Article

Becoming pure: Identifying generational classes of admixed individuals within lesser and greater scaup populations

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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.

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... Delineating population boundaries is critical for understanding demography, migratory connectivity and population dynamics, which are all important factors in effective management and conservation (Lande 1988, Supple and Shapiro 2018, Sonsthagen et al. 2019. However, directly documenting regional population structure and individual dispersal events can be challenging, especially for species that reside in remote landscapes and occupy large distributions across their annual cycle (Lavretsky et al. 2016, Sonsthagen et al. 2019. Quantifying genetic structure and rates and directionality of gene flow within a species can provide valuable information on these various stochastic and demographic factors. ...
... After ddRAD library prep, all samples were pooled in equimolar amounts, and 150 bp, single-end sequencing was completed on an Illumina HiSeq 2500 at the Tufts University Core Genomics Facility. Specific protocols for ddRAD-seq library preparation followed DaCosta and Sorenson (2014, and also see Lavretsky et al. 2015Lavretsky et al. , 2016Lavretsky et al. , 2019 and are outlined in detail in Supplementary information. Raw Illumina reads were deposited in NCBI's sequence read archive (SRA; <http:// www.ncbi.nlm.nih.gov/sra>; ...
... Final output files were generated for downstream analyses (e.g. fasta, Nexus, ADMIXTURE) using custom python scripts (Lavretsky et al. 2016). Only loci with ≥ 5× coverage and < 10% missing data were retained for downstream analyses. ...
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Delineation of population structure provides valuable information for conservation and management of species, as levels of demographic and genetic connectivity not only affect population dynamics but also have important implications for adaptability and resiliency of populations and species. Here, we measure population genetic structure and connectivity across the ranges of two sister species of sea ducks: Barrow's Goldeneye (Bucephala islandica) and Common Goldeneye (B. clangula). We use two different marker types: 7–8 nuclear microsatellite loci assayed across 229 samples and 3,678 double digest Restriction‐site Associated DNA Sequencing (ddRAD‐seq) loci assayed across 61 samples. First, both datasets found no evidence of genetic structure within Common or Barrow's Goldeneye, including between North American and European samples of Common Goldeneye. These results are in contrast with previous mitochondrial DNA, band recovery, and telemetry data which suggest that goldeneyes are structured across their range. We posit that the discordance between autosomal genetic markers and other data types suggests that males, possibly subadult males, may be maintaining genetic connectivity across each species’ respective ranges. Next, although mate choice consequences resulting from inter‐specific brood parasitism was hypothesized to cause some level of gene flow between goldeneye species, we only identified a single F1 hybrid with no further evidence of contemporary or historical gene flow. Despite ddRAD‐seq demographic analyses which recovered an optimum evolutionary model of split‐with‐migration (i.e., secondary contact), estimates of gene flow were <<1 migrant per generation in both directions. Together, we conclude that either strong ecological barriers or assortative mating are likely playing a role in preventing further backcrossing. Finally, demographic analyses estimated a relatively deep divergence time between Barrow's Goldeneye and Common Goldeneye of ~1.6 million years before present and suggests that the genomes of both species have been under similar evolutionary constraints. This article is protected by copyright. All rights reserved.
... This gene-tree heterogeneity must be accounted for as it can make reconstructing evolutionary relationships and historical demography challenging (Carstens & Knowles, 2007;Firneno et al., 2020;Liu et al., 2010). The increasing availability of high-throughput sequencing data sets for non-model organisms has improved our ability to discern patterns of introgression in closely related species or populations (Firneno et al., 2020;Graham et al., 2018;Lavretsky et al., 2016) and thus clarify phylogenetic relationships and species limits. This is especially so in large, widely distributed species complexes with limited variation in external morphological traits and hybridization blurring species limits (Guo et al., 2016;Phuong et al., 2017;Potter et al., 2016). ...
... These approaches have transformed our understanding of how landscape and climate changes have contributed to the assembly of regional species pools, for instance by limiting dispersal, promoting speciation, or leading to lineage fusion (Graham et al., 2018;Lavretsky et al., 2016;Leaché et al., 2019;Portik et al., 2017). One flexible approach involves simulating population histories to compare the fit of empirical genome-scale data to data simulated under alternative biogeographical scenarios (Portik et al., 2017;Dal Vechio et al., 2019). ...
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The effects of genetic introgression on species boundaries and how they affect species’ integrity and persistence over evolutionary time have received increased attention. The increasing availability of genomic data has revealed contrasting patterns of gene flow across genomic regions, which impose challenges to inferences of evolutionary relationships and of patterns of genetic admixture across lineages. By characterizing patterns of variation across thousands of genomic loci in a widespread complex of true toads (Rhinella), we assess the true extent of genetic introgression across species thought to hybridize to extreme degrees based on natural history observations and multi‐locus analyses. Comprehensive geographic sampling of five large‐ranged Neotropical taxa revealed multiple distinct evolutionary lineages that span large geographic areas and, at times, distinct biomes. The inferred major clades and genetic clusters largely correspond to currently recognized taxa; however, we also found evidence of cryptic diversity within taxa. While previous phylogenetic studies revealed extensive mito‐nuclear discordance, our genetic clustering analyses uncovered several admixed individuals within major genetic groups. Accordingly, historical demographic analyses supported that the evolutionary history of these toads involved cross‐taxon gene flow both at ancient and recent times. Lastly, ABBA‐BABA tests revealed widespread allele sharing across species boundaries, a pattern that can be confidently attributed to genetic introgression as opposed to incomplete lineage sorting. These results confirm previous assertions that the evolutionary history of Rhinella was characterized by various levels of hybridization even across environmentally heterogeneous regions, posing exciting questions about what factors prevent complete fusion of diverging yet highly interdependent evolutionary lineages.
... Thus, all loci were represented by at least one member of each species. Final output files (e.g., fasta, NEXUS, ADMIXTURE, fineR-ADstructure) were generated using custom python scripts (Lavretsky et al., 2016). ...
... composite estimates of relative differentiation among species were generally high (composite Φ ST > 0.60) across pair-wise species comparisons (Fig. 3A). Although composite Φ ST estimates based on Z-sex chromosome ddRAD-seq loci tended to be higher than those based on autosomal ddRAD-seq loci, the Z:Autosomal (Z:A) Φ ST ratio was mostly around 1 (highest Z:A Φ ST ratio of 2), which are all close to neutral expectations based on Z-sex chromosome loci having three-fourths the effective population size of autosomal markers (i.e., ΦST Z:Autosomal ≤ 1.33; Lavretsky et al., 2015a;Lavretsky et al., 2016 ; Fig. 3). These results suggest that evolutionary processes are similarly shaping the genetic variation across the Z-sex and autosomal chromosomes, which is in contrast to those Z:A Φ ST ratios found in other ducks . ...
Article
Insight into complex evolutionary histories continues to build through broad comparative phylogenomic and population genomic studies. In particular, there is a need to understand the extent and scale that gene flow contributes to standing genomic diversity and the role introgression has played in evolutionary processes such as hybrid speciation. Here, we investigate the evolutionary history of the Mergini tribe (sea ducks) by coupling multi-species comparisons with phylogenomic analyses of thousands of nuclear ddRAD-seq loci, including Z-sex chromosome and autosomal linked loci, and the mitogenome assayed across all extant sea duck species in North America. All sea duck species are strongly structured across all sampled marker types (pair-wise species ΦST >0.2), with clear genetic assignments of individuals to their respective species, and phylogenetic relationships recapitulate known relationships. Despite strong species integrity, we identify at least 18 putative hybrids; with all but one being late generational backcrosses. Most interesting, we provide the first evidence that an ancestral gene flow event between long-tailed ducks (Clangula hyemalis) and true Eiders (Somateria spp.) not only moved genetic material into the former species, but likely generated a novel species — the Steller’s eider (Polysticta stelleri) — via hybrid speciation. Despite generally low contemporary levels of gene flow, we conclude that hybridization has and continues to be an important process that shifts novel genetic variation between species within the tribe Mergini. Finally, we outline methods that permit researchers to contrast genomic patterns of contemporary versus ancestral gene flow when attempting to reconstruct potentially complex evolutionary histories.
... Inc.) to ensure a minimum concentration of 0.02 µg/µl and visualized on an 1% agarose gel for high molecular weight bands. Library preparation for multiplexing followed steps outlined in (DaCosta & Sorenson, 2014; also see Lavretsky et al., 2015Lavretsky et al., , 2016 Raw Illumina reads were de-multiplexed and processed using the computational pipeline described by DaCosta and Sorenson (2014; Python scripts available at http://github.com/BU-RAD-seq/ddRADseq-Pipeline) and following steps outlined in Lavretsky et al. (2015). ...
... Final output files (e.g., FASTA, NEXUS, and ADMIXTURE) were generated with custom python scripts that set a higher minimum sequencing depth to score an allele (Lavretsky et al., 2016). Specifically, to limit any biases due to sequencing error and/or allelic dropout, alleles with <5x coverage were scored as missing, such that a minimum of 10 reads was required to score a locus as heterozygous. ...
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Abstract Dispersal shapes demographic processes and therefore is fundamental to understanding biological, ecological, and evolutionary processes acting within populations. However, assessing population connectivity in scoters (Melanitta sp.) is challenging as these species have large spatial distributions that span remote landscapes, have varying nesting distributions (disjunct vs. continuous), exhibit unknown levels of dispersal, and vary in the timing of the formation of pair bonds (winter vs. fall/spring migration) that may influence the distribution of genetic diversity. Here, we used double‐digest restriction‐associated DNA sequence (ddRAD) and microsatellite genotype data to assess population structure within the three North American species of scoter (black scoter, M. americana; white‐winged scoter, M. deglandi; surf scoter, M. perspicillata), and between their European congeners (common scoter, M. nigra; velvet scoter, M. fusca). We uncovered no or weak genomic structure (ddRAD ΦST 0.086). The pattern of limited genomic structure within North America is shared with other sea duck species and is often attributed to male‐biased dispersal. Further, migratory tendencies (east vs. west) of female surf and white‐winged scoters in central Canada are known to vary across years, providing additional opportunities for intracontinental dispersal and a mechanism for the maintenance of genomic connectivity across North America. In contrast, the black scoter had relatively elevated levels of divergence between Alaska and Atlantic sites and a second genetic cluster found in Alaska at ddRAD loci was concordant with its disjunct breeding distribution suggestive of a dispersal barrier (behavioral or physical). Although scoter populations appear to be connected through a dispersal network, a small percentage (
... The expectations associated with N e are useful in illuminating whether the evolution of these different markers types has been shaped through different selective pressures on specific chromosome types (Charlesworth 2009). Previous work on waterfowl support that ducks fit the ¼ rule for mtDNA and ¾ rule for Z-linked markers (Lavretsky, et al. 2015b;Lavretsky, et al. 2016). Specifically, under a scenario of equal reproductive success between males and females, the mitochondria will have ¼ the effective population size of the nuclear genome, resulting in a 4-fold difference in F ST between mtDNA and nuDNA (Caballero 1995;Dean, et al. 2015;Whitlock and McCauley 1999). ...
... However, with our current data, we are not able to clarify further which of the two possibilities is responsible, thus warranting future research. Nonetheless, in the case of the speckled teal, we see a significant role for nonneutral processes involving Z-linked and autosomal markers -a result consistent with recent findings in other birds (Dean, et al. 2015;Dhami, et al. 2016) as well as other duck species (Lavretsky, et al. 2015b;Lavretsky, et al. 2016). ...
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Local adaptation frequently occurs across populations as a result of migration-selection balance between divergent selective pressures and gene flow associated with life in heterogeneous landscapes. Studying the effects of selection and gene flow on the adaptation process can be achieved in systems that have recently colonized extreme environments. This study utilizes an endemic South American duck species, the speckled teal (Anas flavirostris), which has both high- and low-altitude populations. High-altitude speckled teal (A. f. oxyptera) are locally adapted to the Andean environment and mostly allopatric from low-altitude birds (A. f. flavirostris); however, there is occasional gene flow across altitudinal gradients. In this study, we used next-generation sequencing to explore genetic patterns associated with high-altitude adaptation in speckled teal populations, as well as the extent to which the balance between selection and migration have affected genetic architecture. We identified a set of loci with allele frequencies strongly correlated with altitude, including those involved in the insulin-like signaling pathway, bone morphogenesis, oxidative phosphorylation, responders to hypoxia-induced DNA damage, and feedback loops to the hypoxia-inducible factor (HIF) pathway. These same outlier loci were found to have depressed gene flow estimates, as well as being highly concentrated on the Z-chromosome. Our results suggest a multi-factorial response to life at high altitudes through an array of interconnected pathways that are likely under positive selection and whose genetic components seem to be providing an effective genomic barrier to interbreeding, potentially functioning as an avenue for population divergence and speciation.
