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128 results for “hybrid origin”
Phylogeography of lionfishes (Pterois) indicate taxonomic over splitting and hybrid origin of the invasive Pterois volitans
The evolutionary consequences of hybridization are poorly understood, especially in the marine realm where hybridization was once thought to be a rare occurrence. Previous research indicated that the lionfishes Pterois volitans and P. miles are sister species, both of which have been detected in the recent invasion of the Atlantic. Anecdotal data from the invasive range indicates they may hybridize, but previous studies have not examined the potential for these species to hybridize in the native range, or how such hybridization affects the distribution of genetic diversity. Here we address evolutionary divergence and population structure using mtDNA COI and two nuclear introns from 214 lionfish including four putative sister species (36 P. miles, 90 P. volitans, 32 P. lunulata, and 56 P. russelii) collected at 10 locations. Genetic data are supplemented with a re-examination of key morphological characters: dorsal, anal and pectoral fin ray counts. These data reveal two lineages (d = 0.041 in COI) among the four putative species: an Indian Ocean lineage, represented by P. miles and a Pacific Ocean lineage represented by P. lunulata and P. russelii. Lionfish identified as P. volitans appear to be hybrids between the sister linages of P. miles and P. lunulata/russelii, a conclusion supported by both the genetic data and morphology. The degree and geographic extent of introgression indicates widespread hybridization, or the absence of valid species distinctions between all four species. These findings also indicate that the lionfish invading tropical Atlantic Ocean, usually labeled P. volitans, is a hybrid.
Fig. 1 in Origine hybride de Arthropteris boutoniana (Hook.) Pic. Serm. (Arthropteridaceae) de l'île Maurice et de Madagascar
Fig. 1. – Distribution de Arthropteris monocarpa (Cordem.) C. Chr. (carrés), Arthropteris orientalis (J. F. Gmel.) Posth. var. orientalis (triangles) et Arthropteris ×boutoniana (Hook.) Pic. Serm. (étoiles) sur la carte bioclimatique de Madagascar (CORNET, 1974) et la carte de Maurice. Chaque point représente une station dans laquelle le taxon est présent 1 à x-fois.
Museum genomics reveals the hybrid origin of an extinct crater lake endemic
<p>Crater lake fishes are common evolutionary model systems, with recent studies suggesting a key role for gene flow in promoting rapid adaptation and speciation. However, the study of these young lakes can be complicated by human-mediated extinctions. Museum genomics approaches integrating genetic data from recently extinct species are therefore critical to understanding the complex evolutionary histories of these fragile systems. Here, we examine the evolutionary history of an extinct Southern Hemisphere crater lake endemic, the rainbowfish Melanotaenia eachamensis. We undertook comprehensive sampling of extant rainbowfish populations of the Atherton Tablelands of Australia alongside historical museum material to understand the evolutionary origins of the extinct crater lake population and the dynamics of gene flow across the ecoregion. The extinct crater lake species is genetically distinct from all other nearby populations due to historic introgression between two proximate riverine lineages, similar to other prominent crater lake speciation systems, but this historic gene flow has not been sufficient to induce a species flock. Our results suggest that museum genomics approaches can be successfully combined with extant sampling to unravel complex speciation dynamics involving recently extinct species.</p>
Reciprocal F1 hybrids of two inbred mouse strains reveal parent-of-origin and perinatal diet effects on behavior and expression
<p>Raw data and statistical analyses from an experiment to study parent-of-origin and diet-by-parent-of-origin effects on expression and behavior. </p> <p>In this experiment, female NOD/ShiLtJ x C57Bl/6J and C57Bl/6J x NOD/ShiLtJ mice were exposed in utero to one of four diets. After weaning, their whole-brain gene expression, as well as a set of behaviors that model psychiatric disease, were recorded and analyzed.</p> <p>File_S1_README contains detailed descriptions of all included files.</p>
Museum genomics reveals the hybrid origin of an extinct crater lake endemic
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Phylogeography of lionfishes (Pterois) indicate taxonomic over splitting and hybrid origin of the invasive Pterois volitans
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Natural hybrid origin of a controversial "species", Clematis pinnata (Ranunculaceae), based on multidisciplinary evidence
