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1. Geography shapes the phylogeny of frailejones (Espeletiinae Cuatrec., Asteraceae): a remarkable example of recent rapid radiation in sky islands

   https://doi.org/10.7717/peerj.2968  

   Diazgranados, Mauricio ; Barber, Janet C. ( February 2017 , PeerJ)

   The páramo ecosystem, located above the timberline in the tropical Andes, has been the setting for some of the most dramatic plant radiations, and it is one of the world’s fastest evolving and most diverse high-altitude ecosystems. Today 144+ species of frailejones (subtribe Espeletiinae Cuatrec., Asteraceae) dominate the páramo. Frailejones have intrigued naturalists and botanists, not just for their appealing beauty and impressive morphological diversity, but also for their remarkable adaptations to the extremely harsh environmental conditions of the páramo. Previous attempts to reconstruct the evolutionary history of this group failed to resolve relationships among genera and species, and there is no agreement regarding the classification of the group. Thus, our goal was to reconstruct the phylogeny of the frailejones and to test the influence of the geography on it as a first step to understanding the patterns of radiation of these plants.

   Field expeditions in 70 páramos of Colombia and Venezuela resulted in 555 collected samples from 110 species. Additional material was obtained from herbarium specimens. Sequence data included nrDNA (ITS and ETS) and cpDNA (rpl16), for an aligned total of 2,954 bp. Fragment analysis was performed with AFLP data using 28 primer combinations and yielding 1,665 fragments. Phylogeniesmore »based on sequence data were reconstructed under maximum parsimony, maximum likelihood and Bayesian inference. The AFLP dataset employed minimum evolution analyses. A Monte Carlo permutation test was used to infer the influence of the geography on the phylogeny.

   Phylogenies reconstructed suggest that most genera are paraphyletic, but the phylogenetic signal may be misled by hybridization and incomplete lineage sorting. A tree with all the available molecular data shows two large clades: one of primarily Venezuelan species that includes a few neighboring Colombian species; and a second clade of only Colombian species. Results from the Monte Carlo permutation test suggests a very strong influence of the geography on the phylogenetic relationships. Venezuelan páramos tend to hold taxa that are more distantly-related to each other than Colombian páramos, where taxa are more closely-related to each other.

   Our data suggest the presence of two independent radiations: one in Venezuela and the other in Colombia. In addition, the current generic classification will need to be deeply revised. Analyses show a strong geographic structure in the phylogeny, with large clades grouped in hotspots of diversity at a regional scale, and in páramo localities at a local scale. Differences in the degrees of relatedness between sympatric species of Venezuelan and Colombian páramos may be explained because of the younger age of the latter páramos, and the lesser time for speciation of Espeletiinae in them.

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2. Spintharus flavidus in the Caribbean—a 30 million year biogeographical history and radiation of a ‘widespread species’

   https://doi.org/10.7717/peerj.1422  

   Dziki, Austin ; Binford, Greta J. ; Coddington, Jonathan A. ; Agnarsson, Ingi ( November 2015 , PeerJ)

   The Caribbean island biota is characterized by high levels of endemism, the result of an interplay between colonization opportunities on islands and effective oceanic barriers among them. A relatively small percentage of the biota is represented by ‘widespread species,’ presumably taxa for which oceanic barriers are ineffective. Few studies have explored in detail the genetic structure of widespread Caribbean taxa. The cobweb spiderSpintharus flavidusHentz, 1850 (Theridiidae) is one of two describedSpintharusspecies and is unique in being widely distributed from northern N. America to Brazil and throughout the Caribbean. As a taxonomic hypothesis,Spintharus “flavidus”predicts maintenance of gene flow among Caribbean islands, a prediction that seems contradicted by knownS. flavidusbiology, which suggests limited dispersal ability. As part of an extensive survey of Caribbean arachnids (project CarBio), we conducted the first molecular phylogenetic analysis ofS. flaviduswith the primary goal of testing the ‘widespread species’ hypothesis. Our results, while limited to three molecular loci, reject the hypothesis of a single widespread species. Instead this lineage seems to represent a radiation with at least 16 species in the Caribbean region. Nearly all are short range endemics with several distinct mainland groups and others are single island endemics. While limited taxon sampling, with a single specimenmore »from S. America, constrains what we can infer about the biogeographical history of the lineage, clear patterns still emerge. Consistent with limited overwater dispersal, we find evidence for a single colonization of the Caribbean about 30 million years ago, coinciding with the timing of the GAARLandia landbridge hypothesis. In sum,S. “flavidus”is not a single species capable of frequent overwater dispersal, but rather a 30 my old radiation of single island endemics that provides preliminary support for a complex and contested geological hypothesis.