... Some shared ancestry may also be the result of hybridization that took place in the distant past (late stage backcrossing) between Mottled Ducks and Mallards. Lavretsky et al. (2016) used a simulated breeding experiment between Greater Scaup (Aythya marila) and Lesser Scaup (A. affinis) to create generational hybrids (F1-F10), and found that individuals from F1, F2, F3, and most F4 hybrid classes were distinguishable from 'pure' individuals. However, detection of hybrids in F3þ generations was not reliable and assignment values of q ¼ 0.01-0.04 ...
... Determining the generation of our hybrids is difficult because we cannot assume that we had any 'pure' parental individuals. However, based on the analysis conducted by Lavretsky et al. (2016), we considered individuals with ancestry coefficients of 0.10 q 0.90 to be reliable F1 and F2 hybrids. ...
Article
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Hybridization between species that do not normally interbreed has increased due to human impacts on natural environments, such as habitat alteration or introductions of nonnative species. In particular, the introduction of Mallards (Anas platyrhynchos) globally has led to hybridization with many duck species. In the southeastern United States, hybridization with Mallards is a potential threat to the genetic identity of Mottled Ducks (A. fulvigula), a nonmigratory, coastal duck species. Hybridization between Mallards and Mottled Ducks has been examined in South Carolina and Florida, but not extensively in the remaining part of the Mottled Duck range. Mottled Ducks introduced into South Carolina show considerable admixture with Mallards, whereas in Florida, the hybridization rate between Mallards and Mottled Ducks is ~9%. Given these results, hybridization in the western Gulf Coast region is of potential concern and should be examined to determine the potential impact on the Mottled Duck lineage. In this study, we examined hybridization in the western Gulf Coast region using 36 microsatellite loci and 405 ducks consisting of putative Mottled Ducks (n ¼ 319), Mallards (n ¼ 76), and hybrids (n ¼ 10). Overall, genetic analyses revealed levels of hybridization of ~5–8%, with more individuals genetically assigned as hybrids from birds putatively identified as Mallards (5/76 and 14/76 in STRUCTURE and INSTRUCT, respectively) than as Mottled Ducks (14/319 in both programs). These data suggest that hybridization rates in the western Gulf Coast region are lower than those in Florida. However, projected coastal marsh loss in Texas and Louisiana may drive Mottled Ducks into urban wetland areas, an outcome that may increase contact between Mottled Ducks and Mallards and could result in similar levels of hybridization to those observed in Florida, where Mottled Ducks occupy urban and suburban habitats. Regular monitoring will help to determine future trends in levels of hybridization.
... The incidence of hybridization varies among bird orders with Anseriformes (waterfowl: ducks, geese and swans) showing the greatest propensity to hybridize. The study of waterfowl hybridization is biased towards ducks, as exemplified by an extensive inventory of hybrid ducks (Gillham and Gillham, 1998), an analysis of hybrid duck fertility patterns (Tubaro and Lijtmaer, 2002) and various genetic studies on introgressive hybridization (Kraus et al., 2012, Lavretsky et al., 2016, Peters et al., 2014a, McCracken and Wilson, 2011. The knowledge on goose hybridization is clearly lagging behind. ...
... Indeed, the D-statistic was developed to detect ancient gene flow and to estimate the extent of archaic ancestry in the genomes of extant populations (Durand et al., 2011). The detection and quantification of recent gene flow warrants a population genomic approach whereby multiple individuals of one population are sequenced (Lavretsky et al., 2016, Toews et al., 2016, Ellegren et al., 2012, Poelstra et al., 2014. Second, the relative rarity of goose hybrids diminishes the opportunity for backcrossing and introgression, leading to absence or low levels of recent gene flow (Ottenburghs et al., 2016c). ...
... Signs of hybridization in nuclear DNA might be diluted due to repeated unidirectional backcrossing, as hypothesized for cytoplasmic introgression in a Helianthus population by Rieseberg (1995). Lavretsky et al. (2016) demonstrated that evidence of admixed histories in the nuclear genome was effectively lost after the fourth generation of unidirectional backcrossing, based on the simulation of 3448 SNP S loci. In the contact zone examined in this study, signs of contemporary hybridization in nuclear DNA may have been diluted by repeated introgression to I. longitubus. ...
Article
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Interspecific hybridization between the short (ca. 3.5 mm) corolla tube species, Isodon inflexus, and the long (ca. 12 mm) corolla tube species, Isodonlongitubus, was examined using genetic and morphometric analyses. Bayesian clustering analysis using microsatellites revealed that plants in the contact zone consisted of two I. inflexus individuals, 32 I. longitubus individuals, and 13 hybrid individuals (F2-like and backcrosses to both I. inflexus and I. longitubus). Using the sequences of the psbA-trnH intergenic spacer in chloroplast DNA, three haplotypes were found among pure I. inflexus, while four haplotypes were found among pure I. longitubus. Most hybrid individuals had a haplotype found only in I. inflexus, suggesting that the initial F1 might have been formed by hybridization with I. inflexus as the maternal parent, and that in later hybrid formation, hybrids or I. inflexus tended to serve as the maternal parent. Although strong pre-mating isolation mechanisms contribute to preventing hybridization between the species, human habitat disturbance might have created the contact zone. Although mature hybrids in the contact zone contained equal proportions of backcrosses to both I. inflexus and I. longitubus, seedlings comprised more individuals originating from backcrosses to I. longitubus. The dominance of backcrosses to I. longitubus was probably caused by the quantitative difference between the parental species in the contact zone. In the contact zone, signs of contemporary hybridization in the nuclear genome might have been diluted by repeated backcrossing. The present study could illustrate the process of unidirectional introgression leading to chloroplast capture, a phenomenon frequently observed in Isodon species in Japan.
... The variation in the simulation outcomes was evaluated using 100 bootstrap replicates. The estimated generation time (g) of four years and the mutation rate per generation per site (µ) of 6.4*10 − 9 [48][49][50] were applied to visualize the PSMC graph using "psmc_ plot.pl" script. ...
Article
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The common pochard (Aythya ferina) is a freshwater diving duck found in the Palearctic region that has been classified as vulnerable by the IUCN due to continuous and rapid population declines across their distribution. To gain a better understanding of its genetic mechanism of adaptive evolution, we successfully sequenced and assembled the first high-quality chromosome-level genome of A. ferina using Illumina, Nanopore and Hi-C sequencing technologies. A total assembly length of 1,130.78 Mbp was obtained, with over 98.81% (1,117.37Mbp) of sequence anchored to 35 pseudo-chromosomes. We predicted 17,232 protein-coding genes, 95.9% of which were functionally annotated. We identified 339 expanded and 937 contracted gene families in the genome of A. ferina, and detected 95 genes that have been positively selected. The significantly enriched Gene Ontology and enriched pathways were related to energy metabolism, immune, nervous, and sensory systems, suggests that these factors likely played an important role in its evolution. Importantly, we recovered signatures of positive selection on genes related to vasoconstriction that may be associated with thermoregulatory adaptations of A. ferina for underwater diving. Overall, the high-quality genome assembly and annotation in this study provides valuable genomic resources for ecological and evolutionary studies, as well as toward the conservation of A. ferina.
... Signs of hybridization in nuclear DNA might be diluted due to repeated unidirectional backcrossing, as hypothesized for cytoplasmic introgression in a Helianthus population by Rieseberg (1995). Lavretsky et al. (2016) demonstrated that evidence of admixed histories in the nuclear genome was effectively lost after the fourth generation of unidirectional backcrossing, based on the simulation of 3448 SNP S loci. In the contact zone examined in this study, signs of contemporary hybridization in nuclear DNA may have been diluted by repeated introgression to I. longitubus. ...
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Interspecific hybridization between the short corolla tube species Isodon inflexus and the long corolla tube species I . longitubus was analyzed using genetic and morphometric markers. Bayesian clustering analysis using microsatellites revealed that plants in the contact zone consisted of two I . inflexus individuals, 33 I . longitubus individuals, and 13 hybrid individuals (F 2 -like and backcrosses to both I . inflexus and I . longitubus ). Using the sequences of the psbA-trnH inter genic spacer in chloroplast DNA, three haplotypes were found among pure I . inflexus , while four haplotypes were found among pure I . longitubus . Most hybrid individuals had a haplotype found only in I . inflexus , suggesting that the initial F 1 might have been formed by hybridization with I . inflexus as the maternal parent, and that in later hybrid formation, hybrids or I . inflexus tended to serve as the maternal parent. Although strong prezygotic isolation mechanisms contribute to preventing hybridization between the species, human habitat disturbance might have created the contact zone. Although mature hybrids in the contact zone contained equal proportions of backcrosses to both I . inflexus and I . longitubus , seedlings comprised more individuals originating from backcrosses to I . longitubus . The dominance of backcrosses to I . longitubus was probably caused by the quantitative difference between the parental species in the contact zone. In the contact zone, signs of contemporary hybridization in the nuclear genome might have been diluted by repeated backcrossing. The present study could illustrate the process of unidirectional introgression leading to chloroplast capture, a phenomenon frequently observed in Isodon species in Japan.
... To assess the effectiveness of our molecular dataset in distinguishing between classes of generational hybrids, and to more directly assign putative hybrids to those classes, we simulated expected assignment probabilities with our empirical data for first generation hybrids (F1) and 9 generations of backcrosses (F2-F10) based on methods outlined in Lavretsky et al. [51]. We used the same ddRAD-seq bi-allelic nuclear SNP set analyzed for population structure in simulations, but only including reference wild mallard and game-farm mallards. ...
Article
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The genetic composition of mallards in eastern North America has been changed by release of domestically-raised, game-farm mallards to supplement wild populations for hunting. We sampled 296 hatch-year mallards harvested in northwestern Ohio, October–December 2019. The aim was to determine their genetic ancestry and geographic origin to understand the geographic extent of game-farm mallard introgression into wild populations in more westward regions of North America. We used molecular analysis to detect that 35% of samples were pure wild mallard, 12% were early generation hybrids between wild and game-farm mallards (i.e., F1–F3), and the remaining 53% of samples were assigned as part of a hybrid swarm. Percentage of individuals in our study with some form of hybridization with game-farm mallard (65%) was greater than previously detected farther south in the mid-continent (~4%), but less than the Atlantic coast of North America (~ 92%). Stable isotope analysis using δ²Hf suggested that pure wild mallards originated from areas farther north and west than hybrid mallards. More specifically, 17% of all Ohio samples had δ²Hf consistent with more western origins in the prairies, parkland, or boreal regions of the mid-continent of North America, with 55%, 35%, and 10% of these being genetically wild, hybrid swarm, and F3, respectively. We conclude that continued game-farm introgression into wild mallards is not isolated to the eastern population of mallards in North America, and may be increasing and more widespread than previously detected. Mallards in our study had greater incidence of game-farm hybridization than other locales in the mid-continent but less than eastern North American regions suggesting further need to understand game-farm mallard genetic variation and movement across the continent.
... By examining both mtDNA and nuclear DNA, we obtained a more complete understanding of current and historical hybridization. Previous work has demonstrated that backcrossing only three or four generations into the same parental population can cause complete genetic replacement of nuclear DNA (Lavretsky et al. 2016. Conversely, given the life history and breeding philopatry of female ducks and female progeny Anderson 1988, Anderson et al. 1992), mtDNA can be captured within these maternal lineages and perpetuated for much longer than nuclear DNA. ...
Article
The Mallard (Anas platyrhynchos) duck is a ubiquitous and socio-economically important game bird in North America. Despite their generally abundant midcontinent population, Mallards in eastern North America are declining, which may be partially explained by extensive hybridization with human-released domestically-derived game-farm Mallards. We investigated the genetic composition of Mallards in the middle and lower Mississippi flyway, key wintering regions for the species. We found that nearly 30% of wild Mallards carried mitochondrial (mtDNA) haplotypes derived from domestic Mallards present in North America, indicating that the individuals had female game-farm Mallard lineage in their past; however, nuclear results identified only 4% of the same sample set as putative hybrids. Recovering 30% of samples with Old World (OW) A mtDNA haplotypes is concordant with general trends across the Mississippi flyway and this percentage was stable across Mallards we sampled a decade apart. The capture and perpetuation of OW A mtDNA haplotypes is likely due to female breeding structure, whereas reversal of the nuclear signal back to wild ancestry is due to sequential backcrossing and lower and/or declining admixture with game-farm Mallards. Future studies of wild ancestry of Mississippi flyway Mallards will benefit from coupling molecular and spatial technology across flyways, seasons, and years to search for potential transitions of Mallard populations with different genetic ancestry, and whether the genetic ancestry is somehow linked to an individual’s natal and subsequent breeding location.
... Nuclear population structure was based on independent bi-allelic ddRAD-seq autosomal single nucleotide polymorphisms (SNPs) and without using a priori assignment of individuals to populations or species. Bi-allelic SNPs were extracted from a concatenated fasta file of ddRAD-seq autosomal loci using a custom python script in plink format (i.e., ped & map files) 45 . Following, PLINK v1.07 46 was used to filter for singletons (i.e., minimum allele frequency (-maf 0.005)), any SNP missing ≥ 20% of data across samples (-geno 0.2), as well as any SNPs found to be in linkage disequilibrium (LD) (-indep-pairwise 2 1 0.5). ...
