Population structure and landscape genetics in the endangered subterranean rodent Ctenomys porteousi

Topographic barriers drive the pronounced genetic subdivision of a range-limited fossorial rodent

Due to their limited dispersal ability, fossorial species with predominantly belowground activity usually show increased levels of population subdivision across relatively small spatial scales. This may be exacerbated in harsh mountain ecosystems, where landscape geomorphology limits species' dispersal ability and leads to small effective population sizes, making species relatively vulnerable to environmental change. To better understand the environmental drivers of species' population subdivision in remote mountain ecosystems, particularly in understudied high-elevation systems in Africa, we studied the giant root-rat (Tachyoryctes macrocephalus), a fossorial rodent confined to the afro-alpine ecosystem of the Bale Mountains in Ethiopia. Using mitochondrial and low-coverage nuclear genomes, we investigated 77 giant root-rat individuals sampled from nine localities across its entire ~1000 km2 range. Our data revealed a distinct division into a northern and southern group, with no signs of gene flow, and higher nuclear genetic diversity in the south. Landscape genetic analyses of the mitochondrial and nuclear genomes indicated that population subdivision was driven by slope and elevation differences of up to 500 m across escarpments separating the north and south, potentially reinforced by glaciation of the south during the Late Pleistocene (~42,000-16,000 years ago). Despite this landscape-scale subdivision between the north and south, weak geographic structuring of sampling localities within regions indicated gene flow across distances of at least 16 km at the local scale, suggesting high, aboveground mobility for relatively long distances. Our study highlights that despite the potential for local-scale gene flow in fossorial species, topographic barriers can result in pronounced genetic subdivision. These factors can reduce genetic variability, which should be considered when developing conservation strategies.

An evaluation of isolation by distance and isolation by resistance on genetic structure of the Persian squirrel (Sciurus anomalus) in the Zagros forests of Iran

For the conservation of wild species, it is important to understand how landscape change and land management can affect gene flow and movement. Landscape genetic analyses provide a powerful approach to infer effects of various landscape factors on gene flow, thereby informing conservation actions. The Persian squirrel is a keystone species in the woodlands and oak forests of Western Asia, where it has experienced recent habitat loss and fragmentation. We conducted landscape genetic analyses of individuals sampled in the northern Zagros Mountains of Iran (provinces of Kurdistan, Kermanshah, and Ilam), focusing on the evaluation of isolation by distance (IBD) and isolation by resistance (IBR), using 16 microsatellite markers. The roles of geographical distance and landscape features including roads, rivers, developed areas, farming and agriculture, forests, lakes, plantation forests, rangelands, shrublands, and rocky areas of varying canopy cover, and swamp margins on genetic structure were quantified using individual-based approaches and resistance surface modeling. We found a significant pattern of IBD but only weak support for an effect of forest cover on genetic structure and gene flow. It seems that geographical distance is an important factor limiting the dispersal of the Persian squirrel in this region. The results of the current study inform ongoing conservation programs for the Persian squirrel in the Zagros oak forest.

Appearances are deceptive: a cryptic lineage within the assumed distributional boundaries of Ctenomys talarum (Rodentia, Ctenomyidae)

The coastal dunes of the southeast of Buenos Aires province, Argentina, present two different described species of tuco-tucos: Ctenomys talarum and C. australis. Formerly, C. talarum was subdivided into three subspecies (C. t. talarum, C. t. recessus, and C. t. occidentalis), mainly based on its geographic distribution and phenotypic variation in characters of external morphology (e.g., body size and pelage color). This study assesses the phylogenetic relationships of C. talarum, focusing on the populations at the western end of its coastal distribution (localities of Pehuen-Có and Sauce Grande), which have been previously identified as highly genetically divergent. In this regard, populations distributed throughout the range of the species were sampled. Complete DNA sequences of the mitochondrial cytochrome b gene (1,140 bp), partial sequences of the mitochondrial D-loop region (426 bp), and partial sequences of the nuclear DNA intron 8 of the β-fibrinogen (about 870 bp) gene were used for the analyses. Phylogenetic inferences based on mitochondrial and nuclear markers were performed separately or combined to obtain a species tree. Populations distributed at the western end of the coastal dunes (between Pehuen-Có and Sauce Grande), previously assumed as C. talarum, were found to belong to an independent lineage relative to the other populations from the Pampas region. The average genetic distance between these two lineages is within the order of the genetic distances observed between different species of the genus. Also, our results show that this lineage of Ctenomys presents a high affinity with the magellanicus group, which is distributed further south, in Patagonia. In conclusion, tuco-tuco populations occurring in the coastal expanse between these two localities should be considered a possible distinct cryptic species, highly differentiated from C. talarum.