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3. Combining ultraconserved elements and mtDNA data to uncover lineage diversity in a Mexican highland frog ( Sarcohyla ; Hylidae)

   https://doi.org/10.7717/peerj.6045  

   Zarza, Eugenia ; Connors, Elizabeth M. ; Maley, James M. ; Tsai, Whitney L. E. ; Heimes, Peter ; Kaplan, Moises ; McCormack, John E. ( December 2018 , PeerJ)

   Molecular studies have uncovered significant diversity in the Mexican Highlands, leading to the description of many new endemic species. DNA approaches to this kind of species discovery have included both mitochondrial DNA (mtDNA) sequencing and multilocus genomic methods. While these marker types have often been pitted against one another, there are benefits to deploying them together, as linked mtDNA data can provide the bridge between uncovering lineages through rigorous multilocus genomic analysis and identifying lineages through comparison to existing mtDNA databases. Here, we apply one class of multilocus genomic marker, ultraconserved elements (UCEs), and linked mtDNA data to a species complex of frogs (Sarcohyla bistincta, Hylidae) found in the Mexican Highlands. We generated data from 1,891 UCEs, which contained 1,742 informative SNPs forS. bistinctaand closely related species and captured mitochondrial genomes for most samples. Genetic analyses based on both whole loci and SNPs agree there are six to seven distinct lineages within what is currently described asS. bistincta. Phylogenies from UCEs and mtDNA mostly agreed in their topologies, and the few differences suggested a more complex evolutionary history of the mtDNA marker. Our study demonstrates that the Mexican Highlands still hold substantial undescribed diversity, making their conservation a particularly urgentmore »goal. The Trans-Mexican Volcanic Range stands out as a significant geographic feature inSarcohylaand may have acted as a dispersal corridor forS. bistinctato spread to the north. Combining multilocus genomic data with linked mtDNA data is a useful approach for identifying potential new species and associating them with already described taxa, which will be especially important in groups with undescribed subadult phenotypes and cryptic species.

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4. A new, morphologically cryptic species of fanged frog, genus Limnonectes (Amphibia: Anura: Dicroglossidae), from Mindoro Island, central Philippines.

   Mark W. Herr, Johana Goyes ( January 2021 , Copeia)

   We describe a new species of fanged frog (genus Limnonectes) from Mindoro and Semirara Islands, of the Mindoro Pleistocene Aggregate Island Complex, of the central Philippines. Although morphologically indistinguishable from its closest relative, Limnonectes acanthi, of the Palawan faunal region, the two species can be readily diagnosed on the basis of spectral (dominant frequency) and temporal (pulse number and structure) properties of their advertisement calls, and their allopatric insular geographic ranges on permanently separate geological platforms which have not been connected by dry land in the recent geological past—all of which we interpret as congruent and independent lines of evidence supporting our recognition of two independently evolving evolutionary lineages (species). Ribosomal RNA mitochondrial gene sequences were used to provide genetic identification of specimens and estimate phylogenetic relationships; genetic divergences between Palawan and Mindoro faunal regions exceed those estimated among other, uncontroversial, phenotypically distinct Philippine species with equivalent levels of allopatry and biogeographic isolation. The recognition of the new species further emphasizes the degree to which even well-studied Philippine landmasses still harbor unrecognized biodiversity, and suggests that other widespread Philippine fanged frogs should be scrutinized for non-traditional diagnostic character differences (mate-recognition signal divergence, ecological differences, larval characteristics, life-history trait variation), especiallymore »when their geographic ranges span the archipelago’s permanent, deep-water trenches, which define its well-characterized Pleistocene Aggregate Island Complexes« less
5. The amphibian microbiome exhibits poor resilience following pathogen-induced disturbance

   https://doi.org/10.1038/s41396-020-00875-w  

   Jani, Andrea J. ; Bushell, Jessie ; Arisdakessian, Cédric G. ; Belcaid, Mahdi ; Boiano, Daniel M. ; Brown, Cathy ; Knapp, Roland A. ( February 2021 , The ISME Journal)

   Infectious pathogens can disrupt the microbiome in addition to directly affecting the host. Impacts of disease may be dependent on the ability of the microbiome to recover from such disturbance, yet remarkably little is known about microbiome recovery after disease, particularly in nonhuman animals. We assessed the resilience of the amphibian skin microbial community after disturbance by the pathogen,Batrachochytrium dendrobatidis(Bd). Skin microbial communities of laboratory-reared mountain yellow-legged frogs were tracked through three experimental phases: prior to Bd infection, after Bd infection (disturbance), and after clearing Bd infection (recovery period). Bd infection disturbed microbiome composition and altered the relative abundances of several dominant bacterial taxa. After Bd infection, frogs were treated with an antifungal drug that cleared Bd infection, but this did not lead to recovery of microbiome composition (measured as Unifrac distance) or relative abundances of dominant bacterial groups. These results indicate that Bd infection can lead to an alternate stable state in the microbiome of sensitive amphibians, or that microbiome recovery is extremely slow—in either case resilience is low. Furthermore, antifungal treatment and clearance of Bd infection had the additional effect of reducing microbial community variability, which we hypothesize results from similarity across frogs in the taxa thatmore »colonize community vacancies resulting from the removal of Bd. Our results indicate that the skin microbiota of mountain yellow-legged frogs has low resilience following Bd-induced disturbance and is further altered by the process of clearing Bd infection, which may have implications for the conservation of this endangered amphibian.

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