Mitochondrial DNA variation in the European otter (Lutra lutra) and the use of spatial autocorrelation analysis in conservation

Genomics Reveals Complex Population History and Unexpected Diversity of Eurasian Otters (Lutra lutra) in Britain Relative to Genetic Methods

Conservation genetic analyses of many endangered species have been based on genotyping of microsatellite loci and sequencing of short fragments of mtDNA. The increase in power and resolution afforded by whole genome approaches may challenge conclusions made on limited numbers of loci and maternally inherited haploid markers. Here, we provide a matched comparison of whole genome sequencing versus microsatellite and control region (CR) genotyping for Eurasian otters (Lutra lutra). Previous work identified four genetically differentiated "stronghold" populations of otter in Britain, derived from regional populations that survived the population crash of the 1950s-1980s. Using whole genome resequencing data from 45 samples from across the British stronghold populations, we confirmed some aspects of population structure derived from previous marker-driven studies. Importantly, we showed that genomic signals of the population crash bottlenecks matched evidence from otter population surveys. Unexpectedly, two strongly divergent mitochondrial lineages were identified that were undetectable using CR fragments, and otters in the east of England were genetically distinct and surprisingly variable. We hypothesize that this previously unsuspected variability may derive from past releases of Eurasian otters from other, non-British source populations in England around the time of the population bottleneck. Our work highlights that even reasonably well-studied species may harbor genetic surprises, if studied using modern high-throughput sequencing methods.

Taxonomic status of otter species in Nakai-Nam Theun National Park, Lao PDR, based on DNA evidence

Otter populations are threatened by habitat loss, pollution, conflicts with humans, and illegal wildlife trade to meet the demand for pets, for their fur, and for parts used in traditional medicines. Baseline information on the distribution, population genetic diversity, and connectivity is crucial to inform conservation management decisions; however, reliable data from otter populations in Southeast Asia remain scarce. In this study, we conducted baseline otter fecal DNA surveys based on mitochondrial DNA (mtDNA) to identify species, assess the occurrence, and map the spatial distribution of genetic diversity and evolutionary relationships of otter populations using 1700 bp Cytochrome B - Control Region and mitogenome from Nakai-Nam Theun National Park in the Annamite Mountains of Lao PDR. Of the total 56 samples identified to species, the majority (87.5%) was of the widely distributed Eurasian otter with three haplotypes (Lutra lutra; LLLA01-LLLA03), with a calculated haplotype diversity of 0.600 and a nucleotide diversity of 0.00141 based on mitogenome. The second species was the Asian small-clawed otter with only one haplotype detected (Aonyx cinereus; ACLA01). All Eurasian otter haplotypes were newly characterized and clustered within the strongly supported South-Southeast-North Asian clade of Lutra lutra. Compared with the European clade, the high mtDNA diversity of Lutra lutra in Nakai-Nam Theun National Park potentially reflects long-term demographic stability and lesser degree of population bottleneck during the last glacial maxima (LGM, ~21,000 years ago). The single haplotype detected in Asian small-clawed otters had not been detected in previous genetic studies. Our research is the first otter-specific noninvasive genetic study in Lao PDR and provides baseline insights into the otter population diversity in a regional priority site for biodiversity conservation.

Identification of novel haplotypes and interpretation of gene flow of mitochondrial DNA control region of Eurasian otter (Lutra lutra) for the effective conservation

The number and distribution of Eurasian otters have declined during twentieth century due to human activity and water pollution. The global conservation status of Eurasian otter is presently ‘Near Threatened (NT)’ and strictly protected by being listed on the international legislation and conventions. A number of studies using the mitochondrial DNA (mtDNA) control region (CR) have been conducted in order to effectively apply conservation and reintroduction programs, especially in Europe. However, aside from Europe, there have been few studies concerning genetic diversity and phylogeny of Eurasian otters. Therefore, in this study, we sequenced partial mtDNA CR sequences (232 bp) from five South Korean Eurasian otters and analyzed 27 otters originating from parts of northeast Asia (South Korea, China, Japan and Russia (Sakhalin)), and Europe. Out of 232 bp partial mtDNA CR sequences, 13 polymorphic sites (5.6%) were identified and 4 novel mtDNA CR haplotypes (Lut16–19) were discovered from 12 Eurasian otters originating from northeast Asian region. In this study, a comprehensive analysis of genetic diversity and population structure of Eurasian otter between Europe and northeast Asia continents were conducted. Of these, different past demographic histories in Pleistocene period might have largely impacted the genetic structure of each population differently. In addition, low degree of gene flow, isolation by distance (IBD) pattern from geographically wide distanced dataset and analysis of molecular variance (AMOVA) also represented distinct genetic characteristics of Eurasian otter between Europe and northeast Asia.

