Mitochondrial structure despite nuclear panmixia: sex-specific dispersal dictates population structure in sperm whales.

The Gulf of Mexico (GMx) is a subtropical marginal sea of the western North Atlantic Ocean with a diverse cetacean community. Ship-based, line-transect abundance surveys were conducted in oceanic waters (>200 m deep) of the northern GMx within U.S. waters (380,432 square km) during summer 2003 and spring 2004. Data from these surveys were pooled and minimum abundance estimates were based on 10,933 km of effort and 433 sightings of at least 17 species.The most commonly sighted species (number of groups) were pantropical spotted dolphin, Stenella attenuata (115); sperm whale, Physeter macrocephalus (85); dwarf/pygmy sperm whale, Kogia sima/breviceps (27); Risso’s dolphin, Grampus griseus (26); and bottlenose dolphin, Tursiops truncatus (26). The most abundant species (number of individuals; coefficient of variation) were S. attenuata (34,067; 0.18); Clymene dolphin, S. clymene (6,575; 0.36); T. truncatus (3,708; 0.42); and striped dolphin, S. coeruleoalba (3,325; 0.48). The only large whales sighted were P. macrocephalus (1,665; 0.20) and Bryde’s whale, Balaenoptera edeni (15; 1.98). Abundances for other species or genera ranged from 57 to 2,283 animals. Cetaceanswere sighted throughout the oceanic northern GMx, and whereas many species were widely distributed, some had more regional distributions. Compared to abundance estimates for this area based on 1996-2001 surveys, the estimate for S. attenuata was significantly smaller (P <0.05) and that for the spinner dolphin, S. longirostris, appeared much smaller. Also, P. macrocephalus estimates were based on less negatively biased estimates of group-size using 90-minute counts during 2003 and 2004.

Population genetics and dispersal of a threatened marsupial mammal, Petrogale penicillata, in southeast Queensland

The mechanisms that determine population structure in highly mobile marine species are poorly understood, but useful towards understanding the evolution of diversity, and essential for effective conservation and management. In this study, we compare putative sperm whale populations located in the Gulf of Mexico, western North Atlantic, Mediterranean Sea and North Sea using mtDNA control region sequence data and 16 polymorphic microsatellite loci. The Gulf of Mexico, western North Atlantic and North Sea populations each possessed similar low levels of haplotype and nucleotide diversity at the mtDNA locus, while the Mediterranean Sea population showed no detectable mtDNA diversity. Mitochondrial DNA results showed significant differentiation between all populations, while microsatellites showed significant differentiation only for comparisons with the Mediterranean Sea, and at a much lower level than seen for mtDNA. Samples from either side of the North Atlantic in coastal waters showed no differentiation for mtDNA, while North Atlantic samples from just outside the Gulf of Mexico (the western North Atlantic sample) were highly differentiated from samples within the Gulf at this locus. Our analyses indicate a previously unknown fidelity of females to coastal basins either side of the North Atlantic, and suggest the movement of males among these populations for breeding.

Genetic evidence for regional philopatry of the Bull Shark (Carcharhinus leucas), to nursery areas in estuaries of the Gulf of Mexico and western North Atlantic ocean

Octopus insularis is a shallow‐water octopus distributed throughout the western Atlantic, the Gulf of Mexico and the Caribbean. To evaluate its phylogeographic pattern, mitochondrial markers (16S rRNA and COIII) and genome‐wide nuclear markers (SNP's) were analyzed in individuals from artisanal fishing in different locations of the Colombian Caribbean coast. Mitochondrial analyzes displayed novel haplotypes (16S = H2, H3 and H4; COIII = H2–H7) and haplotypes shared with distant geographic areas (16S = H1 COIII = H1). The COIII gene did not show genetic differentiation between the analyzed localities, while the 16S gene showed significant differences between Santa Marta and Isla Fuerte. COIII's demographic analysis indicated that the species' effective population size has remained constant. Inferences were made from next‐generation genomic data with restriction site‐associated DNA (ddRAD‐seq) and 6769 polymorphic loci. The pairwise FST test indicated that there are low but significant differences between localities; however, the general molecular analysis of variance (AMOVA) and the principal coordinate analysis showed a lack of spatial structure in the populations analyzed. The Mantel test found no correlation between genetic distance and geographic distance, and the genetic structure analyses showed the presence of one genetic stock. The information obtained in this study indicates the genetic connectivity of O. insularis in the southwestern Caribbean, the absence of putative biogeographic barriers that affect its gene flow, and the crucial role played by life history strategies (planktonic paralarvae) and oceanographic factors to define the current distribution of its genetic diversity in this region.

