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Figure 4 from: Espinasa L, Robinson J, Soares D, Hoese G, Toulkeridis T, Toomey III R (2018) Troglomorphic features of Astroblepus pholeter, a cavefish from Ecuador, and possible introgressive hybridization. Subterranean Biology 27: 17-29. https://doi.org/10.3897/subtbiol.27.27098
Figure 4 Cross section of the eye from Astroblepuspholeter (A, E–G) and Chaetostomamicrops (B–D). Notice that the pigmented epithelium (G) and iris of A.pholeter (E) are black, implying that they are not albino. Furthermore, A.pholeter eye has retained its lens, optic nerve, and its retina has all the normal layers, as the surface fish eye.
Figure 2 from: Espinasa L, Robinson J, Soares D, Hoese G, Toulkeridis T, Toomey III R (2018) Troglomorphic features of Astroblepus pholeter, a cavefish from Ecuador, and possible introgressive hybridization. Subterranean Biology 27: 17-29. https://doi.org/10.3897/subtbiol.27.27098
Figure 2 A–C Live specimens of cave AstroblepuspholeterD Two different surface Astroblepus sp. from the Apurimac drainage. Notice contrasting coloration between A and B both of which were collected in 2011. Pigmentation level variability within the cave population in 2011 spanned from pinkish-white white (A) to pigmented (B) at levels equivalent to some surface Astroblepus (D). Specimens collected in 2011 had longer fins (A) than those collected in 2015 (C). Notice as well that some surface Astroblepus (bottom one in D) can have small eyes of a size equivalent to cave specimens. A Modified from Haspel et al. (2012)B Modified from the Soares Lab web-page-photo C Specimen collected on 2015 D Modified from Schaefer et al. (2011).
Figure 3 from: Decker P (2018) Phylogenetic and morphological discord indicates introgressive hybridisation in two genera of Australian millipedes (Diplopoda, Polydesmida, Paradoxosomatidae). ZooKeys 809: 1-14. https://doi.org/10.3897/zookeys.809.30087
Figure 3 Bootstrap consensus tree for the combined mt COI+16S dataset in Pogonosternum; maximum likelihood, 1000 bootstrap replicates. Coloured dotted lines indicate specimens with similar gonopod morphology. Coloured bars indicate last male leg pairs with tibial and tarsal brushes (leg pair 7 = blue, leg pair 9 = green).
Figure 6 from: Decker P (2018) Phylogenetic and morphological discord indicates introgressive hybridisation in two genera of Australian millipedes (Diplopoda, Polydesmida, Paradoxosomatidae). ZooKeys 809: 1-14. https://doi.org/10.3897/zookeys.809.30087
Figure 6 Map of South Australia and southern Mt Lofty Ranges showing localities for Somethus species: S.castaneus (filled triangle), S.inflatus (open triangle), S.lancearius (square), and S.castaneus from Mt. Osmond (yellow star).
Figure 2 from: Decker P (2018) Phylogenetic and morphological discord indicates introgressive hybridisation in two genera of Australian millipedes (Diplopoda, Polydesmida, Paradoxosomatidae). ZooKeys 809: 1-14. https://doi.org/10.3897/zookeys.809.30087
Figure 2 Pogonosternumnigrovirgatum (Carl, 1902), ♂, right gonopod. A, B AMS KS96017 Ferntree Gully C, DNMV K-10248 from Sandringham and Brighton. Pogonosternumjeekeli Decker, sp. n., ♂, right gonopod E, FNMV K-10252 from Dyer Creek G, HNMV K-10250 from Bemm River. A, C Posterior view B, D Mesal view. Scale bar: 0.5 mm.
Figure 1 from: Decker P (2018) Phylogenetic and morphological discord indicates introgressive hybridisation in two genera of Australian millipedes (Diplopoda, Polydesmida, Paradoxosomatidae). ZooKeys 809: 1-14. https://doi.org/10.3897/zookeys.809.30087
Figure 1 Pogonosternumcf.nigrovirgatum "Dargo", male, right gonopod (NMV K-12202). A Posterior view B Lateral view C Anterior view D Mesal view. Abbreviations: fp1 = femoral process 1; fp2 = femoral process 2; lp = lateral process; prof = prolongation of femorite; S = solenomere; F = femorite. Scale bar: 0.5 mm.
