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410 results for “hybrid species”
Development of a panel of SNP loci in the emblematic southern damselfly (Coenagrion mercuriale) using a hybrid method: Pitfalls and recommendations for large-scale SNP genotyping in a non-model endangered species
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Genetic confirmation of a hybrid between two highly divergent cardinalid species: A Rose-breasted Grosbeak (Pheucticus ludovicianus) and a Scarlet Tanager (Piranga olivacea)
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Data from: Are you more than the sum of your parents’ genes? phenotypic plasticity in a clonal vertebrate and F1 hybrids of its parental species
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Data from: Preserving wild pears: Using genomic data to assess species boundaries, interspecific hybridization, and genetic diversity to inform conservation
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Assessing potential hybridization between a hypothetical gene drive-modified Drosophila suzukii and non-target Drosophila species
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Historical climate change dynamics facilitated speciation and hybridization between highland and lowland species of Baripus ground beetles from Patagonia
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Newly discovered cichlid fish biodiversity threatened by hybridization with non-native species - Data supporting published version
<p><span><a name="_Hlk503794553"><span>Invasive freshwater fish systems are known to readily hybridize with indigenous congeneric species, driving loss of unique and irreplaceable genetic resources. Here we reveal that newly discovered (2013-2016) evolutionarily significant populations of Korogwe tilapia (<i>Oreochromis korogwe</i>) from southern Tanzania are threatened by hybridization with the larger invasive Nile tilapia (<i>Oreochromis niloticus</i>). We use a combination of morphology, microsatellite allele frequencies and whole genome sequences to show that <i>O. korogwe</i> from southern lakes (Nambawala, Rutamba and Mitupa) are distinct from geographically-disjunct populations in northern Tanzania (Zigi River and Mlingano Dam). We also provide genetic evidence of <i>O. korogwe</i> x <i>niloticus</i> hybrids in three southern lakes and </span></a><span>demonstrate heterogeneity in the extent of admixture across the genome. Finally, using the least admixed genomic regions we estimate that the northern and southern <i>O. korogwe</i> populations most plausibly diverged approximately 140,000 years ago, suggesting that the geographical separation of the northern and southern groups is not a result of a recent translocation, and instead these populations represent independent evolutionarily significant units. We conclude that these newly-discovered and phenotypically unique </span><span>cichlid populations are already threatened by hybridization with an invasive species, and propose that these irreplaceable genetic resources would benefit from conservation interventions.</span></span></p>
How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels
<p>The <em>Mytilus</em> complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study "replicated" instances of secondary contact between closely-related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry-informative panel of such SNPs. We then compared their frequencies in newly-sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi-stable variants (Dobzhansky-Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact.</p>
Figure 5 in Hybridization patterns in two contact zones of grass snakes reveal a new Central European snake species
Figure 5. Cline analyses of mitochondrial DNA and microsatellite data. Transects (top) through the two different contact zones of grass snake lineages (helvetica/eastern lineages – left; yellow/red lineages – right) and associated Maximum Likelihood clines for microsatellites (centre) and mtDNA (bottom). Grey: fuzzy 95% credible cline region. Red points (top) indicate cline centres. Maps were created using ARCGIS 10.2 (http://www. esri.com/arcgis) and ADOBE ILLUSTRATOR CS6 (http://www.adobe.com/products/illustrator.html).
Figure 4. PCA axes 1–2 in Hybridization patterns in two contact zones of grass snakes reveal a new Central European snake species
Figure 4. PCA axes 1–2 for microsatellite data. Samples are coloured according to mitochondrial lineages (top) or STRUCTURE clusters (bottom). Admixed individuals were identified according to HYBRIDLAB results. PCAs for the yellow and red lineages correspond to the samples from Fig. 3c. Non-native samples were excluded. The oval outlines represent 95% confidential intervals. For helvetica and the eastern lineages (left) the x axis explains 16.6% and the y axis 4.5% of variation. For the eastern lineages (right) the x axis explains 3.8% and the y axis 2.9% of variation. Analyses along axes 1–3 produced nearly identical results (see Supplementary Fig. S4).
