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675 results for “Introgression”
Fig. 2 in Unraveling the Myotis morass: ultraconserved-element analysis reveals introgression, cryptic diversity, and taxonomic trouble
Fig. 2. Comparison of tree conflict by marker for 3 broad phylogeographic Myotis groups: (A) Nearctic group; (B) Neotropical "albescens group"; (C) Neotropical "ruber group." This is a subset of individuals shown in Fig. 1A. For each group, the left tree displays the ASTRAL_I UCE phylogeny while the right displays the maximum likelihood Cyt b phylogeny. The same individuals are shown in each tree pair. Lines between trees denote notable topological differences between markers. Colors for highlighting by species are an approximated average color for that species as determined by the first 3 components of the PCAs shown in Figs. 3–5.
Data from: Introgression from farmed escapees affects the full life cycle of wild Atlantic salmon
<p>After a half a century of salmon farming, we have yet to understand how the influx of genes from farmed escapees affects the full life history of Atlantic salmon (Salmo salar L.) in the wild. Using scale samples of over 6900 wild adult salmon from 105 rivers, we document that increased farmed genetic ancestry is associated with increased growth throughout life and a younger age at both seaward migration and sexual maturity. There was large among-population variation in the effects of introgression. Most saliently, the increased growth at sea following introgression declined with the population's average growth potential. Variation at two major-effect loci previously shown to be associated with age at maturity was little affected by farmed genetic ancestry and could not explain the observed phenotypic effects of introgression. Our study provides knowledge crucial for redicting the ecological and evolutionary consequences of increased aquaculture production worldwide.</p>
Data from: Historical mitochondrial genome introgression confounds species delimitation—evidence from phylogenetic inference in the Odorrana grahami species complex
<p>Species delimitation is essential to informing conservation policy and understanding ecological and evolutionary processes. Most of our recent gains in knowledge on animal diversity rely on morphological characteristics and mitochondrial (mt) DNA variation. Concordant results based on both have led to an unprecedented acceleration in the identification of new species and enriched the field of taxonomy. However, discordances are also found commonly between morphological and mtDNA evidence. This confounds species delimitation, especially when gene flow or mitochondrial genome introgression has occurred. Here we illustrate how mitochondrial genome introgression among species of the <em>Odorrana grahami </em>complex confounds species delimitation using the combined evidence of morphological characters, mitochondrial variation, and thousands of nuclear single nucleotide polymorphisms (SNPs) from genotyping-by-sequencing (GBS). Fifty-eight samples across the distribution of the <em>O. grahami </em>complex were included. The mtDNA matrilineal genealogy indicated two clades, with <em>O. grahami </em>and <em>O. junlianensis</em> clustered together. In contrast, all nuclear evidence including gene trees, species trees, and genetic structure analyses based on GBS data support three species with distinct genetic clusters. These three distinct genetic clusters also correspond to distinct morphological characters. They affirm the distinct taxonomic entities of both <em>O. grahami </em>and <em>O. junlianensis</em>, as well as a third clade distinct from either. Which species the third clade belongs to remains unclear and will require further testing. The nuclear genomic loci contradict the COI evidence, with indications of rampant historical mitochondrial genome introgression among the species of the <em>O. grahami</em> complex. These discordant signals previously confused species delimitation efforts in this group. Based on these findings, we recommend the integration of independent data, especially nuclear genomic evidence, in species delimitation so as to be robust against the pitfalls of mitochondrial introgression.</p>
Range expansion and contraction of Tillandsia landbeckii lomas in hyperarid Chilean Atacama Desert indicate ancient introgression and geneflow
