MICROSATELLITE ANALYSIS OF A HYBRID ZONE BETWEEN CHROMOSOMALLY DIVERGENT POPULATIONS OF CTENOMYS MINUTUS FROM SOUTHERN BRAZIL (RODENTIA: CTENOMYIDAE)

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.

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.

The contribution of incomplete lineage sorting and introgression to the evolutionary history of the fast-evolving genus Ctenomys (Rodentia, Ctenomyidae)

Incomplete lineage sorting and introgression have been increasingly recognized as important processes involved in biological differentiation. Both incomplete lineage sorting and introgression result in incongruences between gene trees and species trees, consequently causing difficulties in phylogenetic reconstruction. This is particularly the case for rapid radiations, as short internodal distances and incomplete reproductive isolation increase the likelihood of both ILS and introgression. Estimation of the relative frequency of these processes requires assessments across many genomic regions. We use transcriptomics to test for introgression and estimate the frequency of incomplete lineage sorting in a set of three closely related and geographically adjacent South American tuco-tucos species (Ctenomys), a genus comprising 64 species resulting from recent, rapid radiation. After cleaning and filtering, 5764 orthologous genes strongly support paraphyly of C. pearsoni relative to C. brasiliensis (putatively represented by the population of Villa Serrana). In line with earlier phylogenetic work, the C. pearsoni - C. brasiliensis pair is closely related to C. torquatus, whereas C. rionegrensis is more distantly related to these three nominal species. Classical Patterson's D-statistic shows significant signals of introgression from C. torquatus into C. brasiliensis. However, a 5-taxon test shows no significant results. Incomplete lineage sorting was estimated to have involved about 9% of the loci, suggesting it represents an important process in the incipient diversification of tuco-tucos.

Hybridization between subterranean tuco-tucos (Rodentia, Ctenomyidae) with contrasting phylogenetic positions

Reproductive compatibility usually decreases according to increasing genetic difference and the time of divergence between species. However, the amount of modification required to influence hybridization may vary in different species. Thus, it is extremely important to conduct studies that seek to understand what and how variables influence the reproductive isolation of species. We have explored a system involving two species of subterranean rodents that present morphological, karyotypic, and evolutionary history differences and are capable of generating hybrids. To gain insight into the karyotype organization of genus Ctenomys, we examined the chromosome evolution by classical and molecular cytogenetics of both parental species and hybrids. Furthermore, we have used different approaches to analyze the differences between the parental species and the hybrids, and determined the origin of the hybrids. The results of our work demonstrate unequivocally that some species that present extensive differences in chromosome organization, phenotype, evolutionary history, sperm morphology and genetic, which are usually associated with reproductive isolation, can generate natural hybrids. The results also demonstrate that females of both species are able to generate hybrids with males of the other species. In addition, the chromosome-specific probes prepared from Ctenomys flamarioni provide an invaluable tool for comparative cytogenetics in closely related species.

Multilocus Characterization of a Woodrat (Genus Neotoma) Hybrid Zone

In order to investigate hybridization between 2 species of woodrats, Neotoma floridana and Neotoma micropus, 103 specimens were collected, in March of 1988, from a known area of sympatry, and compared with reference collections from areas of allopatry. Ten genetic markers, consisting of 7 microsatellite loci, 1 mitochondrial gene (cytochrome-b [Cytb]), and 2 nuclear introns (intron 2 of the vertebrate alcohol dehydrogenase gene [Adh1-I2] and intron 7 of the beta-fibrinogen gene [Fgb-I7]) were used to develop a composite genotype for each individual and for detection of hybridization. Six individuals were identified as pure parental N. micropus, 96 as hybrids, and 1 as pure parental N. floridana Hybrids were formed primarily through matings between complex genotypes, resulting in a high prevalence of individuals classified as backcrosses. The ratio of hybrid classes, population substructure, and presence of significant linkage disequilibrium within the zone of contact could not reject either the hybrid superiority or hybrid equilibrium model as responsible for maintenance of this hybrid zone. The collection date of this dataset (1988) provided not only a point in time assessment of the hybrid zone but also provided opportunities for future comparisons of temporal datasets with the purpose of examining hybrid zone characteristics over multiple generations.

