Uncovering the species diversity of subterranean rodents at the end of the World: three new species of Patagonian tuco-tucos (Rodentia, Hystricomorpha, Ctenomys)

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.

Cranial morphological variation of Ctenomys lami (Rodentia: Ctenomyidae) in a restricted geographical distribution

The relationship between chromosomal and morphological variation in mammals is poorly understood. We analyzed the cranial size and shape variation in Ctenomys lami concerning to the geographic variation in their chromosome numbers. This subterranean rodent occurs in a narrow range of sand-dunes in the Coastal Plain of southern Brazil. This species presents a high karyotypic variation with diploid numbers varying from 2n = 54 to 2n = 58, involving the fission and fusion of chromosome pairs 1 and 2. Due to different chromosome rearrangement frequencies along their geographic distribution, four karyotypic blocks were proposed. This study, explored cranium shape and size variation in geographical, chromosomal polymorphism, and chromosome rearrangements contexts to test whether the four karyotypic blocks reflect morphologically distinct units. For this, we measured 89 craniums using geometric morphometrics and used uni and multivariate statistics to discriminate the predicted groups and test for an association among chromosomal and morphological variation. Our results show the size and shape of sexual dimorphism, with males larger than females, and support the existence of four karyotypic blocks for Ctenomys lami based on morphological variation. However, our results do not support a direct relationship between chromosomal and cranial morphological variation in C. lami.

A new species of the highly polytypic South American rodent Ctenomys increases the diversity of the magellanicus clade

The subterranean rodent Ctenomys is the most polytypic South American mammal genus and one of the most speciose and rapidly diversifying mammal genera in the world. Its systematics is unstable due to the underlying accelerated diversification processes that give rise to evolutionary lineages at different stages of differentiation and to remarkable morphological homogeneity even among long-differentiated species. As a result, species boundaries are often difficult to define. Diversity of this genus in the coastal area of central Argentina has been extensively studied, with two independent lineages currently recognized while a distinct third population had not been previously detected. Through a phylogenetic analysis based on combined morphological and molecular evidence, Bayesian estimates of divergence times, and morphometric and morphological assessments, we recognize this third population as an independently evolving lineage. The new species, Ctenomys pulcersp. nov., is here described for both the living fauna and the fossil record of the Pampean region of central Argentina. According to phylogenetic results, Ctenomys pulcersp. nov. belongs to the essentially Patagonian magellanicus clade, and would have diverged from its sister species, Ctenomys bidaui, during the middle Pleistocene (ca. 0.4 Ma). Its current distribution in the fixed and semifixed dunes of the coastal Pampean region is assumed to represent a relict of a wider and continuous distribution of potentially suitable environments during the late Pleistocene. Ctenomys pulcersp. nov. occurs in a particularly fragile natural system subjected to profound disturbances caused by diverse anthropic actions and therefore measures for the conservation of its habitat will be indispensable.

Filling the gap in distribution ranges and conservation status in Ctenomys (Rodentia: Ctenomyidae)

South American subterranean rodents of the genus Ctenomys (Rodentia, Ctenomyidae, tuco-tuco) are one of the most diverse genera among mammals. Recently described species, new taxonomic revisions, and new distribution range delimitation made the revision of distribution areas and conservation status of these mammals mandatory. Implementing the first part of the DAMA protocol (document, assess, monitor, act), here we compile updated sets of species distribution range maps and use these and the number of collection localities to assess the conservation status of ctenomyids. We integrate potential for conservation in protected areas, and levels of habitat transformation to revise previous conservation status assessments and propose the first assessment for all Data Deficient or not evaluated species of tuco-tucos. Our results indicate that 53 (78%) of these species are threatened and that 47 (69%) have little or no overlap with protected areas, emphasizing the urgent need to conduct conservation efforts. Here, 18 of 22 species previously classified as Data Deficient resulted in them being put in an at-risk category (VU, EN, CR). In addition, nine species that have not been previously evaluated were classified as threatened, with these two groups comprising more than 47% of the known species. These results posit that the Ctenomyidae are the rodent family with the greatest number of species at risk of extinction. Finally, a total of 33 (49%) species have been reported from three or fewer localities; all considered threatened through the approach implemented in this study. These geographically restricted taxa should be given more attention in conservation programs since the richness of this genus relies on the survival of such species.

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.