<p><span>Here we hypothesise that interspecies geneflow as well as secondary contact of formerly isolated clusters of <em>T. landbeckii</em> may have contributed to maintain, restore or even enhance the species´ genetic diversity through space and time. We employed genotyping-by sequencing (GBS) to obtain genetic variation largely retrieved from the nuclear genome on population level, and used the same data to extract sequence information to define maternally inherited plastid types. Reference plastomes from different plastid types via a genome-wide short read sequencing approach (genome skimming) were assembled. Plastome data were analysed in order to provide a robust phylogenetic and temporal framework of the maternal perspective including various epiarenic species of particular interest for the evolutionary history of <em>T. landbeckii</em>. The spatiotemporal scale of our study covers the entire Chilean Atacama Desert with a focus on one population form the central cluster. The aim of our study is to provide reasonable explanations for orphan genetic clusters on different spatial scales, while highlighting the idea of evolutionary significant secondary genetic contact on and between species level, which may have also fostered the evolution of epiarenic growth in Tillandsia. This study should pave the way for future comparative evolutionary studies across epiarenic Tillandsia species to unravel the co-evolution of the Atacama Desert system and biological life.</span></p>
Introgression, admixture and selection facilitate genetic adaptation to high-altitude environments in Chinese cattle
<p>Domestication and subsequent selection of cattle to form breeds and biological types that can adapt to different environments partitioned ancestral genetic diversity into distinct modern lineages. Genome-wide selection particularly for adaptation to extreme environments left detectable signatures genome-wide. We used high-density genotype data for 42 cattle breeds and identified the influence of <em>Bos grunniens</em> and <em>Bos javanicus</em> on the formation of Chinese indicine breeds that led to their divergence from India-origin Zebu. We also found evidence for introgression, admixture, and migration in most of the Chinese breeds. Selection signature analyses between high-altitude (>1800m) and low-altitude adapted breeds (<1500m) revealed candidate genes (<em>ACSS2</em>, <em>ALDOC,</em> <em>EPAS1</em>,<em> EGLN1, NUCB2</em>) and pathways that are putatively involved in hypoxia adaptation. Immunohistochemical, real-time PCR and CRISPR/cas9 <em>ACSS2</em>-knockout analyses suggests that the up-regulation of <em>ACSS2</em> expression in the liver promotes the metabolic adaptation of cells to hypoxia via the hypoxia-inducible factor pathway. High altitude adaptation involved the introgression of alleles from high-altitude adapted Yaks into Chinese <em>B. t. taurus </em>prior to their formation into recognized breeds and followed by selection. In addition to selection, adaptation to high altitude environments has been facilitated by admixture and introgression with locally adapted cattle populations.</p>
Phased genotype data for FILET's analysis of introgression in D. simulans and D. sechellia
<p>This dataset contains all genotype files prepared for Schrider et al.'s analysis of introgression between D. simulans and D. sechellia. For more information see https://www.biorxiv.org/content/early/2017/09/25/170670</p>
Fig. 3 in Non-ultrametric phylogenetic trees shed new light on Neanderthal introgression
Fig. 3 Neanderthals (red square termed N) and ancient non-African humans (blue square termed H) branching from a common ancestor. Two scenarios are illustrated, each of them relying on a square with distinct molecular clock calibration. Our method suggests what follows: if the split took place 400,000 years ago, the introgression occurred about 40,000 years ago (A); if the split took place 600,000 years ago, the introgression occurred about 75,000 years ago (B)
Data from: Differential introgression across newt hybrid zones – evidence from replicated transects
<p>Genomic heterogeneity of divergence between hybridizing species may reflect heterogeneity of introgression, but also processes unrelated to hybridization. Heterogeneous introgression and its repeatability can be directly tested in natural hybrid zones by examining multiple transects. Here, we studied hybrid zones between the European newts: Lissotriton montandoni and two lineages of L. vulgaris, with replicate transects within each zone. Over 1000 nuclear genes located on a linkage map and mtDNA were investigated using geographic and genomic clines. Overall, the five transects were all similar, showing hallmarks of strong reproductive isolation: bimodal distribution of genotypes in central populations and narrow allele frequency clines. However, the extent of introgression differed between the zones, likely as a consequence of their different ages, indicated by the analysis of heterozygosity runs in diagnostic markers. In three transects genomic signatures of small-scale (ca. 2 km) zone movements were detected. We found a limited overlap of cline outliers between transects, and no evidence of stronger differentiation between zones than between transects within zones. Introgression was heterogeneous across linkage groups, with patterns of heterogeneity similar between transects and zones. Predefined candidates for increased or reduced introgression exhibited only a subtle tendency in the expected direction, suggesting that interspecific differentiation is not a reliable indicator for the strength of introgression. These hierarchically sampled hybrid zones of different ages show how introgression unfolds with time and offer an excellent opportunity to dissect the dynamics of hybridization and architecture of reproductive isolation at advanced stages of speciation.</p>