<p>Hybridization is common and has often been viewed as a driving force of plant diversity. However, it may raise problems in taxonomy, biodiversity estimation, and biological conservation. Although previous molecular phylogenetic studies suggested that hybridization may be rather common in <em>Clematis</em>, and artificial hybridization has been widely applied to produce new <em>Clematis</em> cultivars for nearly two centuries, the issue of natural hybridization of <em>Clematis</em> has never been addressed in detail. In this study, we tested the hybrid origin of <em>Clematis</em> <em>pinnata</em>, a rare and taxonomically controversial species distributed in northern China. Using field observations, morphological statistics, flow cytometry, niche modelling, and phylogenomic analysis, we tested the hypothesis of the possible hybrid origin of <em>C. pinnata</em>. The results show morphologically intermediacy of <em>C. pinnata</em> between the putative progenitors. Homoploidy among all the tested species is confirmed by flow cytometric analysis. Niche modelling results demonstrate that <em>C. pinnata</em> had not been adapted to a novel ecological niche independent of its putative parents. The plastome phylogeny indicates that <em>C. pinnata</em> plants in different sampling sites originated by different hybridization events. Phylonet and HyDe analyses based on transcriptome data corroborate the hybrid origins of<em> C. pinnata</em> from <em>C. brevicaudata</em>×<em>C. heracleifolia</em>/<em>C. tubulosa</em>. Rare introgression event between <em>C. brevicaudata</em> and <em>C. heracleifolia</em>/<em>C. tubulosa</em> was also detected in this study. These findings show that <em>C. pinnata</em> is representing F1 progeny or early generation hybrids of its parental species and evolved independently in different sites. The present study also indicates that interspecific or even intersectional hybridization is a common mechanism that the genus <em>Clematis</em> uses to generate diversity and variation, and it may play an important role in the evolution and diversification of this genus. Our study implies that morphological diversity caused by natural hybridization may overstate the real species diversity in <em>Clematis</em>.</p>
Assemblies and annotations from the paper "Interspecies hybridization as a route of accessory chromosome origin in fungal species infecting wild grasses"
<div> <p>This repository contains the whole genome assemblies, gene and TE annotations generated and analyzed in the manuscript entitled "Interspecies hybridization as a route of accessory chromosome origin in fungal species infecting wild grasses". </p> <p>Preprint available on BioRxiv:</p> <p>https://www.biorxiv.org/content/10.1101/2024.10.03.616481v1</p> <p> </p> </div>
Multiple origins of the desert shrub Reaumuria songarica in northern Xinjiang involving homoploid and tetraploid hybrids
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Data from: Evolutionary networks from RADseq loci point to hybrid origins of Medicago carstiensis and Medicago cretacea
Premise: Although hybridization has played an important role in the evolution of many plant species, phylogenetic reconstructions that include hybridizing lineages have been historically constrained by the available models and data. RADseq has been a popular sequencing technique for the reconstruction of hybridization in the Next Generation Sequencing era. However, the utility of RADseq for the reconstruction of complex evolutionary networks has not been thoroughly investigated. Conflicting phylogenetic relationships in the genus Medicago have been mainly attributed to hybridization but the specific hybrid origins of taxa have not been yet clarified. Methods: We obtained new molecular data from diploid species of Medicago section Medicago using single-digest RADseq to reconstruct evolutionary networks from gene trees, an approach that is computationally tractable with datasets that include several species and complex hybridization patterns. Results: Our analyses revealed that assembly filters to exclusively select a small set of loci with high phylogenetic information led to the most divergent network topologies. Conversely, alternative clustering thresholds or filters on the number of samples per locus had a lower impact on networks. A strong hybridization signal was detected for M. carstiensis and M. cretacea, while less clear signals were observed for M. rugosa, M. rhodopea, M. suffruticosa, M. marina, M. scutellata and M. sativa. Conclusions: Complex network reconstructions from RADseq gene trees were not robust under variations of the assembly parameters and filters. But when most divergent networks were discarded, all remaining analyses consistently supported a hybrid origin for M. carstiensis and M. cretacea.