Figure 5 from: Decker P (2018) Phylogenetic and morphological discord indicates introgressive hybridisation in two genera of Australian millipedes (Diplopoda, Polydesmida, Paradoxosomatidae). ZooKeys 809: 1-14. https://doi.org/10.3897/zookeys.809.30087
Figure 5 COI and 28S bootstrap consensus trees for Somethus species; maximum likelihood, 1000 bootstrap replicates.
Figure 4 from: Decker P (2018) Phylogenetic and morphological discord indicates introgressive hybridisation in two genera of Australian millipedes (Diplopoda, Polydesmida, Paradoxosomatidae). ZooKeys 809: 1-14. https://doi.org/10.3897/zookeys.809.30087
Figure 4 Distribution map of Pogonosternumnigrovirgatum (red circles), P.jeekeli (orange diamonds) and P.cf.nigrovirgatum "Dargo" (yellow star) in southeastern Australia. Abbreviation: ACT = Australian Capital Territory.
Data from: Are Parnassius apollo populations from the Pieniny National Park introgressed? A genetic study.
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Fig. 2 in Altai Mountains - cradle of hybrids and introgressants: A case study in Veronica subg. Pseudolysimachium (Plantaginaceae)
Fig. 2. Assignments of individuals to K clusters/populations based on Bayesian, multivariate and likelihood approaches as implemented in STRUCTURE, DAPC (in the adegenet package) and IQ-TREE programs respectively. A, Maximum likelihood unrooted tree reconstructed in IQ-TREE, calibrated with 1000 ultrafast bootstrap replicates. The numbers near the nodes represent bootstrap confidence. This analysis was based on 174 putative pure individuals. B, Probability of ancestry of each individual (horizontal axis; total 174 individuals) to each of K = 5 populations (vertical axis). The five populations correspond mostly to the morphotypes hypothesized for putative pure species. C, Discriminant analysis of principal components using the same dataset as in (B). D, Corresponding morphotypes of K = 5. — Photos: P.A. Kosachev.
Data from: Phylogenetic relationships of toads of the Rhinella granulosa group (Anura: Bufonidae): a molecular perspective with comments on hybridization and introgression
The Rhinella granulosa group consists of 13 species of toads distributed throughout open areas of South America and Panama. In this paper we perform a phylogenetic analysis considering all but one species of the group, employing five nuclear and four mitochondrial genes, for up to 7910 bp per specimen. Separate phylogenetic analyses under direct optimization (DO) of nuclear and mitochondrial sequences recovered the R. granulosa group as monophyletic and revealed topological incongruence that can be explained mainly by multiple events of hybridization and introgression, both mitochondrial and nuclear. The DO combined analysis, after the exclusion of putatively introgressed or heterozygous genomes, resulted in a phylogenetic hypothesis for the R. granulosa group in which most of the species are recovered as monophyletic, but with interspecific relationships poorly supported. The optimization of morphological (adult and larval), chromosomal, and behavioural characters resulted in 12 putative phenotypic synapomorphies for this species group and some other synapomorphies for internal clades. Our results indicate the need for additional population genetic studies on R. dorbignyi and R. fernandezae to corroborate the taxonomic status of both taxa. Finally, we discuss biological and genetic characteristics of Bufonidae, as possible explanations for the common occurrence of hybridization and introgression observed in some lineages of this family.
Data from: Introgression of Chinese haplotypes contributed to the improvement of Danish Duroc pigs
The distribution of Asian ancestry in the genome of Danish Duroc pigs was investigated using whole-genome sequencing data from European wild boars, Danish Duroc, Chinese Meishan and Bamaxiang pigs. Asian haplotypes deriving from Meishan and Bamaxiang occur widely across the genome. Signatures of selection on Asian haplotypes are common in the genome, but few of these haplotypes have been fixed. By defining 50 kb windows with more than 50% Chinese ancestry, which did not exhibit extreme genetic differentiation between Meishan and Bamaxiang as candidate regions, the enrichment of quantitative trait loci in candidate regions support that Asian haplotypes under selection play an important role in contributing genetic variation underlying production, reproduction, meat and carcass, and exterior traits. Gene annotation of regions with the highest proportion of Chinese ancestry revealed genes of biological interest, such as NR6A1. Further haplotype clustering analysis suggested that a haplotype of Chinese origin around the NR6A1 gene was introduced to Europe and then underwent a selective sweep in European pigs. Besides, functional genes in candidate regions, such as AHR and PGRMC2, associated with fertility, and SAL1, associated with meat quality were identified. Our results demonstrate the contribution of Asian haplotypes to the genomes of European pigs. Findings herein facilitate further genomic studies such as genome-wide association study and genomic prediction by providing ancestry information of variants.