Data from: History cleans up messes: the impact of time in driving divergence and introgression in a tropical suture zone
Contact zones provide an excellent arena in which to address questions about how genomic divergence evolves during lineage divergence. They allow us to both infer patterns of genomic divergence in allopatric populations isolated from introgression and to characterize patterns of introgression after lineages meet. Thusly motivated, we analyze genome-wide introgression data from four contact zones in three genera of lizards endemic to the Australian Wet Tropics. These contact zones all formed between morphologically cryptic lineage-pairs within morphologically defined species, and the lineage-pairs meeting in the contact zones diverged anywhere from 3.1 to 5.8 million years ago. By characterizing patterns of molecular divergence across an average of 11K genes and fitting geographic clines to an average of 7.5K variants, we characterize how patterns of genomic differentiation and introgression change through time. Across this range of divergences, we find that genome-wide differentiation increases but becomes no less heterogeneous. In contrast, we find that introgression heterogeneity decreases dramatically, suggesting that time helps isolated genomes "congeal". Thus, this work emphasizes the pivotal role that history plays in driving lineage divergence.
Data from: Nuclear markers reveal a complex introgression pattern among marine turtle species on the Brazilian coast
A surprisingly high frequency of interspecific sea turtle hybrids have been previously recorded in a nesting site along a short stretch of the Brazilian coast. Mitochondrial DNA data indicated that as much as 43% of the females identified as E. imbricata are hybrids in this area (Bahia State of Brazil). It is a remarkable find, since most of the nesting sites surveyed worldwide, including some in northern Brazil, presents no hybrids, and rare Caribbean sites present no more than 2% of hybrids. Thus, a detailed understanding of the hybridization process is needed to evaluate natural or anthropogenic causes of this regional phenomenon in Brazil, which could be an important factor affecting the conservation of this population. We analyzed a set of 12 nuclear markers to investigate the pattern of hybridization involving three species of sea turtles: hawksbill (Eretmochelys imbricata), loggerhead (Caretta caretta), and olive ridley (Lepidochelys olivacea). Our data indicate that most of the individuals in the crossings L. olivacea × E. imbricata and L. olivacea × C. caretta are F1 hybrids, whereas C. caretta × E. imbricata crossings present F1 and backcrosses with both parental species. In addition, the C. caretta × E. imbricata hybridization seems to be gender and species biased, and we also found one individual with evidence of multispecies hybridization among C. caretta × E. imbricata × Chelonia mydas. The overall results also indicate that hybridization in this area is a recent phenomenon, spanning at least two generations or ~40 years.
Data from: Widespread introgression in Chinese indigenous chicken breeds from commercial broiler
Chinese indigenous chickens constitute world-renowned genetic resources due to their excellent traits, including early puberty, good meat quality, and strong resistance to disease. Unfortunately, the introduction of a large number of commercial chickens in the past two decades has had an adverse effect on Chinese indigenous chickens. Using the chicken 60K single-nucleotide polymorphism (SNP) chip, we assessed the genetic diversity and population structure of 1,187 chickens, representing eight Chinese indigenous chicken breeds, two hybrid chicken breeds, two ancestral chicken breeds, two commercial populations, and additional red jungle fowl. By investigating haplotype similarity, we found extensive gene introgression from commercial broiler to almost all Chinese indigenous chickens. Approximately 15% of the genome, on average, of Chinese indigenous chickens was introgressed, ranging from 0.64% for Tibetan chicken to 21.52% for Huiyang Bearded chicken. Further analysis revealed signals consistent with positive selection in the introgression loci. For the first time, we systematically mapped and quantified introgression from commercial broiler to Chinese indigenous chickens at the whole genome level. Our data provided a usable resource for chicken genetic diversity, and our findings indicated a dire need for protecting the genetic resources of Chinese indigenous chickens.
