John E McCormack

Occidental College, Los Ángeles, California, United States

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Publications (36)244.97 Total impact

  • John E. McCormack, James M. Maley
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    ABSTRACT: A recent study by Zink et al. (2013) raises questions about how to interpret negative results in studies when the distinctness of a species of conservation concern is in question. Zink et al. found no evidence for genetic or ecological distinctness of the coastal California Gnatcatcher (Polioptila californica californica). We discuss why the genetic markers they chose were not well suited to the question of distinctness and how they overinterpreted negative results in their genetic and ecological analyses. We reanalyze their genetic data and find evidence that several genetic loci show significant differentiation in the coastal California Gnatcatchers. We provide recommendations for best practices in determining distinctness in phenotype, genetics, and ecology for California Gnatcatchers and other populations of conservation concern.
    The Auk 04/2015; 132(2):380-388. DOI:10.1642/AUK-14-184.1 · 2.63 Impact Factor
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    ABSTRACT: Manakins (Pipridae) are well know for elaborate male sexual displays and ornate plumage coloration, both of which are thought to have evolved as a consequence of lekking breeding, the prevalent mating system in the family. Less attention has been paid to a handful of ‘drab’ manakin species, in which sexual dimorphism appears to be reduced or absent. Using character reconstruction, we show that these ‘exceptions to the rule’ represent phylogenetically independent cases of losses in sexual dimorphism, and as such could provide a focal group to investigate the link between changes in morphology and in life history (e.g. mating system). We take a first step in this direction by focusing on two subspecies of the putatively monomorphic green manakin Xenopipo holochlora to formally confirm that the species is sexually monomorphic in size and plumage color and test the prediction that sexual monomorphism is associated with the loss of lekking behavior in this species. Our results show that size dimorphism is present but limited in the green manakin, with substantial overlap in male and female morphometric measures, and that sexes are largely monochromatic (including from an avian perspective), despite marked coloration differences between subspecies. Behavioral observations indicate that males do not form leks and do not engage in elaborate sexual displays, that there is no stable pair bond formation, and that females provide parental care alone. These findings are consistent with the idea that changes in mating behavior may have driven changes in morphology in Pipridae, and we encourage similar studies on other drab manakins to better understand this relationship.
    Journal of Avian Biology 02/2015; 46(3). DOI:10.1111/jav.00545 · 2.24 Impact Factor
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    ABSTRACT: To provide context for the diversification of archosaurs--the group that includes crocodilians, dinosaurs, and birds--we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs. Copyright © 2014, American Association for the Advancement of Science.
    Science 12/2014; 346. DOI:10.1126/science.1254449 · 31.48 Impact Factor
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    ABSTRACT: To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago. Copyright © 2014, American Association for the Advancement of Science.
    Science 12/2014; 346(6215):1320-1331. DOI:10.1126/science.1253451 · 31.48 Impact Factor
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    ABSTRACT: To provide context for the diversification of archosaurs—the group that includes crocodilians, dinosaurs, and birds—we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs.
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    ABSTRACT: Additional methods, results and references
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    ABSTRACT: Since the recognition that allopatric speciation can be induced by large-scale reconfigurations of the landscape that isolate formerly continuous populations, such as the separation of continents by plate tectonics, the uplift of mountains or the formation of large rivers, landscape change has been viewed as a primary driver of biological diversification. This process is referred to in biogeography as vicariance1. In the most species-rich region of the world, the Neotropics, the sundering of populations associated with the Andean uplift is ascribed this principal role in speciation. An alternative model posits that rather than being directly linked to landscape change, allopatric speciation is initiated to a greater extent by dispersal events, with the principal drivers of speciation being organism-specific abilities to persist and disperse in the landscape. Landscape change is not a necessity for speciation in this model8. Here we show that spatial and temporal patterns of genetic differentiation in Neotropical birds are highly discordant across lineages and are not reconcilable with a model linking speciation solely to landscape change. Instead, the strongest predictors of speciation are the amount of time a lineage has persisted in the landscape and the ability of birds to move through the landscape matrix. These results, augmented by the observation that most species-level diversity originated after episodes of major Andean uplift in the Neogene period, suggest that dispersal and differentiation on a matrix previously shaped by large-scale landscape events was a major driver of avian speciation in lowland Neotropical rainforests.