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Causes for genomic and morphological similarities among recently radiated species are often multifaceted and are further convoluted among species that readily interbreed. Here, we couple genomic and morphological trait comparisons to test the extent that ancestry and gene flow explain the retention of mallard-like traits within a sister species, the Mexican duck. First, we confirm that these taxa remain genetically structured, and that Mexican ducks exhibit an isolation-by-distance pattern. Despite the assumption of wide-spread hybridization, we found only a few late-stage hybrids, all from the southwestern USA. Next, assessing 23 morphological traits, we developed a genetically-vetted morphological key that is > 97% accurate in distinguishing across sex-age cohorts of Mexican ducks, mallards, and hybrids. During key development, we determined that 25% of genetically pure, immature male Mexican ducks of the northern population naturally displayed mallard-like traits in their formative plumage. In fact, applying this key to 55 museum specimens, we identified that only four of the 14 specimens originally classified as phenotypic hybrids were truly hybrids. We discuss how genomic and morphological comparisons shed light into the mechanism(s) underlying the evolution of complex phenotypic traits in recent radiations, and how misunderstanding the true morphological diversity within Mexican ducks resulted in taxonomic revisions that hindered conservation efforts.
... To better assess whether small interspecific admixture assignments reflect hybridization or retained ancestral vari-ation, we employed methods outlined in Lavretsky et al. (2016) to simulate expected assignment probabilities for firstgeneration hybrids (F1) and nine generations of backcrosses (F2-F10) into either Arctogadus or Boreogadus for all ddRADseq markers. In short, a total of ten F1 hybrids were first generated by randomly sampling an allele from Arctogadus and Boreogadus gene pool across biallelic SNP positions--each position was randomly sampled based on a probability proportional to the allelic frequency in each respective gene pool. ...
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As marine ecosystems respond to climate change and other stressors, it is necessary to evaluate current and past hybridization events to gain insight on the outcomes and drivers of such events. Ancestral introgression within the gadids has been suggested to allow cod to inhabit a variety of habitats. Little attention has been given to contemporary hybridization, especially within cold-water-adapted cod (Boreogadus saida Lepechin, 1774 and Arctogadus glacialis Peters, 1872). We used whole-genome, restriction-site associated, and mitochondrial sequence data to explore the degree and direction of hybridization between these species where previous hybridization had not been reported. Although nearly identical morphologically at certain life stages, we detected very distinct nuclear and mitochondrial lineages. We detected one potential hybrid with a Arctogadus mitochondrial haplotype and Boreogadus nuclear genotype, but no early generational hybrids. The presence of a late generation hybrid suggests that at least some hybrids survive to maturity and reproduce. However, a historical introgression event could not be excluded. Contemporary gene flow appears asymmetrical from Arctogadus into Boreogadus, which may be due to overlap in timing of spawning, environmental heterogeneity, or differences in population size. This study provides important baseline information for the degree of potential hybridization between these species within Alaska marine environments.
... However, Qvalue ranges have not been thoroughly investigated with GBS data without creating a panel of diagnostic loci (Randi, 2008;Vaha & Primmer, 2006). In our study, GBS enabled classification of parental species with very high confidence (Q-values > 0.99), and our simulation in HYBRIDLAB suggested a range of 0.05 < Q < 0.95 to classify hybrids, similar to other GBS studies (Ackiss et al., 2020;Lavretsky et al., 2016). Importantly, this Q-value range resulted in 94% agreement between ADMIXTURE and NEWHYBRIDS for identification of hybrids. ...
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Anthropogenic activities may facilitate undesirable hybridization and genomic introgression between fish species. Walleye (Sander vitreus) and sauger (Sander canadensis) are economically valuable freshwater species that can spontaneously hybridize in areas of sympatry. Levels of genomic introgression between walleye and sauger may be increased by modifications to waterbodies (e.g., reservoir development) and inadvertent propagation of hybrids in stocking programs. We used genotyping by sequencing (GBS) to examine 217 fish from two large reservoirs with mixed populations of walleye and sauger in Saskatchewan, Canada (Lake Diefenbaker, Tobin Lake). Analyses with 20,038 (r90) and 478 (r100) SNPs clearly resolved walleye and sauger, and classified hybrids with high confidence. F1, F2, and multi‐generation hybrids were detected in Lake Diefenbaker, indicating potentially high levels of genomic introgression. In contrast, only F1 hybrids were detected in Tobin Lake. Field classification of fish was unreliable; 7% of fish were misidentified based on broad species categories. Important for activities such as brood stock selection, 12/173 (7%) fish field‐identified as pure walleye, and 1/24 (4%) identified as pure sauger were actually hybrids. In addition, 2/15 (13%) field‐identified hybrids were actually pure walleye or sauger. We conclude that hybridization and introgression are occurring in Saskatchewan reservoirs, and that caution is warranted when using these populations in stocking programs. GBS offers a powerful and flexible tool for examining hybridization without pre‐identification of informative loci, eliminating some of the key challenges associated with other marker types.
... For the lice, we called bi-allelic SNPs for one OTU of Goniodes lagpoi (18 louse individuals) and two OTUs of Lagopoecus affinis (18 total louse individuals, 9 from each OTU) identified in the OTU analyses. These lice were sampled from three distinct regions: a northern region ("Arctic"), an interior region ("Denali"), and a south-central re- (Lavretsky et al., 2016). Specifically, to limit any biases due to sequencing error and/or allelic dropout, a minimum of 10 reads was required to score a locus as heterozygous. ...
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Understanding both sides of host–parasite relationships can provide more complete insights into host and parasite biology in natural systems. For example, phylogenetic and population genetic comparisons between a group of hosts and their closely associated parasites can reveal patterns of host dispersal, interspecies interactions, and population structure that might not be evident from host data alone. These comparisons are also useful for understanding factors that drive host–parasite coevolutionary patterns (e.g., codivergence or host switching) over different periods of time. However, few studies have compared the evolutionary histories between multiple groups of parasites from the same group of hosts at a regional geographic scale. Here, we used genomic data to compare phylogenomic and population genomic patterns of Alaska ptarmigan and grouse species (Aves: Tetraoninae) and two genera of their associated feather lice: Lagopoecus and Goniodes . We used whole‐genome sequencing to obtain hundreds of genes and thousands of single‐nucleotide polymorphisms (SNPs) for the lice and double‐digest restriction‐associated DNA sequences to obtain SNPs from Alaska populations of two species of ptarmigan. We found that both genera of lice have some codivergence with their galliform hosts, but these relationships are primarily characterized by host switching and phylogenetic incongruence. Population structure was also uncorrelated between the hosts and lice. These patterns suggest that grouse, and ptarmigan in particular, share habitats and have likely had historical and ongoing dispersal within Alaska. However, the two genera of lice also have sufficient dissimilarities in the relationships with their hosts to suggest there are other factors, such as differences in louse dispersal ability, that shape the evolutionary patterns with their hosts.
... Examples of true hybrid swarms may be rare simply because the backcrossing of hybrids back into large parental populations makes the persistence of large numbers of admixed individuals unlikely (e.g., Lavretsky et al., 2016). However, island populations and those that have recently declined are more susceptible to genetic swamping by an introduced species (Childs, Echelle, & Dowling, 1996;Rhymer, 2006 (Rhymer, 2006;Rhymer & Simberloff, 1996;Todesco et al., 2016). ...
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Interspecific hybridization is recognized as an important process in the evolutionary dynamics of both speciation and the reversal of speciation. However, our understanding of the spatial and temporal patterns of hybridization that erode versus promote species boundaries is incomplete. The endangered, endemic koloa maoli (or Hawaiian duck, Anas wyvilliana) is thought to be threatened with genetic extinction through ongoing hybridization with an introduced congener, the feral mallard (A. platyrhynchos). We investigated spatial and temporal variation in hybrid prevalence in populations throughout the main Hawaiian Islands, using genomic data to characterize population structure of koloa, quantify the extent of hybridization, and compare hybrid proportions over time. To accomplish this, we genotyped 3,308 double‐digest restriction‐site‐associated DNA (ddRAD) loci in 425 putative koloa, mallards, and hybrids from populations across the main Hawaiian Islands. We found that despite a population decline in the last century, koloa genetic diversity is high. There were few hybrids on the island of Kauaʻi, home to the largest population of koloa. By contrast, we report that sampled populations outside of Kauaʻi can now be characterized as hybrid swarms, in that all individuals sampled were of mixed koloa × mallard ancestry. Further, there is some evidence that these swarms are stable over time. These findings demonstrate spatial variation in the extent and consequences of interspecific hybridization, and highlight how islands or island‐like systems with small population sizes may be especially prone to genetic extinction when met with a congener that is not reproductively isolated.
... The evidence suggests any hybridization event would have likely taken place in Asia within the species' normal distribution. Further, Lavretsky et al. (2016) showed that evidence of admixture is effectively lost after the fourth generation; therefore, whole-genome information or genomewide scans would be needed to identify admixture events at this stage. ...
Article
First sighting records of rare occurrences may become increasingly important for recognizing changes in distribution, changes in migratory strategies, or increases in hybridization. We documented the first record of a Tundra Bean Goose in the Mississippi Alluvial Valley, the outlet and historic floodplain for much of North America and one of the most important waterfowl wintering areas on the continent. We also document the first genetically confirmed record in the contiguous USA. Bean Goose (Anser fabalis and A. serrirostris) occurrences in North America are rare, especially outside of Alaska. On 24 January 2018, a Tundra Bean Goose (A. s. serrirostris) was harvested by a hunter in a winter-flooded rice field in Desha County, Arkansas, USA, near Dumas. The goose was mixed with a flock of 50 Greater White-Fronted Geese (A. albifrons). Because this individual was legally, albeit accidentally shot, we had the rare and exciting opportunity to obtain morphometric measurements and biological samples. As a result, we were able to verify the species and subspecies through genetic and morphological analysis. We determined the goose was an adult female Tundra Bean Goose, and mitochondrial DNA control region sequence data indicated this specimen was the subspecies A. s. serrirostris.
... Therefore, because mutation rates are likely to be similar across duck species, we can hypothesize that torrent duck mtDNA genetic diversity probably is influenced by the structure of their habitat leading to extensive branched and subdivided, structured riverine habitat, such that each river may be isolated by distance and genetically distinct from other watersheds. In contrast to mtDNA, diversity estimates from nuclear DNA for the two torrent duck subspecies were lower compared to other waterfowl species (Lavretsky et al., 2015;Lavretsky et al., 2016;Peters et al., 2016;Wilson et al., 2012). A probable explanation for the disparity in diversity estimates of mitochondrial and nuclear genes within torrent ducks could be a combined effect resulting from high mtDNA mutation rate (four orders of magnitude), population subdivision due to the branched structure riverine habitat, the adult territorial behavior, and natural selection associated to high elevation (e.g., low temperatures and hypoxia) affecting nuclear DNA. ...
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Aim: To investigate the structure and rate of gene flow among populations of habitat-specialized species to understand the ecological and evolutionary processes underpinning their population dynamics and historical demography, including speciation and extinction. Location: Peruvian and Argentine Andes. Taxon: Two subspecies of torrent duck (Merganetta armata). Methods: We sampled 156 individuals in Peru (M. a. leucogenis; Chillón River, n = 57 and Pachachaca River, n = 49) and Argentina (M. a. armata; Arroyo Grande River, n = 33 and Malargüe River, n = 17), and sequenced the mitochondrial DNA (mtDNA) control region to conduct coarse and fine-scale demographic analyses of population structure. Additionally, to test for differences between subspecies, and across genetic markers with distinct inheritance patterns, a subset of individuals (Peru, n = 10 and Argentina, n = 9) was subjected to partial genome resequencing, obtaining 4,027 autosomal and 189 Z-linked double-digest restriction-associated DNA sequences. Results: Haplotype and nucleotide diversities were higher in Peru than Argentina across all markers. Peruvian and Argentine subspecies showed concordant species-level differences (ΦST mtDNA = 0.82; ΦST autosomal = 0.30; ΦST Z chromosome = 0.45), including no shared mtDNA haplotypes. Demographic parameters estimated for mtDNA using IM and IMa2 analyses, and for autosomal markers using ∂a∂i (isolation-with-migration model), supported an old divergence (mtDNA = 600,000 years before present (ybp), 95% HPD range = 1.2 Mya to 200,000 ybp; and autosomal ∂a∂i = 782,490 ybp), between the two subspecies, characteristic of deeply diverged lineages. The populations were well-differentiated in Argentina but moderately differentiated in Peru, with low unidirectional gene flow in each country. Main conclusions: We suggest that the South American Arid Diagonal was preexisting and remains a current phylogeographic barrier between the ranges of the two torrent duck subspecies, and the adult territoriality and breeding site fidelity to the rivers define their population structure.
