Circumpolar Diversity and Geographic Differentiation of mtDNA in the Critically Endangered Antarctic Blue Whale (Balaenoptera musculus intermedia)

To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work.\ud This is the publisher’s final pdf. The published article is copyrighted by the Public Library of Science and can be found at: http://www.plosone.org/home.action.The Antarctic blue whale (Balaenoptera musculus intermedia) was hunted to near extinction between 1904 and 1972, declining from an estimated initial abundance of more than 250,000 to fewer than 400. Here, we describe mtDNA control region diversity and geographic differentiation in the surviving population of the Antarctic blue whale, using 218 biopsy samples collected under the auspices of the International Whaling Commission (IWC) during research cruises from 1990-2009. Microsatellite genotypes and mtDNA sequences identified 166 individuals among the 218 samples and documented movement of a small number of individuals, including a female that traveled at least 6,650 km or 131 degrees longitude over four years. mtDNA sequences from the 166 individuals were aligned with published sequences from 17 additional individuals, resolving 52 unique haplotypes from a consensus length of 410 bp. From this minimum census, a rarefaction analysis predicted that only 72 haplotypes (95% CL, 64, 86) have survived in the contemporary population of Antarctic blue whales. However, haplotype diversity was relatively high (0.968 +/- 0.004), perhaps as a result of the longevity of blue whales and the relatively recent timing of the bottleneck. Despite the potential for circumpolar dispersal, we found significant differentiation in mtDNA diversity (F-ST = 0.032, p<0.005) and microsatellite alleles (F-ST = 0.005, p<0.05) among the six Antarctic Areas historically used by the IWC for management of blue whales

A whale's tale of mtDNA diversity and differentiation : the Antarctic blue whale

Twentieth century commercial whaling drastically reduced the abundance of great whale populations in the Southern Ocean. Exploitation began on the south Atlantic island of South Georgia, where catch records account for over 175,000 whales killed. Modern whaling within the Southern Ocean depleted populations rapidly, and by 1966, hunting blue whales south of 40°S was prohibited by the International Whaling Commission (IWC). After 40 years of protection, this species has shown little recovery. A current abundance estimate of 2,280 (CV=0.036) individuals from sighting data (1991/92-2003/04) represents less than 1% the original abundance. With such an intensive demographic 'bottleneck,' it is likely that genetic diversity has been lost from some or all components of the Southern Ocean population. Here I describe historical and contemporary Antarctic blue whale mtDNA diversity and report the first circumpolar analyses of contemporary population structure. In Chapter 2, historical mtDNA diversity is described from whale bones collected from the first Southern Hemisphere whaling stations established in 1904 on the island of South Georgia. A total of 281 whale bones were representative of three prominent species hunted in South Georgian waters. Using ancient DNA methods and sequencing of the mtDNA control region, bone samples were first identified to species, identifying 153 humpback, 49 fin, 18 blue, 2 sei, 1 southern right whale and 1 elephant seal. Within each of the three prominent historic species populations, mtDNA haplotypes were described resulting in 64 humpback, 34 fin, and 16 blue whale haplotypes. Haplotype and nucleotide diversity within each of the three historic species populations ranged from 0.980-0.987 and 1.87-3.16%, respectively. In chapter 3, I update the previous estimate of contemporary Antarctic blue whale mtDNA diversity with biopsy samples of living whales collected during research cruises conducted with IWC oversight from 1990-2009 (n=218) for comparison to historical blue whale mtDNA diversity. After the removal of replicate samples based on 15 microsatellite loci, the dataset described 167 individuals. This dataset was combined with additional published Antarctic blue whale mtDNA control region sequences (LeDuc et al. 2007; n=20) to represent the most comprehensive dataset available for Antarctic blue whale mtDNA diversity (n=187). A high haplotype diversity was described within this contemoporary population (0.968). With this dataset, I report the first evidence of population structure within the IWC Southern Ocean management Areas I-VI through an analysis of genetic differentiation. The identification of recaptures within the dataset through microsatellite genotyping, allows for the first inference of movement of six individuals with the Southern Ocean since the end of the Discovery marking program 50 years ago. In the final chapter of this thesis, I explore the impact of the 20th century commercial whaling industry on the Antarctic blue whale population through a comparison of historical and contemporary Antarctic blue whale mtDNA diversity. The comparison showed that only 6 of the 16 haplotypes from the South Georgian population were found in contemporary worldwide blue whale populations, indicating a potential loss of mtDNA lineages. The loss of mtDNA haplotypes sugges two hypotheses; either a low predicted loss of widespread Antarctic blue whale mtDNA diversity or the loss of a South Georgia local Antarctic blue whale population driven to commercial extinction. The impact of commercial whaling is also assessed through a prediction of the minimum number of maternal lineages, or haplotypes, to have survived the exploitation bottleneck. The number of 51 mtDNA haplotypes identified within the contemporary Antarctic blue whale population is used to update the estimate of haplotypes within the unsampled contemporary population. We predict 69 mtDNA lineages within the contemporary population from the current abundance estimate of 2,280 (1,160-4,500) individuals (Branch 2008). This prediction will increase the lower bound of population abundance used in population dynamic modeling and may reduce an upward bias in population increase estimates used to assess the recovery of this species

