Water samples were collected over two weeks directly behind individual whale sharks at Ningaloo Reef, Australia in May, 2019. A total of 56 seawater samples were collected, filtered immediately through sterile 0.22 μm filters, and stored at -80°C. Tissue biopsy samples were then taken from the same animal using a hand spear with a dart head, totalling 77 individual samples. Individual whale sharks were identified by their unique spot and stipe patters through photographs analysed by I³S Classic Software. Re-sightings of the same individual were removed from the dataset. Following photo-identification, a total of 48 unique individuals were confirmed, of which 42 consisted of both tissue and seawater samples. Additional samples were later discarded from the study, resulting in libraries for 28 seawater samples, and whale shark d-loop haplotypes. DNA extractions of the tissue samples were carried out and PCR amplification of the mitochondrial control region and reaction protocol verified. Seawater samples were processed and environmental DNA was extracted. Statistical analysis was performed with R Studio.

The difficulties associated with detecting population boundaries have long constrained the conservation and management of highly mobile marine species, especially for wide-ranging cetaceans such as killer whales (Orcinus orca). In this study, we use molecular genetic data to test a priori hypotheses about population subdivisions generated from a decade of killer whale surveys across the northern North Pacific. A total of 462 skin biopsies were collected from free-swimming killer whales from 1990 to 2010 between the northern Gulf of Alaska in the east and the Sea of Okhotsk in the west, representing both the piscivorous resident and the mammal-eating Biggs (or transient) killer whales. Geographic patterns of genetic differentiation were supported by significant regions of genetic discontinuity providing evidence of population structuring within both lineages, and corroborating direct observations of restricted movements of individual whales. In the Aleutian Islands (Alaska), population strata were largely delimited by major oceanographic boundaries for resident killer whales. In contrast, subdivisions among Biggs killer whales indicated multiple genetic clusters in the Eastern Aleutians and Bering Sea. The presence of sympatric genetic clusters within Biggs whales suggests the presence of isolating mechanisms other than geographic distance within this highly mobile top predator.

The difficulties associated with detecting population boundaries have long constrained the conservation and management of highly mobile marine species, especially for wide-ranging cetaceans such as killer whales (Orcinus orca). In this study, we use molecular genetic data to test a priori hypotheses about population subdivisions generated from a decade of killer whale surveys across the northern North Pacific. A total of 462 skin biopsies were collected from free-swimming killer whales from 1990 to 2010 between the northern Gulf of Alaska in the east and the Sea of Okhotsk in the west, representing both the piscivorous resident and the mammal-eating Biggs (or transient) killer whales. Geographic patterns of genetic differentiation were supported by significant regions of genetic discontinuity providing evidence of population structuring within both lineages, and corroborating direct observations of restricted movements of individual whales. In the Aleutian Islands (Alaska), population strata were largely delimited by major oceanographic boundaries for resident killer whales. In contrast, subdivisions among Biggs killer whales indicated multiple genetic clusters in the Eastern Aleutians and Bering Sea. The presence of sympatric genetic clusters within Biggs whales suggests the presence of isolating mechanisms other than geographic distance within this highly mobile top predator.

Baseline data collection on Whale Sharks by photo-identification, Whale Shark sex & size and collection of plankton samples to determine Whale Shark prey items.

Samples of skin and other tissues are collected from marine mammals along the North-Central Gulf of Mexico from live animals through remote biopsy or live-capture or stranded animals during 2010-2014. DNA is extracted from these samples, sequenced, and analyzed using a variety of methods to support phylogenetic studies, stock delineation studies, and a variety of other analyses related to cetacean genetics associated with the Natural Resources Damage Assessment associated with the Deepwater Horizon oil spill. These data sets include the sequence and other genetic data collected from these samples along with analytical results. These data support stock delineation studies and a variety of other analyses related to cetacean genetics and are incorporated into the Deepwater Horizon Damage Assessment and Restoration Plan.

To determine Whale Shark numbers at Ningaloo Marine Park by working with whale shark industry videographers to collect footage - part of the Whale Shark Management Program.

This database archives genetic tissue samples from marine mammals collected primarily from the U.S. east coast. The collection includes samples from field programs, fisheries bycatch, and stranding data. A range of researchers have contributed samples to this archive, so some of the data records are confidential. Data includes field identification numbers, location and date information, collection information, and disposition of samples. These samples are primarily intended to support analyses of the genetic relationships and phylogeny of cetaceans in U.S. and Caribbean waters.

This database archives genetic tissue samples from marine mammals collected in the North-Central Gulf of Mexico from 2010-2015. The collection includes samples from field sampling programs and stranding data. Data includes field identification numbers, location and date information, collection information, and disposition of samples. These data support stock delineation studies and a variety of other analyses related to cetacean genetics in the Gulf of Mexico related to the Deepwater Horizon oil spill.

The southern residents face several well-documented external threats. However, the population might also be subject to internal factors that limit population growth, including a reduction in fitness due to inbreeding. Understanding how inbreeding affects individual fitness and thus the health status of the population is critical for evaluating the relative influence of other factors on southern resident recovery. Assessing the risk of inbreeding depression – specifically called for in the NMFS recovery plan – is important for conducting accurate Population Viability Analyses and correctly understanding the urgency of recovery efforts. Here, we propose using genomic methods to evaluate inbreeding and inbreeding depression in the southern resident population and a comparable but healthier Alaskan resident population. Measures of inbreeding will serve as an important health marker, supporting the integration of individual metrics aimed at understanding population performance. Measures of inbreeding can be obtained directly by estimating variation at millions of DNA markers in an individual’s genome. Complete genomic sequences for 100 southern and 50 Alaska residents will be collected in collaboration with the genomics company BGI. Inbreeding values for each individual will be obtained using genome wide measures of homozygosity and relatedness. We will then combine measured of inbreeding with data on individual fitness, to evaluate whether inbreeding leads to inbreeding depression. Generalized additive models will be used to determine whether survivorship, fecundity and size-at-age is influenced by different levels of inbreeding. Using this data, we will measure the degree of current and predicted future of inbreeding in the southern residents and compare this risk with the Alaska residents that have experienced consistent population growth. We will then evaluate whether inbreeding depression explains individual variance in fitness, and estimate its influence on the status of southern residents, using Population Viability Analyses. Microsatellite, SNP, and mtDNA sequence data from southern resident killer whales.

Samples of skin and other tissues are collected from marine mammals along the U.S. east coast by a variety of researchers. Samples may be collected from live animals through remote biopsy or live-capture, stranded animals, or animals captured incidentally during fishery operations. DNA is extracted from these samples, sequenced, and analyzed using a variety of methods to support phylogenetic studies, stock delineation studies, and a variety of other analyses related to cetacean genetics in U.S. waters. These data sets include the sequence and other genetic data collected from these samples along with analytical results. These data contribute to delineation of stocks described in annual Marine Mammal Protection Act stock assessment reports.