Kevin G McCracken

University of Miami, كورال غيبلز، فلوريدا, Florida, United States

Are you Kevin G McCracken?

Claim your profile

Publications (64)249.25 Total impact

  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Many species have Holarctic distributions that extend across Europe, Asia, and North America. Most genetics research on these species has examined only mitochondrial (mt) DNA, which has revealed wide variance in divergence between Old World (OW) and New World (NW) populations, ranging from shallow, unstructured genealogies to deeply divergent lineages. In this study, we sequenced 20 nuclear introns to test for concordant patterns of OW-NW differentiation between mtDNA and nuclear (nu) DNA for six lineages of Holarctic ducks (genus Anas). Genetic differentiation for both marker types varied widely among these lineages (idiosyncratic population histories), but mtDNA and nuDNA divergence within lineages was not significantly correlated. Moreover, compared to the association between mtDNA and nuDNA divergence observed among different species, OW-NW nuDNA differentiation was generally lower than mtDNA divergence, at least for lineages with deeply divergent mtDNA. Furthermore, coalescent estimates indicated significantly higher rates of gene flow for nuDNA than mtDNA for four of the six lineages. Thus, Holarctic ducks show prominent mito-nuclear discord between OW and NW populations, and we reject differences in sorting rates as the sole cause of the within-species discord. Male-mediated intercontinental gene flow is likely a leading contributor to this discord, although selection could also cause elevated mtDNA divergence relative to weak nuDNA differentiation. The population genetics of these ducks contribute to growing evidence that mtDNA can be an unreliable indicator of stage of speciation, and that more holistic approaches are needed for species delimitation.This article is protected by copyright. All rights reserved.
    Molecular Ecology 06/2014; 23(12):2961-2974. · 6.28 Impact Factor
  • Source
    Conservation Genetics 06/2014; 15(3):509–520. · 2.18 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Consistent responses by various organisms to common environmental pressures represent strong evidence of natural selection driving geographical variation. According to Bergmann's and Allen's rules, animals from colder habitats are larger and have smaller limbs than those from warmer habitats to minimize heat loss. Although evidence supporting both rules in different organisms exists, most studies have considered only elevational or latitudinal temperature gradients. We tested for the effects of temperature associated with both elevation and latitude on body and appendage size of torrent ducks (Merganetta armata), a widespread species in Andean rivers. We found a negative relationship between body size and temperature across latitude consistent with Bergmann's rule, whereas there was a positive relationship between these variables along replicate elevational gradients at different latitudes. Limb-size variation did not support Allen's rule along latitude, nor along elevation. High-elevation ducks were smaller and had longer wings than those inhabiting lower elevations within a river. We hypothesize that temperature is likely a major selective pressure acting on morphology across latitudes, although hypoxia or air density may be more important along elevational gradients. We conclude that the effect of temperature on morphology, and hence the likelihood of documenting ecogeographical 'rules', depends on the environmental context in which temperature variation is examined.
    Biological Journal of the Linnean Society 03/2014; 111(4):850–862. · 2.41 Impact Factor
  • Source
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Sheldgeese of the genus Chloephaga are waterfowl (Anatidae) endemic to mainland South America and the Falkland Islands (Malvinas). Continental populations of three species C. picta, C. poliocephala, and C. rubidiceps breed in Patagonia and Tierra del Fuego and migrate northwards to winter in central Argentina and Chile. These continental populations have declined by > 50% in the past 30 years due to direct hunting to control crop damage and by the introduction of the grey fox Dusicyon griseus to their breeding grounds in Tierra del Fuego. The continental population of C. rubidiceps is critically endangered, estimated to be < 1,000 individuals. While no historic popu- lation size estimates exist for C. rubidiceps in its wintering grounds, the breeding population in Tierra del Fuego was estimated to number several thousand individuals in the 1950s. In contrast, the C. rubidiceps population in the Falkland Islands (Malvinas) is non-migratory and stable with > 42,000 individuals, as is the Falkland Islands (Malvinas) population of C. picta leucoptera with > 138,000 individuals. Here we use sequence data from the mitochondrial DNA control region to quantify genetic divergence between insular and continental populations of these two species of sheldgeese. Chloephaga rubidiceps and C. picta showed significant intraspecific differentiation of 1.0% and 0.6%, respectively. In both cases, mainland and insular populations were reciprocally monophyletic and did not share mtDNA haplotypes. These results suggest that the insular and continental populations of C. rubidiceps and C. picta are genetically distinct and that female-mediated gene flow is restricted. We recommend a reevaluation of the threat category status of the continental C. rubidiceps population, under IUCN guidelines. It is necessary to implement urgent actions for the conservation of this critically endangered population.
