Kevin G. McCracken

University of Alaska Fairbanks, Fairbanks, Alaska, United States

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Publications (79)305.29 Total impact

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    ABSTRACT: Documenting patterns of host specificity in parasites relies on the adequate definition of parasite species. In many cases, parasites have simplified morphology, making species delimitation based on traditional morphological characters difficult. Molecular data can help in assessing whether widespread parasites harbour cryptic species and, alternatively, in guiding further taxonomic revision in cases in which there is morphological variation. The duck louse genus Anaticola (Phthiraptera: Philopteridae), based on current taxonomy, contains both host-specific and widespread species. Mitochondrial and nuclear DNA sequences of samples from this genus were used to document patterns of host specificity. The comparison of these patterns with morphological variations in Anaticola revealed a general correspondence between the groups identified by DNA sequences and morphology, respectively. These results suggest that a more thorough taxonomic review of this genus is needed. In general, the groups identified on the basis of molecular data were associated with particular groups of waterfowl (e.g. dabbling ducks, sea ducks, geese) or specific biogeographic regions (e.g. North America, South America, Australia, Eurasia).
    No preview · Article · Jan 2016 · Medical and Veterinary Entomology
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    ABSTRACT: A fundamental question in evolutionary genetics concerns the extent to which adaptive phenotypic convergence is attributable to convergent or parallel changes at the molecular sequence level. Here we report a comparative analysis of hemoglobin (Hb) function in eight phylogenetically replicated pairs of high- and low-altitude waterfowl taxa to test for convergence in the oxygenation properties of Hb, and to assess the extent to which convergence in biochemical phenotype is attributable to repeated amino acid replacements. Functional experiments on native Hb variants and protein engineering experiments based on site-directed mutagenesis revealed the phenotypic effects of specific amino acid replacements that were responsible for convergent increases in Hb-O2 affinity in multiple high-altitude taxa. In six of the eight taxon pairs, high-altitude taxa evolved derived increases in Hb-O2 affinity that were caused by a combination of unique replacements, parallel replacements (involving identical-by-state variants with independent mutational origins in different lineages), and collateral replacements (involving shared, identical-by-descent variants derived via introgressive hybridization). In genome scans of nucleotide differentiation involving high- and low-altitude populations of three separate species, function-altering amino acid polymorphisms in the globin genes emerged as highly significant outliers, providing independent evidence for adaptive divergence in Hb function. The experimental results demonstrate that convergent changes in protein function can occur through multiple historical paths, and can involve multiple possible mutations. Most cases of convergence in Hb function did not involve parallel substitutions and most parallel substitutions did not affect Hb-O2 affinity, indicating that the repeatability of phenotypic evolution does not require parallelism at the molecular level.
    Full-text · Article · Jan 2016 · PLoS Genetics
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    Full-text · Dataset · Dec 2015
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    ABSTRACT: Estimating the frequency of hybridization is important to understand its evolutionary consequences and its effects on conservation efforts. In this study, we examined the extent of hybridization in two sister species of ducks that hybridize. We used mitochondrial control region sequences and 3589 double-digest restriction-associated DNA sequences (ddRADseq) to identify admixture between wild lesser scaup (Aythya affinis) and greater scaup (A. marila). Among 111 individuals, we found one introgressed mitochondrial DNA haplotype in lesser scaup and four in greater scaup. Likewise, based on the site-frequency spectrum from autosomal DNA, gene flow was asymmetrical, with higher rates from lesser into greater scaup. However, using ddRADseq nuclear DNA, all individuals were assigned to their respective species with >0.95 posterior assignment probability. To examine the power for detecting admixture, we simulated a breeding experiment in which empirical data were used to create F1 hybrids and nine generations (F2-F10) of backcrossing. F1 hybrids and F2, F3 and most F4 backcrosses were clearly distinguishable from pure individuals, but evidence of admixed histories was effectively lost after the fourth generation. Thus, we conclude that low interspecific assignment probabilities (0.011-0.043) for two lesser and nineteen greater scaup were consistent with admixed histories beyond the F3 generation. These results indicate that the propensity of these species to hybridize in the wild is low and largely asymmetric. When applied to species-specific cases, our approach offers powerful utility for examining concerns of hybridization in conservation efforts, especially for determining the generational time until admixed histories are effectively lost through backcrossing.
    No preview · Article · Nov 2015
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    Daniela Wilner · Kevin G McCracken · Luis Alza