Collecting baleen whale blow samples by drone : a minimally intrusive tool for conservation genetics

_Carol Newell, Donner Canadian Foundation, Elizabeth Haan, Fisheries and Oceans Canada_ Habitat Stewardship Program for Species at Risk, Save Our Seas Foundation, Willow Grove Foundation_In coastal British Columbia, Canada, marine megafauna such as humpback whales (Megaptera novaeangliae) and fin whales (Balaenoptera physalus velifera) have been subject to a history of exploitation and near extirpation. While their populations have been in recovery, significant threats are posed to these vulnerable species by proposed natural resource ventures in this region, in addition to the compounding effects of anthropogenic climate change. Genetic tools play a vital role in informing conservation efforts, but the associated collection of tissue biopsy samples can be challenging for the investigators and disruptive to the ongoing behaviour of the targeted whales. Here, we evaluate a minimally intrusive approach based on collecting exhaled breath condensate, or respiratory ‘blow’ samples, from baleen whales using an unoccupied aerial system (UAS), within Gitga'at First Nation territory for conservation genetics. Minimal behavioural responses to the sampling technique were observed, with no response detected 87% of the time (of 112 UAS deployments). DNA from whale blow (n = 88 samples) was extracted, and DNA profiles consisting of 10 nuclear microsatellite loci, sex identification and mitochondrial (mt) DNA haplotypes were constructed. An average of 7.5 microsatellite loci per individual were successfully genotyped. The success rates for mtDNA and sex assignment were 80% and 89% respectively. Thus, this minimally intrusive sampling method can be used to describe genetic diversity and generate genetic profiles for individual identification. The results of this research demonstrate the potential of UAS-collected whale blow for conservation genetics from a remote location.Peer reviewe

Assessing population-level variation in the mitochondrial genome of Euphausia superba using 454 next-generation sequencing

The Antarctic krill (Euphausia superba Dana 1852) is widely distributed throughout the southern ocean, where it provides a key link between primary producers and upper trophic levels and supports a major commercial fishery. Despite its ecological and commercial importance, genetic population structure of the Antarctic kill remains poorly described. In an attempt to illuminate genetic markers for future population and phylogenetic analysis, five E. superba mitogenomes, from samples collected west of the Antarctic Peninsula, were sequenced using new 454 next-generation sequencing techniques. The sequences, of lengths between 13310 and 13326 base pairs, were then analyzed in the context of two previously published near-complete sequences. Sequences revealed relatively well-conserved partial mitochondrial genomes which included complete sequences for 11 of 13 protein-coding genes, 16 of 23 tRNAs, and the large ribosomal subunit. Partial sequences were also recovered for Cox1 and the small ribosomal subunit. Sequence analysis suggested that the Cox2, Nad5, and Nad6 genes would be the best candidate for future population genetics analyses, due to their high number of variable sites. Future work to reveal the noncoding control region remains.Keywords: Control region, Euphausia superba, mtDNA, Mitogenome, VariabilityKeywords: Control region, Euphausia superba, mtDNA, Mitogenome, Variabilit

Circumpolar Diversity and Geographic Differentiation of mtDNA in the Critically Endangered Antarctic Blue Whale (Balaenoptera musculus intermedia)

