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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. Bounding the Number of Reticulations in a Tree-Child Network that Displays a Set of Trees

   Yufeng Wu and Louxin Zhang ( July 2023 , Comparative Genomics. RECOMB-CG 2023. Lecture Notes in Computer Science)

   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 paper, 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. 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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4. Topology Testing and Demographic Modeling Illuminate a Novel Speciation Pathway in the Greater Caribbean Sea Following the Formation of the Isthmus of Panama

   https://doi.org/10.1093/sysbio/syae045  

   Titus, Benjamin_M ; Gibbs, H_Lisle ; Simões, Nuno ; Daly, Marymegan ; Burbrink, ed., Frank ( July 2024 , Systematic Biology)

   Recent genomic analyses have highlighted the prevalence of speciation with gene flow in many taxa and have underscored the importance of accounting for these reticulate evolutionary processes when constructing species trees and generating parameter estimates. This is especially important for deepening our understanding of speciation in the sea where fast-moving ocean currents, expanses of deep water, and periodic episodes of sea level rise and fall act as soft and temporary allopatric barriers that facilitate both divergence and secondary contact. Under these conditions, gene flow is not expected to cease completely while contemporary distributions are expected to differ from historical ones. Here, we conduct range-wide sampling for Pederson’s cleaner shrimp (Ancylomenes pedersoni), a species complex from the Greater Caribbean that contains three clearly delimited mitochondrial lineages with both allopatric and sympatric distributions. Using mtDNA barcodes and a genomic ddRADseq approach, we combine classic phylogenetic analyses with extensive topology testing and demographic modeling (10 site frequency replicates × 45 evolutionary models × 50 model simulations/replicate = 22,500 simulations) to test species boundaries and reconstruct the evolutionary history of what was expected to be a simple case study. Instead, our results indicate a history of allopatric divergence, secondary contact, introgression, and endemic hybrid speciation that we hypothesize was driven by the final closure of the Isthmus of Panama and the strengthening of the Gulf Stream Current ~3.5 Ma. The history of this species complex recovered by model-based methods that allow reticulation differs from that recovered by standard phylogenetic analyses and is unexpected given contemporary distributions. The geologically and biologically meaningful insights gained by our model selection analyses illuminate what is likely a novel pathway of species formation not previously documented that resulted from one of the most biogeographically significant events in Earth’s history.

    

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5. 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)

   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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