Riverscape properties contribute to the origin and structure of a hybrid zone in a Neotropical freshwater fish
Understanding the structure of hybrid zones provides valuable insights about species boundaries and speciation, such as the evolution of barriers to gene flow and the strength of selection. In river networks, studying evolutionary processes in hybrid zones can be especially challenging, given the influence of past and current river properties along with biological species-specific traits. Here, we suggest that a natural hybrid zone between two divergent lineages of the sexually dimorphic Neotropical fish Nematocharax venustus was probably established by secondary contact as a result of a river capture event between the Contas and Pardo river basins. This putative river capture is supported by hydrogeological evidence of elbows of capture, wind gaps, and geological faults. The morphological (color pattern) and genetic (mtDNA and RADseq) variation reveal a clinal transition between parental lineages along the main river, with predominance of F2 hybrids at the centre of the hybrid zone, absence of early generation backcrosses, and different levels of hybridization in the tributaries. We highlight that different sources of information are crucial for understanding how the riverscape spatial history influences the connectivity between and within rivers systems and, consequently, the dynamics of gene flow between freshwater lineages/species.
Data from: The cryptic origins of evolutionary novelty: 1,000-fold-faster trophic diversification rates without increased ecological opportunity or hybrid swarm
Ecological opportunity is frequently proposed as the sole ingredient for adaptive radiation into novel niches. An additional trigger may be genome-wide hybridization resulting from 'hybrid swarm'. However, these hypotheses have been difficult to test due to the rarity of comparable control environments lacking adaptive radiations. Here I exploit such a pattern in microendemic radiations of Caribbean pupfishes. I show that a sympatric three-species radiation on San Salvador Island, Bahamas diversified 1,445 times faster than neighboring islands in jaw length due to evolution of a novel scale-eating adaptive zone from a generalist ancestral niche. I then sampled 22 generalist populations on seven neighboring islands and measured morphological diversity, stomach content diversity, dietary isotopic diversity, genetic diversity, lake/island areas, macroalgae richness, and Caribbean-wide patterns of gene flow. None of these standard metrics of ecological opportunity or gene flow were associated with adaptive radiation, except for slight increases in macroalgae richness. Thus, exceptional trophic diversification is highly localized despite myriad generalist populations in comparable environmental and genetic backgrounds. This study provides a strong counterexample to the ecological/hybrid-swarm theories of adaptive radiation and suggests that diversification of novel specialists on a sparse fitness landscape is constrained by more than ecological opportunity and gene flow.
Data from: Ancient hybrid origin of the eastern wolf not yet off the table: a comment on Rutledge et al.
A recent study of North American canids by Rutledge et al. (Biol. Lett. 11, 20150303 (doi:10.1098/rsbl.2015.0303)) refutes the hypothesized hybrid origin of the eastern wolf (EW) based on genomic evidence against very recent hybridization. However, the analyses do not rule out the possibility of more ancient hybridization. Claims to have resolved the evolutionary origin of the EW are therefore inappropriate. Importantly, though, we plead that uncertainty about the ancient history of the taxon should not affect current conservation policy.
Data from: Non-random patterns of genetic admixture expose the complex historical hybrid origin of unisexual leaf beetle species in the genus Calligrapha
Many unisexual animal lineages supposedly arose from hybridization. However, support for their putative hybrid origins mostly comes from indirect methodologies, which are rarely confirmatory. Here we provide compelling data indicating that tetraploid unisexual Calligrapha are true genetic mosaics obtained via analysis of mitochondrial DNA (mtDNA) and allelic variation and coalescence times for three single-copy nuclear genes (CPS, HARS, and Wg) in five of six unisexual Calligrapha and a representative sample of bisexual species. Nuclear allelic diversity in unisexuals consistently segregates in the gene pools of at least two but up to three divergent bisexual species, interpreted as putative parentals of interspecific hybridization crosses. Interestingly, their mtDNA diversity derives from an additional yet undiscovered older evolutionary lineage that is possibly the same for all independently originated unisexual species. One possibly extinct species transferred its mtDNA to several evolutionary lineages in a wave of hybridization events during the Pliocene, whereby descendant species retained a polymorphic mtDNA constitution. Recent hybridizations, in the Pleistocene and always involving females with the old introgressed mtDNA, seemingly occurred in the lineages leading to unisexual species, decoupling mtDNA introgression (and inferences derived from these data, such as timing and parentage) from subsequent acquisition of the new reproductive mode. These results illuminate an unexpected complexity in possible routes to animal unisexuality, with implications for the interpretation of ancient unisexuality. If the origin of unisexuality requires a mechanism where (1) hybridization is a necessary but insufficient condition and (2) multiple bouts of hybridization involving more than two divergent lineages are required, then the origins of several classical unisexual systems may have to be reassessed.