The Antarctic blue whale (Balaenoptera musculus intermedia) was hunted to near extinction between 1904 and 1972, declining from an estimated initial abundance of more than 250,000 to fewer than 400. Here, we describe mtDNA control region diversity and geographic differentiation in the surviving population of the Antarctic blue whale, using 218 biopsy samples collected under the auspices of the International Whaling Commission (IWC) during research cruises from 1990-2009. Microsatellite genotypes and mtDNA sequences identified 166 individuals among the 218 samples and documented movement of a small number of individuals, including a female that traveled at least 6,650 km or 131 degrees longitude over four years. mtDNA sequences from the 166 individuals were aligned with published sequences from 17 additional individuals, resolving 52 unique haplotypes from a consensus length of 410 bp. From this minimum census, a rarefaction analysis predicted that only 72 haplotypes (95% CL, 64, 86) have survived in the contemporary population of Antarctic blue whales. However, haplotype diversity was relatively high (0.968 +/- 0.004), perhaps as a result of the longevity of blue whales and the relatively recent timing of the bottleneck. Despite the potential for circumpolar dispersal, we found significant differentiation in mtDNA diversity (F-ST = 0.032, p<0.005) and microsatellite alleles (F-ST = 0.005, p<0.05) among the six Antarctic Areas historically used by the IWC for management of blue whales

The mitochondrial genomes of Euphausia pacifica and Thysanoessa raschii sequenced using 454 next-generation sequencing, with a phylogenetic analysis of their position in the Malacostracan family tree

Euphausiid krill play a critical role in coastal and oceanic food webs, linking primary producers to upper trophic levels. In addition, some species support commercial fisheries worldwide. Despite their ecological importance, the genetics of these important species remain poorly described. To improve our understanding of the genetics of these ecological links, we sequenced the mitochondrial genomes of two species of North Pacific krill, Euphausia pacifica and Thysanoessa raschii, using long-range PCR and 454 GS Junior next-generation sequencing technology. The E. pacifica mitogenome (14,692 + base pairs (bp)) encodes 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, and at least 22 transfer RNA (tRNA) genes. The T. raschii mitogenome (14,240 + bp) encodes 13 PCGs, two rRNA genes, and at least 19 tRNA genes. The gene order in both species is similar to that of E. superba. Comparisons between Bering Sea and Yellow Sea E. pacifica revealed a total of 644 variable sites. The most variable protein-coding gene were atp8 (7.55 %, 12 of 159 sites variable), nad4 (6.35 %, 85 variable sites) and nad6 (6.32 %, 33 variable sites). Phylogenetic analyses to assess the phylogenetic position of the Euphausiacea, using the concatenated nucleic acid sequences of E. pacifica and T. raschii along with 46 previously published malacostracan mitogenomes, support the monophyly of the order Decapoda and indicate that the Euphausiacea share a common ancestor with the Decapoda. Future research should utilize this sequence data to explore the population genetics and molecular ecology of these species.Keywords: Malacostraca, Euphausiacea, Mitochondrial genome, mtDNA, PhylogenyKeywords: Malacostraca, Euphausiacea, Mitochondrial genome, mtDNA, Phylogen

Ontogenetic and spatial variability in trophic biomarkers of juvenile saffron cod (Eleginus gracilis) from the Beaufort, Chukchi and Bering Seas

Climate models indicate the Arctic will undergo dramatic environmental change with forecasted increases in temperature and river runoff. Saffron cod (Eleginus gracilis) is abundant in nearshore waters and appears in the diet of many Arctic sea birds and marine mammals; however, little is known about its early ecology and consequently how they might be affected by environmental changes. We aimed to characterize the mechanisms of spatial and ontogenetic variation in trophic biomarkers (lipid classes, fatty acids and bulk C and N stable isotopes) of saffron cod from the Western Arctic, Chukchi and Bering Seas. Size-standardized analyses showed a significant difference in lipid condition metrics and trophic biomarkers as a function of survey location. Both ontogeny and sampling location played an important role in determining lipid stores with elevated levels in both small offshore juveniles (75 mm). Higher lipid storage in Arctic juveniles was associated with elevated levels of diatom fatty acid markers, but not with nearshore carbon input. Increased lipids were found in age-1 juveniles from Prudhoe Bay in the Western Beaufort that were feeding at a lower trophic level than similarly sized age-0 juveniles from surface trawls in the Bering Sea. The use of otolith annuli revealed two discrete patterns of growth that help explain the trade-offs between energy storage and rapid growth that diverge between the Arctic and Bering Sea. Laboratory temperature-growth experiments confirmed that saffron cod have a eurythermal growth response and are able to store excess lipids at temperatures as high as 20°C.Keywords: Arctic, Nutrition, Fatty acids, Saffron cod, Lipids, OntogenyKeywords: Arctic, Nutrition, Fatty acids, Saffron cod, Lipids, Ontogen