... The evidence suggests any hybridization event would have likely taken place in Asia within the species' normal distribution. Further, Lavretsky et al. (2016) showed that evidence of admixture is effectively lost after the fourth generation; therefore, whole-genome information or genomewide scans would be needed to identify admixture events at this stage. ...
... (c) PCA and admixture analyses for mallards and black ducks only. Arrows highlight two samples consistently identified as admixed across PCA, admixture, and fineRADstructure (see Figure 3) analyses python scripts ( Lavretsky et al., 2016). Input files for fineRADstructure analyses were created using a custom python script from Stryjewski and Sorenson (2017). ...
Article
Recently evolved species typically share genetic variation across their genomes due to incomplete lineage sorting and/or ongoing gene flow. Given only subtle allele frequency differences at most loci and the expectation that divergent selection may affect only a tiny fraction of the genome, distinguishing closely related species based on multi‐locus data requires substantial genomic coverage. In this study, we used ddRAD‐seq to sample the genomes of five recently diverged, New World “mallards” (Anas spp.), a group of dabbling duck species characterized by diagnosable phenotypic differences but minimal genetic differentiation. With increased genomic sampling, we aimed to characterize population structure within this group and identify genomic regions that may have experienced divergent selection during speciation. We analyzed 3,017 autosomal ddRAD‐seq loci and 177 loci from the Z‐chromosome. In contrast to previous studies, the ddRAD‐seq data were sufficient to assign individuals to their respective species or subspecies and to generate estimates of gene flow in a phylogenetic framework. We find limited evidence of contemporary gene flow between the dichromatic mallard and several monochromatic taxa, but find evidence for historical gene flow between some monochromatic species pairs. We conclude that the overall genetic similarity of these taxa likely reflects retained ancestral polymorphism rather than recent and extensive gene flow. Thus, despite recurring cases of hybridization in this group, our results challenge the current dogma predicting the genetic extinction of the New World monochromatic dabbling ducks via introgressive hybridization with mallards. Moreover, ddRAD‐seq data were sufficient to identify previously unknown outlier regions across the Z‐chromosome and several autosomal chromosomes, regions that may have been involved in the diversification of species in this recent radiation. This article is protected by copyright. All rights reserved.
... First, we employed methods outlined in Lavretsky et al. (2016) to simulate expected assignment probabilities for first-generation hybrids (F1) and nine generations of backcrosses (F2-F10) into either the mallard or black duck parental population for ddRAD-seq markers. In short, a total of ten F1 hybrids were first generated by randomly sampling an allele from the mallard and black duck gene pool across bi-allelic SNP positions-each position was randomly sampled based on a probability proportional to the allelic frequency in each respective gene pool. ...
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Resolving evolutionary relationships and establishing population structure depends on molecular diagnosability that is often limited for closely related taxa. Here, we use 3,200 ddRAD‐seq loci across 290 mallards, American black ducks, and putative hybrids to establish population structure and estimate hybridization rates. We test between traditional assignment probability and accumulated recombination events based analyses to assign hybrids to generational classes. For hybrid identification, we report the distribution of recombination events complements ADMIXTURE simulation by extending resolution past F4 hybrid status; however, caution against hybrid assignment based on accumulated recombination events due to an inability to resolve F1 hybrids. Nevertheless, both analyses suggest that there are relatively few backcrossed stages before a lineage's hybrid ancestry is lost and the offspring are effectively parental again. We conclude that despite high rates of observed interspecific hybridization between mallards and black ducks in the middle part of the 20th century, our results do not support the predicted hybrid swarm. Conversely, we report that mallard samples genetically assigned to western and non‐western clusters. We indicate that these non‐western mallards likely originated from game‐farm stock, suggesting landscape level gene flow between domestic and wild conspecifics. Sample distribution of American black ducks (ABDU), mallards (MALL), and putative hybrids (MBDH). Visualization of population structure based on PCA scatter plots of PC1 (x‐axis) and PC2 (y‐axis) plotted for 3,037 Autosomal and 163 Z‐chromosome ddRAD‐seq loci. Additionally, we present ADMIXTURE based maximum likelihood estimation of individual assignment probabilities for K population values of 2 and 3 based on autosomal or Z‐linked markers, respectively.
... The number of generations since hybridization should be interpreted with an eye to policy. After some number of generations of unidirectional backcrossing, policy will dictate that we consider an individual to be parental species (again) [67]. It is best to make this decision before marker selection because it is impossible to apply policy decisions regarding the acceptability of backcrossed individuals if sufficient detection power is lacking. ...
Article
Hybridization among naturally separate taxa is increasing owing to human impact, and can result in taxon loss. Previous classification of anthropogenic hybridization has largely ignored the case of bimodal hybrid zones, in which hybrids commonly mate with parental species, resulting in many backcrossed individuals with a small proportion of introgressed genome. Genetic markers can be used to detect such hybrids, but until recently too few markers have been used to detect the true extent of introgression. Recent studies of wolves and trout have employed thousands of markers to reveal previously undetectable backcrosses. This improved resolution will lead to increased detection of late-generation backcrosses, shed light on the consequences of anthropogenic hybridization, and pose new management issues for conservation scientists.
... (Hoberg et al. 2012), our inconclusive findings could indicate (I) that M. caurina were not present prior to introductions, (II) that the sampled genes provide insufficient resolution to detect M. caurina, or (III) that M. caurina alleles decayed and eventually disappeared following introductions and subsequent introgressive hybridization. Genetic signatures of introgression can be lost in 4 generations of backcrossing (20 years for marten) (Lavretsky et al. 2016) and swamping may be accelerated by asymmetrical gene flow or a demographic imbalance. Therefore, if M. caurina was swamped by introduced M. americana, there may be no signature of admixture remaining in these populations or the signature is so diluted that it requires whole genome-level analyses to detect it. ...
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The evolutionary consequences of natural introgression provide a rare opportunity to retrospectively evaluate how the introduction of exotics or genetic rescue efforts may impact endemic faunas. Phylogeographic structure among mainland, endemic insular, and introduced North American marten (Martes americana and M. caurina) populations have been shaped by a complex history of natural, post-glacial population expansion followed by a series of anthropogenic introductions. In some cases, both natural colonization and translocations facilitated secondary contact, offering a series of replicated experiments that demonstrate how introgression, in these cases following isolation (insular and refugial), shapes genetic diversity. We test whether genetic exchange is occurring between North American marten species using mitochondrial genomes and ten nuclear loci. We present evidence of biased nuclear introgression from M. caurina into M. americana across two natural hybrid zones (insular and mainland) and found no remnant evidence of M. caurina on islands that received M. americana translocations, suggesting prior absence, potential extirpation, or genetic swamping of M. caurina from these islands. Our results highlight the importance of understanding phylogeographic variation prior to identifying source populations for wildlife translocations and caution the use of genetic rescue for North American marten populations. Although previously managed as a single species, these two species show substantial genetic divergence. When the two are placed into contact, they exhibit unidirectional, asymmetric introgression with potentially negative consequences for M. caurina, underscoring the value of mindful consideration of introgression in wildlife management.
... This is likely the result of purifying selection acting on UCE loci, effecting an apparent lower substitution rate. Our values are more similar to the values for Z-linked loci in other bird species (Balakrishnan & Edwards, 2009;Huynh, Maney & Thomas, 2010;Lavretsky et al., 2016). ...
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Using a large, consistent set of loci shared by descent (orthologous) to study relationships among taxa would revolutionize among-lineage comparisons of divergence and speciation processes. Ultraconserved elements (UCEs), highly conserved regions of the genome, offer such genomic markers. The utility of UCEs for deep phylogenetics is clearly established and there are mature analytical frameworks available, but fewer studies apply UCEs to recent evolutionary events, creating a need for additional example datasets and analytical approaches. We used UCEs to study population genomics in snow and McKay’s buntings ( Plectrophenax nivalis and P. hyperboreus ). Prior work suggested divergence of these sister species during the last glacial maximum (∼18–74 Kya). With a sequencing depth of ∼30× from four individuals of each species, we used a series of analysis tools to genotype both alleles, obtaining a complete dataset of 2,635 variable loci (∼3.6 single nucleotide polymorphisms/locus) and 796 invariable loci. We found no fixed allelic differences between the lineages, and few loci had large allele frequency differences. Nevertheless, individuals were 100% diagnosable to species, and the two taxa were different genetically ( FST = 0.034; P = 0.03). The demographic model best fitting the data was one of divergence with gene flow. Estimates of demographic parameters differed from published mtDNA research, with UCE data suggesting lower effective population sizes (∼92,500–240,500 individuals), a deeper divergence time (∼241,000 years), and lower gene flow (2.8–5.2 individuals per generation). Our methods provide a framework for future population studies using UCEs, and our results provide additional evidence that UCEs are useful for answering questions at shallow evolutionary depths.
... A striking feature of our genomic data is the absence of F1 hybrids, though multigenerational and back-crossed individuals were identified. While this may reflect sampling biases, in other systems hybridisation on a per individual scale can be rare (Abbott et al. 2013) and F1 hybrids uncommon as hybridisation rates decrease (Lavretsky et al. 2016). Therefore, the absence of F1 hybrids may not be an artefact if hybridisation between parental P. adscitus and P. eximius is rare. ...
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The study of hybrid zones advances understanding of the speciation process, and approaches incorporating genomic data are increasingly used to draw significant conclusions about the impact of hybridisation. Despite the progress made, the complex interplay of factors that can lead to substantially variable hybridisation outcomes are still not well understood, and many systems and/or groups remain comparatively poorly studied. Our study aims to broaden the literature on avian hybrid zones, investigating a potentially geographically and temporally complex putative hybrid zone between two native Australian non-sister parrot species, the pale-headed and eastern rosellas (Platycercus adscitus and Platycercus eximius, respectively). We analysed six plumage traits and >1400 RADseq loci and detected hybrid individuals and an unexpectedly complex geographic structure. The hybrid zone is larger than previously described due to either observer bias or its movement over recent decades. It comprises different subregions where genetic and plumage signals of admixture vary markedly in their concordance. Evidence of contemporary hybridisation (later generation and backcrossed individuals) both within and beyond the previously defined zone, when coupled with a lack of F1 hybrids and differential patterns of introgression among potentially diagnostic loci, indicates a lack of post-zygotic barriers to gene flow between species. Despite ongoing gene flow, species boundaries are likely maintained largely by strong pre-mating barriers. These findings are discussed in detail and future avenues for research into this system are proposed, which would be of benefit to the speciation and hybrid zone literature.
... Indeed, the D-statistic was developed to detect ancient gene flow and to estimate the extent of archaic ancestry in the genomes of extant populations [33]. The detection and quantification of recent gene flow warrants a population genomic approach whereby multiple individuals of one population are sequenced [3,9,81,82]. Second, the relative rarity of goose hybrids diminishes the opportunity for backcrossing and introgression, leading to absence or low levels of recent gene flow [19]. ...
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Background The impacts of hybridization on the process of speciation are manifold, leading to distinct patterns across the genome. Genetic differentiation accumulates in certain genomic regions, while divergence is hampered in other regions by homogenizing gene flow, resulting in a heterogeneous genomic landscape. A consequence of this heterogeneity is that genomes are mosaics of different gene histories that can be compared to unravel complex speciation and hybridization events. However, incomplete lineage sorting (often the outcome of rapid speciation) can result in similar patterns. New statistical techniques, such as the D-statistic and hybridization networks, can be applied to disentangle the contributions of hybridization and incomplete lineage sorting. We unravel patterns of hybridization and incomplete lineage sorting during and after the diversification of the True Geese (family Anatidae, tribe Anserini, genera Anser and Branta) using an exon-based hybridization network approach and taking advantage of discordant gene tree histories by re-sequencing all taxa of this clade. In addition, we determine the timing of introgression and reconstruct historical effective population sizes for all goose species to infer which demographic or biogeographic factors might explain the observed patterns of introgression. ResultsWe find indications for ancient interspecific gene flow during the diversification of the True Geese and were able to pinpoint several putative hybridization events. Specifically, in the genus Branta, both the ancestor of the White-cheeked Geese (Hawaiian Goose, Canada Goose, Cackling Goose and Barnacle Goose) and the ancestor of the Brent Goose hybridized with Red-breasted Goose. One hybridization network suggests a hybrid origin for the Red-breasted Goose, but this scenario seems unlikely and it not supported by the D-statistic analysis. The complex, highly reticulated evolutionary history of the genus Anser hampered the estimation of ancient hybridization events by means of hybridization networks. The reconstruction of historical effective population sizes shows that most species showed a steady increase during the Pliocene and Pleistocene. These large effective population sizes might have facilitated contact between diverging goose species, resulting in the establishment of hybrid zones and consequent gene flow. Conclusions Our analyses suggest that the evolutionary history of the True Geese is influenced by introgressive hybridization. The approach that we have used, based on genome-wide phylogenetic incongruence and network analyses, will be a useful procedure to reconstruct the complex evolutionary histories of many naturally hybridizing species groups.
