Karine A Viaud-Martinez’s research while affiliated with Illumina and other places

The morphological differentiation between coastal and offshore ecotypes of bottlenose dolphins (genus Tursiops) has been researched since the 1960s, particularly in T. truncatus (Montagu, 1821), although most morphological studies have focused on localized populations. Therefore, it is unclear how patterns observed in these individual populations integrate within the global morphological variation. Here we carry out a meta‐analysis of global morphological variation between coastal and offshore ecotypes from 532 museum specimens, using both linear measurements (LM; 282 specimens), and shape data using geometric morphometrics (GM; 290 specimens). Together these analyses show consistent differentiation in skull morphology between coastal and offshore ecotypes, and provide a detailed description of variation patterns within each ecotype. These patterns show high individual morphological variation in the coastal ecotype between locations, while the offshore ecotype appears morphologically more uniform across the areas sampled. Overall, most skull shape variation can be described by features noticeable dorsally in the structures of the rostrum, whereas more limited change was found in ventral traits. Our results suggest that individual coastal populations may vary according to local environmental conditions, while those corresponding to the offshore ecotype appear to share similar morphological characteristics that might increase fitness in offshore habitats.

Cetacean taxonomy continues to be in flux and molecular genetic analyses examining alpha taxonomy in cetaceans have relied heavily on the mitochondrial DNA control region. However, there has been little consistency across studies; a variety of metrics and levels of divergence have been invoked when delimiting new cetacean species and subspecies. Using control region sequences, we explored, across pairs of well-recognized cetacean populations, subspecies, and species, a suite of metrics measuring molecular genetic differentiation to examine which metrics best categorize these taxonomic units. Nei's estimate of net divergence (dA) and percent diagnosability performed best. All but a single, recently diverged species were unambiguously identified using these metrics. Many subspecies were found at intermediate values as expected, allowing separation from both populations and species, but several had levels of divergence equivalent to populations, resulting in underclassification errors using this single marker. Coupling dA with additional measures, such as percent diagnosability, examining appropriate nuclear genetic markers, and interpreting results in a broader biological context will improve taxonomic investigations in cetaceans.

The common bottlenose dolphin (Tursiops truncatus) is the only cetacean present in the semiclosed waters of the Gulf of Ambracia, Western Greece. This increasingly degraded coastal ecosystem hosts one of the highest observed densities in the Mediterranean Sea for this species. Photo-identification data and tissue samples collected through skin-swabbing and remote biopsy sampling techniques during boat-based surveys conducted between 2006 and 2015 in the Gulf, were used to examine bottlenose dolphin abundance, population trends, site fidelity, genetic differentiation and toxicological status. Bottlenose dolphins showed high levels of year-round site fidelity throughout the 10-year study period. Dolphin population estimates mostly fell between 130 and 170 with CVs averaging about 10%; a trend in population size over the 10 years was a decline of 1.6% per year (but this was not significant). Genetic differentiation between the bottlenose dolphins of the Gulf and their conspecifics from neighbouring populations was detected, and low genetic diversity was found among individuals sampled. In addition, pesticides where identified as factors posing a real toxicological problem for local bottlenose dolphins. Therefore, in the Gulf of Ambracia, high dolphin density does not seem to be indicative of favourable conservation status or pristine habitat.

Genomic locations, flanking sequences and base calls for the 6,909 SNP on the bovineLD array. (CSV)

The Illumina BovineLD BeadChip was designed to support imputation to higher density genotypes in dairy and beef breeds by including single-nucleotide polymorphisms (SNPs) that had a high minor allele frequency as well as uniform spacing across the genome except at the ends of the chromosome where densities were increased. The chip also includes SNPs on the Y chromosome and mitochondrial DNA loci that are useful for determining subspecies classification and certain paternal and maternal breed lineages. The total number of SNPs was 6,909. Accuracy of imputation to Illumina BovineSNP50 genotypes using the BovineLD chip was over 97% for most dairy and beef populations. The BovineLD imputations were about 3 percentage points more accurate than those from the Illumina GoldenGate Bovine3K BeadChip across multiple populations. The improvement was greatest when neither parent was genotyped. The minor allele frequencies were similar across taurine beef and dairy breeds as was the proportion of SNPs that were polymorphic. The new BovineLD chip should facilitate low-cost genomic selection in taurine beef and dairy cattle.

The Black Sea is a semi-enclosed body of water that differs from the adjacent Mediterranean Sea in terms of its biodiversity, oceanographical and ecological characteristics. There is growing international concern about pollution in the Black Sea and other anthropogenic threats to its fauna. The bottlenose dolphin (Tursiops truncatus) is one of three species of cetaceans living in the Azov-Black Sea basin. Despite considerable research on bottlenose dolphins elsewhere, the extent of human impacts on the Black Sea populations is unknown. Previous attempts to award special conservation status to Black Sea cetaceans have failed specifically because policy makers have viewed their ecological and evolutionary uniqueness as equivocal. This study assessed divergence between Black Sea, Mediterranean Sea and Atlantic Ocean bottlenose dolphins for 26 cranial measurements (n = 75 adult bottlenose dolphin skulls) and mitochondrial DNA (n = 99 individuals). Black Sea bottlenose dolphins are smaller than those in the Mediterranean, and possess a uniquely shaped skull. As in a previous study, we found the Black Sea population to be genetically distinct, with relatively low levels of mtDNA diversity. Population genetic models suggest that Black Sea bottlenose dolphins have so little gene flow with the Mediterranean due to historical isolation that they should be managed separately.

Advances in high-throughput genotyping and the International HapMap Project have enabled association studies at the whole-genome level. We have constructed whole-genome genotyping panels of over 550,000 (HumanHap550) and 650,000 (HumanHap650Y) SNP loci by choosing tag SNPs from all populations genotyped by the International HapMap Project. These panels also contain additional SNP content in regions that have historically been overrepresented in diseases, such as nonsynonymous sites, the MHC region, copy number variant regions and mitochondrial DNA. We estimate that the tag SNP loci in these panels cover the majority of all common variation in the genome as measured by coverage of both all common HapMap SNPs and an independent set of SNPs derived from complete resequencing of genes obtained from SeattleSNPs. We also estimate that, given a sample size of 1,000 cases and 1,000 controls, these panels have the power to detect single disease loci of moderate risk (lambda approximately 1.8-2.0). Relative risks as low as lambda approximately 1.1-1.3 can be detected using 10,000 cases and 10,000 controls depending on the sample population and disease model. If multiple loci are involved, the power increases significantly to detect at least one locus such that relative risks 20%-35% lower can be detected with 80% power if between two and four independent loci are involved. Although our SNP selection was based on HapMap data, which is a subset of all common SNPs, these panels effectively capture the majority of all common variation and provide high power to detect risk alleles that are not represented in the HapMap data.

Power in YRI Samples for Additive Model (103 KB DOC)

The Minimum Risk Detectable for Common SNPs outside of the HapMap Data at 80% Power for Various Sample Sizes (N Cases and N Controls) under Multiplicative (Red) and Additive (Blue) Models Power is calculated using the SeattleSNPs data and defined as the ability to detect a single common risk allele outside the HapMap data in a whole-genome association study within either CHB + JPT (A) or YRI (B) samples. (16 KB PDF)

Tajima's D statistic on PGA genes (31 KB DOC)