Genetic structuring in a relictual population of screaming hairy armadillo (Chaetophractus vellerosus) in Argentina revealed by a set of novel microsatellite loci

The screaming hairy armadillo (Chaetophractus vellerosus) is a mammal species containing disjunct and isolated populations. In order to assess the effect of habitat fragmentation and geographic isolation, we developed seven new microsatellite loci isolated from low-coverage genome shotgun sequencing data for this species. Among these loci, six microsatellites were found to be polymorphic with 8 to 26 alleles per locus detected across 69 samples analyzed from a relictual population of the species located in the northeast of the Buenos Aires Province (Argentina). Mean allelic richness and polymorphic information content were 15 and 0.75, with observed and expected heterozygosities ranging from 0.40 to 0.67 and 0.58 to 0.90, respectively. All loci showed departures from Hardy-Weinberg equilibrium. The analysis of population structure in this relictual population revealed three groups of individuals that are genetically differentiated. These newly developed microsatellites will constitute a very useful tool for the estimation of genetic diversity and structure, population dynamics, social structure, parentage and mating system in this little-studied armadillo species. Such genetic data will be particularly helpful for the development of conservation strategies for this isolated population and also for the endangered Bolivian populations previously recognized as a distinct species (Chaetophractus nationi).Centro de Estudios Parasitológicos y de Vectore

Population Genetics of Franciscana Dolphins (Pontoporia blainvillei): Introducing a New Population from the Southern Edge of Their Distribution

Due to anthropogenic factors, the franciscana dolphin, Pontoporia blainvillei, is the most threatened small cetacean on the Atlantic coast of South America. Four Franciscana Management Areas have been proposed: Espiritu Santo to Rio de Janeiro (FMA I), São Paulo to Santa Catarina (FMA II), Rio Grande do Sul to Uruguay (FMA III), and Argentina (FMA IV). Further genetic studies distinguished additional populations within these FMAs. We analyzed the population structure, phylogeography, and demographic history in the southernmost portion of the species range. From the analysis of mitochondrial DNA control region sequences, 5 novel haplotypes were found, totalizing 60 haplotypes for the entire distribution range. The haplotype network did not show an apparent phylogeographical signal for the southern FMAs. Two populations were identified: Monte Hermoso (MH) and Necochea (NC)+Claromecó (CL)+Río Negro (RN). The low levels of genetic variability, the relative constant size over time, and the low levels of gene flow may indicate that MH has been colonized by a few maternal lineages and became isolated from geographically close populations. The apparent increase in NC+CL+RN size would be consistent with the higher genetic variability found, since genetic diversity is generally higher in older and expanding populations. Additionally, RN may have experienced a recent split from CL and NC; current high levels of gene flow may be occurring between the latter ones. FMA IV would comprise four franciscana dolphin populations: Samborombón West+Samborombón South, Cabo San Antonio+Buenos Aires East, NC+CL+Buenos Aires Southwest+RN and MH. Results achieved in this study need to be taken into account in order to ensure the long-term survival of the species.Fil: Gariboldi, María Constanza. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Maimónides. Área de Investigaciones Biomédicas y Biotecnológicas. Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y de Diagnóstico; ArgentinaFil: Tunez, Juan Ignacio. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Luján; ArgentinaFil: Dejean, Cristina Beatriz. Universidad Maimónides. Área de Investigaciones Biomédicas y Biotecnológicas. Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y de Diagnóstico; Argentina. Universidad de Buenos Aires. Facultad de Filosofía y Letras. Instituto de Ciencias Antropológicas. Sección Antropología Biológica; ArgentinaFil: Failla, Mauricio. Fundación Cethus; ArgentinaFil: Vitullo, Alfredo Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Maimónides. Área de Investigaciones Biomédicas y Biotecnológicas. Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y de Diagnóstico; ArgentinaFil: Negri, Maria Fernanda. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales ; ArgentinaFil: Cappozzo, Humberto Luis. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Maimónides. Área de Investigaciones Biomédicas y Biotecnológicas. Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y de Diagnóstico; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales ; Argentin

Genetic structuring in a relictual population of screaming hairy armadillo (Chaetophractus vellerosus) in Argentina revealed by a set of novel microsatellite loci

International audienceThe screaming hairy armadillo (Chaetophractus vellerosus) is a mammal species containing disjunct and isolated populations. In order to assess the effect of habitat fragmentation and geographic isolation, we developed seven new microsatellite loci isolated from low-coverage genome shotgun sequencing data for this species. Among these loci, six microsatellites were found to be polymorphic with 8-26 alleles per locus detected across 69 samples analyzed from a relictual population of the species located in the northeast of the Buenos Aires Province (Argentina). Mean allelic richness and polymorphic information content were 15 and 0.75, with observed and expected heterozy-gosities ranging from 0.40 to 0.67 and 0.58 to 0.90, respectively. All loci showed departures from Hardy-Weinberg equilibrium. The analysis of population structure in this relictual population revealed three groups of individuals that are genetically differentiated. These newly developed microsatellites will constitute a very useful tool for the estimation of genetic diversity and structure, population dynamics, social structure, parentage and mating system in this little-studied armadillo species. Such genetic data will be particularly helpful for the development of conservation strategies for this isolated population and also for the endangered Bolivian populations previously recognized as a distinct species (Chaetophractus nationi)

Median-joining network based on the mtDNA control region haplotypes of franciscana dolphins.

