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dryad36/100

Data from: Postzygotic barriers persist despite ongoing introgression in hybridizing Mimulus species

The evolution of postzygotic isolation is thought to be a key step in maintaining species boundaries upon secondary contact, yet the dynamics and persistence of hybrid incompatibilities in naturally hybridizing species are not well understood. Here, we explore these issues using genetic mapping in three independent populations of recombinant inbred lines between naturally hybridizing monkeyflowers Mimulus guttatus and M. nasutus from the sympatric Catherine Creek population. We discover that the three M. guttatus founders differ dramatically in admixture history, with nearly a quarter of one founder's genome introgressed from M. nasutus. Comparative genetic mapping in the three RIL populations reveals three new putative inversions, each one segregating among the M. guttatus founders, two due to admixture. We find strong, genome-wide transmission ratio distortion in all RILs, but patterns are highly variable among the three populations. At least some of this distortion appears to be explained by epistatic selection favoring parental genotypes, but tests of inter-chromosomal linkage disequilibrium also reveal multiple candidate Dobzhansky-Muller incompatibilities. We also map several genetic loci for hybrid pollen viability, including two interacting pairs that coincide with peaks of distortion. Remarkably, even with this limited sample of three M. guttatus lines, we discover abundant segregating variation for hybrid incompatibilities with M. nasutus, suggesting this population harbors diverse contributors to postzygotic isolation. Moreover, even with substantial admixture, hybrid incompatibilities between Mimulus species persist, suggesting postzygotic isolation might be a potent force in maintaining species barriers in this system.

opencc-zeroDec 2023View details →

dryad36/100

Detection of ghost introgression requires exploiting topological and branch length information

In recent years, the study of hybridization and introgression has made significant progress, with ghost introgression—the transfer of genetic material from extinct or unsampled lineages to extant species—emerging as a key area for research. Accurately identifying ghost introgression, however, presents a challenge. To address this issue, we focused on simple cases involving three species with a known phylogenetic tree. Using mathematical analyses and simulations, we evaluated the performance of popular phylogenetic methods, including HyDe and PhyloNet/MPL, and the full-likelihood method, Bayesian Phylogenetics and Phylogeography (BPP), in detecting ghost introgression. Our findings suggest that heuristic approaches relying on site-pattern counts or gene-tree topologies struggle to differentiate ghost introgression from introgression between sampled non-sister species, frequently leading to incorrect identification of donor and recipient species. The full-likelihood method BPP using multilocus sequence alignments directly—hence taking into account both gene-tree topologies and branch lengths, by contrast, is capable of detecting ghost introgression in phylogenomic datasets. We analyzed a real-world phylogenomic dataset of 14 species of Jaltomata (Solanaceae) to showcase the potential of full-likelihood methods for accurate inference of introgression.

opencc-zeroJan 2024View details →

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Data from: Introgression of non-native mitochondrial haplotypes from farmed to wild Atlantic salmon

Farmed salmon escape and interbreed with wild Atlantic salmon on a large scale. We studied introgression of mitochondrial haplotypes from farmed Atlantic salmon originating from the Eastern Atlantic phylogenetic group to wild salmon of the Barents-White Sea phylogenetic group. We find that farmed genetic introgression introduced novel, non-native haplotypes into the Barents-White Sea phylogenetic group. The mitochondrial genome has important functional effects and is inherited as a haploid from the mother. Hence, the observed introgression across natural genetic barriers is expected to cause long-lasting functional maladaptation of the hybrids in the maternal line. As the use of farmed Atlantic salmon from non-native phylogenetic groups is widespread in aquaculture, the impact on wild Atlantic salmon may be more severe than previously recognized. Our results highlight the ecological risks of releasing non-native wild and domesticated animals.

opencc-zeroMar 2024View details →

zenodo36/100

Table 2 in Altai Mountains - cradle of hybrids and introgressants: A case study in Veronica subg. Pseudolysimachium (Plantaginaceae)