Redefining the Distributional Boundaries and Phylogenetic Relationships for Ctenomids From Central Argentina

With about 68 recognized living species, subterranean rodents of the genus Ctenomys are found in a multiplicity of habitats, from the dunes of the Atlantic coast to the Andes Mountains, including environments ranging from humid steppes of Pampas to the dry deserts of Chaco region. However, this genus needs an exhaustive reevaluation of its systematic and phylogenetic relationships regarding the different groups that compose it. This knowledge is essential to propose biodiversity conservation strategies both at species level and at higher hierarchical levels. In order to clarify the taxonomy and the recent evolutionary history from populations of Ctenomys in the Pampas region, Argentina, phylogenetic relationships among them were evaluated using mitochondrial DNA sequences: gene encoding cytochrome b protein (1,140 bp) and the non-coding D-loop region (434 bp). To infer the divergence times inside the Ctenomys clade, a Bayesian calibrate tree using fossil remains data from different families within Caviomorpha was performed at first. Secondly, that calibration data was used as priors in a new Bayesian phylogenetic inference within the genus Ctenomys. This phylogenetic tree emphasized on species currently distributed on the Pampas region, more precisely considering both the talarum and mendocinus groups. Bayesian inferences (BI) were integrated with the results of a Maximum Likelihood approach (ML). Based on these results, the distributional limits of the mendocinus and talarum groups appear to be related to the physiognomy of the Pampas region soils. On the other hand, the validity of C. pundti complex as a differentiated species of C. talarum is debated. According to previous evidence from morphological and chromosomal studies, these results show a very low divergence between those species that originally were classified within the talarum group. Mitochondrial DNA sequences from populations associated with these putative species have not recovered as reciprocal monophyletic groups in the phylogenetic analyses. In conclusion, C. talarum and C. pundti complex might be considered as the same biological species, or lineages going through a recent or incipient differentiation process. The results obtained in this study have important implications for conservation policies and practices, since both species are currently categorized as Vulnerable and Endangered, respectively.

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.

Functional connectivity and home range inferred at a microgeographic landscape genetics scale in a desert-dwelling rodent

Gene flow in animals is limited or facilitated by different features within the landscape matrix they inhabit. The landscape representation in landscape genetics (LG) is traditionally modeled as resistance surfaces (RS), where novel optimization approaches are needed for assigning resistance values that adequately avoid subjectivity. Also, desert ecosystems and mammals are scarcely represented in LG studies. We addressed these issues by evaluating, at a microgeographic scale, the effect of landscape features on functional connectivity of the desert-dwelling Dipodomys merriami. We characterized genetic diversity and structure with microsatellites loci, estimated home ranges and movement of individuals using telemetry-one of the first with rodents, generated a set of individual and composite environmental surfaces based on hypotheses of variables influencing movement, and assessed how these variables relate to individual-based gene flow. Genetic diversity and structure results evidenced a family-induced pattern driven by first-order-related individuals, notably determining landscape genetic inferences. The vegetation cover and soil resistance optimized surface (NDVI) were the best-supported model and a significant predictor of individual genetic distance, followed by humidity and NDVI+humidity. Based on an accurate definition of thematic resolution, we also showed that vegetation is better represented as continuously (vs. categorically) distributed. Hence, with a nonsubjective optimization framework for RS and telemetry, we were able to describe that vegetation cover, soil texture, and climatic variables influence D. merriami's functional connectivity at a microgeographic scale, patterns we could further explain based on the home range, habitat use, and activity observed between sexes. We describe the relationship between environmental features and some aspects of D. merriami's behavior and physiology.

Landscape genetics in the subterranean rodent Ctenomys "chasiquensis" associated with highly disturbed habitats from the southeastern Pampas region, Argentina

Studies of genetic differentiation in fragmented environments help us to identify those landscape features that most affect gene flow and dispersal patterns. Particularly, the assessment of the relative significance of intrinsic biological and environmental factors affecting the genetic structure of populations becomes crucial. In this work, we assess the current dispersal patterns and population structure of Ctenomys "chasiquensis", a vulnerable and endemic subterranean rodent distributed on a small area in Central Argentina, using 9 polymorphic microsatellite loci. We use landscape genetics approaches to assess the relationship between genetic connectivity among populations and environmental attributes. Our analyses show that populations of C. "chasiquensis" are moderately to highly structured at a regional level. This pattern is most likely the outcome of substantial gene flow on the more homogeneous sand dune habitat of the Northwest of its distributional range, in conjunction with an important degree of isolation of eastern and southwestern populations, where the optimal habitat is surrounded by a highly fragmented landscape. Landscape genetics analysis suggests that habitat quality and longitude were the environmental factors most strongly associated with genetic differentiation/uniqueness of populations. In conclusion, our results indicate an important genetic structure in this species, even at a small spatial scale, suggesting that contemporary habitat fragmentation increases population differentiation.