Journal Club 2018 Year-in-Review

UNM Ornithologists read about 100 papers together each year. About 1/3 of these are discussed formally in our Journal Club, in which 10-15 participants dissect and critique them. The other papers include joint manuscript reviews, papers that were nominated but not discussed formally, or papers we read for collaborative research projects. Some are high-impact papers, some are New Mexico related, and some are interesting only for highly specific reasons known only to us. I list my ten favorites of 2018 here, unranked; these are the ones that best withstood the criticism of our group. Below the top ten you can find the other papers listed alphabetically.

Our paper choices are somewhat arbitrary cannot be comprehensive for any of the subdisciplines represented. If your favorite paper is not included, link to it in the comments section. The brief commentaries under selected papers are exclusively mine, may be inaccurate or unfair, and might not represent the sentiment of the group. Thanks to these core Journal Club participants for 2018:  Mike Andersen, Chris Anderson, Lisa Barrow, Selina Bauernfeind, Serina Brady, Malé Castro, Paxton Cruz, Chauncey Gadek, Levi Gray, Tina Guo, Ethan Gyllenhaal, Andy Johnson, Xena Mapel, Peter Mattison, Jenna McCullough, Moses Michelsohn, Kristen Oliver, Oona Takano, Bill Talbot, Britt White, Dani Wiley, and Jessie Williamson.

Ten favorites from 2018 (unranked):

  • Antonelli, A., Zizka, A., Carvalho, F. A., Scharn, R., Bacon, C. D., Silvestro, D., & Condamine, F. L. (2018). Amazonia is the primary source of Neotropical biodiversity. Proceedings of the National Academy of Sciences115(23), 6034–6039.
    • The 508-page supplement gives a good indication of the underlying substance of this massive synthetic work. The main conclusion (see title) is important; our group noted that it may have been heavily influenced by the much higher diversity in the Amazon region than elsewhere, plus the fact that ‘Amazonia’ was defined here to include the Guyana Shield, Chocó, Darien, and Andean forests up to treeline. The most interesting part of the paper, IMHO, were the timelines of ‘normalized’ rates of exchange between regions for each of six vertebrate taxa. Those are truly fascinating and deserve further consideration.
  • Barrera-Guzmán, A. O., Aleixo, A., Shawkey, M. D., & Weir, J. T. (2018). Hybrid speciation leads to novel male secondary sexual ornamentation of an Amazonian bird. Proceedings of the National Academy of Sciences of the United States of America115(2), E218–E225.
    • We loved this paper. The one critique that couldn’t be resolved in our discussion was why the authors did not apply the coalescent models to test more possible scenarios of speciation and gene flow. We concluded that the case for hybrid speciation and the case for the mechanistic link between hybridization and plumage signals were short of 100% definitive, but it was a beautiful paper, nonetheless. I consider it a ‘must read’.
  • Bay, R. A., Harrigan, R. J., Underwood, V. L., Gibbs, H. L., Smith, T. B., & Ruegg, K. (2018). Genomic signals of selection predict climate-driven population declines in a migratory bird. Science359(6371), 83–86.
  • Clark, N. J. (2018). Phylogenetic uniqueness, not latitude, explains the diversity of avian blood parasite communities worldwide. Global Ecology and Biogeography27(6), 744–755.
    • Clark is doing fantastic faunal analyses on haemosporidians, of which this is just one example.
  • Freeman, B. G., Scholer, M. N., Ruiz-Gutierrez, V., & Fitzpatrick, J. W. (2018). Climate change causes upslope shifts and mountaintop extirpations in a tropical bird community. Proceedings of the National Academy of Sciences115(47), 11982–11987.
    • This is awesome — a rare glimpse into avifaunal change in one of the most diverse but rapidly changing places on earth.
  • Irwin, D. E., Milá, B., Toews, D. P. L., Brelsford, A., Kenyon, H. L., Porter, A. N., et al. (2018). A comparison of genomic islands of differentiation across three young avian species pairs. Molecular Ecology27(23), 4839–4855.
    • Thorough description of genomic divergence in these three cases reveals some fundamental aspects of speciation.
  • Jones, M. R., Mills, L. S., Alves, P. C., Callahan, C. M., Alves, J. M., Lafferty, D. J. R., et al. (2018). Adaptive introgression underlies polymorphic seasonal camouflage in snowshoe hares. Science360(6395), 1355–1358.
    • An elegant paper demonstrating decisively how, when, and why a gene for seasonal polymorphism jumped species boundaries from a jackrabbit to a snowshoe hare.
  • Morales, H. E., Pavlova, A., Amos, N., Major, R., Kilian, A., Greening, C., & Sunnucks, P. (2018). Concordant divergence of mitogenomes and a mitonuclear gene cluster in bird lineages inhabiting different climates. Nature Ecology & Evolution2(8), 1258–1267.
    • Fantastic description of genetic divergence between inland and coastal forms along the east coast of Australia, highly suggestive of mitonuclear coevolution. There were mtDNA and nuclear DNA clines from coastal to inland, across a temperature gradient. mtDNA and some nuclear loci were locally adapted and segregating, mtDNA divergence was high, indicating a deep history of cold adapted and warm adapted genotypes, respectively. My biggest complaint is that one had to read to the 2nd page of the paper just to find out what species was being studied (Eastern Yellow Robin) — are they embarrassed of their study species? Do species even matter any more? Do we go to the field just to study concepts in order to please our journal-editor overlords?!
  • Lamichhaney, S., Han, F., Webster, M. T., Andersson, L., Grant, B. R., & Grant, P. R. (2018). Rapid hybrid speciation in Darwin’s finches. Science359(6372), 224–228.
    • Fascinating case study and phenomenal dataset.
  • Quintero, I., & Jetz, W. (2018). Global elevational diversity and diversification of birds. Nature, 555(7695), 246–250.
    • A super impressive assemblage of avifaunal data and analyses, revealing some fundamental truths about diversification and diversity of birds in mountains.

The rest of our 2018 selections (alphabetical order by 1st author):

  1. Alcala, N., Jenkins, T., Christe, P., & Vuilleumier, S. (2017). Host shift and cospeciation rate estimation from co-phylogenies. Ecology Letters20(8), 1014–1024.
    • Very welcomed framework for analyzing coevolution of parasites and hosts, even when there’s lots of host-switching, as occurs in haemosporidians.
  2. Anticona, S. J., Olmos, E. F., Parent, J. R., Rutti, D. M., Velasco, B. A., & Hoese, W. J. (2013). Greater Roadrunner (Geococcyx californianus) Kills Juvenile Desert Cottontail (Sylvilagus audubonii). The Southwestern Naturalist58(1), 124–126.
    • The title says it all — we like roadrunner natural history here in New Mexico.
  3. Antonelli, A., Ariza, M., Albert, J., Andermann, T., Azevedo, J., Bacon, C., et al. (2018a). Conceptual and empirical advances in Neotropical biodiversity research. PeerJ6(5), e5644–53.
    • A really nice and comprehensive review with appealing graphics.
  4. Antonelli, A., Kissling, W. D., Flantua, S. G. A., Bermúdez, M. A., Mulch, A., Muellner-Riehl, A. N., et al. (2018b). Geological and climatic influences on mountain biodiversity. Nature Geoscience, 1–10.
    • Biologists and geologists working together? Awesome.
  5. Battey, C. J., 2018. Time Lags and Niche Shifts in a Biological Invasion of Hummingbirds.
    • The expansion of the Anna’s Hummingbird since the early-mid 20th century was a story that needed telling — this paper does so with nice graphics.
  6. Battey, C. J., & Klicka, J. (2017). Cryptic speciation and gene flow in a migratory songbird Species Complex: Insights from the Red-Eyed Vireo (Vireo olivaceus). Molecular Phylogenetics and Evolution113, 67–75.
  7. Beckman, E. J., Benham, P. M., Cheviron, Z. A., & Witt, C. C. (2018). Detecting introgression despite phylogenetic uncertainty: The case of the South American siskins. Molecular Ecology27(22), 4350–4367.
  8. Betts, A., Gray, C., Zelek, M., MacLean, R. C., & King, K. C. (2018). High parasite diversity accelerates host adaptation and diversification. Science360(6391), 907–911.
    • Before you get too excited… this was in a test tube, not in the wild! Nonetheless, it’s a great paper and very thought-provoking.
  9. Birkhead, T. R., Thompson, J. E., Biggins, J. D., & Montgomerie, R. (2018). The evolution of egg shape in birds: selection during the incubation period. Ibis55, 105–14.
    • This is more-or-less a rebuttal to the Stoddard et al. paper in Science the other year. Both are worth reading.
  10. Boast, A. P., Weyrich, L. S., Wood, J. R., Metcalf, J. L., Knight, R., & Cooper, A. (2018). Coprolites reveal ecological interactions lost with the extinction of New Zealand birds. Proceedings of the National Academy of Sciences115(7), 1546–1551.
  11. Bruxaux, J., Gabrielli, M., Ashari, H., Prŷs-Jones, R., Joseph, L., Milá, B., et al. (2017). Recovering the evolutionary history of crowned pigeons (Columbidae_ Goura)_ Implications for the biogeography and conservation of New Guinean lowland birds. Molecular Phylogenetics and Evolution120, 248–258.
  12. Budischak, S. A., Wiria, A. E., Hamid, F., Wammes, L. J., Kaisar, M. M. M., van Lieshout, L., et al. (2018). Competing for blood: the ecology of parasite resource competition in human malaria-helminth co-infections. Ecology Letters21(4), 536–545.
  13. Campbell-Staton, S. C., Bare, A., Losos, J. B., Edwards, S. V., & Cheviron, Z. A. (2018). Physiological and regulatory underpinnings of geographic variation in reptilian cold tolerance across a latitudinal cline. Molecular Ecology27(9), 2243–2255.
  14. Carstens, B. C., Morales, A. E., Field, K., & Pelletier, T. A. (2018). A global analysis of bats using automated comparative phylogeography uncovers a surprising impact of Pleistocene glaciation. Journal of Biogeography45(8), 1795–1805.
    • This paper presented an analysis of 100’s of bat mtdna phylogeography datasets to test for expansion or bottlenecks after LGM. The results were mostly indecisive, with only a handful of datasets supporting either scenario with confidence. Neotropical species tended to have been subject to bottlenecks. The automated data harvesting method revealed weaknesses with Genbank and GBIF datasets. Natural selection effects were ignored (which may be problematic, see Bazin et al. 2006, Some of our group had numerous issues with the paper, some defended it, and the discussion was rollicking.
  15. Chan, W.-P., Chen, I.-C., Colwell, R. K., Liu, W.-C., Huang, C.-Y., & Shen, S.-F. (2018). Response to Qian et al. (2017): Daily and seasonal climate variations are both critical in the evolution of species’ elevational range size. Journal of Biogeography45(12), 2832–2836.
  16. Chase, J. M., McGill, B. J., McGlinn, D. J., May, F., Blowes, S. A., Xiao, X., et al. (2018). Embracing scale-dependence to achieve a deeper understanding of biodiversity and its change across communities. Ecology Letters21(11), 1737–1751.
  17. Chen, N., Cosgrove, E. J., Bowman, R., Fitzpatrick, J. W., & Clark, A. G. (2016). Genomic Consequences of Population Decline in the Endangered Florida Scrub-Jay. Current Biology26(21), 2974–2979.
  18. Cheviron, Z. A., & Swanson, D. L. (2017). Comparative Transcriptomics of Seasonal Phenotypic Flexibility in Two North American Songbirds. Integrative and Comparative Biology57(5), 1040–1054.
    • This is a groundbreaking paper, simple in design (two species X two seasons), but really novel in its rigorous application of transcriptomics to bird seasonal adjustments. There were similar seasonal gene-expression shifts in chickadees and goldfinches overall, with some species specific patterns too. Some imperfect venn diagrams (paging Scott Walker!), but a really interesting and informative paper regarding seasonal gene expression shifts.
  19. Corti, M., Podofillini, S., Griggio, M., Gianfranceschi, L., Ducrest, A.-L., Roulin, A., et al. (2018). Sequence variation in melanocortin-1-receptor and tyrosinase-related protein 1 genes and their relationship with melanin-based plumage trait expression in Lesser Kestrel (Falco naumanni) males. Journal of Ornithology, 1–6.
  20. Divis, P. C. S., Duffy, C. W., Kadir, K. A., Singh, B., & Conway, D. J. (2018). Genome-wide mosaicism in divergence between zoonotic malaria parasite subpopulations with separate sympatric transmission cycles. Molecular Ecology, 27(4), 860–870. Human malaria studies get better data, so they provide useful models for early-stage divergence in avian malaria.