Climate-mediated shifts in Neandertal subsistence behaviors at Pech de l'Azé IV and Roc de Marsal (Dordogne Valley, France)

Neandertals disappeared from Europe just after 40,000 years ago. Some hypotheses ascribe this to numerous population crashes associated with glacial cycles in the late Pleistocene. The goal of this paper is to test the hypothesis that glacial periods stressed Neandertal populations. If cold climates stressed Neandertals, their subsistence behaviors may have changed-requiring intensified use of prey through more extensive nutrient extraction from faunal carcasses. To test this, an analysis of Neandertal butchering was conducted on medium sized bovid/cervid remains composed of predominately red deer (Cervus elaphus), reindeer (Rangifer tarandus), and roe deer (Capreolus caprelous) deposited during global warm and cold phases from two French sites: Pech de l'Azé IV (Pech IV, Bordes' excavation) and Roc de Marsal (RDM). Analysis of surface modification on high survival long bones and proximal and middle phalanges demonstrates that skeletal elements excavated from the cold levels (RDM Level 4, Pech IV Level I2) at each cave have more cut marks and percussion marks than elements from the warm levels (RDM Level 9, Pech IV Level Y-Z) after controlling for fragment size. At both sites, epiphyseal fragments are rare, and although this pattern can result from carnivore consumption, carnivore tooth marks are almost nonexistent (<0.1%). Alternatively, processing epiphyseal ends for bone grease may have been a Neandertal survival strategy, and epiphyses were more intensively percussed in cold levels than in warm levels at both RDM and Pech IV. The exploitation of low marrow yield elements such as phalanges does not show a consistent pattern relating to climate, but may have been a general Neandertal behavioral characteristic, suggesting that these hominids were regularly on the edge of sufficient nutrient availability even during interglacials. Overall, the faunal assemblages from Roc de Marsal and Pech IV provide some support for the hypothesis that Neandertals were processing faunal remains more heavily during glacial periods, suggesting a response to increased nutritional stress during colder time periods.

The effect of a major drainage divide on the gene flow of a semiaquatic carnivore, the Eurasian otter

Major drainage divides (separating the water flow draining to different seas) may significantly affect the dispersal, distribution, and genetic structure of semiaquatic animals. Assessing this effect is important for the proper management of both endangered and invasive riparian species. Here, I determined the fine-scale impact of the drainage divide between the Baltic Sea and the Black Sea drainage basins on the genetic structure and dispersal of the Eurasian otter (Lutra lutra) in the Bieszczady Mountains (Poland and Slovakia). I investigated the genetic structure of the otter population and assessed 3 alternative dispersal models using 6 landscape genetics methods. The analyses were based on 48 individual genotypes obtained from 622 fecal and gland secretion samples collected in 2008–2011. Results indicate that the major drainage divide is not a barrier to gene flow for this population. This was established by analyses of population genetic structure and confirmed by analysis of the spatial distribution of samples originating from closely related individuals. In line with these findings, the best-supported dispersal model assumed that otters migrate through mountain passes, away from streams, thus revealing that they are able to cross a drainage divide. The genetic structure of the population studied exhibits an isolation-by-distance pattern; however, the locations of several repeatedly recorded or closely related individuals revealed the occurrence of long-distance movements. Confirmation of the high mobility of otters and their ability to cross a major drainage divide ridge suggest that landscape obstacles and discontinuity of river network are unlikely to stop otter dispersal, gene flow, and recolonization of new areas.

Hantavirus pulmonary syndrome and rodent reservoirs in the savanna-like biome of Brazil's southeastern region

This paper describes the diversity of rodent fauna in an area endemic for hantavirus cardiopulmonary syndrome (HCPS) in Brazil, the population dynamics and the relationship of rodents with hantavirus in the Cerrado (savanna-like) biome. Additionally, an analysis is made of the partial S segment sequences of the hantaviruses obtained from serologically confirmed human HCPS cases and from rodent specimens. Rodents were collected during four campaigns. Human serum samples were collected from suspected cases of HCPS at hospitals in the state of Minas Gerais. The samples antibody-reactive by ELISA were processed by RT-PCR. The PCR product was amplified and sequenced. Hantavirus was detected only in Necromys lasiurus, the wild rodent species most prevalent in the Cerrado biome (min-max: 50-83·7%). All the six human serum samples were hantavirus seropositive and five showed amplified PCR products. The analysis of the nucleotide sequences showed the circulation of a single genotype, the Araraquara hantavirus. The environmental changes that have occurred in the Cerrado biome in recent decades have favoured N. lasiurus in interspecific competition of habitats, thus increasing the risk of contact between humans and rodent species infected with hantavirus. Our data corroborate the definition of N. lasiurus as the main hantavirus reservoir in the Cerrado biome.

