High Levels Of Introgression Research Articles

Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles.

Introgression allows polyploid species to acquire new genomic content from diploid progenitors or from other unrelated diploid or polyploid lineages, contributing to genetic diversity and facilitating adaptive allele discovery. In some cases, high levels of introgression elicit the replacement of large numbers of alleles inherited from the polyploid's ancestral species, profoundly reshaping the polyploid's genomic composition. In such complex polyploids, it is often difficult to determine which taxa were the progenitor species and which taxa provided additional introgressive blocks through subsequent hybridization. Here, we use population-level genomic data to reconstruct the phylogenetic history of Betula pubescens (downy birch), a tetraploid species often assumed to be of allopolyploid origin and which is known to hybridize with at least four other birch species. This was achieved by modeling polyploidization and introgression events under the multispecies coalescent and then using an approximate Bayesian computation rejection algorithm to evaluate and compare competing polyploidization models. We provide evidence that B. pubescens is the outcome of an autoploid genome doubling event in the common ancestor of B. pendula and its extant sister species, B. platyphylla, that took place approximately 178,000-188,000 generations ago. Extensive hybridization with B. pendula, B. nana, and B. humilis followed in the aftermath of autopolyploidization, with the relative contribution of each of these species to the B. pubescens genome varying markedly across the species' range. Functional analysis of B. pubescens loci containing alleles introgressed from B. nana identified multiple genes involved in climate adaptation, while loci containing alleles derived from B. humilis revealed several genes involved in the regulation of meiotic stability and pollen viability in plant species.

Surrounding landscape, habitat and hybridization dynamics drive population structure and genetic diversity in the Saltmarsh Sparrow

Abstract Determining factors that shape a species’ population genetic structure is beneficial for identifying effective conservation practices. We assessed population structure and genetic diversity for Saltmarsh Sparrow (Ammospiza caudacuta), an imperiled tidal marsh specialist, using 13 microsatellite markers and 964 individuals sampled from 24 marshes across the breeding range. We show that Saltmarsh Sparrow populations are structured regionally by isolation-by-distance, with gene flow occurring among marshes within ~110 to 135 km of one another. Isolation-by-resistance and isolation-by-environment also shape genetic variation; several habitat and landscape features are associated with genetic diversity and genetic divergence among populations. Human development in the surrounding landscape isolates breeding marshes, reducing genetic diversity, and increasing population genetic divergence, while surrounding marshland and patch habitat quality (proportion high marsh and sea-level-rise trend) have the opposite effect. The distance of the breeding marsh to the Atlantic Ocean also influences genetic variation, with marshes farther inland being more divergent than coastal marshes. In northern marshes, hybridization with Nelson’s Sparrow (A. nelsoni) strongly influences Saltmarsh Sparrow genetic variation, by increasing genetic diversity in the population; this has a concomitant effect of increasing genetic differentiation of marshes with high levels of introgression. From a conservation perspective, we found that the majority of population clusters have low effective population sizes, suggesting a lack of resiliency. To conserve the representative breadth of genetic and ecological diversity and to ensure redundancy of populations, it will be important to protect a diversity of marsh types across the latitudinal gradient of the species range, including multiple inland, coastal, and urban populations, which we have shown to exhibit signals of genetic differentiation. It will also require maintaining connectivity at a regional level, by promoting high marsh habitat at the scale of gene flow (~130 km), while also ensuring “stepping stone” populations across the range.