Data from: Reproductive isolation and cryptic introgression in a sky island enclave of Appalachian birds
Reproductive isolation is central to the speciation process, and cases where the strength of reproductive isolation varies geographically can inform our understanding of speciation mechanisms. Although generally treated as separate species, Black-capped chickadees (Poecile atricapillus) and Carolina chickadees (P. carolinensis) hybridize and undergo genetic introgression in many areas where they come into contact across the eastern United States and in the northern Appalachian Mountains. The Great Smoky Mountains harbor the last large breeding population of atricapillus in the southern Appalachians, isolated from the species' main range by nearly 200 km. This population is believed to be reproductively isolated from local carolinensis due to an unusual, behaviorally mediated elevational range gap, which forms during the breeding season and may function as an incipient reproductive isolating mechanism. We examined the effectiveness of this putative isolating mechanism by looking for genetic introgression from carolinensis in Great Smoky Mountain atricapillus. We characterized this population and parental controls genetically using hundreds of amplified fragment length polymorphism (AFLP) loci as well as mitochondrial DNA (mtDNA) sequence data from cytochrome-b. Great Smoky Mountain atricapillus have experienced nuclear genetic introgression from carolinensis, but at much lower levels than other populations near the hybrid zone to the north. No mitochondrial introgression was detected, in contrast to northern contact areas. Thus, the seasonal elevational range gap appears to have been effective in reducing gene flow between these closely related taxa.
Data from: Maintenance of genetic and morphological identity in two sibling Syrrhopodon species (Calymperaceae, Bryopsida) despite extensive introgression
Bryophytes are a group of land plants wherein the role of hybridization has long been challenged. Using Genotyping by Sequencing to circumvent the lack of molecular variation at selected loci previously used for phylogeny and morphology, we determine the level of genetic and morphological divergence and reproductive isolation between the sibling Syrrhopodon annotinus and S. simmondsii (Calymperaceae, Bryopsida) that occur in sympatry but in different habitats in lowland Amazonian rainforests. A clear morphological differentiation and a low (0.06), but significant Fst derived from the analysis of 183 SNPs were observed between the two species. Conspecific pairs of individuals consistently exhibited higher average kinship coefficients along a gradient of geographic isolation than interspecific pairs. The weak, but significant genetic divergence observed is consistent with growing evidence that ecological specialization can lead to genetic differentiation among bryophyte species. Nevertheless, the spatial genetic structures of the two species were significantly correlated, as evidenced by the significant slope of the Mantel test based on kinship coefficients between pairs of interspecific individuals and the geographic distance separating them. Interspecific pairs of individuals are thus more closely related when they are geographically closer, suggesting that isolation-by-distance is stronger than the interspecific reproductive barrier and pointing to interspecific gene flow. We conclude that interspecific introgression, whose role has long been questioned in bryophytes, may take place even in species wherein sporophyte production is scarce due to dioicy, raising the question as to what mechanisms maintain differentiation despite weak reproductive isolation.
Data from: Heterogeneity and concordance in locus-specific differentiation and introgression between species of towhees
The maintenance or breakdown of reproductive isolation are observable outcomes of secondary contact between species. In cases where hybrids beyond the F1 are formed, the representation of each species' ancestry can vary dramatically among genomic regions. This genomic heterogeneity in ancestry and introgression can offer insight into evolutionary processes, particularly if introgression is compared in multiple hybrid zones. Similarly, considerable heterogeneity exists across the genome in the extent to which populations and species have diverged, reflecting the combined effects of different evolutionary processes on genetic variation. We studied hybridization across two hybrid zones of two phenotypically well-differentiated bird species in Mexico (Pipilo maculatus and P. ocai), to investigate genomic heterogeneity in differentiation and introgression. Using genotyping by sequencing (GBS) and hierarchical Bayesian models, we genotyped 460 birds at over 41,000 single nucleotide polymorphism (SNP) loci. We identified loci exhibiting extreme introgression relative to the genome-wide expectation using a Bayesian genomic cline model. We also estimated locus-specific FST and identified loci with exceptionally high genetic divergence between the parental species. We found some concordance of locus-specific introgression in the two independent hybrid zones (6-20% of extreme loci shared across zones), reflecting areas of the genome that experience similar gene flow when the species interact. Additionally, heterogeneity in introgression and divergence across the genome revealed another subset of loci under the influence of locally specific factors. These results are consistent with a history in which reproductive isolation has been influenced by a common set of loci in both hybrid zones, but where local environmental and stochastic factors also lead to genomic differentiation.