Table 2. Details of AMOVA in each group with different combination without including the putative hybrid.<table><tbody><tr><th></th><th>Source of variation</th><th>Variance components</th><th>Percentage of variation</th><th>Fixation index</th></tr></tbody><tbody><tr><th>Global AMOVA based on K = 5 results of STRUCTURE including all the putative pure 174 individuals</th><td>Among Species</td><td>14</td><td>16</td><td></td></tr><tr><td>Within Species</td><td>74</td><td>84</td><td></td></tr><tr><td>TOTAL</td><td>88</td><td>100</td><td>F ST: 0.16*</td></tr><tr><th>Hierarchical AMOVA based on K = 5 results of STRUCTURE including all the putative pure 174 individuals</th><td>Among Groups</td><td>7.2</td><td>8.13</td><td>F CT: 0.08*</td></tr><tr><td>Among Species</td><td>7.1</td><td>8.01</td><td>F SC: 0.09*</td></tr><tr><td>Within Species</td><td>74.3</td><td>83.86</td><td>F ST: 0.16*</td></tr><tr><td>TOTAL</td><td>88.6</td><td>100</td><td></td></tr></tbody></table>F ST, correlation within populations relative to total; F CT, correlation within groups relative to total; F SC, correlation within populations relative to groups.* P <0.001, 10,000 permutations.

opencc-by-4.0Apr 2024View details →

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Table 1 in Altai Mountains - cradle of hybrids and introgressants: A case study in Veronica subg. Pseudolysimachium (Plantaginaceae)

Table 1. Details of sampled morphotypes and their geographical distribution.<table><tbody><tr><th>Serial no.</th><th>Species</th><th>Distribution</th><th>Latitude</th><th>Longitude</th><th>Number of individuals</th></tr></tbody><tbody><tr><th>1</th><td>V. ×altaica</td><td>Russia</td><td>50.9158</td><td>82.3274</td><td>12</td></tr><tr><th>2</th><td>V. ×grisea</td><td>Russia</td><td>50.6399</td><td>86.3131</td><td>9</td></tr><tr><th>3</th><td>V. ×kolyvanensis</td><td>Russia</td><td>51.7684</td><td>82.1381</td><td>6</td></tr><tr><th>4</th><td>V. ×sapozhnikovii</td><td>Mongolia</td><td></td><td></td><td>1</td></tr><tr><th>5</th><td>V. ×schmakovii</td><td>Russia</td><td>50.1567</td><td>88.2953</td><td>11</td></tr><tr><th>6</th><td>V. ×sessiliflora</td><td>Russia</td><td>50.3437</td><td>87.4315</td><td>13</td></tr><tr><th>7</th><td>V. ×smirnovii</td><td>Mongolia</td><td>46.3533</td><td>91.2095</td><td>6</td></tr><tr><th>8</th><td>V. arenosa</td><td>Mongolia</td><td></td><td></td><td>3</td></tr><tr><th>9a</th><td>V. incana</td><td>Russia</td><td>50.6461</td><td>86.3144</td><td>10</td></tr><tr><th>9b</th><td>V. incana</td><td>Russia</td><td>51.3924</td><td>82.2084</td><td>24</td></tr><tr><th>10</th><td>V. longifolia</td><td>Russia</td><td>53.3346</td><td>84.2004</td><td>27</td></tr><tr><th>11</th><td>V. pinnata</td><td>Russia</td><td>50.3501</td><td>87.4125</td><td>22</td></tr><tr><th>12</th><td>V. porphyriana</td><td>Russia</td><td>51.0431</td><td>85.6399</td><td>36</td></tr><tr><th>13</th><td>V. reverdattoi</td><td>Russia</td><td>50.4940</td><td>91.3311</td><td>1</td></tr><tr><th>14</th><td>V. sajanensis</td><td>Russia</td><td>56.1262</td><td>92.9057</td><td>2</td></tr><tr><th>15</th><td>V. spicata</td><td>Russia</td><td>50.3605</td><td>82.2448</td><td>37</td></tr><tr><th>16</th><td>V. spuria</td><td>Russia</td><td>51.7684</td><td>82.1381</td><td>7</td></tr><tr><th>17</th><td>V. taigischensis</td><td>Russia</td><td>53.0584</td><td>93.3399</td><td>3</td></tr><tr><th>TOTAL</th><td>17 morphotypes (10 taxonomically described pure forms; 7 taxonomically described putative hybrids forms; 3 individuals were not identified, they are listed in suppl. Table S1)</td></tr></tbody></table>