The genome of the pygmy right whale illuminates the evolution of rorquals

BackgroundBaleen whales are a clade of gigantic and highly specialized marine mammals. Their genomes have been used to investigate their complex evolutionary history and to decipher the molecular mechanisms that allowed them to reach these dimensions. However, many unanswered questions remain, especially about the early radiation of rorquals and how cancer resistance interplays with their huge number of cells. The pygmy right whale is the smallest and most elusive among the baleen whales. It reaches only a fraction of the body length compared to its relatives and it is the only living member of an otherwise extinct family. This placement makes the pygmy right whale genome an interesting target to update the complex phylogenetic past of baleen whales, because it splits up an otherwise long branch that leads to the radiation of rorquals. Apart from that, genomic data of this species might help to investigate cancer resistance in large whales, since these mechanisms are not as important for the pygmy right whale as in other giant rorquals and right whales.ResultsHere, we present a first de novo genome of the species and test its potential in phylogenomics and cancer research. To do so, we constructed a multi-species coalescent tree from fragments of a whole-genome alignment and quantified the amount of introgression in the early evolution of rorquals. Furthermore, a genome-wide comparison of selection rates between large and small-bodied baleen whales revealed a small set of conserved candidate genes with potential connections to cancer resistance.ConclusionsOur results suggest that the evolution of rorquals is best described as a hard polytomy with a rapid radiation and high levels of introgression. The lack of shared positive selected genes between different large-bodied whale species supports a previously proposed convergent evolution of gigantism and hence cancer resistance in baleen whales.

Native Population Structure beyond Hatchery Introgression in the Endemic Sicilian Trout

Brown trout populations living in the limit of the distribution of the species face challenging environmental conditions. In islands, this vulnerable situation is exacerbated by geographical isolation. Sicilian trout persist only in the south-eastern part of the island and, based on their morphological characteristics, they have been recognized as a distinct species named Salmo cettii. We present the most extensive genetic study on Sicilian trout, based on 213 individuals from nine different streams in four basins. Sequencing of the mitochondrial control region and genotyping of the LDH-C* locus and eight microsatellite markers were carried out to evaluate hatchery introgression from past stocking practices in natural populations and to estimate the gene diversity distribution in populations. Results showed that only trout from the Tellesimo River remained free of hatchery introgression. Gene diversity was low in this native population, but increased in the rest of the samples, probably because of the introduction of hatchery genes. Despite the high level of introgression, the distribution of gene diversity depicted a clear natural pattern of population structure related to the hydrographic hierarchy. Because they represent long evolutionary histories, Sicilian trout populations should be considered of high conservation priority and managed according to at least four different genetic units.

Dual Domestication, Diversity, and Differential Introgression in Old World Cotton Diploids.

Domestication in the cotton genus is remarkable in that it has occurred independently four different times at two different ploidy levels. Relatively little is known about genome evolution and domestication in the cultivated diploid species Gossypium herbaceum and Gossypium arboreum, due to the absence of wild representatives for the latter species, their ancient domestication, and their joint history of human-mediated dispersal and interspecific gene flow. Using in-depth resequencing of a broad sampling from both species, we provide support for their independent domestication, as opposed to a progenitor-derivative relationship, showing that diversity (mean π = 6 × 10-3) within species is similar, and that divergence between species is modest (FST = 0.413). Individual accessions were homozygous for ancestral single-nucleotide polymorphisms at over half of variable sites, while fixed, derived sites were at modest frequencies. Notably, two chromosomes with a paucity of fixed, derived sites (i.e., chromosomes 7 and 10) were also strongly implicated as having experienced high levels of introgression. Collectively, these data demonstrate variable permeability to introgression among chromosomes, which we propose is due to divergent selection under domestication and/or the phenomenon of F2 breakdown in interspecific crosses. Our analyses provide insight into the evolutionary forces that shape diversity and divergence in the diploid cultivated species and establish a foundation for understanding the contribution of introgression and/or strong parallel selection to the extensive morphological similarities shared between species.

Molecular Insights into the Centaurea Calocephala Complex (Compositae) from the Balkans—Does Phylogeny Match Systematics?

Groups of recent speciation are characterized by high levels of introgression and gene flow, which often confounds delimitation of species on a DNA basis. We analyzed nuclear DNA sequences (ETS spacer and the AGT1 gene) obtained from a large sample of the C. calocephala complex from the Balkan clade of Centaurea sect. Acrocentron (Compositae, Cardueae-Centaureinae) together with a wide representation of other species from the section. Our main goals were to verify the monophyly of the complex as currently defined and to examine the possible presence of introgression and gene flow. Within the complex, species are well-delimited from a morphological point of view and probably originated by allopatric speciation in the Balkan Peninsula. Our results confirm that the Balkan–Eurasian complex is a natural group, but the Centaurea calocephala complex shows a very complicated pattern and its phylogeny is not resolved. Our hypothesis suggests that altitudinal shifts in the transits from glacial to interglacial periods caused successive hybridization events, which are very evident from the DNA networks, between taxa not currently sympatric. As a result, confirmation of interspecific boundaries using molecular markers is extremely complicated.