Data from: Parapatric genetic introgression and phenotypic assimilation: testing conditions for introgression between Hercules beetles (Dynastes, Dynastinae)
The prevalence and consequences of genetic introgression between species have been intensively debated. I used Hercules beetles as examples to test for conditions that may be associated with the occurrence of introgression. RADseq data were used to reconstruct the species tree and history of introgression between Hercules beetles. Image data from museum specimens were used to investigate the phenotypic similarity of two adaptive traits between species from two distinct climatic realms (Nearctic vs. Neotropical). Genetic introgression was identified between Hercules beetles living in geographic proximity (parapatric). Phylogenetic relatedness and phenotypic similarity did not predict nor preclude genetic introgression between species. Phenotypic assimilation in body coloration was evident between distantly related Hercules beetles codistributed in Central America, where directional introgression was also statistically supported from the putative donor to receiver lineages. The number of introgressed loci was significantly higher between species with than without phenotypic similarity. I discuss the implications of recent studies on adaptive genetic introgression by providing supporting evidence from the Hercules beetle system.
Data from: Reindeer introgression and the population genetics of caribou in Southwestern Alaska
Alaska caribou (Rangifer tarandus granti) in southwestern Alaska are a poorly understood system, with differing descriptions of their regional population structure, population abundance that has varied greatly through time and instances of the release of domestic reindeer (R. t. tarandus) into their range. Here, we use 21 microsatellites and 297 individuals to investigate the genetic population structure of herds and examine for population bottlenecks. Then, using genetic characteristics of existing reindeer populations, we examine introgression into the wild caribou populations. Caribou of the area are genetically diverse (HE between 0.69 – 0.84), with diversity decreasing along the Alaska Peninsula (AP). Using GST and Jost's D, we find extensive structuring among all herds; MIGRATE-N finds AP herds share few effective migrants with other herds, with South AP and Unimak Island herds having the least. Bayesian clustering techniques are able to resolve all but Denali and Mulchatna caribou herds. Using a conservative assignment threshold of qreindeer ≥ 0.2, 3% of caribou show signs of domestic introgression. Denali herd has the most introgressed individuals (6.9%); those caribou herds that were historically adjacent to smaller reindeer herds, or were historically without adjacent herding, show no admixture. This domestic introgression persists despite the lack of managed reindeer in the region since the 1940s. Our results suggest that despite previous movement data indicating metapopulation like dispersal in this region, there may be unknown barriers to reproduction by dispersing individuals. Finally, our results support findings that wild and domestic Rangifer can hybridize, and show this introgression may persist dozens of generations after domestics are no longer present.
Data from: Introgression threatens the survival of the critically endangered freshwater crayfish Cherax tenuimanus (Decapoda : Parastacidae) in the wild
Hybridization and genetic introgression following the introduction of exotic species can pose a significant threat to the survival of geographically restricted species. A remnant population of the critically endangered freshwater crayfish Cherax tenuimanus in the upper reaches of the Margaret River in southwestern Australia is under threat following the introduction and spread of its congener Cherax cainii. Here, we examine the extent of hybridization and introgression between the two species using twelve polymorphic microsatellite loci. Our study reveals there are three times more C. cainii than C. tenuimanus at our study site in the upper reaches of the Margaret River. There is also evidence of hybridization and introgression between C. tenuimanus and C. cainii at this site, with F1, F2 and backcrossed individuals identified. While interbreeding was confirmed in this study, our simulations suggest that the levels of introgression are much lower than would be expected under random mating, indicating partial reproductive barriers exist. Nevertheless, it is apparent that hybridization and introgression with C. cainii pose a serious threat to C. tenuimanus and their survival in the wild will require active adaptive management and continued genetic monitoring to evaluate management effectiveness.