  21. Drury, J. P., Tobias, J. A., Burns, K. J., Mason, N. A., Shultz, A. J., & Morlon, H. (2018). Contrasting impacts of competition on ecological and social trait evolution in songbirds. PLOS Biology16(1), e2003563–23.
    • This probably goes a little too far — inferring competition based on distribution and phylogenetic patterns alone is still fraught. Nonetheless, the analyses and ideas are interesting in their own right.
  22. Ellis, V. A., & Bensch, S. (2018). Host specificity of avian haemosporidian parasites is unrelated among sister lineages but shows phylogenetic signal across larger clades. International Journal for Parasitology, 1–6.
  23. Fecchio, A., Bell, J. A., Collins, M. D., Farias, I. P., Trisos, C. H., Tobias, J. A., Tkach, V. V., Weckstein, J. D., Ricklefs, R. E., & Batalha-Filho, H. (2018a). Diversification by host switching and dispersal shaped the diversity and distribution of avian malaria parasites in Amazonia. Oikos127(9), 1233–1242.
  24. Felice, R. N., & Goswami, A. (2018). Developmental origins of mosaic evolution in the avian cranium. Proceedings of the National Academy of Sciences of the United States of America115(3), 555–560.
    • Not really surprising that the face (i.e. beak) is under a lot of selection. Back of head not so much. Also, if you atomize into parts, you’ll find mosaic evolution. But the paper was nifty anyway.
  25. Field, R., & Qian, H. (2018). No empirical evidence to support the hypothesis that daily climate variation has an effect on species’ elevational range size: Reply to Chan et al. Journal of Biogeography45(12), 2827–2832.
  26. Fitt, R. N. L., Palmer, S., Hand, C., Travis, J. M. J., & Lancaster, L. T. (2018). Towards an interactive, process-based approach to understanding range shifts: developmental and environmental dependencies matter. Ecography147, 381–24.
  27. Funk, V. A. (2018). Collections-based science in the 21st Century. Journal of Systematics and Evolution56(3), 175–193.
  28. Gallo, S. S. M., Ederli, N. B., & Oliveira, F. C. R. (2017). Hematological and morphometric differences of blood cells from rheas, Rhea americana (Struthioniformes: Rheidae) on two conservation farms. Brazilian Journal of Biology77(2), 227–233.
  29. George, R. J., Plog, S., Watson, A. S., Schmidt, K. L., Culleton, B. J., Harper, T. K., et al. (2018). Archaeogenomic evidence from the southwestern US points to a pre-Hispanic scarlet macaw breeding colony. Proceedings of the National Academy of Sciences115(35), 8740–8745.
  30. Gilbert, K. J., Peischl, S., & Excoffier, L. (2018). Mutation load dynamics during environmentally-driven range shifts. PLoS Genetics14(9), e1007450–14.
  31. Glassman, S. I., Wang, I. J., & Bruns, T. D. (2017). Environmental filtering by pH and soil nutrients drives community assembly in fungi at fine spatial scales. Molecular Ecology26(24), 6960–6973.
  32. Gómez-Sánchez, D., Olalde, I., Sastre, N., Enseñat, C., Carrasco, R., Marques-Bonet, T., et al. (2018). On the path to extinction: Inbreeding and admixture in a declining grey wolf population. Molecular Ecology27(18), 3599–3612.
  33. Grant, P. R., & Grant, B. R. (2018). Role of sexual imprinting in assortative mating and premating isolation in Darwin’s finches. Proceedings of the National Academy of Sciences115(46), E10879–E10887.
  34. Halbritter, A. H., Fior, S., Keller, I., Billeter, R., Edwards, P. J., Holderegger, R., et al. (2018). Trait differentiation and adaptation of plants along elevation gradients. Journal of Evolutionary Biology31(6), 784–800.
  35. Haupaix, N., Curantz, C., Bailleul, R., Beck, S., Robic, A., & Manceau, M. (2018). The periodic coloration in birds forms through a prepattern of somite origin. Science361(6408), eaar4777–8.
  36. Hazzi, N. A., Moreno, J. S., Ortiz-Movliav, C., & Palacio, R. D. (2018). Biogeographic regions and events of isolation and diversification of the endemic biota of the tropical Andes. Proceedings of the National Academy of Sciences115(31), 7985–7990.
    • This synthesis paper only analyzed 14 small clades, ignoring many recent phylogenies. Misspellings of bird names were also an issue :-/
  37. Hoffmann, F. G., Vandewege, M. W., Storz, J. F., & Opazo, J. C. (2018). Gene Turnover and Diversification of the α- and β-Globin Gene Families in Sauropsid Vertebrates. Genome Biology and Evolution10(1), 344–358.
  38. Holt, R. D., & Bonsall, M. B. (2017). Apparent Competition. Annual Review of Ecology, Evolution, and Systematics48(1), 447–471.
  39. Huang, X., Ellis, V. A., Jönsson, J., & Bensch, S. (2018). Generalist haemosporidian parasites are better adapted to a subset of host species in a multiple host community. Molecular Ecology27(21), 4336–4346.
  40. Jax, E., Wink, M., & Kraus, R. H. S. (2018). Avian transcriptomics: opportunities and challenges. Journal of Ornithology159(3), 599–629.
  41. Judson, O. P. (2017). The energy expansions of evolution. Nature Ecology & Evolution1(6), 0138–10.
  42. Kearns, A. M., Restani, M., Szabo, I., Schrøder-Nielsen, A., Kim, J. A., Richardson, H. M., et al. (2018). Genomic evidence of speciation reversal in ravens. Nature Communications, 1–13.
    • “Speciation reversal” is a tough sell here, but a fascinating case study anyway.
  43. Kingsolver, J. G., & Buckley, L. B. (2017). Evolution of plasticity and adaptive responses to climate change along climate gradients. Proceedings of the Royal Society of London B: Biological Sciences284(1860), 20170386–7.
  44. Londoño, G. A., Chappell, M. A., Jankowski, J. E., & Robinson, S. K. (2016). Do thermoregulatory costs limit altitude distributions of Andean forest birds? Functional Ecology31(1), 204–215.
  45. Manzoli, D. O. E., Saravia-Pietropaolo, M. J., Antoniazzi, L. R., Barengo, E., Arce, S. I., Quiroga, M. A., & Beldomenico, P. M. (2018). Contrasting consequences of different defence strategies in a natural multihost-parasite system. International Journal for Parasitology48(6), 445–455.
    • Same parasite has really different effects on different host species in the same communities, and this paper disentangles tolerance and resistance to show how different defense strategies underlie the different outcomes.
  46. Miles, M. C., Goller, F., eLife, M. F., 2018. Physiological constraint on acrobatic courtship behavior underlies rapid sympatric speciation in bearded manakins. Elife.
    • The sympatric speciation part is not the strongest part of this paper, but it’s worth reading.
  47. Mueller, J. C., Kuhl, H., Boerno, S., Tella, J. L., Carrete, M., & Kempenaers, B. (2018). Evolution of genomic variation in the burrowing owl in response to recent colonization of urban areas. Proceedings of the Royal Society of London B: Biological Sciences285(1878), 20180206–9.
    • Great to see this Mueller Report issued in a timely fashion.
  48. Mueller, N. F., Ogilvie, H., Zhang, C. (2018). Inference of species histories in the presence of gene flow.
  49. Naka, L. N., & Brumfield, R. T. (2018). The dual role of Amazonian rivers in the generation and maintenance of avian diversity. Science Advances4(8), eaar8575.
    • First off, this is an excellent paper with a sizable, original empirical dataset. And it’s beautifully written. The “dual roles” of rivers were defined as (1) primary divergence and (2) maintenance of separation; but it was never easy to distinguish one from the other. Divergences were mostly recent, with fewer old ones, and were broadly consistent with neutral process of diversification. Interesting contrast with our “dual roles of Andean topography” paper, in which the dual roles were barriers and divergent selection pressures ( Naturally, I prefer the latter framework 😉
  50. Ng, J. W., Knight, E. C., Scarpignato, A. L., Harrison, A. L., Bayne, E. M., & Marra, P. P. (2018). First full annual cycle tracking of a declining aerial insectivorous bird, the Common Nighthawk ( Chordeiles minor), identifies migration routes, nonbreeding habitat, and breeding site fidelity. Canadian Journal of Zoology96(8), 869–875.
    • This is just so cool. Nighthawks rock.
  51. Pacheco, M. A. N., Cepeda, A. S., Bernotienė, R., Lotta, I. A., Matta, N. E., Valkiūnas, G., & Escalante, A. A. (2018a). Primers targeting mitochondrial genes of avian haemosporidians: PCR detection and differential DNA amplification of parasites belonging to different genera. International Journal for Parasitology48(8), 657–670.
    • A tool we’ll use.
  52. Pan, S., Zhang, T., Rong, Z., Hu, L., Gu, Z., Wu, Q., et al. (2017). Population transcriptomes reveal synergistic responses of DNA polymorphism and RNA expression to extreme environments on the Qinghai-Tibetan Plateau in a predatory bird. Molecular Ecology26(11), 2993–3010.
    • EPAS1! We liked this study overall. Tip 1: if you do a single-species study, put the name of the species in the title (see also Morales et al. 2018, above). Tip 2: if you studied a bird as cool as the Saker Falcon, put the name of the species in the title!
  53. Patricelli, G. L., Hebets, E. A., & Mendelson, T. C. (2018). Book review of Prum, R. O. 2018. The evolution of beauty: How Darwin’s forgotten theory of mate choice shapes the animal world-and us (2017), Doubleday, 428 pages, ISBN: 9780385537216. Evolution323, 152–10.
    • This is a must-read for anyone interested in both sex and controversy.
  54. Paxton, E. H., Camp, R. J., Gorresen, P. M., Crampton, L. H., Leonard, D. L., Jr., & VanderWerf, E. A. (2016). Collapsing avian community on a Hawaiian island. Science Advances2(9), e1600029–9.
    • Depressing.
  55. Penn, J. L., Deutsch, C., Payne, J. L., & Sperling, E. A. (2018). Temperature-dependent hypoxia explains biogeography and severity of end-Permian marine mass extinction. Science362(6419), eaat1327–8.
  56. Phillips, A. G., Töpfer, T., Rahbek, C., Böhning-Gaese, K., & Fritz, S. A. (2018). Effects of phylogeny and geography on ecomorphological traits in passerine bird clades. Journal of Biogeography45(10), 2337–2347.
  57. Pulido-Santacruz, P., Aleixo, A., & Weir, J. T. (2018). Morphologically cryptic Amazonian bird species pairs exhibit strong postzygotic reproductive isolation. Proceedings of the Royal Society of London B: Biological Sciences285(1874), 20172081–9.
  58. Pulgarín, P., Gómez, C., Bayly, N. J., Bensch, S., FitzGerald, A. M., Starkloff, N., et al. (2018a). Migratory birds as vehicles for parasite dispersal? Infection by avian haemosporidians over the year and throughout the range of a long‐distance migrant. Journal of Biogeography331, 296.
  59. Pulgarín, P., Gómez, J. P., Robinson, S., Ricklefs, R. E., & Cadena, C. D. (2018b). Host species, and not environment, predicts variation in blood parasite prevalence, distribution, and diversity along a humidity gradient in northern South America. Ecology and Evolution8(8), 3800–3814.
  60. Ramos, J. S. L., Delmore, K. E., & Liedvogel, M. (2017). Candidate genes for migration do not distinguish migratory and non-migratory birds. Journal of Comparative Physiology A203(6), 383–397.
  61. Rangel, T. F., Edwards, N. R., Holden, P. B., Diniz-Filho, J. A. F., Gosling, W. D., Coelho, M. T. P., et al. (2018). Modeling the ecology and evolution of biodiversity: Biogeographical cradles, museums, and graves. Science361(6399), eaar5452–15.
    • Still coming to grips with this impressive modeling effort and what it means.
  62. Ribas, C. C., Aleixo, A., Gubili, C., d’Horta, F. M., Brumfield, R. T., & Cracraft, J. (2018). Biogeography and diversification of Rhegmatorhina (Aves: Thamnophilidae): Implications for the evolution of Amazonian landscapes during the Quaternary. Journal of Biogeography45(4), 917–928.
  63. Ricklefs, R. E., Ellis, V. A., Medeiros, M. C., & Svensson-Coelho, M. (2018). Duration of embryo development and the prevalence of haematozoan blood parasites in birds. The Auk135(2), 276–283.
  64. Roesti, M. (2018). Varied Genomic Responses to Maladaptive Gene Flow and Their Evidence. Genes9(6), 298–16.
  65. Ruegg, K., Bay, R. A., Anderson, E. C., Saracco, J. F., Harrigan, R. J., Whitfield, M., et al. (2018). Ecological genomics predicts climate vulnerability in an endangered southwestern songbird. Ecology Letters21(7), 1085–1096.
    • See also Bay et al., above.
  66. Sackton, T. B., Grayson, P., Cloutier, A., Hu, Z., Liu, J. S., Wheeler, N. E., et al. (2018). Convergent regulatory evolution and the origin of flightlessness in palaeognathous birds, 1–31. Biorxiv.
  67. Santos, J. C., Tarvin, R. D., O’Connell, L. A., Blackburn, D. C., & Coloma, L. A. (2018). Diversity within diversity: Parasite species richness in poison frogs assessed by transcriptomics. Molecular Phylogenetics and Evolution125, 40–50.
    • Nifty, yes, but ultimately this method has a ways to go.
  68. Schindel, D. E., & Cook, J. A. (2018). The next generation of natural history collections. PLOS Biology16(7), e2006125–8.
  69. Schmitt, C. J., Cook, J. A., Zamudio, K. R., & Edwards, S. V. (2019). Museum specimens of terrestrial vertebrates are sensitive indicators of environmental change in the Anthropocene. Philosophical Transactions of the Royal Society of London B: Biological Sciences374(1763), 20170387–10.
  70. Schweizer, M., Warmuth, V., Alaei Kakhki, N., Aliabadian, M., Förschler, M., Shirihai, H., et al. (2018). Parallel plumage colour evolution and introgressive hybridization in wheatears. Journal of Evolutionary Biology26, 229–12.
  71. Scridel, D., Brambilla, M., Martin, K., Lehikoinen, A., Iemma, A., Matteo, A., et al. (2018). A review and meta-analysis of the effects of climate change on Holarctic mountain and upland bird populations. Ibis160(3), 489–515.
  72. Seeholzer, G. F., & Brumfield, R. T. (2017). Isolation by distance, not incipient ecological speciation, explains genetic differentiation in an Andean songbird (Aves: Furnariidae: Cranioleuca antisiensis, Line-cheeked Spinetail) despite near threefold body size change across an environmental gradient. Molecular Ecology27(1), 279–296.
    • This is a great paper to help us understand ecogeographic variation in Andean birds.
  73. Sheldon, K. S., Huey, R. B., Kaspari, M., & Sanders, N. J. (2018). Fifty Years of Mountain Passes: A Perspective on Dan Janzen’s Classic Article. American Naturalist191(5), 553–565.
  74. Sjöberg, S., Pedersen, L., Malmiga, G., Alerstam, T., Hansson, B., HASSELQUIST, D., et al. (2018). Barometer logging reveals new dimensions of individual songbird migration. Journal of Avian Biology49(9), e01821–9.
  75. Smith, C. C. R., Flaxman, S. M., Scordato, E. S. C., Kane, N. C., Hund, A. K., Sheta, B. M., & Safran, R. J. (2018). Demographic inference in barn swallows using whole-genome data shows signal for bottleneck and subspecies differentiation during the Holocene. Molecular Ecology27(21), 4200–4212.
  76. Sukumaran, J., & Knowles, L. L. (2018). Trait-Dependent Biogeography: (Re)Integrating Biology into Probabilistic Historical Biogeographical Models. Trends in Ecology & Evolution33(6), 390–398.
  77. Sun, Y.-B., Fu, T.-T., Jin, J.-Q., Murphy, R. W., Hillis, D. M., Zhang, Y.-P., & Che, J. (2018). Species groups distributed across elevational gradients reveal convergent and continuous genetic adaptation to high elevations. Proceedings of the National Academy of Sciences115(45), E10634–E10641.
    • Finally, a genomic adaptation study treats altitude as a gradient, rather than a dichotomy.
  78. Tang, Y., Winkler, J. A., Viña, A., Liu, J., Zhang, Y., Zhang, X., et al. (2018). Uncertainty of future projections of species distributions in mountainous regions. PloS One13(1), e0189496–23.
  79. Thom, G., Amaral, F. R. D., Hickerson, M. J., Aleixo, A., Araujo-Silva, L. E., Ribas, C. C., et al. (2018). Phenotypic and Genetic Structure Support Gene Flow Generating Gene Tree Discordances in an Amazonian Floodplain Endemic Species. Systematic Biology67(4), 700–718.
  80. Torres, C. R., & Clarke, J. A. (2018). Nocturnal giants: evolution of the sensory ecology in elephant birds and other palaeognaths inferred from digital brain reconstructions. Proceedings of the Royal Society of London B: Biological Sciences285(1890), 20181540–8.
  81. Troudet, J., Vignes-Lebbe, R., Grandcolas, P., & Legendre, F. (2018). The Increasing Disconnection of Primary Biodiversity Data from Specimens: How Does It Happen and How to Handle It? Systematic Biology67(6), 1110–1119.
  82. Uyeda, J. C., Zenil-Ferguson, R., & Pennell, M. W. (2017). Rethinking phylogenetic comparative methods, 1–44. Systematic Biology.
  83. Valencia, B. G., Bush, M. B., Coe, A. L., Orren, E., & Gosling, W. D. (2018). Polylepis woodland dynamics during the last 20,000 years. Journal of Biogeography45(5), 1019–1030.
  84. Van Doren, B. M., & Horton, K. G. (2018). A continental system for forecasting bird migration. Science361(6407), 1115–1118.
  85. Velotta, J. P., Ivy, C. M., Wolf, C. J., Scott, G. R., & Cheviron, Z. A. (2018). Maladaptive phenotypic plasticity in cardiac muscle growth is suppressed in high-altitude deer mice. Evolution72(12), 2712–2727.
  86. Vickrey, A., Bruders, R., Kronenberg, Z., Mackey, E., Bohlender, R. J., Maclary, E., et al. (2018). Protein-coding variation and introgression of regulatory alleles drive plumage pattern diversity in the rock pigeon eLife.
  87. Videvall, E. (2018). Plasmodium parasites of birds have the most AT-rich genes of eukaryotes. Microbial Genomics4(2), 907–9.
  88. Wen, Z., Wu, Y., Cheng, J., Cai, T., Du, Y., Ge, D., et al. (n.d.). Abundance of small mammals correlates with their elevational range sizes and elevational distributions in the subtropics. Ecography
  89. Xu, B., Sun, G., Wang, X., Lu, J., Wang, I. J., & Wang, Z. (2017). Population genetic structure is shaped by historical, geographic, and environmental factors in the leguminous shrub Caragana microphylla on the Inner Mongolia Plateau of China. BMC Plant Biology
  90. Zenzal, T. J., Jr, Moore, F. R., Diehl, R. H., Ward, M. P., & Deppe, J. L. (2018). Migratory hummingbirds make their own rules: the decision to resume migration along a barrier. Animal Behaviour137, 215–224.
    • A notable advance in the application of micro-tracking devices to small birds (0.28 g transmitter glued to a 4-g bird), successful for short-distance tracking to understand local movements and departure of fall-migrant Ruby-throated Hummingbirds on the Alabama Gulf Coast.