Iguanainsularis (Iguanidae) from the southern Lesser Antilles: An endemic lineage endangered by hybridization.

The newly described horned iguanaIguanainsularis from the southern Lesser Antilles is separated in two easily recognized subspecies: I.insularissanctaluciae from St. Lucia and I.insularisinsularis from the Grenadines. Its former description is completed by the use of 38 new samples for genetic and morphological analysis. Seventeen microsatellites were used to estimate genetic diversity, population structure and the level of introgression with other Iguana species over nearly the whole range of the species. ND4 and PAC sequences were also used to better characterize hybridization and to complete the description of this lineage. The I.insularis population of St. Vincent shows a high level of introgression from I.iguana whereas in the Grenadines, most islands present pure insularis populations but several show evidence of introgressions. Of the two remaining populations of I.insularissanctaluciae, only one is still purebred. The recent identification of this and other distinct insular species and subspecies in the eastern Caribbean, and evaluation of where hybridization has occurred, are timely and important because the native iguanas are in urgent need of conservation action. Among the greatest threats is the ongoing human-mediated spread of invasive iguanas from Central and South America, which are destroying the endemic insular lineages through multiple diachronic introgression events.

Genetic Diversity and Population Structure of Japanese Plum-Type (Hybrids of P. salicina) Accessions Assessed by SSR Markers

Japanese plum (Prunus salicina Lindl.) is widely distributed in temperate zones across the world. Since its introduction to USA in the late 19th century, this species has been hybridized with up to 15 different diploid Prunus species. This high level of introgression has resulted in a wide range of traits and agronomic behaviors among currently grown cultivars. In this work, 161 Japanese plum-type accessions were genotyped using a set of eight Simple Sequence Repeats (SSR) markers to assess the current genetic diversity and population structure. A total of 104 alleles were detected, with an average of 13 alleles per locus. The overall Polymorphic Informative Content (PIC) value of SSR markers was 0.75, which indicates that these SSR markers are highly polymorphic. The Unweighted Pair Group Method with Arithmetic (UPGMA) dendrogram and the seven groups inferred by Discriminant Analysis of Principal Components (DAPC) revealed a strong correlation of the population structure to the parentage background of the accessions, supported by a moderate but highly significant genetic differentiation. The results reported herein provide useful information for breeders and for the preservation of germplasm resources.

500 years of breeding in the Carthusian Strain of Pura Raza Español horse: An evolutional analysis using genealogical and genomic data

The Carthusian horse is a Pura Raza Español (PRE) strain (CS), bred as a closed population since its creation more than 500years ago. The aim of this study was to analyse for the first time its population structure and situation of variability combining both genealogical (GEL) and genomic (GEN) data. The GEL data comprised 348,429 pedigree records (56,105 CS horses), while the GEN analysis included the high-density genotypes (670,804 SNPs) of 287 horses. Pedigree completeness demonstrated its accuracy, showing a good correlation of GEL (F) and GEN (FROH ) inbreeding coefficient in the case of PRE subpopulations partially related and non-related to Carthusian strain (0.68) but a lower value in the 100% Carthusian horses (0.42), due to the high weight of founders not detected by GEL analysis. GEN (PCA, AMOVA, and Admixture) and GEL analysis showed a good differentiation of subpopulations, but also a high level of introgression of the CS in the breed during past decades. A recent change in this trend was noteworthy, with a considerable reduction in CS variability and a genetic bottleneck (effective population sizes of 31.57 and 30.20 in GEL and GEN analysis, respectively, in last generation). The PRE has maintained its variability, and a considerable difference in estimated Ne by GEL (60.77) and GEN (188.0) data was observed. Using two sources of complementary information, it was found the existence of an ancient PRE strain with a unique genetic landmark, practically free from the influence of other equine populations.