... Genome reduction approaches, particularly ddRAD, are being increasingly used in studies of hybridization and admixture in vertebrates [28][29][30]. To date, the DArTseq platform has infrequently been used in vertebrate systems. ...
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Next-generation sequencing (NGS) approaches are increasingly being used to generate multi-locus data for phylogeographic and evolutionary genetics research. We detail the applicability of a restriction enzyme-mediated genome complexity reduction approach with subsequent NGS (DArTseq) in vertebrate study systems at different evolutionary and geographical scales. We present two case studies using SNP data from the DArTseq molecular marker platform. First, we used DArTseq in a large phylogeographic study of the agamid lizard Ctenophorus caudicinctus, including 91 individuals and spanning the geographical range of this species across arid Australia. A low-density DArTseq assay resulted in 28 960 SNPs, with low density referring to a comparably reduced set of identified and sequenced markers as a cost-effective approach. Second, we applied this approach to an evolutionary genetics study of a classic frog hybrid zone (Litoria ewingii–Litoria paraewingi) across 93 individuals, which resulted in 48 117 and 67 060 SNPs for a low- and high-density assay, respectively. We provide a docker-based workflow to facilitate data preparation and analysis, then analyse SNP data using multiple methods including Bayesian model-based clustering and conditional likelihood approaches. Based on comparison of results from the DArTseq platform and traditional molecular approaches, we conclude that DArTseq can be used successfully in vertebrates and will be of particular interest to researchers working at the interface between population genetics and phylogenetics, exploring species boundaries, gene exchange and hybridization.
... However, several studies have argued that identifying individuals with hybrid ancestry could become increasingly difficult after the first three generations using the methods we employed in this article (e.g. Lavretsky et al. 2016). Thus, we cannot reject the hypothesis that these later hybrid generations were misidentified. ...
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We aimed to study the importance of hybridization between two cryptic species of the genus Ectocarpus, a group of filamentous algae with haploid-diploid life cycles that include the principal genetic model organism for the brown algae. In haploid-diploid species, the genetic structure of the two phases of the life cycle can be analysed separately in natural populations. Such life cycles provide a unique opportunity to estimate the frequency of hybrid genotypes in diploid sporophytes and meiotic recombinant genotypes in haploid gametophytes allowing the effects of reproductive barriers preventing fertilization or preventing meiosis to be untangle. The level of hybridization between E. siliculosus and E. crouaniorum was quantified along the European coast. Clonal cultures (568 diploid, 336 haploid) isolated from field samples were genotyped using cytoplasmic and nuclear markers to estimate the frequency of hybrid genotypes in diploids and recombinant haploids. We identified admixed individuals using microsatellite loci, classical assignment methods and a newly developed Bayesian method (XPloidAssignment), which allows the analysis of populations that exhibit variations in ploidy level. Over all populations, the level of hybridization was estimated at 8.7%. Hybrids were exclusively observed in sympatric populations. More than 98% of hybrids were diploids (40% of which showed signs of aneuploidy) with a high frequency of rare alleles. The near absence of haploid recombinant hybrids demonstrates that the reproductive barriers are mostly post-zygotic and suggests that abnormal chromosome segregation during meiosis following hybridisation of species with different genome sizes could be a major cause of interspecific incompatibility in this system. This article is protected by copyright. All rights reserved.
... The vigour expressed in some F1 hybrids is often lost in subsequent generations (F2 and/or backcrosses) [54]. Distinguishing between pure individuals and later generation backcrosses (F4 or later) can represent a challenge and may not be particularly useful, because the signal of hybridisation is lost [65]. Further, the limited sample size did not allow for the subdivision of individuals into discrete hybrid classes (e.g F1, backcrosses) for the statistical analyses presented here. ...
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Hybridisation can produce evolutionary novelty by increasing fitness and adaptive capacity. Heterosis, or hybrid vigour, has been documented in many plant and animal taxa, and is a notable consequence of hybridisation that has been exploited for decades in agriculture and aquaculture. On the contrary, loss of fitness in naturally occurring hybrid taxa has been observed in many cases. This can have negative consequences for the parental species involved (wasted reproductive effort), and has raised concerns for species conservation. This study evaluates the relative fitness of previously documented butterflyfish hybrids of the genus Chaetodon from the Indo-Pacific suture zone at Christmas Island. Histological examination confirmed the reproductive viability of Chaetodon hybrids. Examination of liver lipid content showed that hybrid body condition was not significantly different from parent species body condition. Lastly, size at age data revealed no difference in growth rates and asymptotic length between hybrids and parent species. Based on the traits measured in this study, naturally occurring hybrids of Chaetodon butterflyfishes have similar fitness to their parental species, and are unlikely to supplant parental species under current environmental conditions at the suture zone. However, given sufficient fitness and ongoing genetic exchange between the respective parental species, hybrids are likely to persist within the suture zone.
... At the second backcross generation (BC2), an average of two-and-a-quarter Red-tailed Hawk alleles would be expected in our data, but the stochastic nature of Mendelian segregation makes it reasonably probable that our microsatellite data would fail to detect Red-tailed Hawk ancestry, even while one-eighth of the genome would be of Red-tailed Hawk origin. At subsequent backcross generations with eastern Red-shouldered Hawk, the genetic contribution of Red-tailed Hawk would certainly be too dilute to detect with a data set of this size (Lavretsky et al., 2016). In contrast to our microsatellite data, the results of our analyses of phenotype were inconsistent with the conclusion of Pyle et al. (2004) that the specimen represented a eastern Red-shouldered Hawk. ...
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An adult Buteo was found dead as a road-kill south of Sacramento, California, and was thought to represent the first state record of the eastern Red-shouldered Hawk ( B. lineatus lineatus ;). It is now a specimen in the Museum of Wildlife and Fisheries Biology (WFB 4816) at the University of California, Davis. We examined this specimen and found that many of its plumage characters differed from all other adult Red-shouldered Hawks examined, including nominate adults. Plumage markings and measurements were intermediate between Red-tailed Hawk ( Buteo jamaicensis, ssp calurus ) and Red-shouldered Hawk (ssp elegans ), leading us to hypothesize that the bird was a hybrid. However, mtDNA sequences and nuDNA microsatellites proved definitively that the bird was a Red-shouldered Hawk, most likely of eastern origin. This case illustrates that apparent hybrids or apparent vagrants could be individuals with anomalous phenotypes caused by rare genetic variation or novel epigenetic effects.
... At the second backcross generation (BC2), an average of two-and-a-quarter Red-tailed Hawk alleles would be expected in our data, but the stochastic nature of Mendelian segregation makes it reasonably probable that our microsatellite data would fail to detect Red-tailed Hawk ancestry, even while one-eighth of the genome would be of Red-tailed Hawk origin. At subsequent backcross generations with eastern Red-shouldered Hawk, the genetic contribution of Red-tailed Hawk would certainly be too dilute to detect with a data set of this size (Lavretsky et al., 2016). In contrast to our microsatellite data, the results of our analyses of phenotype were inconsistent with the conclusion of Pyle et al. (2004) that the specimen represented a eastern Red-shouldered Hawk. ...
Article
Full-text available
An adult Buteo was found dead as a road-kill south of Sacramento, California, and was thought to represent the first state record of the eastern Red-shouldered Hawk (B. lineatus lineatus; Pyle et al. 2004). It is now a specimen in the Museum of Wildlife and Fish Biology (WFB 4816) at the U. of California, Davis. We examined this specimen and found that many of its plumage characters differed from all other adult Red-shouldered Hawks examined, including nominate adults. Plumage markings and measurements were intermediate between Red-tailed Hawk (Buteo jamaicensis, ssp calurus) and Red-shouldered Hawk (ssp elegans), leading us to hypothesize that the bird was a hybrid. However, mtDNA sequences and nuDNA microsatellites proved definitively that the bird was a Red-shouldered Hawk, most likely of eastern origin. This case illustrates that apparent hybrids or apparent vagrants could be individuals with anomalous phenotypes caused by rare genetic variation or novel epigenetic effects.
... These two A. ''p.'' albivitta specimens also demonstrate that phenotypic evidence of hybridization, which does occur and has been useful in past evaluations in A. ''prasinus'', can be absent despite gene flow (but even nuclear genomic evidence of hybridization can disappear over a few generations of backcrossing; Lavretsky et al., 2016). ...
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The number of species recognized in Aulacorhynchus toucanets has varied tremendously over the past century. Revisors seem to disagree on whether head and bill coloration are useful indicators of species limits, especially in the A. “prasinus” complex. Using morphometrics, I tested the hypothesis that the major color-based subspecific groups of A. “prasinus” sensu lato are simply “cookie-cutter” (i.e., morphologically nearly identical) toucanets with different head and bill colorations. Univariate and multivariate analyses show that they are not simply morphological replicates of different colors: a complex array of morphometric similarities and dissimilarities occur between the major subspecific groups, and these variations differ between the sexes. Latitude and longitude had a small but significant association with female (but not male) PC1 and PC2. Hybridization and intergradation were also considered using plumage and bill characters as a surrogate to infer gene flow. Hybridization as indicated by phenotype appears to be substantial between A. “p.” cyanolaemus and A. “p.” atrogularis and nonexistent between other major groups, although from genetic evidence it is likely rare between A. “p.” albivitta and A. “p.” cyanolaemus. The congruence and complexities of the morphological and color changes occurring among these groups suggest that ecological adaptation (through natural selection) and social selection have co-occurred among these groups and that species limits are involved. Further, hybridization is not evident at key places, despite in many cases (hypothetical) opportunity for gene flow. Consequently, I recommend that this complex be recognized as comprising five biological species: A. wagleri, prasinus, caeruleogularis, albivitta, and atrogularis. Four of these also have valid subspecies within them, and additional work may eventually support elevation of some of these subspecies to full species. Species limits in South America especially need more study.
... Few studies attempt to standardize their hybrid identification and classification through comparative methods or simulations, and those that have done so generally found increasing difficulty in delimiting hybrids from parents past the first two to three generations (e.g. Cullingham et al. 2011, Lavretsky et al. 2016. However, these studies, as well as ours, are limited by their ability to describe older hybrid interactions without resorting to discrete hybrid classes, which can be misleading in systems that are beyond the first two generations of hybridization (Fitzpatrick 2012). ...
Article
Hybrid zones provide unique natural laboratories for studying mechanisms of evolution. But identification and classification of hybrid individuals (F1, F2, backcross, etc.) can be complicated by real population changes over time as well as by use of different marker types, both of which challenge documentation of hybrid dynamics. Here we use multiple genetic markers (mitochondrial DNA, microsatellites, and genome-wide single nucleotide polymorphisms) to reexamine population structure in a hybrid zone between two species of swallowtail butterflies in western Canada, Papilio machaon and P. zelicaon. Our aim was to test whether their hybrid dynamics remain the same as found 30 years ago using morphology and allozymes, and we compared different genetic datasets as well as alternative hybrid identification and classification methods. Overall, we found high differentiation between the two parental species, corroborating previous research from the 1980's. We identified fewer hybrid individuals in the main zone of hybridization in recent years, but this finding depended on the genetic markers considered. Comparison of methods with simulated datasets generated from our data showed that single nucleotide polymorphisms were more powerful than microsatellites for both hybrid identification and classification. Moreover, substantial variation among comparisons underlined the value of multiple markers and methods for documenting evolutionarily dynamic systems. This article is protected by copyright. All rights reserved.
... Hybridization does appear to be a recurrent evolutionary force within at least some species of white-headed gulls, notably the North American species/subspecies. If hybridization were limited to a single nuclear introgression event, the genetic legacy of the event would be lost within six generations (Lavretsky et al., 2015). As noted with other species, perhaps just a few genes are driving the speciation process within this complex (Poelstra et al., 2014;Mason and Taylor, 2015). ...
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Species complexes that have undergone recent radiations are often characterized by extensive allele sharing due to recent ancestry and (or) introgressive hybridization. This can result in discordant evolutionary histories of genes and heterogeneous genomes, making delineating species limits difficult. Here we examine the phylogenetic relationships among a complex group of birds, the white-headed gulls (Aves: Laridae), which offer a unique window into the speciation process due to their recent evolutionary history and propensity to hybridize. Relationships were examined among 17 species (61 populations) using a multilocus approach, including mitochondrial and nuclear intron DNA sequences and microsatellite genotype information. Analyses of microsatellite and intron data resulted in some species-based groupings, although most species were not represented by a single cluster. Considerable allele and haplotype sharing among white-headed gull species was observed; no locus contained a species-specific clade. Despite this, our multilocus approach provided better resolution among some species than previous studies. Interestingly, most clades appear to correspond to geographic locality: our BEAST analysis recovered strong support for a northern European/Icelandic clade, a southern European/Russian clade, and a western North American/canus clade, with weak evidence for a high latitude clade spanning North America and northwestern Europe. This geographical structuring is concordant with behavioral observations of pervasive hybridization in areas of secondary contact. The extent of allele and haplotype sharing indicates that ecological and sexual selection are likely not strong enough to complete reproductive isolation within several species in the white-headed gull complex. This suggests that just a few genes are driving the speciation process.
