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1. Biogeography of the Caribbean Cyrtognatha spiders

   https://doi.org/10.1038/s41598-018-36590-y  

   Čandek, Klemen ; Agnarsson, Ingi ; Binford, Greta J. ; Kuntner, Matjaž ( January 2019 , Scientific Reports)

   Island systems provide excellent arenas to test evolutionary hypotheses pertaining to gene flow and diversification of dispersal-limited organisms. Here we focus on an orbweaver spider genusCyrtognatha(Tetragnathidae) from the Caribbean, with the aims to reconstruct its evolutionary history, examine its biogeographic history in the archipelago, and to estimate the timing and route of Caribbean colonization. Specifically, we test ifCyrtognathabiogeographic history is consistent with an ancient vicariant scenario (the GAARlandia landbridge hypothesis) or overwater dispersal. We reconstructed a species level phylogeny based on one mitochondrial (COI) and one nuclear (28S) marker. We then used this topology to constrain a time-calibrated mtDNA phylogeny, for subsequent biogeographical analyses in BioGeoBEARS of over 100 originally sampledCyrtognathaindividuals, using models with and without a founder event parameter. Our results suggest a radiation of CaribbeanCyrtognatha, containing 11 to 14 species that are exclusively single island endemics. Although biogeographic reconstructions cannot refute a vicariant origin of the Caribbean clade, possibly an artifact of sparse outgroup availability, they indicate timing of colonization that is much too recent for GAARlandia to have played a role. Instead, an overwater colonization to the Caribbean in mid-Miocene better explains the data. From Hispaniola,Cyrtognathasubsequently dispersed to, and diversified on, the other islands of themore »Greater, and Lesser Antilles. Within the constraints of our island system and data, a model that omits the founder event parameter from biogeographic analysis is less suitable than the equivalent model with a founder event.

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2. Using natural history to guide supervised machine learning for cryptic species delimitation with genetic data

   https://doi.org/10.1186/s12983-022-00453-0  

   Derkarabetian, Shahan ; Starrett, James ; Hedin, Marshal ( February 2022 , Frontiers in Zoology)

   The diversity of biological and ecological characteristics of organisms, and the underlying genetic patterns and processes of speciation, makes the development of universally applicable genetic species delimitation methods challenging. Many approaches, like those incorporating the multispecies coalescent, sometimes delimit populations and overestimate species numbers. This issue is exacerbated in taxa with inherently high population structure due to low dispersal ability, and in cryptic species resulting from nonecological speciation. These taxa present a conundrum when delimiting species: analyses rely heavily, if not entirely, on genetic data which over split species, while other lines of evidence lump. We showcase this conundrum in the harvesterTheromaster brunneus, a low dispersal taxon with a wide geographic distribution and high potential for cryptic species. Integrating morphology, mitochondrial, and sub-genomic (double-digest RADSeq and ultraconserved elements) data, we find high discordance across analyses and data types in the number of inferred species, with further evidence that multispecies coalescent approaches over split. We demonstrate the power of a supervised machine learning approach in effectively delimiting cryptic species by creating a “custom” training data set derived from a well-studied lineage with similar biological characteristics asTheromaster. This novel approach uses known taxa with particular biological characteristics to inform unknown taxamore »with similar characteristics, using modern computational tools ideally suited for species delimitation. The approach also considers the natural history of organisms to make more biologically informed species delimitation decisions, and in principle is broadly applicable for taxa across the tree of life.

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3. Phylogeographic inference of Sumatran ranids bearing gastromyzophorous tadpoles with regard to the Pleistocene drainage systems of Sundaland

   https://doi.org/10.1038/s41598-022-14722-9  

   Arifin, Umilaela ; Smart, Utpal ; Husemann, Martin ; Hertwig, Stefan T. ; Smith, Eric N. ; Iskandar, Djoko T. ; Haas, Alexander ( July 2022 , Scientific Reports)