    Nature 09/2014; DOI:10.1038/nature13687 · 42.35 Impact Factor
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    ABSTRACT: Haldane's Rule, the tendency for the heterogametic sex to show reduced fertility in hybrid crosses, can obscure the signal of gene flow in mtDNA between species where females are heterogametic. Therefore, it is important when studying speciation and species limits in female-heterogametic species like birds to assess the signature of gene flow in the nuclear genome as well. We studied introgression of microsatellites and mtDNA across a secondary contact zone between coastal and interior lineages of Western Scrub-Jays (Aphelocoma californica) to test for a signature of Haldane's Rule: a narrower cline of introgression in mtDNA compared to nuclear markers.
    BMC Evolutionary Biology 06/2014; 14(1):135. DOI:10.1186/1471-2148-14-135 · 3.41 Impact Factor
  • John E. McCormack, Madhvi X. Venkatraman
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    ABSTRACT: Ancient hybridization is difficult to detect and is often surmised from conflicting patterns between phenotypic and genetic data sets that are difficult to explain with alternative hypotheses. Here, a fortuitous macromutation in a microsatellite locus allows an unusually distinctive footprint of ancient introgression to be inferred between two highly divergent bird species that began to speciate in the Late Miocene. A cline of distinctive high-repeat-number (large) alleles at a locus in the Mexican Jay (Aphelocoma wollweberi), which predominantly has low-repeat-number (small) alleles, reaches its highest frequency near the range border with Transvolcanic Jays (A. ultramarina), which are fixed for large alleles, indicating gene flow. The gene flow is not recent, however, because very few of the allelic states are shared between Mexican Jays and Transvolcanic Jays. Ancient gene flow is also more plausible than current gene flow because prior mitochondrial DNA results show no evidence of current dispersal between the ranges of the species, and Mexican Jays with introgressed large alleles are not phenotypically more similar to Transvolcanic Jays, as would be expected with recent hybridization. Although bifurcations in the tree of life are often assumed to belie complex histories of introgression, our results provide some of the clearest evidence that speciation can survive one or multiple bouts of gene flow with no detectable trace in the phenotypes and mtDNA of the constituent species. Received 31 October 2012, accepted 16 March 2013.
    The Auk 07/2013; 130(3):469-475. DOI:10.1525/auk.2013.12208 · 2.63 Impact Factor
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    ABSTRACT: Evolutionary relationships among birds in Neoaves, the clade comprising the vast majority of avian diversity, have vexed systematists due to the ancient, rapid radiation of numerous lineages. We applied a new phylogenomic approach to resolve relationships in Neoaves using target enrichment (sequence capture) and high-throughput sequencing of ultraconserved elements (UCEs) in avian genomes. We collected sequence data from UCE loci for 32 members of Neoaves and one outgroup (chicken) and analyzed data sets that differed in their amount of missing data. An alignment of 1,541 loci that allowed missing data was 87% complete and resulted in a highly resolved phylogeny with broad agreement between the Bayesian and maximum-likelihood (ML) trees. Although results from the 100% complete matrix of 416 UCE loci were similar, the Bayesian and ML trees differed to a greater extent in this analysis, suggesting that increasing from 416 to 1,541 loci led to increased stability and resolution of the tree. Novel results of our study include surprisingly close relationships between phenotypically divergent bird families, such as tropicbirds (Phaethontidae) and the sunbittern (Eurypygidae) as well as between bustards (Otididae) and turacos (Musophagidae). This phylogeny bolsters support for monophyletic waterbird and landbird clades and also strongly supports controversial results from previous studies, including the sister relationship between passerines and parrots and the non-monophyly of raptorial birds in the hawk and falcon families. Although significant challenges remain to fully resolving some of the deep relationships in Neoaves, especially among lineages outside the waterbirds and landbirds, this study suggests that increased data will yield an increasingly resolved avian phylogeny.
    PLoS ONE 01/2013; 8(1):e54848. DOI:10.1371/journal.pone.0054848 · 3.53 Impact Factor
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    Molecular Phylogenetics and Evolution 01/2013; 66(1):440. DOI:10.1016/j.ympev.2012.09.009 · 4.02 Impact Factor
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    John E McCormack, Brant C Faircloth
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    ABSTRACT: It has been a tumultuous 5 years in phylogeography and phylogenetics during which both fields have struggled to harness the power of next‐generation sequencing (NGS) (Ekblom & Galindo ; McCormack et al. ). Fortunately, several methodological approaches appear to be taking root. In this issue of Molecular Ecology, O'Neill et al. ) employ one such method – parallel tagged sequencing (PTS) – to elucidate the phylogeography of a tiger salamander (Ambystoma tigrinum) species complex. This study demonstrates a practical application of NGS on a scale appropriate (and not overkill) for most biologists interested in phylogeography (~100 loci for ~100 individuals), and their results highlight several analytical challenges that lie ahead for researchers employing NGS techniques.
    Molecular Ecology 01/2013; 22(1):19-20. DOI:10.1111/mec.12050 · 5.84 Impact Factor
