Patterns of chloroplast diversity among western European Dactylorhiza species (Orchidaceae)

In Europe, the genus Dactylorhiza comprises a bewildering variety of forms that are difficult to sort into discrete species. Most Dactylorhiza species are diploid or tetraploid and contrasting hypotheses have been proposed to explain the complex variation within this group. Using PCR-RFLP analysis in eight putative species, we could identify four highly differentiated chloroplast DNA lineages. The first lineage (clade A) included the unique haplotype found in D. sambucina. Clade B grouped four haplotypes belonging mostly to D. incarnata. Clades C and D included 27 haplotypes detected in diploid D. fuchsii and in all tetraploid species investigated. Eighty percent of the chloroplast variation were consistent with currently accepted species boundaries. The imperfect agreement between chloroplast variation and species boundaries may be ascribed to incomplete lineage sorting and/or reticulation. Our cpDNA results provide strong evidence that the allotetrapolyploids have been formed through asymmetric hybridization with a member of the D. fuchsii / maculata group as the maternal parent.     

Genetic structure among populations in the endemic Hawaiian Plantago lineage: insights from microsatellite variation

Endemic Hawaiian species in the genus Plantago show considerable morphological and ecological diversity. Despite their variation, a recent phylogenetic analysis based on DNA sequence data showed that the group is monophyletic and that sequence variation among species and morphotypes is low. This lack of sequence polymorphisms resulted in an inability to resolve species and population affinities within the most recently derived clade of this lineage. To assess species boundaries, population genetic structure and interpopulation connectivity among the morphologically and ecologically distinct populations within this clade, genetic variation was examined using eight microsatellite loci. Within‐population genetic diversity was found to be lowest in the Maunaiu, Hawai'i population of the endangered P. hawaiensis, and highest in the large P. pachyphylla population from 'Eke, West Maui. Isolation by distance across the range of populations was detected and indicated restricted dispersal. This result is likely to be attributable to few interisland dispersal events in the evolutionary history of this lineage. Genetic differentiation within islands tended to be higher among populations occurring in contrasting bog and woodland habitats, suggesting ecological barriers to gene flow and the potential role of ecological divergence in population diversification. Overall, these results are consistent with findings from phylogenetic analysis of the entire lineage. Our data bring new insights regarding patterns of dispersal and population genetic structure to this endemic and endangered group of island taxa. As island environments become increasingly fragmented, information of this type has important implications for the successful management of these fragile populations and habitats.     

Cryptic species,gene recombination and hybridization in the genus Spiraeanthemum (Cunoniaceae) from New Caledonia

The Oceanian plant genus Spiraeanthemum (Cunoniaceae) has a centre of diversity in New Caledonia, where it is represented by seven species. Its diversification was investigated using two low‐copy nuclear genes, ncpGS and GapC, and phylogenetic analyses were based on maximum parsimony, maximum likelihood and recombination networks. We detected several cases of gene recombination in both datasets, and these have obscured the history within the genus. For S. ellipticum and S. pubescens, accessions from southern populations on ultramafic soils were genetically distinct from accessions from northern populations on non‐ultramafic soils. Given that no obvious morphological characters distinguish northern and southern populations in either taxon, both may be considered as examples of cryptic species. Incongruence between gene trees and species' delimitation may be explained by the parallel evolution of similar morphology, differential lineage sorting leading to differential fixation of alleles or different introgression patterns in the north and south leading to allele displacement. In New Caledonia, some species with broad ecological preferences may thus be artificial concepts. This suggests that they should be treated more critically in monographs and that the species' richness of the New Caledonian flora may be underestimated. Problems associated with the typification of S. ellipticum and evidence of hybridization events in the history of Spiraeanthemum are also discussed. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 161 , 137–152.     