Golden age for the study of bird movements

It is easy to take for granted the scientific methods that allow us to measure and track bird migration. Without them, it is hard or impossible to understand bird movements. Consider the Ancient Greeks, who believed that certain summer resident species transformed themselves into winter resident species, while others went into winter hibernation. These explanations must have seemed more probable than the truth, which is that Greek songbirds lighter than a four-drachma coin1 fly twice annually across the Mediterranean Sea and Sahara Desert. Similar myths persist today, including that swallows hibernate underwater, and that hummingbirds migrate on the backs of geese. At least the latter myth should fool nobody in New Mexico, where the departure of the hummingbirds and the arrival of the geese are offset by at least a month in fall (and vice versa in spring).

In order to know the true nature of migration, we need coordination among people to advance collective knowledge through controlled observations or experiments. In other words, we need science. Several types of scientific of data have been used traditionally to understand bird migration, including observational records, specimens, and bird banding records. And these traditional methods continue to be useful; for example, the long-term bird-banding effort at the Rio Grande Nature Center has produced a detailed record of the migratory passage of small birds through Albuquerque, allowing for detection of population changes. With these types of data, ornithologists have been able to describe species ranges during the summer, winter, and migration.

Over the last couple of decades, technology has enabled new ways of measuring bird movements and understanding them in detail. The key methods have included stable isotopes, genetics, weather radar, citizen science, and micro-tracking devices. We can now ask questions that are much more detailed and in many ways more important than just the species range. For example, we can ask whether specific populations have different wintering sites, what are their migratory routes, where do they rest and feed along the way, how fast do they fly, how high do they fly, and whether individuals, age classes, or sexes vary in migratory behavior.

Micro-tracking devices are currently yielding some of the most exciting discoveries in bird migration. The most basic form of micro-tracking device is the light-level geolocator, a device consisting of a light sensor, a memory chip, a clock, and a battery. These can weigh less than a half of a gram and can be strapped, backpack style, to a bird as small as a warbler or flycatcher. The geolocator can be programmed to record light measurements every few minutes in order to capture the sunrise and sunset times for each day until the battery runs out. If a geolocator device is recovered after months or years of riding around on a bird, its latitude and longitude can then be estimated for each day that the bird carried it around. (A slightly more precise micro-tracking device employs GPS instead of a light sensor, but it makes a more expensive package to release to the wild with uncertain chance of recovery!).

The next generation of micro-tracking devices are those that transmit signals so that birds can be tracked remotely, without recapture. Of course, telemetry has been around for several decades, whether short-range (VHF) or satellite-based, but what’s exciting now is the small size of the devices. There are two types that are currently ‘pushing the envelope’ in ornithological research. First, there are Motus tags2. These are lightweight and inexpensive transmitters that emit unique codes to Motus antennas that have been strategically placed along bird migration routes, mostly in eastern North America (and increasingly elsewhere). The unique signal can be detected when the device passes within about 15 km of an antenna. In this way, Motus data is similar to band-recovery data because the bird was released at ‘point a’ and detected later at ‘point b’. However, whereas bird bands are recovered at rates of around 0.01%, Motus has far higher success. As birds migrate, they can be detected by multiple antennas and thus can yield reliable data about migratory routes, timing, and speed. The major limitations are that the Motus antenna network needs to be sufficiently dense in the study area, and that the position of the bird is not specified with great precision.

The second emerging micro-tracker technology is the satellite transmitter known as a PTT (Platform Transmitter Terminal)3. These are larger than the Motus tags or geolocators, but they are more exciting because they can track the exact geographic position of a bird (within ~150 meters) over the entire course of its migration, and they transmit the positions to a satellite so that they do not need to be recovered. Technological innovations are now allowing PTT’s small enough to apply to migratory birds weighing ~20 grams (only slightly larger than a four-drachma coin!). Fortunately, most migratory birds have built-in capacity to fly with substantial extra weight — they are built to do so in order to support fat loads for fuel that can comprise 50% or more of their normal body mass.

The spectacular cross-continental tracks of Common Cuckoos as revealed by satellite telemetry (

There are several spectacular case studies of migratory behaviors and routes revealed by micro-tracking devices. For example, Hedenstrom and colleagues used geolocators with ‘micro-accelerometers’ to show that Common Swifts from southern Sweden spend the entire 10-month non-breeding season in flight (!), even sleeping on the wing, high above the landscape of sub-Saharan Africa4. Bar-tailed Godwits from western Alaska have been tracked with satellite telemetry and have been shown to fly thousands of kilometers at a time; in fall they fly direct to New Zealand; in spring they fly to China’s Yellow Sea to feed for about 40 days before flying non-stop back to Alaska5. The Bar-tailed Godwit population from Russia, a separate subspecies, undergoes similar migrations, but it winters in northwest Australia instead of New Zealand. By affixing geolocators to Barn Swallows from across North America, Hobson and colleagues discovered that western populations winter in Central America, southeastern populations winter in northeast Brazil, and northeastern populations winter in south-central South America6.