opencc-by-4.0Apr 2024View details →

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Selection against individuals from genetic introgression of escaped farmed salmon in a natural population of Atlantic salmon

The viability of wild Atlantic salmon populations is threatened by genetic introgression from escaped farmed salmon. Farmed Atlantic salmon are genetically improved for important commercial traits and a life in captivity but are poorly adapted to the natural environment. The rate of geneflow from escaped farmed to wild salmon depends on their spawning success and on offspring survival at various life-stages. We here investigate relative survival of introgressed juvenile Atlantic salmon (parr) in a river in northern Norway. The studied population has experienced genetic introgression from farmed salmon for about four generations (20 years). We followed two cohorts of parr from the year of hatching (0+) to the age of two years (2+). Farmed genetic introgression was quantified at the individual level and on a continuous scale using diagnostic SNPs. Population-level genetic introgression decreased from 0+ to 2+ by 64% (2011 cohort) and 37% (2013 cohort) . This change was driven by a 70% (2011 cohort) and 49% (2013 cohort) lower survival from age 0+ to 2+ in introgressed parr compared to parr of wild origin. Our observations show that there is natural selection against genetic introgression with a potential cost of lower productivity.The viability of wild Atlantic salmon populations is threatened by genetic introgression from escaped farmed salmon. Farmed Atlantic salmon are genetically improved for important commercial traits and a life in captivity but are poorly adapted to the natural environment. The rate of geneflow from escaped farmed to wild salmon depends on their spawning success and on offspring survival at various life-stages. We here investigate relative survival of introgressed juvenile Atlantic salmon (parr) in a river in northern Norway. The studied population has experienced genetic introgression from farmed salmon for about four generations (20 years). We followed two cohorts of parr from the year of hatching (0+) to the age of two years (2+). Farmed genetic introgression was quantified at the individual level and on a continuous scale using diagnostic SNPs. Population-level genetic introgression decreased from 0+ to 2+ by 64% (2011 cohort) and 37% (2013 cohort) . This change was driven by a 70% (2011 cohort) and 49% (2013 cohort) lower survival from age 0+ to 2+ in introgressed parr compared to parr of wild origin. Our observations show that there is natural selection against genetic introgression with a potential cost of lower productivity.

opencc-zeroOct 2021View details →

dryad36/100

Plastid introgression and evolution of African miombo woodlands: new insights from the plastome-based phylogeny of Brachystegia trees