Figure 3 in Hybridization patterns in two contact zones of grass snakes reveal a new Central European snake species
Figure 3. Genotypic structuring of grass snakes. On the left, the mitochondrial lineage of each sample is shown above the STRUCTURE diagrams, with haplotypes of Natrix natrix helvetica indicated in blue and haplotypes of the eastern lineages in colours corresponding to Fig. 1 (yellow, red, lilac, grey, green; white = missing data). In (a), orange and dark blue corresponds to non-native snakes (Italian lineages). Samples in STRUCTURE diagrams are arranged within each country from west to east (a) or from north to south (b,c). In STRUCTURE diagrams, an individual sample is represented by a vertical bar reflecting its inferred ancestry. In (a), the blue cluster corresponds to N. n. helvetica and the light green cluster to all other lineages. The isolated red/light green block (first row) represents the allochthonous population from the Neander valley, Germany. In (b), samples with genetic impact of helvetica are excluded. The pink cluster corresponds to samples from the yellow and red lineages. Brown percentages indicate genetic impact of adjacent lineages (lilac, grey, green). In (c) only samples from the yellow and red lineages and their hybrids, without genetic signatures of other lineages, were processed. Country abbreviations: Ba – Balkans (Albania, Bosnia and Herzegovina, Montenegro, Serbia, Kosovo, Former Yugoslav Republic of Macedonia, Romania, Bulgaria, and Greece), CH – Switzerland, CRO – Croatia, CZ – Czech Republic, FI – Finland, H – Hungary, N – Norway, NL – Netherlands, PL – Poland, S – Sweden. Maps were created using ARCGIS 10.2 (http://www.esri.com/arcgis) and ADOBE ILLUSTRATOR CS6 (http://www.adobe. com/products/ illustrator.html).
Figure 1 in Hybridization patterns in two contact zones of grass snakes reveal a new Central European snake species
Figure 1. Distribution of mitochondrial lineages of 1,580 grass snakes used in this study. Total sample size of each clade shown in the legend. Eight allochthonous grass snakes with haplotypes of Italian lineages caught in southern Great Britain and Hesse, Germany, not shown. Map was created using ARCGIS 10.2 (http://www.esri. com/arcgis) and ADOBE ILLUSTRATOR CS6 (http://www.adobe.com/products/illustrator.html). Inset: Natrix natrix helvetica (Linz am Rhein, Germany); photo: Wolfgang Böhme.
Figure 2 in Hybridization patterns in two contact zones of grass snakes reveal a new Central European snake species
Figure 2. Parsimony networks of mtDNA sequences. Symbol sizes reflect haplotype frequencies. Small black circles are missing node haplotypes; each line connecting two haplotypes corresponds to one mutation step, if not otherwise indicated by numbers. Haplotype colours correspond to lineages, i.e. Natrix natrix helvetica (h) in blue; eastern lineages in yellow (y) and in red (r).
Species distribution, hybridization and connectivity in the genus Chionodraco: unveiling unknown icefish diversity in Antarctica
<p><strong>Aim</strong></p> <p>The species of the genus <em>Chionodraco</em> (Notothenioidei) are the most abundant icefish on the continental shelf of the Weddell Sea. While previous studies indicated that only <em>Chionodraco hamatus</em> and <em>Chionodraco myersi</em> inhabit the Weddell Sea, the third <em>Chionodraco</em> species, <em>Chionodraco rastrospinosus</em>, was recently sampled in the area. Since <em>C. rastrospinosus</em> is supposed to be found only at the Antarctic Peninsula and Scotia Arc, this study aimed at confirming the species classification of <em>C. rastrospinosus</em> by molecular methods and identifying its putative source population. Given the documented evidence of introgression among the three species, we tested whether the newly found <em>C. rastrospinosus</em> shared any genetic variability with the other <em>Chionodraco</em> species. To explain the pattern of distribution of the <em>Chionodraco</em> species, we aimed at estimating the hydrodynamic connectivity between the Antarctic Peninsula and the Weddell Sea.</p> <p><strong>Location</strong></p> <p>Antarctic Peninsula, southern Scotia Arc and the south-eastern Weddell Sea</p> <p><strong>Methods</strong></p> <p>We genotyped 19 microsatellites and sequenced the mitochondrial D-loop for 560 <em>Chionodraco</em> individuals. We simulated the dispersal of more than 3 million drifters (Lagrangian model).</p> <p><strong>Results</strong></p> <p>The molecular analyses support the presence of <em>C. rastrospinosus</em> in the Weddell Sea and its homogeneity with <em>C. rastrospinosus</em> from the Antarctic Peninsula. Bayesian clustering identifies three putative hybrids among <em>C. rastrospinosus</em> and the other congenerics. Lagrangian simulations do not support connectivity driven by the oceanographic features of the Antarctic Peninsula and Weddell Sea via passive larval dispersal only.</p> <p><strong>Main conclusions</strong></p> <p>This study documents, for the first time, the presence of <em>C. rastrospinosus</em> in the Weddell Sea unveiling more biodiversity than previously known in this region. The sympatry of the three <em>Chionodraco</em> species explains the occurrence of occasional, ongoing events of hybridization in the genus. Alternative possible hypotheses need to be tested in future studies about the mechanisms maintaining the interspecific connectivity in <em>Chionodraco</em> spp.</p>