Genomic Organization of Microsatellites and LINE-1-like Retrotransposons: Evolutionary Implications for Ctenomys minutus (Rodentia: Ctenomyidae) Cytotypes

Simple Summary

In animals, several species contain substantial chromosomal and genomic variation among their populations, but as to what could have driven such diversification is still a puzzle for most cases. Here, we used molecular cytogenetic analysis to expose the main genomic elements involved in the population variation observed in the Neotropical underground rodents of the genus Ctenomys (Rodentia: Ctenomyidae), which harbor the most significant chromosomal variation among mammals (2n = 10 to 2n = 70). These data provide evidence for a correlation between repetitive genomic content and localization of evolutionary breakpoint regions (EBRs) and highlight their direct impact in promoting chromosomal rearrangements.

Abstract

The Neotropical underground rodents of the genus Ctenomys (Rodentia: Ctenomyidae) comprise about 65 species, which harbor the most significant chromosomal variation among mammals (2n = 10 to 2n = 70). Among them, C. minutus stands out with 45 different cytotypes already identified, among which, seven parental ones, named A to G, are parapatrically distributed in the coastal plains of Southern Brazil. Looking for possible causes that led to such extensive karyotype diversification, we performed chromosomal mapping of different repetitive DNAs, including microsatellites and long interspersed element-1 (LINE-1) retrotransposons in the seven parental cytotypes. Although microsatellites were found mainly in the centromeric and telomeric regions of the chromosomes, different patterns occur for each cytotype, thus revealing specific features. Likewise, the LINE-1-like retrotransposons also showed a differential distribution for each cytotype, which may be linked to stochastic loss of LINE-1 in some populations. Here, microsatellite motifs (A)₃₀, (C)₃₀, (CA)₁₅, (CAC)₁₀, (CAG)₁₀, (CGG)₁₀, (GA)₁₅, and (GAG)₁₀ could be mapped to fusion of chromosomes 20/17, fission and inversion in the short arm of chromosome 2, fusion of chromosomes 23/19, and different combinations of centric and tandem fusions of chromosomes 22/24/16. These data provide evidence for a correlation between repetitive genomic content and localization of evolutionary breakpoints and highlight their direct impact in promoting chromosomal rearrangements.

Disentangling the taxonomic status of Ctenomys (Rodentia: Ctenomyidae) populations inhabiting northern areas of La Rioja Province, Argentina

The Ctenomys population from Anillaco, La Rioja Province, Argentina has been the subject of detailed studies of circadian rhythms, vocalization, ecology and spatial dynamics. However, the taxonomy and systematics of this population as well as populations of Ctenomys inhabiting Andean areas of this province is unknown. In this study, we present the phylogenetic relationship of the “Anillaco tuco-tuco” as well as of two other populations of Ctenomys, all distributed in the northern portion of La Rioja Province, Argentina. Based on molecular analyses and morphological comparisons, we reached to the conclusion that the “Anillaco tuco-tuco” population corresponds to the species Ctenomys famosus. In addition, an undescribed species, member of the “mendocinus” lineage of Ctenomys, is recognized in the Andean portions of the province.

Disentangling the complex alpha taxonomy of Andean populations of Ctenomys (Rodentia: Ctenomyidae) from northern Patagonia: the need for extensive sampling in heterogeneous landscapes

In the Andean portion of northern Patagonia, populations of Ctenomys are found from low-elevation plains to high-elevation meadows and valleys. Despite their prevalence, the taxonomy of these subterranean rodents remains poorly resolved. Using genetic and morphological data obtained from museum specimens and animals collected in the field, we examined the taxonomy of Ctenomys from southwestern Mendoza Province, Argentina. Our analyses suggest the presence of at least five species of Ctenomys within the study area. The highest, innermost portion of the Andes is occupied by C. maulinus. To the east, the mountains and foothills are inhabited by two forms associated with the “mendocinus” and the “magellanicus” lineages, respectively. The former appears to be a local variant of C. emilianus, while the latter is sister to C. pontifex. Although C. pontifex was not encountered during our field sampling, it remains a valid species that likely is restricted to the isolated Valle Hermoso in westernmost Mendoza Province. In addition, we report an undescribed form from Las Leñas Valley that is associated with the “mendocinus” lineage. This complex alpha taxonomic scenario occurs within less than one degree of latitude, thereby highlighting the need to conduct detailed field collections to improve our knowledge of the systematics of Ctenomys.

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.