   Rivers are known to act as biogeographic barriers in several strictly terrestrial taxa, while possibly serving as conduits of dispersal for freshwater-tolerant or -dependent species. However, the influence of river systems on genetic diversity depends on taxa-specific life history traits as well as other geographic factors. In amphibians, several studies have demonstrated that river systems have only minor influence on their divergence. Here, we assess the role of the paleodrainage systems of the Sunda region (with a focus on the island of Sumatra) in shaping the evolutionary history of two genera of frogs (SumateranaandWijayarana) whose tadpoles are highly dependent on cascading stream habitats. Our phylogenetic results show no clear association between the genetic diversification patterns of both anurans genera and the existence of paleodrainage systems. Time-calibrated phylogenies and biogeographical models suggest that these frogs colonized Sumatra and diversified on the island before the occurrence of the Pleistocene drainage systems. Both genera demonstrate phylogenetic structuring along a north–south geographic axis, the temporal dynamics of which coincide with the geological chronology of proto Sumatran and -Javan volcanic islands. Our results also highlight the chronic underestimation of Sumatran biodiversity and call for more intense sampling efforts on the island.
4. Dynamic colonization history in a rediscovered Isle Royale carnivore

   https://doi.org/10.1038/s41598-018-31130-0  

   Manlick, Philip J. ; Romanski, Mark C. ; Pauli, Jonathan N. ( August 2018 , Scientific Reports)

   Island ecosystems are globally threatened, and efforts to restore historical communities are widespread. Such conservation efforts should be informed by accurate assessments of historical community composition to establish appropriate restoration targets. Isle Royale National Park is one of the most researched island ecosystems in the world, yet little is actually known about the biogeographic history of most Isle Royale taxa. To address this uncertainty and inform restoration targets, we determined the phylogeographic history of American martens (Martes americana), a species rediscovered on Isle Royale 76 years after presumed extirpation. We characterized the genetic composition of martens throughout the Great Lakes region using nuclear and mitochondrial markers, identified the source of Isle Royale martens using genetic structure analyses, and used demographic bottleneck tests to evaluate (eliminate redundancy of test). 3 competing colonization scenarios. Martens exhibited significant structure regionally, including a distinct Isle Royale cluster, but mitochondrial sequences revealed no monophyletic clades or evolutionarily significant units. Rather, martens were historically extirpated and recolonized Isle Royale from neighbouring Ontario, Canada in the late 20^thcentury. These findings illustrate the underappreciated dynamics of island communities, underscore the importance of historical biogeography for establishing restoration baselines, and provide optimism for extirpated and declining Isle Royalemore »vertebrates whose reintroductions have been widely debated.

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5. Ancient DNA Reconstructs the Genetic Legacies of Precontact Puerto Rico Communities

   https://doi.org/10.1093/molbev/msz267  

   Nieves-Colón, Maria A. ; Pestle, William J. ; Reynolds, Austin W. ; Llamas, Bastien ; de la Fuente, Constanza ; Fowler, Kathleen ; Skerry, Katherine M. ; Crespo-Torres, Edwin ; Bustamante, Carlos D. ; Stone, Anne C. ; et al ( November 2019 , Molecular Biology and Evolution)

   Indigenous peoples have occupied the island of Puerto Rico since at least 3000 BC. Due to the demographic shifts that occurred after European contact, the origin(s) of these ancient populations, and their genetic relationship to present-day islanders, are unclear. We use ancient DNA to characterize the population history and genetic legacies of precontact Indigenous communities from Puerto Rico. Bone, tooth, and dental calculus samples were collected from 124 individuals from three precontact archaeological sites: Tibes, Punta Candelero, and Paso del Indio. Despite poor DNA preservation, we used target enrichment and high-throughput sequencing to obtain complete mitochondrial genomes (mtDNA) from 45 individuals and autosomal genotypes from two individuals. We found a high proportion of Native American mtDNA haplogroups A2 and C1 in the precontact Puerto Rico sample (40% and 44%, respectively). This distribution, as well as the haplotypes represented, supports a primarily Amazonian South American origin for these populations and mirrors the Native American mtDNA diversity patterns found in present-day islanders. Three mtDNA haplotypes from precontact Puerto Rico persist among Puerto Ricans and other Caribbean islanders, indicating that present-day populations are reservoirs of precontact mtDNA diversity. Lastly, we find similarity in autosomal ancestry patterns between precontact individuals from Puerto Ricomore »and the Bahamas, suggesting a shared component of Indigenous Caribbean ancestry with close affinity to South American populations. Our findings contribute to a more complete reconstruction of precontact Caribbean population history and explore the role of Indigenous peoples in shaping the biocultural diversity of present-day Puerto Ricans and other Caribbean islanders.

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