* denotes undergraduate coauthor

40. Bryson, Jr. RW, WE Savary, AJ Zellmer, RB Bury & JE McCormack. 2016. Genomic data reveal ancient microendemism in forest scorpions across the California Floristic Province. Molecular Ecology. Accepted. Link to early view article

39. Bryson, Jr. RW, BC Faircloth, WLE Tsai, JE McCormack & J Klicka. 2016. Target enrichment of thousands of ultraconserved elements sheds new light on the early relationships within New World sparrows (Aves: Passerellidae). The Auk: Ornithological Advances: 133: 451-458. (PDF)

38. Alvarez S, JF Salter*, JE McCormack & B Milá. 2016. Speciation in mountain refugia: phylogeography and demographic history of the pine siskin and black-capped siskin complex. Journal of Avian Biology: 47: 335-345. (PDF)

37. Edwards SV, Z Xi, A Janke, BC Faircloth, JE McCormack, TC Glenn, B Zhong, S Wu, EM Lemmon, AR Lemmon, AD Leache, L Liu, CC Davis. 2015. Implementing and testing the multispecies coalescent model: a valuable paradigm for phylogenomics. Molecular Phylogenetics & Evolution 94: 447-462. Link to open access PDF

36. Toews DPL, L Campagna, SA Taylor, CN Balakrishnan, DT Baldassarre, PE Deane-Coe, MG Harvey, DM Hooper, DE Irwin, CD Judy, NA Mason, JE McCormack, KG McCracken, CH Oliveros, RJ Safran, ESC Scordato, K Faust Stryjewski, A Tigano, JAC Uy, BM Winger. 2016. Genomic approaches to understanding population divergence and speciation in birds. The Auk: Ornithological Advances 133: 13-30. (PDF)

35. McCormack JE, WLE Tsai & BC Faircloth. 2016. Sequence capture of ultraconserved elements from bird museum specimens. Molecular Ecology Resources, forthcoming in special issue on sequence capture. (PDF)

34. Kaplan M, P Heimes & McCormack JE. 2015. Contributions to the morphology of Plectrohyla mykter (Anura: Hylidae), with comments on some controversial characters and the diagnosis of this species. Caldasia 37: 211-220. Link to open access PDF

33. Ribiero RD, McCormack JE, HG Alvarez, L Carrasco, GF Grether, P Mena, R Sedano, TB Smith & J Karubian. 2015. Loss of sexual dimorphism is associated with loss of lekking behavior in the green manakin Xenopipo holochora. Journal of Avian Biology 46: 307-314. (PDF)

32. McCormack JE & JM Maley. 2014. Commentary: Interpreting negative results with conservation implications: another look at distinctness of coastal California Gnatcatchers. The Auk: Ornithological Advances 132: 380-388. Link to open access PDF.

31. Green RE & 54 co-authors. 2014. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science 346: 1254449. (PDF)

30. Jarvis ED & 109 co-authors. 2014. Whole genome analyses resolve early branches in the tree of life of modern birds. Science 346: 1320-1331. (PDF)

29. Smith BT, JE McCormack, AM Cuervo, MJ Hickerson, A Aleixo, CD Cadena, J Pérez-Emán, CW Burney, X Xie, MG Harvey, BC Faircloth, TC Glenn, EP Derryberry, J Prejean*, S Fields* & RT Brumfield. 2014. The drivers of tropical speciation. Nature 515: 406-409. (PDF)

28. Gowen FC, JM Maley, C Cicero, AT Peterson, BC Faircloth, TC Warr* & JE McCormack. 2014. Speciation in Western Scrub-Jays, Haldane's rule, and genetic clines in secondary contact. BMC Evolutionary Biology. Link to open access PDF.