Matched breeding (stars) and wintering (squares) localities of Barn Swallows. Note that New Mexico populations have not yet been studied! (

A similar finding was made with Golden-winged Warblers, where populations from different parts of the species range winter in distinct areas of Central America or northern South America7. Such findings are groundbreaking because they indicate spatial isolation of migratory populations throughout the annual cycle. However, this isn’t the rule for all species; for example, Brewer’s Sparrows and Sagebrush Sparrows appear to have no precise connectivity between breeding and wintering areas8. In some cases, winter ranges are totally unknown before tracking studies; this was the case for the Black Swift before it was tracked from Colorado to western Brazil, connecting the Rocky Mountains to the Amazon rainforests9. Similarly, Common Cuckoos from China have recently been tracked using PTT’s to their previously unknown wintering grounds in sub-Saharan Africa10. At least for migratory birds, continental ecosystems appear to be small and interdependent. Sometimes, micro-tracking devices implicate pervasive human effects on the environment, as when it was discovered that Lesser Black-backed Gulls on the coast of the North Sea were not feasting on the bounty of seafood, but rather were making daily 130-km commutes to visit an inland potato chip factory11.

jessie with giant hummingbird glam shot
Jessie Williamson, UNM graduate student, prepares to release a Giant Hummingbird with a geolocator.

Use of micro-tracking devices is undergoing a boom, so there are probably even more ongoing studies than those that have been published to date. These will improve our understanding of the connections between breeding and wintering populations, allowing us to see connections with much finer spatial resolution than that of the species range alone. For example, UNM graduate student Jessie Williamson is using two types of micro-tracking devices to uncover the mysterious migration of the southern Giant Hummingbird. The Giant Hummingbird is the largest hummingbird in the world, and its annual migrations are completely unstudied previously; however, we know from anecdotes that it can fly over some of the highest mountain passes and harshest deserts of South America. Closer to home, a collaborative project by the University of Toledo, USFWS, and Sandia Labs is working to track New Mexico populations of Gray Vireo and identify their wintering grounds12.

Silas Fischer, graduate student at the University of Toledo, prepares to release a Gray Vireo with a radio transmitter (to examine local movements), in central New Mexico. Fischer and colleagues are also currently analyzing the first geolocator data for this species to reveal connectivity between breeding and wintering grounds.

But even most of the familiar New Mexico breeding bird populations remain unstudied. Consider, for example, American Robin, Bullock’s Oriole, Audubon’s Warbler, and Cliff Swallow; all four have broad ranges in winter, and we have little or no idea of where our New Mexico populations go within that range. For those species and just about every other bird population found in New Mexico, new tracking studies would advance scientific knowledge in important ways. Until such studies are completed, we will have substantial gaps in our understanding of their annual cycles and potentially critical conservation issues related to winter habitats.


1. A four-drachma coin in ancient Greece weighed 17.2 grams.



4. Hedenström, A., et al. (2016). Annual 10-Month Aerial Life Phase in the Common Swift Apus apus. Current Biology, 26(22), 3066–3070.

5. Battley, P. F., et al. (2012). Contrasting extreme long-distance migration patterns in bar-tailed godwits Limosa lapponica. Journal of Avian Biology, 43(1), 21–32.

6. Hobson, K. A., et al. (2015). A Continent-Wide Migratory Divide in North American Breeding Barn Swallows (Hirundo rustica). PloS One, 10(6), e0129340.

7. Kramer, G. R., et al. (2017). Nonbreeding isolation and population-specific migration patterns among three populations of Golden-winged Warblers. The Condor, 119(1), 108–121.

8. Knick, S. T., et al. (2013). Diffuse migratory connectivity in two species of shrubland birds: evidence from stable isotopes. Oecologia, 174(2), 595–608.

9. Beason, J. P., et al. (2012). The Northern Black Swift: Migration Path And Wintering Area Revealed. Wilson Journal of Ornithology, 124(1), 1–8.



12. Led by graduate student, Silas Fischer, and their advisor, Dr. Henry Streby.

The Changing Birds of New Mexico

New Mexico is warming up and its avifauna is responding. Some consequences of warming will be predictable; for example, species will tend to shift their ranges northward and breed earlier in spring. But shifting species will encounter new predators, parasites, and competitors, the effects of which will be unpredictable. Furthermore, even species that live in the same places can vary in sensitivity to heat, drought, and habitat changes.

‘Black hawk and the white-winged dove’ is a mournful lyric from an Emmylou Harris song, but also a reminder of the large set of bird species that are expanding their ranges in New Mexico. Sandy Williams, Research Associate at UNM’s Museum of Southwestern Biology (MSB), reports that at least 50 bird species have expanded their breeding ranges within New Mexico, with northward and westward expansions being most common. In addition to the Common Black-Hawk and White-winged Dove mentioned by Harris, a suite of warm-climate species have expanded northward over the couple of centuries since the ‘Little Ice Age’. These expanding species include Greater Roadrunner, Curve-billed Thrasher, Cactus Wren, and Lucy’s Warbler, each of which reaches its northern limits in (or near) New Mexico. Williams is working on a book on the birds of New Mexico that will describe these and other historical changes. There are fewer species whose ranges have shrunk in New Mexico over the same time period, but Williams points out that declines are harder to detect. In the Albuquerque area, species that have clearly declined over recent decades include Yellow Warbler, Lewis’ Woodpecker, and Yellow-billed Cuckoo (1).

Two species that could be vulnerable to climate warming in New Mexico: Mexican Spotted Owl (left) and Northern Goshawk (right), represented by specimens at the Museum of Southwestern Biology of the University of New Mexico. These series of salvaged specimens, accumulated over decades, provide irreplaceable documentation of these populations, their genetics, diet, and other characteristics.

There are many breeding bird species whose southern range limits are in New Mexico. These include three sage specialists — Sage Thrasher, Sagebrush Sparrow, and Sage Grouse (the latter species was extirpated during the 20th century) — and many montane forest species, including Gray Jay, American Three-toed Woodpecker, Dusky Grouse, Pine Grosbeak, Clark’s Nutcracker, ruby-crowned and golden-crowned kinglets, White-crowned Sparrow, Wilson’s Snipe, and Boreal Owl. As temperatures warm, we predict that these species will contract their ranges or withdraw from New Mexico. Montane forest species are typically restricted to above ~7000 ft and are predicted to shift toward mountain peaks, a phenomenon known as the ‘escalator to extinction’. This is even likely to affect species that are currently abundant, such as Dark-eyed Junco and Flammulated Owl.

Disappearance of New Mexico’s forests would sharply reduce bird diversity. A study of ponderosa and piñon pines recently showed that warming temperatures accelerate tree death during drought, adding to the evidence that New Mexico’s forests have no long-term future (2). As forests decline, top predators such as Northern Goshawks and Mexican Spotted Owls would likely be among the first species to disappear. Pinecone predators like the Red Crossbill are abundant and closely dependent on pine forests, but a study of Old World crossbill species showed how these birds could disappear even sooner than the pine trees due to a phenomenon called ‘phenological mismatch’ (3). In short, earlier opening of pinecones in spring is predicted to lead to a period of food scarcity for crossbills in late summer. Such shifts in timing, or ‘phenology’, are happening everywhere. For example, a study of California species showed that they are nesting one week earlier, on average, than a century ago; this might allow species to track their preferred temperature for nesting, even without shifting their geographic ranges (4).

Climate change doesn’t just cause population fluctuations and range shifts, it also is likely to cause evolution that is rapid enough to be measured over years or decades. I don’t yet know of examples of ‘real-time’ adaptation in New Mexico birds, but examples elsewhere suggest that it’s happening here too. For example, a recent study of Great Tits in Britain showed that their beaks have gotten larger over a few decades in order to better exploit bird feeders, and their genome sequences revealed exactly which beak-enlarging genes had been favored by natural selection (5). Natural selection on birds must also be occurring in New Mexico towns and cities where we have created thriving ‘bird-seed economies’. In fact, House Finches in urban Tucson, Arizona, have larger beaks than neighboring populations that eat native plant seeds, mostly likely because the urban birds have adapted to eating thick-hulled sunflower seeds (6). And the latest study on rapid bird beak evolution showed that Florida Snail Kites have adapted to eat a large invasive snail species by an increase in their beak sizes that occurred over less than two generations (7).

Body size and plumage color are also expected to evolve in response to a warming climate. In the eastern U.S., measurements of banded birds showed that several species are getting smaller due to warming (8). In southwestern Arizona, museum specimens revealed that Horned Larks have evolved darker back coloration as an adaptation for background matching in response to agriculture, which has darkened the color of the soil (9). Tests for historical changes in traits of New Mexico birds would be timely and, fortunately, UNM has one of the best and fastest growing bird-specimen collections with which to conduct these studies.

Another way that warming will affect birds is by affecting their parasites, diseases, and disease vectors, many of which have yet to even be discovered. Researchers at UNM Ornithology are surveying the malaria-related parasites of birds in New Mexico pine forests and have found that approximately two-thirds of infections represent previously unknown parasite species (10). In New Mexico on the whole, there are likely to be hundreds of malaria-related parasite species, and each has the potential to harm susceptible bird populations if distributions shift in response to warming.

In summary, many environmental changes are affecting New Mexico’s birds, and changes are occurring with shocking speed. Scientists and citizen-scientists will need to work fast to detect these changes in real time.

  1. J. S. Findley, Birds in Corrales. Occasional Papers of the Museum of Southwestern Biology (2013).
  2. H. D. Adams et al., Temperature response surfaces for mortality risk of tree species with future drought. Environmental Research Letters. 12 (2017), doi:10.1088/1748-9326/aa93be.
  3. E. T. Mezquida, J.-C. Svenning, R. W. Summers, C. W. Benkman, Higher spring temperatures increase food scarcity and limit the current and future distributions of crossbills. Diversity Distrib. 16, 743 (2017).
  4. J. B. Socolar, P. N. Epanchin, S. R. Beissinger, M. W. Tingley, Phenological shifts conserve thermal niches in North American birds and reshape expectations for climate-driven range shifts. Proc. Natl. Acad. Sci. U.S.A. 114, 12976–12981 (2017).
  5. M. Bosse et al., Recent natural selection causes adaptive evolution of an avian polygenic trait. Science. 358, 365–368 (2017).
  6. A. V. Badyaev, R. L. Young, K. P. Oh, C. Addison, Evolution on a local scale: Developmental, functional, and genetic bases of divergence in bill form and associated changes in song structure between adjacent habitats. Evolution. 62, 1951–1964 (2008).
  7. C. E. Cattau, R. J. Fletcher, R. T. Kimball, C. W. Miller, W. M. Kitchens, Rapid morphological change of a top predator with the invasion of a novel prey. Nat Ecol Evol. 21, 1 (2017).
  8. J. Van Buskirk, R. S. Mulvihill, R. C. Leberman, Declining body sizes in North American birds associated with climate change. Oikos. 119, 1047–1055 (2010).
  9. N. A. Mason, P. Unitt, Rapid phenotypic change in a native bird population following conversion of the Colorado Desert to agriculture. Journal of Avian Biology (2017), doi:10.1111/jav.01507.
  10. R. A. Marroquin-Flores et al., Diversity, abundance, and host relationships of avian malaria and related haemosporidians in New Mexico pine forests. PeerJ. 5, e3700 (2017).

Reprinted from Bosque Tracks, Winter 2018 issue.

Will we soon see another wave of bird extinctions in the Americas?

by Alexander C. Lees, Cornell University and Jacob B. Socolar, Princeton University

In the shady recesses of unassuming forest patches in eastern Brazil, bird species are taking their final bows on the global evolutionary stage, and winking out.

These are obscure birds with quaint names: Alagoas Foliage-Gleaner, Pernambuco Pygmy-Owl, Cryptic Treehunter. But their disappearance portends a turning point in a global biodiversity crisis.

Bird extinctions are nothing new. Human activity has already wiped out over a thousand species. But the vast majority of these occurred on oceanic islands. Today, although island species remain disproportionately threatened, we are witnessing a historic shift towards the endangerment of continental species of birds. The Alagoas Foliage-Gleaner, last seen in 2011, looks increasingly like the tip of an iceberg.

This new wave of threats, driven primarily by habitat loss, is deeply troubling because South American forests are home to such a concentration of bird diversity, yet our conservation strategies are still a work in progress.

The trouble with the tropics

To appreciate the significance of today’s looming extinctions in the tropics, we must travel north to the great deciduous forests of the eastern United States, which are haunted by the ghosts of extinctions past. Here, the opportunity to experience the double raps of Ivory-billed Woodpeckers, sun-obscuring clouds of Passenger Pigeons, raucous flocks of Carolina Parakeets, and the monotone song of the Bachman’s Warbler is seemingly forever lost.

The blame for these four infamous extinctions has been laid firmly at the door of historic deforestation.