Zoonotic Bartonella species in wild rodents in the state of Mato Grosso do Sul, Brazil

Several rodent-associated Bartonella species cause disease in humans but little is known about their epidemiology in Brazil. The presence of Bartonella spp. in wild rodents captured in two municipalities of the Mato Grosso do Sul state was assessed by polymerase chain reaction (PCR). Fragments of heart tissue from 42 wild rodents were tested using primers targeting the Bartonella 16S-23S intergenic transcribed spacer (ITS) region and citrate synthase gltA gene. The wild rodents were identified based on external and cranial morphology and confirmed at species level by mitochondrial DNA (cytochrome B) sequencing and karyotype. Overall, 42.9% (18/42) of the wild rodents were PCR positive for Bartonella spp.: Callomys callosus (04), Cerradomys maracajuensis (04), Hylaeamus megacephalus (01), Necromys lasiurus (06), Nectomys squamipes (01), Oecomys catherinae (01) and Oxymycterus delator (01). Bartonella vinsonii subsp. arupensis was detected in N. lasiurus (46%) and C. callosus (21%) captured in the two study sites. We reported the first molecular detection of B. vinsonii subsp. arupensis in different species of wild rodents collected in the Brazilian territory. Further studies are needed to examine the role of these mammals in the eco-epidemiology of bartonellosis in Brazil.

Co-circulation of Clade C New World Arenaviruses: New geographic distribution and host species

Clade C, of the New World Arenaviruses, is composed of only the Latino and Oliveros viruses and, besides the geographic range of their rodent reservoirs, the distribution of these viruses has been restricted to Bolivia and Argentina. In this study, the genetic detection and phylogenetic analysis of the complete S segment sequences of sympatric arenaviruses from Brazil revealed a new geographic distribution of clade C arenaviruses, as well as the association of Oliveros virus with a new rodent reservoir.

Phylogeography and demographic history of the neotropical otter (Lontra longicaudis)

The Neotropical otter (Lontra longicaudis) is a medium-sized semiaquatic carnivore with a broad distribution in the Neotropical region. Despite being apparently common in many areas, it is one of the least known otters, and genetic studies on this species are scarce. Here, we have investigated its genetic diversity, population structure, and demographic history across a large portion of its geographic range by analyzing 1471 base pairs (bp) of mitochondrial DNA from 52 individuals. Our results indicate that L. longicaudis presents high levels of genetic diversity and a consistent phylogeographic pattern, suggesting the existence of at least 4 distinct evolutionary lineages in South America. The observed phylogeographic partitions are partially congruent with the subspecies classification previously proposed for this species. Coalescence-based analyses indicate that Neotropical otter mitochondrial DNA lineages have shared a rather recent common ancestor, approximately 0.5 Ma, and have subsequently diversified into the observed phylogroups. A consistent scenario of recent population expansion was identified in Eastern South America based on several complementary analyses of historical demography. The results obtained here provide novel insights on the evolutionary history of this largely unknown Neotropical mustelid and should be useful to design conservation and management policies on behalf of this species and its habitats.

Phylogeography of the Patagonian otter Lontra provocax: adaptive divergence to marine habitat or signature of southern glacial refugia?

BACKGROUND

A number of studies have described the extension of ice cover in western Patagonia during the Last Glacial Maximum, providing evidence of a complete cover of terrestrial habitat from 41°S to 56°S and two main refugia, one in south-eastern Tierra del Fuego and the other north of the Chiloé Island. However, recent evidence of high genetic diversity in Patagonian river species suggests the existence of aquatic refugia in this region. Here, we further test this hypothesis based on phylogeographic inferences from a semi-aquatic species that is a top predator of river and marine fauna, the huillín or Southern river otter (Lontra provocax).

RESULTS

We examined mtDNA sequences of the control region, ND5 and Cytochrome-b (2151 bp in total) in 75 samples of L. provocax from 21 locations in river and marine habitats. Phylogenetic analysis illustrates two main divergent clades for L. provocax in continental freshwater habitat. A highly diverse clade was represented by haplotypes from the marine habitat of the Southern Fjords and Channels (SFC) region (43°38' to 53°08'S), whereas only one of these haplotypes was paraphyletic and associated with northern river haplotypes.

CONCLUSIONS

Our data support the hypothesis of the persistence of L. provocax in western Patagonia, south of the ice sheet limit, during last glacial maximum (41°S latitude). This limit also corresponds to a strong environmental change, which might have spurred L. provocax differentiation between the two environments.