<p>The size of the circle is proportional to frequency. Branch length reflects the number of mutations separating any two haplotypes. AA and AB: haplotypes with unknown exact sampling site and/or frequency, collected from Argentina [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0132854#pone.0132854.ref003" target="_blank">3</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0132854#pone.0132854.ref033" target="_blank">33</a>] and Brazil [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0132854#pone.0132854.ref034" target="_blank">34</a>], respectively. The frequency for AA and AB was set to one individual. RJ: Rio de Janeiro; RG: Rio Grande do Sul; UY: Uruguay; SCL: San Clemente del Tuyú; PN: Pinamar; NC: Necochea; CL: Claromecó; MH: Monte Hermoso; BB: Bahía Blanca; RN: Río Negro. Haplotype SJ-L3-M4-M5-M12 is shown with a shorter nomenclature, SJL3.</p

Franciscana Management Areas (FMAs) and sampled sites.

<p>Previously proposed FMAs (FMA I-VI) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0132854#pone.0132854.ref024" target="_blank">24</a>] are delineated with solid lines. The number of samples is shown between brackets. ES: Espíritu Santo; RJ: Rio de Janeiro; SP: São Paulo; PR: Paraná; SCA: Santa Catarina; RG: Rio Grande do Sul; SCL: San Clemente del Tuyú; PN: Pinamar; NC: Necochea; CL: Claromecó; MH: Monte Hermoso; BB: Bahía Blanca; RN: Río Negro. Note: Sample size for CL (N = 51) corresponds to 31 samples from Lázaro <i>et al</i>. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0132854#pone.0132854.ref005" target="_blank">5</a>] and 20 samples from this study.</p

Demographic history based on the mtDNA control region sequences from populations NC+CL+NC and MH.

<p>A) Mismatch distributions. Observed and expected distributions are shown with bars and lines, respectively. B) Bayesian skyline plots. The black line is the median estimated and the blue lines show the 95% highest posterior density (HPD) intervals. NC: Necochea; CL: Claromecó; RN: Río Negro; MH: Monte Hermoso.</p

Pairwise genetic differentiation between putative populations.

<p>* Significant values at <i>P</i> < 0.01 are shown in bold.</p><p>Pairwise genetic differentiation between putative populations.</p

Ancient female philopatry, asymmetric male gene flow, and synchronous population expansion support the influence of climatic oscillations on the evolution of South American sea lion (Otaria flavescens)

The South American sea lion (Otaria flavescens) is widely distributed along the southern Atlantic and Pacific coasts of South America with a history of significant commercial exploitation. We aimed to evaluate the population genetic structure and the evolutionary history of South American sea lion along its distribution by analyses of mitochondrial DNA (mtDNA) and 10 nuclear microsatellites loci. We analyzed 147 sequences of mtDNA control region and genotyped 111 individuals of South American sea lion for 10 microsatellite loci, representing six populations (Peru, Northern Chile, Southern Chile, Uruguay (Brazil), Argentina and Falkland (Malvinas) Islands) and covering the entire distribution of the species. The mtDNA phylogeny shows that haplotypes from the two oceans comprise two very divergent clades as observed in previous studies, suggesting a long period (>1 million years) of low inter-oceanic female gene flow. Bayesian analysis of bi-parental genetic diversity supports significant (but less pronounced than mitochondrial) genetic structure between Pacific and Atlantic populations, although also suggested some inter-oceanic gene flow mediated by males. Higher male migration rates were found in the intra-oceanic population comparisons, supporting very high female philopatry in the species. Demographic analyses showed that populations from both oceans went through a large population expansion ~10,000 years ago, suggesting a very similar influence of historical environmental factors, such as the last glacial cycle, on both regions. Our results support the proposition that the Pacific and Atlantic populations of the South American sea lion should be considered distinct evolutionarily significant units, with at least two managements units in each ocean

Mitochondrial genetic and microsatellites diversities in each locality: N number of individuals analyzed (averaged over loci for microsatellites); Hd, haplotype diversity; π, nucleotide diversity; H, number of haplotypes; K, average number of alleles; Ho, observed heterozygosity; He, expected heterozygosity.

<p>Mitochondrial genetic and microsatellites diversities in each locality: N number of individuals analyzed (averaged over loci for microsatellites); Hd, haplotype diversity; π, nucleotide diversity; H, number of haplotypes; K, average number of alleles; Ho, observed heterozygosity; He, expected heterozygosity.</p

Extended Bayesian skyline plot showing the effective population size fluctuation of three South American sea lions populations throughout time based on the mtDNA control region.

<p>Internal thick lines are median estimates and thin lines and coloured areas are the 95% Central Posterior Density (CPD) intervals. Nef, effective female population size (log scale), ka, thousands of years ago. Time was truncated at 50 ka.</p