In the early 20th century, the last remaining old-growth fell to the sawmills, almost without exception. Given the ubiquity of the logging, perhaps the most noteworthy feature of this extinction episode is that it did not involve more species.

The European experience was even more striking. The wholesale clearing of Europe’s primeval forest apparently did not cause a single bird extinction. The logical conclusion is that it is very difficult to drive continental birds extinct.

Why then are forest birds beginning to go extinct on mainland South America, home of the largest and most intact tropical forests on Earth?

We must face two equally unsettling conclusions. The first is that forest destruction, particularly in Brazil’s Atlantic rainforest, has reached continental-scale proportions, with almost no nook or cranny spared. And the second is that it may not be nearly as difficult to drive extinct in the tropics as in the temperate zone.

Biologists Stuart Pimm and Robert Askins have argued that the eastern USA witnessed few avian extinctions simply because most of its birds have very large geographic ranges. In South America, the situation is dramatically different.

South America is both the evolutionary cradle and current champion of global bird biodiversity; the authoritative regional list totals 3,368 species – around one third of all the word’s birds. Many of these species have small ranges, restricted to particular countries or even to particular mountains or forest types.

Unique features of the life history of tropical birds led to an overly rosy assessment of their future. Author and academic Bjorn Lomborg, for example, claimed that the lack of extinctions following the destruction of Brazil’s Atlantic forest showed that the biodiversity crisis is overblown.

But extinctions may lag far behind forest loss, a phenomenon known as the “extinction debt” which may be paid over hundreds of years.

Tropical birds typically live for longer than their temperate counterparts. Thus, the last pairs of rare species may make their last stand in their fragmented forest redoubts for decades. Indeed, several species have paid this price, and more may already be committed to extinction.

The last known Alagoas Foliage-gleaner photographed in Pernambuco, Brazil in November 2010
Ciro Albano/NE Brazil Birding

Need to develop strategies

The situation in northeast Brazil is particularly dire.

A few dozen Alagoas Antwrens cling to survival in less than six tiny forest patches. The Alagoas Foliage-gleaner, presented to science along with the Antwren for the first time in the 1980s, was known from only two patches. The last known individual was photographed for the final time in November 2011. We can only guess how many more species will be lost from this region where new species are discovered and others are disappearing on a near-annual basis.

But what of Amazonia, the last great tropical forest wilderness and bastion of tropical biodiversity?

Although deforestation rates have fallen since 2004, there are still grounds for concern. Pressure on existing protected areas from dam-building and mining interests is increasing, and the existing reserve network poorly protects the hardest hit regions.

Arable fields in eastern Amazonia, former forest haunts of the endemic Belem Curassow, illustrated in the inset to the right of the similar Bare-faced Curassow. This former species was last documented in the wild decades ago.
both images Alexander Charles Lees, curassow specimens ©Museu Paraense Emílio Goeldi

Furthermore, Amazonia is divided into different biogeographic regions known as ‘areas of endemism’ that each contain species found nowhere else. Even today, taxonomists continue to recognize new divisions in Amazonian birds, often elevating former subspecies to species status. The Belem Curassow was recently recognized as a species and occurs only in the most deforested part of the Amazon. The last documented record in the wild was over 35 years ago.

Unless a population is discovered in the embattled Gurupi reserve, this species may be the first recorded Amazonian bird extinction. Hot on its heels is the Iquitos Gnatcatcher, known only from a tiny and heavily deforested area of unique stunted forest in Peru. Only six pairs are known, and the bird has proven harder to find every year.

The Iquitos Gnatcatcher hangs by a thread in small patches of stunted forest near Iquitos, Peru. Only six pairs are known.
José Álvarez Alonso, used with permission

Some of these species need immediate and drastic conservation interventions, but their plight seems to be largely ignored by governments and international environmental groups. Restoring forest around these last fragments is crucial for long-term population viability.

However, for some species captive breeding with an eye to future reintroduction may be the only way forward. Such measures have already saved the Spix’s Macaw and Alagoas Curassow from global extinction – populations of these species exist only in captivity. However, while we have centuries of experience breeding parrots and gamebirds, we know far less about breeding small songbirds.

In fact, most of what we know about managing songbird populations comes from islands, and it is unclear how well this knowledge will translate to the mainland. Island species are adapted to maintain small populations and may be better able to recover from genetic bottlenecks. And, quick fixes such as controlling invasive predators have helped to restore populations. But mainland birds face a different suite of threats, dominated by habitat loss.

Clearly, we must not assume that tropical forest birds will prove as resilient to human activity as their temperate brethren. But though the situation is critical, we also see grounds for optimism.

In Peru, for instance, new endangered species legislation has convened a working group to develop a conservation strategy for the Iquitos Gnatcatcher. In the meantime, a small reserve has been created that protects the few remaining territories. Across the border in Brazil exciting plans are being drawn up to reintroduce the Alagoas Curassow back into the wild.

There is an immediate need to support and expand such actions. The next five to ten years will be critical for many species of South American birds teetering on the brink of extinction.

The Conversation

Alexander C. Lees, Postdoctoral Fellow at the Cornell Lab of Ornithology, Cornell University and Jacob B. Socolar, PhD Candidate in Ecology and Evolution, Princeton University

This article was originally published on The Conversation. Read the original article.

Journal Club 2015 Year-in-Review

Our UNM Ornithology Journal Club read 101 papers this year, ranging in year-of-publication from 1970-2016, and in impact-factor from below zero to 41. In addition to bird evolution & ecology, topics ranged from human genetics to geology, butterflies to malaria. Though we didn’t have time to discuss all 101, our consensus favorites were #’s 1, 12, 18, 20, 24, 25, 26, 30, 31, 40, 42, 48, 50, 52, 56, 64, 85, 88, 94, 101.

We originally intended to blog about each paper, but who has time to do that? Instead, here are our super-brief commentaries on each paper, in red text following each entry.

We welcome your opinions in the Comments section – particularly regarding ‘must-reads’ that we missed.