Penial morphology in three species of Brazilian tuco-tucos, Ctenomys torquatus, C. minutus, and C. flamarioni (Rodentia: Ctenomyidae)

The present study analyses the glans penis and baculum morphology of three Brazilian tuco-tucos, Ctenomys torquatus Lichtenstein, 1830, Ctenomys minutus Nehring, 1887 and Ctenomys flamarioni Travi, 1981, in order to identify possible variations and understand some more about this taxonomically complex group. We used fixed penis from 15 previously listed adult specimens. For a more detailed baculum analysis, the penis underwent dissection and diaphanisation, whereas to analyse the glans penis surface we used Scanning Electron Microscopy (SEM). Results showed striking differences in baculum morphology among the three species. While C. minutus have a particular V-shaped proximal baculum tip, C. flamarioni baculum is thin throughout the shaft with rounded proximal and distal tips. Ctenomys torquatus have a shorter and larger baculum, similar to what has previously been described for the species. Glans penis surface microstructure analyses also revealed inter-specific differences, with penial spines varying in shape, size and, especially density. Although C. torquatus has a relatively small penis, it has the largest penial spine density, which suggests a more complex penial ornamentation in this species.

A hybrid zone of the genus Ctenomys: A case study in southern Brazil

We describe variation at microsatellite loci and the chromosomal polymorphisms of a hybrid population, and hybridizing populations of Ctenomys minutus (the minor tuco-tuco) from the coastal plain of Rio Grande do Sul, southern Brazil. Cytogenetic analysis and a survey of six microsatellite loci included 101 specimens of C. minutus from the parental populations (2n/AN = 42/74 and 48a/76) and their contact zone. Cytogenetic analysis recorded 26 different karyotypes exhibited by 50 individuals from the hybrid population. Of the 26 karyotypes, only 14% presented a parental-like configuration, and none had the combinations of 2n and AN expected for an F1 hybrid. The remaining karyotypes were alternative hybrid forms, with 2n varying from 42 to 46 and AN from 68 to 80. These results suggest chromosomal rearrangements are only of minor significance in the establishment of reproductive barriers for this species.

Cuticular compounds bring new insight in the post-glacial recolonization of a Pyrenean area: Deutonura deficiens Deharveng, 1979 complex, a case study

Background

In most Arthropod groups, the study of systematics and evolution rely mostly on neutral characters, in this context cuticular compounds, as non-neutral characters, represent an underexplored but potentially informative type of characters at the infraspecific level as they have been routinely proven to be involved in sexual attraction.

Methods and Findings

The collembolan species complex Deutonura deficiens was chosen as a model in order to test the utility of these characters for delineating four infraspecific entities of this group. Specimens were collected for three subspecies (D. d. deficiens, D. d. meridionalis, D. d. sylvatica) and two morphotypes (D. d. sylvatica morphoype A and B) of the complex; an additional species D. monticola was added. Cuticular compounds were extracted and separated by gas chromatography for each individual. Our results demonstrate that cuticular compounds succeeded in separating the different elements of this complex. Those data allowed also the reconstruction of the phylogenetic relationships among them.

Conclusions

The discriminating power of cuticular compounds is directly related to their involvement in sexual attraction and mate recognition. These findings allowed a discussion on the potential involvement of intrinsic and paleoclimatic factors in the origin and the diversification of this complex in the Pyrenean zone. This character type brings the first advance from pattern to process concerning the origin of this species complex.

The conservation status of the tuco-tucos, genus Ctenomys (Rodentia: Ctenomyidae), in southern Brazil

The goal of conservation biology should be related to the preservation of species and also to the evolutionary and ecological processes that were responsible to form them and that are still acting. We review the conservation status of the species of tuco-tuco (Ctenomys torquatus, C. lami, C. minutus, and C. flamarioni) from southern Brazil, and relate these data to the geological history of a particular area in that region, the Coastal Plain of the States of Rio Grande do Sul and Santa Catarina. The implications of the data on these species from the Southeastern Brazil are also discussed in relation to the evolution and risk of extinction of these subterranean rodents.

Cytogenetics Status of Four Ctenomys Species in the South of Brazil

This report is a review of 20 years of cytogenetics studies in tuco-tucos from the south of Brazil and the implications for the evolution of these species as well as the relation of these data with the geological history of the Coastal Plain of southern Brazil. Two forms of Ctenomys torquatus, 2n = 44 and 46, are separated by a geographic barrier. Ctenomys flamarioni shows a constant karyotype (2n = 48) and presents high variability in FN due to constitutive heterochromatin variation. Ctenomys minutus presents the highest chromosomic variation among the species in the south of Brazil (2n = 42-50) with three chromosomic hybrid zones. Ctenomys lami, like C. minutus, presents a high chromosomic variation due to fusions and fissions of chromosome pairs 1 and 2. Both species present a close evolutionary relationship, including a chromosomic hybrid zone.