Genetic sampling for identification of species, subspecies or stock of whales, dolphins and porpoises at sea remains challenging. Most samples have been collected with some form of a biopsy dart ...requiring a close approach of a vessel while the individual is at the surface. Here we have adopted droplet digital (dd)PCR technology for detection and species identification of cetaceans using environmental (e)DNA collected from seawater. We conducted a series of eDNA sampling experiments during 25 encounters with killer whales, Orcinus orca, in Puget Sound (the Salish Sea). The regular habits of killer whales in these inshore waters allowed us to locate pods and collect seawater, at an initial distance of 200 m and at 15-minute intervals, for up to two hours after the passage of the whales. To optimize detection, we designed a set of oligonucleotide primers and probes to target short fragments of the mitochondrial (mt)DNA control region, with a focus on identification of known killer whale ecotypes. We confirmed the potential to detect eDNA in the wake of the whales for up to two hours, despite movement of the water mass by several kilometers due to tidal currents. Re-amplification and sequencing of the eDNA barcode confirmed that the ddPCR detection included the ‘southern resident community’ of killer whales, consistent with the calls from hydrophone recordings and visual observations.
Detection and identification of species, subspecies or stocks of whales, dolphins and porpoises at sea remain challenging, particularly for cryptic or elusive species like beaked whales (Family: ...Ziphiidae). Here we investigated the potential for using an acoustically assisted sampling design to collect environmental (e)DNA from beaked whales on the U.S. Navy’s Atlantic Undersea Test and Evaluation Center (AUTEC) in The Bahamas. During 12 days of August 2019, we conducted 9 small-boat surveys and collected 56 samples of seawater (paired subsamples of 1L each, including controls) using both a spatial collection design in the absence of visual confirmation of whales, and a serial collection design in the proximity of whales at the surface. There were 7 sightings of whales, including 11 Blainville’s beaked whales (
Mesoplodon densirostris
). All whales were located initially with the assistance of information from a bottom-mounted acoustic array available on the AUTEC range. Quantification by droplet digital (dd)PCR from the four spatial design collections showed no samples of eDNA above the threshold of detection and none of these 20 samples yielded amplicons for conventional or next-generation sequencing. Quantification of the 31 samples from four serial collections identified 11 likely positive detections. eDNA barcoding by conventional sequencing and eDNA metabarcoding by next-generation sequencing confirmed species identification for 9 samples from three of the four serial collections. We further resolved five intra-specific variants (i.e., haplotypes), two of which showed an exact match to previously published haplotypes and three that have not been reported previously to the international repository, GenBank. A minimum spanning network of the five eDNA haplotypes, with all other published haplotypes of Blainville’s beaked whales, suggested the potential for further resolution of differences between oceanic populations.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The interplay of natural selection and genetic drift, influenced by geographic isolation, mating systems and population size, determines patterns of genetic diversity within species. The sperm whale ...provides an interesting example of a longâlived species with few geographic barriers to dispersal. Worldwide mtDNA diversity is relatively low, but highly structured among geographic regions and social groups, attributed to female philopatry. However, it is unclear whether this female philopatry is due to geographic regions or social groups, or how this might vary on a worldwide scale. To answer these questions, we combined mtDNA information for 1091 previously published samples with 542 newly obtained DNA profiles (394âbp mtDNA, sex, 13 microsatellites) including the previously unsampled Indian Ocean, and social group information for 541 individuals. We found low mtDNA diversity (ÏÂ =Â 0.430%) reflecting an expansion event <80Â 000Â years bp, but strong differentiation by ocean, among regions within some oceans, and among social groups. In comparison, microsatellite differentiation was low at all levels, presumably due to maleâmediated gene flow. A hierarchical amova showed that regions were important for explaining mtDNA variance in the Indian Ocean, but not Pacific, with social group sampling in the Atlantic too limited to include in analyses. Social groups were important in partitioning mtDNA and microsatellite variance within both oceans. Therefore, both geographic philopatry and social philopatry influence genetic structure in the sperm whale, but their relative importance differs by sex and ocean, reflecting breeding behaviour, geographic features and perhaps a more recent origin of sperm whales in the Pacific. By investigating the interplay of evolutionary forces operating at different temporal and geographic scales, we show that sperm whales are perhaps a unique example of a worldwide population expansion followed by rapid assortment due to female social organization.
