Exploitation of mitochondrial nad6 as a complementary marker for studying population variability in Lepidoptera

The applicability of mitochondrial nad6 sequences to studies of DNA and population variability in Lepidoptera was tested in four species of economically important moths and one of wild butterflies. The genetic information so obtained was compared to that of cox1 sequences for two species of Lepidoptera. nad6 primers appropriately amplified all the tested DNA targets, the generated data proving to be as informative and suitable in recovering population structures as that of cox1. The proposal is that, to obtain more robust results, this mitochondrial region can be complementarily used with other molecular sequences in studies of low level phylogeny and population genetics in Lepidoptera

Successful application of ancient DNA extraction and library construction protocols to museum wet collection specimens

Millions of scientific specimens are housed in museum collections, a large part of which are fluid preserved. The use of formaldehyde as fixative and subsequent storage in ethanol is especially common in ichthyology and herpetology. This type of preservation damages DNA and reduces the chance of successful retrieval of genetic data. We applied ancient DNA extraction and single stranded library construction protocols to a variety of vertebrate samples obtained from wet collections and of different ages. Our results show that almost all samples tested yielded endogenous DNA. Archival DNA extraction was successful across different tissue types as well as using small amounts of tissue. Conversion of archival DNA fragments into single-stranded libraries resulted in usable data even for samples with initially undetectable DNA amounts. Subsequent target capture approaches for mitochondrial DNA using homemade baits on a subset of 30 samples resulted in almost complete mitochondrial genome sequences in several instances. Thus, application of ancient DNA methodology makes wet collection specimens, including type material as well as rare, old or extinct species, accessible for genetic and genomic analyses. Our results, accompanied by detailed step-by-step protocols, are a large step forward to open the DNA archive of museum wet collections for scientific studies.publishedVersio

Taxonomic Review of South American Butter Frogs: Phylogeny, Geographic Patterns, and Species Delimitation in the Leptodactylus latrans Species Group (Anura: Leptodactylidae)

The Leptodactylus latrans species group currently comprises eight medium- to large-sized frog species with a convoluted taxonomic history, particularly related to the specific limits of the L. latrans complex, and the species pair Leptodactylus chaquensis–Leptodactylus macrosternum. Their homogeneous external morphology and continental geographic distribution in South America have posed severe limitations to a comprehensive review, such that taxonomic consensus and species limits remain uncertain. This is further worsened by the presence of chromatic polymorphism among coexisting species that can hardly be distinguished by external morphology. Based on a large-scale geographic sampling including multilocus DNA analyses, and acoustic and morphological data, we provide a comprehensive evaluation of the taxonomic status and species limits of the L. latrans group, focusing on the resolution of the L. latranscomplex and the species pair L. chaquensis–L. macrosternum. We gathered 728 mitochondrial sequences from 429 localities, encompassing the entire geographic distribution of the group. Both generalized mixed Yule coalescent and automatic barcode gap discovery species delimitation methods recovered four major mitochondrial evolutionary lineages within the L. latrans complex, also supported by distribution patterns, multilocus molecular, morphological and/or bioacoustic data. One lineage is linked to nominal L. latrans,one revalidated as Leptodactylus luctator, and the other two are formally named and described. Another lineage encompasses all specimens previously assigned to the species pair L. chaquensis–L. macrosternum, clustered as a single evolutionary entity and is now regarded as L. macrosternum. We provide a revised diagnosis for these species based on acoustic data, morphological/chromatic variation, and phylogenetic relationships of all species currently included in the L. latrans group. Our findings reinforce the view that Neotropical diversity is highly underestimated and stress that appropriate geographic sampling in an integrative framework is crucial for the establishment of specific limits among broadly distributed and morphologically cryptic Neotropical frogs

Seeing the forest through many trees: multi-taxon patterns of phylogenetic diversity in the Atlantic Forest hotspot

We combine phylogenetic and point locality data from selected lineages of the Atlantic Forest flora and fauna to compare spatial patterns of biodiversity sustained by the current configuration of forest remnants to a scenario of complete forest preservation. We then ask the question "how much biodiversity is likely lost, already"? Specifically, we assess how habitat loss likely impacted the climatic spaces occupied by the local species, the inferred composition of local communities and the spatial distribution of phylogenetic diversity and endemism

Environmental correlates of taxonomic and phylogenetic diversity in the Atlantic Forest