... We assumed an approximate mutation rate of 10 À9 mutations per bp per generation (Kumar & Subramanian, 2002) to convert the posterior distribution for the estimates of different parameters from mutation scale to generations (s) and individuals (h). A similar value has been used for RAD loci in other Anatidae species (Lavretsky et al., 2016). Because this mutation rate is a rough approximation, we are cautious to interpret the absolute values of the estimated parameters, and focus mainly on relative comparisons, which are not impacted by assumptions on the mutation rate. ...
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Aim The Malvinas/Falkland Islands ( MFI ) constitute the largest archipelago in the southern Atlantic, and harbour endemic lineages that presumably evolved after sea‐level rise, associated with glacial periods, isolated ancestral populations. We investigate the role of the MFI in isolating populations from continental counterparts of two highly vagile species: the sheldgeese Chloephaga picta and Chloephaga rubidiceps . Location Patagonia and the Malvinas/Falkland Islands. Methods We sampled C. picta and C. rubidiceps on the continent and MFI . Using a reduced‐representation genomic approach, we quantified the genetic differentiation between insular and continental populations of both species, and used coalescent‐based analyses to model their demography. Results The MFI harbour independently evolving lineages of C. picta and C. rubidiceps , which diverged from their continental counterparts during the Middle‐Late Pleistocene and have since experienced negligible gene flow. Main conclusions The c . 450 km that separate the archipelago from the continent are sufficient to isolate populations of these putatively highly vagile species. Ancestral lineages may have reached the MFI refugium during glacial cycles. Without conservation measures, the drastic decline of the morphologically, behaviourally and ecologically distinct continental population of C. rubidiceps , to < 1000 individuals, may lead to the extinction of an independently evolving taxon.
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Hybrid zones are dynamic systems where natural selection, sexual selection, and other evolutionary forces can act on reshuffled combinations of distinct genomes. The movement of hybrid zones, individual traits, or both are of particular interest for understanding the interplay between selective processes. In a hybrid zone involving two lek-breeding birds, secondary sexual plumage traits of Manacus vitellinus, including bright yellow collar and olive belly color, have introgressed asymmetrically ~50 km across the genomic center of the zone into populations more genetically similar to Manacus candei. Males with yellow collars are preferred by females and are more aggressive than parental M. candei, suggesting that sexual selection was responsible for the introgression of male traits. We assessed the spatial and temporal dynamics of this hybrid zone using historical (1989 - 1994) and contemporary (2017 - 2020) transect samples to survey both morphological and genetic variation. Genome-wide SNP data and several male phenotypic traits show that the genomic center of the zone has remained spatially stable, whereas the olive belly color of male M. vitellinus has continued to introgress over this time period. Our data suggest that sexual selection can continue to shape phenotypes dynamically, independent of a stable genomic transition between species.
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Anthropogenic hybridization, or higher and non‐natural rates of gene flow directly and indirectly induced by human activities, is considered a significant threat to biodiversity. The primary concern for conservation is the potential for genomic extinction and loss of adaptiveness for native species due to the extensive introgression of non‐native genes. To alleviate or reverse trends for such scenarios requires the direct integration of genomic data within a model framework for effective management. Towards this end, we developed the simRestore R program as a decision‐making tool that integrates ecological and genomic information to simulate ancestry outcomes from optimized conservation strategies. In short, the program optimizes supplementation and removal strategies across generations until a set native genetic threshold is reached within the studied population. Importantly, in addition to helping with initial decision‐making, simulations can be updated with the outcomes of ongoing efforts, allowing for the adaptive management of populations. After demonstrating functionality, we apply and optimize among actionable management strategies for the endangered Hawaiian duck for which the current primary threat is genetic extinction through ongoing anthropogenic hybridization with feral mallards. Simulations demonstrate that supplemental and removal efforts can be strategically tailored to move the genetic ancestry of Hawaii's hybrid populations towards Hawaiian duck without the need to completely start over. Further, we discuss ecological parameter sensitivity, including which factors are most important to ensure genetic outcomes (i.e. number of offspring). Finally, to facilitate use, the program is also available online as a Shiny Web application.
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Aim Connectivity is vital to the resiliency of populations to environmental change and stochastic events, especially for cold-adapted species as Arctic and alpine tundra habitats retract as the climate warms. We examined the influence of past and current landscapes on genomic connectivity in cold-adapted galliformes as a critical first step to assess the vulnerability of Alaska ptarmigan and grouse to environmental change. We hypothesize that the mosaic of physical features and habitat within Alaska promoted the formation of genetic structure across species. Location Alaska, United States of America. Taxa Ptarmigan and Grouse (Galliformes: Tetraoninae). Methods We collected double digest restriction-site-associated DNA sequence data from six ptarmigan and grouse species (N = 13–145/species) sampled across multiple ecosystems up to ~10 degrees of latitude. Spatial genomic structure was analysed using methods that reflect different temporal scales: (1) principal components analysis to identify major trends in the distribution of genomic variation; (2) maximum likelihood clustering analyses to test for the presence of multiple genomic groupings; (3) shared co-ancestry analyses to assess contemporary relationships and (4) effective migration surfaces to identify regions that deviate from a null model of isolation by distance. Results Levels of genomic structure varied across species (ΦST =0.009–0.042). Three general patterns of structure emerged: (1) east-west partition located near the Yukon-Tanana uplands; (2) north-south split coinciding with the Alaska Range and (3) northern group near the Brooks Range. Species-specific patterns were observed; not all landscape features were barriers to gene flow for all ptarmigan and grouse and temporal contrasts were detected at the Brooks Range. Main conclusions Within Alaska galliformes, patterns of genomic structure coincide with physiographic features and highlight the importance of physical and ecological barriers in shaping how genomic diversity is arrayed across the landscape. Lack of concordance in spatial patterns indicates that species behaviour and habitat affinities play key roles in driving the contrasting patterns of genomic structure.
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Translocating species is an important management tool to establish or expand the range of species. Success of translocations requires an understanding of potential consequences, including whether a sufficient number of individuals were used to minimize founder effects and if interspecific hybridization poses a threat. We provide an updated and comprehensive genetic assessment of a 1970s–1980s translocation and now established mottled duck (Anas fulvigula) population in South Carolina, USA. In addition to examining the population genetics of these mottled ducks, we simulated expected genetic assignments for generational hybrids (F1–F10), permitting formal purity assignment across samples to identify true hybrids and establish hybridization rates. In addition to wild mallards (A. platyrhynchos), we tested for presence of hybrids with migrant American black ducks (A. rubripes) and released domestic game‐farm mallards (A. p. domesticus). We used wild reference populations of North American mallard‐like ducks and sampled game‐farm mallards from 2 sites in South Carolina that could potentially interbreed with mottled ducks. Despite 2 different subspecies of mottled duck (Florida [A. f. fulvigula] and the Western Gulf Coast [A. f. maculatlus]) used in original translocations, we determined the gene pool of the Western Gulf Coast mottled duck was overwhelmingly represented in South Carolina's current population. We found no evidence of founder effects or inbreeding and concluded the original translocation of 1,285 mottled ducks was sufficient to maintain current genetic diversity. We identified 7 hybrids, including an F1 and 3 late‐staged (i.e., F2–F3 backcrosses) mottled duck × black duck hybrids, 1 F2‐mottled duck backcrossed with a wild mallard, and 2 F3‐mottled ducks introgressed with game‐farm mallard. We estimated a 15% hybridization rate in our mottled duck dataset; however, the general lack of F1 and intermediate hybrids were inconsistent with scenarios of high hybridization rates or presence of a hybrid swarm. Instead, our results suggested a scenario of infrequent interspecific hybridization between South Carolina's mottled ducks and congeners. We concluded that South Carolina's mottled duck population is sufficiently large now to absorb current hybridization rates because 85% of sampled mottled ducks were pure. These results demonstrate the importance in managing and maintaining large parental populations to counter hybridization. As such, future population management of mottled ducks in South Carolina will benefit from increased geographical and continued sampling to monitor hybridization rates with closely related congeners. We also suggest that any future translocations of mottled ducks to coastal South Carolina should originate from the Western Gulf Coast. © 2021 The Wildlife Society. We determined that the translocation of mottled ducks to South Carolina, USA, established a sustainable population of largely genetically pure Western Gulf Coast mottled ducks. Genetic monitoring of post‐established populations is important when establishing the outcomes of management efforts.
Article
Aim Numerous glacial refugia have been hypothesized along North America's North Pacific Coast that may have increased divergence of refugial taxa, leading to elevated endemism and subsequently clustered hybrid zones following deglaciation. The locations and community composition of these ice‐free areas remains controversial, but whole‐genome sequences now enable detailed analysis of the demographic and evolutionary histories of refugial taxa. Here, we use genomic data to test spatial and temporal processes of diversification among martens with respect to the Coastal Refugium Hypothesis, to understand the role of climate cycling in shaping diversity across complex landscapes. Location North America and North Pacific Coast archipelagos. Taxon North American martens (Martes). Methods Short‐read whole‐genome resequencing data were generated for 11 martens: four M. americana, four M. caurina, two hybrids, and one outgroup (Martes zibellina). Sampling was representative of known genetic clades within New World martens, including sampling within insular and continental hybrid zones and along the North Pacific Coast (five island populations). ADMIXTURE, F‐statistics, and D‐statistics (ABBA‐BABA) were used to identify introgression and infer directionality. Heterozygosity densities, estimated via PSMC, were used to characterize historical demography at and below the species level to infer refugial and colonization processes. Results Forest‐associated Pacific martens (M. caurina) are divided into distinct insular and continental clades consistent with the Coastal Refugium Hypothesis. There was no evidence of introgression on islands that received historical translocations of American pine martens (M. americana), but introgression was detected in two active zones of secondary contact: one insular and one continental. Only early‐generational hybrids were identified across multiple hybrid zones, a pattern consistent with potential genetic swamping of M. caurina by M. americana. Main conclusions Despite an incomplete fossil record, genomic evidence supports the persistence of forest‐associated martens, likely the insular Pacific marten lineage, along the western edges of the Alexander Archipelago during the Last Glacial Maximum. This discovery informs our understanding of refugial paleoenvironments, critical to interpreting refugial timing, duration, and community composition. Genomic reevaluations of other taxa along North America's North Pacific Coast may yield new and deeper perspectives on the history of refugial forest communities and the role of dynamic climate shifts in shaping high‐latitude diversity across complex insular landscapes.
Chapter
The ability to identify population structure, estimate rates of hybridization, and genetic sources of gene flow is critical when attempting to conserve wild populations. Recently diverged species with few pre- or post-zygotic isolating mechanisms are prone to exchange genetic material during secondary contact events, potentially causing the breakup of important coadapted genes and resulting in maladapted populations. Such events are especially exacerbated when domestic versions come into contact with their wild congeners and exchange genetic variation that had been under artificial selection. Being able to genetically identify individuals to populations or species, and thus potential hybrids, is essential when attempting to assess impacts from hybridization. Until recently, molecular methods often resulted in insufficient marker coverage to confidently assign individuals to populations for organisms comprised of closely related taxa. Advances in partial genome sequencing methods (e.g., ddRAD-seq, sequence capture) and decreasing sequencing costs have made it possible to readily access thousands of genetic markers across hundreds of samples, providing a population genomics across the landscapes of wild systems. Here, I review what landscape-level sampling coupled with thousands of nuclear markers has uncovered for a group of recently radiated ducks of the Mallard Complex (genus Anas). Deploying the latest population genomics approaches, researchers have been able to reconstruct complex evolutionary histories, assign individuals to species with confidence, as well as identify genetic hybrids. These population genomics studies have produced findings that are in contrast to what was thought to be known for many of these species. Among results, studies consistently found that the problem of hybridization for many of these species was due to feral mallard populations. In fact, the result of these anthropogenic hybridization events is the formation of hybrid swarms on Hawaii, North America, Eurasia, and New Zealand. Wildlife biologists are now incorporating these population genomics-based results into their management planning, demonstrating the need and importance of population genomics in wildlife conservation.
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Along with manipulating habitat, the direct release of domesticated individuals into the wild is a practice used world-wide to augment wildlife populations. We test between possible outcomes of human-mediated secondary contact using genomic techniques at both historical and contemporary time scales for two iconic duck species. First, we sequence several thousand ddRAD-seq loci for contemporary mallards (Anas platyrhynchos) throughout North America, and two domestic mallard-types (i.e., known game-farm mallards and feral Khaki Campbell's). We show that North American mallards may well be becoming a hybrid swarm due to interbreeding with domesticated game-farm mallards released for hunting. Next, to attain a historical perspective, we applied a bait-capture array targeting thousands of loci in century-old (1842-1915) and contemporary (2009-2010) mallard and American black duck (A. rubripes) specimens. We conclude that American black ducks and mallards have always been closely related, with a divergence time of ~ 600,000 years before present, and likely evolved through prolonged isolation followed by limited bouts of gene flow (i.e., secondary contact). They continue to maintain genetic separation, a finding that overturns decades of prior research and speculation suggesting the genetic extinction of the American black duck due to contemporary interbreeding with mallards. Thus, despite having high rates of hybridization, actual gene flow is limited between mallards and American black ducks. Conversely, our historical and contemporary data confirm that the intensive stocking of game-farm mallards during the last ~ 100 years has fundamentally changed the genetic integrity of North America's wild mallard population, especially in the east. It thus becomes of great interest to ask whether the iconic North American mallard is declining in the wild due to introgression of maladaptive traits from domesticated forms. Moreover, we hypothesize that differential gene flow from domestic game-farm mallards into the wild mallard population may explain the overall temporal increase in differentiation between wild black ducks and mallards, as well as the uncoupling of genetic diversity and effective population size estimates across time in our results. Finally, our findings highlight how genomic methods can recover complex population histories by capturing DNA preserved in traditional museum specimens.
