Underground speciation: Unraveling the systematics and evolution of the highly diverse tuco-tucos (genus Ctenomys) with genomic data.

Subterranean rodents of the genus Ctenomys (tuco-tucos) are endemic to South America and have experienced relatively recent radiation. There are about 67 recognized species that originated in approximately 1-2 MY. They stand out for their species richness, extraordinary chromosomal diversity, and wide range of habitat they occupy in the continent. Phylogenetic relationships among species of tuco-tucos have been challenging to resolve. Groups of closely-related species have been suggested, but their relationships must be resolved. This study estimates the phylogeny of the genus using massive sequencing, generating thousands of independent molecular markers obtained by RADseq, with a taxonomic sampling that includes 66% of the recognized species. The sequences obtained were mapped against the C. sociabilis genome, recovering up to 1,215 widely shared RAD loci with more than 19,000 polymorphic sites. Our new phylogenetic hypothesis corroborated the species groups previously proposed with cytochrome b gene sequences and provided a much greater resolution of the relationships among species groups. The frater group is sister to all other tuco-tucos, whereas some of the earlierliest proposals placed the sociabilis group as sister to all other tuco-tucos. Ctenomys leucodon, previously proposed as an independent lineage, is associated with the frater group with moderate statistical support. The magellanicus and mendocinus are sister groups in a major clade formed by the boliviensis, talarum, tucumanus, torquatus, and opimus groups. Ctenomys viperinus, included in the phylogeny for the first time, belongs to the tucumanus group. This multi-locus phylogenetic hypothesis provides insights into the historical biogeography of understanding this highly diverse genus.

Influences of landscape characteristics and historical barriers on the population genetic structure in the endangered sand-dune subterranean rodent Ctenomys australis.

Understanding the processes and patterns of local adaptation and migration involves an exhaustive knowledge of how landscape features and population distances shape the genetic variation at the geographical level. Ctenomys australis is an endangered subterranean rodent characterized by having a restricted geographic range immerse in a highly fragmented sand dune landscape in the Southeast of Buenos Aires province, Argentina. We use 13 microsatellite loci in a total of 194 individuals from 13 sampling sites to assess the dispersal patterns and population structure in the complete geographic range of this endemic species. Our analyses show that populations are highly structured with low rates of gene flow among them. Genetic differentiation among sampling sites was consistent with an isolation by distance pattern, however, an important fraction of the population differentiation was explained by natural barriers such as rivers and streams. Although the individuals were sampled at locations distanced from each other, we also use some landscape genetics approaches to evaluate the effects of landscape configuration on the genetic connectivity among populations. These analyses showed that the sand dune habitat availability (the most suitable habitat for the occupation of the species), was one of the main factors that explained the differentiation patterns of the different sampling sites located on both sides of the Quequén Salado River. Finally, habitat availability was directly associated with the width of the sand dune landscape in the Southeast of Buenos Aires province, finding the greatest genetic differentiation among the populations of the Northeast, where this landscape is narrower.

The role of sigmodontine rodents as sylvatic hosts of Trypanosoma cruzi in the Argentinean Chaco.