    Bird Conservation International 03/2014; 24(1):59–71. · 1.07 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Heteropatric differentiation is a mode of speciation with gene flow in which divergence occurs between lineages that are in sympatry and allopatry at different times during cyclic spatial movements. Empirical evidence suggests that heteropatric differentiation may prove to be common among seasonally migratory organisms. We examined genetic differentiation between the sedentary Aleutian Islands population of green-winged teal (Anas crecca nimia) and its close migratory relative, the Eurasian, or Old World (OW), Anas c. crecca population, a portion of which passes through the range of nimia during its seasonal migrations. We also examined its relationship with the parapatric North American, New World (NW), A. c. carolinensis population. Sequence data from eight nuclear introns and the mtDNA control region showed that the nimia-crecca divergence occurred much more recently than the deeper crecca-carolinensis split (~83,000 y vs. ~1.1 My). Despite considerable spatial overlap between crecca and nimia during seasonal migration, three key predictions of heteropatric differentiation are supported: significant genetic divergence (overall mean Φst = 0.07), low gene flow (2Ne m ~1.8), and an effective population size in nimia that is not especially low (Ne ~ 80,000 individuals). Similar levels of gene flow have come into nimia from carolinensis, but no detectable nuclear gene flow has gone out of nimia into either OW (crecca) or NW (carolinensis) populations. We infer that adaptations of these populations to local optima in different places (e.g., each matching their reproductive effort to different resource blooms) promote genetic isolation and divergence despite periods of sympatry between them, as the heteropatric model predicts. This article is protected by copyright. All rights reserved.
    Molecular Ecology 09/2013; · 6.28 Impact Factor
  • Source
    Philip Lavretsky, Kevin G McCracken, Jeffrey L Peters
    [Show abstract] [Hide abstract]
    ABSTRACT: Reconstructing species trees by incorporating information from many independent gene trees reduces the confounding influence of stochastic lineage sorting. Such analyses are particularly important for taxa that share polymorphisms due to incomplete lineage sorting or introgressive hybridization. We investigated phylogenetic relationships among 13 closely related species from the mallard (Anas spp.) complex using the multispecies coalescent and 20 nuclear loci sampled from a genomic transect. We also examined how treating recombining loci and hybridizing species influences results by partitioning the data using various protocols. In general, topologies were similar among the various species trees, with major clades consistently composed of the same taxa. However, relationships among these clades and among taxa within clades changed among partitioned data sets. Posterior support generally decreased when filtering for recombination, whereas excluding mallards (Anas platyrhynchos) increased posterior support for taxa known to hybridize with them. Furthermore, branch lengths decreased substantially for recombination-filtered data. Finally, concordance between nuclear and morphometric topologies conflicted with those in the mitochondrial tree, particularly with regard to the placement of the Hawaiian duck (A. wyvilliana), Philippine duck (A. luzonica), and two spot-billed ducks (A. zonorhyncha and A. poecilorhyncha). These results demonstrate the importance of maximizing sequence length and taxon sampling when inferring taxonomic relationships that are confounded by extensive allele sharing.
