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1. No link between population isolation and speciation rate in squamate reptiles

   https://doi.org/10.1073/pnas.2113388119  

   Singhal, Sonal ; Colli, Guarino R. ; Grundler, Maggie R. ; Costa, Gabriel C. ; Prates, Ivan ; Rabosky, Daniel L. ( January 2022 , Proceedings of the National Academy of Sciences)

   Rates of species formation vary widely across the tree of life and contribute to massive disparities in species richness among clades. This variation can emerge from differences in metapopulation-level processes that affect the rates at which lineages diverge, persist, and evolve reproductive barriers and ecological differentiation. For example, populations that evolve reproductive barriers quickly should form new species at faster rates than populations that acquire reproductive barriers more slowly. This expectation implicitly links microevolutionary processes (the evolution of populations) and macroevolutionary patterns (the profound disparity in speciation rate across taxa). Here, leveraging extensive field sampling from the Neotropical Cerrado biome in a biogeographically controlled natural experiment, we test the role of an important microevolutionary process—the propensity for population isolation—as a control on speciation rate in lizards and snakes. By quantifying population genomic structure across a set of codistributed taxa with extensive and phylogenetically independent variation in speciation rate, we show that broad-scale patterns of species formation are decoupled from demographic and genetic processes that promote the formation of population isolates. Population isolation is likely a critical stage of speciation for many taxa, but our results suggest that interspecific variability in the propensity for isolation has little influence on speciation rates.more »These results suggest that other stages of speciation—including the rate at which reproductive barriers evolve and the extent to which newly formed populations persist—are likely to play a larger role than population isolation in controlling speciation rate variation in squamates.« less
2. Population expansion, divergence, and persistence in Western Fence Lizards (Sceloporus occidentalis) at the northern extreme of their distributional range

   https://doi.org/10.1038/s41598-022-10233-9  

   Davis, Hayden R. ; Des Roches, Simone ; Anderson, Roger A. ; Leaché, Adam D. ( April 2022 , Scientific Reports)

   Population dynamics within species at the edge of their distributional range, including the formation of genetic structure during range expansion, are difficult to study when they have had limited time to evolve. Western Fence Lizards (Sceloporus occidentalis) have a patchy distribution at the northern edge of their range around the Puget Sound, Washington, where they almost exclusively occur on imperiled coastal habitats. The entire region was covered by Pleistocene glaciation as recently as 16,000 years ago, suggesting that populations must have colonized these habitats relatively recently. We tested for population differentiation across this landscape using genome-wide SNPs and morphological data. A time-calibrated species tree supports the hypothesis of a post-glacial establishment and subsequent population expansion into the region. Despite a strong signal for fine-scale population genetic structure across the Puget Sound with as many as 8–10 distinct subpopulations supported by the SNP data, there is minimal evidence for morphological differentiation at this same spatiotemporal scale. Historical demographic analyses suggest that populations expanded and diverged across the region as the Cordilleran Ice Sheet receded. Population isolation, lack of dispersal corridors, and strict habitat requirements are the key drivers of population divergence in this system. These same factors may prove detrimental tomore »the future persistence of populations as they cope with increasing shoreline development associated with urbanization.

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3. Sufficient versus optimal climatic stability during the Late Quaternary: using environmental quality to guide phylogeographic inferences in a Neotropical montane system

   https://doi.org/10.1093/jmammal/gyz162  

   Soley-Guardia, Mariano ; Carnaval, Ana Carolina ; Anderson, Robert P ( November 2019 , Journal of Mammalogy)

   Powell, Roger (Ed.)