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Using a large, consistent set of loci shared by descent (orthologous) to study relationships among taxa would revolutionize among-lineage comparisons of divergence and speciation processes. Ultraconserved elements (UCEs), highly conserved regions of the genome, offer such genomic markers. The utility of UCEs for deep phylogenetics is clearly established and there are mature analytical frameworks available, but fewer studies apply UCEs to recent evolutionary events, creating a need for additional example datasets and analytical approaches. We used UCEs to study population genomics in snow and McKay’s buntings ( Plectrophenax nivalis and P. hyperboreus ). Prior work suggested divergence of these sister species during the last glacial maximum (~18-74 Kya). With a sequencing depth of ~30× from four individuals of each species, we used a series of analysis tools to genotype both alleles, obtaining a complete dataset of 2,635 variable loci (~3.6 single nucleotide polymorphisms [SNPs]/locus) and 796 invariable loci. We found no fixed allelic differences between the lineages, and few loci had large allele frequency differences. Nevertheless, individuals were 100% diagnosable to species, and the two taxa were different genetically ( F ST = 0.034; P = 0.03). The demographic model best fitting the data was one of divergence with gene flow. Estimates of demographic parameters differed from published mtDNA research, with UCE data suggesting lower effective population sizes (~92,500 - 240,500 individuals), a deeper divergence time (~241,000 yrs), and lower gene flow (2.8-5.2 individuals per generation). Our methods provide a framework for future population studies using UCEs, and our results provide additional evidence that UCEs are useful for answering questions at shallow evolutionary depths.
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Las técnicas de análisis genómico que se basan en la secuenciación masiva han supuesto una revolución en la última década no sólo en biomedicina o agronomía, sino también en el estudio de la diversidad biológica. Las plataformas de secuenciación de segunda y tercera generación que vienen a complementar a la tradicional secuenciación por el método Sanger, permiten analizar un gran número de individuos obteniendo una profundidad de secuenciación significativa de sus genomas o transcriptomas. Así, aunque todavía de manera incipiente, se vienen realizando estudios sobre la flora y fauna silvestre a escala poblacional, con especial énfasis en la determinación de patrones adaptativos frente a los cambios ambientales. En la presente revisión se describe la situación actual de las plataformas de secuenciación masiva, señalando sus ventajas y limitaciones para el análisis en organismos no modelo, para a continuación detallar las bases de dos de las técnicas más populares que se benefician de la secuenciación masiva (RAD-seq y RNA-seq) y señalar algunos ejemplos de su uso para el estudio de la diversidad biológica.
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The role of hybridization in adaptive evolution is contentious. While many cases of adaptive trait introgression have been proposed, the relevant traits have rarely been identified, resulting in a lack of clear examples of this process. Here, we examine a purported case of adaptive introgression in which the annual sunflower Helianthus annuus annuus has captured alleles from a congener (Helianthus debilis) to form a stabilized hybrid, Helianthus annuus texanus. We tested the hypotheses that herbivore resistance traits have introgressed from H. debilis to H. annuus and have increased adaptation in the latter. In two common gardens, fitness (estimated by seed production) was on average 55% higher in H. a. texanus than in H. a. annuus. For H. a. texanus, three damage traits (of seven tested) differed significantly from the H. a. annuus parent in one or both sites and were shifted in the direction of the more resistant H. debilis. Natural selection favored H. a. \landscape $annuus\times H. debilis BC1 hybrids (synthesized to mimic the ancestors of H. a. texanus) with H. debilis–like resistance to seed midges Neolasioptera helianthis and to receptacle/seed feeding Lepidoptera at one or both sites. Assuming similar herbivore pressures in the past, these results suggest that introgression of biotic resistance traits was important in the adaptation of H. annuus to central and southern Texas.
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Background Sex chromosomes exhibit many unusual patterns in sequence and gene expression relative to autosomes. Birds have evolved a female heterogametic sex system (male ZZ, female ZW), through stepwise suppression of recombination between chrZ and chrW. To address the broad patterns and complex driving forces of Z chromosome evolution, we analyze here 45 newly available bird genomes and four species’ transcriptomes, over their course of recombination loss between the sex chromosomes. Results We show Z chromosomes in general have a significantly higher substitution rate in introns and synonymous protein-coding sites than autosomes, driven by the male-to-female mutation bias (‘male-driven evolution’ effect). Our genome-wide estimate reveals that the degree of such a bias ranges from 1.6 to 3.8 among different species. G + C content of third codon positions exhibits the same trend of gradual changes with that of introns, between chrZ and autosomes or regions with increasing ages of becoming Z-linked, therefore codon usage bias in birds is probably driven by the mutational bias. On the other hand, Z chromosomes also evolve significantly faster at nonsynonymous sites relative to autosomes (‘fast-Z’ evolution). And species with a lower level of intronic heterozygosities tend to evolve even faster on the Z chromosome. Further analysis of fast-evolving genes’ enriched functional categories and sex-biased expression patterns support that, fast-Z evolution in birds is mainly driven by genetic drift. Finally, we show in species except for chicken, gene expression becomes more male-biased within Z-linked regions that have became hemizygous in females for a longer time, suggesting a lack of global dosage compensation in birds, and the reported regional dosage compensation in chicken has only evolved very recently. Conclusions In conclusion, we uncover that the sequence and expression patterns of Z chromosome genes covary with their ages of becoming Z-linked. In contrast to the mammalian X chromosomes, such patterns are mainly driven by mutational bias and genetic drift in birds, due to the opposite sex-biased inheritance of Z vs. X.
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Speciation is a continuous and dynamic process, and studying organisms during the early stages of this process can aid in identifying speciation mechanisms. The mallard (Anas platyrhynchos) and Mexican duck (A. [p.] diazi) are two recently diverged taxa with a history of hybridization and controversial taxonomy. To understand their evolutionary history, we conducted genomic scans to characterize patterns of genetic diversity and divergence across the mitochondrial DNA (mtDNA) control region, 3523 autosomal loci, and 172 Z-linked sex chromosome loci. Between the two taxa, Z-linked loci (ΦST = 0.088) were 5.2 times more differentiated than autosomal DNA (ΦST = 0.017) but comparable to mtDNA (ΦST = 0.092). This elevated Z-differentiation deviated from neutral expectations inferred from simulated data that incorporated demographic history and differences in effective population sizes between marker types. Furthermore, 3% of Z-linked loci, compared to <0.1% of autosomal loci, were detected as outlier loci under divergent selection with elevated relative (ΦST ) and absolute (dXY ) estimates of divergence. In contrast, the ratio of Z-linked and autosomal differentiation among the seven Mexican duck sampling locations was close to 1:1 (ΦST = 0.018 for both markers). We conclude that between mallards and Mexican ducks, divergence at autosomal markers is largely neutral, whereas greater divergence on the Z-chromosome (or some portions thereof) is likely the product of selection that has been important in speciation. Our results contribute to a growing body of literature indicating elevated divergence on the Z chromosome and its likely importance in avian speciation. This article is protected by copyright. All rights reserved.
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Hybridization, the interbreeding of different species, plays an important role in several evolutionary processes, such as adaptive trait transfer (Arnold 2006, Arnold et al. 2008, Hedrick 2013), adaptive radiations (Seehausen 2004), and the origin of new species (Mavarez & Linares 2008, Abbott et al. 2013, Schumer et al. 2014). However, hybridization can have detrimental effects for the species involved: one of the species can be driven to extinction (Rhymer & Simberloff 1996) or two species can merge into one leading to a loss in biodiversity (Seehausen 2006, Seehausen et al. 2008), so hybridization has also become a relevant topic in conservation (Allendorf et al. 2001, Brumfield 2010).
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The role of hybridization in the origin, maintenance, and loss of biodiversity has been the subject of speculation and debate for more than two centuries (Linnaeus 1760; Kölreuter 1893; Arnold 1997). Some authors have emphasized the creative role of hybridization in fostering species or community diversity (Linnaeus 1760; Kerner von Marilaun 1894–1895; Lotsy 1916; Stebbins 1942; Anderson 1949; Whitham and Maschinski 1996; Arnold 1997), whereas others have focused on its role as a destructive evolutionary force, contributing to the extinction of rare populations or species (Cade 1983; Rieseberg 1991; Ell-strand 1992; Levin et al. 1996; Rhymer and Simberloff 1996; Carney et al. 2000). Although the emphasis of these authors may vary, most appear to recognize the diversity of possible evolutionary outcomes of hybridization.
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The elevated rate of evolution for genes on sex chromosomes compared to autosomes (Fast-X or Fast-Z evolution) can result either from positive selection in the heterogametic sex, or from non-adaptive consequences of reduced relative effective population size. Recent work in birds suggests that Fast-Z of coding sequence is primarily due to relaxed purifying selection resulting from reduced relative effective population size. However, gene sequence and gene expression are often subject to distinct evolutionary pressures, therefore we tested for Fast-Z in gene expression using next-generation RNA-sequencing data from multiple avian species. Similar to studies of Fast-Z in coding sequence, we recover clear signatures of Fast-Z in gene expression, however in contrast to coding sequence, our data indicate that Fast-Z in expression is due to positive selection acting primarily in females. In the soma, where gene expression is highly correlated between the sexes, we detected Fast-Z in both sexes, although at a higher rate in females, suggesting that many positively selected expression changes in females are also expressed in males. In the gonad, where inter-sexual correlations in expression are much lower, we detected Fast-Z for female gene expression, but crucially, not males. This suggests that a large amount of expression variation is sex-specific in its effects within the gonad. Taken together, our results indicate that Fast-Z evolution of gene expression is the product of positive selection acting on recessive beneficial alleles in the heterogametic sex. More broadly, our analysis suggests that the adaptive potential of Z chromosome gene expression may be much greater than that of gene sequence, results which have important implications for the role of sex chromosomes in speciation and sexual selection. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
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Speciation is regarded primarily as a bifurcation from an ancestral species into two distinct taxonomic units, but gene flow can create different signals of phylogenetic relationships among different loci. We evaluated several hypotheses that could account for phylogenetic discord between mitochondrial DNA (mtDNA) and nuclear DNA (nuDNA) within Hawaiian ducks (Anas wyvilliana), including stochastic lineage sorting, mtDNA capture, and widespread genomic introgression. Our results best support the hypothesis that the contemporary Hawaiian duck is descended from an ancient hybridization event between the mallard (A. platyrhynchos) and Laysan duck (A. laysanensis). Whereas mtDNA clearly shows a sister-relationship between Hawaiian ducks and mallards, nuDNA is consistent with a genetic mosaic with nearly equal contributions from Laysan ducks and mallards. In addition, coalescent analyses suggest that gene flow from either mallard or Laysan duck, depending on the pre-defined tree topology, is necessary to explain contemporary genetic diversity in Hawaiian ducks, and these estimates are more consistent with ancient, rather than contemporary, hybridization. Time since divergence estimates suggest that the genetic admixture event occurred around the Pleistocene-Holocene boundary, which is further supported by circumstantial evidence from the Hawaiian sub-fossil record. Although the extent of reproductive isolation from either putative parental taxon is not currently known, these species are phenotypically, genetically, and ecologically different, and they meet primary criteria used in avian taxonomy for species designation. Thus, the available data are consistent with an admixed origin, and support the hypothesis that the Hawaiian duck may represent a young hybrid species. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
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The polytypic species concept unites populations that theoretically could and would interbreed were the opportunity to arise-This concept places the burden of proof of reproductive in-capability and species status on those claiming species or higher rank. Advances in our understanding of the nature of reproductive isolation, the genetics of speciation, the limited role of gene flow, the power of directional selection, and the dynamics of hybridization support a different null hypothesis for taxonomic decisions, one that places the burden of proof on 'lumping' rather than on 'splitting' taxa at the species level. Switching the burden of proof provides an improved conceptual basis for the recognition of many allopatric island taxa and subspecies groups that merit species status. Taxonomic revisions based on these advances predictably confirm that distinct sister populations once lumped as polytypic species are independent evolutionary lineages that exhibit essential reproductive isolation. Release from the concerns about hybridization also positions proposed species for timely taxonomic decisions. The stage is set to proactively redefine polytypic species to separate component species for the 21' century. The improved species classification will better reflect phylogeny and evolutionary status, characterize biodiversity more accurately, guide improved sampling patterns of bird populations for systematic studies, and enable informed conservation decisions.