Building time-budgets from bioacoustic signals to measure population-level changes in behavior: a case study with sperm whales in the Gulf of Mexico

Marine mammals are important models for studying convergent evolution and aquatic adaption, and thus reference genomes of marine mammals can provide evolutionary insights. Here, we present the first chromosome-level marine mammal genome assembly based on the data generated by the BGISEQ-500 platform, for a stranded female sperm whale (Physeter macrocephalus). Using this reference genome, we performed chromosome evolution analysis of the sperm whale, including constructing ancestral chromosomes, identifying chromosome rearrangement events and comparing with cattle chromosomes, which provides a resource for exploring marine mammal adaptation and speciation. We detected a high proportion of long interspersed nuclear elements and expanded gene families, and contraction of major histocompatibility complex region genes which were specific to sperm whale. Using comparisons with sheep and cattle, we analysed positively selected genes to identify gene pathways that may be related to adaptation to the marine environment. Further, we identified possible convergent evolution in aquatic mammals by testing for positively selected genes across three orders of marine mammals. In addition, we used publicly available resequencing data to confirm a rapid decline in global population size in the Pliocene to Pleistocene transition. This study sheds light on the chromosome evolution and genetic mechanisms underpinning sperm whale adaptations, providing valuable resources for future comparative genomics.

The Gulf of Mexico is a subtropical ocean basin with a diverse oceanic cetacean community. Cetacean research in the Gulf of Mexico has been driven by mandates of the US Marine Mammal Protection Act as well as concerns over the rapidly expanding oil and natural gas industry and related potential threats (e.g. seismic surveys, increased ship traffic, oil spills). Previously, cetacean distribution and abundances for specific Gulf of Mexico areas or species have been described based on work over periods of several years, and recently abundance estimates were made for the entire oceanic northern Gulf of Mexico (1996-2001). For each cetacean species, the paper describes distribution, group size, associated sea surface temperature and water depth and interspecific associations based on surveys conducted over 11 years that span the entire northern Gulf of Mexico. This dataset is the most comprehensive to date for the oceanic northern Gulf. Nine ship surveys totalling 45,462km of effort were conducted during spring seasons (1991-2001) in continental shelf-edge and oceanic waters ( 100m) of the northern Gulf of Mexico. Eighteen species were identified from 1,868 sightings. Cetaceans were found throughout the area although some species had localised distributions or occurred in restricted ranges of water depths. Spinner dolphins (Stenella longirostris) had the largest mean group size (n = 40, x – = 151.5, SE = 30.90), followed by melon-headed whales (Peponocephala electra), clymene dolphins (S. clymene), pantropical spotted dolphins (S. attenuata), Fraser’s dolphins (Lagenodelphis hosei) and striped dolphins (S. coeruleoalba) (range of means 46.1-99.6). Beaked whales (Ziphiidae), Bryde’s whales (Balaenoptera edeni/brydei), sperm whales (Physeter macrocephalus) and pygmy/dwarf sperm whales (Kogia spp.) were found in the smallest groups (x – &lt; 3). Twenty-seven sightings (1.4% of all sightings) were composed of two cetacean species. Common bottlenose dolphins (Tursiops truncatus) were recorded in mixedspecies groups with more species than any other cetacean. Forty-five cetacean sightings (2.4% of all sightings) were associated with at least one bird species, and 21 (1.1% of all sightings) were associated with schools of fish. Contrary to previous reports, pantropical spotted dolphins were observed in association with both fish (including surface tunas) and seabirds, although to a lesser extent than for other tropical oceans. No mixed pantropical spotted and spinner dolphin groups were sighted despite their regular co-occurrence in other tropical oceans.

We examined the age and growth of the blacknose shark, Carcharhinus acronotus, in the western North Atlantic Ocean by obtaining direct age estimates using vertebral centra. We verified annual deposition of growth increments with marginal increment analysis and validated it by analyzing vertebrae marked with oxytetracycline from a female blacknose shark held in captivity. Von Bertalanffy growth parameters indicated that female blacknose sharks have a lower growth constant (k), a larger theortical maximum size (L∞), and are longer lived than males. We compared these growth parameters for blacknose sharks in the western North Atlantic Ocean to growth parameters for blacknose sharks collected in the eastern Gulf of Mexico to test for differences between regions. Females in the western North Atlantic Ocean have a significantly lower L∞, lower k, and a higher theoretical longevity than females in the Gulf of Mexico. Males in the western North Atlantic Ocean have a higher L∞ , lower k, and higher theoretical longevity than males in the Gulf of Mexico. The significant differences between these life history parameters for blacknose sharks suggest that, when possible, future management initiatives concerning blacknose sharks should consider managing the populations in the western North Atlantic and the Gulf of Mexico as separate stocks.