   Abstract Quaternary climatic oscillations affected species distributions worldwide, creating cycles of connectivity and isolation that impacted population demography and promoted lineage divergence. These effects have been well studied in temperate regions. Taxa inhabiting mesic montane habitats in tropical ecosystems show high levels of endemism and diversification in the distinct mountain ranges they inhabit; such a pattern has commonly been ascribed to past climatic oscillations, but few phylogeographic studies have tested this hypothesis. Here, we combine ecological niche models of species distributions with molecular data to study phylogeographic patterns in two rodents endemic to the highlands of Costa Rica and western Panama (Reithrodontomys creper and Nephelomys devius). In so doing, we apply a novel approach that incorporates a basic ecological principle: the expected positive relationship between environmental suitability and population abundance. Specifically, we use niche models to predict potential patterns of population connectivity and stability of different suitability levels during climatic extremes of the last glacial–interglacial cycle; we then test these predictions with population genetic analyses of a mitochondrial and a nuclear marker. The detailed predictions arising from the different levels of suitability were moderately to highly congruent with the molecular data depending on the species. Overall, results suggest that inmore »these tropical montane ecosystems, cycles of population connectivity and isolation followed a pattern opposite to that typically described for temperate or lowland tropical ecosystems: namely, higher connectivity during the colder glacials, with isolation in montane refugia during the interglacials, including today. Nevertheless, the individualistic patterns for each species indicate a potentially wide gamut of phylogeographic histories reflecting particularities of their niches. Taken together, this study illustrates how phylogeographic inferences may benefit from niche model outputs that provide more detailed predictions of connectivity and finer characterizations of potential refugia through time.« less
4. Linking Biodiversity Data Using Evolutionary History

   https://doi.org/10.3897/biss.3.36207  

   McTavish, Emily Jane ( June 2019 , Biodiversity Information Science and Standards)

   All life on earth is linked by a shared evolutionary history. Even before Darwin developed the theory of evolution, Linnaeus categorized types of organisms based on their shared traits. We now know these traits derived from these species’ shared ancestry. This evolutionary history provides a natural framework to harness the enormous quantities of biological data being generated today. The Open Tree of Life project is a collaboration developing tools to curate and share evolutionary estimates (phylogenies) covering the entire tree of life (Hinchliff et al. 2015, McTavish et al. 2017). The tree is viewable at https://tree.opentreeoflife.org, and the data is all freely available online. The taxon identifiers used in the Open Tree unified taxonomy (Rees and Cranston 2017) are mapped to identifiers across biological informatics databases, including the Global Biodiversity Information Facility (GBIF), NCBI, and others. Linking these identifiers allows researchers to easily unify data from across these different resources (Fig. 1). Leveraging a unified evolutionary framework across the diversity of life provides new avenues for integrative wide scale research. Downstream tools, such as R packages developed by the R OpenSci foundation (rotl, rgbif) (Michonneau et al. 2016, Chamberlain 2017) and others tools (Revell 2012), make accessing and combining thismore »information straightforward for students as well as researchers (e.g. https://mctavishlab.github.io/BIO144/labs/rotl-rgbif.html). Figure 1. Example linking phylogenetic relationships accessed from the Open Tree of Life with specimen location data from Global Biodiversity Information Facility. For example, a recent publication by Santorelli et al. 2018 linked evolutionary information from Open Tree with species locality data gathered from a local field study as well as GBIF species location records to test a river-barrier hypothesis in the Amazon. By combining these data, the authors were able test a widely held biogeographic hypothesis across 1952 species in 14 taxonomic groups, and found that a river that had been postulated to drive endemism, was in fact not a barrier to gene flow. However, data provenance and taxonomic name reconciliation remain key hurdles to applying data from these large digital biodiversity and evolution community resources to answering biological questions. In the Amazonian river analysis, while they leveraged use of GBIF records as a secondary check on their species records, they relied on their an intensive local field study for their major conclusions, and preferred taxon specific phylogenetic resources over Open Tree where they were available (Santorelli et al. 2018). When Li et al. 2018 assessed large scale phylogenetic approaches, including Open Tree, for measuring community diversity, they found that synthesis phylogenies were less resolved than purpose-built phylogenies, but also found that these synthetic phylogenies were sufficient for community level phylogenetic diversity analyses. Nonetheless, data quality concerns have limited adoption of analyses data from centralized resources (McTavish et al. 2017). Taxonomic name recognition and reconciliation across databases also remains a hurdle for large scale analyses, despite several ongoing efforts to improve taxonomic interoperability and unify taxonomies, such at Catalogue of Life + (Bánki et al. 2018). In order to support innovative science, large scale digital data resources need to facilitate data linkage between resources, and address researchers' data quality and provenance concerns. I will present the model that the Open Tree of Life is using to provide evolutionary data at the scale of the entire tree of life, while maintaining traceable provenance to the publications and taxonomies these evolutionary relationships are inferred from. I will discuss the hurdles to adoption of these large scale resources by researchers, as well as the opportunities for new research avenues provided by the connections between evolutionary inferences and biodiversity digital databases.« less
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 contentiousmore »historically.

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