Humpback whales (Megaptera novaeangliae) annually undertake the longest migrations between seasonal feeding and breeding grounds of any mammal. Despite this dispersal potential, discontinuous ...seasonal distributions and migratory patterns suggest that humpbacks form discrete regional populations within each ocean. To better understand the worldwide population history of humpbacks, and the interplay of this species with the oceanic environment through geological time, we assembled mitochondrial DNA control region sequences representing approximately 2700 individuals (465 bp, 219 haplotypes) and eight nuclear intronic sequences representing approximately 70 individuals (3700 bp, 140 alleles) from the North Pacific, North Atlantic and Southern Hemisphere. Bayesian divergence time reconstructions date the origin of humpback mtDNA lineages to the Pleistocene (880 ka, 95% posterior intervals 550–1320 ka) and estimate radiation of current Northern Hemisphere lineages between 50 and 200 ka, indicating colonization of the northern oceans prior to the Last Glacial Maximum. Coalescent analyses reveal restricted gene flow between ocean basins, with long-term migration rates (individual migrants per generation) of less than 3.3 for mtDNA and less than 2 for nuclear genomic DNA. Genetic evidence suggests that humpbacks in the North Pacific, North Atlantic and Southern Hemisphere are on independent evolutionary trajectories, supporting taxonomic revision of M. novaeangliae to three subspecies.
Heteroplasmy in the mitochondrial genome offers a rare opportunity to track the evolution of a newly arising maternal lineage in populations of non-model species. Here, we identified a previously ...unreported mitochondrial DNA haplotype while assembling an integrated database of DNA profiles and photo-identification records from humpback whales in southeastern Alaska (SEAK). The haplotype, referred to as A8, was shared by only 2 individuals, a mature female with her female calf, and differed by only a single base pair from a common haplotype in the North Pacific, referred to as A-. To investigate the origins of the A8 haplotype, we reviewed n = 1,089 electropherograms (including replicate samples) of n = 710 individuals with A- haplotypes from an existing collection. From this review, we found 20 individuals with clear evidence of heteroplasmy for A-/A8 (parental/derived) haplotypes. Of these, 15 were encountered in SEAK, 4 were encountered on the Hawaiian breeding ground (the primary migratory destination for whales in SEAK), and 1 was encountered in the northern Gulf of Alaska. We used genotype exclusion and likelihood to identify one of the heteroplasmic females as the likely mother of the A8 cow and grandmother of the A8 calf, establishing the inheritance and germ-line fixation of the new haplotype from the parental heteroplasmy. The mutation leading to this heteroplasmy and the fixation of the A8 haplotype provide an opportunity to document the population dynamics and regional fidelity of a newly arising maternal lineage in a population recovering from exploitation.
The genus Stenella is comprised of five species occurring in all oceans. Despite its wide distribution, genetic diversity information on these species is still scarce especially in the Southwest ...Atlantic Ocean. Some features of this genus can enhance opportunities for potential introgressive hybridization, e.g. sympatric distibution along the Brazilian coast, mixed known associations among species, karyotype uniformity and genome permeability. In this study we analyzed three genes of the mitochondrial genome to investigate the genetic diversity and occurrence of genetic mixture among eighty specimens of Stenella. All species exhibited moderate to high levels of genetic diversity (h = 0.833 to h = 1.000 and qi = 0.006 to qi = 0.015). Specimens of S. longirostris, S. attenuata and S. frontalis were clustered into differentiated haplogroups, in contrast, haplotypes of S. coeruleoalba and S. clymene were clustered together. We detected phylogenetic structure of mixed clades for S. clymene and S. coeruleoalba specimens, in the Southwest Atlantic Ocean, and also between S. frontalis and S. attenuata in the Northeast Atlantic Ocean, and between S. frontalis and S. longirostris in the Northwest Atlantic Ocean. These specimes were morphologically identified as one species but exhibited the maternal lineage of another species, by mitochondrial DNA. Our results demonstrate that ongoing gene flow is occurring among species of the genus Stenella reinforcing that this process could be one of the reasons for the confusing taxonomy and difficulties in elucidating phylogenetic relationships within this group.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Antarctic humpback whales are recovering from near extirpation from commercial whaling. To understand the dynamics of this recovery and establish a baseline to monitor impacts of a rapidly changing ...environment, we investigated sex ratios and pregnancy rates of females within the Western Antarctic Peninsula (WAP) feeding population. DNA profiling of 577 tissue samples (2010–2016) identified 239 males and 268 females. Blubber progesterone levels indicated 63.5% of the females biopsied were pregnant. This proportion varied significantly across years, from 36% in 2010 to 86% in 2014. A comparison of samples collected in summer versus fall showed significant increases in the proportion of females present (50% to 59%) and pregnant (59% to 72%), consistent with demographic variation in migratory timing. We also found evidence of annual reproduction among females; 54.5% of females accompanied by a calf were pregnant. These high pregnancy rates are consistent with a population recovering from past exploitation, but appear inconsistent with recent estimates of WAP humpback population growth. Thus, our results will help to better understand population growth potential and set a current baseline from which to determine the impact of climate change and variability on fecundity and reproductive rates.
