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134 results for “genomics of speciation”

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dryad36/100

Data from: A test of genomic modularity among life-history adaptations promoting speciation with gene flow

Speciation with gene flow may require adaptive divergence of multiple traits to generate strong ecologically based reproductive isolation. Extensive negative pleiotropy or physical linkage of genes in the wrong phase affecting these diverging traits may therefore hinder speciation, while genetic independence or "modularity" among phenotypic traits may reduce constraints and facilitate divergence. Here, we test whether the genetics underlying two components of diapause life history, initial diapause intensity and diapause termination timing, constrain differentiation between sympatric hawthorn and apple-infesting host races of the fly Rhagoletis pomonella through analysis of 10,256 SNPs measured via genotyping-by-sequencing (GBS). Loci genetically associated with diapause termination timing were mainly observed for SNPs mapping to chromosomes 1–3 in the genome, most notably for SNPs displaying higher levels of linkage disequilibrium (LD), likely due to inversions. In contrast, selection on initial diapause intensity affected loci on all five major chromosomes of the genome, specifically those showing low levels of LD. This lack of overlap in genetically associated loci suggests that the two diapause phenotypes are largely modular. On chromosome 2, however, intermediate level LD loci and a subgroup of high LD loci displayed significant negative relationships between initial diapause intensity and diapause termination time. These gene regions on chromosome 2 therefore affected both traits, while most regions were largely independent. Moreover, loci associated with both measured traits also tended to exhibit highly divergent allele frequencies between the host races. Thus, the presence of nonoverlapping genetic modules likely facilitates simultaneous, adaptive divergence for the measured life-history components.

opencc-zeroDec 2016View details →

dryad36/100

Data from: Transitions between phases of genomic differentiation during stick-insect speciation

Speciation can involve a transition from a few genetic loci that are resistant to gene flow to genome-wide differentiation. However, only limited data exist concerning this transition and the factors promoting it. Here, we study phases of speciation using data from >100 populations of 11 species of Timema stick insects. Consistent with early phases of genic speciation, adaptive colour-pattern loci reside in localized genetic regions of accentuated differentiation between populations experiencing gene flow. Transitions to genome-wide differentiation are also observed with gene flow, in association with differentiation in polygenic chemical traits affecting mate choice. Thus, intermediate phases of speciation are associated with genome-wide differentiation and mate choice, but not growth of a few genomic islands. We also find a gap in genomic differentiation between sympatric taxa that still exchange genes and those that do not, highlighting the association between differentiation and complete reproductive isolation. Our results suggest that substantial progress towards speciation may involve the alignment of multi-faceted aspects of differentiation.

opencc-zeroDec 2016View details →

dryad36/100

Genome-wide SNP analysis elucidates the evolution of Prunus takesimensis in Ulleung Island: Genetic consequences of anagenetic speciation

Of two major speciation modes of endemic plants on oceanic islands, cladogenesis and anagenesis, the latter has been recently emphasized as an effective mechanism for increasing plant diversity in isolated, ecologically homogeneous insular setting. As a single flowering cherry occurring on Ulleung Island in East Sea, Prunus takesimensis Nakai has been presumed as derived through anagenetic speciation on the Island. Based on morphological similarities, P. sargentii distributed in adjacent continental areas and islands has been suggested as its purported continental progenitor. However, the overall genetic complexity and resultant non-monophylies of closely related flowering cherries have hindered determining their phylogenetic relationships as well as establishing concrete continental progenitor and insular derivative relationship. Based on extensive sampling of wild flowering cherries including P. takesimensis and P. sargentii from Ulleung Island and its adjacent areas, this study inferred the origin and evolution of P. takesimensis using multiple different molecular markers. As the result of phylogeny and population genetic structure analyses based on SNPs detected by MIG-Seq and complementary cpDNA haplotypes, we could provide the extensive and convincing evidence for (1) the monophyly of P. takesimensis, (2) clear genetic differentiation between P. takesimensis (insular derivative) and P. sargentii (continental progenitor), (3) the geographic origin of P. takesimensis via single introduction from source population of P. sargentii in Korean Peninsula, (4) no significant genetic reduction in anagenetically derived insular species P. takesimsnsis compared to continental progenitor P. sargentii, (5) no strong population genetic structuring or geographical patters in the insular derived species, and (6) Mig-seq method as an effective tool to unravel complex evolutionary history of plant groups.

opencc-zeroAug 2021View details →

dryad36/100

Speciation in coastal basins driven by staggered headwater captures: Dispersal of a species complex, Leporinus bahiensis, as revealed by genome-wide SNP data

