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1. The rises and falls of turritellid gastropods during the Cenozoic in the western Atlantic

   Allmon, WD; Anderson, BM (July 2024, Museum of Paleontology, The University of Michigan; Papers on Paleontology)

   and frequently-occurring marine macrofossil groups of the past 100+ million years worldwide. From their apparent origin in central Tethys in the late Jurassic they spread across most of the world’s oceans by the Late Cretaceous. They suffered substantial extinction at the K-Pg but diversified quickly thereafter, and they were present on every continent during the Paleogene. The record of their diversity, abundance, and morphology during the Cenozoic has become clearer due to recent studies of body size, molecular phylogenetic analysis, and systematic treatments of Paleogene, Miocene, and Plio-Pleistocene fossils from the Western Atlantic region (southeastern North America, the Caribbean, Central America, and northern South America). A database (still a work in progress) of more than 230 described species from this region shows turritellid diversity of more than 20 species in the Paleocene, a low of fewer than 10 in the early Eocene, a peak of more than 80 in the Miocene, a decline to around 20 in the Pliocene, and a decline to only 4 species in the central Western Atlantic today. Diversity within single formations shows a slightly different pattern, with highs of 11–16 species in the Late Miocene of Colombia and 18 species in the Late Pliocene Pinecrest Sand of Florida. Overall abundance has also declined, with turritellid-dominated assemblages common across the region throughout the Cenozoic, but limited today to only small areas of northern Venezuela. Higher taxonomic assignments of fossil and Recent turritellids and their phylogenetic relationships are still poorly known (and are likely to remain so for many species), but recent molecular data and systematic work on fossil turritellids indicate that several clades (e.g., Torcula) persisted in the region throughout the Cenozoic, while other groups which became significant likely appeared in the Miocene, including Vermicularia and Caviturritella. A common pattern in all of this change is correlation with likely patterns of primary productivity. Hyperdiverse assemblages and high regional diversity of turritellids appear to occur at times and places of high productivity, frequently in association with upwelling or significant terrestrial runoff, and patterns of extinction (temporal and geographic) correlate with declines in productivity. Funding source: NSF DEB 2225014 

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2. A general approach for inferring the ancestry of recent ancestors of an admixed individual

   https://doi.org/10.1073/pnas.2316242120  

   Zhang, Yiming; Zhang, Haotian; Wu, Yufeng (January 2024, Proceedings of the National Academy of Sciences)

   The genome of an individual from an admixed population consists of segments originated from different ancestral populations. Most existing ancestry inference approaches focus on calling these segments for the extant individual. In this paper, we present a general ancestry inference approach for inferring recent ancestors from an extant genome. Given the genome of an individual from a recently admixed population, our method can estimate the proportions of the genomes of the recent ancestors of this individual that originated from some ancestral populations. The key step of our method is the inference of ancestors (called founders) right after the formation of an admixed population. The inferred founders can then be used to infer the ancestry of recent ancestors of an extant individual. Our method is implemented in a computer program called PedMix2. To the best of our knowledge, there is no existing method that can practically infer ancestors beyond grandparents from an extant individual’s genome. Results on both simulated and real data show that PedMix2 performs well in ancestry inference. 

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3. Selectivity of mass extinctions: Patterns, processes, and future directions

   https://doi.org/10.1017/ext.2023.10  

   Payne, Jonathan L.; Al Aswad, Jood A.; Deutsch, Curtis; Monarrez, Pedro M.; Penn, Justin L.; Singh, Pulkit (January 2023, Cambridge Prisms: Extinction)

