Find research datasets worth reusing

opencc-zeroDec 2018View details →

Data from: Asymmetric introgression between fishes in the Red River basin of Texas is associated with variation in water quality

When ecologically divergent taxa encounter one another, hybrid zones can form when reproductive isolation is incomplete. The location of such hybrid zones can be influenced by environmental variables, and an ecological context can provide unique insights into the mechanisms by which species diverge and are maintained. Two ecologically differentiated species of small benthic fishes, the endemic and imperiled prairie chub, Macrhybopsis australis, and the shoal chub, Macrhybopsis hyostoma, are locally sympatric within the upper Red River Basin of Texas. We integrated population genomic data and environmental data to investigate species divergence and the maintenance of species boundaries in these two species. We found evidence of advanced-generation asymmetric hybridization and introgression, with shoal chub alleles introgressing more frequently into prairie chubs than the reciprocal. Using a Bayesian Genomic Cline framework, patterns of genomic introgression were revealed to be quite heterogeneous, yet shoal chub alleles were found to have likely selectively introgressed across species boundaries significantly more often than prairie chub alleles, potentially explaining some of the observed asymmetry in hybridization. These patterns were remarkably consistent across two sampled geographic regions of hybridization. Several environmental variables were found to significantly predict individual admixture, suggesting ecological isolation might maintain species boundaries.

opencc-zeroJul 2021View details →

Multigenerational backcrossing and introgression between two woodrat species at an abrupt ecological transition

When organisms experience secondary contact after allopatric divergence, genomic regions can introgress differentially depending on their relationships with adaptation, reproductive isolation, recombination, and drift. Analyses of genome-wide patterns of divergence and introgression could provide insight into the outcomes of hybridization and the potential relationship between allopatric divergence and reproductive isolation. Here, we generate population genetic data (26,262 SNPs; 353 individuals) using a reduced-representation sequencing approach to quantify patterns of ancestry, differentiation, and introgression between a pair of ecologically distinct mammals – the desert woodrat (N. lepida) and Bryant's woodrat (N. bryanti) – that hybridize at a sharp ecotone in southern California. Individual ancestry estimates confirmed that hybrids were rare in this bimodal hybrid zone, and entirely consisted of a few F1 individuals and a broad range of multigenerational backcrosses. Genomic cline analyses indicated more than half of loci had elevated introgression from one genomic background into the other. However, introgression was not associated with relative or absolute measures of divergence, and loci with extreme values for both were not typically found near detoxification enzymes previously implicated in dietary specialization for woodrats. The decoupling of differentiation and introgression suggests that processes other than adaptation, such as drift, may underlie the extreme clines at this contact zone.

opencc-zeroDec 2017View details →

Data from: Phylogenomic signatures of ancient introgression in a rogue lineage of darters (Teleostei: Percidae)

Evolutionary history is typically portrayed as a branching phylogenetic tree, yet not all evolution proceeds in a purely bifurcating manner. Introgressive hybridization is one process that results in reticulate evolution. Most known examples of genome-wide introgression occur among closely related species with relatively recent common ancestry; however, we present evidence for ancient hybridization and genome-wide introgression between major stem lineages of darters, a species-rich clade of North American freshwater fishes. Previous attempts to resolve the relationships of darters have been confounded by the uncertain phylogenetic resolution of the lineage Allohistium. In this study we investigate the phylogenomics of darters, specifically the relationships of Allohistium, through analyses of ~30,000 RADseq loci sampled from 112 species. Our phylogenetic inferences are based on traditional approaches in combination with strategies that accommodate reticulate evolution. These analyses result in a novel phylogenetic hypothesis for darters that includes ancient introgression involving Allohistium and other two major darter lineages, minimally occurring 20 million years ago. Darters offer a compelling case for the necessity of incorporating phylogenetic networks in reconstructing the evolutionary history of diversification in species-rich lineages. We anticipate that the growing wealth of genomic data for clades of non-model organisms will reveal more examples of ancient hybridization, eventually requiring a re-evaluation of how evolutionary history is visualized and utilized in macroevolutonary investigations.

opencc-zeroDec 2017View details →

Data from: Unraveling historical introgression and resolving phylogenetic discord within Catostomus (Osteichthys: Catostomidae)