Abstract
The age of an individual is an essential demographic parameter but is difficult to estimate without long‐term monitoring or invasive sampling. Epigenetic approaches are increasingly used to ...age organisms, including nonmodel organisms such as cetaceans. Māui dolphins (
Cephalorhynchus hectori maui
) are a critically endangered subspecies endemic to Aotearoa New Zealand, and the age structure of this population is important for informing conservation. Here we present an epigenetic clock for aging Māui and Hector's dolphins (
C. h. hectori
) developed from methylation data using DNA from tooth aged individuals (
n
= 48). Based on this training data set, the optimal model required only eight methylation sites, provided an age correlation of .95, and had a median absolute age error of 1.54 years. A leave‐one‐out cross‐validation analysis with the same parameters resulted in an age correlation of .87 and median absolute age error of 2.09 years. To improve age estimation, we included previously published beluga whale (
Delphinapterus leucas
) data to develop a joint beluga/dolphin clock, resulting in a clock with comparable performance and improved estimation of older individuals. Application of the models to DNA from skin biopsy samples of living Māui dolphins revealed a shift from a median age of 8–9 years to a younger population aged 7–8 years 10 years later. These models could be applied to other dolphin species and demonstrate the ability to construct a clock even when the number of known age samples is limited, removing this impediment to estimating demographic parameters vital to the conservation of critically endangered species.
Historical exploitation, and a combination of current anthropogenic impacts, such as climate change and habitat degradation, impact the population dynamics of marine mammalian megafauna. Right whales ...(Eubalaena spp.) are large cetaceans recovering from hunting, whose reproductive and population growth rate appear to be impacted by climate change. We apply noninvasive genetic methods to monitor southern right whale (E. australis, SRW) and test the application of noninvasive genetics to minimise the observer effects on the population. Our aim is to describe population structure, and interdecadal and interannual changes to assess species status in the Great Acceleration period of Anthropocene. As a basis for population genetic analyses, we collected samples from sloughed skin during post-migration epidermal moult. Considering the exploration-exploitation dilemma, we collaborated with whale watching companies, as part of a citizen science approach and to reduce ad hoc logistic operations and biopsy equipment. We used mitochondrial and microsatellite data and population genetic tools. We report for the first time the genetic composition and differentiation of the Namibian portion of the range. Population genetic parameters suggest that South Africa hosts the largest population. This corresponds with higher estimates of current gene flow from Africa compared to older samples. We have observed considerable interannual variation in population density at the breeding ground and an interdecadal shift in genetic variability, evidenced by an increase in the point estimate inbreeding. Clustering analyses confirmed differentiation between the Atlantic and Indo-Pacific, presumably originating during the ice ages. We show that population monitoring of large whales, essential for their conservation management, is feasible using noninvasive sampling within non-scientific platforms. Observed patterns are concurrent to changes of movement ecology and decline in reproductive success of the South African population, probably reflecting a large-scale restructuring of pelagic marine food webs.
We present genetic and morphological evidence supporting the recognition of a previously synonymized species of Mesoplodon beaked whale in the tropical Indo‐Pacific, Mesoplodon hotaula. Although the ...new species is closely‐related to the rare ginkgo‐toothed beaked whale M. ginkgodens, we show that these two lineages can be differentiated by maternally (mitochondrial DNA), biparentally (autosomal), and paternally (Y chromosome) inherited DNA sequences, as well as by morphological features. The reciprocal monophyly of the mtDNA genealogies and the largely parapatric distribution of these lineages is consistent with reproductive isolation. The new lineage is currently known from at least seven specimens: Sri Lanka (1), Gilbert Islands, Republic of Kiribati (1+), Palmyra Atoll, Northern Line Islands, U.S.A. (3), Maldives (1), and Seychelles (1). The type specimen (Sri Lanka) was described as a new species, M. hotaula, in 1963, but later synonymized with M. ginkgodens. This discovery brings the total number of Mesoplodon species to 15, making it, by far, the most speciose yet least known genus of cetaceans.
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