  1. Asghar, M., Hasselquist, D., Hansson, B., Zehtindjiev, P., Westerdahl, H., & Bensch, S. (2015). Chronic infection. Hidden costs of infection: chronic malaria accelerates telomere degradation and senescence in wild birds. Science, 347(6220), 436–438.
    This is the best paper we read all year. Novel empirical data convincingly showed that low-level chronic malaria infection leads to shortened telomeres and early death. This has profound implications for mechanisms of longevity and avian population biology in general (since avian malaria is everywhere).
  2. Assaf, Z. J., Petrov, D. A., & Blundell, J. R. (2015). Obstruction of adaptation in diploids by recessive, strongly deleterious alleles. Proceedings of the National Academy of Sciences, 112(20), E2658–E2666.
    A theoretical demonstration of a powerful idea that was completely new to us, but makes perfect sense — that deleterious recessive alleles that lurking in the genome pose an obstacle to rapid adaptation if they are linked to a beneficial allele. 
  3. Bacon, C. D., Silvestro, D., Jaramillo, C., Smith, B. T., Chakrabarty, P., & Antonelli, A. (2015). Biological evidence supports an early and complex emergence of the Isthmus of Panama. Proceedings of the National Academy of Sciences, 112(19), 6110–6115.
    This is a huge claim for Neotropical biogeography, and that makes this a very important paper. The devil is in the “and complex” part. Molecular clocks are still a bitch though, just as mid-Cenozoic animal dispersal between continents is still a conundrum.
  4. Bailey, R. I., Tesaker, M. R., Trier, C. N., & Saetre, G. P. (2015). Strong selection on male plumage in a hybrid zone between a hybrid bird species and one of its parents. Journal of Evolutionary Biology, 28(6), 1257–1269. fascinating narrow cline between Italian Sparrow and House Sparrow, centered on a high ridge of the Alps, near the Italy-Switzerland border. Crown color is claimed to be under strong selection, reinforcing reproductive isolation… there’s probably a lot more to this story.
  5. Barker, F. K., Burns, K. J., Klicka, J., Lanyon, S. M., & Lovette, I. J. (2015). New insights into New World biogeography: An integrated view from the phylogeny of blackbirds, cardinals, sparrows, tanagers, warblers, and allies. The Auk, 132(2), 333–348.
    We loved this paper, as the simple, rigorous description of the species-level phylogeny of the biggest New World songbird clade continues to illuminate how American bird communities came to be.
  6. Bhullar, B.-A. S., Morris, Z. S., Sefton, E. M., Tok, A., Tokita, M., Namkoong, B., et al. (2015). A molecular mechanism for the origin of a key evolutionary innovation, the bird beak and palate, revealed by an integrative approach to major transitions in vertebrate history. Evolution, 69(7), 1665–1677.
    This is nifty evo-devo. The authors pinpoint a “gene expression region” unique to birds that probably is responsible for the development of the beak. Then they knock it out in chicken embryos and produce something more similar to a dinosaur.
  7. Bloch, N. I., Price, T. D., & Chang, B. S. W. (2015). Evolutionary dynamics of Rh2 opsins in birds demonstrate an episode of accelerated evolution in the New World warblers (Setophaga). Molecular Ecology, 24(10), 2449–2462. liked this paper, even though statistical support for central finding was modest.
  8. Borowiec, M. L., Lee, E. K., Chiu, J. C., & Plachetzki, D. C. (2015). Dissecting phylogenetic signal and accounting for bias in whole-genome data sets: a case study of the Metazoa (pp. 1–39). and cnidarians are not sister taxa. Interesting. Our interest in this paper, however, was the proposed workflow for “minimizing systematic bias in whole genome-based phylogenetic analyses”.
  9. Brusatte, S. L., O’Connor, J. K., & Jarvis, E. D. (2015). The Origin and Diversification of Birds. Current Biology, 25(19), R888–R898.
    Nice 3-page summary of state of knowledge.
  10. Campagna, L., Gronau, I., Silveira, L. F., Siepel, A., & Lovette, I. J. (2015). Distinguishing noise from signal in patterns of genomic divergence in a highly polymorphic avian radiation. Molecular Ecology, 24(16), 4238–4251.
    Really nice empirical paper on a rapid radiation of seedeaters (little ground-dwelling tanagers). ddRad-Seq finds genes that can distinguish the species from one-another… but these skeptical authors then randomized the species-assignments for each individual and they found the same result — an important cautionary tale that highlights the seedeaters as a biological conundrum. A good reminder that it’s an exciting time to be studying bird speciation.
  11. Careau, V., & Garland, T., Jr. (2015). Energetics and behavior: many paths to understanding. Trends in Ecology & Evolution, 30(7), 365–366.
    A thought-provoking short commentary that points out that energy use does not necessarily reveal energy constraints. It concludes that correlative studies of links between energetics and personality (or other aspects of behavior) could be misleading. It’s always important to keep challenging the assumptions that prop up evolutionary claims of comparative studies.
  12. Claramunt, S., & Cracraft, J. (2015). A new time tree reveals Earth history’s imprint on the evolution of modern birds. Science Advances, 1(11), e1501005–e1501005.
    This was a great paper. The link here between cold climate and fast bird diversification will become text-book paradigm, and the basis for a new module in Ornithology class at UNM.
  13. Clarkson, C. S., Weetman, D., Essandoh, J., Yawson, A. E., Maslen, G., Manske, M., et al. (1AD). Adaptive introgression between Anopheles sibling species eliminates a major genomic island but not reproductive isolation. Nature Communications, 5, 1–10. Inter-species introgression is so hot right now.
  14. Cooper, N., Thomas, G. H., & Venditti, C. (2015). A cautionary note on the use of Ornstein Uhlenbeck models in macroevolutionary studies. Biological Journal of … Important for anyone thinking of applying O-U models for comparative analyses. We’ve always suspected there was a bit of voodoo in applying a “mean-reverting” model. These three smarter minds have now begun to clarify that for us.
  15. Cracraft, J., Houde, P., Ho, S. Y. W., Mindell, D. P., Fjeldså, J., Lindow, B., et al. (2015). Response to Comment on “Whole-genome analyses resolve early branches in the tree of life of modern birds”. Science, 349(6255), 1460–1460.
    This blustery, hand-wavey argument is remarkably informative — a great read! Summary: yes, the Mitchell et al. criticism of our methods is correct, but our results are probably close to correct anyway.
  16. De-Silva, D. L., Elias, M., Willmott, K., Mallet, J., & Day, J. J. (2015). Diversification of clearwing butterflies with the rise of the Andes. Journal of Biogeography, n/a–n/a.
    This is a good demonstration of a really thorough biogeographic analysis of a diverse Neotropical groups. Of course we love it every time the Andes are implicated, fitting our confirmation bias, just as we expected!
  17. Dierickx, E. G., Shultz, A. J., Sato, F., Hiraoka, T., & Edwards, S. V. (2015). Morphological and genomic comparisons of Hawaiian and Japanese Black-footed Albatrosses ( Phoebastria nigripes) using double digest RADseq: implications for conservation. Evolutionary Applications, 8(7), 662–678.
    Nice dataset showing that Black-footed Albatross have low evolutionary effective population size, and very recent divergence between Japan and Hawaii. So they have strong philopatry in real time — it does NOT mean that they can’t colonize new areas rapidly in evolutionary time.
  18. Duckworth, R. A., Belloni, V., & Anderson, S. R. (2015). Evolutionary ecology. Cycles of species replacement emerge from locally induced maternal effects on offspring behavior in a passerine bird. Science, 347(6224), 875–877.
    The connection between the maternal effects and the cycle of species replacement were a little fuzzy, but it didn’t matter — this paper was extremely interesting, and helped us understand the connections between post-fire regeneration and community composition in western US forest birds (specifically Mountain and Western Bluebirds).
  19. Duret, L., & Galtier, N. (2009). Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes. Annual Review of Genomics and Human Genetics, 10(1), 285–311.
    A 6-yr old paper, but describes a mechanism of increasing importance in comparative genomics: “This apparently unimportant feature of our molecular machinery, [GC-biased gene-conversion], has major evolutionary consequences.”
  20. Edwards, S. V., Xi, Z., Janke, A., Faircloth, B. C., McCormack, J. E., Glenn, T. C., et al. (2016). Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics. Molecular Phylogenetics and Evolution, 94(Part A), 447–462.
    Must-read for phylogeneticists. A convincing response to the biting criticisms of species-tree methods that were launched by Springer and Gatesy (and were unfortunately vituperative).
  21. Enard, D., Messer, P. W., & Petrov, D. A. (2014). Genome-wide signals of positive selection in human evolution. Genome Research, 24(6), 885–895.
    1000 genomes showed that adaptation was frequent during human evolution, and targeted mostly regulatory sequences.
  22. Engler, J. O., Secondi, J., Dawson, D. A., Elle, O., & Hochkirch, A. (2015). Range expansion and retraction along a moving contact zone has no effect on the genetic diversity of two passerine birds. Ecography, n/a–n/a.
    In mobile species such as Hippolais warblers, there’s no reason to expect differences in genetic diversity or structure between range edges and range center.
  23. Feduccia, A. (2014). Avian extinction at the end of the Cretaceous: Assessing the magnitude and subsequent explosive radiation. Cretaceous Research, 50, 1–15.
    An essay that provides perspective from a knowledgeable paleo-ornithologist. Although he has many controversial ideas on other topics, his 1995 Science paper on the avian big bang has been corroborated by many subsequent studies of fossils and DNA. 
  24. Fitzpatrick, M. C., & Keller, S. R. (2014). Ecological genomics meets community-level modelling of biodiversity: mapping the genomic landscape of current and future environmental adaptation. Ecology Letters, 18(1), 1–16.
    “We identify a threshold response to temperature in the circadian clock gene GIGANTEA-5 (GI5) [in balsam poplar].” That’s freaking cool!
  25. Foll, M., Gaggiotti, O. E., Daub, J. T., Vatsiou, A., & Excoffier, L. (2014). Widespread Signals of Convergent Adaptation to High Altitude in Asia and America. The American Journal of Human Genetics, 95(4), 394–407.
    This is an amazing demonstration of convergence on different continents — will definitely be core reading in our UNM High Altitude Biology Class.
  26. Fontaine, M. C., Pease, J. B., Steele, A., Waterhouse, R. M., Neafsey, D. E., Sharakhov, I. V., et al. (2015). Extensive introgression in a malaria vector species complex revealed by phylogenomics. Science, 347(6217), 1258524–1258524.
    A/The premier example of inter-species introgression.
  27. Frantz, L. A. F., Madsen, O., Megens, H.-J., Schraiber, J. G., Paudel, Y., Bosse, M., et al. (2015). Evolution of Tibetan wild boars. Nature Publishing Group, 47(3), 188–189.
    A critique of boar genomics paper (Li et al.) previously published in Nature; it seems that genomics can’t get enough of these cautionary tales. Yes, some genomics is sleight-of-hand.
  28. Freeman, B. G. (2015). Competitive Interactions upon Secondary Contact Drive Elevational Divergence in Tropical Birds. The American Naturalist, 186(4), 470–479.
    We were initially critical of this — circular reasoning, sampling biases, etc. — but the patterns as illustrated are pretty cool, even if some of our group thought that they were only masquerading as novel, and Freeman’s interpretations are probably right — yeah, we’re going to cite this afterall. Recommended reading.
  29. Friedman, N. R., & Remeš, V. (2015). Global geographic patterns of sexual size dimorphism in birds: support for a latitudinal trend? Ecography, n/a–n/a.
    A respectable ‘negative-results’ paper.
  30. Galen, S. C., Natarajan, C., Moriyama, H., Weber, R. E., Fago, A., Benham, P. M., et al. (2015). Contribution of a mutational hot spot to hemoglobin adaptation in high-altitude Andean house wrens. Proceedings of the National Academy of Sciences, 112(45), 13958–13963.
    OK, this is our paper — but hey, we love it.
  31. Giarla, T. C., & Esselstyn, J. A. (2015). The Challenges of Resolving a Rapid, Recent Radiation: Empirical and Simulated Phylogenomics of Philippine Shrews. Systematic Biology, 64(5), 727–740.
    This is an important paper because it showed that for a difficult phylogenetic problem, concatenation provided an answer, but species-tree analysis didn’t. The authors argued convincingly that concatenation was probably providing false high support.
  32. Gill, F. B. (2014). Species taxonomy of birds: Which null hypothesis? The Auk, 131(2), 150–161.
    We disagree.
  33. Good, J. M., Vanderpool, D., Keeble, S., & Bi, K. (2015). Negligible nuclear introgression despite complete mitochondrial capture between two species of chipmunks. Evolution, 69(8), 1961–1972.
    Two thumbs up — in many cases we have suspected that this is happening (mtDNA alone in jumping btwn taxa), but Good et al. show it convincingly. This is very important to keep in mind when interpreting phylogeographic datasets.
  34. Gossmann, T. I., Santure, A. W., Sheldon, B. C., Slate, J., & Zeng, K. (2014). Highly Variable Recombinational Landscape Modulates Efficacy of Natural Selection in Birds. Genome Biology and Evolution, 6(8), 2061–2075.
    Recombination abets selection. Cool.
  35. Guillot, G., & Rousset, F. (2013). Dismantling the Mantel tests. Methods in Ecology and Evolution, 4(4), 336–344.
    Wow, this is important. We’ve seen some 2014 and 2015 papers whose authors should have read this before using partial Mantel tests (which are very likely biased!).
  36. Hartmann, S. A., Schaefer, H. M., & Segelbacher, G. (2014). Genetic depletion at adaptive but not neutral loci in an endangered bird species. Molecular Ecology, 23(23), 5712–5725.
    The Pale-headed Brushfinch has a 200-hectare range! It’s microsats indicate ample genetic diversity. But an immune gene complex, TLR, has very low diversity, and TLR diversity was inversely related to survival (!). This is intriguing, even though sample sizes were necessarily small.
  37. Heers, A. M., & Dial, K. P. (2015). Wings versus legs in the avian bauplan: Development and evolution of alternative locomotor strategies. Evolution, 69(2), 305–320.
    Ornithologists should read this. Great illustration of developmental and evolutionary tradeoffs.
  38. Ho, S. Y. W., & Duchêne, S. (2014). Molecular-clock methods for estimating evolutionary rates and timescales. Molecular Ecology, 23(24), 5947–5965.
    We try to keep up with Ho’s papers on time-dependency of molecular rate calibrations. Fascinating, and still emerging. More empirical data needed.
  39. Ho, S., Duchêne, S., Molak, M., & Shapiro, B. (2015). Time‐dependent estimates of molecular evolutionary rates: evidence and causes. Molecular Ecology.
    See above.
  40. Hooper, D. M., & Price, T. D. (2015). Rates of karyotypic evolution in Estrildid finches differ between island and continental clades. Evolution, 69(4), 890–903.
    Highly recommended: “These results point to adaptation as the dominant mechanism driving fixation and suggest a role for gene flow in karyotype divergence.”
  41. Hosner, P. A., Braun, E. L., & Kimball, R. T. (2015). Land connectivity changes and global cooling shaped the colonization history and diversification of New World quail (Aves: Galliformes: Odontophoridae). Journal of Biogeography, 42(10), 1883–1895.
    This is the best example yet of Miocene avian colonization of the New World across the Bering landbridge.
  42. James, F. C. (1970). Geographic size variation in birds and its relationship to climate. Ecology.
    A classic, and still a great read. Wet-bulb Temperature. Dry-bulb Temperature. Gotta understand these to understand temperature effects on animal traits.
  43. Jehl, J. R., Jr, Henry, A. E., & Swanson, D. L. (2014). Ratios, adaptations, and the differential metabolic capability of avian flight muscles. Journal of Avian Biology, 46(2), 119–124.
  44. Jetz, W., Thomas, G. H., Joy, J. B., Redding, D. W., Hartmann, K., & Mooers, A. O. (2014). Global Distribution and Conservation of Evolutionary Distinctness in Birds. Current Biology, 24(9), 919–930.
    Data-rich. Put aside a full hour to stare at Figure 2’s global maps of evolutionary distinctness.
  45. Jones, M. R., & Good, J. M. (2015). Targeted capture in evolutionary and ecological genomics. Molecular Ecology, n/a–n/a.
    Authors are alum & friend of UNM Ornithology, and the technique is one that we’re investing in heavily, so naturally, we recommend this highly!
  46. Jønsson, K. A., Lessard, J.-P., & Ricklefs, R. E. (2015). The evolution of morphological diversity in continental assemblages of passerine birds. Evolution, 69(4), 879–889.
    A big analysis, with kind of a negative result (“idiosyncratic” patterns prevail. But we found this one bit of wisdom to be a gem: “…species within passerine clades are continuously replacing each other, which may lead to a more gradual filling of niche space over time, as opposed to rapid filling during an initial burst.”
  47. Kress, W. J. (2014). Valuing collections. Science, 346(6215), 1310–1310.
    Understated case, perhaps, but this pro-collecting editorial was a nice bonus to the Avian Phylogenomics burst of pubs in late 2014.
  48. Lamichhaney, S., Berglund, J., Almén, M. S., Maqbool, K., Grabherr, M., Martinez-Barrio, A., et al. (2015). Evolution of Darwin’s finches and their beaks revealed by genome sequencing. Nature, 1–16.
    Timed for Darwin Day, but influence will last. Recommended.