Phylogeography of the Marine Otter (Lontra felina): historical and contemporary factors determining its distribution

The evolutionary history of a species can be revealed by phylogeographical analysis; nevertheless, not only historical but also contemporary processes can imprint on the distribution of genetic diversity. We report on the phylogeny of Lontra ssp. in South America, and the role of spatial heterogeneity in shaping the distribution and population structure of the endangered marine otter, Lontra felina. Analyzing a total of 2261 bp of mitochondrial DNA (mtDNA) revealed the recent divergence of L. felina from L. provocax. A strong population structure (Φ(st) = 0.83, P < 0.0001) and a significant pattern of isolation by distance were described for L. felina (n = 168) across a wide geographical distribution (13°53'S to 43°36'S). Lontra felina mtDNA phylogeny is composed of 2 main clades: a clade from Peru and another composed of Chilean haplotypes. Northern populations show different divergent lineages and higher genetic diversity when compared with more recently colonized southern populations. Furthermore, long sandy beaches seem to act as barriers to dispersal, creating 2 evolutionary significant units in agreement with subspecies previous description, and at least 5 different management units (MUs). At a fine spatial scale, the size of rocky seashore patches, the distance between patches and anthropogenic factors also play important roles in species gene flow.

Genetic diversity of the Neotropical otter (Lontra longicaudis Olfers, 1818) in Southern and Southeastern Brazil

The Neotropical otter is one of the least known otter species, and it is considered to be threatened to various degrees throughout its geographic range. Little information exists on the ecological characteristics of this species, and no genetic study has been published about it until now, hampering the design of adequate conservation strategies for its populations. To contribute with genetic information to comprehensive conservation efforts on behalf of L. longicaudis, we characterized the molecular diversity of the 5 portion of the mtDNA control region in samples from this species collected in Southern and Southeastern Brazil. The sequence analysis revealed a high level of haplotype diversity (h=0.819; SE=0.0052) and nucleotide variability ranging from 0.0039 to 0.0067. One of the sampled haplotypes was the most common in both regions and, from this sequence, several other (locally occurring) haplotypes could be derived by single point mutations. No significant genetic differentiation was observed between the Southern and Southeastern regions.

Diversity of mtDNA in Southern River Otter (Lontra provocax) from Argentinean Patagonia

Lontra provocax is an endemic species from Patagonia that has been categorized as "endangered" by the International Union for Conservation of Nature. In this study, noninvasive molecular methods were used to investigate the genetic diversity and haplotype distribution of L. provocax in Argentinean Patagonia. We analyzed 150 scat samples collected from 1995 to 2006 and obtained 13 sequences of control region with 1 haplotype and 34 sequences of cytochrome b with 4 haplotypes. The population of the south of Patagonia (Tierra del Fuego and De los Estados Island) showed a relatively high haplotype diversity (h = 0.71) and was statistically different to the population of the north (analysis of molecular variance, F(ST) = 0.15, P = 0.018). We concluded that there are 2 different subpopulations of L. provocax that deserve conservation attention and that the southern population appears not to have suffered a human-induced population bottleneck of the sort typically experienced by various otter species around the world.

Applying new inter-individual approaches to assess fine-scale population genetic diversity in a neotropical frog, Eleutherodactylus ockendeni

We assess patterns of genetic diversity of a neotropical leaflitter frog, Eleutherodactylus ockendeni, in the upper Amazon of Ecuador without a priori delineation of biological populations and with sufficiently intensive sampling to assess inter-individual patterns. We mapped the location of each collected frog across a 5.4 x 1 km landscape at the Jatun Sacha Biological Station, genotyped 185 individuals using five species-specific DNA microsatellite loci, and sequenced a fragment of mitochondrial cytochrome b for a subset of 51 individuals. The microsatellites were characterized by high allelic diversity and homozygote excess across all loci, suggesting that when pooled the sample is not a panmictic population. We conclude that the lack of panmixia is not attributable to the influence of null alleles or biased sampling of consanguineous family groups. Multiple methods of population cluster analysis, using both Bayesian and maximum likelihood approaches, failed to identify discrete genetic clusters across the sampled area. Using multivariate spatial autocorrelation, kinship coefficients and relatedness coefficients, we identify a continuous isolation by distance population structure, with a first patch size of ca. 260 m and apparently large population sizes. Analysis of mtDNA corroborates the observation of high genetic diversity at fine scales: there are multiple haplotypes, they are non-randomly distributed and a binary haplotype correlogram shows significant spatial genetic autocorrelation. We demonstrate the utility of inter-individual genetic methods and caution against making a priori assumptions about population genetic structure based simply on arbitrary or convenient patterns of sampling.

