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opencc-zeroNov 2023View details →

Genomic landscape of introgression from the ghost lineage in a gobiid fish uncovers the generality of forces shaping hybrid genomes

Extinct lineages can leave legacies in the genomes of extant lineages through ancient introgressive hybridization. The patterns of genomic survival of these extinct lineages provide insight into the role of extinct lineages in current biodiversity. However, our understanding of the genomic landscape of introgression from extinct lineages remains limited due to challenges associated with locating the traces of unsampled "ghost" extinct lineages without ancient genomes. Herein, we conducted population genomic analyses on the East China Sea (ECS) lineage of Chaenogobius annularis, which was suspected to have originated from ghost introgression, with the aim of elucidating its genomic origins and characterizing its landscape of introgression. By combining phylogeographic analysis and demographic modeling, we demonstrated that the ECS lineage originated from ancient hybridization with an extinct ghost lineage. Forward simulations based on the estimated demography indicated that the statistic γ of the HyDe analysis can be used to distinguish the differences in local introgression rates in our data. Consistent with introgression between extant organisms, we found reduced introgression from extinct lineage in regions with low-recombination rates and with functional importance, thereby suggesting a role of linked selection that has eliminated the extinct lineage in shaping the hybrid genome. Moreover, we identified enrichment of repetitive elements in regions associated with ghost introgression, which was hitherto little-known but was also observed in the reanalysis of published data on introgression between extant organisms. Overall, our findings underscore the unexpected similarities in the characteristics of introgression landscapes across different taxa, even in cases of ghost introgression.

Fig. 4 in Altai Mountains - cradle of hybrids and introgressants: A case study in Veronica subg. Pseudolysimachium (Plantaginaceae)

Fig. 4. STRUCTURE results showing the probability of ancestry of each individual (horizontal axis) to each of K = 2 populations (vertical axis) in all the five scenarios. A, Veronica spicata × V. pinnata; B, V. incana and V. longifolia; C, V. longifolia and V. porphyriana; D & E, V. pinnata and V. porphyriana involving putative hybrids of V. ×schmakovii and V. ×sessiliflora. Details of the exact posterior probabilities of each putative hybrid individual and their corresponding parents are given in suppl. Table S3.

opencc-zeroFeb 2022View details →

Genome-wide sequence data show no evidence of hybridization and introgression among pollinator wasps associated with a community of Panamanian strangler figs

The specificity of pollinator host choice influences opportunities for reproductive isolation in their host plants. Similarly, host plants can influence opportunities for reproductive isolation in their pollinators. For example, in the fig and fig wasp mutualism, offspring of fig pollinator wasps mate inside the inflorescence that the mothers pollinate. Although often host specific, multiple fig pollinator species are sometimes associated with the same fig species, potentially enabling hybridization between wasp species. Here we study the 19 pollinator species (Pegoscapus spp.) associated with an entire community of 16 Panamanian strangler fig species (Ficus subgenus Urostigma, section Americanae) to determine whether the previously documented history of pollinator host switching and current host sharing predicts genetic admixture among the pollinator species, as has been observed in their host figs. Specifically, we use genome-wide ultraconserved element (UCE) loci to estimate phylogenetic relationships and test for hybridization and introgression among the pollinator species. In all cases, we recover well-delimited pollinator species that contain high interspecific divergence. Even among pairs of pollinator species that currently reproduce within syconia of shared host fig species, we found no evidence of hybridization or introgression. This is in contrast to their host figs, where hybridization and introgression have been detected within this community, and more generally, within figs worldwide. Consistent with general patterns recovered among other obligate pollination mutualisms (e.g., yucca moths and yuccas), our results suggest that while hybridization and introgression are processes operating within the host plants, these processes are relatively unimportant within their associated insect pollinators.

opencc-zeroDec 2021View details →

Introgression between Sphyrapicus nuchalis and S. varius sapsuckers in a hybrid zone in west-central Alberta