    Molecular Phylogenetics and Evolution 08/2013; · 4.07 Impact Factor
  • Source
    Dataset: FigureS2
  • Source
    Dataset: FigureS1
  • [Show abstract] [Hide abstract]
    ABSTRACT: Andean uplift played a key role in Neotropical bird diversification, yet past dispersal and genetic adaptation to high-altitude environments remain little understood. Here we use multilocus population genetics to study population history and historical demographic processes in the ruddy duck (Oxyura jamaicensis), a stiff-tailed diving duck comprising three subspecies distributed from Canada to Tierra del Fuego and inhabiting wetlands from sea level to 4500 m in the Andes. We sequenced the mitochondrial DNA, four autosomal introns and three haemoglobin genes (α(A) , α(D) , β(A) ) and used isolation-with-migration (IM) models to study gene flow between North America and South America, and between the tropical and southern Andes. Our analyses indicated that ruddy ducks dispersed first from North America to the tropical Andes, then from the tropical Andes to the southern Andes. While no nonsynonymous substitutions were found in either α globin gene, three amino acid substitutions were observed in the β(A) globin. Based on phylogenetic reconstruction and power analysis, the first β(A) substitution, found in all Andean individuals, was acquired when ruddy ducks dispersed from low altitude in North America to high altitude in the tropical Andes, whereas the two additional substitutions occurred more recently, when ruddy ducks dispersed from high altitude in the tropical Andes to low altitude in the southern Andes. This stepwise colonization pattern accompanied by polarized β(A) globin amino acid replacements suggest that ruddy ducks first acclimatized or adapted to the Andean highlands and then again to the lowlands. In addition, ruddy ducks colonized the Andean highlands via a less common route as compared to other waterbird species that colonized the Andes northwards from the southern cone of South America.
    Molecular Ecology 01/2013; · 6.28 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: AimGlacial cycles had a major influence on the distribution of high‐latitude species, and while genetic consequences of these cycles have been well studied in the Circumpolar North, notably fewer studies have been undertaken in the Antarctic. Here, we use multilocus genetic data from the South Georgia pintail (Anas georgica georgica) as a proxy to study the presence and timing of ice‐free refugia on South Georgia, a glaciated subantarctic island in the South Atlantic Ocean that has been the subject of intense geomorphological and palaeoenvironmental study. LocationSouth Georgia. Methods Multilocus DNA sequence data from five nuclear loci and the mitochondrial DNA control region were analysed for South Georgia pintails (n = 60) and the neighbouring population of yellow‐billed pintails (A. georgica spinicauda) in Argentina (n = 64). Population genetic structure and gene flow were examined using ΦST, assignment tests, and multilocus coalescent analyses. ResultsIsolation‐with‐migration (IM) analysis revealed that the South Georgia pintail population was founded by pintails dispersing from South America. Although the confidence intervals on divergence dates inferred from genetic data are generally wide and there may be time‐dependency in rate calibrations, our analysis suggests that this founding event probably occurred c. 34,000 years ago, prior to the Last Glacial Maximum (LGM). Our findings further suggest that South Georgia pintails might have experienced a bottleneck coinciding with complete replacement of mitochondrial DNA prior to 8700 years ago following the final advance of glaciers. Main conclusionsThese findings suggest that ice‐free refugia existed earlier in the chronology of deglaciation in contrast with earlier studies, but in agreement with observations that the plant community was also established on South Georgia prior to the end of the Pleistocene. Like other recent studies that have utilized genetic data to date dispersal and vicariance events in the Antarctic, our results provide a constraint on the extent of ice sheets, suggesting that past ice coverage on South Georgia through the LGM was overestimated.
    Journal of Biogeography 01/2013; 40(12):2348–2360. · 4.86 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Since the late 18th century bird populations residing in the Aleutian Archipelago have been greatly reduced by introduced arctic foxes (Alopex lagopus). We analyzed data from microsatellite, nuclear intron, and mitochondrial (mtDNA) loci to examine the spatial genetic structure, demography, and gene flow among four Aleutian Island populations of the Common Eider (Somateria mollissima) much reduced by introduced foxes. In mtDNA, we found high levels of genetic structure within and between island groups (ФST = 0.643), but we found no population subdivision in microsatellites or nuclear introns. Differences in genetic structure between the mitochondrial and nuclear genomes are consistent with the Common Eider's breeding and winter biology, as females are highly philopatric and males disperse. Nevertheless, significant differences between islands in the mtDNA of males and marginal significance (P = 0.07) in the Z-linked locus Smo1 suggest that males may also have some level of fidelity to island groups. Severe reduction of populations by the fox, coupled with females' high philopatry, may have left the genetic signature of a bottleneck effect, resulting in the high levels of genetic differentiation observed in mtDNA (ФST = 0.460–0.807) between