Dispersal, philopatry and intergroup relatedness: fine-scale genetic structure in the white-breasted thrasher, Ramphocinclus brachyurus

Dispersal is a fundamental process influencing evolution, social behaviour, and the long-term persistence of populations. We use both observational and genetic data to investigate dispersal, kin-clustering and intergroup relatedness in the white-breasted thrasher, Ramphocinclus brachyurus, a cooperatively breeding bird that is globally endangered. Mark-resighting data suggested sex-biased dispersal, with females dispersing over greater distances while males remained philopatric. Accordingly, spatial autocorrelation analysis showed highly significant fine-scale genetic structure among males, but not among females. This fine-scale genetic structuring of the male population resulted in very high levels of relatedness between dominant males at neighbouring nests, similar to that seen within cooperative groups in many species where kin selection is cited as a cause of cooperation. By implication, between-group as well as within-group cooperation may be important, potentially creating a feedback loop in which short-distance dispersal by males leads to the formation of male kin clusters that in turn facilitate nepotistic interactions and favour further local recruitment. The strength of spatial autocorrelation, as measured by the autocorrelation coefficient, r, was approximately two to three times greater than that reported in previous studies of animals. Relatively short dispersal distances by both males and females may have a negative impact on the white-breasted thrasher's ability to colonize new areas, and may influence the long-term persistence of isolated populations. This should be taken into account when designating protected areas or selecting sites for habitat restoration.

The Population History of Extant and Extinct Hyenas

We have analyzed partial DNA sequences of the mitochondrial cytochrome b gene from extant striped, brown, and spotted hyenas as well as from Pleistocene cave hyenas. Sequences of the Pleistocene cave hyenas from Eurasia and modern spotted hyenas from Africa are intermixed in phylogenetic analyses, questioning any taxonomic delineation between the two groups. Contrary to cave hyenas in Eurasia, spotted hyenas in Africa show a phylogeographic pattern with little geographical overlap between two mitochondrial DNA (mtDNA) clades, suggesting two Pleistocene refugia in the north and south of Africa. Our results, furthermore, suggest three waves of migration from Africa to Eurasia for spotted hyenas, around 3, 1, and 0.3 MYA. A recent emigration of striped hyenas from Africa to Eurasia took place less than 0.1 MYA, resulting in a dramatic expansion of the geographical range of striped hyenas. In striped hyenas and within the geographical range of mtDNA clades in spotted hyenas, we found identical sequences several thousand kilometers apart, indicating a high rate of migration during the Pleistocene as well as the Holocene. Both striped and brown hyenas show low amounts of genetic diversity, with the latter ones displaying just a single haplotype.

Conservation genetics and population history of the threatened European mink Mustela lutreola, with an emphasis on the west European population

In species of great conservation concern, special attention must be paid to their phylogeography, in particular the origin of animals for captive breeding and reintroduction. The endangered European mink lives now in at least three well-separated populations in northeast, southeast and west Europe. Our aim is to assess the genetic structure of these populations to identify 'distinct population segments' (DPS) and advise captive breeding programmes. First, the mtDNA control region was completely sequenced in 176 minks and 10 polecats. The analysis revealed that the western population is characterized by a single mtDNA haplotype that is closely related to those in eastern regions but nevertheless, not found there to date. The northeast European animals are much more variable (pi = 0.012, h = 0.939), with the southeast samples intermediate (pi = 0.0012, h = 0.469). Second, 155 European mink were genotyped using six microsatellites. The latter display the same trends of genetic diversity among regions as mtDNA [gene diversity and allelic richness highest in northeast Europe (H(E) = 0.539, R(S) = 3.76), lowest in west Europe (H(E) = 0.379, R(S) = 2.12)], and provide evidences that the southeast and possibly the west populations have undergone a recent bottleneck. Our results indicate that the western population derives from a few animals which recently colonized this region, possibly after a human introduction. Microsatellite data also reveal that isolation by distance occurs in the western population, causing some inbreeding because related individuals mate. As genetic data indicate that the three populations have not undergone independent evolutionary histories for long (no phylogeographical structure), they should not be considered as distinct DPS. In conclusion, the captive breeding programme should use animals from different parts of the species' present distribution area.