Combining population genomics and ecological niche modeling to assess taxon limits between Carex jemtlandica and C. lepidocarpa

Abstract Carex section Ceratocystis (Cyperaceae) is a group of recently evolved plant species, in which hybridization is frequent, introgression is documented, taxonomy is complex, and morphological boundaries are vague. Within this section, a unified taxonomic treatment of the Carex jemtlandica–Carex lepidocarpa species complex does not exist, and Norway may currently be the sole country accepting species rank for both. Carex jemtlandica is mainly confined to Fennoscandia and is thus a Fennoscandian conservation responsibility. This motivated us to test the principal hypothesis that both C. jemtlandica and C. lepidocarpa represent evolutionary significant units, and that both deserve their current recognition at species level. We investigated their evolutionary distinctiveness in Norway, using restriction site‐associated DNA sequencing and ecological niche modeling. Our genomic results reveal two genetic clusters, largely corresponding to C. jemtlandica and C. lepidocarpa that also remain distinct in sympatry, despite clear indications of ongoing hybridization and introgression. The ecological niche modeling suggests that they occupy different environmental niches. Jointly, our results clearly show that C. jemtlandica and C. lepidocarpa represent separately evolving entities that should qualify recognition as evolutionary significant units. Given the high level of introgression compared to other hybridizing species pairs in Carex we recommend treating C. jemtlandica as a subspecies of C. lepidocarpa.

Landscape resistance constrains hybridization across contact zones in a reproductively and morphologically polymorphic salamander

Explicitly accounting for phenotypic differentiation together with environmental heterogeneity is crucial to understand the evolutionary dynamics in hybrid zones. Species showing intra-specific variation in phenotypic traits that meet across environmentally heterogeneous regions constitute excellent natural settings to study the role of phenotypic differentiation and environmental factors in shaping the spatial extent and patterns of admixture in hybrid zones. We studied three environmentally distinct contact zones where morphologically and reproductively divergent subspecies of Salamandra salamandra co-occur: the pueriparous S. s. bernardezi that is mostly parapatric to its three larviparous subspecies neighbours. We used a landscape genetics framework to: (i) characterise the spatial location and extent of each contact zone; (ii) assess patterns of introgression and hybridization between subspecies pairs; and (iii) examine the role of environmental heterogeneity in the evolutionary dynamics of hybrid zones. We found high levels of introgression between parity modes, and between distinct phenotypes, thus demonstrating the evolution to pueriparity alone or morphological differentiation do not lead to reproductive isolation between these highly divergent S. salamandra morphotypes. However, we detected substantial variation in patterns of hybridization across contact zones, being lower in the contact zone located on a topographically complex area. We highlight the importance of accounting for spatial environmental heterogeneity when studying evolutionary dynamics of hybrid zones.

The Negative Impact of the Hominin’s DPP4 Gene Inherited from Neanderthals to Pandemic of COVID-19

Background: According to preliminary sequences from 2010, 99.7% of the nucleotide sequences of the modern human and Neanderthal genomes are identical, compared to humans sharing around 98.8% of sequences with the chimpanzee. In contrast, the difference between chimpanzees and modern humans is approximately 1,462 mtDNA base pairs. Materials and Methods: Neanderthal-inherited genetic material is found in all non-African populations and was initially reported to comprise 1 to 4 percent of the genome. This fraction was later refined to 1.5 to 2.1 percent. We had gone through many researches of Neanderthals affected gene flow in humans. Results: It is estimated that 20 percent of Neanderthal DNA currently survives in modern humans. Modern human genes involved in making keratin, a protein constituent of skin, hair, and nails, have especially high levels of introgression. For example, approximately 66% of East Asians contain a POUF23L variant introgressed from Neanderthals, while 70% of Europeans possess an introgressed allele of BNC2. Our finding shines a light on an enzyme called dipeptidyl peptidase-4 (DPP4). Scientists already know the protein allows another coronavirus, which causes Middle Eastern respiratory syndrome (MERS), to bind to and enter human cells. The new analysis, of DPP4 gene variants among COVID-19 patients, suggests the enzyme also provides SARS-CoV-2 with a second door into our cells, along with its usual infection route via the angiotensinconverting enzyme 2 (ACE2) receptor on cell surfaces. Conclusion: Most Europeans, Asians, and Native Americans harbor a handful of genes from Neanderthals, up 1.8% to 2.6% of their DNA. Studies of ancient DNA in Neanderthal fossils have shown the hominin’s DPP4 gene subtly differs from the typical human one. Conclusion: The hominin’s DPP4 gene inherited from Neanderthals plays a major role in Immune System Disorders and Lower Immune response in many diseases. This gene plays a major role in affecting humans with COVID-19 and spreading it through the world. All humans contain this gene from 1 to 4 percent. East Asians, Europeans, Middle and South Americans conveys more, hence; native Africans contain less amounts of hominin’s DPP4 gene. Therefore; East Asians, Europeans, Middle and South Americans are prone to severe COVID-19.

