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Tomasco IH, Ceballos SG, Austrich A, Brook F, Caraballo DA, Fernández GP, Lanzone C, Mora MS, Parada A, Sánchez RT, Lessa EP. Underground speciation: Unraveling the systematics and evolution of the highly diverse tuco-tucos (genus Ctenomys) with genomic data. Mol Phylogenet Evol 2024; 199:108163. [PMID: 39079596 DOI: 10.1016/j.ympev.2024.108163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/19/2024] [Accepted: 07/26/2024] [Indexed: 08/10/2024]
Abstract
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.
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Affiliation(s)
- Ivanna H Tomasco
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República. Montevideo, 11300, Uruguay.
| | - Santiago G Ceballos
- Universidad Nacional de Tierra del Fuego (ICPA-UNTDF), Centro Austral de Investigaciones Científicas (CADIC-CONICET), Argentina
| | - Ailin Austrich
- Instituto de Investigaciones Marinas y Costeras (IIMyC) - (UNMDP-CONICET), Argentina
| | - Federico Brook
- Laboratorio de Investigaciones en Evolución y Biodiversidad. Facultad de Ciencias Naturales y de la Salud, Universidad Nacional de la Patagonia San Juan Bosco, sede Esquel, Argentina
| | - Diego A Caraballo
- Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), UBA-CONICET, Ciudad Universitaria-Pabellón II, Buenos Aires, Argentina
| | - Gabriela P Fernández
- Centro de Bioinvestigaciones CeBio, UNNOBA-CICBA - Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires CITNOBA UNNOBA-CONICET, Pergamino, Argentina
| | - Cecilia Lanzone
- Laboratorio de Genética Evolutiva, FCEQyN, IBS, UNaM-CONICET, CPA N3300LQF Posadas, Misiones, Argentina
| | - Matías S Mora
- Instituto de Investigaciones Marinas y Costeras (IIMyC) - (UNMDP-CONICET), Argentina
| | - Andrés Parada
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República. Montevideo, 11300, Uruguay
| | - R Tatiana Sánchez
- Instituto de Investigaciones de Biodiversidad Argentina (PIDBA), Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, 4000 Tucumán, Argentina
| | - Enrique P Lessa
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República. Montevideo, 11300, Uruguay
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Austrich A, Tomasco IH, Mapelli FJ, Kittlein MJ, Cutrera AP, Mora MS. Appearances are deceptive: a cryptic lineage within the assumed distributional boundaries of Ctenomys talarum (Rodentia, Ctenomyidae). J Mammal 2023. [DOI: 10.1093/jmammal/gyac116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Abstract
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.
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Affiliation(s)
- Ailin Austrich
- Departamento de Biologia, Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones Marinas y Costeras (IIMyC, CONICET), Universidad Nacional de Mar del Plata , Dean Funes 3250, 3rd Floor, 7600 Mar del Plata , Argentina
| | - Ivanna Haydée Tomasco
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República , Iguá 4225, Montevideo 11400 , Uruguay
| | - Fernando Javier Mapelli
- División Mastozoología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” CONICET , Angel Gallardo 470, Buenos Aires C1405DJR , Argentina
| | - Marcelo Javier Kittlein
- Departamento de Biologia, Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones Marinas y Costeras (IIMyC, CONICET), Universidad Nacional de Mar del Plata , Dean Funes 3250, 3rd Floor, 7600 Mar del Plata , Argentina
| | - Ana Paula Cutrera
- Departamento de Biologia, Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones Marinas y Costeras (IIMyC, CONICET), Universidad Nacional de Mar del Plata , Dean Funes 3250, 3rd Floor, 7600 Mar del Plata , Argentina
| | - Matías Sebastián Mora
- Departamento de Biologia, Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones Marinas y Costeras (IIMyC, CONICET), Universidad Nacional de Mar del Plata , Dean Funes 3250, 3rd Floor, 7600 Mar del Plata , Argentina
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Carnovale CS, Fernández GP, Merino ML, Mora MS. Redefining the Distributional Boundaries and Phylogenetic Relationships for Ctenomids From Central Argentina. Front Genet 2021; 12:698134. [PMID: 34422000 PMCID: PMC8372524 DOI: 10.3389/fgene.2021.698134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/06/2021] [Indexed: 11/13/2022] Open
Abstract
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.