Data from: Integrating phylogeography and paleoecology to investigate the origin and dynamics of hybrid zones: insights from two widespread North American firs
Secondary contact between closely related taxa routinely occurs during postglacial migrations. After initial contact, the location of hybrid zones may shift geographically or remain spatially stable over time in response to various selective pressures or neutral processes. Studying the extent and direction of introgression using markers having contrasted levels of gene flow can help unravel the historical dynamics of hybrid zones. Thanks to their contrasted maternal and paternal inheritance, resulting in different levels of gene flow for mitochondrial and chloroplast DNA (mtDNA and cpDNA), the Pinaceae stand out as a relevant biological model for this purpose. The objective of the study was to assess whether the hybrid zone between Abies balsamea and Abies lasiocarpa (two largely distributed Pinaceae) has moved or remained stable over time by analysing the distribution of cytoplasmic DNA variation as well as published palaeobotanical data. Interspecific gene flow was higher for cpDNA than mtDNA markers; hence, the geographic distribution of mitotypes was more congruent with species distributions than chlorotypes. This genetic signature was contrary to expectations under a moving hybrid zone scenario, as well as empirical observations in other conifers. Genetic evidence for this rare instance of stable hybrid zone was corroborated by the colonization chronology derived from published fossil data, indicating that the two fir species initially came into contact in the area corresponding to the current sympatric zone 11 kyr ago. While an explanatory analysis suggested the putative influence of various environmental factors on the relative abundance of cytoplasmic genome combinations, further research appears necessary to assess the role of both demographic history and selective factors in driving the dynamics of hybrid zones.
Data from: Integrative taxonomy refutes a species hypothesis: the asymmetric hybrid origin of Arsapnia arapahoe (Plecoptera, Capniidae)
Molecular tools are commonly directed at refining taxonomies and the species that constitute their fundamental units. This has been especially insightful for groups for which species hypotheses are ambiguous and have largely been based on morphological differences between certain life stages or sexes, and has added importance when taxa are a focus of conservation efforts. Here we examine the taxonomic status of Arsapnia arapahoe, a winter stonefly in the family Capniidae that is a species of conservation concern because of its limited abundance and restricted range in northern Colorado, USA. Phylogenetic analyses of sequences of mitochondrial and nuclear genes of this and other capniid stoneflies from this region and elsewhere in western North America indicated extensive haplotype sharing, limited genetic differences, and a lack of reciprocal monophyly between A. arapahoe and the sympatric A. decepta, despite distinctive and consistent morphological differences in the sexual apparatus of males of both species. Analyses of autosomal and sex-linked single nucleotide polymorphisms detected using genotyping by sequencing, however, indicated that all individuals of A. arapahoe consisted of F1 hybrids between female A. decepta and males of another sympatric stonefly, Capnia gracilaria. Rather than constitute a self-sustaining evolutionary lineage, A. arapahoe appears to represent the product of nonintrogressive hybridization in the limited area of syntopy between two widely distributed taxa. This offers a cautionary tale for taxonomists and conservation biologists working on the less-studied components of the global fauna.
