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. http://doi.org/10.1126/science.1261121
    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. http://doi.org/10.1073/pnas.1424949112
    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. http://doi.org/10.1073/pnas.1423853112
    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. http://doi.org/10.1111/jeb.12652A 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. http://doi.org/10.1642/AUK-14-110.1
    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. http://doi.org/10.1111/evo.12684
    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. http://doi.org/10.1111/mec.13180We 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). http://dx.doi.org/10.1101/013946Ctenophores 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. http://doi.org/10.1016/j.cub.2015.08.003
    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. http://doi.org/10.1111/mec.13314
    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. http://doi.org/10.1016/j.tree.2015.04.007
    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. http://doi.org/10.1126/sciadv.1501005
    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. http://doi.org/10.1038/ncomms5248 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 …http://onlinelibrary.wiley.com/doi/10.1111/bij.12701/full. 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. http://doi.org/10.1126/science.aab1578
    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. http://doi.org/10.1111/jbi.12611
    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. http://doi.org/10.1111/eva.12274
    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. http://doi.org/10.1126/science.1260154
    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. http://doi.org/10.1146/annurev-genom-082908-150001
    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. http://doi.org/10.1016/j.ympev.2015.10.027
    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. http://doi.org/10.1101/gr.164822.113
    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. http://doi.org/10.1111/ecog.01520
    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. http://doi.org/10.1016/j.cretres.2014.03.009
    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. http://doi.org/10.1111/ele.12376
    “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. http://doi.org/10.1016/j.ajhg.2014.09.002
    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. http://doi.org/10.1126/science.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. http://doi.org/10.1038/ng.3197
    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. http://doi.org/10.1086/682703
    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. http://doi.org/10.1111/ecog.01531
    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. http://doi.org/10.1073/pnas.1507300112
    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. http://doi.org/10.1093/sysbio/syv029
    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. http://doi.org/10.1642/AUK-13-206.1
    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. http://doi.org/10.1111/evo.12712
    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. http://doi.org/10.1093/gbe/evu157
    Recombination abets selection. Cool.
  35. Guillot, G., & Rousset, F. (2013). Dismantling the Mantel tests. Methods in Ecology and Evolution, 4(4), 336–344. http://doi.org/10.1111/2041-210x.12018
    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. http://doi.org/10.1111/mec.12975
    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. http://doi.org/10.1111/evo.12576
    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. http://doi.org/10.1111/mec.12953
    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. http://doi.org/10.1111/evo.12633
    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. http://doi.org/10.1111/jbi.12555
    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. http://doi.org/10.1111/jav.00506
    Recommended.
  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. http://doi.org/10.1016/j.cub.2014.03.011
    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. http://doi.org/10.1111/mec.13304
    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. http://doi.org/10.1111/evo.12622
    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. http://doi.org/10.1126/science.aaa4115
    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. http://doi.org/10.1038/nature14181
    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. http://doi.org/10.1111/jeb.12637
    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. http://doi.org/10.1186/s13059-015-0711-4
    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. http://doi.org/10.1111/jav.00509
    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. http://doi.org/10.1111/1365-2435.12348
    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. http://doi.org/10.1093/molbev/msu309
    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. http://doi.org/10.1038/nature14419
    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. http://doi.org/10.1642/AUK-13-061.1
    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. http://doi.org/10.1016/j.coi.2014.06.004
    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. http://doi.org/10.1111/evo.12695
    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. http://doi.org/10.1111/mec.13140
    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. http://doi.org/10.1111/1755-0998.12466
    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. http://doi.org/10.1093/jmammal/gyv178
    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. http://doi.org/10.1038/nature14949
    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. http://doi.org/10.1126/science.aab1062
    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. http://doi.org/10.1126/science.aaa2815Important 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. http://doi.org/10.1093/molbev/msu403
    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. http://doi.org/10.1073/pnas.1418892112
    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. http://doi.org/10.1371/journal.pone.0143311
    “…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. http://doi.org/10.1371/journal.pgen.1002752
    Repeated adaptive introgression from one species to another — awesome.
  68. Patterson, N., Moorjani, P., Luo, Y., & Mallick, S. (2012). Ancient admixture in human history. . http://doi.org/10.1534/genetics.112.145037/-/DC1
    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. http://doi.org/10.1111/evo.12634
    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. http://doi.org/10.1073/pnas.1421515112
    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. http://doi.org/10.1038/nature15697
    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. http://doi.org/10.1016/j.tree.2015.04.016
    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. http://doi.org/10.1038/srep14256
    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. http://doi.org/10.1098/rspb.2014.2889
    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. http://doi.org/10.1111/ecog.01622
    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. http://doi.org/10.1676/13-162.1
    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. http://doi.org/10.1098/rspb.2015.0861
    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. http://doi.org/10.1111/zsc.12088
    Recommended only for fans of this clade.
  80. Schluter, D. (2016). Speciation, Ecological Opportunity, and Latitude. The American Naturalist, 187(1), 1–18. http://doi.org/10.1086/684193
    Wisdom.
  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. http://doi.org/10.1073/pnas.1403666111. 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. http://doi.org/10.1642/AUK-14-203.1
    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. http://doi.org/10.1016/j.ympev.2015.07.018
    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. http://doi.org/10.1073/pnas.1516490112
    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. http://doi.org/10.1073/pnas.1518490112Outstanding 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. http://doi.org/10.1152/ajpregu.00100.2015
    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. http://doi.org/10.1371/journal.pbio.1002224
    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. http://doi.org/10.1642/AUK-14-138.1
    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. http://doi.org/10.1093/molbev/msu311
    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. http://doi.org/10.1007/s11252-010-0126-7
    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. http://doi.org/10.1073/pnas.1415442111
    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. http://doi.org/10.1111/mec.12938
    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. http://doi.org/10.1016/j.tree.2014.08.003
    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. http://doi.org/10.1111/evo.12696
    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. http://doi.org/10.1242/jeb.065144
    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. http://doi.org/10.1126/science.348.6236.766-a
    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. http://doi.org/10.1111/evo.12607
    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. http://doi.org/10.1111/mec.13477
    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. http://doi.org/10.1111/mec.12921
    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. http://doi.org/10.1126/science.1251385. 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.
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3 thoughts on “Journal Club 2015 Year-in-Review