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    ABSTRACT: We present the first genomic-scale analysis addressing the phylogenetic position of turtles, using over 1000 loci from representatives of all major reptile lineages including tuatara. Previously, studies of morphological traits positioned turtles either at the base of the reptile tree or with lizards, snakes and tuatara (lepidosaurs), whereas molecular analyses typically allied turtles with crocodiles and birds (archosaurs). A recent analysis of shared microRNA families found that turtles are more closely related to lepidosaurs. To test this hypothesis with data from many single-copy nuclear loci dispersed throughout the genome, we used sequence capture, high-throughput sequencing and published genomes to obtain sequences from 1145 ultraconserved elements (UCEs) and their variable flanking DNA. The resulting phylogeny provides overwhelming support for the hypothesis that turtles evolved from a common ancestor of birds and crocodilians, rejecting the hypothesized relationship between turtles and lepidosaurs.
    Biology letters 05/2012; 8(5):783-6. DOI:10.1098/rsbl.2012.0331 · 3.43 Impact Factor
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    ABSTRACT: The International Crocodilian Genomes Working Group (ICGWG) will sequence and assemble the American alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus porosus) and Indian gharial (Gavialis gangeticus) genomes. The status of these projects and our planned analyses are described.
    Genome biology 01/2012; 13(1):415. DOI:10.1186/gb-2012-13-1-415 · 10.47 Impact Factor
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    ABSTRACT: Although massively parallel sequencing has facilitated large-scale DNA sequencing, comparisons among distantly related species rely upon small portions of the genome that are easily aligned. Methods are needed to efficiently obtain comparable DNA fragments prior to massively parallel sequencing, particularly for biologists working with non-model organisms. We introduce a new class of molecular marker, anchored by ultraconserved genomic elements (UCEs), that universally enable target enrichment and sequencing of thousands of orthologous loci across species separated by hundreds of millions of years of evolution. Our analyses here focus on use of UCE markers in Amniota because UCEs and phylogenetic relationships are well-known in some amniotes. We perform an in silico experiment to demonstrate that sequence flanking 2030 UCEs contains information sufficient to enable unambiguous recovery of the established primate phylogeny. We extend this experiment by performing an in vitro enrichment of 2386 UCE-anchored loci from nine, non-model avian species. We then use alignments of 854 of these loci to unambiguously recover the established evolutionary relationships within and among three ancient bird lineages. Because many organismal lineages have UCEs, this type of genetic marker and the analytical framework we outline can be applied across the tree of life, potentially reshaping our understanding of phylogeny at many taxonomic levels.
    Systematic Biology 01/2012; 61(5):717-26. DOI:10.1093/sysbio/sys004 · 11.53 Impact Factor
  • J E McCormack, J M Maley, S M Hird
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    ABSTRACT: Next generation sequencing (NGS) technologies are revolutionizing many biological disciplines but have been slow to take root in phylogeography . This is partly due to the difficulty of using NGS to sequence orthologous DNA fragments for many individuals at ...
    Molecular Phylogenetics and Evolution 01/2012; 62:397-406. · 4.02 Impact Factor
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    ABSTRACT: Phylogenomics offers the potential to fully resolve the Tree of Life, but increasing genomic coverage also reveals conflicting evolutionary histories among genes, demanding new analytical strategies for elucidating a single history of life. Here, we outline a phylogenomic approach using a novel class of phylogenetic markers derived from ultraconserved elements and flanking DNA. Using species-tree analysis that accounts for discord among hundreds of independent loci, we show that this class of marker is useful for recovering deep-level phylogeny in placental mammals. In broad outline, our phylogeny agrees with recent phylogenomic studies of mammals, including several formerly controversial relationships. Our results also inform two outstanding questions in placental mammal phylogeny involving rapid speciation, where species-tree methods are particularly needed. Contrary to most phylogenomic studies, our study supports a first-diverging placental mammal lineage that includes elephants and tenrecs (Afrotheria). The level of conflict among gene histories is consistent with this basal divergence occurring in or near a phylogenetic "anomaly zone" where a failure to account for coalescent stochasticity will mislead phylogenetic inference. Addressing a long-standing phylogenetic mystery, we find some support from a high genomic coverage data set for a traditional placement of bats (Chiroptera) sister to a clade containing Perissodactyla, Cetartiodactyla, and Carnivora, and not nested within the latter clade, as has been suggested recently, although other results were conflicting. One of the most remarkable findings of our study is that ultraconserved elements and their flanking DNA are a rich source of phylogenetic information with strong potential for application across Amniotes.
    Genome Research 12/2011; 22(4):746-54. DOI:10.1101/gr.125864.111 · 13.85 Impact Factor