Data from: Mechanical incompatibility caused by modifications of multiple male genital structures using genomic introgression in Drosophila
Mechanical incompatibility of male and female genitalia is common in animals with internal fertilization. However, our knowledge regarding the precise mechanisms is limited. One key question regards the susceptibility of the match between male and female genitalia to morphological modification. To address this issue, we generated six different second-chromosome introgression lines possessing partially Drosophila mauritiana-like genital morphology in multiple structures in D. simulans background. Three of the six introgression males showed elevated mobility at some stages during copulation with D. simulans females; this was assumed to be an indication of genital mismatch. Notably, one of the introgression males with D. mauritiana-like enlarged anal plates showed occasional leakage of adhesive ejaculate on the body surface when mated with pure D. simulans females, suggesting apparent structural incompatibility in genital coupling. These observations suggested that both sexual and natural selection shape the anal plate morphology, highlighting the role of this structure as an important component of mechanical isolation. Partial replacement (introgression) by a sibling species genome can induce perturbations in genital coupling mechanics, suggesting that genital compatibility can be susceptible to subtle genomic changes at the early stages of divergence in these species.
Data from: Resequencing of common bean identifies regions of inter-gene pool introgression and provides comprehensive resources for molecular breeding
Common bean is the most important grain legume for human consumption and a main nutrition source in the tropics. Because bean production is reduced by both abiotic and biotic constraints, current breeding efforts are focused on the development of improved varieties with tolerance to these stresses. We characterized materials from different breeding programs spanning three continents to understand their sequence diversity and advance the development of molecular breeding tools. For this, 37 varieties belonging to P. vulgaris, P. acutifolius, and P. coccineus were sequenced by whole-genome sequencing (WGS), identifying more than 40 million genomic variants. Evaluation of nuclear DNA content and analysis of copy number variation revealed important differences in genomic content not only between P. vulgaris and two other domesticated Phaseolus species, but also within P. vulgaris, affecting hundreds of protein-coding genomic regions. A large number of inter-gene-pool introgressions were identified. Furthermore, interspecific introgressions for disease resistance in breeding lines were mapped. Evaluation of newly developed SNP markers within previously discovered QTL for common bacterial blight and angular leaf spot provide improved specificity to tag sources of resistance to these diseases. We expect that this dataset will provide a deeper molecular understanding of breeding germplasm and deliver molecular tools for germplasm development, aiming to increase the efficiency of bean breeding programs.
Deep ancestral introgression shapes evolutionary history of dragonflies and damselflies
<p>Introgression is arguably one of the most important biological processes in the evolution of groups of related species, affecting at least 10% of the extant species in the animal kingdom. Introgression reduces genetic divergence between species, and in some cases can be highly beneficial, facilitating rapid adaptation to ever-changing environmental pressures. Introgression also significantly impacts inference of phylogenetic species relationships where a strictly binary tree model cannot adequately explain reticulate net-like species relationships. Here we use phylogenomic approaches to understand patterns of introgression along the evolutionary history of a unique, non-model insect system: dragonflies and damselflies (Odonata). We demonstrate that introgression is a pervasive evolutionary force across various taxonomic levels within Odonata. In particular, we show that the morphologically "intermediate" species of Anisozygoptera (one of the three primary suborders within Odonata besides Zygoptera and Anisoptera), which retain phenotypic characteristics of the other two suborders, experienced high levels of introgression likely coming from zygopteran genomes. Additionally, we find evidence for multiple cases of deep inter-superfamilial ancestral introgression.</p>
Data from: The genetic architecture of hybrid incompatibilities and their effect on barriers to introgression in secondary contact
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Data from: The genomic landscape at a late stage of stickleback speciation: high genomic divergence interspersed by small localized regions of introgression
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Data from: Introgression maintains the genetic integrity of the sex-determining chromosome of the fungus Neurospora tetrasperma
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Data from: Multiple hybridization events between Drosophila simulans and Drosophila mauritiana are supported by mtDNA introgression
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Data from: Introgression study reveals two quantitative trait loci involved in interspecific variation in memory retention among Nasonia wasp species
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