  1. Thanks a lot for this excellent review; it’s great to see how many interesting papers escaped me this year! I’m not sure how to interpret the following quote, though:

    Some call him crazy. Yeah, right… crazy as a Hesperornis. If you’re calling the skeptic crazy, it might be time to check your own kool-aid.

    Is this about Feduccia’s “big bang” model of neornithine evolution? That’d make sense, because that’s what the paper in question dealt with, but it also seems quite unlikely, since something very close to Feduccia’s views on the topic is mainstream within the paleornithological community, and has been so for some time now. A lot of other paleontologists have argued that the absence of neornithine fossils from Cretaceous rocks is real rather than artifactual, and that the explosive basal radiation of Neoaves supported by multiple lines of evidence must have happened after the K/Pg boundary rather than before it, contrary to molecular dating analyses. Besides Feduccia, this was also the position of Bleiweiss (1998), Benton (1999), Fara & Benton (2000), Fountaine et al. (2005), Longrich et al. (2011), or Ksepka & Boyd (2012), to list just a few papers that were published prior to Feduccia’s (2014) review. Sure, many other people (especially molecular workers) have disagreed, but Feduccia’s model is far from heterodox, and I don’t think he’s ever been called “crazy” because of it.

    Presenting Feduccia as someone who’s called “crazy” for being a “skeptic” would make much more sense if it were a reference to his views on the origin of birds, which are entirely unrelated to the focus of his 2014 paper cited above. If that’s the case, well, yeah, he’s worked hard to earn that reputation. I fail to see how he can justifiably be called a skeptic — to me, at least, skepticism means refusing to accept a belief until it has been supported with sufficiently robust evidence, but not afterwards. If you still reject a hypothesis even though there’s an overwhelming amount of evidence supporting it, the proper term is not “skeptic” but “denier”, and that’s arguably the best way to describe Feduccia with regard to his views on the origin of birds after 1998 or so. His publications on the issue often have more in common with creationist writing than with science: numerous factual inaccuracies, blatant self-contradictions (detailed in Paul 2002; Prum 2003), straw man arguments, false dichotomies, conflation of unrelated questions (notably, the idea that birds can either have a terrestrial dinosaurian ancestor that evolved flight from the ground up, or an arboreal basal-archosaurian ancestor that developed flight from the trees down — arboreal dinosaurs are assumed to be impossible virtually by definition), confirmation bias (algorithmic phylogenetics is bad, unless the analysis in question supports one of Feduccia’s pet hypotheses), exaggerated rhetoric, and self-pitying cries of “censorship by lack of citation” (Feduccia 2009: 415). This has been detailed in a number of papers of which the Smith et al. (2015) review cited above is just the most recent example: see (if you don’t already know them) Norell & Chiappe (1996), Padian (2001), Witmer (2002), or Prum (2003).

    Some people react to all of this with platitudes about how Feduccia’s “criticisms” are healthy and useful for science since they can at least provoke a critical reexamination of the evidence for the theropod origin of birds, but that’s just not true — his critique lacks both substance and logical coherence. (Leaving aside the logic of the argument, which is itself highly suspect — do we really want more papers out there about the luminiferous aether, you know, just to prevent special relativity from turning into a dogma? Are we justified in “punish[ing] non-conformity”, to use your own words, when it comes to the phlogiston theory of combustion?) In short, I don’t think that “crazy” is the right word to use, but I don’t think Feduccia’s doing science with his writings on bird origins, either — “old sage” or not.