islands only 440 km apart. Reestablishment of the Common Eider following the fox's eradication was likely through recruitment from within the islands and bolstered by dispersal from neighboring islands, as suggested by the lack of genetic structure and asymmetry in gene flow between Attu and the other Near Islands. Desde finales del siglo 18, las poblaciones de aves que residen en el archipiélago aleutiano han sido diezmadas por la introducción del zorro del ártico (Alopex lagopus). Analizamos datos de microsatélites, intrones nucleares y loci mitocondriales (ADNmt) para examinar la estructura genética espacial, la demografía y el flujo génico en las islas Aleutianas entre cuatro poblaciones de Somateria mollissima muy reducidas por los zorros introducidos. Encontramos altos niveles de estructura genética dentro y entre grupos de islas (ФST = 0.643) en ADNmt, pero no encontramos subdivisiones poblacionales en los microsatélites o los intrones nucleares. Las diferencias en estructura genética entre los genomas mitocondriales y nucleares son consistentes con la biología reproductiva e invernal de S. mollissima, ya que las hembras son altamente filopátricas y los machos se dispersan. Sin embargo, las diferencias significativas entre islas en el ADNmt de los machos y la significancia marginal (P = 0.07) en el locus Smo1 ligado a Z sugiere que los machos pueden también tener algún nivel de fidelidad a los grupos de islas. Una reducción severa de las poblaciones debido al zorro, sumada a la alta filopatría de las hembras, puede haber dejado la señal genética de un efecto de cuello de botella, dando como resultado los altos niveles de diferenciación genética que se observan en el ADNmt (ФST = 0.460–0.807) entre islas separadas por tan solo 440 km. El restablecimiento de S. mollissima luego de la erradicación del zorro se dio probablemente por reclutamiento desde dentro de las islas y estuvo reforzado por dispersión desde las islas vecinas, como sugiere la falta de estructura genética y la asimetría en flujo génico entre Attu y las otras Islas Near.
    The Condor 01/2013; 115(1):28-39. · 1.37 Impact Factor
  • Robert E Wilson, Jeffrey L Peters, Kevin G McCracken
    [Show abstract] [Hide abstract]
    ABSTRACT: Spatial variation in the environment can lead to divergent selection between populations occupying different parts of a species' range, and ultimately lead to population divergence. The colonization of new areas can thus facilitate divergence in beneficial traits, yet with little differentiation at neutral genetic markers. We investigated genetic and phenotypic patterns of divergence between low- and high-altitude populations of cinnamon teal inhabiting normoxic and hypoxic regions in the Andes and adjacent lowlands of South America. Cinnamon teal showed strong divergence in body size (PC1; P(ST) = 0.56) and exhibited significant frequency differences in a single nonsynonymous α-hemoglobin amino acid polymorphism (Asn/Ser-α9; F(ST) = 0.60) between environmental extremes, despite considerable admixture of mtDNA and intron loci (F(ST) = 0.004-0.168). Inferences of strong population segregation were further supported by the observation of few mismatched individuals in either environmental extreme. Coalescent analyses indicated that the highlands were most likely colonized from lowland regions but following divergence, gene flow has been asymmetric from the highlands into the lowlands. Multiple selection pressures associated with high-altitude habitats, including cold and hypoxia, have likely shaped morphological and genetic divergence within South American cinnamon teal populations.
    Evolution 01/2013; 67(1):170-84. · 4.86 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Five species of migratory thrushes (Turdidae) occupy a transcontinental distribution across northern North America. They have largely overlapping breeding ranges, relatively similar ecological niches, and mutualistic relationships with northern woodland communities as insectivores and seed-dispersing frugivores. As an assemblage of ecologically similar species, and given other vertebrate studies, we predicted a shared pattern of genetic divergence among these species between their eastern and western populations, and also that the timing of the coalescent events might be similar and coincident with historical glacial events. To determine how these five lineages effectively established transcontinental distributions, we used mitochondrial cytochrome b sequences to assess genetic structure and lineage coalescence from populations on each side of the continent. Two general patterns occur. Hermit and Swainson's thrushes (Catharus guttatus and C. ustulatus) have relatively deep divergences between eastern and western phylogroups, probably reflecting shared historic vicariance. The Veery (C. fuscescens), Gray-cheeked Thrush (C. minimus), and American Robin (Turdus migratorius) have relatively shallow divergences between eastern and western populations. However, coalescent and approximate Bayesian computational analyses indicated that among all species as many as five transcontinental divergence events occurred. Divergence within both Hermit and Swainson's thrushes resembled the divergence between Gray-cheeked Thrushes and Veeries and probably occurred during a similar time period. Despite these species' ecological similarities, the assemblage exhibits heterogeneity at the species level in how they came to occupy transcontinental northern North America but two general continental patterns at an among-species organizational level, likely related to lineage age.
