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410 results for “hybrid species”
Supporting data and codes for: A new biological species in the Mercurialis annua polyploid complex: functional divergence in inflorescence morphology, hybrid sterility and possible introgression
<p>This GitHub repository includes R codes and datasets for the paper: A new biological species in the Mercurialis annua polyploid complex: functional divergence in inflorescence morphology, hybrid sterility and possible introgression</p>
Data from: Genomic analysis reveals limited hybridization among three giraffe species in Kenya
<p>The data deposited here was generated by and reported in Coimbra <em>et al.</em> (2023).</p> <p><em>SNP calling and linkage pruning</em></p> <ul> <li><strong>snp_calling_per_species.tar.gz:</strong> includes a genotype likelihoods (GL) file estimated with ANGSD for each giraffe species.</li> <li><strong>sampled_ld.tar.gz:</strong> contains a random sample of estimated pairwise <em>r<sup>2</sup></em> values for each species used to fit linkage disequilibrium (LD) decay curves.</li> <li><strong>ld_pruned_snps.tar.gz:</strong> contains an LD-pruned ANGSD GL file per species.</li> <li><strong>snp_calling_combined.tar.gz:</strong> includes a single LD-pruned ANGSD GL file comprising all sampled individuals of the three giraffe species analyzed in this study.</li> </ul> <p><em>Relatedness</em></p> <ul> <li><strong>relatedness.tar.gz:</strong> contains the input and output files used with NGSremix to estimate relatedness among giraffe in the dataset.</li> <li><strong>snp_calling_combined_unrelated.tar.gz:</strong> includes a single LD-pruned ANGSD GL file comprising all unrelated individuals of the three giraffe species analyzed in this study.</li> </ul> <p><em>Population structure and admixture</em></p> <ul> <li><strong>pcangsd.tar.gz:</strong> contains the covariance matrix generated by PCAngsd.</li> <li><strong>ngsadmix.tar.gz:</strong> includes run likelihood lists for each K value ranging from 1 to 11, as well as the admixture proportions (stored in '.qopt' files) inferred from the run with the highest log-likelihood for each K in NGSadmix.</li> <li><strong>evaladmix.tar.gz:</strong> contains the pairwise correlation of residuals between individuals estimated with evalAdmix for the NGSadmix runs with the highest log-likelihood run for each K.</li> </ul> <p><em>SNP-based phylogenomic inference</em></p> <ul> <li><strong>snp_phylogeny.tar.gz:</strong> contains the input PHYLIP file and the IQ-TREE output tree and log files.</li> </ul> <p><em>Phylogeny of mitochondrial genomes</em></p> <ul> <li><strong>mtdna_phylogeny.tar.gz:</strong> includes the 13 mitochondrial protein-coding gene alignments, the partitions file, and the IQ-TREE output tree and log files.</li> </ul> <p><em>Inference of migration events</em></p> <ul> <li><strong>admixture_graphs.tar.gz:</strong> contains the TreeMix / OrientAGraph input file ('treemix.frq.strat.gz'), the output files for all TreeMix and OrientAGraph runs, and the OptM summary table of TreeMix runs ('optm.tsv').</li> </ul> <p><em>Test for introgression</em></p> <ul> <li><strong>dsuite_introgression.tar.gz:</strong> includes the input VCF, the admixture graph topology reconstructed by OrientAGraph, and the Dsuite output files for the estimation of Patterson's D, f4-ratio, and f-branch statistics.</li> </ul> <p><em>Contemporary migration rates</em></p> <ul> <li><strong>ba3-snps.tar.gz:</strong> contains the input and output files for the BA3-SNPs-autotune and BA3-SNPs runs.</li> </ul> <p><em>Demographic reconstruction</em></p> <ul> <li><strong>demographic_inference.tar.gz:</strong> includes the SFS files generated with ANGSD and realSFS and the StairwayPlot2 blueprint and output files.</li> </ul> <p>Other:</p> <ul> <li><strong>metadata.csv:</strong> a companion file containing sample information used in conjunction with R scripts to plot the figures in the paper.</li> </ul>
Data from: Genetic and morphological evidence of a geographically widespread hybrid zone between two crocodile species, Crocodylus acutus and Crocodylus moreletii
<p>Hybrid zones represent natural laboratories to study gene flow, divergence and the nature of species boundaries between closely related taxa. We evaluated the level and extent of hybridization between <em>Crocodylus moreletii </em>and<em> C. acutus </em>using genetic and morphological data on 300 crocodiles from 65 localities. To our knowledge, this is the first genetic study that includes the entire historic range and sympatric zone of the two species. Contrary to expectations, Bayesian admixture proportions and maximum likelihood estimates of hybrid indexes revealed that most sampled crocodiles were admixed and that the hybrid zone is geographically extensive, extending well beyond their historical region of sympatry. We identified a few geographically isolated, non-admixed populations of both parental species. Hybrids do not appear to be F<sub>1</sub>s or recent backcrosses, but rather are more likely later-generation hybrids, suggesting that hybridization has been going on for several to many generations and is mostly the result of natural processes. <em>C. moreletii </em>is not the sister species of <em>C. acutus,</em> suggesting that the hybrid zone formed from secondary contact rather than primary divergence. Non-admixed individuals from the two species were distinguishable based on morphological characters, whereas hybrids had a complex mosaic of morphological characters that hinders identification in the wild. Very few non-admixed <em>C. acutus</em> and <em>C. moreletii</em> populations exist in the wild. Consequently, the last non-admixed <em>C. moreletii</em> populations have become critically endangered. Indeed, not only the parental species but also the naturally occurring hybrids should be considered for their potential conservation value.</p>
Fig. 6 in Morphometric Variation Of Hybridizing Species And Gynogenetic Biotypes Of Spined Loaches (Cobitidae, Cobitis) In River Systems Of Ukraine
Fig. 6. UPGMA clustering of biotypes by Mahalanobis distances calculated for body measurements and indices separately. Rectangles bounds the clusters with more than 90 % AU-support.
