Phylogeographic analysis and species distribution modelling of the wood frog Batrachyla leptopus (Batrachylidae) reveal interglacial diversification in south western Patagonia

Comparing skin swabs, buccal swabs, and toe clips for amphibian genetic sampling, a case study with a small anuran (Acris blanchardi)

Multiple methods for collecting genetic samples from amphibians exist, each with their own implications for study design, animal welfare, and costs. Toe clipping is one common method, but there is ongoing debate regarding its potential detriment. Less invasive methods should be implemented, if efficacious, as amphibians are a particularly vulnerable vertebrate group. Skin and buccal swabbing are less invasive methods for genetic sampling, but the potential for contamination and a lower yield of DNA may exist. To compare these methods, we gathered skin swabs, buccal swabs, and toe clips from the same individuals of a relatively small anuran species, Blanchard's Cricket Frog (Acris blanchardi). We then compared DNA yield, DNA purity, amplification success rate, and genotypic data quality among sample types. We found toe clips and buccal swabs generated similar DNA yield and purity, with skin swabs yielding significantly less DNA of significantly lower purity than the other sample types. Amplification success rate was significantly higher using toe clips compared to the other sample types, though buccal swab samples amplified more readily than skin swabs. Genotypic data from toe clips and buccal swabs did not differ significantly in quality, but skin swab data quality was significantly lowest among sample types. Thus, skin swabbing could produce erroneous data in some situations, but buccal swabbing is likely an effective substitute to toe clipping, even for small species. Our results can help future researchers select which genetic sampling method might best suit their research needs.

Genomic diversity and Demographic History of the Dromiciops genus (Marsupialia: Microbiotheriidae)

Three orders represent the South American fauna of marsupials. Of these, Microbiotheria was until recently known as a monotypic genus with the only surviving species Dromiciops gliroides (monito del monte). The recent proposal of a new Dromiciops species (Dromiciops bicinovici), together with new information on the origin and diversification of living microbioterians has changed the prevailing paradigm around the evolutionary history of these emblematic marsupials. Here, we used a RADseq approach to test for evidence of admixture and past or current gene flow among both species of Dromiciops and evaluate the genetic structure within D. gliroides. We analyzed 127 samples of Dromiciops distributed across the known distribution range of both species. We also inferred the joint demographic history of these lineages, thus corroborating the status of D. bozinovici as a distinct species. Demographic history reconstruction indicated that D. bozinovici diverged from D. gliroides around 4my ago and has remained isolated and demographically stable ever since. In contrast, D. gliroides is subdivided into three subclades that experienced recent expansions and moderate gene flow among them (mostly from north to south). Furthermore, genetic distances among populations within D. gliroides were significantly correlated with geographic distances. These results suggest that some of the D. gliroides populations would have survived in glacial refuges, with posterior expansions after ice retreat. Our results have important implications for the systematics of the genus and have profound conservation consequences for the new species, especially considering the fragmentation level of the temperate rainforest.

Onthophagus pilauco sp. nov. (Coleoptera, Scarabaeidae): evidence of beetle extinction in the Pleistocene-Holocene transition in Chilean Northern Patagonia

The South American Pleistocene-Holocene transition has been characterized by drastic climatic and diversity changes. These rapid changes induced one of the largest and most recent extinctions in the megafauna at the continental scale. However, examples of the extinction of small animals (e.g., insects) are scarce, and the underlying causes of the extinction have been little studied. In this work, a new extinct dung beetle species is described from a late Pleistocene sequence (~15.2 k cal yr BP) at the paleoarcheological site Pilauco, Chilean Northern Patagonia. Based on morphological characters, this fossil is considered to belong to the genus Onthophagus Latreille, 1802 and named Onthophagus pilauco sp. nov. We carried out a comprehensive revision of related groups, and we analyzed the possible mechanism of diversification and extinction of this new species. We hypothesize that Onthophagus pilauco sp. nov. diversified as a member of the osculatii species-complex following migration processes related to the Great American Biotic Interchange (~3 Ma). The extinction of O. pilauco sp. nov. may be related to massive defaunation and climatic changes recorded in the Plesitocene-Holocene transition (12.8 k cal yr BP). This finding is the first record of this genus in Chile, and provides new evidence to support the collateral-extinction hypothesis related to the defaunation.

Genetic Diversity and Demographic History of the Shaggy Soft-Haired Mouse Abrothrix hirta (Cricetidae; Abrotrichini)

Genetic information on species can inform decision making regarding conservation of biodiversity since the response of organisms to changing environments depend, in part, on their genetic makeup. Territories of central-southern Chile and Argentina have undergone a varying degree of impact during the Quaternary, where the response of local fauna and flora was rather species-specific. Here, we focus on the sigmodontine rodent Abrothrix hirta, distributed from 35° S in Chile and Argentina to northern Tierra del Fuego. Based on 119,226 transcriptome-derived SNP loci from 46 individuals of A. hirta, we described the geographic distribution of the genetic diversity of this species using a maximum likelihood tree, principal component and admixture analyses. We also addressed the demographic history of the main intraspecific lineages of A. hirta using GADMA. We found that A. hirta exhibited four allopatric intraspecific lineages. Three main genetic groups were identified by a Principal Component Analysis and by Ancestry analysis. The demographic history of A. hirta was characterized by recent population stability for populations at the northernmost part of the range, while southern populations experienced a recent population expansion.