The impact of multiple biogeographic barriers and hybridization on species-level differentiation

• Premise of the study: The glacial cycles of the Quaternary did not impact Australia in the same way as Europe and North America. Here we investigate the history of population isolation, species differentiation, and hybridization in the southeastern Australian landscape, using five species of Lomatia (Proteaceae). We use a chloroplast DNA phylogeography to assess chloroplast haplotype (chlorotype) sharing among these species and whether species with shared distributions have been affected by shared biogeographic barriers. • Methods: We used six chloroplast DNA simple sequence repeats (cpSSR) across five species of Lomatia, sampled across their entire distributional range in southeastern Australia. Resulting size data were combined, presented as a network, and visualized on a map. Biogeographical barriers were tested using AMOVA. To explore hypotheses of chlorotype origin, we converted the network into a cladogram and reconciled with all possible species trees using parsimony-based tree mapping. • Key results: Some chlorotypes were shared across multiple species of Lomatia in the study, including between morphologically differentiated species. Chlorotypes were either widespread in distribution or geographically restricted to specific regions. Biogeographical structure was identified across the range of Lomatia. The most parsimonious reconciled tree incorporated horizontal transfer of chlorotypes. • Conclusions: Lomatia shows evidence of both incomplete lineage sorting and extensive hybridization between co-occurring species. Although the species in the study appear to have responded to a number of biogeographic barriers to varying degrees, our findings identified the Hunter River Valley as the most important long-term biogeographic barrier for the genus in southeastern Australia.     

Timing major conflict between mitochondrial and nuclear genes in species relationships of Polygonia butterflies (Nymphalidae: Nymphalini)

Background  

Major conflict between mitochondrial and nuclear genes in estimating species relationships is an increasingly common finding in animals. Usually this is attributed to incomplete lineage sorting, but recently the possibility has been raised that hybridization is important in generating such phylogenetic patterns. Just how widespread ancient and/or recent hybridization is in animals and how it affects estimates of species relationships is still not well-known.     

PHYLOGENOMICS REVEALS EXTENSIVE RETICULATE EVOLUTION IN XIPHOPHORUS FISHES

Hybridization is increasingly being recognized as a widespread process, even between ecologically and behaviorally divergent animal species. Determining phylogenetic relationships in the presence of hybridization remains a major challenge for evolutionary biologists, but advances in sequencing technology and phylogenetic techniques are beginning to address these challenges. Here we reconstruct evolutionary relationships among swordtails and platyfishes (Xiphophorus: Poeciliidae), a group of species characterized by remarkable morphological diversity and behavioral barriers to interspecific mating. Past attempts to reconstruct phylogenetic relationships within Xiphophorus have produced conflicting results. Because many of the 26 species in the genus are interfertile, these conflicts are likely due to hybridization. Using genomic data, we resolve a high‐confidence species tree of Xiphophorus that accounts for both incomplete lineage sorting and hybridization. Our results allow us to reexamine a long‐standing controversy about the evolution of the sexually selected sword in Xiphophorus, and demonstrate that hybridization has been strikingly widespread in the evolutionary history of this genus.     

Molecular evidence for hybridization between two Australian desert skinks, Ctenotus leonhardii and Ctenotus quattuordecimlineatus (Scincidae: Squamata)

Australian scincid lizards in the genus Ctenotus constitute the most diverse vertebrate radiation in Australia. However, the evolutionary processes that have generated this diversity remain elusive, in part because both interspecific phylogenetic relationships and phylogeographic structure within Ctenotus species remain poorly known. Here we use nucleotide sequences from a mitochondrial locus and two nuclear introns to investigate broad-scale phylogeographic patterns within Ctenotus leonhardii and C. quattuordecimlineatus, two geographically widespread species of skinks that were found to have a surprisingly close genetic relationship in a previous molecular phylogenetic study. We demonstrate that the apparent close relationship between these ecologically and phenotypically distinct taxa is attributable to mitochondrial introgression from C. quattuordecimlineatus to C. leonhardii. In the western deserts, Ctenotus leonhardii individuals carry mtDNA lineages that are derived from C. quattuordecimlineatus mtDNA lineages from that geographic region. Coalescent simulations indicate that this pattern is unlikely to have resulted from incomplete lineage sorting, implicating introgressive hybridization as the cause of this regional gene-tree discordance.     