Aim: Miombo woodlands form a characteristic vegetation type covering 2.7 million km2 in southern and eastern Africa. Despite their wide geographical extent, their origin, floristic and spatial evolution through time remain understudied. To fill this gap, we studied the evolution of Brachystegia trees, one of the most representative genera of these woodlands (20 species), also represented in Guineo-Congolian rain forests (8 species). Location: Tropical Africa, Guineo-Congolian forests and Zambezian savannahs. Methods: We used a genome skimming approach to sequence the plastomes of 45 Brachystegia samples, covering 25 of the 29 existing species, and one outgroup (Julbernardia paniculata). The phylogeny of the plastomes was reconstructed and time-calibrated. We tested if the genetic divergence between lineages reflected taxonomic and/or geographic distances using Mantel tests. Finally, we inferred the evolutionary history of Brachystegia based on the age and spatial distribution of its lineages. Results: Surprisingly, species represented by multiple specimens appear rarely monophyletic while plastid clades display strong geographical structuring, independently of the species. Two main clades separate woodland and rain forest species, which diverged during the late Miocene-Pliocene (95% HPD = 2.78-8.59 Ma). In miombo woodlands, three subclades occur in parapatry along an East-West axis, ranging from Angola to East Africa. Their divergence started from the Plio-Pleistocene (95% HPD = 1.17-3.69 Ma). Divergence dates (TMRCA) within miombo subclades decrease from East Africa (1.53 Ma) to Angola (0.76 Ma). Main Conclusions: Brachystegia plastomes appear unreliable to identify species, probably due to species introgression leading to recurrent chloroplast captures. However, they prove very informative for tracking the past dynamics of the genus, and suggest a historical westwards expansion of miombo Brachystegia, and possibly of miombo vegetation, during the Plio-Pleistocene. Further investigations using nuclear DNA are needed to assess the species tree as well as speciation and hybridisation events between species.

opencc-zeroNov 2021View details →

zenodo36/100

Hybridization dynamics and extensive introgression in the Daphnia longispina species complex: new insights from a high-quality Daphnia galeata reference genome

Supplementary data for the Genome Biology and Evolution paper <a href="http://dx.doi.org/10.1093/gbe/evab267">10.1093/gbe/evab267</a>

opencc-by-4.0Jan 2021View details →

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Extensive introgression at late stages of species formation: Insights from grasshopper hybrid zones

The process of species formation is characterised by the accumulation of multiple reproductive barriers. The evolution of hybrid male sterility, or Haldane's rule, typically characterises later stages of species formation, when total reproductive isolation is strongest. Yet, understanding how quickly reproductive barriers evolve and their consequences for maintaining genetic boundaries between emerging species remains a challenging task because it requires studying taxa that hybridise in nature. Here, we address these questions using the meadow grasshopper Pseudochorthippus parallelus, where populations that show multiple reproductive barriers, including hybrid male sterility, hybridise in two natural hybrid zones. Using mitochondrial data, we infer that such populations have diverged some 100,000 years ago, at the beginning of the last glacial cycle in Europe. Nuclear data shows that contractions at multiple glacial refugia, and post-glacial expansions have facilitated genetic differentiation between lineages that today interact in hybrid zones. We find extensive introgression throughout the sampled species range, irrespective of current strength of reproductive isolation. Populations exhibiting hybrid male sterility in two hybrid zones show repeatable patterns of genomic differentiation, consistent with shared genomic constraints affecting ancestral divergence or with the role of those regions in reproductive isolation. Together, our results suggest that reproductive barriers that characterise late stages of species formation can evolve relatively quickly within species, particularly when associated with strong demographic changes. Moreover, we show that such barriers persist in the face of extensive gene flow, allowing future studies to identify associated genomic regions.

opencc-zeroDec 2021View details →

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Phylogenomic analyses highlight innovation and introgression in the continental radiations of Fagaceae across the Northern Hemisphere

Northern Hemisphere forests changed drastically in the early Eocene with the diversification of the oak family (Fagaceae). Cooling climates over the next 20 million years fostered the spread of temperate biomes that became increasingly dominated by oaks and their chestnut relatives. Here we investigate the timing and pattern of major macroevolutionary events and ancient genome-wide signatures of hybridization across Fagaceae. An unparalleled transformation of forest dynamics began with the rapid diversification of major lineages within 15 million years following the K-Pg extinction. Innovations related to seed and pollen dispersal are implicated in triggering waves of continental radiations, while fungal symbioses fortified a competitive edge underground. We detected introgression at multiple time scales, including ancient events predating the origination of genus-level diversity. As oak lineages moved into newly available temperate habitats in the early Miocene, secondary contact between previously isolated species occurred. This resulted in adaptive introgression, further amplifying global proliferation.