27. McCormack JE & MX Venkatraman*. 2013. A distinctive genetic footprint of ancient hybridization. The Auk: 130: 469-475. (PDF)

26. McCormack JE, MG Harvey, BC Faircloth, NG Crawford, TC Glenn & RT Brumfield. 2013. A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing. PLoS One 8(1): e54848. Link to open access article

Over 10,000 views and 100 social shares on PLoS One. Great blog coverage here and here. Altmetric score of 120, placing it top 99%ile of nearly 2 million articles in terms of media attention.

25. McCormack JE & BC Faircloth. 2013. Next-generation phylogenetics takes root. Molecular Ecology 22: 19-21. doi: 10.1111/mec.12050 (PDF)

24. McCormack JE, SM Hird, AJ Zellmer, BC Carstens & RT Brumfield. 2013. Applications of next-generation sequencing to phylogeography and phylogenetics. Molecular Phylogenetics and Evolution 66: 526-538. doi: 10.1016/j.ympev.2011.12.007 (PDF)

Still the most highly downloaded paper at MPE over a year after being published.

23. Crawford NG, BC Faircloth, JE McCormack, RT Brumfield, K Winker, and TC Glenn. 2012. More than 1000 ultraconserved elements provide evidence that turtles are the sister group to archosaurs. Biology Letters 8: 783-786. doi: 10.1098/rsbl.2012.0331 (PDF)

Popular press coverage at The Reptile Channel and Elements and Science Friday Blog.

22. St. John JA and 47 co-authors. 2012. Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biology 13: 415. Link to open access article

21. McCormack JE, BC Faircloth, NG Crawford, PA Gowaty, RT Brumfield, TC Glenn. 2012. Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species tree analysis. Genome Research 22: 746-754. doi: 10:1101/gr.125864.111 (PDF)

*** Must Read Article according to Faculty of 1000 ***

20. BC Faircloth, JE McCormack, NG Crawford, MG Harvey, RT Brumfield & TC Glenn. 2012. Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Systematic Biology 61: 717-726. doi: 10.1093/sysbio/sys004 (PDF)

19. McCormack JE, JM Maley, SM Hird, EP Derryberry, GR Graves & RT Brumfield. 2012. Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences. Molecular Phylogenetics and Evolution 62: 397-406. doi: 10.1016/j.ympev.2011.10.012 (PDF)

Important note: there is a type-o in the primer sequence for one of the EcoRI adaptors listed in Table 1. It should read AATTGGTACGCAGTCTAC. In the paper, the last two base pairs are reversed. A corrigendum can be found here.

18. Berg EC, RA Aldredge, AT Peterson & JE McCormack. 2012. New phylogenetic information suggests both an increase and at least one loss of cooperative breeding during the evolutionary history of Aphelocoma jays. Evolutionary Ecology 26: 43-54. doi: 10.1007/s10682-011-9492-8 (PDF)

17. Arteaga MC, JE McCormack, LA Eguiarte & RA Medellín. 2011. Genetic admixture in multidimensional niche space: asymmetrical niche similarity promotes gene flow in armadillos (Dasypus novemcinctus). Evolution 65: 2470-2480. (PDF)

*** Recommended Article by Faculty of 1000 ***

16. McCormack JE, J Heled, KS Delaney, AT Peterson & LL Knowles. 2011. Calibrating divergence times on species tree versus gene trees: Implications for speciation history of Aphelocoma jays. Evolution 65:184-202 (PDF)

Note: the ability to add fossil calibrations to species trees has been added as a feature of BEAST v.1.7

15. McCormack JE, AJ Zellmer & LL Knowles. 2010. Does niche divergence accompany allopatric divergence in Aphelocoma jays as predicted under ecological speciation?: Insights from tests with niche models. Evolution 64:1231-1244 (PDF)

Madhvi Venkatraman's annotated Niche Tests for Dummies
Joe Manthey's detailed instructions for conducting niche divergence tests
My instructions for conducting niche divergence test
Stata routine for calculating observed niche divergence
Stata routine for conducting jackknife replicates of background divergence
Note: on 10/2/13 the jackknife background routine was modified so that the PCA occurs before the resampling, meaning that the PCA only occurs once and is not repeated for every replicate. While there is no evidence the previous way was wrong, the new way seems more theoretically sound. Also, users might want to play around with the % resampling, changing 75 to lower, more conservative values like 25 or the actual number of observed points. Again, there does not seem to be sound theoretical reasons for any particular value, but users are always encouraged to perform sensitivity analyses.