Frequent chloroplast capture among Isodon (Lamiaceae) species in Japan revealed by phylogenies based on variation in chloroplast and nuclear DNA

A recent phylogenetic study based only on chloroplast DNA (cpDNA) variation revealed that populations of an Isodon species are frequently embedded paraphyletically among other Isodon species. This phylogenetic discrepancy between species taxonomy and molecular phylogeny was considered to have resulted from chloroplast DNA captures and/or incomplete lineage sorting. To elucidate which of these factors was mainly responsible for the observed phylogenetic pattern, we performed phylogenetic analyses of multiple populations of Isodon species in Japan using cpDNA variation, three single-copy nuclear genes, and double-digest restriction-site-associated DNA sequencing (ddRAD-seq). Although a species often shared chlorotypes with other species, our phylogenetical analyses based on variation in the three single-copy nuclear genes and the ddRAD-seq data showed that most populations belonging to the same species were monophyletic at the species level, suggesting that chloroplast capture may have frequently occurred between Isodon species. Some populations of an intraspecific taxon were embedded paraphyletically within the species, regardless of the large amount of phylogenetic information in nuclear DNA; this incongruity may have resulted from incomplete lineage sorting.     

Diversification of Hawaiian Cyrtandra (Gesneriaceae) under the influence of incomplete lineage sorting and hybridization

Cyrtandra (Gesneriaceae) is a genus of flowering plants with over 800 species distributed throughout Southeast Asia and the Pacific Islands. On the Hawaiian Islands, 60 named species and over 89 putative hybrids exist, most of which are identified on the basis of morphology. Despite many previous studies on the Hawaiian Cyrtandra lineage, questions regarding the reconciliation of morphology and genetics remain, many of which can be attributed to the relatively young age and evidence of hybridization between species. We utilized targeted enrichment, high‐throughput sequencing, and modern phylogenomics tools to test 31 Hawaiian Cyrtandra samples (22 species, two putative hybrids, four species with two samples each, one species with four samples) and two outgroups for species relationships and hybridization in the presence of incomplete lineage sorting (ILS). Both concatenated and species‐tree methods were used to reconstruct species relationships, and network analyses were conducted to test for hybridization. We expected to see high levels of ILS and putative hybrids intermediate to their parent species. Phylogenies reconstructed from the concatenated and species‐tree methods were highly incongruent, most likely due to high levels of incomplete lineage sorting. Network analyses inferred gene flow within this lineage, but not always between taxa that we expected. Multiple hybridizations were inferred, but many were on deeper branches of the island lineages suggesting a long history of hybridization. We demonstrated the utility of high‐throughput sequencing and a phylogenomic approach using 569 loci to understanding species relationships and gene flow in the presence of ILS.     

Exon primed intron-crossing (EPIC) markers reveal natural hybridization and introgression in Actinidia (Actinidiaceae) with sympatric distribution

Interspecific hybridization is widespread among plants. Understanding the phylogenetic relationships among species is necessary for revealing the potential hybridization events. Actinidia, best known as kiwifruit genus found throughout a wide range in eastern Asian from Indonesia to Siberia. In this study, phylogenetic relationships of Actinidia species with sympatric distributions were investigated using three chloroplast introns (trnL-F, atpB-rbcL and rpl32-trnL) and three Exon primed intron-crossing (EPIC) markers. Chloroplast phylogeny supports non-monophyly of the five species studied excluding Actinidia fulvicoma var. lanata. The non-monophyly was also revealed by EPIC markers. Our results showed EPIC markers are more variable and informative for phylogenetic inference than that of chloroplast markers. The incongruences between loci from the plastid and nuclear DNA phylogenic trees may stem from incomplete lineage sorting or historical introgression hybridization. Incomplete lineage sorting may explain the non-monophyly between Actinidia chrysantha (section Maculatae) and other four species (section Stellatae), and introgression hybridization and high level of interspecific gene flow may explain the non-monophyly among the species of sect. Stellatae. Thus, natural hybridization and introgression may be common in Actinidia with sympatric distribution.     

Congeneric phylogeography: hypothesizing species limits and evolutionary processes in Patagonian lizards of the Liolaemus boulengeri group (Squamata: Liolaemini)