    A loosely connected series of vignettes, suffering from writing-by-committee (factual mistakes and frustrating omissions of key citations).

    Interesting — what factual mistakes are there in Zhang et al. (2014)? If you already discussed this somewhere online, a link would be much appreciated.

    Refs:

    Benton MJ 1999 Early origins of modern birds and mammals: molecules vs. morphology. BioEssays 21(12): 1043–51

    Bleiweiss R 1998 Fossil gap analysis supports early Tertiary origin of trophically diverse avian orders. Geology 26(4): 323–6

    Fara E, Benton MJ 2000 The fossil record of Cretaceous tetrapods. Palaios 15: 161–5

    Feduccia A 2009 A colorful mesozoic [sic] menagerie. [Review of: Feathered Dinosaurs: The Origin of Birds by John Long.] Trends Ecol Evol 24(8): 415–6

    Fountaine TMR, Benton MJ, Dyke GJ, Nudds RL 2005 The quality of the fossil record of Mesozoic birds. Proc R Soc B 272(1560): 289–94

    Ksepka DT, Boyd CA 2012 Quantifying historical trends in the completeness of the fossil record and the contributing factors: an example using Aves. Paleobiol 38(1): 112–25

    Longrich NR, Tokaryk T, Field DJ 2011 Mass extinction of birds at the Cretaceous–Paleogene (K–Pg) boundary. Proc Natl Acad Sci USA 108(37): 15253–7

    Norell MA, Chiappe LM 1996 Flight from reason [Review of: The Origin and Evolution of Birds by Alan Feduccia.] Nature 384(6606): 230

    Padian K 2001 The false issues of bird origins: an historiographic perspective. 485–99 in Gauthier JA, Gall LF, eds. New Perspectives on the Origin and Early Evolution of Birds. New Haven, CT: Yale Univ Press

    Paul GS 2002 Dinosaurs of the Air: The Evolution and Loss of Flight in Dinosaurs and Birds. Baltimore, MD: Johns Hopkins Univ Press

    Prum RO 2003 Are current critiques of the theropod origin of birds science? Rebuttal to Feduccia (2002). Auk 120(2): 550–61

    Witmer LM 2002 The debate on avian ancestry: phylogeny, function, and fossils. 3–30 in Chiappe LM, Witmer LM, eds. Mesozoic Birds: Above the Heads of Dinosaurs. Berkeley, CA: Univ of California Press

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    • Dear David,
      Your eloquent reply makes me feel slightly ashamed of my hasty, flippant remarks (which I’m about to edit for tone). Feduccia is clearly a lightning rod, and means many things to different people. He clearly was a pioneer in describing the avian big bang in his 1995 Science paper, subsequently corroborated by the other references that you provided, and more. Regarding bird-dinosaur relationships, I suspect that Feduccia has committed all of the rhetorical sins of which he has been accused. I also don’t doubt that his basal-archosaur hypothesis is wrong. So why does he still get sympathy and admiration? I think it boils down to this: the phylogenetic position of birds among theropods is frequently asserted with too much certainty, while the pitfalls that are inherent to morphological cladistics are overlooked. And that is as far as I wish to wade into the issue — thanks again for your point of view.

      Chris W.
      PS. Regarding Zhang et al., one of the mistakes regards the range of genome sizes reported in birds, a mistake that would have been easily remedied looking at Wright et al. 2014, Proc. Roy. Soc. B 281(1779) (published 11 months earlier). If I went on I’d be picking nits, when I really should just acknowledge that it’s landmark paper, because it is.

      Liked by 1 person

      • Hi Chris,

        Thanks a lot for your reply and for editing the original article. I still disagree slightly with the notion that too much certainty is sometimes attributed to the theropod origin of birds. It’s not obvious why it should be viewed as any less certain than comparable hypotheses whose acceptance is entirely uncontroversial – say, the therapsid origin of mammals. It’s true that the current consensus on the phylogenetic position of birds only emerged in the late 1970s, while a synapsid origin for mammals has been well-established since the 19th century, but as far as the amount of supporting data is concerned, the two hypotheses are quite well matched. I do agree that there are lots of problems with morphological phylogenetics, and that paleontologists would probably do well to acknowledge them and think about them more often than they currently do. However, suggesting that every single analysis published in the last 30 years came to the same wrong conclusion (which would have to be the case if the theropod hypothesis of the origin of birds were wrong) would require a mind-boggling amount of special pleading. A lot more could be said, but I want to respect your wish not to dig into the issue any further – in fact, what I wrote above is probably already too long.

        Also, many thanks for answering my question about Zhang et al. (2014), and for the ref to the Wright et al. paper, which I’ll be sure to read. I’m really happy to have discovered your blog (it’s an awesome addition to my bird evo blogroll), and I’ll definitely continue to follow it. If you’re thinking about making some of your Journal Club discussions public (either here, or on Twitter, or maybe even as a podcast), I’d be extremely interested in hearing what you have to say!

        Liked by 1 person

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