The Heard Island Feasibility Test source transmitted a hum at 209-220 dB re: 1 microPa at 175-m depth, centered on 57 Hz with a maximum bandwidth of 30 Hz for 1 h of every 3. Experienced marine mammal observers conducted line-transect surveys and monitored marine mammal behavior visually and acoustically in a 70 x 70 km square centered on the transmission site. Thirty-nine groups of cetaceans and 19 of pinnipeds were sighted from both vessels before the start of transmissions. Thirty-nine groups of cetaceans and 23 of pinnipeds were sighted during transmissions. Blue (Balaenoptera musculus), fin (B. physalus), and sperm (Physeter macrocephalus) whales were sighted during the base line period; blue, sperm, and possibly sei (B. borealis) whales were sighted during the transmission period. More schools of hourglass dolphins (Lagenorhynchus cruciger) were sighted during transmissions, but fewer groups of pilot whales (Globicephala melas), southern bottlenose whales (Hyperoodon planifrons), and minke whales (B. acutorostrata). The density of all cetaceans was 0.0157 groups/km2 before the transmissions and 0.0166 groups/km2 during. Antarctic fur seals (Arctocephalus gazella) and southern elephant seals (Mirounga leonina) were seen, but not in sufficient numbers to estimate abundance. One blue whale tracked before, during and after a transmission changed respiration and reorientation rates, but did not avoid the source detectably. Sperm whales and pilot whales were heard in 23% of 1181 min of baseline acoustic surveys; but in none of 1939 min during the transmission period. Both species were heard within 48 h after the end of the test.

The northern Gulf of Mexico has a long history of polycyclic aromatic hydrocarbon (PAH) contamination from anthropogenic activities, natural oil seepages, and the 2010 Deepwater Horizon explosion and oil spill. The continental shelf of the same area is a known breeding ground for sperm whales (Physeter macrocephalus). To evaluate PAH-DNA damage, a biomarker for potential cancer risk, we compared skin biopsies collected from Gulf of Mexico sperm whales in 2012 with skin biopsies collected from sperm whales in areas of the Pacific Ocean in 1999-2001. All samples were obtained by crossbow and comprised both epidermis and subcutaneous blubber. To evaluate exposure, 7 carcinogenic PAHs were analyzed in lipids extracted from Pacific Ocean sperm whale blubber, pooled by sex, and location. To evaluate PAH-DNA damage, portions of all tissue samples were formalin-fixed, paraffin-embedded, sectioned, and examined for PAH-DNA adducts by immunohistochemistry (IHC) using an antiserum elicited against benzo[a]pyrene-modified DNA, which crossreacts with several high molecular weight carcinogenic PAHs bound to DNA. The IHC showed widespread epidermal nuclear localization of PAH-DNA adducts in the Gulf of Mexico whales (n = 15) but not in the Pacific Ocean whales (n = 4). A standard semiquantitative scoring system revealed significantly higher PAH-DNA adducts in the Gulf of Mexico whales compared to the whales from the Pacific Ocean study (p = .0002).

Summary Arid landscapes pose arguably one of the greatest challenges to dispersal of aquatic insects, and may drive speciation in taxa with low dispersal potential. We investigated genetic divergence in aquatic insects with high and low dispersal potential between two regions within the Australian arid zone. We used two dragonfly species to infer patterns for strong‐dispersing species, and mayfly species from two genera to represent weak‐dispersing species. Based on dispersal‐related traits of the taxa, we predicted that dragonflies would show little divergence between and within the two geographical regions, while mayflies would show evidence of genetic isolation, with divergence timing associated with aridification in Australia. Samples were collected from perennial pools in ephemeral stream networks in central and western Australia. The two study regions are separated by approximately 1,500 km of predominantly dune desert. Collected insects were sequenced for one mitochondrial and one nuclear marker. We investigated spatial distribution of haplotypes, estimated divergence dates for identified mayfly lineages, and performed phylogenetic reconstruction to investigate relationships with known congeners. Both dragonfly species showed evidence of recent or ongoing gene flow between the central and western Australian study regions. In contrast, mayflies showed evidence of ancient, but not recent, gene flow between regions, with species‐level CO1 divergence within regions. We found 11 previously unknown putative mayfly species, that if confirmed could double the known diversity within these genera in Australia. Timing of divergence events for mayflies coincided with the development of the Australian arid zone, and phylogenetic relationships are similar to divergence patterns found in other Australian arid taxa. The findings of this study suggest that aridification is more likely to be a driver of diversification in taxa with low dispersal potential than in those with high dispersal potential. This is because effective aerial dispersal is integral for maintaining gene flow when aquatic connections are lost between distant populations, and reduced gene flow can promote genetic divergence.

