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1. Adaptive Divergence of Meiotic Recombination Rate in Ecological Speciation

   https://doi.org/10.1093/gbe/evaa182  

   Neupane, Swatantra ; Xu, Sen ( October 2020 , Genome Biology and Evolution)

   Baer, Charles (Ed.)

   Abstract Theories predict that directional selection during adaptation to a novel habitat results in elevated meiotic recombination rate. Yet the lack of population-level recombination rate data leaves this hypothesis untested in natural populations. Here, we examine the population-level recombination rate variation in two incipient ecological species, the microcrustacean Daphnia pulex (an ephemeral-pond species) and Daphnia pulicaria (a permanent-lake species). The divergence of D. pulicaria from D. pulex involved habitat shifts from pond to lake habitats as well as strong local adaptation due to directional selection. Using a novel single-sperm genotyping approach, we estimated the male-specific recombination rate of two linkage groups in multiple populations of each species in common garden experiments and identified a significantly elevated recombination rate in D. pulicaria. Most importantly, population genetic analyses show that the divergence in recombination rate between these two species is most likely due to divergent selection in distinct ecological habitats rather than neutral evolution. 

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2. Ancient divergence of Indian and Tibetan wolves revealed by recombination‐aware phylogenomics

   https://doi.org/10.1111/mec.16127  

   Hennelly, Lauren M. ; Habib, Bilal ; Modi, Shrushti ; Rueness, Eli K. ; Gaubert, Philippe ; Sacks, Benjamin N. ( August 2021 , Molecular Ecology)

   The grey wolf (Canis lupus) expanded its range across Holarctic regions during the late Pleistocene. Consequently, most grey wolves share recent (<100,000 years ago) maternal origins corresponding to a widespread Holarctic clade. However, two deeply divergent (200,000–700,000 years ago) mitochondrial clades are restricted, respectively, to the Indian subcontinent and the Tibetan Plateau, where remaining wolves are endangered. No genome‐wide analysis had previously included wolves corresponding to the mitochondrial Indian clade or attempted to parse gene flow and phylogeny. We sequenced four Indian and two Tibetan wolves and included 31 additional canid genomes to resolve the phylogenomic history of grey wolves. Genomic analyses revealed Indian and Tibetan wolves to be distinct from each other and from broadly distributed wolf populations corresponding to the mitochondrial Holarctic clade. Despite gene flow, which was reflected disproportionately in high‐recombination regions of the genome, analyses revealed Indian and Tibetan wolves to be basal to Holarctic grey wolves, in agreement with the mitochondrial phylogeny. In contrast to mitochondrial DNA, however, genomic findings suggest the possibility that the Indian wolf could be basal to the Tibetan wolf, a discordance potentially reflecting selection on the mitochondrial genome. Together, these findings imply that southern regions of Asia have been important centers for grey wolf evolution and that Indian and Tibetan wolves represent evolutionary significant units (ESUs). Further study is needed to assess whether these ESUs warrant recognition as distinct species. This question is especially urgent regarding the Indian wolf, which represents one of the world's most endangered wolf populations.

    

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3. The roles of recombination and selection in shaping genomic divergence in an incipient ecological species complex

   https://doi.org/10.1111/mec.16383  

   Wersebe, Matthew J. ; Sherman, Ryan E. ; Jeyasingh, Punidan D. ; Weider, Lawrence J. ( February 2022 , Molecular Ecology)

   Speciation genomic studies have revealed that genomes of diverging lineages are shaped jointly by the actions of gene flow and selection. These evolutionary forces acting in concert with processes such as recombination and genome features such as gene density shape a mosaic landscape of divergence. We investigated the roles of recombination and gene density in shaping the patterns of differentiation and divergence between the cyclically parthenogenetic ecological sister‐taxa,Daphnia pulicariaandDaphnia pulex. First, we assembled a phased chromosome‐scale genome assembly using trio‐binning forD.pulicariaand constructed a genetic map using an F2‐intercross panel to understand sex‐specific recombination rate heterogeneity. Finally, we used a ddRADseq data set with broad geographic sampling ofD.pulicaria,D.pulex, and their hybrids to understand the patterns of genome‐scale divergence and demographic parameters. Our study provides the first sex‐specific estimates of recombination rates for a cyclical parthenogen, and unlike other eukaryotic species, we observed male‐biased heterochiasmy inD.pulicaria, which may be related to this somewhat unique breeding mode. Additionally, regions of high gene density and recombination are generally more divergent than regions of suppressed recombination. Outlier analysis indicated that divergent genomic regions are probably driven by selection onD.pulicaria, the derived lineage colonizing a novel lake habitat. Together, our study supports a scenario of selection acting on genes related to local adaptation shaping genome‐wide patterns of differentiation despite high local recombination rates in this species complex. Finally, we discuss the limitations of our data in light of demographic uncertainty.

    

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4. Recombination-aware phylogeographic inference using the structured coalescent with ancestral recombination

   https://doi.org/10.1371/journal.pcbi.1010422  

   Guo, Fangfang ; Carbone, Ignazio ; Rasmussen, David A. ( August 2022 , PLOS Computational Biology)

   Schiffels, Stephan (Ed.)

   Movement of individuals between populations or demes is often restricted, especially between geographically isolated populations. The structured coalescent provides an elegant theoretical framework for describing how movement between populations shapes the genealogical history of sampled individuals and thereby structures genetic variation within and between populations. However, in the presence of recombination an individual may inherit different regions of their genome from different parents, resulting in a mosaic of genealogical histories across the genome, which can be represented by an Ancestral Recombination Graph (ARG). In this case, different genomic regions may have different ancestral histories and so different histories of movement between populations. Recombination therefore poses an additional challenge to phylogeographic methods that aim to reconstruct the movement of individuals from genealogies, although also a potential benefit in that different loci may contain additional information about movement. Here, we introduce the Structured Coalescent with Ancestral Recombination (SCAR) model, which builds on recent approximations to the structured coalescent by incorporating recombination into the ancestry of sampled individuals. The SCAR model allows us to infer how the migration history of sampled individuals varies across the genome from ARGs, and improves estimation of key population genetic parameters such as population sizes, recombination rates and migration rates. Using the SCAR model, we explore the potential and limitations of phylogeographic inference using full ARGs. We then apply the SCAR to lineages of the recombining fungus Aspergillus flavus sampled across the United States to explore patterns of recombination and migration across the genome. 

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5. Surface-Radical Mobility Test by Self-Sorted Recombination: Symmetrical Product upon Recombination (SPR)

   https://doi.org/10.1021/acs.jpcb.1c01099  

   Belh, Sarah J. ; Ghosh, Goutam ; Greer, Alexander ( April 2021 , The Journal of Physical Chemistry B)

   null (Ed.)