Fig 5. 95 in Morphometric Variation Of Hybridizing Species And Gynogenetic Biotypes Of Spined Loaches (Cobitidae, Cobitis) In River Systems Of Ukraine
Fig 5. 95 % confidence ellipses of the biotypes in the morphospace of four between-group principal components calculated for indices. Mean groups of each biotype is marked with black point and designation.
Fig. 3. 95 in Morphometric Variation Of Hybridizing Species And Gynogenetic Biotypes Of Spined Loaches (Cobitidae, Cobitis) In River Systems Of Ukraine
Fig. 3. 95 % confidence interval ellipses of the biotypes in the morphospace of bgPC1 and bgPC2 calculated for log10-transformed absolute traits. Each biotype means are marked with black points and names. The biotypes are explained in table 1.
Fig. 4. 95 in Morphometric Variation Of Hybridizing Species And Gynogenetic Biotypes Of Spined Loaches (Cobitidae, Cobitis) In River Systems Of Ukraine
Fig. 4. 95% confidence interval ellipses of the biotypes in the morphospace of bg PC3 and bgPC4 A calculated for log10 transformed absolute traits. Designations the same as on fig. 3.
Fig. 2 in Morphometric Variation Of Hybridizing Species And Gynogenetic Biotypes Of Spined Loaches (Cobitidae, Cobitis) In River Systems Of Ukraine
Fig. 2. Body measurements for Cobitis. Th e original fish image is from Wilhelm von Wright out of Fries, 1895.
Fig. 1 in Morphometric Variation Of Hybridizing Species And Gynogenetic Biotypes Of Spined Loaches (Cobitidae, Cobitis) In River Systems Of Ukraine
Fig. 1. Collection points of spined loaches in the river systems of Ukraine. Th e decoding of the numbering of samples is given in Material and methods.
Data for: Assortative mating in an ecological context: Effects of mate choice errors and relative species abundance on the frequency and asymmetry of hybridization
<p><span>The frequency and asymmetry of mixed-species mating set the initial stage for the ecological and evolutionary implications of hybridization. How such patterns of mixed-species mating, in turn, are influenced by the combination of mate choice errors and relative species abundance remain largely unknown. We develop a mathematical model that generates predictions for how relative species abundances and mate choice errors affect hybridization patterns. When mate choice errors are small (<5%) the highest frequency of hybridization occurs when one of the hybridizing species is at low abundance, but when mate choice errors are high (>5%) the highest hybridization frequency occurs when species occur in equal proportions. Furthermore, females of the less abundant species are overrepresented in mixed-species matings. We compare our theoretical predictions with empirical data on naturally hybridizing Ficedula flycatchers and find that hybridization is highest when the two species occur in equal abundance, implying rather high mate choice errors. We discuss ecological and evolutionary implications of our findings and encourage future work on hybrid zone dynamics that take demographic aspects, such as relative species abundance, into account.</span></p>
On the impermanence of species: The collapse of genetic incompatibilities in hybridizing populations
<p>Species pairs often become genetically incompatible during divergence, which is an important source of reproductive isolation. An idealized picture is often painted where incompatibility alleles accumulate and fix between diverging species. However, recent studies have shown both that incompatibilities can collapse with ongoing hybridization, and that incompatibility loci can be polymorphic within species. This paper suggests some general rules for the behavior of incompatibilities under hybridization. In particular, we argue that redundancy of genetic pathways can strongly affect the dynamics of intrinsic incompatibilities. Since fitness in genetically redundant systems is unaffected by introducing a few foreign alleles, higher redundancy decreases the stability of incompatibilities during hybridization, but also increases tolerance of incompatibility polymorphism within species. We use simulations and theories to show that this principle leads to two types of collapse: in redundant systems, exemplified by classical Dobzhansky-Muller incompatibilities, collapse is continuous and approaches a quasi-neutral polymorphism between broadly sympatric species, often as a result of isolation-by-distance. In non-redundant systems, exemplified by coevolution among genetic elements, incompatibilities are often stable, but can collapse abruptly with spatial traveling waves. As both types are common, the proposed principle may be useful in understanding the abundance of genetic incompatibilities in natural populations.</p>
Fig. 1 in Genetic identification of interspecific hybrid of Neotropical catfish species (Pseudoplatystoma corruscans vs. Pseudoplatystoma reticulatum) in rivers of Mato Grosso do Sul State, Brazil
Fig. 1. Map of collection sites of the biological material. Upper Paraná River basin: Dourados River (1 to 16), Brilhante River (17), and Ivinhema River (18 to 20). Paraguay River basin: Miranda River (21), Aquidauana River (22), Negro River (23), and Paraguay River (24).