Data from: Hybridization, natural selection and evolution of reproductive isolation: a 25-years survey of an artificial sympatric area between two mosquito sibling species of the Aedes mariae complex
Natural selection can act against maladaptive hybridization between co-occurring divergent populations leading to evolution of reproductive isolation among them. A critical unanswered question about this process that provides a basis for the theory of speciation by reinforcement, is whether natural selection can cause hybridization rates to evolve to zero. Here we investigated this issue in two sibling mosquitoes species, Aedes mariae and Ae. zammitii, that show post-mating reproductive isolation (F1 males sterile) and partial pre-mating isolation (different height of mating swarms) that could be reinforced by natural selection against hybridization. In 1986, we created an artificial sympatric area between the two species and sampled about 20,000 individuals over the following 25 years. Between 1986 to 2011, the composition of mating swarms and the hybridization rate between the two species were investigated across time in the sympatric area. Our results showed that Ae. mariae and Ae. zammitii have not completed reproductive isolation since their first contact in the artificial sympatric area. We have discussed the relative role of factors such as time of contact, gene flow, strength of natural selection, and biological mechanisms causing prezygotic isolation to explain the observed results.
Data from: Species diversification in a lineage of Mexican red oak (Quercus section Lobatae subsection Racemiflorae)—the interplay between distance, habitat, and hybridization
In widespread taxa in which hybridization is suspected of being an important aspect of species biology, the patterns and drivers of lineage diversification are not always clear. Here, we examine the patterns of species diversification in a monophyletic lineage of oaks endemic to western Mexico, a center of global oak diversity. This group of four species inhabits a variety of soil types and exhibits varying patterns of species distribution ranging from widespread to restricted, with the range bisected by the Trans-Mexican Volcanic Belt (TVB). Using chloroplast and nuclear microsatellites, we evaluated genetic diversity, diversification, and genetic group assignment across 49 populations. Chloroplast data identified 29 haplotypes in three distinct lineages, many of these found occurring on opposite sides of the TVB. Individual species were only loosely associated to specific chloroplast haplotypes but the distribution of shared haplotypes supports a one-time wider distribution. One lineage was highly divergent and geographically isolated, likely representing a case of chloroplast capture via hybridization and may indicate a range expansion of Racemiflorae into new territory. Nuclear gene diversity varied little across species and populations; however, differentiation and genetic assignment analysis was strongly structured geographically and tended to cluster with broad soil types. Soil specialist taxa produced homogeneous genetic structure while soil generalists showed varying patterns of mixed ancestry and high levels of admixture. Speciation appears driven by a combination of distance and edaphic factors leading to drift. Hybridization appears to be complementary, occurring most often in non-specific soil environments and in marginal areas, and contributes to a long-scale pattern of gene exchange as species ranges fluctuate with time.
Data from: Species integrity enhanced by a predation cost to hybrids in the wild
Species integrity can be challenged, and even eroded, if closely related species can hybridize and produce fertile offspring of comparable fitness to that of parental species. The maintenance of newly diverged or closely related species therefore hinges on the establishment and effectiveness of pre- and/or post-zygotic reproductive barriers. Ecological selection, including predation, is often presumed to contribute to reduced hybrid fitness, but field evidence for a predation cost to hybridization remains elusive. Here we provide proof-of-concept for predation on hybrids being a postzygotic barrier to gene flow in the wild. Cyprinid fishes commonly produce fertile, viable hybrid offspring and therefore make excellent study organisms to investigate ecological costs to hybrids. We electronically tagged two freshwater cyprinid fish species (roach Rutilus rutilus and bream Abramis brama) and their hybrids in 2005. Tagged fish were returned to their lake of origin, exposing them to natural predation risk from apex avian predators (great cormorant, Phalacrocorax carbo). Scanning for regurgitated tags under cormorant roosts 3–4 years later identified cormorant-killed individual fish and allowed us to directly test for a predation cost to hybrids in the wild. Hybrid individuals were found significantly more susceptible to cormorant predation than individuals from either parental species. Such ecological selection against hybrids contributes to species integrity, and can enhance species diversification.