  49. Lavretsky, P., Engilis, A., Jr, Eadie, J. M., & Peters, J. L. (2015). Genetic admixture supports an ancient hybrid origin of the endangered Hawaiian duck. Journal of Evolutionary Biology, 28(5), 1005–1015.
    Very stimulating paper… not 100% convincing with respect to ‘ancient hybrid origin’, but debatable.
  50. Le Duc, D., Renaud, G., Krishnan, A., Almén, M. S., Huynen, L., Prohaska, S. J., et al. (2015). Kiwi genome provides insights into evolution of a nocturnal lifestyle. Genome Biology, 1–15.
    Typical of a genomics paper in that actual insights into biology were few, but we came away impressed with this paper anyway.
  51. Leisler, B., & Winkler, H. (2015). Evolution of island warblers: beyond bills and masses. Journal of Avian Biology, 46(3), 236–244.
    This is a great paper — bunches of morphological traits examined over bunches of island populations. Robust analyses, insightful interpretations.
  52. Londoño, G. A., Chappell, M. A., Castañeda, M. D. R., Jankowski, J. E., & Robinson, S. K. (2014). Basal metabolism in tropical birds: latitude, altitude, and the “pace of life.” Functional Ecology, 29(3), 338–346.
    One of our favorite papers of the year. Kudos to our colleagues at UF, UBC, UCR, and Cali. We’re looking forward to the next paper from this project.
  53. Lowe, C. B., Clarke, J. A., Baker, A. J., Haussler, D., & Edwards, S. V. (2015). Feather development genes and associated regulatory innovation predate the origin of Dinosauria. Molecular Biology and Evolution, 32(1), 23–28.
    Textbook demo of how genomes can be used to pinpoint trait origins.
  54. Lumley, A. J., Michalczyk, Ł., Kitson, J. J. N., Spurgin, L. G., Morrison, C. A., Godwin, J. L., et al. (2015). Sexual selection protects against extinction. Nature, 522(7557), 470–473.
    No. No it doesn’t. Not our fav paper, but perhaps a good illustration of a different perspective and approach to evolutionary biology.
  55. Macías-Duarte, A., & Conway, C. J. (2015). Spatial patterns in hydrogen isotope ratios in feathers of Burrowing Owls from western North America. The Auk, 132(1), 25–36.
    Deuterium is a low-resolution tool. Try something else.
  56. Mangano, V. D., & Modiano, D. (2014). ScienceDirect An evolutionary perspective of how infection drives human genome diversity: the case of malaria. Current Opinion in Immunology, 30, 39–47.
    Pathogens drive diversity, this review summarizes the empirical evidence for the co-evolutionary arms race that is closest to home.
  57. Marki, P. Z., Fabre, P.-H., Jønsson, K. A., Rahbek, C., Fjeldså, J., & Kennedy, J. D. (2015). Breeding system evolution influenced the geographic expansion and diversification of the core Corvoidea (Aves: Passeriformes). Evolution, 69(7), 1874–1924.
    Interesting to look at diversification and geography in light of breeding system. On the other hand, some dubious ancestral state estimation here, and I’m skeptical that the rate of cooperative breeding -> pair breeding transitions is much higher than the reverse, and that cooperative breeding is ancestral state for the clade.
  58. Mason, N. A., & Taylor, S. A. (2015). Differentially expressed genes match bill morphology and plumage despite largely undifferentiated genomes in a Holarctic songbird. Molecular Ecology, 24(12), 3009–3025.
    This is one of our favorite papers on the year. The apparent genetic identity between redpolls despite gene expression differences is a conundrum that needs solving.
  59. McCormack, J. E., Tsai, W. L. E., & Faircloth, B. C. (2015). Sequence capture of ultraconserved elements from bird museum specimens. Molecular Ecology Resources, n/a–n/a.
    Two thumbs up — more justification for the extensive time and effort we spend on collecting, specimen prep, and curation. Kudos to McCormack et al.
  60. McLean, B. S., Bell, K. C., Dunnum, J. L., Abrahamson, B., Colella, J. P., Deardorff, E. R., et al. (2015). Natural history collections-based research: progress, promise, and best practices. Journal of Mammalogy, gyv178–12.
    Our sister collection at MSB produced a damn good review. As useful for ornithologists as mammalogists (continuing the long-term convergence among the vertebrate-ologies).
  61. Merckx, V. S. F. T., Hendriks, K. P., Beentjes, K. K., Mennes, C. B., Becking, L. E., Peijnenburg, K. T. C. A., et al. (2015). Evolution of endemism on a young tropical mountain. Nature, 524(7565), 347–350.
    Kinabalu is awesome. This paper is futuristic in its comprehensive phylo treatment of a tropical biota. Impressive.
  62. Mitchell, K. J., Cooper, A., & Phillips, M. J. (2015). Comment on “Whole-genome analyses resolve early branches in the tree of life of modern birds.” Science, 349(6255), 1460–1460.
    A must read. We agree (but we don’t think it undercuts the importance of Jarvis et al. 2014).
  63. Montes, C., Cardona, A., Jaramillo, C., Pardo, A., Silva, J. C., Valencia, V., et al. (2015). Middle Miocene closure of the Central American Seaway. Science, 348(6231), 226–229. in light of Bacon et al., 2015, above.
  64. Natarajan, C., Hoffmann, F. G., Lanier, H. C., Wolf, C. J., Cheviron, Z. A., Spangler, M. L., et al. (2015). Intraspecific Polymorphism, Interspecific Divergence, and the Origins of Function-Altering Mutations in Deer Mouse Hemoglobin. Molecular Biology and Evolution, 32(4), 978–997.
    Outstanding integrative evolutionary genetics.
  65. Norris, L. C., Main, B. J., Lee, Y., Collier, T. C., Fofana, A., Cornel, A. J., & Lanzaro, G. C. (2015). Adaptive introgression in an African malaria mosquito coincident with the increased usage of insecticide-treated bed nets. Proceedings of the National Academy of Sciences, 112(3), 815–820.
    Awesome illustration of introgression as well as human-driven evolution.
  66. Ocampo-Peñuela, N., & Pimm, S. L. (2015). Elevational Ranges of Montane Birds and Deforestation in the Western Andes of Colombia. PloS One, 10(12), e0143311–15.
    “…as expected, [elevational] ranges were larger in forested transects.” Simple but profound.
  67. Pardo-Diaz, C., Salazar, C., Baxter, S. W., Merot, C., Figueiredo-Ready, W., Joron, M., et al. (2012). Adaptive Introgression across Species Boundaries in Heliconius Butterflies. PLoS Genetics, 8(6), e1002752–13.
    Repeated adaptive introgression from one species to another — awesome.
  68. Patterson, N., Moorjani, P., Luo, Y., & Mallick, S. (2012). Ancient admixture in human history. .
    Yes, there was a lot of admixture — a highly recommended analysis by the gurus in the field.
  69. Persons, W. S., IV, & Currie, P. J. (2015). Bristles before down: A new perspective on the functional origin of feathers. Evolution, 69(4), 857–862.
    This paper was popular among our undergrad evolution students. Very simple, clear evolutionary logic; as a result, it’s convincing that the first function of feathers was unlikely to have been insulation.
  70. Polechová, J., & Barton, N. H. (2015). Limits to adaptation along environmental gradients. Proceedings of the National Academy of Sciences, 112(20), 6401–6406.
    OK, this was too heavily theoretical for many of us… but we’re convinced of it’s importance, e.g.: “The theory predicts sharp range margins even in the absence of abrupt changes in the environment.” That’s pretty freaking cool. As is this: “gradual worsening of conditions across a species’ habitat may lead to a sudden range fragmentation, when adaptation to a wide span of conditions within a single species becomes impossible.”
  71. Prum, R. O., Berv, J. S., Dornburg, A., Field, D. J., Townsend, J. P., Lemmon, E. M., & Lemmon, A. R. (2015). A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature, 526(7574), 569–573.
    Ok, this is an undeniably excellent study. But in light of its hype we feel justified in being critical — this is no big advance over Jarvis et al. 2014. Possibly taxon-sampling effects on topology might have been over-played, but the next few years of progress in genomics will tell us whether or not that’s the case. The topological conflicts with Jarvis’ Figure 1 tree highlight the challenges that remain in deep Neoavian phylogeny.  I don’t think it would be going out on a limb to say that the exaBayes tree of Prum’s Fig. 1 has inflated node support values (nonetheless, it’s a spectacular figure). 
  72. Pyle, P., Engilis, A., Jr, & Kelt, D. A. (2015). Manual for Ageing and Sexing Birds of Bosque Fray Jorge National Park and Northcentral Chile, with Notes on Range and Breeding Seasonality, 1–156.
    Yeah, we bet this one went under your radar, but it is a trove of natural history for west slope Andean birds of northern Chile (and, by extension, sw Peru).
  73. Pyron, R. A. (2015). Post-molecular systematics and the future of phylogenetics. Trends in Ecology & Evolution, 30(7), 384–389.
    Useful, concise perspective on recent development in the field, but insufficiently nuanced. Appropriately skeptical of diversification analyses (but probably too harsh on comparative methods in general, by extension). Definitely worth a read, must-read for students.
  74. Qu, Y., Tian, S., Han, N., Zhao, H., Bin Gao, Fu, J., et al. (2015). Genetic responses to seasonal variation in altitudinal stress: whole-genome resequencing of great tit in eastern Himalayas. Nature Publishing Group, 1–10.
    Outstanding advance in high-altitude biology & ornithology.
  75. Rabosky, D. L., Title, P. O., & Huang, H. (2015). Minimal effects of latitude on present-day speciation rates in New World birds. Proceedings of the Royal Society of London B: Biological Sciences, 282(1809), 20142889–8.
    Great ‘negative-result’ paper.
  76. Reeve, A. H., Borregaard, M. K., & Fjeldså, J. (2015). Negative range size-abundance relationships in Indo-Pacific bird communities. Ecography, n/a–n/a.
    Very curious & counterintuitive findings, demands followup.
  77. Robbins, M. B., & Nyári, Á. S. (2014). Canada to Tierra del Fuego: species limits and historical biogeography of the Sedge Wren (Cistothorus platensis). The Wilson Journal of Ornithology, 126(4), 649–662.
    Widespread clade with lots of local adaptation and under-appreciated diversity — this is a super-valuable first-pass at its range-wide phylogeography.
  78. Robin, V. V., Vishnudas, C. K., Gupta, P., & Ramakrishnan, U. (2015). Deep and wide valleys drive nested phylogeographic patterns across a montane bird community. Proceedings of the Royal Society of London B: Biological Sciences, 282(1810), 20150861–8.
    Himalayan bird phylogeography emerging.
  79. Sánchez-González, L. A., Navarro-Sigüenza, A. G., Krabbe, N. K., Fjeldså, J., & García-Moreno, J. (2014). Diversification in the Andes: the Atlapetes brush-finches. Zoologica Scripta, 44(2), 135–152.
    Recommended only for fans of this clade.
  80. Schluter, D. (2016). Speciation, Ecological Opportunity, and Latitude. The American Naturalist, 187(1), 1–18.
  81. Serrano, D. A., & Hickerson, M. J. (2015). Model misspecification confounds the estimation of rates and exaggerates their time dependency. Molecular ….
    Critical accompaniment to the Ho papers.
  82. Slater, G. J. (2015). Iterative adaptive radiations of fossil canids show no evidence for diversity-dependent trait evolution. Proceedings of the National Academy of Sciences, 112(16), 4897–4902. This is a tremendous paleo dataset; eye-opening regarding canid-diversity during the Cenozoic (though we thought the power of the diversity-dependence thing was probably overplayed). Recommened.
  83. Smith, N. A., Chiappe, L. M., Clarke, J. A., Edwards, S. V., Nesbitt, S. J., Norell, M. A., et al. (2015). Rhetoric vs. reality: A commentary on “Bird Origins Anew” by A. Feduccia. The Auk, 132(2), 467–480.
    Originally, we flippantly wrote “‘Big Dino’ punishes non-conformity,” but it’s been pointed out to us that that is an unfair characterization. Hey, it’s a heavy-hitting author line — have a read for yourself.
  84. Springer, M. S., & Gatesy, J. (2016). Molecular Phylogenetics and Evolution. Molecular Phylogenetics and Evolution, 94(Part A), 1–33.
    Second in a series of though-provoking but overly aggressive attacks on species-tree methods. One one hand, the discussion of recombination effects on species-trees is fascinating. On the other hand, it’s written in a take-no-prisoners, combative style (a rarity for MPE, but another sign that the journal may have lost its edge).
  85. Steadman, D. W., Albury, N. A., Kakuk, B., Mead, J. I., Soto-Centeno, J. A., Singleton, H. M., & Franklin, J. (2015). Vertebrate community on an ice-age Caribbean island. Proceedings of the National Academy of Sciences, 201516490–9.
    One of the coolest papers of the year if you’re interested in global change. Utterly shocking to see how much the Bahamas avifauna has changed (for the worse!) over the past few thousand years.
  86. Stoltzfus, A., & McCandlish, D. M. (2015). Mutation-biased adaptation in Andean house wrens. Proceedings of the National Academy of Sciences, 112(45), 13753–13754. persepective piece on mutational influences on adaptation.
  87. Storz, J. F., Bridgham, J. T., Kelly, S. A., & Garland, T., Jr. (2015). Genetic approaches in comparative and evolutionary physiology. American Journal of Physiology – Regulatory, Integrative and Comparative Physiology, 309(3), R197–R214.
    Important review on evolutionary genetics and physiology from a UNM Ornithology collaborator.
  88. Suh, A., Smeds, L., & Ellegren, H. (2015). The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds. PLOS Biology, 13(8), e1002224–18.
    Figure 1 went viral on Twitter, for good reason. This is an outstanding followup to Jarvis et al. 2014, an enlightening analysis of the intractable nodes at the base of Neoaves.
  89. Toews, D. P. L. (2015). Biological species and taxonomic species: Will a new null hypothesis help? (A comment on Gill 2014). The Auk, 132(1), 78–81.
    We agree.
  90. Tufts, D. M., Natarajan, C., Revsbech, I. G., Projecto-Garcia, J., Hoffmann, F. G., Weber, R. E., et al. (2015). Epistasis Constrains Mutational Pathways of Hemoglobin Adaptation in High-Altitude Pikas. Molecular Biology and Evolution, 32(2), 287–298.
    Outstanding study of hemoglobin adaptation, demonstrating  interactions among different mutations (epistasis).
  91. Villegas, M., & Garitano-Zavala, Á. (2010). Bird community responses to different urban conditions in La Paz, Bolivia. Urban Ecosystems, 13(3), 375–391.
    You probably missed this one, but we think that an analysis of the avifauna of the world’s highest-altitude capital is fascinating for what’s on it and what’s not. Urban ornithology is emerging and La Paz’s unique bird list is pretty freaking cool.
  92. Violle, C., Reich, P. B., Pacala, S. W., Enquist, B. J., & Kattge, J. (2014). The emergence and promise of functional biogeography. Proceedings of the National Academy of Sciences, 111(38), 13690–13696.
    Yeah, we buy in bigtime – functional biogeography is the future.
  93. Wang, I. J., & Bradburd, G. S. (2014). Isolation by environment. Molecular Ecology, 23(23), 5649–5662.
    IBE. A must read.
  94. Warren, D. L., Cardillo, M., Rosauer, D. F., & Bolnick, D. I. (2014). Mistaking geography for biology: inferring processes from species distributions. Trends in Ecology & Evolution, 29(10), 572–580.
    Although inferring processes from species distributions is one of our fav things to do, it should not be attempted at home. Seriously, we applaud this much-needed critique. Macroecologists take note of this, please!
  95. Weir, J. T., Faccio, M. S., Pulido-Santacruz, P., Barrera-Guzmán, A. O., & Aleixo, A. (2015). Hybridization in headwater regions, and the role of rivers as drivers of speciation in Amazonian birds. Evolution, 69(7), 1823–1834.
    We liked this paper a lot, but we don’t think it was a story about headwaters, but rather one about environmental gradients causing the confluence of multiple hybrid zones in one small area. The conceptual framework, while elegant, was simplified in a way that probably missed the mark. Nonetheless, highly recommended for those interested in Amazonian biogeography.
  96. Wiersma, P., Nowak, B., & Williams, J. B. (2012). Small organ size contributes to the slow pace of life in tropical birds. Journal of Experimental Biology, 215(10), 1662–1669.
    We missed this when it came out, but now think that organ size holds many more secrets. Great paper with nice data.
  97. Willis, C. G., & Davis, C. C. (2015). Rethinking migration. Science, 348(6236), 766–766.
    Important background in light of Bacon et al. 2015, above.
  98. Winger, B. M., & Bates, J. M. (2015). The tempo of trait divergence in geographic isolation: Avian speciation across the Marañon Valley of Peru. Evolution, 69(3), 772–787.
    Plumage divergence and mtDNA divergence are linked. This is a very convincing demonstration of that link.
  99. Winger, B. M., Hosner, P. A., Bravo, G. A., Cuervo, A. M., Aristizábal, N., Cueto, L. E., & Bates, J. M. (2015). Inferring speciation history in the Andes with reduced-representation sequence data: an example in the bay-backed antpittas (Aves; Grallariidae; Grallaria hypoleucas. l.). Molecular Ecology, 24(24), 6256–6277.
    Elegant phylogeography study of a charasmatic Andean taxon. Recommended.
  100. Zancolli, G., Rödel, M.-O., Steffan-Dewenter, I., & Storfer, A. (2014). Comparative landscape genetics of two river frog species occurring at different elevations on Mount Kilimanjaro. Molecular Ecology, 23(20), 4989–5002.
    Nice study of African frog landscape genetics — effects of elevation (high species more fragmented), and human settlements (on low elev species).
  101. Zhang, G., Li, C., Li, Q., Li, B., Larkin, D. M., Lee, C., et al. (2014). Comparative genomics reveals insights into avian genome evolution and adaptation. Science, 346(6215), 1311–1320. Undeniably a landmark paper, even if not a fine work of literature.  Rather, it’s a loosely connected series of vignettes, suffering from writing-by-committee (factual mistakes and frustrating omissions of key citations). Nonetheless important and pioneering in several ways. A must-read.