    Full-text · Poster · Apr 2015
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    Full-text · Dataset · Apr 2015
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    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.
    Full-text · Article · Jun 2014 · Molecular Ecology
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    ABSTRACT: Under drift-mutation equilibrium, genetic diversity is expected to be correlated with effective population size (N e ). Changes in population size and gene flow are two important processes that can cause populations to deviate from this expected relationship. In this study, we used DNA sequences from six independent loci to examine the influence of these processes on standing genetic diversity in endemic mottled ducks (Anas fulvigula) and geographically widespread mallards (A. platyrhynchos), two species known to hybridize. Mottled ducks have an estimated census size that is about two orders-of-magnitude smaller than that of mallards, yet these two species have similar levels of genetic diversity, especially at nuclear DNA. Coalescent analyses suggest that a population expansion in the mallard at least partly explains this discrepancy, but the mottled duck harbors higher genetic diversity and apparent N e than expected for its census size even after accounting for a population decline. Incorporating gene flow into the model, however, reduced the estimated N e of mottled ducks to 33 % of the equilibrium N e and yielded an estimated N e consistent with census size. We also examined the utility of these loci to distinguish among mallards, mottled ducks, and their hybrids. Most putatively pure individuals were correctly assigned to species, but the power for detecting hybrids was low. Although hybridization with mallards potentially poses a conservation threat to mottled ducks by creating a risk of extinction by hybridization, introgression of mallard alleles has helped maintain high genetic diversity in mottled ducks and might be important for the adaptability and survival of this species.
    Full-text · Article · Jun 2014 · Conservation Genetics
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    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.
    Full-text · Article · Mar 2014 · Biological Journal of the Linnean Society
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    Full-text · Dataset · Mar 2014
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    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.
    Full-text · Article · Mar 2014 · Bird Conservation International
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    Kevin G McCracken · Robert E Wilson · Anthony R Martin
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    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.
    Full-text · Article · Dec 2013 · PLoS ONE
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    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.
    No preview · Article · Dec 2013 · Journal of Biogeography
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    Carrie M Topp · Christin L Pruett · Kevin G McCracken · Kevin Winker
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    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.
    Full-text · Article · Nov 2013 · PeerJ
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    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.
    Full-text · Article · Nov 2013 · The Condor
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    Kevin Winker · Kevin G McCracken · Daniel D Gibson · Jeffrey L Peters
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    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.
    Full-text · Article · Sep 2013 · Molecular Ecology
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    Philip Lavretsky · Kevin G McCracken · Jeffrey L Peters
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    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.
    Full-text · Article · Aug 2013 · Molecular Phylogenetics and Evolution
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    Dataset: FigureS2

    Full-text · Dataset · Apr 2013
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    Dataset: FigureS1

    Full-text · Dataset · Apr 2013
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    Full-text · Poster · Apr 2013

Publication Stats

1k Citations
305.29 Total Impact Points

Institutions

  • 2001-2016
    • University of Alaska Fairbanks
      • • Institute of Arctic Biology
      • • Department of Biology and Wildlife
      Fairbanks, Alaska, United States
    • Brigham Young University - Provo Main Campus
      Provo, Utah, United States
  • 2011
    • Drake University
      • Biology
      Des Moines, Iowa, United States
  • 1998-2009
    • Louisiana State University
      • Museum of Natural Science
      Baton Rouge, Louisiana, United States