14. McCormack JE & EC Berg. 2010. Small-scale divergence in egg color along an elevation gradient in the Mexican Jay: a condition-dependent response? The Auk 127:35-43 (PDF)

13. McCormack JE, H Huang & LL Knowles. 2009. Maximum-likelihood estimates of species trees: how accuracy of phylogenetic inference depends upon the divergence history and sampling design. Systematic Biology 58:501-508 (PDF)

12. Pease KM, A Freedman, JP Pollinger, WP Buermann, JE McCormack, J Rodzen, J Banks, E Meredith, V Bleich, K Jones & RK Wayne. 2009. Landscape genetics of California mule deer (Odocoileus hemionus): the roles of ecological and historical factors in generating differentiation. Molecular Ecology 18:1848-1862 (PDF)

11. Berg EC, JE McCormack & TB Smith. 2009. Test of an adaptive hypothesis for egg speckling along an elevational gradient in a population of Mexican jays (Aphelocoma ultramarina). Journal of Avian Biology 40:448-452 (PDF)

10. McCormack JE, H Huang & LL Knowles. 2009. Sky islands. Pages 839-843 in Encyclopedia of Islands (Gillespie, RG and D Clague, eds.). University of California Press: Berkeley, CA (PDF)

9. McCormack JE & TB Smith. 2008. Niche expansion leads to small-scale adaptive divergence along an elevation gradient in a medium-sized passerine bird. Proceedings of the Royal Society B 275:2155-2164 (PDF)

8. McCormack JE, BS Bowen & TB Smith. 2008. Integrating paleoecology and genetics of bird populations in two sky island archipelagos. BMC Biology 6:28 (PDF)

Focus of minireview: Baker, AJ. 2008. Islands in the sky: the impact of Pleistocene climate cycles on biodiversity. Journal of Biology 7:32 Link

7. McCormack JE, AT Peterson, E Bonaccorso & TB Smith. 2008. Speciation in the highlands of Mexico: genetic and phenotypic divergence in the Mexican jay (Aphelocoma ultramarina). Molecular Ecology 17:2505-2521 (PDF)

6. McCormack JE & JL Brown. 2008. Mexican jay (Aphelocoma ultramarina). In The Birds of North America Online (ed. A Poole). Cornell Laboratory of Ornithology: Ithaca, NY. Available at: http://bna.birds.cornell.edu/bna/species/118/articles/introduction

5. Milá B, JE McCormack, G Castañeda, TB Smith & RK Wayne. 2007. Recent postglacial range expansion drives the rapid diversification of a songbird lineage in the genus Junco. Proceedings of the Royal Society B 274:2653-2660 (PDF)

4. McCormack JE, P Jablonski & JL Brown. 2007. Producer-scrounger roles and the effect of dominance on preferential joining in a free-living group of Mexican jays (Aphelocoma ultramarina). Behaviour 144:967-982 (PDF)

3. McCormack JE, G Castañeda-Guayasamin & G Levandoski. 2007. Sierra Santa Rosa: an oasis of bird diversity in arid northern Mexico. Ornitología Neotropical 18:369-377 (PDF)

2. McCormack JE, G Castañeda Guayasamin, B Milá & F Heredia-Pineda. 2005. Slate-throated redstarts (Myioborus miniatus) breeding in Maderas del Carmen, Coahuila, Mexico. Southwestern Naturalist 50:501-503 (PDF)

1. Avilés L, J McCormack, A Cutter & T Bukowski. 2000. Precise, highly female-biased sex ratios in a social spider. Proceedings of the Royal Society B 267:1445-1449 (PDF)