Birds in the Anthropocene: Scientific evidence of rapid change

The world is changing at an unprecedented pace. Warming of two to four degrees Celsius appears to be inevitable by the end of this century, at which time the human population will exceed 10 billion. This is the Anthropocene, a new geological epoch in which humans are the dominant ecological force. Emerging scientific evidence shows that our impacts are dramatically affecting birds.

We need not look further than Albuquerque backyards to see that bird populations respond quickly to environmental change. Before the post-war expansion of the city, most of it was desert grassland, with Horned Larks aplenty. Now the larks have been replaced by species that subsist wholly on urban subsidies: water, trees, and birdseed. The birdseed feeds White-winged Doves and House Sparrows, which are then eaten by Cooper’s Hawks and Greater Roadrunners, respectively. Native species such as Bullock’s Orioles, Black-headed Grosbeaks, and Black-chinned Hummingbirds have expanded their populations into the mulberries and Chinese elms that line the streets.

Consistent with our local experience, ornithologists measuring bird populations are reporting evidence of rapid change throughout the world. Here are four striking examples:

  1. Humans are directly eliminating one of the world’s most intelligent bird species, the African Gray Parrot, from its wild habitats in west Africa. A new study has shown that populations have declined by 90-99% in Ghana over the past two decades (Annorbah, Collar, & Marsden, 2015). The primary cause is trapping for the pet trade. Like wild elephants, wild African Gray Parrots cannot withstand unfettered market forces.
  2. Indirect human impacts are also contributing to bird population declines. In a pristine Amazonian rainforest, the entire avifauna has declined in abundance by 40-50% since 2008 (Blake & Loiselle, 2015). The study site in northeastern Ecuador has been monitored since 2001 by Bette Loiselle and John Blake of the University of Florida. The leading hypothesis for the decline, according to Loiselle and Blake, is climate change.
  3. Long-term declines in survival rates of North American birds seem to have both direct and indirect anthropogenic causes. A recent study of data from breeding-season banding stations revealed persistently reduced survival rates following the invasion of West Nile Virus, ~15 years ago (George et al., 2015). Particularly hard-hit species include Purple Finch, Swainson’s Thrush, Wrentit, and White-crowned Sparrow. The authors found significant declines in survival rates for about half of the North American species that they examined (23 out of 49). They argued that disease effects could be magnified by habitat destruction and climate warming.
  4. Climate change may help some bird populations, at least temporarily. A new study showed that understory forest birds are thriving in high-altitude forests on Kilimanjaro, where both low and high elevation species increased in abundance over a 20-year period (Dulle et al., 2015). Even this news could be seen as ominous, however, as anyone can see that the cone-shaped Kilimanjaro gets smaller towards the top. Other recent studies have shown that bird species are moving upslope in New Guinea, Costa Rica, and Peru. The ‘climate escalator’ seems to be a global phenomenon.

Figure for Bosque Tracks 2015 Anthropocene articleWhat can we do to help bird populations survive the Anthropocene?

First, we can think globally. Our leading climate scientist, Dr. James Hansen, argues that preventing catastrophic global warming is only possible if we put a price on fossil fuel consumption that accounts for its true cost. This suggests that those of us who abhor the prospect of avian mass extinction should advocate a carbon tax, an idea that has support from both the left (Bernie Sanders) and right (Gregory Mankiw) sides of the political spectrum.

Second, we can act locally. It is possible to reduce bird mortality by our direct actions. For example, we can keep our cats inside. The outdoor cats that we feed and the feral cats that our communities tolerate are major sources of mortality for birds. A 2013 study scientifically estimated the impacts of domestic cats on birds (Loss, Will, & Marra, 2013). Out of ~84 million pet cats in the contiguous United States, about half are allowed outside, and these kill ~1 billion birds per year; feral (unowned) domestic cats kill another ~1.8 billion. This year, Australia launched an effort to cull ~2 million feral cats to reduce stress on its native wildlife populations. In the United States, public awareness of the wildlife carnage inflicted by free-ranging domestic cats is relatively low. Compared to rising carbon dioxide and melting icecaps, lack of awareness seems eminently solvable.

Annorbah, N. N. D., Collar, N. J., & Marsden, S. J. (2015). Trade and habitat change virtually eliminate the Grey Parrot Psittacus erithacus from Ghana. Ibis, in press.

Blake, J. G., & Loiselle, B. A. (2015). Enigmatic declines in bird numbers in lowland forest of eastern Ecuador may be a consequence of climate change. PeerJ, 3, e1177.

Dulle, H. I., Ferger, S. W., Cordeiro, N. J., Howell, K. M., Schleuning, M., Böhning-Gaese, K., & Hof, C. (2015). Changes in abundances of forest understorey birds on Africa’s highest mountain suggest subtle effects of climate change. Diversity and Distributions, in press.

George, T. L., Harrigan, R. J., LaManna, J. A., DeSante, D. F., Saracco, J. F., & Smith, T. B. (2015). Persistent impacts of West Nile virus on North American bird populations. Proceedings of the National Academy of Sciences of the United States of America, 112(46), 14290–14294.

Loss, S. R., Will, T., & Marra, P. P. (2013). The impact of free-ranging domestic cats on wildlife of the United States. Nature Communications, 4, 1396.

Best Clade Ever? The New World nine-primaried songbirds.

They’re ~811 species of songbirds that share a common ancestor. They’re small to medium-sized, handsome to gaudy, fast-moving, abundant to rare, temperate to tropical, highly migratory to completely sedentary. From the North Slope of Alaska to Tierra del Fuego, the New World avifauna wouldn’t be the same without them. They are the New World nine-primaried oscines (also known as superfamily Emberizoidea), and they included the warblers, blackbirds, sparrows, cardinals, tanagers, and a grab-bag of less notable groups.

A recent phylogenetic study by Keith Barker, and with collaborators John Klicka, Irby Lovette, Kevin Burns, and Scott Lanyon, has provided a near complete, time-calibrated species-level phylogeny of this group (Barker et al. 2013, Barker et al. 2015). This has finally given us a firm basis for a revision of the family and genus-level classification of this group. Inspired by the species-level phylogeny and proposed new phylogenetic classification of this major group, our journal-club group at UNM set out to [re-]learn the families and their characteristics. We teamed up to build an informal Powerpoint ‘guide’ to the families and genera, including the basics of their diversity and distribution. We included images of nearly all of the 201 genera, in 90 slides. We share it with you here on Slideshare.

Images from allaboutbirds blogpost on gaudiest tanagers, clockwise from upper left: Golden-hooded Tanager by Raúl Vega, Opal-rumped Tanager by Joao Quental, Paradise Tanager by Joao Quental, Blue-winged Mountain-Tanager by Bryan Hix, Grass-green Tanager by chris.w.birder, Black-chinned Mountain-Tanager by Ian Billenness, via Neotropical Birds.

One of the coolest things resulting from the Barker et al. studies was a robust description of the history of dispersal between North and South America with the group, summarized in Figure 2 from Barker et al. (2015):

barker et al 15-fig-backbonejpg

The figure shows how the North American ancestor of the nine-primaried oscines colonized South America several times as it diversified, starting way before the closure of the Isthmus of Panama. Overall, there are a surprisingly small number of dispersal events between the continents, and huge variation in diversity and distributional extent among subclades. Most interestingly, it appears that a common ancestor of tanagers and cardinals lived in South America ~13 million years ago. Other groups of nine-primaried oscines that made it to South America (blackbirds, warblers, sparrows) are recent arrivals in comparison.

These papers are a joy to peruse. They allow an ornithologist or birder to organize their existing knowledge of bird traits and distributions according to evolutionary descent. A couple of things that jump out as truly surprising are the deep phylogenetic distinctness of several Caribbean lineages and the extensive inter-continental dispersal that occurred before the closure of the Isthmus of Panama, in both directions. Sometimes the purest and most elegant scientific advances come from improving our description of diversity in the form of a robust, informative phylogeny — we now have that for the nine-primaried oscines songbirds.

Literature cited:

Barker, F. K., K. J. Burns, J. Klicka, S. M. Lanyon, and I. J. Lovette. 2013. Going to extremes: Contrasting rates of diversification in a recent radiation of New World passerine birds. Systematic Biology 62:298-320.

Barker, F. K., K. J. Burns, J. Klicka, S. M. Lanyon, and I. J. Lovette. 2015. New insights into New World biogeography: An integrated view from the phylogeny of blackbirds, cardinals, sparrows, tanagers, warblers, and allies. The Auk: 132(2):333-348.