Distribution of mtDNA haplotypes in North-Atlantic humpback whales:The influence of behavior on population structure

Samples from 136 humpback whales Megaptera novaeangliae, representing 5 feeding aggregations in the North Atlantic and 1 in the Antarctic, were analyzed with respect to the sequence variation in the mitochondrial (mt) control region. A total of 288 base pairs was sequenced by direct sequencing of asymmetrically amplified DNA. Thirty-one different haplotypes were identified. The nucleotide diversity for the total sample was estimated to be 2.6 %, which is high relative to other North Atlantic cetaceans. The degree of genetic differentiation in various subsets of the samples was estimated and tested for statistical significance by Monte Carlo simulations. Significant degrees of heterogeneity were found between the Antarctic and all North Atlantic areas, as well as between Iceland and the western North Atlantic samples. A genealogical tree was estimated for the 31 haplotypes and rooted with the homologous sequence from a fin whale Balaenoptera physalus. The branching pattern in the genealogical tree suggests that the North Atlantic Ocean has been populated by 2 independent influxes of humpback whales. The combined results from the homogeneity tests and the genealogical tree indicate that behaviour (in this case maternally directed site fidelity to a foraging area) can influence the population structure of marine cetaceans on an evolutionary time scale

Distribution of mtDNA haplotypes in North-Atlantic humpback whales:The influence of behavior on population structure

Samples from 136 humpback whales Megaptera novaeangliae, representing 5 feeding aggregations in the North Atlantic and 1 in the Antarctic, were analyzed with respect to the sequence variation in the mitochondrial (mt) control region. A total of 288 base pairs was sequenced by direct sequencing of asymmetrically amplified DNA. Thirty-one different haplotypes were identified. The nucleotide diversity for the total sample was estimated to be 2.6 %, which is high relative to other North Atlantic cetaceans. The degree of genetic differentiation in various subsets of the samples was estimated and tested for statistical significance by Monte Carlo simulations. Significant degrees of heterogeneity were found between the Antarctic and all North Atlantic areas, as well as between Iceland and the western North Atlantic samples. A genealogical tree was estimated for the 31 haplotypes and rooted with the homologous sequence from a fin whale Balaenoptera physalus. The branching pattern in the genealogical tree suggests that the North Atlantic Ocean has been populated by 2 independent influxes of humpback whales. The combined results from the homogeneity tests and the genealogical tree indicate that behaviour (in this case maternally directed site fidelity to a foraging area) can influence the population structure of marine cetaceans on an evolutionary time scale

High interannual variability in connectivity and genetic pool of a temperate clingfish matches oceanographic transport predictions

Adults of most marine benthic and demersal fish are site-attached, with the dispersal of their larval stages ensuring connectivity among populations. In this study we aimed to infer spatial and temporal variation in population connectivity and dispersal of a marine fish species, using genetic tools and comparing these with oceanographic transport. We focused on an intertidal rocky reef fish species, the shore clingfish Lepadogaster lepadogaster, along the southwest Iberian Peninsula, in 2011 and 2012. We predicted high levels of self-recruitment and distinct populations, due to short pelagic larval duration and because all its developmental stages have previously been found near adult habitats. Genetic analyses based on microsatellites countered our prediction and a biophysical dispersal model showed that oceanographic transport was a good explanation for the patterns observed. Adult sub-populations separated by up to 300 km of coastline displayed no genetic differentiation, revealing a single connected population with larvae potentially dispersing long distances over hundreds of km. Despite this, parentage analysis performed on recruits from one focal site within the Marine Park of Arrabida (Portugal), revealed self-recruitment levels of 2.5% and 7.7% in 2011 and 2012, respectively, suggesting that both long-and short-distance dispersal play an important role in the replenishment of these populations. Population differentiation and patterns of dispersal, which were highly variable between years, could be linked to the variability inherent in local oceanographic processes. Overall, our measures of connectivity based on genetic and oceanographic data highlight the relevance of long-distance dispersal in determining the degree of connectivity, even in species with short pelagic larval durations