    PeerJ. 01/2013; 1:e206.
  • Source
    Kevin G McCracken, Robert E Wilson, Anthony R Martin
    [Show abstract] [Hide abstract]
    ABSTRACT: Hybridization is common between species of animals, particularly in waterfowl (Anatidae). One factor shown to promote hybridization is restricted mate choice, which can occur when 2 species occur in sympatry but one is rare. According to the Hubbs principle, or "desperation hypothesis," the rarer species is more likely to mate with heterospecifics. We report the second of 2 independent examples of hybridization between 2 species of ducks inhabiting island ecosystems in the Subantarctic and South Atlantic Ocean. Yellow-billed pintails (Anas georgica) and speckled teal (Anas flavirostris) are abundant in continental South America, where they are sympatric and coexist in mixed flocks. But on South Georgia, an isolated island in the Subantarctic, the pintail population of approximately 6000 pairs outnumbers a small breeding population of speckled teal 300∶1. Using 6 genetic loci (mtDNA and 5 nuclear introns) and Bayesian assignment tests coupled with coalescent analyses, we identified hybrid-origin speckled teal alleles in 2 pintails on South Georgia. While it is unclear whether introgression has also occurred into the speckled teal population, our data suggest that this hybridization was not a recent event, but occurred some time ago. We also failed to identify unequivocal evidence of introgression in a much larger sample of pintails and speckled teal from Argentina using a 3-population "Isolation-with-Migration" coalescent analysis. Combined with parallel findings of hybridization between these same 2 duck species in the Falkland Islands, where population ratios are reversed and pintails are outnumbered by speckled teal 1:10, our results provide further support for the desperation hypothesis, which predicts that scarcity in one population and abundance of another will often lead to hybridization. While the South Georgia pintail population appears to be thriving, it's possible that low density of conspecific mates and inverse density dependence (Allee effect) may be one factor limiting the reproductive output of the speckled teal population, and this situation may persist unless speckled teal increase in abundance on South Georgia.
    PLoS ONE 01/2013; 8(12):e82664. · 3.53 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Pleistocene refugia likely contributed to the modern biodiversity of northern areas. Using the mitochondrial DNA cytochrome-b gene, we compared 11 forest-dwelling bird species from Haida Gwaii (formerly the Queen Charlotte Islands) with populations from Alaska, Washington, and other locations in the United States. If Haida Gwaii was an unglaciated refugium, its modern populations should feature a high number of endemic lineages and divergence times that predate the end of the last glacial maximum, ca. 13,000–19,000 years before present (ybp). Furthermore, the genetic diversity of these populations should be higher than that in areas colonized after the glacial retreat. Four of the species examined from Haida Gwaii showed old divergences and a high percentage of endemic lineages: the Northern Saw-whet Owl (Aegolius acadicus), Hairy Woodpecker (Picoides villosus), Steller's Jay (Cyanocitta stelleri), and Pine Grosbeak (Pinicola enucleator); all four have endemic subspecies on these islands. The Pacific Wren (Troglodytes pacificus) and Song Sparrow (Melospiza melodia) showed genetic trends associated with populations in refugia, including high genetic diversity on Haida Gwaii. Estimated divergence dates of these six species were fairly uniform (~20,000–30,000 ybp), being greatest for the Hairy Woodpecker (>70,000 ybp) and Pine Grosbeak (>120,000 ybp). There was an association between apparent occurrence in a refugium and a sedentary life-history strategy and a trend for endemic subspecies (4 of 6) also to show this association. Our findings suggest that the Haida Gwaii area hosted a forested refugium during the cycles of climatic change in the late Pleistocene. Los refugios pleistocénicos probablemente contribuyeron a la biodiversidad moderna de las áreas del norte. Usando el gen citocromo-b del ADN mitocondrial, comparamos 11 especies de aves del bosque de Haida Gwaii (anteriormente conocidas como las Islas de la Reina Charlotte) con poblaciones de Alaska, Washington y otras lugares de los Estados Unidos. Si Haida Gwaii fue un refugio glaciar, sus poblaciones modernas deberían presentar un alto número de linajes endémicos y tiempos de