In poorly known groups for which data are insufficient to develop biologically plausible model‐based approaches to phylogeographical analyses, a ‘first hypotheses’ protocol is suggested as offering the best way to generate hypotheses for subsequent model‐based tests. Preliminary hypotheses are formulated about species boundaries and population processes in three species complexes of the Liolaemus boulengeri group in the context of mtDNA ‘congeneric phylogeography’. The temperate South American Liolaemus provides a model with ancient and recent allopatric divergence across ecologically and geologically complex landscapes, incipient speciation, secondary contact, and discordance between molecular and morphological patterns of variation. Moderately dense sampling of widely distributed ‘inertial’ species in the Patagonian Steppe has revealed hidden genetic and probably species diversity, and also hinted at demographic and historical processes that may have shaped the histories of these taxa. Five of the seven focal species of the present study were paraphyletic for mtDNA genealogies, suggesting that they represent complexes of species, and nested clade phylogeographical analysis (NCPA) analyses suggest that different historical and demographic processes have shaped the observed patterns. Introgression and incomplete lineage sorting are hypothesized as being the cause of some of the observed paraphyly. Provisional delimitations of species are proposed and NCPA is used to generate hypotheses of population history, all of which are subject to further testing. Multi‐faceted studies, involving phylogenetic assessments of independent molecular markers and morphological variation across codistributed taxa with estimates of niche breadths in a landscape context, will likely yield the most promising returns for cross‐validation of hypotheses of population and speciation histories. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 89 , 241–275.     

Allopolyploidy and homoploid hybridization in the Sphagnum subsecundum complex (Sphagnaceae: Bryophyta)

Several complexes of species in Sphagnum (peat mosses) originated through hybridization and allopolyploidy, suggesting that these processes have played a major evolutionary role in this genus. The Sphagnum subsecundum complex includes gametophytically haploid and diploid species in North America. Analyses of 12 microsatellite loci and sequences from two plastid DNA markers show that the evolutionary history of this group is substantially more complex than previously thought. Two taxonomic species, Sphagnum lescurii and Sphagnum inundatum, include both haploid and diploid populations. Within each ploidal level, S. lescurii and S. inundatum are not genetically differentiated. The diploid taxa show patterns of fixed heterozygosity for the microsatellite markers, consistent with an allopolyploid origin. Diploid S. lescurii is an allopolyploid between haploid S. lescurii and (haploid) S. subsecundum. Sphagnum carolinianum is an allopolyploid between haploid S. lescurii and an unknown parent. We detected homoploid hybridization between the haploids Sphagnum contortum and S. subsecundum. Finally, we report three samples of diploid Sphagnum platyphyllum (otherwise haploid) that have an allopolyploid origin involving north‐eastern haploid S. platyphyllum and an unidentified taxon. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 135–151.     

Multilocus genetic analyses provide insight into speciation and hybridization in aquatic grasses,genus Ruppia

Aquatic plants of the genus Ruppia inhabit some of the most threatened habitats in the world, such as coastal lagoons and inland saline to brackish waters where their meadows play several key roles. The evolutionary history of this genus has been affected by the processes of hybridization, polyploidization, and vicariance, which have resulted in uncertainty regarding the number of species. In the present study, we apply microsatellite markers for the identification, genetic characterization, and detection of hybridization events among populations of putative Ruppia species found in the southern Iberian Peninsula, with the exception of a clearly distinct species, the diploid Ruppia maritima. Microsatellite markers group the populations into genetically distinct entities that are not coincident with geographical location and contain unique diagnostic alleles. These results support the interpretation of these entities as distinct species: designated here as (1) Ruppia drepanensis, (2) Ruppia cf. maritima, and (3) Ruppia cirrhosa. A fourth distinct genetic entity was identified as a putative hybrid between R. cf. maritima and R. cirrhosa because it contained a mixture of microsatellite alleles that are otherwise unique to these putative species. Hence, our analyses were able to discriminate among different genetic entities of Ruppia and, by adding multilocus nuclear markers, we confirm hybridization as an important process of speciation within the genus. In addition, careful taxonomic curation of the samples enabled us to determine the genotypic and genetic diversity and differentiation among populations of each putative Ruppia species. This will be important for identifying diversity hotspots and evaluating patterns of population genetic connectivity.     

Nuclear ribosomal DNA sequence polymorphism and hybridization in checker mallows (Sidalcea, Malvaceae)