   Abstract A central question in the study of mass extinction is whether these events simply intensify background extinction processes and patterns versus change the driving mechanisms and associated patterns of selectivity. Over the past two decades, aided by the development of new fossil occurrence databases, selectivity patterns associated with mass extinction have become increasingly well quantified and their differences from background patterns established. In general, differences in geographic range matter less during mass extinction than during background intervals, while differences in respiratory and circulatory anatomy that may correlate with tolerance to rapid change in oxygen availability, temperature, and pH show greater evidence of selectivity during mass extinction. The recent expansion of physiological experiments on living representatives of diverse clades and the development of simple, quantitative theories linking temperature and oxygen availability to the extent of viable habitat in the oceans have enabled the use of Earth system models to link geochemical proxy constraints on environmental change with quantitative predictions of the amount and biogeography of habitat loss. Early indications are that the interaction between physiological traits and environmental change can explain substantial proportions of observed extinction selectivity for at least some mass extinction events. A remaining challenge is quantifying the effects of primary extinction resulting from the limits of physiological tolerance versus secondary extinction resulting from the loss of taxa on which a given species depended ecologically. The calibration of physiology-based models to past extinction events will enhance their value in prediction and mitigation efforts related to the current biodiversity crisis. 

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4. Climate change, extinction, and Sky Island biogeography in a montane lizard

   https://doi.org/10.1111/mec.15073  

   Wiens, John J.; Camacho, Agustín; Goldberg, Aaron; Jezkova, Tereza; Kaplan, Matthew E.; Lambert, Shea M.; Miller, Elizabeth C.; Streicher, Jeffrey W.; Walls, Ramona L. (May 2019, Molecular Ecology)

   Abstract Around the world, many species are confined to “Sky Islands,” with different populations in isolated patches of montane habitat. How does this pattern arise? One scenario is that montane species were widespread in lowlands when climates were cooler, and were isolated by local extinction caused by warming conditions. This scenario implies that many montane species may be highly susceptible to anthropogenic warming. Here, we test this scenario in a montane lizard (Sceloporus jarrovii) from the Madrean Sky Islands of southeastern Arizona. We combined data from field surveys, climate, population genomics, and physiology. Overall, our results support the hypothesis that this species' current distribution is explained by local extinction caused by past climate change. However, our results for this species differ from simple expectations in several ways: (a) their absence at lower elevations is related to warm winter temperatures, not hot summer temperatures; (b) they appear to exclude a low‐elevation congener from higher elevations, not the converse; (c) they are apparently absent from many climatically suitable but low mountain ranges, seemingly “pushed off the top” by climates even warmer than those today; (d) despite the potential for dispersal among ranges during recent glacial periods (~18,000 years ago), populations in different ranges diverged ~4.5–0.5 million years ago and remained largely distinct; and (e) body temperatures are inversely related to climatic temperatures among sites. These results may have implications for many other Sky Island systems. More broadly, we suggest that Sky Island species may be relevant for predicting responses to future warming. 

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5. Microgeographic population structuring in a genus of California trapdoor spiders and discovery of an enigmatic new species (Euctenizidae: Promyrmekiaphila korematsui sp. nov.)

   https://doi.org/10.1002/ece3.10983  

   Starrett, James; Jochim, Emma_E; Quayle, Iris_L; Zahnle, Xavier_J; Bond, Jason_E (March 2024, Ecology and Evolution)

   Abstract The recognition and delineation of cryptic species remains a perplexing problem in systematics, evolution, and species delimitation. Once recognized as such, cryptic species complexes provide fertile ground for studying genetic divergence within the context of phenotypic and ecological divergence (or lack thereof). Herein we document the discovery of a new cryptic species of trapdoor spider,Promyrmekiaphila korematsuisp. nov. Using subgenomic data obtained via target enrichment, we document the phylogeography of the California endemic genusPromyrmekiaphilaand its constituent species, which also includesP. clathrataandP. winnemem. Based on these data we show a pattern of strong geographic structuring among populations but cannot entirely discount recent gene flow among populations that are parapatric, particularly for deeply diverged lineages withinP. clathrata. The genetic data, in addition to revealing a new undescribed species, also allude to a pattern of potential phenotypic differentiation where species likely come into close contact. Alternatively, phenotypic cohesion among genetically divergentP. clathratalineages suggests that some level of gene flow is ongoing or occurred in the recent past. Despite considerable field collection efforts over many years, additional sampling in potential zones of contact for both species and lineages is needed to completely resolve the dynamics of divergence inPromyrmekiaphilaat the population–species interface. 

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