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Higher rates of coding sequence evolution have been observed on the Z chromosome relative to the autosomes across a wide range of species. However, despite a considerable body of theory, we lack empirical evidence explaining variation in the strength of the Faster-Z Effect. To assess the magnitude and drivers of Faster-Z Evolution, we assembled six de novo transcriptomes, spanning 90 million years of avian evolution. Our analysis combines expression, sequence and polymorphism data with measures of sperm competition and promiscuity. In doing so, we present the first empirical evidence demonstrating the positive relationship between Faster-Z Effect and measures of promiscuity, and therefore variance in male mating success. Our results from multiple lines of evidence indicate that selection is less effective on the Z chromosome, particularly in promiscuous species, and that Faster-Z Evolution in birds is due primarily to genetic drift. Our results reveal the power of mating system and sexual selection in shaping broad patterns in genome evolution. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
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Sex chromosomes exhibit many unusual patterns in sequence and gene expression relative to autosomes. Birds have evolved a female heterogametic sex system (male ZZ, female ZW), through stepwise suppression of recombination between chrZ and chrW. To address the broad patterns and complex driving forces of Z chromosome evolution, we analyze here 45 newly available bird genomes and four species' transcriptomes, over their course of recombination loss between the sex chromosomes. We show Z chromosomes in general have a significantly higher substitution rate in introns and synonymous protein-coding sites than autosomes, driven by the male-to-female mutation bias ('male-driven evolution' effect). Our genome-wide estimate reveals that the degree of such a bias ranges from 1.6 to 3.8 among different species. G + C content of third codon positions exhibits the same trend of gradual changes with that of introns, between chrZ and autosomes or regions with increasing ages of becoming Z-linked, therefore codon usage bias in birds is probably driven by the mutational bias. On the other hand, Z chromosomes also evolve significantly faster at nonsynonymous sites relative to autosomes ('fast-Z' evolution). And species with a lower level of intronic heterozygosities tend to evolve even faster on the Z chromosome. Further analysis of fast-evolving genes' enriched functional categories and sex-biased expression patterns support that, fast-Z evolution in birds is mainly driven by genetic drift. Finally, we show in species except for chicken, gene expression becomes more male-biased within Z-linked regions that have became hemizygous in females for a longer time, suggesting a lack of global dosage compensation in birds, and the reported regional dosage compensation in chicken has only evolved very recently. In conclusion, we uncover that the sequence and expression patterns of Z chromosome genes covary with their ages of becoming Z-linked. In contrast to the mammalian X chromosomes, such patterns are mainly driven by mutational bias and genetic drift in birds, due to the opposite sex-biased inheritance of Z vs. X.
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The package adegenet for the R software is dedicated to the multivariate analysis of genetic markers. It extends the ade4 package of multivariate methods by implementing formal classes and functions to manipulate and analyse genetic markers. Data can be imported from common population genetics software and exported to other software and R packages. adegenet also implements standard population genetics tools along with more original approaches for spatial genetics and hybridization. Availability: Stable version is available from CRAN: http://cran.r-project.org/mirrors.html. Development version is available from adegenet website: http://adegenet.r-forge.r-project.org/. Both versions can be installed directly from R. adegenet is distributed under the GNU General Public Licence (v.2). Contact:jombart@biomserv.univ-lyon1.fr Supplementary information:Supplementary data are available at Bioinformatics online.
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An accurately resolved gene tree may not be congruent with the species tree because of lineage sorting of ancestral polymorphisms. DNA sequences from the mitochondrially encoded genes (mtDNA) are attractive sources of characters for estimating the phylogenies of recently evolved taxa because mtDNA evolves rapidly, but its utility is limited because the mitochondrial genes are inherited as a single linkage group (haplotype) and provide only one independent estimate of the species tree. In contrast, a set of nuclear genes can be selected from distinct chromosomes, such that each gene tree provides an independent estimate of the species tree. Another aspect of the gene-tree versus species-tree problem, however, favors the use of mtDNA for inferring species trees. For a three-species segment of a phylogeny, the branching order of a gene tree will correspond to that of the species tree if coalescence of the alleles or haplotypes occurred in the internode between the first and second bifurcation. From neutral theory, it is apparent that the probability of coalescence increases as effective population size decreases. Because the mitochondrial genome is maternally inherited and effectively haploid, its effective population size is one-fourth that of a nuclear-autosomal gene. Thus, the mitochondrial-haplotype tree has a substantially higher probability of accurately tracking a short internode than does a nuclear-autosomal-gene tree. When an internode is sufficiently long that the probability that the mitochondrial-haplotype tree will be congruent with the species tree is 0.95, the probability that a nuclear-autosomalgene tree will be congruent is only 0.62. If each of k independently sampled nuclear-gene trees has a probability of congruence with the species tree of 0.62, then a sample of 16 such trees would be required to be as confident of the inference based on the mitochondrial-haplotype tree. A survey of mtDNA-haplotype diversity in 34 species of birds indicates that coalescence is generally very recent, which suggests that coalescence times are typically much shorter than internodal branch lengths of the species tree, and that sorting of mtDNA lineages is not likely to confound the species tree. Hybridization resulting in transfer of mtDNA haplotypes among branches could also result in a haplotype tree that is incongruent with the species tree; if undetected, this could confound the species tree. However, hybridization is usually easy to detect and should be incorporated in the historical narrative of the group, because reticulation, as well as cladistic events, contributed to the evolution of the group.
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A summary classification of 175 modern species and 30 well-represented fossil forms of waterfowl (Aves: Anseriformes) is presented, based on a series of phylogenetic (cladistic) analyses of the group using morphological characters (Livezey, 1986a, 1986b, 1986c, 1989a, 1989b, 1990, 1991, 1993a, 1993b, 1995a, 1995b, 1995c, 1996a, 1996b, 1996c, 1997a, 1997b). The proposed classification includes a superordinal grouping with the Order Galliformes, and subdivides the Anseriformes into two suborders (Anhimae and Anseres), two superfamilies (Anseranatoidea and Anatoidea), and five families (Anhimidae, Anseranatidae, †Presbyornithidae, †,Cnemiornithidae, and Anatidae). Among the latter, the Anatidae is the largest and comprises six subfamilies: Dendrocygninae (comprising two tribes and two genera), Dendrocheninae (two genera), Anserinae (four tribes, nine genera), Stictonettinae (one genus), Tadorninae (four tribes, 15 genera), and Anatinae (five tribes, 31 genera). The classification also incorporates: phylogenetic inferences and associated taxonomic decisions subsequent to the preliminary work by Livezey (1986a); corrections of classifications included with the earlier analyses; recognition of two species of comb-duck (Sarkdiornis); and provisional partitions of several problematic species groups (Branta canadensis, Merganetta armata, and Somateria mollissima). Also included are a concise historical review of the classification of the order, an assessment of the relative support documented for the taxonomic groups defined within the classification, and suggestions for future investigations.
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Over the past decade, many studies documented high genetic divergence between closely related species in genomic regions experiencing restricted recombination in hybrids, such as within chromosomal rearrangements or areas adjacent to centromeres. Such regions have been called 'islands of speciation' because of their presumed role in maintaining the integrity of species despite gene flow elsewhere in the genome. Here, we review alternative explanations for such patterns. Segregation of ancestral variation or artifacts of nucleotide diversity within species can readily lead to higher F(ST) in regions of restricted recombination than other parts of the genome, even in the complete absence of interspecies gene flow, and thereby cause investigators to erroneously conclude that islands of speciation exist. We conclude by discussing strengths and weaknesses of various means for testing the role of restricted recombination in maintaining species.
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A phylogenetic analysis of all Recent genera of the Anseriformes using 120 morphological characters supports much of the current consensus regarding intraordinal relationships. I found that (1) Anseranas should be placed in a monotypic family; (2) Dendrocygna, Thalassornis, geese and swans, and Stictonetta are paraphyletic to the rest of the Anatidae; (3) Cereopsis is the sister group to Anser and Branta, and Coscoroba is the sister group to Cygnus and Olor; (4) Plectropterus is the sister group to the Tadorninae (shelducks) and the Anatinae (typical ducks); (5) the shelducks are monophyletic and include Sarkidiornis (provisionally), Malacorhynchus, Hymenolaimus, Merganetta, and Tachyeres; (6) the tribe "Cairinini" ("perching ducks") is an unnatural, polyphyletic assemblage and is rejected; (7) the dabbling ducks (including the smaller "perching ducks") comprise an unresolved, probably paraphyletic group; (8) tribal monophyly of the pochards (including Marmaronetta and Rhodonessa), sea ducks (including the eiders), and stiff-tailed ducks (including Heteronetta) is confirmed; and (9) the retention of Mergellus and resurrection of Nomonyx are recommended based on clarifications of intratribal relationships. Problematic groups, effects of homoplasy, phenetic comparisons, life-history correlates, biogeographic patterns, and fossil species are discussed, and a phylogenetic classification of Recent genera is proposed.
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Weights of 1,281 diving ducks of five species livetrapped on Seneca Lake, Ontario County, New York, during January, February, and March of 1960, 1961, 1962, 1965, and 1971 are reported. Body weights drop significantly from early January through late February and March. The weight loss by redheads (Aythya americana) is emphasized with significant differences shown in the 11-year time span between 1960 and 1971. To make conjectures as to this difference, it is suggested that periods of zero to subzero temperatures occurring in 1971 and not in 1960 influenced weight loss. Also, dramatically different, and possibly less suitable, food resources dominating the aquatic environment of the lake in 1971 contributed to weight loss.
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Species hybrids have long been undervalued in conservation and are often perceived as a threat to pure species. Recently, the conservation value of hybrids, especially those of natural origin, has gained recognition; however, hybrid conservation remains controversial. We reviewed hybrid management policies, including laws, regulations, and management protocols, from a variety of organizations, primarily in Canada and the United States. We found that many policies are based on limited ethical and ecological considerations and provide little opportunity for hybrid conservation. In most policies, hybrids are either unrepresented or considered a threat to conservation goals. This is problematic because our review of the hybrid conservation literature identified many ethical and ecological considerations relevant to determining the conservation value of a hybrid, all of which are management-context specific. We also noted a lack of discussion of the ethical considerations regarding hybrid conservation. Based on these findings, we created a policy framework outlining situations in which hybrids could be eligible for conservation in Canada and the United States. The framework comprises a decision tree that helps users determine whether a hybrid should be eligible for conservation based on multiple ecological and ethical considerations. The framework may be applied to any hybrid and is flexible in that it accommodates context-specific management by allowing different options if a hybrid is a threat to or could benefit conservation goals. The framework can inform policy makers and conservationists in decision-making processes regarding hybrid conservation by providing a systematic set of decision criteria and guidance on additional criteria to be considered in cases of uncertainty, and it fills a policy gap that limits current hybrid management. © 2015 Society for Conservation Biology.
Article
Sexual coercion was defined previously as "use by a male of force, or threat of force, that functions to increase the chances that a female will mate with him at a time when she is likely to be fertile, and to decrease the chances that she will mate with other males, at some cost to the female." Forced extrapair copulation (FEPC), a well-known phenomenon in waterfowl, is reexamined in detail as a prime example of sexual coercion in birds. Monogamy is the basic mating system in almost all waterfowl, opportunities for polygyny are rare, and males of many species seek extra-pair copulations (EPCs). Presence of a male intromittent organ in waterfowl, thought to have evolved in association with copulation while swimming, makes forced EPC feasible. Evidence (as follows) for FEPC as a secondary male reproductive strategy is reviewed: males involved are usually paired, eggs can be fertilized, FEPC attempts focus on fertile females, males have elaborate tactics to secure FEPCs, males defend their mates against FEPC by other males, and males perform forced pair copulation after FEPC has occurred on their mates. Females resist FEPC and show elaborate escape behavior (flying, diving, hiding, sneaking). Female resistance may be a tactic to preserve the pair-bond and the investment of the mate. Incubating female dabbling ducks have special "repulsion" behavior that indicates their nonfertile status and seems to discourage males from FEPC. Females incur costs from FEPC, including risk of injury or death during multimale FEPC attempts, energetic costs of escape behavior, and abandonment of nesting attempts caused by harassment. FEPC has been recorded in 55 species of waterfowl in 17 genera. FEPC apparently is absent in swans, shelducks and sheldgeese, steamer ducks, and most sea ducks. In some of these cases, there may be a trade-off between territoriality and FEPC. Other avian groups in which FEPC has been reported include albatrosses, pelicans, herons, gulls, auks, bee-eaters, swallows, waxbills, and corvids. Females may be especially vulnerable to FEPC in breeding colonies when left unguarded by the mate. In general, FEPC appears to be uncommon in birds other than waterfowl, but there are some species in which males do appear to be able to overpower females. Many opportunities for future research are noted.