Microsatellite analyses reveal fine-scale genetic structure in grey mouse lemurs (Microcebus murinus)

Information on genetic structure can be used to complement direct inferences on social systems and behaviour. We studied the genetic structure of the solitary grey mouse lemur (Microcebus murinus), a small, nocturnal primate endemic to western Madagascar, with the aim of getting further insight on its breeding structure. Tissue samples from 167 grey mouse lemurs in an area covering 12.3 km2 in Kirindy Forest were obtained from trapping. The capture data indicated a noncontinuous distribution of individuals in the study area. Using 10 microsatellite markers, significant genetic differentiation in the study area was demonstrated and dispersal was found to be significantly male biased. Furthermore, we observed an overall excess of homozygotes in the total population (F(IT) = 0.131), which we interpret as caused by fine-scale structure with breeding occurring in small units. Evidence for a clumped distribution of identical homozygotes was found, supporting the notion that dispersal distance for breeding was shorter than that for foraging, i.e. the breeding neighbourhood size is smaller than the foraging neighbourhood size. In conclusion, we found a more complex population structure than what has been previously reported in studies performed on smaller spatial scales. The noncontinuous distribution of individuals and the effects of social variables on the genetic structure have implications for the interpretation of social organization and the planning of conservation activities that may apply to other solitary and endangered mammals as well.

Streams over mountains: influence of riparian connectivity on gene flow in the Pacific jumping mouse (Zapus trinotatus)

In species affiliated with heterogeneous habitat, we expect gene flow to be restricted due to constraints placed on individual movement by habitat boundaries. This is likely to impact both individual dispersal and connectivity between populations. In this study, a GIS-based landscape genetics approach was used, in combination with fine-scale spatial autocorrelation analysis and the estimation of recent intersubpopulation migration rates, to infer patterns of dispersal and migration in the riparian-affiliated Pacific jumping mouse (Zapus trinotatus). A total of 228 individuals were sampled from nine subpopulations across a system of three rivers and genotyped at eight microsatellite loci. Significant spatial autocorrelation among individuals revealed a pattern of fine-scale spatial genetic structure indicative of limited dispersal. Geographical distances between pairwise subpopulations were defined following four criteria: (i) Euclidean distance, and three landscape-specific distances, (ii) river distance (distance travelled along the river only), (iii) overland distance (similar to Euclidean, but includes elevation), and (iv) habitat-path distance (a least-cost path distance that models movement along habitat pathways). Pairwise Mantel tests were used to test for a correlation between genetic distance and each of the geographical distances. Significant correlations were found between genetic distance and both the overland and habitat-path distances; however, the correlation with habitat-path distance was stronger. Lastly, estimates of recent migration rates revealed that migration occurs not only within drainages but also across large topographic barriers. These results suggest that patterns of dispersal and migration in Pacific jumping mice are largely determined by habitat connectivity.

Structure of the mitochondrial control region of the Eurasian otter (Lutra lutra; Carnivora, Mustelidae): patterns of genetic heterogeneity and implications for conservation of the species in Italy

In this study we determined the complete sequence of the mitochondrial DNA (mtDNA) control region of the Eurasian otter (Lutra lutra). We then compared these new sequences with orthologues of nine carnivores belonging to six families (Mustelidae, Mephitidae, Canidae, Hyaenidae, Ursidae, and Felidae). The comparative analyses identified all the conserved regions previously found in mammals. The Eurasian otter and seven other species have a single location with tandem repeats in the right domain, while the spotted hyena (Hyaenidae) and the tiger (Felidae) have repeated sequences in both the right and left domains. To assess the degree of genetic heterogeneity of the Eurasian otter in Italy we sequenced two fragments of the gene and analyzed length polymorphisms of repeated sequences and heteroplasmy in 32 specimens. The study includes 23 museum specimens collected in northern, central, and southern Italy; most of these specimens are from extinct populations, while the southern Italian samples belong to the sole extant Italian population of the Eurasian otter. The study also includes all the captive-reared animals living in the colony "Centro Lontra, Caramanico Terme" (Pescara, central Italy). The colony is maintained for reintroduction of the species. We found a low level of genetic polymorphism; a single haplotype is dominant, but our data indicate the presence in central and southern Italy of two slightly divergent haplotypes. One haplotype belongs to an extinct population, the other is present in the single extant Italian population. Analyses of length polymorphisms and heteroplasmy indicate that the autochthonous Italian samples are characterized by a distinct array of repeated sequences from captive-reared animals.

Lack of phylogeography in European mammals before the last glaciation

In many extant animal and plant species in Europe and North America a correlation exists between the geographical location of individuals and the genetic relatedness of the mitochondrial (mt) DNA sequences that they carry. Here, we analyze mtDNA sequences from cave bears, brown bears, cave hyenas, and Neandertals in Europe before the last glacial maximum and fail to detect any phylogeographic patterns similar to those observed in extant species. We suggest that at the beginning of the last glacial maximum, little phylogeographic patterns existed in European mammals over most of their geographical ranges and that current phylogeographic patterns are transient relics of the last glaciation. Cycles of retreat of species in refugia during glacial periods followed by incomplete dispersal from one refugium into other refugia during interglacial periods is likely to be responsible for the deep genetic divergences between phylogeographic clusters of mtDNA seen today.