Checker mallows (Sidalcea, Malvaceae) constitute a western North American genus of annuals and perennials that have been regarded as taxonomically difficult because of complex patterns of morphological variation putatively stemming from hybridization and polyploidy. In recent molecular phylogenetic investigations extensive polymorphism was observed in the internal and external transcribed spacers (ITS and ETS) of 18S–26S nuclear ribosomal DNA for some Sidalcea samples. To resolve the evolutionary basis for this polymorphism and to readdress the evolutionary impact of hybridization in Sidalcea we cloned and sequenced the polymorphic DNAs and included the clones in phylogenetic analyses together with direct sequences of non-polymorphic samples. The positions of cloned spacer sequences in the phylogenetic trees suggest that S. reptans and two subspecies of S. malviflora may have been influenced by past hybridization with lineages of the “glaucescens” clade. Polymorphic sequence patterns in other taxa may be a result of extensive interbreeding within young clades, in keeping with the minimal sequence divergence, largely overlapping geographic distributions and morphology, and ploidy variation in these groups. Other possible explanations for polymorphic sequences in members of Sidalcea include slow concerted evolution relative to mutation rates, incomplete lineage sorting, and recent pseudogene formation.     

Genome‐wide sequence information reveals recurrent hybridization among diploid wheat wild relatives

Many conflicting hypotheses regarding the relationships among crops and wild species closely related to wheat (the genera Aegilops, Amblyopyrum, and Triticum) have been postulated. The contribution of hybridization to the evolution of these taxa is intensely discussed. To determine possible causes for this, and provide a phylogeny of the diploid taxa based on genome‐wide sequence information, independent data were obtained from genotyping‐by‐sequencing and a target‐enrichment experiment that returned 244 low‐copy nuclear loci. The data were analyzed using Bayesian, likelihood and coalescent‐based methods. D statistics were used to test if incomplete lineage sorting alone or together with hybridization is the source for incongruent gene trees. Here we present the phylogeny of all diploid species of the wheat wild relatives. We hypothesize that most of the wheat‐group species were shaped by a primordial homoploid hybrid speciation event involving the ancestral Triticum and Am. muticum lineages to form all other species except Ae. speltoides. This hybridization event was followed by multiple introgressions affecting all taxa except Triticum. Mostly progenitors of the extant species were involved in these processes, while recent interspecific gene flow seems insignificant. The composite nature of many genomes of wheat‐group taxa results in complicated patterns of diploid contributions when these lineages are involved in polyploid formation, which is, for example, the case for tetraploid and hexaploid wheats. Our analysis provides phylogenetic relationships and a testable hypothesis for the genome compositions in the basic evolutionary units within the wheat group of Triticeae.     

A Six Nuclear Gene Phylogeny of Citrus (Rutaceae) Taking into Account Hybridization and Lineage Sorting

Background

Genus Citrus (Rutaceae) comprises many important cultivated species that generally hybridize easily. Phylogenetic study of a group showing extensive hybridization is challenging. Since the genus Citrus has diverged recently (4–12 Ma), incomplete lineage sorting of ancestral polymorphisms is also likely to cause discrepancies among genes in phylogenetic inferences. Incongruence of gene trees is observed and it is essential to unravel the processes that cause inconsistencies in order to understand the phylogenetic relationships among the species.

Methodology and Principal Findings

(1) We generated phylogenetic trees using haplotype sequences of six low copy nuclear genes. (2) Published simple sequence repeat data were re-analyzed to study population structure and the results were compared with the phylogenetic trees constructed using sequence data and coalescence simulations. (3) To distinguish between hybridization and incomplete lineage sorting, we developed and utilized a coalescence simulation approach. In other studies, species trees have been inferred despite the possibility of hybridization having occurred and used to generate null distributions of the effect of lineage sorting alone (by coalescent simulation). Since this is problematic, we instead generate these distributions directly from observed gene trees. Of the six trees generated, we used the most resolved three to detect hybrids. We found that 11 of 33 samples appear to be affected by historical hybridization. Analysis of the remaining three genes supported the conclusions from the hybrid detection test.

Conclusions

We have identified or confirmed probable hybrid origins for several Citrus cultivars using three different approaches–gene phylogenies, population structure analysis and coalescence simulation. Hybridization and incomplete lineage sorting were identified primarily based on differences among gene phylogenies with reference to null expectations via coalescence simulations. We conclude that identifying hybridization as a frequent cause of incongruence among gene trees is critical to correctly infer the phylogeny among species of Citrus.     

