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1. Whole exome sequencing identifies the potential for genetic rescue in iconic and critically endangered Panamanian harlequin frogs

   https://doi.org/10.1111/gcb.15405  

   Byrne, Allison Q.; Richards‐Zawacki, Corinne L.; Voyles, Jamie; Bi, Ke; Ibáñez, Roberto; Rosenblum, Erica Bree (November 2020, Global Change Biology)

   Abstract Avoiding extinction in a rapidly changing environment often relies on a species’ ability to quickly adapt in the face of extreme selective pressures. In Panamá, two closely related harlequin frog species (Atelopus variusandAtelopus zeteki) are threatened with extinction due to the fungal pathogenBatrachochytrium dendrobatidis(Bd). Once thought to be nearly extirpated from Panamá,A. variushave recently been rediscovered in multiple localities across their historical range; however,A. zetekiare possibly extinct in the wild. By leveraging a unique collection of 186Atelopustissue samples collected before and after theBdoutbreak in Panama, we describe the genetics of persistence for these species on the brink of extinction. We sequenced the transcriptome and developed an exome‐capture assay to sequence the coding regions of theAtelopusgenome. Using these genetic data, we evaluate the population genetic structure of historicalA. variusandA. zetekipopulations, describe changes in genetic diversity over time, assess the relationship between contemporary and historical individuals, and test the hypothesis that someA. variuspopulations have rapidly evolved to resist or tolerateBdinfection. We found a significant decrease in genetic diversity in contemporary (compared to historical)A. variuspopulations. We did not find strong evidence of directional allele frequency change or selection forBdresistance genes, but we uncovered a set of candidate genes that warrant further study. Additionally, we found preliminary evidence of recent migration and gene flow in one of the largest persistingA. variuspopulations in Panamá, suggesting the potential for genetic rescue in this system. Finally, we propose that previous conservation units should be modified, as clear genetic breaks do not exist beyond the local population level. Our data lay the groundwork for genetically informed conservation and advance our understanding of how imperiled species might be rescued from extinction. 

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2. Nutrient addition drives declines in grassland species richness primarily via enhanced species loss

   https://doi.org/10.1111/1365-2745.14038  

   Muehleisen, Andrew J.; Watkins, Carmen R. E.; Altmire, Gabriella R.; Shaw, E. Ashley; Case, Madelon F.; Aoyama, Lina; Brambila, Alejandro; Reed, Paul B.; LaForgia, Marina; Borer, Elizabeth T.; et al (November 2022, Journal of Ecology)

   Abstract Declines in grassland diversity in response to nutrient addition are a general consequence of global change. This decline in species richness may be driven by multiple underlying processes operating at different time‐scales. Nutrient addition can reduce diversity by enhancing the rate of local extinction via competitive exclusion, or by reducing the rate of colonization by constraining the pool of species able to colonize under new conditions. Partitioning net change into extinction and colonization rates will better delineate the long‐term effect of global change in grasslands.We synthesized changes in richness in response to experimental fertilization with nitrogen, phosphorus and potassium with micronutrients across 30 grasslands. We quantified changes in local richness, colonization, and extinction over 8–10 years of nutrient addition, and compared these rates against control conditions to isolate the effect of nutrient addition from background dynamics.Total richness at steady state in the control plots was the sum of equal, relatively high rates of local colonization and extinction. On aggregate, 30%–35% of initial species were lost and the same proportion of new species were gained at least once over a decade. Absolute turnover increased with site‐level richness but was proportionately greater at lower‐richness sites relative to starting richness. Loss of total richness with nutrient addition, especially N in combination with P or K, was driven by enhanced rates of extinction with a smaller contribution from reduced colonization. Enhanced extinction and reduced colonization were disproportionately among native species, perennials, and forbs. Reduced colonization plateaued after the first few (<5) years after nutrient addition, while enhanced extinction continued throughout the first decade.Synthesis. Our results indicate a high rate of colonizations and extinctions underlying the richness of ambient communities and that nutrient enhancement drives overall declines in diversity primarily by exclusion of previously established species. Moreover, enhanced extinction continues over long time‐scales, suggesting continuous, long‐term community responses and a need for long‐term study to fully realize the extinction impact of increased nutrients on grassland composition. 

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3. Range reduction of Oblong Rocksnail, Leptoxis compacta , shapes riverscape genetic patterns

   https://doi.org/10.7717/peerj.9789  

   Wright, Aaliyah D.; Garrison, Nicole L.; Williams, Ashantye’ S.; Johnson, Paul D.; Whelan, Nathan V. (January 2020, PeerJ)

   null (Ed.)