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Affiliation(s)
- Cecilia Soledad Carnovale
- Centro de Bioinvestigaciones (CeBio), Universidad Nacional del Noroeste de la Provincia de Buenos Aires (UNNOBA-CICBA) / Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires CITNOBA (UNNOBA-CONICET), Pergamino, Argentina
| | - Gabriela Paula Fernández
- Centro de Bioinvestigaciones (CeBio), Universidad Nacional del Noroeste de la Provincia de Buenos Aires (UNNOBA-CICBA) / Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires CITNOBA (UNNOBA-CONICET), Pergamino, Argentina
| | - Mariano Lisandro Merino
- Centro de Bioinvestigaciones (CeBio), Universidad Nacional del Noroeste de la Provincia de Buenos Aires (UNNOBA-CICBA) / Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires CITNOBA (UNNOBA-CONICET), Pergamino, Argentina.,Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CICBA), La Plata, Argentina
| | - Matías Sebastián Mora
- Grupo de Investigación: Ecología y Genética de Poblaciones de Mamíferos, Instituto de Investigaciones Marinas y Costeras (IIMyC, CONICET), Universidad Nacional de Mar del Plata (UNMdP), Mar del Plata, Argentina
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Austrich A, Mora MS, Mapelli FJ, Fameli A, Kittlein MJ. Influences of landscape characteristics and historical barriers on the population genetic structure in the endangered sand-dune subterranean rodent Ctenomys australis. Genetica 2020; 148:149-164. [PMID: 32451787 DOI: 10.1007/s10709-020-00096-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/20/2020] [Indexed: 11/29/2022]
Abstract
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.
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Affiliation(s)
- Ailin Austrich
- Departamento de Biología, Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones Marinas y Costeras, (IIMyC, CONICET),, Universidad Nacional de Mar del Plata, Funes 3250, 3th Floor, 7600, Mar del Plata, Argentina.
| | - Matías S Mora
- Departamento de Biología, Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones Marinas y Costeras, (IIMyC, CONICET),, Universidad Nacional de Mar del Plata, Funes 3250, 3th Floor, 7600, Mar del Plata, Argentina
| | - Fernando J Mapelli
- Grupo de Genética y Ecología Para la Conservación de la Biodiversidad, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", CONICET, Ángel Gallardo 470, Buenos Aires, Argentina
| | - Alberto Fameli
- Grupo de Genética y Ecología Para la Conservación de la Biodiversidad, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", CONICET, Ángel Gallardo 470, Buenos Aires, Argentina
| | - Marcelo J Kittlein
- Departamento de Biología, Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones Marinas y Costeras, (IIMyC, CONICET),, Universidad Nacional de Mar del Plata, Funes 3250, 3th Floor, 7600, Mar del Plata, Argentina
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Mapelli FJ, Mora MS, Lancia JP, Gómez Fernández MJ, Mirol PM, Kittlein MJ. Evolution and phylogenetic relationships in subterranean rodents of the Ctenomys mendocinus species complex: Effects of Late Quaternary landscape changes of Central Argentina. Mamm Biol 2017. [DOI: 10.1016/j.mambio.2017.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Mora MS, Mapelli FJ, López A, Gómez Fernández MJ, Mirol PM, Kittlein MJ. Landscape genetics in the subterranean rodent Ctenomys "chasiquensis" associated with highly disturbed habitats from the southeastern Pampas region, Argentina. Genetica 2017; 145:575-591. [PMID: 28905157 DOI: 10.1007/s10709-017-9983-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 09/07/2017] [Indexed: 11/29/2022]
Abstract
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.
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Affiliation(s)
- Matías Sebastián Mora
- Departamento de Biología, Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones Marinas y Costeras, (IIMyC, CONICET), Universidad Nacional de Mar del Plata, Funes 3250, 3rd floor, 7600, Mar del Plata, Argentina.
| | - Fernando J Mapelli
- Departamento de Biología, Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones Marinas y Costeras, (IIMyC, CONICET), Universidad Nacional de Mar del Plata, Funes 3250, 3rd floor, 7600, Mar del Plata, Argentina
| | - Aldana López
- Área de Recursos Naturales, CONICET INTA EEA Bariloche, CC 277 8400, Bariloche, Río Negro, Argentina
| | - María Jimena Gómez Fernández
- Grupo de Genética y Ecología en Conservación y Biodiversidad, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", CONICET, Ángel Gallardo 470, Buenos Aires, Argentina
| | - Patricia M Mirol
- Grupo de Genética y Ecología en Conservación y Biodiversidad, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", CONICET, Ángel Gallardo 470, Buenos Aires, Argentina
| | - Marcelo J Kittlein
- Departamento de Biología, Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones Marinas y Costeras, (IIMyC, CONICET), Universidad Nacional de Mar del Plata, Funes 3250, 3rd floor, 7600, Mar del Plata, Argentina
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