Background: Porous species boundaries can be a source of conflicting hypotheses, particularly when coupled with variable data and/or methodological approaches. Their impacts can often be magnified when non-model organisms with complex histories of reticulation are investigated. One such example is the genus Catostomus (Osteichthys, Catostomidae), a freshwater fish clade with conflicting morphological and mitochondrial phylogenies. The former is hypothesized as reflecting the presence of admixed genotypes within morphologically distinct lineages, whereas the latter is interpreted as the presence of distinct morphologies that emerged multiple times through convergent evolution. We tested these hypotheses using multiple methods, to including multispecies coalescent and concatenated approaches. Patterson's D-statistic was applied to resolve potential discord, examine introgression, and test the putative hybrid origin of two species. We also applied naïve binning to explore potential effects of concatenation. Results: We employed 14,007 loci generated from ddRAD sequencing of 184 individuals to derive the first highly supported nuclear phylogeny for Catostomus. Our phylogenomic analyses largely agreed with a morphological interpretation,with the exception of the placement of Xyrauchen texanus, which differs from both morphological and mitochondrial phylogenies. Additionally, our evaluation of the putative hybrid species C. columbianus revealed a lack introgression and instead matched the mitochondrial phylogeny. Furthermore, D-statistic tests clarified all discrepancies based solely on mitochondrial data, with agreement among topologies derived from concatenation and multispecies coalescent approaches. Extensive historic introgression was detected across six species-pairs. Potential endemism in the Virgin and Little Colorado Rivers was also apparent, and the former genus Pantosteus was derived as monophyletic, save for C. columbianus. Conclusions: Complex reticulated histories detected herein support the hypothesis that introgression was responsible for conflicts that occurred within the mitochondrial phylogeny, and explains discrepancies found between it and previous morphological phylogenies. Additionally, the hybrid origin of C. columbianus was refuted, but with the caveat that more fine-grain sampling is still needed. Our diverse phylogenomic approaches provided largely concordant results, with naïve binning useful in exploring the single conflict. Considerable diversity was found within Catostomus across southwestern North America, with two drainages [Virgin River (UT) and Little Colorado River (AZ)] reflecting unique composition.

FIGURE 3 in Phylogeography of the Habronattus amicus species complex (Araneae: Salticidae) of western North America, with evidence for localized asymmetrical mitochondrial introgression

FIGURE 3. Bayesian majority-rule consensus phylogram resulting from the three partitions analysis. Branch lengths are averaged from across the posterior distribution (post burn-in), and drawn proportional to this average length (an exception is the branch leading to "right hand" clades – this branch is less than one scale unit in length). Clade designations follow those described in text. Asterisks denote posterior probability values> 0.95, although these are not shown for tip clades involving only two haplotypes. Haplotypes derived from different species are represented by different colours; focal site haplotypes are named by location and bolded.

FIGURE 5 in Phylogeography of the Habronattus amicus species complex (Araneae: Salticidae) of western North America, with evidence for localized asymmetrical mitochondrial introgression

FIGURE 5. Neighbor-net haplotype networks. Filled circles denote interior nodes with extant haplotypes. Clade designations follow those described in text. Haplotypes derived from different species are represented by different colours; focal site haplotypes are named by location and bolded. Dashed lines are used for graphical purposes only, linking haplotypes with interior nodes. Networks are drawn at different mutational scales – maximum pairwise observed differences as follows: A Interior amicus II (22), B Interior amicus I (18), C southern II derived (3).

FIGURE 1 in Phylogeography of the Habronattus amicus species complex (Araneae: Salticidae) of western North America, with evidence for localized asymmetrical mitochondrial introgression

FIGURE 1. Distribution of H. amicus group members in western North America. Collection localities are designated by location numbers, corresponding to those found in the Appendix. Sites 60–62 are found further south in Baja California than portrayed on the map. Different species are represented by different colours, except for the OR focal sites where H. amicus and H. ustulatus occur in syntopy. Inset shows the relative locations of OR focal sites (16=Alkali Lake, 17=Fossil Lake, 18=Summer Lake).

FIGURE 7 in Phylogeography of the Habronattus amicus species complex (Araneae: Salticidae) of western North America, with evidence for localized asymmetrical mitochondrial introgression

FIGURE 7. Habitat use by H. amicus and H. ustulatus at OR focal sites. Pie charts depict the proportion of times a member of a species was collected on each of the available substrate types. Mantel R values as follows: Alkali Lake (R = 0.439, P = 0.001), Fossil Lake (R = 0.825, P = 0.001), Summer Lake (R = 0.079, P = 0.105).

FIGURE 4 in Phylogeography of the Habronattus amicus species complex (Araneae: Salticidae) of western North America, with evidence for localized asymmetrical mitochondrial introgression

FIGURE 4. Summary diagram of phylogeny plus phylogeographic clade distributions. For the tree diagram, haplotypes derived from different species are represented by different colours. Clade designations follow those described in text.