High cryptic diversity and persistent lineage segregation in endemic Romecytheridea (Crustacea,Ostracoda) from the ancient Lake Tanganyika (East Africa)

Ostracods form a substantial part of the endemic fauna of ancient lakes. Here, we have investigated the phylogenetic and phylogeographic patterns and genetic diversities of species of the endemic genus Romecytheridea from the Southern and Central part of Lake Tanganyika. We found that ostracod populations from four different localities are genetically highly differentiated from each other when analyzing the mitochondrial 16S region, while they are almost identical with genetic markers from the nuclear genome (D1-D2 from the large ribosomal subunit (LSU) and ITS). The criteria of the K/θ method for the evolutionary species concepts are fulfilled when analyzing 16S DNA sequence data, indicating that these populations are in fact different (cryptic) species with allopatric distribution. We discuss various hypotheses on how this high diversity could have originated. The complete lineage segregation can partly be explained by geographic isolation during periods of low lake level stands. But, other factors must have contributed to genetic isolation and speciation, as the two closest populations (Chimba and Katoto) from shallow parts of the Southern basin of Tanganyika are also geographically fully segregated.     

Strong postmating reproductive isolation in Mimulus section Eunanus

Postmating reproductive isolation can help maintain species boundaries when premating barriers to reproduction are incomplete. The strength and identity of postmating reproductive barriers are highly variable among diverging species, leading to questions about their genetic basis and evolutionary drivers. These questions have been tackled in model systems but are less often addressed with broader phylogenetic resolution. In this study we analyse patterns of genetic divergence alongside direct measures of postmating reproductive barriers in an overlooked group of sympatric species within the model monkeyflower genus, Mimulus. Within this Mimulus brevipes species group, we find substantial divergence among species, including a cryptic genetic lineage. However, rampant gene discordance and ancient signals of introgression suggest a complex history of divergence. In addition, we find multiple strong postmating barriers, including postmating prezygotic isolation, hybrid seed inviability and hybrid male sterility. M. brevipes and M. fremontii have substantial but incomplete postmating isolation. For all other tested species pairs, we find essentially complete postmating isolation. Hybrid seed inviability appears linked to differences in seed size, providing a window into possible developmental mechanisms underlying this reproductive barrier. While geographic proximity and incomplete mating isolation may have allowed gene flow within this group in the distant past, strong postmating reproductive barriers today have likely played a key role in preventing ongoing introgression. By producing foundational information about reproductive isolation and genomic divergence in this understudied group, we add new diversity and phylogenetic resolution to our understanding of the mechanisms of plant speciation.     

Genetic diversity enhanced by ancient introgression and secondary contact in East Pacific black mangroves

Regional distribution of genetic diversity in widespread species may be influenced by hybridization with locally restricted, closely related species. Previous studies have shown that Central American East Pacific populations of the wide-ranged Avicennia germinans , the black mangrove, harbour higher genetic diversity than the rest of its range. Genetic diversity in this region might be enhanced by introgression with the locally restricted Avicennia bicolor . We tested the hypotheses of ancient hybridization using phylogenetic analysis of the internal transcribed spacer region (ITS) of the nuclear ribosomal DNA and intergenic chloroplast DNA; we also tested for current hybridization by population level analysis of nuclear microsatellites. Our results unveiled ancient ITS introgression between a northern Pacific Central American A. germinans lineage and A. bicolor . However, microsatellite data revealed contemporary isolation between the two species. Polymorphic ITS sequences from Costa Rica and Panama are consistent with a zone of admixture between the introgressant ITS A. germinans lineage and a southern Central American lineage of A. germinans . Interspecific introgression influenced lineage diversity and divergence at the nuclear ribosomal DNA; intraspecific population differentiation and secondary contact are more likely to have enhanced regional genetic diversity in Pacific Central American populations of the widespread A. germinans .     

Genetic admixture supports an ancient hybrid origin of the endangered Hawaiian duck

Speciation is regarded primarily as a bifurcation from an ancestral species into two distinct taxonomic units, but gene flow can create complex signals of phylogenetic relationships, especially among different loci. We evaluated several hypotheses that could account for phylogenetic discord between mitochondrial DNA (mtDNA) and nuclear DNA (nuDNA) within Hawaiian duck (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 (Anas platyrhynchos) and Laysan duck (Anas laysanensis). Whereas mtDNA clearly shows a sister relationship between Hawaiian duck and mallard, nuDNA is consistent with a genetic mosaic with nearly equal contributions from Laysan duck and mallard. In addition, coalescent analyses suggest that gene flow from either mallard or Laysan duck, depending on the predefined 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 subfossil 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.