The role of rodents in the sylvatic transmission of Trypanosoma cruzi has seldom been investigated using parasitological and molecular methods. We assessed the occurrence of T. cruzi in wild small rodents from Pampa del Indio, in the Argentinean Chaco, and identified the taxonomic status of positive rodents by sequencing a fragment of cytochrome b gene (cytb) and performing BLAST searches and phylogenetic analyses. A total of 176 Sigmodontinae rodents was captured in six surveys using 5425 trap-nights in a wide range of sylvatic habitats between 2009 and 2011. Host infection was determined by xenodiagnosis and by polymerase chain reaction amplification of the hyper-variable region of kinetoplast DNA minicircles of T. cruzi (kDNA-PCR) from blood samples. None of the 176 rodents examined was xenodiagnosis-positive. The prevalence of infection determined by kDNA-PCR from blood samples was 16.2% (95% confidence interval, 10.1-21.9%). Half of the infections detected by kDNA-PCR were confirmed by nuclear satellite DNA-PCR or by kDNA-PCR of the rectal contents of xenodiagnostic bugs. The 24 positive specimens were assigned to eight species, providing the first records of T. cruzi in Akodon montensis, Akodon toba, Graomys chacoensis, and Oligoryzomys chacoensis. The occurrence of T. cruzi infection in Oligoryzomys nigripes, Calomys callosus, Necromys lasiurus and Oecomys sp. (most probably Oecomys mamorae) from the Gran Chaco is also reported for the first time. Although sigmodontine rodents were frequently infected, the intensity of bug rectal infection with T. cruzi was below the detection limit of xenodiagnosis (subpatent infectiousness to bugs), indicating they had a low reservoir host competence.

Dispersal and population structure at different spatial scales in the subterranean rodent Ctenomys australis.

BACKGROUND: The population genetic structure of subterranean rodent species is strongly affected by demographic (e.g. rates of dispersal and social structure) and stochastic factors (e.g. random genetic drift among subpopulations and habitat fragmentation). In particular, gene flow estimates at different spatial scales are essential to understand genetic differentiation among populations of a species living in a highly fragmented landscape. Ctenomys australis (the sand dune tuco-tuco) is a territorial subterranean rodent that inhabits a relatively secure, permanently sealed burrow system, occurring in sand dune habitats on the coastal landscape in the south-east of Buenos Aires province, Argentina. Currently, this habitat is threatened by urban development and forestry and, therefore, the survival of this endemic species is at risk. Here, we assess population genetic structure and patterns of dispersal among individuals of this species at different spatial scales using 8 polymorphic microsatellite loci. Furthermore, we evaluate the relative importance of sex and habitat configuration in modulating the dispersal patterns at these geographical scales. RESULTS: Our results show that dispersal in C. australis is not restricted at regional spatial scales (approximately 4 km). Assignment tests revealed significant population substructure within the study area, providing support for the presence of two subpopulations from three original sampling sites. Finally, male-biased dispersal was found in the Western side of our study area, but in the Eastern side no apparent philopatric pattern was found, suggesting that in a more continuous habitat males might move longer distances than females. CONCLUSIONS: Overall, the assignment-based approaches were able to detect population substructure at fine geographical scales. Additionally, the maintenance of a significant genetic structure at regional (approximately 4 km) and small (less than 1 km) spatial scales despite apparently moderate to high levels of gene flow between local sampling sites could not be explained simply by the linear distance among them. On the whole, our results support the hypothesis that males disperse more frequently than females; however they do not provide support for strict philopatry within females.

Phylogeographical structure in the subterranean tuco-tuco Ctenomys talarum (Rodentia: Ctenomyidae): contrasting the demographic consequences of regional and habitat-specific histories.

In this work we examined the phylogeography of the South American subterranean herbivorous rodent Ctenomys talarum (Talas tuco-tuco) using mitochondrial DNA (mtDNA) control region (D-loop) sequences, and we assessed the geographical genetic structure of this species in comparison with that of subterranean Ctenomys australis, which we have shown previously to be parapatric to C. talarum and to also live in a coastal sand dune habitat. A significant apportionment of the genetic variance among regional groups indicated that putative geographical barriers, such as rivers, substantially affected the pattern of genetic structure in C. talarum. Furthermore, genetic differentiation is consistent with a simple model of isolation by distance, possibly evidencing equilibrium between gene flow and local genetic drift. In contrast, C. australis showed limited hierarchical partitioning of genetic variation and departed from an isolation-by-distance pattern. Mismatch distributions and tests of neutrality suggest contrasting histories of these two species: C. talarum appears to be characterized by demographic stability and no significant departures from neutrality, whereas C. australis has undergone a recent demographic expansion and/or departures from strict neutrality in its mtDNA.