opencc-zeroFeb 2022View details →

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Introgressive hybridisation between domestic pigs (Sus scrofa domesticus) and endemic Corsican wild boars (S. s. meridionalis): effects of human-mediated interventions

Owing to the intensified domestication process with artificial trait selection, introgressive hybridisation between domestic and wild species poses a management problem. Traditional free-range livestock husbandry, as practiced in Corsica and Sardinia, is known to facilitate hybridisation between wild boars and domestic pigs (Sus scrofa). Here, we assessed the genetic distinctness and genome-wide domestic pig ancestry levels of the Corsican wild boar subspecies S. s. meridionalis, with reference to its Sardinian conspecifics, employing a genome-wide single nucleotide polymorphism (SNP) assay and mitochondrial control region (mtCR) haplotypes. We also assessed the reliance of morphological criteria and the melanocortin-1 receptor (MC1R) coat colour gene to identify individuals with domestic introgression. While Corsican wild boars showed closest affinity to Sardinian and Italian wild boars compared to other European populations based on principal component analysis, the observation of previously undescribed mtCR haplotypes and high levels of nuclear divergence (Weir's 0.14) highlighted the genetic distinctness of Corsican S. s. meridionalis. Across three complementary analyses of mixed ancestry (i.e., STRUCTURE, PCADMIX, and ELAI), proportions of domestic pig ancestry were estimated at 9.5% in Corsican wild boars, which was significantly higher than in wild boars in Sardinia, where free-range pig keeping was banned in 2012. Comparison of morphologically pure- and hybrid-looking Corsican wild boars suggested a weak correlation between morphological criteria and genome-wide domestic pig ancestry. The study highlighted the usefulness of molecular markers to assess the direct impacts of management practices on gene flow between domestic and wild species.

opencc-zeroFeb 2022View details →

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Archived data for: Balancing selection, genetic drift, and human mediated-introgression interplay to shape MHC (functional) diversity in Mediterranean brown trout

The extraordinary polymorphism of Major Histocompatibility Complex (MHC) genes is considered a paradigm of pathogen-mediated balancing selection, although empirical evidence is still scarce. Furthermore, the relative contribution of balancing selection to shape MHC population structure and diversity, compared to that of neutral forces, as well as its interaction with other evolutionary processes such as hybridization, remains largely unclear. To investigate these issues, we analysed adaptive (MHC-DAB gene) and neutral (11 microsatellite loci) variation in 156 brown trout (Salmo trutta complex) from six wild populations in central Italy exposed to introgression from domestic hatchery lineages (assessed with the LDH gene). MHC diversity and structuring correlated with those at microsatellites, indicating the substantial role of neutral forces. However, individuals carrying locally rare MHC alleles/supertypes (regardless of the zygosity status and degree of sequence dissimilarity of MHC) were in better body condition (a proxy of individual fitness/parasite load), hence supporting balancing selection under rare allele advantage, but not heterozygote advantage or divergent allele advantage. The association between specific MHC supertypes and body condition confirmed in part this finding. Across populations, MHC allelic richness increased with increasing admixture between native and domestic lineages, indicating introgression as a source of MHC variation. Furthermore, introgression across populations appeared more pronounced for MHC than microsatellites, possibly because initially-rare MHC variants are expected to introgress more readily under rare allele advantage. Providing evidence for the complex interplay among neutral evolutionary forces, balancing selection and human-mediated introgression in shaping the pattern of MHC (functional) variation, our findings contribute to a deeper understanding of the evolution of MHC genes in wild populations exposed to anthropogenic disturbance.

opencc-zeroMar 2022View details →

zenodo36/100

Selection strategies to introgress water deficit tolerance derived from Solanum galapagense accession LA1141 into cultivated tomato (datasets)

This dataset includes best linear unbiased predictors (BLUPs) used for composite interval mapping in the LA1141 × OH8245 BC2S3 families (tab - BC2S3_BLUP_data_for_CIM), greenhouse data corresponding to the BC2S5 advanced lines (tab - BC2S5_GH_trial), and field performance data corresponding to the BC2S5 advanced lines (tab - BC2S5_Field_Trial).

