Genetic structure and evidence for recent population decline in Eurasian otter populations in the Czech and Slovak Republics: implications for conservation

Abstract

Over the latter part of the 20th century, Eurasian otter Lutra lutra populations suffered dramatic declines, resulting in extinction or fragmentation of populations in many western and central European countries. Part of the Czech otter population became totally isolated while the Slovak population remained partly connected to the relatively continuous central and eastern European otter distribution range. This paper examines the genetic structure and past demographic history of otters in the Czech and Slovak Republics, using microsatellite nuclear markers amplified from DNA extracted from tissue and faecal samples. A relatively high level of genetic differentiation was found between the Czech and Slovak populations (F ST = 0.154, P = 0.0002), supported by a perfect assignment in Bayesian cluster analysis. Both the Czech and Slovak populations showed significant heterozygosity excess (assuming an infinite allele model), indicating recent population bottlenecks. A very recent population decline was also suggested by coalescent analysis, inferring a drop to c. 25% of past effective population size in both populations. The timing of the decline was in accordance with published data from otter surveys, suggesting that the strongest decline probably occurred between the 1970s and the mid-1990s. The results of this study confirm that otter populations remain vulnerable to any violent demographic change and, despite the claims of fish-farmers and anglers for legal culls, it is highly desirable that they remain a strongly protected species in both countries. The spreading and reconnection of otter populations observed recently is essential for the future health of the populations, and should be supported through habitat conservation.

Genetic diversity and landscape genetic structure of otter (Lutra lutra) populations in Europe

“…Landscape genetic structure of otter populations Microsatellite allelic diversity and heterozygosity were moderate in the European otter populations, concordant with other published studies (Dallas et al 1999(Dallas et al , 2002Pertoldi et al 2001;Arrendal et al 2004;Hajkova et al 2007). In this study, we could not find evidence for any clear global trend in the geographical distribution of genetic diversity.…”

“…The intra-specific taxonomy of otter populations is uncertain, because the species exhibits unusually low levels of mtDNA variation, and shows almost no mtDNA geographic structure (Effenberger and Suchentrunk 1999;Mucci et al 1999;Cassens et al 2000;Arrendal et al 2004;Ferrando et al 2004;Ketmaier and Bernardini 2005;Pérez-Haro et al 2005;Finnegan and Néill 2009;Stanton et al 2009). Autosomal microsatellites are polymorphic in otters, but the populations studied so far showed little geographical differentiation also at the nuclear level (Dallas et al 1999;Pertoldi et al 2001;Dallas et al 2002;Randi et al 2003;Arrendal et al 2004;Hajkova et al 2007;Janssens et al 2008). The scope of published studies was limited by restricted geographical sampling collections.…”

An evaluation of field and noninvasive genetic methods for estimating Eurasian otter population size

“…In the first round, six microsatellites and the SRY marker were genotyped for individual identification, yielding acceptable probability of identity values (Table 1). As it was planned that genotypes would be included in larger datasets used for population genetic studies (Hájková et al 2007), the samples were subsequently genotyped for four additional loci, resulting in multilocus genotypes composed of ten loci for each identified individual. When the individual was represented by several samples, those of the highest quality were used in preference for the second round of genotyping.…”

“…Detailed protocols are described in Hájková et al (2007). PCR products were electrophoresed on ABI Prism 310 and 3130 Genetic Analysers (Applied Biosystems, Foster City, CA, USA) and analysed using GeneScan 3.7 or GeneMapper 3.7 software (Applied Biosystems).…”

Effects of Linked Selective Sweeps on Demographic Inference and Model Selection

“…In particular, genomescale variation data allows for inference of demographic factors such as population size changes, the timing and ordering of population splits, migration rates between populations, and the founding of admixed populations (Pool et al 2010;Pickrell and Pritchard 2012;Sousa and Hey 2013). Such efforts can refine our picture of demographic events inferred from the archaeological record (e.g., Fagundes et al 2007;Goebel et al 2008), or reveal such events in species where no archaeological data are available, and can aid conservation efforts by complementing census data (e.g., Hájková et al 2007;Garrick et al 2015).Population genomic data sets are well suited for this task simply because demographic changes leave their mark on patterns of genetic variation. Recent population growth, for example, will result in an excess of rare variation compared to equilibrium expectations (Fu 1997), while population contraction will result in an excess of intermediate frequency alleles (Maruyama and Fuerst 1985).…”