Figures 1−6 in Polymorphism and hybridization in species of Hottentotta Birula, 1908 (Scorpiones: Buthidae)
Figures 1−6: 1. F0 female of Hottentotta salei (pale morph). 2. F0 male of Hottentotta jayakari (dark morph). 3. Courtship and mating between F0 male (dark morph) and F0 female (pale morph). 4. F1 brood, on instar I. 5. F1 brood, on instar II. 6. F1 adult female (dark morph).
Fig. 8. Karyotype from a Northern Site x Central Site L. spenceri unsexed tadpole hybrid. A representative karyotype demonstrates the L. spenceri 2n in The critically endangered species Litoria spenceri demonstrates subpopulation karyotype diversity
Fig. 8. Karyotype from a Northern Site x Central Site L. spenceri unsexed tadpole hybrid. A representative karyotype demonstrates the L. spenceri 2n = 26 karyotype and DAPI negative areas in the long arm of chromosome 9, as well as one matched chromosome of chromosome 11. The chromosome 11 matched chromosome that does not contain the DAPI negative area is submetacentric.
Fig.14 in Molecular and morphological approaches for species delimitation and hybridization investigations of two Cichla species
Fig.14. Cluster similarity based on the meristic data of Cichla Bloch & Schneider, 1801 specimens, indicating the relationship among Cichla kelberi Kullander & Ferreira, 2006, Cichla piquiti Kullander & Ferreira, 2006 and carijó samples.
Figs 9-12. Fig. 9 in Molecular and morphological approaches for species delimitation and hybridization investigations of two Cichla species
Figs 9-12. Fig. 9, patterns of PCR-multiplex for the COI mitochondrial gene. Fig. 10, PCR-RFLP patterns of the COI gene with NlaIV enzymes. Fig. 11, patterns of PCR-multiplex for the RAG nuclear gene. Fig. 12, PCR-RFLP patterns of the RAG gene with the BsrI enzyme. The species are indicated as: column 1, Cichla kelberi Kullander & Ferreira, 2006; column 2, Cichla piquiti Kullander & Ferreira, 2006; column 3 and 4, Cichla kelberi; column 5 and 6, Cichla piquiti; column 7 and 8, carijó; M, 1 kb molecular weight marker.
Fig. 8 in Molecular and morphological approaches for species delimitation and hybridization investigations of two Cichla species
Fig. 8. Restriction maps of the COI gene and RAG1 gene for the species Cichla kelberi Kullander & Ferreira, 2006 and Cichla piquiti Kullander & Ferreira, 2006.
Fig. 13 in Molecular and morphological approaches for species delimitation and hybridization investigations of two Cichla species
Fig. 13. Principal Component Analysis (PCA) for Cichla Bloch & Schneider, 1801 specimens using morphological data. Highlight: Cichla kelberi Kullander & Ferreira, 2006, Cichla piquiti Kullander & Ferreira, 2006 and carijó samples distribution.
Figs 4-6. Fig. 4 in Molecular and morphological approaches for species delimitation and hybridization investigations of two Cichla species
Figs 4-6. Fig. 4: Cichla kelberi Kullander & Ferreira, 2006; Fig. 5: Cichla piquiti Kullander & Ferreira, 2006; Fig. 6: carijó.
Fig. 7 in Molecular and morphological approaches for species delimitation and hybridization investigations of two Cichla species
Fig. 7. Recognition and orientation sites of universal and species-specific primers within regions of the mitochondrial (COI) and nuclear (RAG1) genes of Cichla Bloch & Schneider, 1801 species.
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OpenNeuro
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