The alsodid ground frogs of the Eupsophus genus are divided into two groups, the roseus (2n = 30) and vertebralis (2n = 28), which are distributed throughout the temperate Nothofagus forests of South America. Currently, the roseus group is composed by four species, while the vertebralis group consists of two. Phylogenetic relationships and species delimitation within each group are controversial. In fact, previous analyses considered that the roseus group was composed of between four to nine species. In this work, we evaluated phylogenetic relationships, diversification times, and species delimitation within the roseus group using a multi-locus dataset. For this purpose, mitochondrial (D-loop, Cyt b, and COI) and nuclear (POMC and CRYBA1) partial sequences from 164 individuals were amplified, representing all species. Maximum Likelihood (ML) and Bayesian approaches were used to reconstruct phylogenetic relationships. Species tree was estimated using BEAST and singular value decomposition scores for species quartets (SVDquartets). Species limits were evaluated with six coalescent approaches. Diversification times were estimated using mitochondrial and nuclear rates with LogNormal relaxed clock in BEAST. Nine well-supported monophyletic lineages were recovered in Bayesian, ML, and SVDquartets, including eight named species and a lineage composed by specimens from the Villarrica population (Bootstrap:>70, PP:> 0.99). Single-locus species delimitation analyses overestimated the species number in E. migueli, E. calcaratus, and E. roseus lineages, while multi-locus analyses recovered as species the nine lineages observed in phylogenetic analyses (Ctax = 0.69). It is hypothesized that Eupsophus diversification occurred during Mid-Pleistocene (0.42–0.14 Mya), with most species having originated after the Last Southern Patagonian Glaciation (0.18 Mya). Our results revitalize the hypothesis that the E. roseus group is composed of eight species and support the Villarrica lineage as a new putative species.

BackgroundMorphological divergences of snake retinal structure point to complex evolutionary processes and adaptations. The Colubridae family has a remarkable variety of retinal structure that can range from all-cone and all-rod to duplex (cone/rod) retinas. To explore whether nocturnal versus diurnal activity is responsible for constraints on molecular evolution and plays a role in visual opsin spectral tuning of colubrids, we carried out molecular evolution analyses of the visual opsin genes LWS, RH1, and SWS1 from 17 species and performed morphological analyses.ResultsPhylogenetic reconstructions of the RH1 and LWS recovered major clades characterized by primarily diurnal or primarily nocturnal activity patterns, in contrast with the topology for SWS1, which is very similar to the species tree. We found stronger signals of purifying selection along diurnal and nocturnal lineages for RH1 and SWS1, respectively. A blue-shift of the RH1 spectral peak is associated with diurnal habits. Spectral tuning of cone opsins did not differ among diurnal and nocturnal species. Retinas of nocturnal colubrids had many rows of photoreceptor nuclei, with large numbers of rods, labeled by wheat germ agglutinin (WGA), and two types of cones: large cones sensitive to long/medium wavelengths (L/M) and small cones sensitive to ultra-violet/violet wavelengths (UV/VS). In contrast, retinas of diurnal species had only one row of photoreceptor nuclei, with four types of cones: large and double L/M cones, small UV/VS cones, and a second group of small cones, labeled by WGA.ConclusionsFor LWS gene, selection tests did not confirm different constraints related to activity pattern. For SWS1, stronger purifying selection in nocturnal lineages indicates divergent evolutionary pressures related to the activity pattern, and the importance of the short wavelength sensitivity at low light condition. Activity pattern has a clear influence on the signatures of selection and spectral tuning of RH1, with stronger purifying selection in diurnal lineages, which indicates selective pressure to preserve rhodopsin structure and function in pure-cone retinas. We suggest that the presence of four cone types in primarily diurnal colubrids might be related to the gain of color discrimination capacity.Electronic supplementary materialThe online version of this article (10.1186/s12862-017-1110-0) contains supplementary material, which is available to authorized users.

Oecomys is a genus of Neotropical arboreal rodents composed of 17 species with diploid number ranging from 2n = 54 to 86. Despite this high taxonomic and karyotypic diversity, the species-level systematics remains uncertain. We investigated the phylogenetic relationships and species delimitation of Oecomys using multiple approaches based on cytogenetic, molecular (mtDNA and nuDNA sequences) and morphological data sets. Sampling included 73 individuals from 25 localities in Amazonia, Cerrado, Pantanal and the Atlantic Forest, as well as 128 DNA sequences from GenBank. Molecular species boundaries associated with karyotype, morphological characters and geographic distribution led us to recognize 15 distinct lineages in Oecomys. These include five major well-supported clades composed of O. bicolor, O. catherinae, O. cleberi, O. mamorae, O. paricola and O. roberti, which were hypothesized as species complexes with at least eight putative new taxa. Three new karyotypes are also reported for the genus: 2n = 54 (FN = 54), 2n = 62 (FN = 62) and 2n = 70 (FN = 74). Sympatry of up to four species with different diploid numbers recovered in distinct clades illustrates the complex evolutionary history in Oecomys. These data highlight the importance of combining cytogenetic, morphological and geographic information along with molecular coalescent analyses in developing species delimitation scenarios.