opencc-by-4.0Apr 2022View details →

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Data from: Species limits and introgression in Pimelodus from the Magdalena-Cauca River basin

Low morphological differentiation among taxa hampers its appropriate identification, basic biological studies, and promotion of any conservation effort. Aiming to clarify the evolution and speciation among members of Pimelodus from the Magdalena-Cauca River basin, this study tested the hypothesis that P. yuma, P. grosskopfii and P. crypticus represent three independently evolving species and explored signals of interspecific hybridization. Likewise, we test the ancient hypothesis that the trans-Andean Pimelodus yuma and P. crypticus belong to the cis-Andean P. blochii species complex. The outcomes based on mitochondrial (cox1) and nuclear [RADseq (Illumina Hi-Seq), microsatellites and rag2] markers combined with coalescence-based and allele-frequency methods, confirm that each studied trans-Andean species represent an independently evolving unit. We used Stacks v.2.52 for de novo SNP genotyping. Contrary to expectations, P. yuma was found as a sister clade of P. blochii, while P. crypticus (confused for a long time with P. blochii) was phylogenetic closer to P. grosskopfii. Additionally, we found strong evidence of historical introgression between the non-sibling species Pimelodus yuma and P. grosskopfii, breaking the absence of interbreeding and the independent evolutionary trajectory among Trans-Andean Pimelodus during their diversification history, a pre-requisite to define species limits. However, non-significant values of current gene flow were evidenced between them, supporting the hypothesis of full isolation.

opencc-zeroApr 2022View details →

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Ecological speciation by sympatric host shifts in a clade of herbivorous sea slugs, with introgression and localized mitochondrial capture between species

Host shifting in insect-plant systems was historically important to the development of ecological speciation theory, yet surprisingly few studies have examined whether host shifting drives the diversification of marine herbivores. When small-bodied consumers feed and also mate on a preferred host, disruptive selection can split a population into host races despite gene flow. Support for host shifts is notably lacking for invertebrates associated with macroalgae, where the scale of dispersal by planktonic larvae often far exceeds the grain of host patchiness, and adults are typically less specialized than terrestrial herbivores. Here, we present a candidate example of ecological speciation in a clade of sea slugs that primarily consume green algae in the genus Caulerpa, including highly invasive species. Ancestral character state reconstructions supported 'sea grapes' (C. racemosa, C. lentillifera) as the ancestral host for a tropical radiation of 12 Elysia spp., with one shift onto alternative Caulerpa spp. in the Indo-Pacific. A Caribbean radiation of three species included symaptric host shifts to Rhipocephalus brevicaulis in the ancestor of E. pratensis Ortea & Espinosa, 1996, and to C. prolifera in E. hamanni Krug, Vendetti & Valdes 2016, plus a niche expansion to a range of Caulerpa spp. in E. subornata Verrill, 1901. All three species are broadly sympatric across the Caribbean but are host-partitioned at a fine grain, and distinct by morphology and at nuclear loci. However, non-recombining mtDNA revealed a history of gene flow between E. pratensis and E. subornata: COI haplotypes from E. subornata were 10.4% divergent from E. pratensis haplotypes from four sites, but closely related to all E. pratensis haplotypes sampled from six Bahamian islands, indicating historical introgression and localized "mitochondrial capture." Disruptive selective likely fueled divergence and adaptation to distinct host environments, indicating ecological speciation may be an under-appreciated driver of diversification for marine herbivores as well as epibionts and other resource specialists.

opencc-zeroJun 2022View details →

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Benefit of introgression depends on genetic variation in cereal breeding programs