Data from: Hybridization and geographic distribution shapes the spatial genetic structure of two co-occurring orchid species
Multiple ecological and life-history traits shape the fine-scale spatial genetic structure (FSGS) of a given population. The occurrence in core versus peripheral populations, levels of outcrossing, pollen and seed dispersal, and hybridization are important biological properties that influence the kinship of individuals within populations. We examined spatial genetic structure within 15 populations of Epidendrum fulgens and E. puniceoluteum distributed along a linear gradient of Brazilian coastal vegetation, including both allopatric and sympatric populations where the two orchid species hybridize. We analyzed 581 mapped specimens using nine simple sequence repeat loci, aiming to investigate how geographic distribution and hybridization shape within-population FSGS. A significant increase in FSGS was found towards peripheral populations, compared to core populations. Analysis of short- and long-distance components of FSGS identified biparental inbreeding and higher levels of FSGS at peripheral populations, when compared to core populations. In contrast, the relatively high density of reproductive adults in core populations potentially leads to highly overlapping seed and pollen movement, decreasing FSGS. Hybridization was an important factor shaping within-population spatial genetic structure at sympatric sites, decreasing the FSGS observed in parental species. Our results indicate that different ecological forces act in concert to create a gradient of FSGS along species distribution ranges, shaped by extensive levels of intra- and interspecific gene exchange.
Data from: Genetic evidence for species cohesion, substructure, and hybrids in spruce
The origin and history of species are shaped by various evolutionary dynamics, including their persistence in the face of potential gene flow from related taxa. In this study we use broad geographic and taxonomic sampling (2,219 individuals) to establish the distribution of species, hybrids, and cryptic genetic variation within the conifer genus Picea (spruce) across western North America. We demonstrate that the six species of spruce in this region are distinguishable based on their genetic composition, and that the more closely related Engelmann spruce (P. engelmannii) and white spruce (P. glauca) have generated numerous and widespread hybrids. These hybrids occur in the central Rocky Mountains, well to the south of the well-established region of admixture in Canada. Additionally, we provide evidence for subdivision within Engelmann spruce, manifested as a southern Rocky Mountains form, and a northern Rocky Mountain and Cascade mountains (western) form. In the intervening central Rocky Mountains region (forests in Wyoming and adjacent states) we found primarily individuals with admixed ancestry. Following their origin, these species of spruce have interacted repeatedly and in different geographic contexts. Multiple pairs of species have been shown to hybridize, yet the species persist and retain distinguishable compositions. At the same time, large geographic areas exist where hybrids are pervasive. Consequently, spruce provide a case study for the maintenance of species boundaries, particularly for how widespread hybridization need not lead to the collapse and loss of species.
Data from: Integration of conflict into integrative taxonomy: fitting hybridization in species delimitation of Mesocarabus (Coleoptera: Carabidae)
In species differentiation, characters do not usually diverge synchronously and there are also processes that effectively shuffle character states present in lineages descendant from a common ancestor. Species are thus expected to show some degree of incongruence among characters, and we argue that taxonomic delimitation actually benefits from integrative approaches and objective strategies dealing with character conflict. We illustrate the potential of exploiting conflict for species delimitation in a study-case of ground beetles of the subgenus Carabus (Mesocarabus), where traditional taxonomy fails to accurately delimit species. The molecular phylogenies of four mitochondrial and three nuclear genes, cladistic analysis of the aedeagus, ecological niche divergence, and morphometry of pronotal shape in altogether more than 500 specimens of Mesocarabus, show that none of these character sets are fully congruent with each other. For these data, a three-steps operational strategy is proposed for species delimitation by (1) delineating candidate species based on the integration of incongruence among conclusive lines of evidence, (2) corroborating candidate species with inconclusive lines of evidence, and (3) refining a final species proposal based on an integrated characterization of candidate species based on the evolutionary analysis of incongruence. This procedure provided a general understanding of the reticulate process of hybridization and introgression acting on Mesocarabus and generated the hypothesis of seven Mesocarabus species, including two putative hybrid lineages. Our work emphasizes the importance of incorporating critical analyses of character and phylogenetic conflict to infer both the evolutionary history and species boundaries through an integrative taxonomic approach.
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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.