Great genome size (GS) variations described in desert-specialist octodontid rodents include diploid species ( Octomys mimax and Octodontomys gliroides ) and putative tetraploid species ( Tympanoctomys barrerae and Pipanacoctomys aureus ). Because of its high DNA content, elevated chromosome number, and gigas effect, the genome of T. barrerae is claimed to have resulted from tetraploidy. Alternatively, the origin of its GS has been attributed to the accumulation of repetitive sequences. To better characterize the extent and origin of these repetitive DNA, self-genomic in situ hybridization (self-GISH), whole-comparative genomic hybridization (W-CGH), and conventional GISH were conducted in mitotic and meiotic chromosomes. Self-GISH on T. barrerae mitotic plates together with comparative self-GISH (using its closest relatives) discriminate a pericentromeric and a telomeric DNA fraction. As most of the repetitive sequences are pericentromeric, it seems that the large GS of T. barrerae is not due to highly repeated sequences accumulated along chromosomes arms. W-CGH using red-labeled P. aureus DNA and green-labeled O. mimax DNA simultaneously on chromosomes of T. barrerae revealed a yellow-orange fluorescence over a repetitive fraction of the karyotype. However, distinctive red-only fluorescent signals were also detected at some centromeres and telomeres, indicating closer homology with the DNA sequences of P. aureus. Conventional GISH using an excess of blocking DNA from either P. aureus or O. mimax labeled only a fraction of the T. barrerae genome, indicating its double genome composition. These data point to a hybrid nature of the T. barrerae karyotype, suggesting a hybridization event in the origin of this species.

The allotetraploid Tympanoctomys barrerae has a broad, patchy distribution around salt flats in western Argentina. To gain insights into its phylogenetic relationships, phylogeographical patterns, and origin, seven populations of T. barrerae and its allied taxa were studied through a 1075-bp fragment of cytochrome b and cytochrome oxidase I. Matrilineal phylogenetic relationships were explored with maximum likelihood and Bayesian approaches. The intraspecific genealogy was inferred by median-joining networks. The populational structure was assessed by molecular variance, and the demographic history through coalescence. The tree topology depicted sister-group relationship between Octomys mimax to the pair T. barrerae-Pipanacoctomys aureus, suggesting P. aureus belongs to the maternal lineage that gave rise to T. barrerae. High degrees of intrapopulational variation and the several instances of interpopulational polyphyly suggest range shifts and secondary contact. Consistent with the phylogenetic results, the network analysis revealed two haplotypic lineages depicting genetic admixtures unrelated to the current geographical distribution, and a deep split with the southernmost lineage of Chubut. The origin of T barrerae was estimated at approximately 2.52 Mya, whereas the divergence estimate for Chubut coincides with the end of largest Patagonian glaciation, at 1.47 Mya. Apparently, this population remained isolated during a northward Pleistocenic range shift. The historical demographic patterns of the lineages of T. barrerae fit with a contraction-expansion model coincident with Quaternary cycling events.

Endemic to South America, octodontid rodents are remarkable by being the only mammal taxa where allotetraploidy has been documented. The taxon's extensive morpho-physiological radiation associated to niche shifts has allowed testing phylogeographic hypotheses. Using maximum likelihood and Bayesian inference analyses, applied to all nominal species of octodontids, phylogenetic reconstructions based on sequences of 12S rRNA and growth hormone receptor gene are presented. Species boundaries were determined by coalescent analyses and divergence times among taxa were estimated based on mutation rates. Two main clades associated to the Andean orogenesis were recognized. The essentially western clade comprises genera Aconaemys, Octodon, Spalacopus, and Octodontomys whereas the eastern one included genera Octomys, Pipanacoctomys, Salinoctomys, and Tympanoctomys. Genetic relationships, coalescent analyses, and genetic distance supported the specific status given to Octodon pacificus and that given to Pipanacoctomys aureus as a species of Tympanoctomys. However, these analyses failed to recognize Salinoctomys loschalchalerosorum as a valid taxon considering its position within the diversity of Tympanoctomys barrerae. Although the origin of genome duplication remains contentious, the coincidence of the basal clade split with distinctive modes of karyotypic evolution across the Andes emphasizes the role of physiographic barriers and westerlies in shaping different edaphological conditions, selective grounds, and concomitantly distinct adaptations within the octodontids.

No abstract

We report the sequencing and compare the mitochondrial genomes of the South American ground frogs Eupsophus vertebralis and E. emiliopugini and reconstruct phylogenetic relationships among Eupsophus species. These genomes consist of 16,156 and 16,711 bp in length, respectively and contain 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes (tRNA), and partial non-coding D-loop region. Both genomes share 94.5% identity with 879 variable sites. A phylogenetic analysis with other available mitogenomes recovered both species as the sister clade of Alsodes gargola. Sequences from D-loop, CO1, and Cyt b, amplified and sequenced with primers developed from the mitochondrial genomes, allowed us to reconstruct phylogenetic relationships among Eupsophus species. Since our report represents the first mitogenomes for the genus Eupsophus, we expect these data will be valuable for further studies on conservation genetics and on the evolution of Patagonian amphibians.