Data from: Contemporary ecotypic divergence during a recent range expansion was facilitated by adaptive introgression
Although rapid phenotypic evolution during range expansion associated with colonization of contrasting habitats has been documented in several taxa, the evolutionary mechanisms that underlie such phenotypic divergence have less often been investigated. A strong candidate for rapid ecotype formation within an invaded range is the three-spine stickleback in the Lake Geneva region of central Europe. Since its introduction only about 140 years ago, it has undergone a significant expansion of its range and its niche, now forming phenotypically differentiated parapatric ecotypes that occupy either the pelagic zone of the large lake or small inlet streams, respectively. By comparing museum collections from different times with contemporary population samples, we here reconstruct the evolution of parapatric phenotypic divergence through time. Using genetic data from modern samples, we infer the underlying invasion history. We find that parapatric habitat-dependent phenotypic divergence between the lake and stream was already present in the first half of the twentieth century, but the magnitude of differentiation increased through time, particularly in antipredator defence traits. This suggests that divergent selection between the habitats occurred and was stable through much of the time since colonization. Recently, increased phenotypic differentiation in antipredator defence traits likely results from habitat-dependent selection on alleles that arrived through introgression from a distantly related lineage from outside the Lake Geneva region. This illustrates how hybridization can quickly promote phenotypic divergence in a system where adaptation from standing genetic variation was constrained.
Data from: Bayesian analysis of hybridization and introgression between the endangered european mink (Mustela lutreola) and the polecat (Mustela putorius)
Human-mediated global change will probably increase the rates of natural hybridization and genetic introgression between closely related species, and this will have major implications for conservation of the taxa involved. In this study, we analyse both mitochondrial and nuclear data to characterize ongoing hybridization and genetic introgression between two sympatric sister species of mustelids, the endangered European mink (Mustela lutreola) and the more abundant polecat (M. putorius). A total of 317 European mink, 114 polecats and 15 putative hybrid individuals were collected from different localities in Europe and genotyped with 13 microsatellite nuclear markers. Recently developed Bayesian methods for assigning individuals to populations and identifying admixture proportions were applied to the genetic data. To identify the direction of hybridization, we additionally sequenced mtDNA and Y chromosomes from 78 individuals and 29 males respectively. We found that both hybridization and genetic introgression occurred at low levels (3% and 0.9% respectively) and indicated that hybridization is asymmetric, as only pure polecat males mate with pure European mink females. Furthermore, backcrossing and genetic introgression was detected only from female first-generation (F1) hybrids of European mink to polecats. This latter result implies that Haldane's rule may apply. Our results suggest that hybridization and genetic introgression between the two species should be considered a rather uncommon event. However, the current low densities of European mink might be changing this trend.
Data from: Genome-wide markers reveal a complex evolutionary history involving divergence and introgression in the Abert's squirrel (Sciurus aberti) species group
Background: Genetic introgression between divergent lineages is now considered more common than previously appreciated, with potentially important consequences for adaptation and speciation. Introgression is often asymmetric between populations and patterns can vary for different types of loci (nuclear vs. organellar), complicating phylogeographic reconstruction. The taxonomy of the ecologically specialized Abert's squirrel species group has been controversial, and previous studies based on mitochondrial data have not fully resolved the evolutionary relationships among populations. Moreover, while these studies identified potential areas of secondary contact between divergent lineages, the possibility for introgression has not been tested. Results: We used RAD-seq to unravel the complex evolutionary history of the Abert's squirrel species group. Although some of our findings reinforce inferences based on mitochondrial data, we also find significant areas of discordance. Discordant signals generally arise from previously undetected introgression between divergent populations that differentially affected variation at mitochondrial and nuclear loci. Most notably, our results support earlier claims (disputed by mitochondrial data) that S. aberti kaibabensis, found only on the north rim of the Grand Canyon, is highly divergent from other populations. However, we also detected introgression of S. aberti kaibabensis DNA into other S. aberti populations, which likely accounts for the previously inferred close genetic relationship between this population and those south of the Grand Canyon. Conclusions: Overall, the evolutionary history of Abert's squirrels appears to be shaped largely by divergence during periods of habitat isolation. However, we also found evidence for interbreeding during periods of secondary contact resulting in introgression, with variable effects on mitochondrial and nuclear markers. Our results support the emerging view that populations often diversify under scenarios involving both divergence in isolation and gene flow during secondary contact, and highlight the value of genome-wide datasets for resolving such complex evolutionary histories.
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