Individual assignment test reveals differential restriction to dispersal between two salmonids despite no increase of genetic differences with distance

In many species genes move over limited distances, such that genetic differences among populations or individuals are expected to increase as a function of geographical distance. In other species, however, genes may move any distance over a single generation time, such that no increase of genetic differences is expected to occur with distance. Patterns of gene dispersal have been assessed typically using this theoretical property. In this study, this classical approach based on a Mantel test was compared to a new method using individual assignment to reveal contrasts in dispersal patterns between 15 populations of brook charr Salvelinus fontinalis and 10 populations of Atlantic salmon Salmo salar sampled in eastern Canada, where both species co-occur naturally. Based on the Mantel test, we found evidence for neither an increase of genetic differences with distance in either species nor a significant contrast between them. The individual-based method, in contrast, revealed that individual assignment in both species was non random, being significantly biased toward geographically proximate locations. Furthermore, brook charr were on average assigned to a closer river than were salmon, according to a priori expectations based on the dispersal behaviour of the two species. We thus propose that individual assignment methods might be a promising and more powerful alternative to Mantel tests when isolation by distance cannot be postulated a priori.

Phylogenetic relationships and divergence times among mustelids (Mammalia: Carnivora) based on nucleotide sequences of the nuclear interphotoreceptor retinoid binding protein and mitochondrial cytochrome b genes

Phylogenetic relationships among 20 species-group taxa of Mustelidae, representing Mustelinae (Mustela, Martes, Gulo), Lutrinae (Enhydra), and Melinae (Meles), were examined using nucleotide sequences of the nuclear interphotoreceptor retinoid binding protein (IRBP) and mitochondrial cytochrome b genes. Neighbor-joining and maximum-parsimony phylogenetic analyses on these genes separately and combined were conducted. While IRBP performed better than cytochrome b in recovering more-inclusive clades, cytochrome b demonstrated more resolving power in recovering less-inclusive clades. Strong support was found for a close affinity of Enhydra with Mustela to the exclusion of Martes and Gulo (causing Mustelinae to be paraphyletic); the most-basal position of Mustela vison within Mustela, followed by Mustela erminea; an association of Mustela lutreola, Mustela itatsi, Mustela sibirica, and the subgenus Putorius (including Mustela putorius and Mustela eversmanii), to the exclusion of Mustela nivalis and Mustela altaica; and a basal position of Mustela itatsi to a clade containing Mustela sibirica and Putorius. Whereas cytochrome b strongly supported Mustela lutreola as the sister species to Putorius, IRBP strongly supported its basal placement to the Mustela itatsi-Mustela sibirica-Putorius clade. The low level of sequence divergence in cytochrome b between Mustela lutreola and Putorius is therefore a result of interspecific mitochondrial introgression between these taxa, rather than a recent origin of Mustela lutreola in a close relationship to Putorius. Time estimates inferred from IRBP and cytochrome b for mustelid divergence events are mostly in agreement with the fossil record.

Similar estimates of population genetic composition and sex ratio derived from carcasses and faeces of Eurasian otter Lutra lutra

Collecting faeces is viewed as a potentially efficient way to sample elusive animals. Nonetheless, any biases in estimates of population composition associated with such sampling remain uncharacterized. The goal of this study was to compare estimates of genetic composition and sex ratio derived from Eurasian otter Lutra lutra spraints (faeces) with estimates derived from carcasses. Twenty per cent of 426 wild-collected spraints from SW England yielded composite genotypes for 7-9 microsatellites and the SRY gene. The expected number of incorrect spraint genotypes was negligible, given the proportions of allele dropout and false allele detection estimated using paired blood and spraint samples of three captive otters. Fifty-two different spraint genotypes were detected and compared with genotypes of 70 otter carcasses from the same area. Carcass and spraint genotypes did not differ significantly in mean number of alleles, mean unbiased heterozygosity or sex ratio, although statistical power to detect all but large differences in sex ratio was low. The genetic compositions of carcass and spraint genotypes were very similar according to confidence intervals of theta and two methods for assigning composite genotypes to groups. A distinct group of approximately 11 carcass and spraint genotypes was detected using the latter methods. The results suggest that spraints can yield unbiased estimates of population genetic composition and sex ratio.