FIGURE 6 in Phylogeography of the Habronattus amicus species complex (Araneae: Salticidae) of western North America, with evidence for localized asymmetrical mitochondrial introgression

FIGURE 6. Bivariate scattergram of carapace width (CW) versus length of the first tibia (ITL) for male and female H. amicus and H. ustulatus specimens from OR focal sites. All measurements are in millimeters.

opennotspecifiedAug 2014View details →

Figure 4 in The role of mitochondrial introgression in illuminating the evolutionary history of Nearctic treefrogs

Figure 4. Species-tree reconstructions for Hyla eximia group treefrogs estimated from mitochondrial DNA (mtDNA) or nuclear DNA (nuDNA) using *BEAST. Bars indicate 95% posterior credibility intervals of divergence dates. All major nodes that received ≥ 0.95 Bayesian posterior probability are depicted with black dots. Bayesian posterior probability support values at all other nodes are provided. Inset shows oscillograms of the advertisement calls (90 s) of four H. eximia group species. Note call similarities between Hyla wrightorum and H. eximia and call differences between H. wrightorum and Hyla arenicolor (data from Klymus, Humfeld & Gerhardt, 2012). Abbreviations: CD, Chihuahuan Desert; CMP, Central Mexican Plateau; CMPsw, south-western Central Mexican Plateau; CP, Colorado Plateau; DGO, Durango; E, eastern; OcS, southern Sierra Madre Occidental; Oligo, Oligocene; OrS, southern Sierra Madre Oriental; Pleis, Pleistocene; Plio, Pliocene; SD, Sonoran Desert; W, western.

opennotspecifiedAug 2014View details →

Figure 1 in The role of mitochondrial introgression in illuminating the evolutionary history of Nearctic treefrogs

Figure 1. Distribution of Hyla eximia group treefrogs (thick black lines). Black dots indicate localities sampled in this study (listed in Table S1). The Balsas Basin lineage represents an undescribed species within the group (Bryson et al., 2010; Klymus & Gerhardt, 2012).

opencc-zeroSep 2021View details →

Weak coupling among barrier loci and waves of neutral and adaptive introgression across an expanding hybrid zone

Hybridization can serve as an evolutionary stimulus, but we have little understanding of introgression at early stages of hybrid zone formation. We analyze reproductive isolation and introgression between a range-limited and a widespread species. Reproductive barriers are estimated based on differences in flowering time, ecogeographic distributions, and seed set from crosses. We find an asymmetrical mating barrier due to cytonuclear incompatibility that is consistent with observed clusters of coincident and concordant tension zone clines (barrier loci) for mtDNA haplotypes and nuclear SNPs. These groups of concordant clines are spread across the hybrid zone, resulting in weak coupling among barrier loci and extensive introgression. Neutral clines had nearly equal introgression into both species' ranges, while putative cases of adaptive introgression had exceptionally wide clines with centers shifted towards one species. Analyses of cline shape indicate that secondary contact was initiated within the last 800 generations with the per-generation dispersal between 200 and 400 meters, and provide some of the first estimates of the strength of selection required to account for observed levels of adaptive introgression. The weak species boundary between these species appears to be in early stages of dissolution, and ultimately will precipitate genetic swamping of the range-limited species.

opencc-zeroOct 2021View details →

Seeing through the hedge: Phylogenomics of Thuja (Cupressaceae) reveals prominent incomplete lineage sorting and ancient introgression for Tertiary relict flora

The eastern Asia (EA) – eastern North America (ENA) disjunction is a typical and well known biogeographic. Although its origin has been the topic of many studies, some new insights will arise when more complex evolutionary histories are revealed using phylogenomic methods. Here, we used targeted exon capture and sequenced >1,000 single copy nuclear, plus 73 chloroplast genes, to resolve interspecific relationships and the biogeographic history of an intercontinental disjunct genus Thuja. Two separate clades were detected: the "EA clade" comprised two species (<a name="_Hlk63130225">T. standishii</a> and <a name="_Hlk63130201">T. sutchuenensis</a>) from EA, and the "disjunct clade" comprising T. koraiensis, T. occidentalis, and T. plicata, with the first two comprising an EA–ENA disjunct pattern and T. plicata in western North America. The disjunct clade experienced a rapid radiation in the Mid–Miocene, and furthermore multispecies coalescent analysis revealed that ancient lineages of Thuja had large population sizes. These two factors might have contributed to the significant levels of incomplete lineage sorting (ILS) we detected within Thuja, and especially the disjunct clade. Because of this, EA–ENA disjunct pattern of T. koraiensis and T. occidentalis is exhibited by only 13.98% of genes examined. In addition, we found that ~20% of the T. sutchuenensis nuclear genome is derived from an as–yet–unrecognized ancestral lineage of Thuja, which might explain the close resemblance of cone morphology between T. sutchuenensis and the Paleocene fossil species T. ehrenswaerdii. Overall, our study demonstrates that single genes may produce incomplete or inaccurate phylogenies for disjunct taxa, and that more accurate results will come from using genomic data, revealing a more complex evolutionary history. This will steadily improve our understanding of their origin and evolution.

