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1. Evolutionary impacts of introgressive hybridization in a rapidly evolving group of jumping spiders (F. Salticidae, Habronattus americanus group)

   https://doi.org/https://doi.org/10.1016/j.ympev.2021.107165  

   Bougie, T.C.; Brelsford, A.; Hedin, M. (January 2021, Molecular phylogenetics and evolution)

   null (Ed.)

   Introgressive hybridization can be a powerful force impacting patterns of evolution at multiple taxonomic levels. We aimed to understand how introgression has affected speciation and diversification within a species complex of jumping spiders. The Habronattus americanus subgroup is a recently radiating group of jumping spiders, with species now in contact after hypothesized periods of isolation during glaciation cycles of the Pleistocene. Effects of introgression on genomes and morphology were investigated using phylogenomic and clustering methods using RADseq, ultraconserved elements (UCEs), and morphological data. We characterized 14 unique species/morphs using non-metric multidimensional scaling of morphological data, a majority of which were not recovered as monophyletic in our phylogenomic analyses. Morphological clusters and genetic lineages are highly incongruent, such that geographic region was a greater predictor of phylogenetic relatedness and genomic similarity than species or morph identity. STRUCTURE analyses support this pattern, revealing clusters corresponding to larger geographic regions. A history of rapid radiation in combination with frequent introgression seems to have mostly homogenized the genomes of species in this system, while selective forces maintain distinct male morphologies. GEMMA analyses support this idea by identifying SNPs correlated with distinct male morphologies. Overall, we have uncovered a system at odds with a typical bifurcating evolutionary model, instead supporting one where closely related species evolve together connected through multiple introgression events, creating a reticulate evolutionary history. 

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2. Computing the Bounds of the Number of Reticulations in a Tree-Child Network That Displays a Set of Trees

   https://doi.org/10.1089/cmb.2023.0309  

   Wu, Yufeng; Zhang, Louxin (April 2024, Journal of Computational Biology)

   Phylogenetic network is an evolutionary model that uses a rooted directed acyclic graph (instead of a tree) to model an evolutionary history of species in which reticulate events (e.g., hybrid speciation or horizontal gene transfer) occurred. Tree-child network is a kind of phylogenetic network with structural constraints. Existing approaches for tree-child network reconstruction can be slow for large data. In this study, we present several computational approaches for bounding from below the number of reticulations in a tree-child network that displays a given set of rooted binary phylogenetic trees. In addition, we also present some theoretical results on bounding from above the number of reticulations. Through simulation, we demonstrate that the new lower bounds on the reticulation number for tree-child networks can practically be computed for large tree data. The bounds can provide estimates of reticulation for relatively large data. 

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3. Allopatric divergence and secondary contact with gene flow: a recurring theme in rattlesnake speciation

   https://doi.org/10.1093/biolinnean/blz077  

   Schield, Drew R.; Perry, Blair W.; Adams, Richard H.; Card, Daren C.; Jezkova, Tereza; Pasquesi, Giulia I. M.; Nikolakis, Zachary L.; Row, Kristopher; Meik, Jesse M.; Smith, Cara F.; et al (June 2019, Biological Journal of the Linnean Society)

   Abstract The study of recently diverged lineages whose geographical ranges come into contact can provide insight into the early stages of speciation and the potential roles of reproductive isolation in generating and maintaining species. Such insight can also be important for understanding the strategies and challenges for delimiting species within recently diverged species complexes. Here, we use mitochondrial and nuclear genetic data to study population structure, gene flow and demographic history across a geographically widespread rattlesnake clade, the western rattlesnake species complex (Crotalus cerberus, Crotalus viridis, Crotalus oreganus and relatives), which contains multiple lineages with ranges that overlap geographically or contact one another. We find evidence that the evolutionary history of this group does not conform to a bifurcating tree model and that pervasive gene flow has broadly influenced patterns of present-day genetic diversity. Our results suggest that lineage diversity has been shaped largely by drift and divergent selection in isolation, followed by secondary contact, in which reproductive isolating mechanisms appear weak and insufficient to prevent introgression, even between anciently diverged lineages. The complexity of divergence and secondary contact with gene flow among lineages also provides new context for why delimiting species within this complex has been difficult and contentious historically. 