Data from: A phylogeographic investigation of the hybrid origin of a species of swordtail fish from Mexico
Hybrid speciation may contribute significantly to generating biodiversity, but only a few well-documented examples for it exist so far that do not involve polyploidization as a mechanism. The swordtail fish, Xiphophorus clemenciae, shows common hall-marks of a hybrid origin and still overlaps in its current geographic distribution with its putative ancestral species (X. helleri and X. maculatus). Xiphophorus clemenciae provides an ideal system for investigating the possible continued genetic interactions between a hybrid and its parental species. Here we use microsatellite and mitochondrial markers to investigate the population structure of these species of swordtails and search for signs of recent hybridization. Individuals were sampled from 21 localities across the known range of X. clemenciae – the Isthmus of Tehuantepec (IT) Mexico, and several environmental parameters that might represent barriers to dispersal were recorded. The hybridization event that gave rise to X. clemenciae appears to be rather ancient and a single origin is likely. We find negligible evidence for ongoing hybridization and introgression between the putative ancestral species, since they now occupy distinct ecological niches, and a common haplotype is shared by most populations of X. clemenciae. The population structure within these species shows an isolation-by-distance (IBD) pattern and genetic differentiation between most populations is significant and high. We infer that tectonic evolution in the Isthmus has greatly restricted gene flow between the southern and central IT populations of X. clemenciae and X. helleri and provide preliminary information to aid in conservation management of this geographically restricted hybrid species, X. clemenciae.
Data from: Hybrid origin of Audubon's warbler
Several animal species have recently been shown to have hybrid origins, but no avian examples have been documented with molecular evidence. We investigate whether the Audubon's warbler, one of four visually distinct species in the yellow-rumped warbler (Dendroica coronata) complex, may have originated through hybridization between two other species in this group, the myrtle warbler and black-fronted warbler. Analysis of nuclear AFLP and sequence markers shows that Audubon's warblers are genetically intermediate, and carry a mixture of alleles otherwise found only in one or the other of their putative parental species. Audubon's warblers also carry two deeply divergent mitochondrial DNA lineages, each shared with only one putative parental form. Broad clines between Audubon's and black-fronted warblers in AFLP markers call into question the validity of these two forms as full species; nevertheless, our results suggest that the Audubon's warbler likely originated through hybridization between two long-diverged species. It is likely that more cases of avian species of hybrid origin will be revealed by surveys of variation in nuclear DNA and other traits.
Data from: Demographic modelling with whole-genome data reveals parallel origin of similar Pundamilia cichlid species after hybridization
Modes and mechanisms of speciation are best studied in young species pairs. In older taxa, it is increasingly difficult to distinguish what happened during speciation from what happened after speciation. Lake Victoria cichlids in the genus Pundamilia encompass a complex of young species and polymorphic populations. One Pundamilia species pair, P. pundamilia and P. nyererei, is particularly well suited to study speciation because sympatric population pairs occur with different levels of phenotypic differentiation and reproductive isolation at different rocky islands within the lake. Genetic distances between allopatric island populations of the same nominal species often exceed those between the sympatric species. It thus remained unresolved whether speciation into P. nyererei and P. pundamilia occurred once, followed by geographical range expansion and interspecific gene flow in local sympatry, or if the species pair arose repeatedly by parallel speciation. Here, we use genomic data and demographic modelling to test these alternative evolutionary scenarios. We demonstrate that gene flow plays a strong role in shaping the observed patterns of genetic similarity, including both gene flow between sympatric species and gene flow between allopatric populations, as well as recent and early gene flow. The best supported model for the origin of P. pundamilia and P. nyererei population pairs at two different islands is one where speciation happened twice, whereby the second speciation event follows shortly after introgression from an allopatric P. nyererei population that arose earlier. Our findings support the hypothesis that very similar species may arise repeatedly, potentially facilitated by introgressed genetic variation.
FIGURE 8 in Evidence of hybrid origin for Tachyphonus nattereri Pelzeln, 1870 (Aves: Thraupidae)
FIGURE 8. Range of Tachyphonus cristatus (circles) and T. luctuosus (triangles) in southwestern Brazil. Type locality of T. nattereri (Cáceres) is indicated by the white star. The place of collection of the purported female of T. nattereri (Salto do Jirau) is indicated by the black star. Limits of the ecoregions follow Olson et al. (2001). Occurrences of the taxa studied are based on the specimens examined, records in the Wikiaves Portal (www.wikiaves.com.br) and key references (Naumburg 1930; Willis 1976; Lopes et al. 2009).
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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.
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.
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.
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.
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.