Genetic characterisation and social structure of the East Scotland population of bottlenose dolphins (Tursiops truncatus)

The Eastern Scottish population of bottlenose dolphins (Tursiops truncatus) is the northernmost population of this species. The resident core of this population consists of 120 to 150 different individuals. This small size and its geographical isolation from other populations raises questions about its viability and whether the population has behavioural patterns that differ from those common to other populations of the same species. Microsatellite genetic diversity was low and mitochondrial DNA genetic diversity values were lowest in East Scotland compared to other populations worldwide and to neighbouring populations around UK waters. It has been well documented, from four different field sites worldwide, that male bottlenose dolphins form alliances with preferred male associates. These alliances can last for several years and the males involved show association coefficients similar to those of mothers and calves (0.8-1.0). These alliances appear to be of great importance in obtaining matings for the males. In the Eastern Scottish population males do not form alliances. No evidence of strong associations between individuals of either sex was found and there was no correlation between association and relatedness patterns. I suggest that the isolation and small size of the population together with reduced genetic diversity affects the pressure of kin selection for altruistic behaviours. There is no gain in competing or associating with close relatives for access to mates and it might be more important to avoid inbreeding by dispersing. Although evidence of gene flow between East Scotland and its neighbouring populations was not confirmed with Bayesian clustering analysis, a small set of individuals from Wales were found to be closely related to individuals from the East Coast of Scotland. In general the dynamics found in UK water populations resemble those of the Western North Atlantic with sympatric populations of coastal as well as pelagic individuals

Research in association with New Seal Licensing System : Research on the population structure of harbour seals

The population structure of harbour seals (Phoca vitulina) around Scotland was investigated using different genetic markers and approaches. This allowed discrete population units or metapopulations to be identified. The population genetic structure is compared to the recently defined harbour seal management regions (SCOS, 2011), ensuring Scottish Government’s regional management procedures and plans for harbour seals are based on genetic data as well as the currently employed ecological haulout and pupping site data. Analysis of DNA samples from a total of 453 individuals around Scotland including samples from comparative regions in the UK and Europe (including an out-group of Pacific harbour seals) was carried out. Following some initial trials the most appropriate population differentiation analysis comprised 10 putative populations across all the samples analysed. Focusing on Scotland, Bayesian clustering analysis clearly separated Scotland from England, France and the Dutch Wadden Sea. In this scenario 3 clusters were generally identified: a) Norway, b)West Coast of Scotland/Northern Ireland and c) Pentland Firth / Orkney / Shetland / Moray Firth / Tay and Eden with some degree of shared individuals between them. Examining the Scottish populations alone indicated there might be some additional separation between the Tay and Eden compared to the other north and east coast groups. Within the Scottish populations a number of harbour seal Management Areas have been assigned based on haul outs and breeding sites (SCOS, 2011). The result of the genetic analyses reported here clearly supports the designation and definition of these Areas. Allelic diversity and heterozygosity are standard measures that assess the level of inbreeding which populations display as a reflection of their ‘genetic health’. The populations with relatively good sample sizes and low levels of genetic diversity were Shetland (n=2.545, HO=0.363) and the Outer Hebrides (2.467, HO= 0.331). It has been widely shown that inbreeding, translated as very low levels of genetic diversity in wild populations is correlated with disease such as cancer (Acevedo-Whitehouse et al. 2003) and with susceptibility to pathogens such as parasites (Rijks et al. 2008) among others.Publisher PDFPublisher PD

Genetic population structure of harbour seals in the United Kingdom and neighbouring waters

Natural Environment Research Council (GrantNumber(s): SMRU1001; Grant recipient(s): Ailsa Hall)1.  In the United Kingdom (UK), several harbour seal (Phoca vitulina) populations have been declining over the past decade. In order to understand the effect of these changes in abundance, this study seeks to determine the population structure of harbour seals in the UK, and in Scotland in particular, on a wider and finer spatial scale than has previously been reported. 2.  Harbour seals were genotyped from 18 different localities throughout the UK and neighbouring localities in mainland Europe, at 12 microsatellite loci. Results from Bayesian and frequency based tests of population structure suggested an initial structural division into two main groups consisting of localities in northern UK and southern UK-mainland Europe, respectively. 3.  These two clusters were further divided into four geographically distinct genetic clusters. 4.  An overall agreement between the genetic results and the existing management areas for UK harbour seals was observed, but it is also clear that an adaptive management approach should be adopted, in which the delineation of the current management areas is maintained until further genetic and ecological information has been accumulated and analysed.Publisher PDFPeer reviewe

Monitoring of benthic eukaryotic communities in two tropical coastal lagoons through eDNA metabarcoding: a spatial and temporal approximation

Tropical coastal lagoons are important ecosystems that support high levels of biodiversity and provide several goods and services. Monitoring of benthic biodiversity and detection of harmful or invasive species is crucial, particularly in relation to seasonal and spatial variation of environmental conditions. In this study, eDNA metabarcoding was used in two tropical coastal lagoons, Chacahua (CH) and Corralero (C) (Southern Mexican Pacific), to describe the benthic biodiversity and its spatial–temporal dynamics. The distribution of benthic diversity within the lagoons showed a very particular pattern evidencing a transition from freshwater to seawater. Although the two lagoon systems are similar in terms of the species composition of metazoans and microeukaryotes, our findings indicate that they are different in taxa richness and structure, resulting in regional partitioning of the diversity with salinity as the driving factor of community composition in CH. Harmful, invasive, non-indigenous species, bioindicators and species of commercial importance were detected, demonstrating the reach of this technique for biodiversity monitoring along with the continued efforts of building species reference libraries

Postglacial Colonization of Northern Coastal Habitat by Bottlenose Dolphins: A Marine Leading-Edge Expansion?