Investigating Population Genetic Structure in a Highly Mobile Marine Organism: The Minke Whale Balaenoptera acutorostrata acutorostrata in the North East Atlantic

Inferring the number of genetically distinct populations and their levels of connectivity is of key importance for the sustainable management and conservation of wildlife. This represents an extra challenge in the marine environment where there are few physical barriers to gene-flow, and populations may overlap in time and space. Several studies have investigated the population genetic structure within the North Atlantic minke whale with contrasting results. In order to address this issue, we analyzed ten microsatellite loci and 331 bp of the mitochondrial D-loop on 2990 whales sampled in the North East Atlantic in the period 2004 and 2007–2011. The primary findings were: (1) No spatial or temporal genetic differentiations were observed for either class of genetic marker. (2) mtDNA identified three distinct mitochondrial lineages without any underlying geographical pattern. (3) Nuclear markers showed evidence of a single panmictic population in the NE Atlantic according STRUCTURE's highest average likelihood found at K = 1. (4) When K = 2 was accepted, based on the Evanno's test, whales were divided into two more or less equally sized groups that showed significant genetic differentiation between them but without any sign of underlying geographic pattern. However, mtDNA for these individuals did not corroborate the differentiation. (5) In order to further evaluate the potential for cryptic structuring, a set of 100 in silico generated panmictic populations was examined using the same procedures as above showing genetic differentiation between two artificially divided groups, similar to the aforementioned observations. This demonstrates that clustering methods may spuriously reveal cryptic genetic structure. Based upon these data, we find no evidence to support the existence of spatial or cryptic population genetic structure of minke whales within the NE Atlantic. However, in order to conclusively evaluate population structure within this highly mobile species, more markers will be required

Genomic and proteomic identification of Late Holocene remains: Setting baselines for Black Sea odontocetes

A critical challenge of the 21st century is to understand and minimise the effects of human activities on biodiversity. Cetaceans are a prime concern in biodiversity research, as many species still suffer from human impacts despite decades of management and conservation efforts. Zooarchaeology constitutes a valuable approach for informing conservation and management decisions by providing baseline information on the past distribution and human uses of species. However, traditional morphological species identification of mixed assemblage bones can be challenging, particularly in the case of cetaceans. To address this issue, we applied and evaluated the performance of three biomolecular approaches – Sanger sequencing, shotgun sequencing and collagen peptide fingerprinting (ZooMS) – for species identification in a mixed assemblage of 800 to 1600 years old odontocete (toothed whale) samples from the site of Chersonesus in Crimea, Ukraine. We found that ZooMS allowed for identification to the taxonomic level for 28 of our 30 samples (> 90%), identifying them as either “porpoise” or “dolphin”, and approximately half of those samples could be further identified to species level with the shotgun sequencing approach. In addition, shotgun sequencing produced several complete ancient odontocete mitogenomes and auxiliary nuclear genomic data for further exploration in a population genetic context. In contrast, both morphological identification and Sanger sequencing lacked taxonomic resolution and/or resulted in misclassification of samples. We found that the combination of ZooMS and shotgun sequencing provides a powerful tool in zooarchaeology, and here allowed for a deeper understanding of past marine resource use and its implication for current management and conservation of Black Sea odontocetes

A Study of Behavior Issues in the Early Childhood Classroom after the Pandemic

Research has shown that children entering the classroom environment after the COVID-19 pandemic are struggling with behavioral issues. Due to a lack of social-emotional skills and heightened anxiety and depression, schools are seeing children act out more violently and emotionally than ever before. With a strict focus on the findings of the importance of school readiness and play-based learning skills, this project is aimed to minimize these outbursts of negative behavior by teaching parents on how to get involved in the home and teach these necessary skills for school success. Parental involvement has shown high correlations with success for children in school on all levels but with this project being focused on socio-emotional skills, parents will have a booklet that can easily guide them through how to accomplish teaching these skills and local resources that can come to the home and help