divergencia anteriores al final del último máximo glaciar, ca. 13,000–19,000 años antes del presente (AP). Más aún, la diversidad genética de estas poblaciones debería ser mayor que la de áreas colonizadas luego del retroceso glaciar. Cuatro de las especies examinadas de Haida Gwaii mostraron divergencias viejas y un alto porcentaje de linajes endémicos: Aegolius acadicus, Picoides villosus, Cyanocitta stelleri y Pinicola enucleator; las cuatro tienen subespecies endémicas en estas islas. Troglodytes pacificus y Melospiza melodía mostraron tendencias genéticas asociadas con poblaciones en refugios, incluyendo una alta diversidad genética en Haida Gwaii. Las fechas estimadas de divergencia de estas seis especies fueron bastante uniformes (~20,000–30,000 años AP), siendo mayores para P. villosus (>70,000 años AP) y P. enucleator (>120,000 años AP). Hubo una asociación entre la presencia aparente en un refugio y una estrategia de historia de vida sedentaria, y una tendencia de las subespecies endémicas (4 de 6) también a mostrar esta asociación. Nuestros resultados sugieren que el área de Haida Gwaii hospedó un refugio de bosque durante los ciclos de cambio climático de fines del Pleistoceno.
    The Condor 01/2013; 115(4):725-737. · 1.37 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Speciation is a process in which genetic drift and selection cause divergence over time. However, there is no rule dictating the time required for speciation, and even low levels of gene flow hinder divergence, so that taxa may be poised at the threshold of speciation for long periods of evolutionary time. We sequenced mitochondrial DNA (mtDNA) and eight nuclear introns (nuDNA) to estimate genomic levels of differentiation and gene flow between the Eurasian common teal (Anas crecca crecca) and the North American green-winged teal (Anas crecca carolinensis). These ducks come into contact in Beringia (north-eastern Asia and north-western North America) and have probably done so, perhaps cyclically, since the Pliocene-Pleistocene transition, ∼2.6 Ma, when they apparently began diverging. They have diagnosable differences in male plumage and are 6.9% divergent in the mtDNA control region, with only 1 of 58 crecca and 2 of 86 carolinensis having haplotypes grouping with the other. Two nuclear loci were likewise strongly structured between these teal (Φ(st)  ≥ 0.35), but six loci were undifferentiated or only weakly structured (Φ(st)  = 0.0-0.06). Gene flow between crecca and carolinensis was ∼1 individual per generation in both directions in mtDNA, but was asymmetrical in nuDNA, with ∼1 and ∼20 individuals per generation immigrating into crecca and carolinensis, respectively. This study illustrates that species delimitation using a single marker oversimplifies the complexity of the speciation process, and it suggests that even with divergent selection, moderate levels of gene flow may stall the speciation process short of completion.
    Molecular Ecology 07/2012; 21(18):4563-4577. · 6.28 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Inferring aspects of the population histories of species using coalescent analyses of non-coding nuclear DNA has grown in popularity. These inferences, such as divergence, gene flow, and changes in population size, assume that genetic data reflect simple population histories and neutral evolutionary processes. However, violating model assumptions can result in a poor fit between empirical data and the models. We sampled 22 nuclear intron sequences from at least 19 different chromosomes (a genomic transect) to test for deviations from selective neutrality in the gadwall (Anas strepera), a Holarctic duck. Nucleotide diversity among these loci varied by nearly two orders of magnitude (from 0.0004 to 0.029), and this heterogeneity could not be explained by differences in substitution rates alone. Using two different coalescent methods to infer models of population history and then simulating neutral genetic diversity under these models, we found that the observed among-locus heterogeneity in nucleotide diversity was significantly higher than expected for these simple models. Defining more complex models of population history demonstrated that a pre-divergence bottleneck was also unlikely to explain this heterogeneity. However, both selection and interspecific hybridization could account for the heterogeneity observed among loci. Regardless of the cause of the deviation, our results illustrate that violating key assumptions of coalescent models can mislead inferences of population history.