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    ABSTRACT: This is a time of unprecedented transition in DNA sequencing technologies. Next-generation sequencing (NGS) clearly holds promise for fast and cost-effective generation of multilocus sequence data for phylogeography and phylogenetics. However, the focus on non-model organisms, in addition to uncertainty about which sample preparation methods and analyses are appropriate for different research questions and evolutionary timescales, have contributed to a lag in the application of NGS to these fields. Here, we outline some of the major obstacles specific to the application of NGS to phylogeography and phylogenetics, including the focus on non-model organisms, the necessity of obtaining orthologous loci in a cost-effective manner, and the predominate use of gene trees in these fields. We describe the most promising methods of sample preparation that address these challenges. Methods that reduce the genome by restriction digest and manual size selection are most appropriate for studies at the intraspecific level, whereas methods that target specific genomic regions (i.e., target enrichment or sequence capture) have wider applicability from the population level to deep-level phylogenomics. Additionally, we give an overview of how to analyze NGS data to arrive at data sets applicable to the standard toolkit of phylogeography and phylogenetics, including initial data processing to alignment and genotype calling (both SNPs and loci involving many SNPs). Even though whole-genome sequencing is likely to become affordable rather soon, because phylogeography and phylogenetics rely on analysis of hundreds of individuals in many cases, methods that reduce the genome to a subset of loci should remain more cost-effective for some time to come.
    Molecular Phylogenetics and Evolution 12/2011; 66(2). DOI:10.1016/j.ympev.2011.12.007 · 4.02 Impact Factor
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    ABSTRACT: Next generation sequencing (NGS) technologies are revolutionizing many biological disciplines but have been slow to take root in phylogeography. This is partly due to the difficulty of using NGS to sequence orthologous DNA fragments for many individuals at low cost. We explore cases of recent divergence in four phylogenetically diverse avian systems using a method for quick and cost-effective generation of primary DNA sequence data using pyrosequencing. NGS data were processed using an analytical pipeline that reduces many reads into two called alleles per locus per individual. Using single nucleotide polymorphisms (SNPs) mined from the loci, we detected population differentiation in each of the four bird systems, including: a case of ecological speciation in rails (Rallus); a rapid postglacial radiation in the genus Junco; recent in situ speciation among hummingbirds (Trochilus) in Jamaica; and subspecies of white-crowned sparrows (Zonotrichia leucophrys) along the Pacific coast. The number of recovered loci aligning closely to chromosomal locations on the zebra finch (Taeniopygia guttata) genome was highly correlated to the size of the chromosome, suggesting that loci are randomly distributed throughout the genome. Using eight loci found in Zonotrichia and Junco lineages, we were also able to generate a species tree of these sparrow sister genera, demonstrating the potential of this method for generating data amenable to coalescent-based analysis. We discuss improvements that should enhance the method's utility for primary data generation.
    Molecular Phylogenetics and Evolution 10/2011; 62(1):397-406. DOI:10.1016/j.ympev.2011.10.012 · 4.02 Impact Factor
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    ABSTRACT: We unite genetic data with a robust test of niche divergence to test the hypothesis that patterns of gene flow between two lineages of the nine-banded armadillo are influenced by their climatic niches. We collected Geographical Information System (GIS) data on climate using locality information from 111 individuals from two lineages that had associated genetic material. We tested whether niches of these lineages were more conserved or divergent than the background environments of their geographic ranges and found evidence for niche conservatism on two axes and no evidence for divergence on any axis. To address the role of niche similarity in gene flow, we genotyped the 111 individuals at five microsatellite loci and tested whether admixed individuals tended to be located in parts of multidimensional environmental space (E-space) shared between the two lineages. We observed an asymmetrical pattern of overlap, in which the West lineage's E-space was almost completely included inside East lineage's E-space. Genetic admixture levels were significantly higher in the West lineage and, for both lineages, in shared portions of E-space. This suggests that niche similarity can facilitate gene flow among disjunct groups with moderate-to-good dispersal capabilities, contrasting with the prevailing view of niche conservatism as a diversifying force.
    Evolution 09/2011; 65(9):2470-80. DOI:10.1111/j.1558-5646.2011.01329.x · 4.66 Impact Factor

Publication Stats

1k Citations
244.97 Total Impact Points

Institutions

  • 2011–2015
    • Occidental College
      Los Ángeles, California, United States
  • 2011–2013
    • Louisiana State University
      • Museum of Natural Science
      Baton Rouge, Louisiana, United States
  • 2009–2011
    • University of Michigan
      • Department of Ecology and Evolutionary Biology
      Ann Arbor, Michigan, United States
  • 2005–2009
    • University of California, Los Angeles
      • Department of Ecology and Evolutionary Biology
      Los Angeles, California, United States
  • 2007
    • The University of Arizona
      • Department of Ecology and Evolutionary Biology
      Tucson, AZ, United States