We investigated the benefit from introgression of external lines into a cereal breeding program and strategies that accelerated introgression of the favourable alleles while minimising linkage drag using stochastic computer simulation. We simulated genomic selection for disease resistance and grain yield in two environments with a high level of genotype-by-environment (G×E) for the latter trait, using genomic data of a historical barley breeding program as the base generation. Two populations (existing and external) were created from this base population with different allele frequencies for few (N=10) major and many (N~990) minor simulated disease quantitative trait loci (QTL). The major disease QTL only existed in the external population and lines from the external population were introgressed into the existing population which had minor disease QTL with low, medium, and high allele frequencies. The study revealed that the benefit of introgression depended on the level of genetic variation for the target trait in the existing cereal breeding program. Introgression of external resources into the existing population was beneficial only when the existing population lacked variation in disease resistance or when minor disease QTL were already at medium or high frequency. When minor disease QTL were at low frequencies, no extra genetic gain was achieved from introgression. More benefit in the disease trait was obtained from the introgression if the major disease QTL had larger effect sizes, more selection emphasis was applied on disease resistance, or more external lines were introgressed. While our strategies to increase introgression of major disease QTL were generally successful, most were not able to completely avoid negative impacts on selection for grain yield with the only exception being when major introgression QTL effects were very large. Breeding programs are advised to carefully consider the level of genetic variation in a trait available in their breeding program before deciding to introgress germplasms.

opencc-zeroJun 2022View details →

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Supplementary material for: Impact of ghost introgression on coalescent-based species tree inference and estimation of divergence time

The species studied in any evolutionary investigation generally constitute a small proportion of all the species currently existing or that have gone extinct. It is therefore likely that introgression, which is widespread across the tree of life, involves "ghosts," i.e., unsampled, unknown, or extinct lineages. However, the impact of ghost introgression on estimations of species trees has rarely been studied and is poorly understood. Here, we use mathematical analysis and simulations to examine the robustness of species tree methods based on the multispecies coalescent model to introgression from a ghost or extant lineage. We found that many results originally obtained for introgression between extant species can easily be extended to ghost introgression, such as the strongly interactive effects of incomplete lineage sorting (ILS) and introgression on the occurrence of anomalous gene trees (AGTs). The relative performance of the summary species tree method (ASTRAL) and the full-likelihood method (*BEAST) varies under different introgression scenarios, with the former being more robust to gene flow between non-sister species whereas the latter performing better under certain conditions of ghost introgression. When an outgroup ghost (defined as a lineage that diverged before the most basal species under investigation) acts as the donor of the introgressed genes, the time of root divergence among the investigated species generally was overestimated, whereas ingroup introgression, as commonly perceived, can only lead to underestimation. In many cases of ingroup introgression that may or may not involve ghost lineages, the stronger the ILS, the higher the accuracy achieved in estimating the time of root divergence, although the topology of the species tree is more prone to be biased by the effect of introgression.

opencc-zeroJun 2022View details →

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Data from: Pervasive introgression during rapid diversification of the European mountain genus Soldanella (L.) (Primulaceae)

Hybridization is a key mechanism involved in lineage diversification and speciation, especially in ecosystems that experienced repeated environmental oscillations. Recently radiated plant groups, which have evolved in mountain ecosystems impacted by historical climate change provide an excellent model system for studying the impact of gene flow on speciation. We combined organellar (whole plastome) and nuclear genomic data (RAD-seq) with a cytogenetic approach (rDNA FISH) to investigate the effects of hybridization and introgression on evolution and speciation in the genus Soldanella (snowbells, Primulaceae). Pervasive introgression has already occurred among ancestral lineages of snowbells and has persisted throughout the entire evolutionary history of the genus, regardless of the ecology, cytotype, or distribution range size of the affected species. The highest extent of introgression has been detected in the Carpathian species, which is also reflected in their extensive karyotype variation. Introgression occurred even between species with dysploid and euploid cytotypes, which were considered to be reproductively isolated. The magnitude of introgression detected in snowbells is unprecedented in other mountain genera of the European Alpine System investigated hitherto. Our study stresses the prominent evolutionary role of hybridization in facilitating speciation and diversification on the one hand, but also enriching previously isolated genetic pools.