Mitochondrial phylogeography and population history of pine martens Martes martes compared with polecats Mustela putorius

The flora and fauna of Europe are linked by a common biogeographic history, most recently the Pleistocene glaciations that restricted the range of most species to southern refugial populations. Changes in population size and migration, as well as selection, have all left a signature on the genetic differentiation. Thus, three paradigms of postglacial recolonization have been described, inferred from the patterns of DNA differentiation. Yet some species, especially wide-ranging carnivores, exhibit little population structuring between the proposed refugia, although relatively few have been studied due to the difficulty of obtaining samples. Therefore, we investigated mitochondrial variation in pine martens, Martes martes, in order to understand the extent to which they were affected by glacial cycles, and compared the results with an analysis of sequences from polecats, Mustela putorius. A general lack of ancient lineages, and a mismatch distribution that is consistent with an expanding population, is evidence that the present-day M. martes and Mu. putorius in central and northern Europe colonized from a single European refugium following a recent glaciation. There has also been interspecific mitochondrial introgression between M. martes and the sable M. zibellina in Fennoscandia.

Genetic consequences of population decline in the European otter (Lutra lutra): an assessment of microsatellite DNA variation in Danish otters from 1883 to 1993

The European otter (Lutra lutra) was common in Denmark until the 1960s, but its present distribution encompasses only a minor part of the country. The aim of this study was to assess whether the recent population decline has resulted in loss of genetic variability and to gain further insight into the dynamics of the population decline. This was done by analysing microsatellite DNA variation in contemporary and historical samples, the latter encompassing DNA samples extracted from museum specimens covering a time-span from the 1880s to the 1960s. Tests for differences in expected heterozygosity and the numbers of alleles in contemporary versus historical samples and a test for detecting population bottlenecks provided few indications of a recent bottleneck and loss of variability. However, a procedure for detecting population expansions and declines, based on the genealogical history of microsatellite alleles, suggested that a drastic long-term population decline has taken place, which could have started more than 2000 years ago, possibly due to ancient anthropogenic pressure. Finally, assignment tests and pairwise F(ST) values suggested weak but statistically significant genetic differentiation between the extant population and historical samples of otters from other regions in Denmark, more likely reflecting differentiation among original populations rather than recent drift.

Genetic variation and population structure in Scandinavian wolverine (Gulo gulo) populations

Wolverine (Gulo gulo) numbers in Scandinavia were significantly reduced during the early part of the century as a result of predator removal programmes and hunting. Protective legislation in both Sweden and Norway in the 1960s and 1970s has now resulted in increased wolverine densities in Scandinavia. We report here the development of 15 polymorphic microsatellite markers in wolverine and their use to examine the population sub-structure and genetic variability in free-ranging Scandinavian wolverine populations as well as in a sample of individuals collected before 1970. Significant subdivision between extant populations was discovered, in particular for the small and isolated population of southern Norway, which represents a recent recolonization. Overall genetic variability was found to be lower than previously reported for other mustelids, with only two to five alleles per locus and observed heterozygosities (H(O)) ranging from 0.269 to 0.376 across the examined populations, being lowest in southern Norway. Analysis of the mitochondrial DNA control region revealed no variation throughout the surveyed populations. As the historical sample did not show higher levels of genetic variability, our results are consistent with a reduction in the genetic variation in Scandinavian wolverines that pre-dates the demographic bottleneck observed during the last century. The observed subdivision between populations calls for management caution when issuing harvest quotas, especially for the geographically isolated south Norwegian population.

Assessing non-metric skeleton characters as a morphological tool

The appearance of non-metric skeletal characters in vertebrates results mainly from basic genetic control, as proved and documented for house mice and humans. Although the heritability of non-metric traits, mainly the presence of foramina and similar structures for blood vessels and nerves or dental occlusal variants, have been evaluated as rather low, the simultaneous consideration of several traits allows estimation of epigenetic variation in time and space as a result of genetic relationship. Thus, the main use of non-metric characters has been aimed at assessing epigenetic variability and divergence among populations. Applications extend from the problem of genetic isolation of populations, the lack of reproductive contact, detection of genetic drift, systematic studies to clarify species taxonomy, to phylogenetic interpretation. Additionally, non-directional deviations from bilateral symmetry in non-metric characters, e.g. fluctuating asymmetry, could be caused by current environmental conditions in general. Fluctuating asymmetry is regarded as a measure of developmental instability to indicate the presence of genomic changes or the influence of contamination and/or habitat deterioration, and is also used as a further population parameter with integrated information. However, standpoints on the use of fluctuating asymmetry are quite inconsistent, fluctuating themselves between considering it a powerful biomonitoring tool to being merely a curious scientific toy.