Past sea level changes and geological instability along watershed boundaries have largely influenced fish distribution across coastal basins, either by dispersal via palaeodrainages now submerged or by headwater captures, respectively. Accordingly, the South American Atlantic coast encompasses several small and isolated drainages that share a similar species composition, representing a suitable model to infer historical processes. Leporinus bahiensis is a freshwater fish species widespread along adjacent coastal basins over narrow continental shelf with no evidence of palaeodrainage connections at low sea level periods. Therefore, this study aimed to reconstruct its evolutionary history to infer the role of headwater captures in the dispersal process. To accomplish this, we employed molecular-level phylogenetic and population structure analyses based on Sanger sequences (5 genes) and genome-wide SNP data. Phylogenetic trees based on Sanger data were inconclusive, but SNPs data did support the monophyletic status of L. bahiensis. Both COI and SNP data revealed structured populations according to each hydrographic basin. Species delimitation analyses revealed from 3 (COI) to 5 (multilocus approach) MOTUs, corresponding to the sampled basins. An intricate biogeographic scenario was inferred and supported by Approximate Bayesian Computation (ABC) analysis. Specifically, a staggered pattern was revealed and characterized by sequential headwater captures from basins adjacent to upland drainages into small coastal basins at different periods. These headwater captures resulted in dispersal throughout contiguous coastal basins, followed by deep genetic divergence among lineages. To decipher such recent divergences, as herein represented by L. bahiensis populations, we used genome-wide SNPs data. Indeed, the combined use of genome-wide SNPs data and ABC method allowed us to reconstruct the evolutionary history and speciation of L. bahiensis. This framework might be useful in disentangling the diversification process in other neotropical fishes subject to a reticulate geological history.

opencc-zeroJan 2023View details →

dryad36/100

Genomic diversity gradients and functional differentiation put Northeast Pacific ribbon kelp lineages in the speciation grey zone

The transition from reproductively isolated populations to species is not well understood. Genotyping entire genomes holds promise to enhance insights into the process of speciation and the evolutionary relationships among related taxa. Gulf of Alaska ribbon kelp was once recognized as four species before they were folded into Alaria marginata on the basis of DNA barcode markers, though several lineages have continued to be recognized. Here, we used whole genome sequencing datasets to test the hypothesis that these lineages represent incipient species. Whole genomes of 69 individuals from five genetically distinctive lineages in the Gulf of Alaska (USA) and Salish Sea (Canada) were analyzed, along with 63 genomes from three other species of Alaria. Our analysis of >3.4 million Single Nucleotide Polymorphisms reaffirms that organellar and nuclear phylogenetic signals are incongruent in Alaria, producing different topologies among five organellar and six nuclear A. marginata lineages. Lineages also display reproductive isolation, evidenced by a lack of recent admixture across genomes. Genetic distances between A. marginata lineages exceed levels expected of population-level divergence but fall short of distances between species of Alaria. Moreover, we provide evidence of functional genomic differences between the A. marginata lineages, exceeding differences expected between populations, but falling short of larger differences among species. Our results place A. marginata lineages in an evolutionary grey zone, where lineages display substantial differentiation, but not to the level expected of Alaria species. This information shifts taxonomic conversations towards a genome-scale framework that provides a more comprehensive picture of divergence, connectivity, and functional innovation for defining lineages.

opencc-zeroDec 2021View details →

dryad36/100

Genomic insights into diversification and ecological speciation of three Saccharina species

Aim: Saccharina is a genus within the brown algae that is of ecological and economic importance and shows rapid adaptive radiation, while the process and genetic mechanism of diversification and speciation remains unclear. In this study, we conducted genome resequencing of three typical Saccharina species, including the four varieties of S. japonica, and its two sister species (S. angustata and S. longissima) to investigate the genetic mechanism of ecological speciation. Location: coast of Japan Methods: We assess the genomic differentiation and genetic diversity of these Saccharina kelps based on whole-genome resequencing. We applied composite-likelihood approach to identify the ancestral species and reconstruct the evolutionary history. Selective sweep analysis was conducted to detect selective signatures when they adapted to diverse habitat. Results: The demography suggested that S. angustata, S. longissima and S. japonica var. japonica underwent adaptive speciation early, with S. japonica var. japonica as the oldest variant that diverged into three other varieties. The newly evolved variety SR has the highest genetic diversity, and the variety SD has the lowest genetic diversity. Interspecific hybridization among these congeneric species was low, indicating these species exist in genetic isolation in nature. We detected that some stress response genes (e.g. ubiquitin-like protein) and growth-related genes (e.g. imm upregulated 3) were under positive selection during the ecological speciation. Low linkage disequilibrium decay rate and extensive signals of selective sweeps are present in these Saccharina species, providing strong support for adaptive differentiation under natural selection as the driving force for its ecological speciation. Main conclusions: The main driving force of speciation in this genus appears to be not natural hybridization, but genetic isolation and adaptive differentiation by nature selection. The evolutionary history and ecological speciation of Saccharina species allow us to predict how common the species responds to environmental change, and whether they require different management strategies.

opencc-zeroSep 2023View details →

dryad36/100