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4. Understanding Species Boundaries that Arise from Complex Histories: Gene Flow Across the Speciation Continuum in the Spotted Whiptail Lizards

   https://doi.org/10.1093/sysbio/syae040  

   Barley, Anthony J; Nieto-Montes_de_Oca, Adrián; Manríquez-Morán, Norma L; Thomson, Robert C (July 2024, Systematic Biology)

   Carstens, Bryan (Ed.)

   Gene flow between diverging lineages challenges the resolution of species boundaries and the understanding of evolutionary history in recent radiations. Here, we integrate phylogenetic and coalescent tools to resolve reticulate patterns of diversification and use a perspective focused on evolutionary mechanisms to distinguish interspecific and intraspecific taxonomic variation. We use this approach to resolve the systematics for one of the most intensively studied but difficult to understand groups of reptiles: the spotted whiptail lizards of the genus Aspidoscelis (A. gularis complex). Whiptails contain the largest number of unisexual species known within any vertebrate group and the spotted whiptail complex has played a key role in the generation of this diversity through hybrid speciation. Understanding lineage boundaries and the evolutionary history of divergence and reticulation within this group is therefore key to understanding the generation of unisexual diversity in whiptails. Despite this importance, long-standing confusion about their systematics has impeded understanding of which gonochoristic species have contributed to the formation of unisexual lineages. Using reduced representation genomic data, we resolve patterns of divergence and gene flow within the spotted whiptails and clarify patterns of hybrid speciation. We find evidence that biogeographically structured ecological and environmental variation has been important in morphological and genetic diversification, as well as the maintenance of species boundaries in this system. Our study elucidates how gene flow among lineages and the continuous nature of speciation can bias the practice of species delimitation and lead taxonomists operating under different frameworks to different conclusions (here we propose that a 2 species arrangement best reflects our current understanding). In doing so, this study provides conceptual and methodological insights into approaches to resolving diversification patterns and species boundaries in rapid radiations with complex histories, as well as long-standing taxonomic challenges in the field of systematic biology. 

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5. Strong postmating reproductive isolation in Mimulus section Eunanus

   https://doi.org/10.1111/jeb.14219  

   Farnitano, Matthew C.; Sweigart, Andrea L. (October 2023, Journal of Evolutionary Biology)

   Abstract Postmating reproductive isolation can help maintain species boundaries when premating barriers to reproduction are incomplete. The strength and identity of postmating reproductive barriers are highly variable among diverging species, leading to questions about their genetic basis and evolutionary drivers. These questions have been tackled in model systems but are less often addressed with broader phylogenetic resolution. In this study we analyse patterns of genetic divergence alongside direct measures of postmating reproductive barriers in an overlooked group of sympatric species within the model monkeyflower genus, Mimulus. Within this Mimulus brevipes species group, we find substantial divergence among species, including a cryptic genetic lineage. However, rampant gene discordance and ancient signals of introgression suggest a complex history of divergence. In addition, we find multiple strong postmating barriers, including postmating prezygotic isolation, hybrid seed inviability and hybrid male sterility. M. brevipes and M. fremontii have substantial but incomplete postmating isolation. For all other tested species pairs, we find essentially complete postmating isolation. Hybrid seed inviability appears linked to differences in seed size, providing a window into possible developmental mechanisms underlying this reproductive barrier. While geographic proximity and incomplete mating isolation may have allowed gene flow within this group in the distant past, strong postmating reproductive barriers today have likely played a key role in preventing ongoing introgression. By producing foundational information about reproductive isolation and genomic divergence in this understudied group, we add new diversity and phylogenetic resolution to our understanding of the mechanisms of plant speciation. Abstract Hybrid seed inviability and other postmating reproductive barriers isolate species in Mimulus section Eunanus. Variation in seed size may help explain hybrid seed failure. Whole-genome sequencing indicates a complex history of divergence, including signals of ancient introgression and cryptic diversity. 

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