Introgression does not influence the positive ecological and functional role of dingo populations

The impact of hybridisation between dingoes and domestic dogs, and the subsequent introgression of domestic dog genes into dingo populations, remains a topic of significant impact. It has been claimed, but with little evidence or logical argumentation, that dingoes with significant dog introgression have different effects on agriculture and ecosystems than dingoes with no dog introgression. Introgression is a natural process in evolution, occurring in many species, although this is sometimes human assisted. Canid species in particular show high levels of introgression, due to their genetic and phylogenetic similarities, and human persecution creates scenarios encouraging hybridisation. Dingoes are no exception and demonstrate high levels of introgression of domestic dog genes, particularly in the temperate areas of south-eastern Australia. The available evidence shows that this introgression has minimal effects on the functional morphology of the dingo skull. There is also some preliminary evidence that introgression has not had a major impact on dingo reproductive biology. Studies on the impacts of dingoes on arid, tropical and temperate ecosystems, where levels of introgression vary greatly, all show consistent positive impacts of dingoes, regardless of the amount of domestic dog genes within the dingo population, on these ecosystems. Hence, hybridisation and resultant introgression from domestic dog genes appear to have little effect on aspects of the functional morphology or ecological role of the dingo. Accordingly, introgression does not diminish the conservation status of the dingo.

Hybridization and introgression between Helicoverpa armigera and H. zea: an adaptational bridge

BackgroundInvasion of organisms into new ecosystems is increasingly common, due to the global trade in commodities. One of the most complex post-invasion scenarios occurs when an invasive species is related to a native pest, and even more so when they can hybridize and produce fertile progeny. The global pest Helicoverpa armigera was first detected in Brazil in 2013 and generated a wave of speculations about the possibility of hybridization with the native sister taxon Helicoverpa zea. In the present study, we used genome-wide single nucleotide polymorphisms from field-collected individuals to estimate hybridization between H. armigera and H. zea in different Brazilian agricultural landscapes.ResultsThe frequency of hybridization varied from 15 to 30% depending on the statistical analyses. These methods showed more congruence in estimating that hybrids contained approximately 10% mixed ancestry (i.e. introgression) from either species. Hybridization also varied considerably depending on the geographic locations where the sample was collected, forming a ‘mosaic’ hybrid zone where introgression may be facilitated by environmental and landscape variables. Both landscape composition and bioclimatic variables indicated that maize and soybean cropland are the main factors responsible for high levels of introgression in agricultural landscapes. The impact of multiple H. armigera incursions is reflected in the structured and inbred pattern of genetic diversity.ConclusionsOur data showed that the landscape composition and bioclimatic variables influence the introgression rate between H. armigera and H. zea in agricultural areas. Continuous monitoring of the hybridization process in the field is necessary, since agricultural expansion, climatic fluctuations, changing composition of crop species and varieties, and dynamic planting seasons are some factors in South America that could cause a sudden alteration in the introgression rate between Helicoverpa species. Introgression between invasive and native pests can dramatically impact the evolution of host ranges and resistance management.

RADseq and mate choice assays reveal unidirectional gene flow among three lamprey ecotypes despite weak assortative mating: Insights into the formation and stability of multiple ecotypes in sympatry.