Incorporating non-equilibrium dynamics into demographic history inferences of a migratory marine species

ELC was supported while writing this paper by a EU Horizon 2020 Marie Slodowska Curie Fellowship, project BEHAVIOUR-CONNECT, by a Newton Fellowship from the Royal Society of London and Bayesian statistical training was supported by National Science Foundation (award DEB- 1145200). Laboratory analyses conducted by ELC were funded by a small grant from the British Ecological Society 5076 / 6118 and Bayesian analysis was supported by training from the National Science Foundation under Grant No. DEB-1145200. OEG was supported by the Marine Alliance for Science and Technology for Scotland (MASTS) funded by the Scottish Founding Council (grant reference HR09011). Genetic data from the South African right whale samples were generated by MB and PJP with the support of UC Berkeley, University of Stockholm and University of Groningen. Computational Biology analyses were supported by the University of St Andrews Bioinformatics Unit which is funded by a Wellcome Trust ISSF award.Understanding how dispersal and gene flow link geographically separated populations over evolutionary history is challenging, particularly in migratory marine species. In southern right whales (SRWs, Eubalaena australis), patterns of genetic diversity are likely influenced by the glacial climate cycle and recent history of whaling. Here we use a dataset of mitochondrial DNA (mtDNA) sequences (n=1,327) and nuclear markers (17 microsatellite loci, n=222) from major wintering grounds to investigate circumpolar population structure, historical demography, and effective population size. Analyses of nuclear genetic variation identify two population clusters that correspond to the South Atlantic and Indo-Pacific ocean basins that have similar effective breeder estimates. In contrast, all wintering grounds show significant differentiation for mtDNA, but no sex-biased dispersal was detected using the microsatellite genotypes. An approximate Bayesian computation (ABC) approach with microsatellite markers compared scenarios with gene flow through time, or isolation and secondary contact between ocean basins, while modeling declines in abundance linked to whaling. Secondary-contact scenarios yield the highest posterior probabilities, implying that populations in different ocean basins were largely isolated and came into secondary contact within the last 25,000 years, but the role of whaling in changes in genetic diversity and gene flow over recent generations could not be resolved. We hypothesis that these findings are driven by factors that promote isolation, such as female philopatry, and factors that could promote dispersal, such oceanographic changes. These findings highlight the application of ABC approaches to infer connectivity in mobile species with complex population histories and currently low levels of differentiation.PostprintPeer reviewe

Identification of sex in Cetaceans by multiplexing with three ZFX and ZFY specific primers

We sequenced 540 nucleotides of the last exon in the ZFY/ZFX gene in two males and two females for eight cetacean species; four odontocetes (toothed whales) and four mysticetes (baleen whales). Based upon the obtained nucleotide sequences, we designed two sets of oligonucleotide primers for specific amplification of the ZFX and the ZFY sequence in odontocetes and mysticetes, respectively. Each primer set consisted of three oligonucleotides; one forward-orientated primer, which anneals to the ZFY as well as the ZFX sequence, and two reverse-orientated primers that anneal to either the ZFX or the ZFY sequence. The resulting two amplification products (specific for the ZFY and ZFX sequences) can be distinguished by gel-electrophoresis through 2% NuSieve(TM). The accuracy of the technique was tested by determination of gender in 214 individuals of known sex. Finally we applied the technique to determine the sex of 3570 cetacean specimens; 2284 humpback whales, 315 fin whales, 37 blue whales, 7 minke whales, as well as 592 belugas, 335 narwhals and 25 harbour porpoises

Primers for animal mitochondrial DNA: the importance of species-specific primers

In this chapter we outline the procedure for designing oligonucleotide primers for the direct-sequencing of in vitro amplified animal mitochondrial DNA (mtDNA). Although this chapter deals with animal mtDNA in particular, the approach is of course applicable to any gene, nuclear or mitochondrial. There are four main ‘steps’:identification of a suitable target region;design of a preliminary set of oligonucleotide primers;confirmation of sequence identity;optimization of amplification protocol