   Many freshwater gastropod species face extinction, including 79% of species in the family Pleuroceridae. The Oblong Rocksnail, Leptoxis compacta , is a narrow range endemic pleurocerid from the Cahaba River basin in central Alabama that has seen rapid range contraction in the last 100 years. Such a decline is expected to negatively affect genetic diversity in the species. However, precise patterns of genetic variation and gene flow across the restricted range of L. compacta are unknown. This lack of information limits our understanding of human impacts on the Cahaba River system and Pleuroceridae. Here, we show that L. compacta has likely seen a species-wide decline in genetic diversity, but remaining populations have relatively high genetic diversity. We also report a contemporary range extension compared to the last published survey. Our findings indicate that historical range contraction has resulted in the absence of common genetic patterns seen in many riverine taxa like isolation by distance as the small distribution of L. compacta allows for relatively unrestricted gene flow across its remaining range despite limited dispersal abilities. Two collection sites had higher genetic diversity than others, and broodstock sites for future captive propagation and reintroduction efforts should utilize sites identified here as having the highest genetic diversity. Broadly, our results support the hypothesis that range contraction will result in the reduction of species-wide genetic diversity, and common riverscape genetic patterns cannot be assumed to be present in species facing extinction risk. 

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4. West Indian Mammals The Old, the New, and the Recently Extinct

   Dávalos, L.M.; Turvey, S. (June 2012, Bones, Clones, and Biomes: An Extended History of Recent Neotropical Mammals)

   The West Indian mammal fauna has played a key role in the development of biogeographic ideas for over a century, but a synthesis explaining regional patterns of mammal diversity and distribution in a historical framework has not emerged. We review recent phylogenetic, population genetic, and radiocarbon dating studies of West Indian mammals and explore the biological and historical drivers of colonization, speciation, and extinction in this region of endemism. We also present the first complete list of all its extant and extinct mammals. The mammalian biota is older than was earlier presumed, with many ancient endemic lineages, even among highly vagile organisms such as bats. Land bridges, Cenozoic eustatic sea-level changes, and Pleistocene glacial cycles have been proposed to explain the colonization of the islands, but phylogenetic divergence analyses often conlict with the timing of these events and favor alternative biogeographic histories. The loss of West Indian biodiversity is incompletely understood, but new radiometric chronologies indicate that anthropogenic impacts rather than glacial-interglacial environmental changes are responsible for most Quaternary extinction and extirpation events involving land mammals. However, many outstanding questions of historical biogeography remain unresolved, including appropriate methods for interpreting phylogenies and divergence estimates in a biogeographic context, and whether to use vicariance or dispersal as the null hypothesis when investigating regional patterns of colonization, speciation, and extinction in comparative analyses. We propose synthetic approaches drawing from phylogenetics, population genetics, paleogeography, paleontology, and even archaeology to resolve persisting questions in Caribbean biogeography. 

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5. Oceanic islands of Wallacea as a source for dispersal and diversification of murine rodents

   https://doi.org/10.1111/jbi.13720  

   Rowe, Kevin_C; Achmadi, Anang_S; Fabre, Pierre‐Henri; Schenk, John_J; Steppan, Scott_J; Esselstyn, Jacob_A (October 2019, Journal of Biogeography)

   Abstract AimTo determine the historical dynamics of colonization and whether the relative timing of colonization predicts diversification rate in the species‐rich, murine rodent communities of Indo‐Australia. LocationIndo‐Australian Archipelago including the Sunda shelf of continental Asia, Sahul shelf of continental Australia, the Philippines and Wallacea of Indonesia. TaxonOrder Rodentia, Family Muridae. MethodsWe used a fossil‐calibrated molecular phylogeny and Bayesian biogeographical modelling to infer the frequency and temporal sequence of biogeographical transitions among Sunda, Sahul, the Philippines and Wallacea. We estimated diversification rates for each colonizing lineage using a method‐of‐moments estimator of net diversification and Bayesian mixture model estimates of diversification rate shifts. ResultsWe identified 17 biogeographical transitions, including nine originating from Sunda, seven originating from Sulawesi and broader Wallacea and one originating from Sahul. Wallacea was colonized eight times, the Phillipines five times, Sunda twice and Sahul twice. Net diversification rates ranged from 0.2 to 2.12 species/lineage/My with higher rates in secondary and later colonizers than primary colonizers. The highest rates were in the genusRattusand their closest relatives, irrespective of colonization history. Main ConclusionsOur inferences from murines demonstrate once again the substantial role of islands as sources of species diversity in terrestrial vertebrates of the IAA with most speciation events occurring on islands. Sulawesi and broader Wallacea have been a major source of colonists for both island and continental systems. Crossings of Wallace's Line were more common than subsequent transitions across Lydekker's Line to the east. While speciation following colonization of oceanic archipelagos and large islands is consistent with adaptive radiation theory and ideas regarding ecological opportunity, we did not observe a strong signal of incumbency effects. Rather, subsequent colonists of landmasses radiated unhindered by previous radiations. 

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