opencc-zeroAug 2022View details →

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Introgressive hybridization erodes morphological divergence between lentic and lotic habitats in an endangered minnow

Introgressive hybridization may erode phenotypic divergence along environmental gradients, collapsing locally adapted populations into a hybrid swarm. Alternatively, introgression may promote phenotypic divergence by providing variation on which natural selection can act. In freshwater fishes, water flow often selects for divergent morphological traits in lake versus stream habitats. We tested the effects of introgression on lake-stream morphological divergence in the minnow Owens Tui Chub (Siphateles bicolor snyderi), which has been rendered endangered by introgression from the introduced Lahontan Tui Chub (Siphateles bicolor obesa). Using geometric morphometric analysis of 457 individual Tui Chub from thirteen populations, we found that both the native and introgressing parent taxa exhibited divergent body and caudal fin shapes in lake vs. stream habitats, but their trajectories of divergence were distinct. In contrast, introgressed populations exhibited intermediate body and caudal fin shapes that were not differentiated by habitat type, indicating that introgression has eroded phenotypic divergence along the lentic-lotic gradient throughout the historic range of the Owens Tui Chub. Individuals within hybrid populations were less morphologically variable than those within parent populations, suggesting hybrid adaptation to selective agents other than water flow or loss of variance by drift.

opencc-zeroAug 2022View details →

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Linked selection, differential introgression and recombination rate variation promote heterogeneous divergence in a pair of yellow croakers

Understanding the mechanisms underlying heterogeneous genomic divergence is of particular interest in evolutionary biology. Highly differentiated genomic regions, known as genomic islands, often evolve between diverging lineages. These genomic islands may be related to selection promoting adaptation or reproductive isolation. Based on whole genome assembly and genome-wide RAD sequencing in a pair of yellow croakers (genus: Larimichthys), we investigated the evolutionary processes shaping genomic landscapes of divergence. Demographic modelling indicated that the two species diverged following a secondary contact scenario, where differential introgression and linked selection were suggested to be involved in heterogeneous genomic divergence. We identified reduced recombination rate in genomic islands and a relatively good conservation of both genetic diversity and recombination landscapes between species, which highlight the roles of linked selection and recombination rate variation in promoting heterogeneous divergence in the common ancestral lineage of the two species. In addition, we found a positive correlation between differentiation (FST) and absolute sequence divergence (Dxy), and elevated Dxy in genomic islands, which were different from the patterns under linked selection. Restricted gene flow in highly differentiated regions has likely remodeled the landscape of heterogeneous genomic divergence. Moreover, genomic islands showed little evidence of overlapping within and between species, implying that high gene flow and divergent selection when colonizing new habitats have reshaped the patterns of intraspecific divergence. This study highlights that highly differentiated genomic regions can also be from linked selection and variation of recombination rate, and thus are not necessarily related to speciation islands or local adaptation.

opencc-zeroSep 2022View details →

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Allen Brain Atlas

Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.

allen-brain-atlas

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Last verified 2026-04-30Open record

Annotated Behaviour and Observability Dataset (ABODe)

ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.

abode-home-cage

behavioral-neuroscienceopenThe DataShare record exposes download links for annotations, documentation, license text, and the zipped per-snippet data directory.

Last verified 2026-04-30Open record

DANDI Archive for NWB datasets

DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.

dandi-nwb

electrophysiologyopenPublished Dandiset metadata and archive endpoints are available through the production DANDI API.

Last verified 2026-04-30Open record

International Brain Laboratory public data

The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.

ibl

behavioral-neuroscienceopenPublic sessions can be searched and loaded from the IBL public data server through ONE.

Last verified 2026-04-29Open record

OpenNeuro

OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.

openneuro

neuroscienceopenPublished datasets are available on demand over the internet.

Last verified 2026-04-29Open record