Adaptive divergence with gene flow often results in complex patterns of variation within taxa exhibiting substantial ecological differences among populations. One example where this may have occurred is the parallel evolution of freshwater-resident nonparasitic lampreys from anadromous-parasitic ancestors. Previous studies have focused on transitions between these two phenotypic extremes, but here, we considered more complex evolutionary scenarios where an intermediate freshwater form that remains parasitic is found sympatrically with the other two ecotypes. Using population genomic analysis (restriction-associated DNA sequencing), we found that a freshwater-parasitic ecotype was highly distinct from an anadromous-parasitic form (Qlake-P =96.8%, Fst =0.154), but that a freshwater-nonparasitic form was almost completely admixed in Loch Lomond, Scotland. Demographic reconstructions indicated that both freshwater populations likely derived from a common freshwater ancestor. However, while the nonparasitic ecotype has experienced high levels of introgression from the anadromous-parasitic ecotype (Qanad-P =37.7%), there is no evidence of introgression into the freshwater-parasitic ecotype. Paradoxically, mate choice experiments predicted high potential for gene flow: Males from all ecotypes were stimulated to spawn with freshwater-parasitic females, which released gametes in response to all ecotypes. Differentially fixed single nucleotide polymorphisms identified genes associated with growth and development, which could possibly influence the timing of metamorphosis, resulting in significant ecological differences between forms. This suggests that multiple lamprey ecotypes can persist in sympatry following shifts in adaptive peaks, due to environmental change during their repeated colonization of post-glacial regions, followed by periods of extensive gene flow among such diverging populations.

Identification of Molecular Markers Differentiating Betula papyrifera and B. pumila Populations from Northern Ontario (Canada)

Betula is a polyploid and highly polymorphic genus with several species known to hybridize very readily. This high level of introgression has resulted in hybrid populations where different species are sympatric. The main objectives of the present study were to identify putative hybrids between B. papyrifera and B. pumila in the Greater Sudbury Region (Northern Ontario) and to develop ISSR and RAPD markers that can differentiate B. papyrifera and B. pumila and their respective populations. This study revealed extensive introgression of B. papyrifera genes into B. pumila based on morphological characterization in the Greater Sudbury region (Northern Ontario) where these two species coexist. Genomic DNAs were extracted from all the collected genotypes from seven B. papyrifera and five B. pumila populations within the GSR. Additional samples from B. pumila from Wisconsin were also analyzed. All the DNA samples were amplified using ISSR and RAPD primers. No – species – diagnostic markers was identified because in part to a high level of polymorphic loci observed within and among populations. A close look of all the amplified products revealed a number of ISSR and RAPD diagnostic markers that differentiate P. papyrifera populations from different origins. Likewise, diagnostic bands distinguishing B. pumila from Wisconsin to the GSR population were identified.

Scale and direction of adaptive introgression between black cottonwood (Populus trichocarpa) and balsam poplar (P.balsamifera).

Introgression can introduce novel genetic variation at a faster rate than mutation alone and result in adaptive introgression when adaptive alleles are maintained in the recipient genome over time by natural selection. A previous study from our group demonstrated adaptive introgression from Populus balsamifera into P.trichocarpa in a target genomic region. Here we expand our local ancestry analysis to the whole genome of both parents to provide a comprehensive view of introgression patterns and to identify additional candidate regions for adaptive introgression genomewide. Populus trichocarpa is a large, fast-growing tree of mild coastal regions of the Pacific Northwest, whereas P.balsamifera is a smaller stature tree of continental and boreal regions with intense winter cold. The species hybridize where they are parapatric. We detected asymmetric patterns of introgression across the whole genome of these two poplar species adapted to contrasting environments, with stronger introgression from P.balsamifera to P.trichocarpa than vice versa. Admixed P.trichocarpa individuals contained more genomic regions with unusually high levels of introgression (19 regions) and also the largest introgressed genome fragment (1.02Mb) compared with admixed P.balsamifera (nine regions). Our analysis also revealed numerous candidate regions for adaptive introgression with strong signals of selection, notably related to disease resistance, and enriched for genes that may play crucial roles in survival and adaptation. Furthermore, we detected a potential overrepresentation of subtelomeric regions in P.balsamifera introgressed into P.trichocarpa and possible protection of sex-determining regions from interspecific gene flow.

Gene flow from domesticated escapes alters the life history of wild Atlantic salmon.

