Microsatellite genotyping from faeces of Lontra longicaudis from southern Brazil

Abstract

ABSTRACT.A genetic study of the neotropical river otter Lontra longicaudis (Olfers, 1818), which has an unknown conservation status, was carried out at the Taim Ecological Station and the margins of the Vargas stream, Rio Grande do Sul, southern Brazil. Faecal samples were collected, and DNA was extracted using a silica-guanidine method. Five microsatellite loci were amplified using PCR with heterologous primers previously described for Lutra lutra (Linnaeus, 1758). Sixteen faecal samples out of 29 from Taim and 11 out of 14 from Vargas stream margins contained enough DNA for genetic analysis. A total of 49 different alleles were found at both localities, from which 18 were exclusively found in individuals from Taim and 17 were exclusives from Vargas individuals. The most common allele was the same at both locations for three loci (Lut715, Lut733, and Lut818). A high level of genetic diversity was found at both sites (Ne Taim =4.1, Ho Taim =0.299, He Taim =0.681; Ne Vargas =4.9, Ho Vargas =0.355, He Vargas =0.724), being higher at the Vargas stream site. A high and significant level of heterozygote deficiency was observed at most loci according to the χ 2 test. The homogeneity χ 2 test (P≤0.001) showed that there were significant differences in the allele frequencies between the two locations. Genotyping for more than one locus was possible in 81.5% of samples, from which only 37% were possible to genotype for more than three loci. A low degree of relatedness was found among individuals from Taim (R=0.055±0.310), but an even lower value of relatedness was found at the Vargas site (R= -0.285±0.440). The significant degree of differentiation (I=0.890; F ST =0.059) found between Taim and Vargas individuals suggests that there is more than one population of otters in the southern extreme of Brazil, which probably are associated with the water body systems found in this region, the Mirim and the Caiuvá/Flores/Mangueira Lagoons. The high genetic diversity and low relatedness found at the Vargas stream, lead us to believe that the Vargas stream may be acting as a corridor between these water bodies for otter dispersion. KEYWORDS.Neotropical river otter, genetic markers, Taim, non-invasive sampling, genetic diversity.RESUMO. Genotipagem através de microsatélites extraídos de amostras fecais em Lontra longicaudis do sul do Brasil. A lontra neotropical de rio Lontra longicaudis (Olfers, 1818), cujo estado de conservação é ainda desconhecido, foi estudada geneticamente na Estação Ecológica do Taim e nas margens do arroio Vargas, RS, sul do Brasil. Amostras de fezes foram coletadas e o DNA foi extraído por um método de sílica-guanidina. Cinco locos de microsatélites foram amplificados por PCR utilizando primers heterólogos previamente descritos para Lutra lutra (Linnaeus, 1758). Dezesseis amostras de fezes de um total de 29 coletadas no Taim e onze das 14 obtidas no arroio Vargas contiveram DNA suficiente para prosseguir com a analise genética. Um total de 49 alelos foram obtidos, dos quais 18 foram exclusivos de indivíduos...

Molecular ecology of the Neotropical otter (Lontra longicaudis): non-invasive sampling yields insights into local population dynamics

“…Interestingly, seven alleles detected in the studied population were not observed in the blood/tissue set of samples from southern Brazil, also highlighting the great potential of these loci for local genetic studies. Levels of microsatellite polymorphism such as observed heterozygosity (H O = 0.832) and mean number of alleles (6.5) were higher in the present study than those reported for two other populations from southernmost Brazil (HO = 0.299/0.355; Weber et al, 2009) based on a partially overlapping set of loci, and also higher than that estimated for a wild population in Mexico (HO range = 0.48-0.59; Ortega et al, 2012).…”

“…Gallo-Reynoso, Ramos-Rosas & Rangel-Aguilar, 2008;Chemes, Giraudo & Gil, 2010). Molecular studies are so far few, focusing mostly on the characterization of genetic diversity and/or population structure (Trinca, Waldemarin & Eizirik, 2007;Weber et al, 2009;Ortega, Navarrete & Maldonado, 2012;. There is thus a need to investigate its biology in more detail, including the use of molecular tools to address outstanding questions.…”

Non–invasive sampling of endangered neotropical river otters reveals high levels of dispersion in the Lacantun River System of Chiapas, Mexico

“…Furthermore, our estimates of dispersion levels between rivers suggest that they are high enough to prevent genetic differentiation. The pattern of low genetic structure is also strongly supported by the high resolution provided by microsatellite markers in these types of studies (Selkoe & Toonen 2006;Weber et al, 2009). In particular, Latch et al (2008) found that the North American river otter (L. canadensis) in Louisiana is affected by a variety of landscape habitats that have structured the river otter populations and have prohibited an adequate level of gene flow, but the scale of that study is several times larger than the area surveyed in this study.…”

“…Information concerning population dynamics of the species is scarce, and even less is known about the genetic structure of their populations. Only two studies related to the genetic structure of the neotropical river otter have been conducted previously in Brazil, but both were carried out in larger areas than our present study (Trinca et al, 2007;Weber et al, 2009). The first study found no significant mtDNA genetic differentiation between populations in the southern and south-eastern regions of Brazil and the latter study, using microsatellite markers, found significant levels of genetic differentiation in populations in the southernmost part of Brazil.…”

Conservation genetics of otters: Review about the use of non-invasive samples

“…In the first study of L. longicaudis using nuclear markers, Weber et al (2009) collected 43 stool samples in the state of Rio Grande do Sul and tested the amplification of five microsatellites developed for Lutra lutra. The genotyping efficiency reached 37 % and 24 genotypes were detected.…”