opencc-zeroNov 2022View details →

Integrative taxonomy of two thrush complexes (Aves: Turdidae) reveals introgression across sister species

The classification of some Turdus species, such as the Naumann's and dusky thrush complexes and the red-throated and black-throated thrush complexes, is controversial. Herein, we used molecular data and morphological characters to review the taxonomy of these thrush complexes and analyze the genetic differentiation between them. Herein, we examined the genetic characteristics of 13 microsatellite loci in all individuals and total of 129 alleles were detected. In parallel, we have a further judgment on their classification status by measuring 5 morphological features (tail length, wing length, toe length, claw length and instep length).

opencc-zeroFeb 2023View details →

Large-scale phylogenomics reveals ancient introgression in Asian Hepatica and new insights into the origin of the insular endemic Hepatica maxima

Hepatica maxima is native to Ulleungdo, which is one of the oceanic islands in Korea, and it likely originated via anagenetic speciation from the Korean mainland species H. asiatica. However, the relationships among the Asian lineages remain unresolved. Phylogenomics based on plant genomes can provide new insights into the evolutionary history of plants. We first generated plastid, mitochondrial and transcriptome sequences of the insular endemic species H. maxima. Using the genomic data for H. maxima, we obtained a phylogenomic dataset consisting of 76 plastid, 37 mitochondrial and 413 nuclear genes from Asian Hepatica and two outgroups. Coalescent- and concatenation-based methods revealed cytonuclear and organellar discordance in the lineage. The presence of gynodioecy with cytoplasmic male sterility in Asian Hepatica suggests that the discordance is correlated with potential disruption of linkage disequilibrium between the organellar genomes. Species network analyses revealed a deep history of hybridization and introgression in Asian Hepatica. We discovered that ancient and recent introgression events occurred throughout the evolutionary history of the insular endemic species H. maxima. The introgression may serve as an important source of genetic variation to facilitate adaptation to the Ulleungdo environment.

opencc-zeroMay 2023View details →

Biased gene introgression and adaptation in face of chloroplast capture in Aquilegia

Chloroplast capture, a phenomenon that can occur through interspecific hybridization and introgression, has been frequently suggested as an explanation for cytonuclear discordance in plants. In theory, the captured donor chloroplasts may not cooperate with the recipient nuclear genome, especially chloroplast-targeted nuclear genes. However, relatively few studies have documented the mechanisms of cytonuclear coevolution and its potential species differentiation and possible functional differences in the face of chloroplast capture. To explore this crucial question, we chose the Aquilegia genus, which is known for having minimal sterility among the species, and we inferred that A. amurensis captured the plastome of A. parviflora based on cytonuclear discordance and gene flow between these two species. We focused on the introgression region and its differentiation with closely related species, especially its composition in a chloroplast capture scenario. We found that nuclear genes encoding cytonuclear enzyme complexes or organelle localized (CECs) were significantly enriched in the introgression regions, indicating that the CEC genes of chloroplast donor species were selectively retained and displaced the original CEC genes in chloroplast receptor species due to cytonuclear interactions during introgression. Notably, the intrinsic factor of cytonuclear compatibility may have a higher degree of evolutionary distance for the introgressed CEC genes between A. amurensis and A. parviflora. Introgression from A. parviflora promotes the differentiation of A. amurensis and A. japonica. Furthermore, we found that one of the overrepresented gene ontology terms in these introgressed genes was terpene synthase activity (GO: 0010333) in which more than one-third of the genes were CEC genes, showing that A. amurensis had similar release patterns for terpenes in flowers of A. parviflora when compared with A. japonica. Altogether, this study helps to clarify the mechanisms of cytonuclear coevolution, species differentiation and functional differences in face of chloroplast capture and highlights a critical role of chloroplast capture in adaptation.

publicDec 2020View details →

Towards the introgression of PvPdh1 for increased resistance to pod shattering in common bean

Open the record for dataset details and reuse information.

publicJan 2016View details →

Data from: Genomic and functional approaches reveal a case of adaptive introgression from Populus balsamifera (balsam poplar) in P. trichocarpa (black cottonwood)

Open the record for dataset details and reuse information.