Taxonomy of Ctenomys (Rodentia: Ctenomyidae) in northwestern Patagonia, Argentina: the occurrence of the “mendocinus” lineage

Subterranean rodents Ctenomys are iconic representatives of the mammalian fauna from southern South America. Based on molecular data, eight lineages have been identified within the genus, although species-level identifications and relationships are still debated. Until now, the “magellanicus” clade has been the only lineage mentioned from arid, extra-Andean portions of Patagonia. Here, we report the presence of a Ctenomys population from northern Patagonia that is unambiguously associated with the Central Argentinean “mendocinus” lineage. Most of the 160,000 km2 comprising the northern portion of Patagonia – an area consisting primarily of Monte Desert shrub-land – are inhabited by Ctenomys populations of unknown taxonomy.

The number of species of degus (genus Octodon) is currently underestimated: An appraisal of species limits and their phylogenetic relationships (Rodentia: Hystricomorpha: Octodontidae)

As currently understood, the genus Octodon contains five species degus, lunatus, bridgesii, pacificus, and ricardojeda. Previous phylogenetic studies suggest that genus specific diversity is underestimated. In order to evaluate the taxonomic diversity of Octodon, we implemented unilocus (cytochrome-b) and multilocus (cytochrome-b + 4 nuclear genes) species delimitation methods. Octodon degus was recovered as a sister of the other species of the genus. The unilocus bGMYC and mPTP methods, based on cytochrome-b sequences, delimits 11 and 7 candidate species respectively, and both methods fail to recognize O. pacificus from O. ricardojeda. Results of the multilocus analysis (BPP) vary as a function of the dataset used. When the five genes are used 11 species are delimited, while eight species are delimited when only the nuclear genes are used. Octodon bridgesii is shown as comprising at least two species (one on the Pacific coast and the typical form found on the Andean slopes), while O. ricardojeda may comprise two species (one on the Chilean side of the Andes and the other in Argentina). Likewise, both multilocus matrices recover O. pacificus as a distinct species. This shows that species diversity of Octodon is underestimated. Remarkably, many of the delimited species based on genetic data are morphologically differentiated in cranio-dental characteristics. However, a pair of species has not achieved morphological differentiation, being cryptic species. Finally, the incongruence between mitochondrial and nuclear phylogenies suggests that processes such as incomplete lineage sorting and/or introgression have been present during the radiation of the genus.

Effects of size, phylogeny and locomotor habits on the pelvic and femoral morphology of South American spiny rats (Rodentia: Echimyidae)

The rodent family Echimyidae (spiny rats, hutias and coypu) is notable for its high phylogenetic and ecological diversity, encompassing ~100 living species with body mass ranging from 70 to 4500 g, including arboreal, epigean (non-arboreal or scansorial), fossorial and semi-aquatic taxa. In view of this diversity, it was hypothesized that echimyid morphological variation in the pelvis and femur should reflect: (1) allometric association with body mass; (2) morphofunctional specializations for the different locomotor habits; and (3) phylogenetic history. To test these propositions, we examined 30 echimyid species, in addition to eight species of two other octodontoid families, Abrocomidae and Octodontidae. Pelvic and femoral variation was assessed with linear morphometry, using bivariate and multivariate statistical methods, part of which was phylogenetically informed. Approximately 80% of the total variation among echimyids was explained by body mass, and some univariate measurements were found potentially to be effective as body mass estimators after simple allometric procedures, notably in the pelvis. Even considering the significant phylogenetic signal, variation in shape was largely structured by locomotor habits, mainly in the pelvis, suggesting that the echimyid hindlimb diversification was driven, in part, by selective pressures related to locomotor habits. Finally, echimyid femoral disparity was considerably greater than in other octodontoids, contrasting with their relatively modest cranial variation. Thus, this study suggests that hindlimb diversity constitutes a key factor for the exceptional echimyid ecological and phyletic diversification.

Genetic diversity and conservation of the endemic tuco-tuco Ctenomys ibicuiensis (Rodentia: Ctenomyidae)

Endemic, small range species are susceptible to environmental changes and landscape modification. Understanding genetic diversity and distributional patterns is important for implementation of effective conservation measures. In this context, genetic diversity was evaluated to update the conservation status of an endemic tuco-tuco, Ctenomys ibicuiensis. Phylogeographic and population genetic analyses of mitochondrial DNA and microsatellite loci were carried out using 46 individuals sampled across the species’ distribution. Ctenomys ibicuiensis presented moderate to high genetic diversity and highly structured populations with low levels of gene flow and isolation by distance. Anthropogenic landscape changes threaten this restricted-range tuco-tuco. Considering its limited geographic distribution and highly structured populations with low gene flow, we consider C. ibicuiensis to be at significant risk of extinction.