Aim There is little consensus on which environmental variables are best at predicting multiple dimensions of diversity. We ask whether there are common environmental correlates of diversity, despite ecological differences, across nine clades of plants and animals distributed along a single rainforest domain. For that, we compare the environmental correlates of species richness, phylogenetic diversity, and phylogenetic endemism. Location Brazilian Atlantic Forest. Taxon:Five clades of plants (Bromelioideae, Miconieae, Bertolonia, Cambessedesieae, and the Fridericia and allies) and four clades of animals (butterlies in the tribe Ithomiini, frogs in the genera Boana and Proceratophrys, and birds in the subfamily Thraupinae). Methods Using curated occurrence localities and phylogenetic data, we generated maps of (a) species richness, (b) phylogenetic diversity, (c) residuals of phylogenetic diversity regressed on species richness, and (d) phylogenetic endemism for all groups. We also compiled a set of 30 environmental descriptors, including records of current temperature and precipitation, climatic stability over time, and topography. Through a machine learning framework, we explored the environmental correlates of each of these diversity measures for each group. Results The environmental variables used here were strong predictors of diversity for all studied groups. However, models for phylogenetic endemism had lower predictive power. Although patterns of diversity are different among groups, correlates of diversity are consistent across taxa. For both species richness and phylogenetic diversity, current precipitation and precipitation stability over time were consistently ranked among the variables that strongly correlate with diversity patterns. The correlates of phylogenetic endemism were less homogeneous across groups. The results suggest that including climate stability over time is important when predicting diversity measures that reflect historical components. Main conclusions Investigating environmental correlates of diversity for multiple clades and diversity measures in a single geographic area allows for a better understanding of common patterns across taxa. This study shows that environmental conditions, particularly precipitation, are good predictors of the patterns of species richness and phylogenetic diversity‐but not phylogenetic endemism‐across different Atlantic Forest groups.Additional co-authors: Marcelo Reginato, Karina Lucas Silva‐Brandão, André Victor Lucci Freitas, Renato Goldenberg, Lúcia G. Lohmann, Fabián A. Michelangeli, Cristina Miyaki, Miguel T. Rodrigues, Ana C. Carnava

Determinants of anti-PD-1 response and resistance in clear cell renal cell carcinoma.

ADAPTeR is a prospective, phase II study of nivolumab (anti-PD-1) in 15 treatment-naive patients (115 multiregion tumor samples) with metastatic clear cell renal cell carcinoma (ccRCC) aiming to understand the mechanism underpinning therapeutic response. Genomic analyses show no correlation between tumor molecular features and response, whereas ccRCC-specific human endogenous retrovirus expression indirectly correlates with clinical response. T cell receptor (TCR) analysis reveals a significantly higher number of expanded TCR clones pre-treatment in responders suggesting pre-existing immunity. Maintenance of highly similar clusters of TCRs post-treatment predict response, suggesting ongoing antigen engagement and survival of families of T cells likely recognizing the same antigens. In responders, nivolumab-bound CD8+ T cells are expanded and express GZMK/B. Our data suggest nivolumab drives both maintenance and replacement of previously expanded T cell clones, but only maintenance correlates with response. We hypothesize that maintenance and boosting of a pre-existing response is a key element of anti-PD-1 mode of action

High Levels of Diversity Uncovered in a Widespread Nominal Taxon: Continental Phylogeography of the Neotropical Tree Frog

Species distributed across vast continental areas and across major biomes provide unique model systems for studies of biotic diversification, yet also constitute daunting financial, logistic and political challenges for data collection across such regions. The tree frog Dendropsophus minutus (Anura: Hylidae) is a nominal species, continentally distributed in South America, that may represent a complex of multiple species, each with a more limited distribution. To understand the spatial pattern of molecular diversity throughout the range of this species complex, we obtained DNA sequence data from two mitochondrial genes, cytochrome oxidase I (COI) and the 16S rhibosomal gene (16S) for 407 samples of D. minutus and closely related species distributed across eleven countries, effectively comprising the entire range of the group. We performed phylogenetic and spatially explicit phylogeographic analyses to assess the genetic structure of lineages and infer ancestral areas. We found 43 statistically supported, deep mitochondrial lineages, several of which may represent currently unrecognized distinct species. One major clade, containing 25 divergent lineages, includes samples from the type locality of D. minutus. We defined that clade as the D. minutus complex. The remaining lineages together with the D. minutus complex constitute the D. minutus species group. Historical analyses support an Amazonian origin for the D. minutus species group with a subsequent dispersal to eastern Brazil where the D. minutus complex originated. According to our dataset, a total of eight mtDNA lineages have ranges >100,000 km2. One of them occupies an area of almost one million km2 encompassing multiple biomes. Our results, at a spatial scale and resolution unprecedented for a Neotropical vertebrate, confirm that widespread amphibian species occur in lowland South America, yet at the same time a large proportion of cryptic diversity still remains to be discovered

FIGURE 2 in A lost species or the loss of stripes? The case of Contomastix lizards from Cabo Polonio, Uruguay, with observations on C. lacertoides (Duméril & Bibron) and Cnemidophorus grandensis Cope (Squamata, Teiidae)

FIGURE 2. Uruguayan specimens of Contomastix lacertoides. On top, unvouchered adult male photographed while basking at La Palma, Rivera (orange color corresponds to parasitic mites); inset: detail of sexual color dimorphism in a male from Quebrada de los Cuervos, Treinta y Tres (MNHN 9460). Bottom, adult female from Quebrada de los Cuervos, (MNHN 9461, total length 196 mm).Published as part of <i>Borteiro, Claudio, Kolenc, Francisco, Prigioni, Carlos, Lyra, Mariana L. & Baldo, Diego, 2013, A lost species or the loss of stripes? The case of Contomastix lizards from Cabo Polonio, Uruguay, with observations on C. lacertoides (Duméril & Bibron) and Cnemidophorus grandensis Cope (Squamata, Teiidae), pp. 245-259 in Zootaxa 3620 (2)</i> on page 248, DOI: 10.11646/zootaxa.3620.2.3, <a href="http://zenodo.org/record/10097469">http://zenodo.org/record/10097469</a&gt