    PLoS ONE 01/2012; 7(2):e31972. · 3.53 Impact Factor
  • Robert Edward Wilson, Muir D. Eaton, Kevin G. McCracken
    [Show abstract] [Hide abstract]
    ABSTRACT: Blue-winged Teal (Anas discors) and Cinnamon Teal (A. cyanoptera septentrionalium) are two closely related North American dabbling duck species that are ecological equivalents. Cinnamon Teal are primarily restricted to regions west of the Great Plains, whereas Blue-winged Teal occur primarily in the central and eastern part of the continent, only recently expanding westward. Males of the two species exhibit striking plumage color differences, while females are difficult to differentiate by plumage, and it is unclear if interspecific size differences exist between either sex due to inconsistencies in previous reports. Here we reassess body size differences, and quantify plumage color differences using avian color discrimination modeling. Like previous studies, significant differences were found for bill morphology; mean bill length was 7-10% longer in Cinnamon Teal. Based on avian visual modeling of plumage reflectance data, color differences not visible to human vision were found between species for several female feather patches (e.g. breast coloration) and male wing speculum coloration, potentially representing previously unrecognized interspecific signals to the avian visual system. Although color reflectance data yielded higher accuracy than morphometrics for identifying females, body size measurements (in addition to plumage to a lesser degree) also proved to be reliable in correctly classifying males of each species. In combination, morphometrics and plumage reflectance data represent useful identification tools for avian species that are otherwise difficult to distinguish.
    Avian biology research 01/2012; 5(2):107-116. · 0.67 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Hypoxia is a key factor determining survival, and haemoglobins are targets of selection in species native to high-altitude regions. We studied population genetic structure and evaluated evidence for local adaptation in the crested duck (Lophonetta specularioides). Differentiation, gene flow and time since divergence between highland and lowland populations were assessed for three haemoglobin genes (α(A) , α(D) , β(A) ) and compared to seven reference loci (six autosomal introns and mtDNA). Four derived amino acid replacements were found in the globin genes that had elevated Φ(ST) values between the Andean highlands and Patagonian lowlands. A single β(A) -globin polymorphism at a site known to influence O(2) affinity was fixed for different alleles in the two populations, whereas three α(A) - and α(D) -globin polymorphisms exhibited high heterozygosity in the highlands but not in the lowlands. Coalescent analyses supported restricted gene flow for haemoglobin alleles and mitochondrial DNA but nonzero gene flow for the introns. Simulating genetic data under a drift-migration model of selective neutrality, the β(A) -globin fell outside the 95% confidence limit of simulated data, suggesting that directional selection is maintaining different variants in the contrasting elevational environments, thereby restricting migration of β(A) -globin alleles. The α(A) - and α(D) -globins, by contrast, did not differ from the simulated values, suggesting that variants in these genes are either selectively neutral, or that the effects of selection could not be differentiated from background levels of population structure and linkage disequilibrium. This study illustrates the combined effects of selection and population history on inferring levels of population divergence for a species distributed across an altitudinal gradient in which selection for hypoxia resistance has likely played an important role.
    Molecular Ecology 12/2011; 21(2):350-68. · 6.28 Impact Factor

Publication Stats

751 Citations
249.25 Total Impact Points

Institutions

  • 2014
    • University of Miami
      كورال غيبلز، فلوريدا, Florida, United States
  • 2001–2014
    • University of Alaska Fairbanks
      • • Department of Biology and Wildlife
      • • Institute of Arctic Biology
      Fairbanks, Alaska, United States
    • Brigham Young University - Provo Main Campus
      Provo, Utah, United States
  • 2013
    • Uppsala University
      Uppsala, Uppsala, Sweden
  • 2012–2013
    • Wright State University
      • Department of Biological Sciences
      Dayton, Ohio, United States
  • 2009
    • University of Alaska System
      Fairbanks, Alaska, United States
  • 1997–2009
    • Louisiana State University
      • Museum of Natural Science
      Baton Rouge, Louisiana, United States
  • 2006
    • United States Department of Agriculture
      • Agricultural Research Service (ARS)
      Washington, D. C., DC, United States