Studying species interactions at hybrid zones allows biologists to understand the forces that promote speciation. Hybridization among Sphyrapicus nuchalis, S. varius, and S. ruber has long been acknowledged, and hybrid zones between S. nuchalis/S. ruber and S. varius/S. ruber have been characterized with both genetic and genomic data. Using a combination of next-generation Restriction Site-Associated DNA sequencing (RAD-Seq) and traditional genetic methods, we examined patterns of introgression in the poorly characterized S. nuchalis/S. varius contact zone; the two most similar species in the complex, though they are not each other's closest relatives. We found high introgression rates, with several early and many advanced generation hybrids along a 275 km stretch of Rocky Mountain foothill, pointing to a well-established hybrid zone with hybrid individuals backcrossing with individuals from the parental species and each other. Plumage colouration in the hybrid zone was a relatively poor indicator of parental or hybrid status, which could be attributed to the possible involvement of few large effect genes.

opencc-by-4.0Jul 2022View details →

Molecular evidence for introgressive hybridization in New Zealand masked gulls

Genetic data and codes to reproduce the analyses from the manuscript : Given, A. D., Mills, J. A., Momigliano, P., & Baker, A. J. (2022). Molecular evidence for introgressive hybridization in New Zealand masked gulls. Ibis. https://doi.org/10.1111/ibi.13117 The data and codes are  in  two zipped folders <ol> <li>FSC.zip</li> <li>PopGen.zip</li> </ol> The FSC.zip folder contains data and scripts to reproduce the fastsimcoal simulations and to calculate summary statistics from observed and simulated data. It also includes the results from these analyses and an R script to run ABC model selection via random forest.   The PopGen.zip folder contains the microsatellite dataset in both genepop (RB-BB.gen) and structure (RB-BB.str) formats , the results from STRUCTURE analyses (folder RB-BB_STRUCT), and an R script (Popgen_analyses.r) to reproduce population genetic analyses (PCA and summary statistics: FST, and estimate HWE,  HO and HE) and plots.

Fig. 1 in Morphological characters and SNP markers suggest hybridization and introgression in sympatric populations of the pleurocarpous mosses Homalothecium lutescens and H. sericeum

Fig. 1 Measurements of branch leaf characteristics of Homalothecium spp. Leaf characters (L1-L18) are explained in Table 3

Fig. 4 in Morphological characters and SNP markers suggest hybridization and introgression in sympatric populations of the pleurocarpous mosses Homalothecium lutescens and H. sericeum

Fig. 4 Relationship between width and length of leaf lamina of Homalothecium leaf specimens (N = 240) collected from the allopatric populations of H. lutescens (N = 60) and H. sericeum (N = 59) and the

Fig. 6 in Morphological characters and SNP markers suggest hybridization and introgression in sympatric populations of the pleurocarpous mosses Homalothecium lutescens and H. sericeum

Fig. 6 The positions of putatively hybrid sporophytes from the sympatric populations of H. lutescens and H. sericeum superimposed in the PCA from Fig. 5, based on leaf morphology of the maternal gametophytes. The morphospace of leaves from allopatric populations of H. lutescens and H. sericeum are shown as encircled surfaces (blue circle = H. lutescens and yellow circle = H. sericeum). The red circle represents the morphospace of individuals from the sympatric populations. Each square represents a hybrid sporophyte specimen, collected on its

Fig. 5 in Morphological characters and SNP markers suggest hybridization and introgression in sympatric populations of the pleurocarpous mosses Homalothecium lutescens and H. sericeum

Fig. 5 Principal component analysis of 14 leaf characters from 240 specimens representing allopatric and sympatric populations of Homalothecium lutescens and H. sericeum. The first two axes (PC1 and PC2) representing together 36% of variation are shown. The colours and shapes of data points correspond to the population of the specimens. Leaf

Fig. 2 in Morphological characters and SNP markers suggest hybridization and introgression in sympatric populations of the pleurocarpous mosses Homalothecium lutescens and H. sericeum

Fig. 2 (a) Measurement of capsule orientation in relation to the seta in Homalothecium as the angle (in degrees) between the seta and spore capsule at the basis of the spore capsule. (b) Capsule inclinations of individuals from the allopatric populations fell into the black ranges of variation; in the sympatric populations individuals occurred with capsule inclinations ranging outside typical capsule inclinations of the pure species (red zone: 150°- 164°), indicating hybrid origin