Interbreeding between domesticated and wild animals occurs in several species. This gene flow has long been anticipated to induce genetic changes in life-history traits of wild populations, thereby influencing population dynamics and viability. Here, we show that individuals with high levels of introgression (domesticated ancestry) have altered age and size at maturation in 62 wild Atlantic salmon Salmo salar populations, including seven ancestral populations to breeding lines of the domesticated salmon. This study documents widespread changes to life-history traits in wild animal populations following gene flow from selectively bred, domesticated conspecifics. The continued high abundance of escaped, domesticated Atlantic salmon thus threatens wild Atlantic salmon populations by inducing genetic changes in fitness-related traits. Our results represent key evidence and a timely warning concerning the potential ecological impacts of the globally increasing use of domesticated animals.

Does genetic distance between parental species influence outcomes of hybridization among coral reef butterflyfishes?

Christmas Island is located at the overlap of the Indian and Pacific Ocean marine provinces and is a hot spot for marine hybridization. Here, we evaluate the ecological framework and genetic consequences of hybridization between butterflyfishes Chaetodon guttatissimus and Chaetodon punctatofasciatus. Further, we compare our current findings to those from a previous study of hybridization between Chaetodon trifasciatus and Chaetodon lunulatus. For both species groups, habitat and dietary overlap between parental species facilitate frequent heterospecific encounters. Low abundance of potential mates promotes heterospecific pair formation and the breakdown of assortative mating. Despite similarities in ecological frameworks, the population genetic signatures of hybridization differ between the species groups. Mitochondrial and nuclear data from C.guttatissimus×C.punctatofasciatus (1% divergence at cyt b) show bidirectional maternal contributions and relatively high levels of introgression, both inside and outside the Christmas Island hybrid zone. In contrast, C.trifasciatus×C.lunulatus (5% cyt b divergence) exhibit unidirectional mitochondrial inheritance and almost no introgression. Back-crossing of hybrid C.guttatissimus×C.punctatofasciatus and parental genotypes may eventually confound species-specific signals within the hybrid zone. In contrast, hybrids of C.trifasciatus and C.lunulatus may coexist with and remain genetically distinct from the parents. Our results, and comparisons with hybridization studies in other reef fish families, indicate that genetic distance between hybridizing species may be a factor influencing outcomes of hybridization in reef fish, which is consistent with predictions from terrestrially derived hybridization theory.

Introgression and Phenotypic Assimilation in Zimmerius Flycatchers (Tyrannidae): Population Genetic and Phylogenetic Inferences from Genome-Wide SNPs

Genetic introgression is pervasive in nature and may lead to large-scale phenotypic assimilation and/or admixture of populations, but there is limited knowledge on whether large phenotypic changes are typically accompanied by high levels of introgression throughout the genome. Using bioacoustic, biometric, and spectrophotometric data from a flycatcher (Tyrannidae) system in the Neotropical genus Zimmerius, we document a mosaic pattern of phenotypic admixture in which a population of Zimmerius viridiflavus in northern Peru (henceforth "mosaic") is vocally and biometrically similar to conspecifics to the south but shares plumage characteristics with a different species (Zimmerius chrysops) to the north. To clarify the origins of the mosaic population, we used the RAD-seq approach to generate a data set of 37,361 genome-wide single nucleotide polymorphisms (SNPs). A range of population-genetic diagnostics shows that the genome of the mosaic population is largely indistinguishable from southern Z. viridiflavus and distinct from northern Z. chrysops, and the application of parsimony and species tree methods to the genome-wide SNP data set confirms the close affinity of the mosaic population with southern Z. viridiflavus. Even so, using a subset of 2710 SNPs found across all sampled lineages in configurations appropriate for a recently proposed statistical ("ABBA/BABA") test that distinguishes gene flow from incomplete lineage sorting, we detected low levels of gene flow from northern Z. chrysops into the mosaic population. Mapping the candidate loci for introgression from Z. chrysops into the mosaic population to the zebra finch genome reveals close linkage with genes significantly enriched in functions involving cell projection and plasma membranes. Introgression of key alleles may have led to phenotypic assimilation in the plumage of mosaic birds, suggesting that selection may have been a key factor facilitating introgression.