Oscillations in the Earth’s temperature and the subsequent retreating and advancing of ice-sheets around the polar regions are thought to have played an important role in shaping the distribution and genetic structuring of contemporary high-latitude populations. After the Last Glacial Maximum (LGM), retreating of the ice-sheets would have enabled early colonizers to rapidly occupy suitable niches to the exclusion of other conspecifics, thereby reducing genetic diversity at the leading-edge. Bottlenose dolphins (genus Tursiops) form distinct coastal and pelagic ecotypes, with finer-scale genetic structuring observed within each ecotype. We reconstruct the postglacial colonization of the Northeast Atlantic (NEA) by bottlenose dolphins using habitat modeling and phylogenetics. The AquaMaps model hindcasted suitable habitat for the LGM in the Atlantic lower latitude waters and parts of the Mediterranean Sea. The time-calibrated phylogeny, constructed with 86 complete mitochondrial genomes including 30 generated for this study and created using a multispecies coalescent model, suggests that the expansion to the available coastal habitat in the NEA happened via founder events starting ~15 000 years ago (95% highest posterior density interval: 4 900–26 400). The founders of the 2 distinct coastal NEA populations comprised as few as 2 maternal lineages that originated from the pelagic population. The low effective population size and genetic diversity estimated for the shared ancestral coastal population subsequent to divergence from the pelagic source population are consistent with leading-edge expansion. These findings highlight the legacy of the Late Pleistocene glacial cycles on the genetic structuring and diversity of contemporary populations

The east coast of Scotland bottlenose dolphin population : improving understanding of ecology outside the Moray Firth SAC

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Research in association with New Seal Licensing System:research on the population structure of harbour seals

The population structure of harbour seals (Phoca vitulina) around Scotland was investigated using different genetic markers and approaches. This allowed discrete population units or metapopulations to be identified. The population genetic structure is compared to the recently defined harbour seal management regions (SCOS, 2011), ensuring Scottish Government’s regional management procedures and plans for harbour seals are based on genetic data as well as the currently employed ecological haulout and pupping site data. Analysis of DNA samples from a total of 453 individuals around Scotland including samples from comparative regions in the UK and Europe (including an out-group of Pacific harbour seals) was carried out. Following some initial trials the most appropriate population differentiation analysis comprised 10 putative populations across all the samples analysed. Focusing on Scotland, Bayesian clustering analysis clearly separated Scotland from England, France and the Dutch Wadden Sea. In this scenario 3 clusters were generally identified: a) Norway, b)West Coast of Scotland/Northern Ireland and c) Pentland Firth / Orkney / Shetland / Moray Firth / Tay and Eden with some degree of shared individuals between them. Examining the Scottish populations alone indicated there might be some additional separation between the Tay and Eden compared to the other north and east coast groups.Within the Scottish populations a number of harbour seal Management Areas have been assigned based on haul outs and breeding sites (SCOS, 2011). The result of the genetic analyses reported here clearly supports the designation and definition of these Areas.Allelic diversity and heterozygosity are standard measures that assess the level of inbreeding which populations display as a reflection of their ‘genetic health’. The populations with relatively good sample sizes and low levels of genetic diversity were Shetland (n=2.545, HO=0.363) and the Outer Hebrides (2.467, HO= 0.331). It has been widely shown that inbreeding, translated as very low levels of genetic diversity in wild populations is correlated with disease such as cancer (Acevedo-Whitehouse et al. 2003) and with susceptibility to pathogens such as parasites (Rijks et al. 2008) among others.<br/

Geographic variation in the advertisement calls of Hyla eximia and its possible explanations

Populations of species occupying large geographic ranges are often phenotypically diverse as a consequence of variation in selective pressures and drift. This applies to attributes involved in mate choice, particularly when both geographic range and breeding biology overlap between related species. This condition may lead to interference of mating signals, which would in turn promote reproductive character displacement (RCD). We investigated whether variation in the advertisement call of the mountain treefrog (Hyla eximia) is linked to geographic distribution with respect to major Mexican river basins (Panuco, Lerma, Balsas and Magdalena), or to coexistence with its sister (the canyon treefrog, Hyla arenicolor) or another related species (the dwarf treefrog, Tlalocohyla smithii). We also evaluated whether call divergence across the main river basins could be linked to genetic structure. We found that the multidimensional acoustic space of calls from two basins where H. eximia currently interacts with T. smithii, was different from the acoustic space of calls from H. eximia elsewhere. Individuals from these two basins were also distinguishable from the rest by both the phylogeny inferred from mitochondrial sequences, and the genetic structure inferred from nuclear markers. The discordant divergence of H. eximia advertisement calls in the two separate basins where its geographic range overlaps that of T. smithii can be interpreted as the result of two independent events of RCD, presumably as a consequence of acoustic interference in the breeding choruses, although more data are required to evaluate this possibility