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

Fig. 1. A, Genetic composition based on K = 5 of first-level STRUCTURE results and number of individuals included from that particular locality. Genetic composition of the localities with more than one individual has been averaged. Key to the colors is given in a separate inset. B–D, Probability of ancestry of each individual (horizontal axis; total 233 individuals) to each of K = 4, 5, 6 populations (vertical axis). The five populations correspond mostly to the morphotypes hypothesized for species and putative hybrids. V. ×alt, V. ×altaica; V. ×gri, V. ×grisea; V. ×kol, V. ×kolyvanensis; V. ×sap, V. ×sapozhnikovii; V. ×sch, V. ×schmakovii; V. ×ses, V. ×sessiliflora; V. ×smi, V. ×smirnovii; V. are, V. arenosa; V. inca, V. incana; V. lon, V. longifolia; V. pinn, V. pinnata; V. porp, V. porphyriana; V. reve, V. reverdattoi; V. saj, V. sajanensis; V. spic, V. spicata; V. spur, V. spuria; V. ×taig, V. ×taigischensis; uniden, unidentified.

Fig. 5 in Altai Mountains - cradle of hybrids and introgressants: A case study in Veronica subg. Pseudolysimachium (Plantaginaceae)

Fig. 5. Results of the G-PhoCS analysis for effective population sizes, and gene flow using only pure individuals (no admixture). The inferred current effective population size (Ne) of each species are given for all the five species. The direction of the arrows represents the probability of migration among the species both in forward and reverse directions. The width of the bars represents the effective population size of each species. For population size estimation, we used the equations Ne (effective population size) = θ / 4μg; and T (divergence time) = τ · g / μ; where substitution rate/site/year (μ) = 2.44E-9, generation time for population (g) = 10 years. Migration rates are based on per generation parameter (Msx = msx · θx / 4), which is the proportion of individuals in population x arrived by migration from another population per generation. Gene flow has been calculated using the total migration rate, cases where the total rate is low, it approximates the probability of gene flow between the two species. However, for higher rates, we adjusted probabilities into rates with the equation P = 1 − e−m (where P = the probability of gene flow, e = exponent, and m = total migration rate; following vonHoldt & al., 2016). The phylogenetic tree on which the G-PhoCS analysis has been based is given in suppl. Fig. S2. For complete details, see in Materials and Methods as well as suppl. Tables S4 and S5 for migration rates (msx), τ and θ values, and divergence times.

Fig. 3 in Altai Mountains - cradle of hybrids and introgressants: A case study in Veronica subg. Pseudolysimachium (Plantaginaceae)

Fig. 3. Chromosome localization of rDNA and genomic in situ hybridization (GISH) in Veronica. Mitotic chromosome complements of: A, V. porphyriana; B, V. ×schmakovii; C, V. spicata; D, V. pinnata; E, V. longifolia; and F, V. incana hybridized with 35S (red fluorescence) and 5S (purple) rDNA probes. G, Mitotic chromosomes of V. ×schmakovii hybridized with gDNA of V. longifolia (red) and V. porphyriana (green). — Chromosomes were counterstained with DAPI. Scale bars, 10 μm.

opencc-zeroDec 2022View details →

Pollinator and host sharing lead to hybridization and introgression in Panamanian free-standing figs, but not in their pollinator wasps

Obligate pollination mutualisms, in which plant and pollinator lineages depend on each other for reproduction, often exhibit high levels of species-specificity. However, cases in which two or more pollinator species share a single host species (host sharing), or two or more host species share a single pollinator species (pollinator sharing), are known to occur in the current ecological time. Further, evidence for host switching in evolutionary time is increasingly being recognized in these systems. The degree to which departures from strict specificity differentially affect the potential for hybridization and introgression in the associated host or pollinator is unclear. We addressed this question using genome-wide sequence data from five sympatric Panamanian free-standing fig species (Ficus subgenus Pharmacosycea, section Pharmacosycea) and their six associated fig pollinator wasp species (Tetrapus). Two of the five fig species, F. glabrata and F. maxima, were found to regularly share pollinators. In these species, ongoing hybridization was demonstrated by the detection of several first-generation (F1) hybrid individuals, and historical introgression was indicated by phylogenetic network analysis. In contrast, although two of the pollinator species regularly share hosts, all six species were genetically distinct and deeply divergent, with no evidence for either hybridization or introgression. This pattern is consistent with results from other obligate pollination mutualisms, suggesting that, in contrast to their host plants, pollinators appear to be reproductively isolated, even when different species of pollinators mate in shared hosts.