Despite numerous studies across the large geographic range of the sperm whale (Physeter macrocephalus), little is known about the diet and mitochondrial DNA haplotypes of this strongly female philopatric species in waters off Southeast Asia. A female sperm whale found dead in Singapore waters provided the opportunity to study her diet and mitochondrial DNA haplotype. Here we report on the identification of stomach contents and mitochondrial DNA haplotype of this individual, and we include coastal hydrodynamic modelling to determine the possible geographic origin of the whale. At least 28 species of prey were eaten by this adult female whale, most of which were cephalopods. The mesopelagic squids Taonius pavo, Histioteuthis pacifica, Chiroteuthis imperator,and Ancistrocheirus lesueurii made up over 65% of the whale’s stomach contents. Plastic debris was also found in the whale’s stomach. Based on the diet, genetics, and coastal hydrodynamic modelling that suggest an easterly drift of the whale carcass over several days, the dead sperm whale in Singapore probably originated from a pod in the Southern Indian Ocean. This study provides an increase in the understanding the diet and natural history of the sperm whale in Southeast Asia. The combined analyses of stomach contents, DNA, and hydrodynamic modeling could provide a context to future studies on the sperm whale strandings, and have broader applicability for other marine mammals in the region.

The Gulf of Mexico is a subtropical marginal sea of the western North Atlantic Ocean with a diverse cetacean community. Ship‐based, line‐transect abundance surveys were conducted in oceanic waters (&gt;200 m deep) of the northern Gulf within U. S. waters (380,432 km2) during spring from 1996 to 1997 and from 1999 to 2001. Data from these five surveys were pooled and minimum abundance estimates were based on 12,162 km of effort and 512 sightings of at least 19 species. The most commonly sighted species (number of groups) were pantropical spotted dolphin,Stenella attenuata(164); sperm whale,Physeter macrocephalus(67); dwarf/pygmy sperm whale,Kogia simalbreviceps(58); Risso's dolphin,Grampus griseus(38); and bottlenose dolphin,Tursiops truncatus(24). The most abundant species (number of individuals; coefficient of variation) wereS. attenuata(91,321; 0.16); Clymene dolphin,S. clymene(17,355; 0.65); spinner dolphin,S. longirostris(11,971; 0.71); and striped dolphin,S. coeruleoalba(6,505; 0.43). The only large whales sighted wereP. macrocephalus(1,349; 0.23) and Bryde's whale,Balaenopteraedeni(40; 0.61). Abundances for other species or genera ranged from 95 to 2,388 animals. Cetaceans were sighted throughout the oceanic northern Gulf and, whereas many species were widely distributed, some had more regional distributions.

The southern flounder Paralichthys lethostigma is a key species in recreational flatfish fisheries in the Gulf of Mexico and the northwestern Atlantic Ocean. Effective management of this species relies on knowing how many populations occur within the range of the species, as knowledge of the underlying genetic structure may be used in stock assessments or in the establishment of management units. Here, the evolutionary history of the southern flounder was elicited with genetic data, and the geographic extent and long‐term female effective population size (Nef) of extant populations were estimated. Mitochondrial DNA sequence data (415 base pairs, control region) were analyzed with a combination of traditional hypothesis testing (analysis of molecular variance) and the coalescent‐based maximum likelihood approach (analysis with the program Migrate). Three main findings resulted from this work. First, two distinct genetic populations of southern flounder exist in the Gulf of Mexico and western Atlantic Ocean, and there is a measured genetic divergence (i.e., FST) of 0.374 between them. Within ocean basins, there was little significant genetic structure among samples. Second, coalescent modeling suggests that the two populations of southern flounder have expanded rapidly in numbers in the past 10,000–22,000 years, timing that approximately coincides with the end of the last North American glacial retreat. Third, historical population growth is coupled with high estimates of long‐term Nef, both of which contrast with present‐day declines in abundance measured by stock assessments. Present‐day southern flounder populations persist in two independent evolutionarily significant units that have divergent evolutionary backgrounds.