C. Scott Baker

C. Scott Baker
Oregon State University | OSU · Department of Fisheries and Wildlife

PhD

About

714
Publications
84,942
Reads
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12,436
Citations
Additional affiliations
July 2006 - present
Oregon State University
Position
  • Professor (Full)
May 1993 - present
University of Auckland
Position
  • Professor (Full)
March 1990 - March 1991
Victoria University of Wellington
Position
  • PostDoc Position

Publications

Publications (714)
Article
Full-text available
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 Brazi...
Article
Rough‐toothed dolphins (Steno bredanensis) have a global tropical and subtropical distribution with oceanic, neritic, and island‐associated populations. To inform conservation and management for this species, we used sequences from the mtDNA control region (n = 360), mitogenomes (n = 19), and six nuclear introns (n = 35) to provide multiple lines o...
Article
Full-text available
Understanding the ecosystem effects of ocean warming is increasingly important as marine heatwaves become more common and increase in severity. Here, we used Glacier Bay National Park long-term monitoring data (1985–2020) to investigate a sudden, sharp decline in humpback whale reproductive success and survival following the onset of the 2014–2016...
Article
Full-text available
Unoccupied aerial system (UAS) technologies applied to health assessments of large whales can have positive implications for progressive management. We focused on the collection of cetacean respiratory blow samples for endocrine, DNA profiling, microbial metabarcoding, and metagenomics analyses, with the goal of improving management of large whale...
Article
Full-text available
Commerson’s dolphins ( Cephalorhynchus commersonii ) are separated into the subspecies C. c. commersonii , found along southern South America (SA) and the Falkland Islands/Islas Malvinas (FI/IM), and C. c. kerguelenensis , restricted to the subantarctic Kerguelen Islands (KI). Following the dispersal model proposed for the genus, the latter is thou...
Article
Full-text available
Abstract available in English, Spanish and Portuguese. The deep sea has been described as the last major ecological frontier, as much of its biodiversity is yet to be discovered and described. Beaked whales (ziphiids) are among the most visible inhabitants of the deep sea, due to their large size and worldwide distribution, and their taxonomic div...
Technical Report
Full-text available
https://www.doc.govt.nz/globalassets/documents/conservation/native-animals/marine-mammals/maui-hectors-dolphins/maui-abundance/maui-dolphin-abundance-2021.pdf
Article
• The sei whale (Balaenoptera borealis) presents a disjointed geographic distribution. Significant genetic divergence between sei whales from the North Atlantic (NA) and North Pacific (NP) have been recorded; however, limited samples from the Southern Hemisphere (SH) have precluded a global analysis. • The largest recorded mass mortality event occu...
Article
Runs of homozygosity (ROH) occur when offspring inherit haplotypes that are identical by descent from each parent. Length distributions of ROH are informative about population history; specifically, the probability of inbreeding mediated by mating system and/or population demography. Here, we investigate whether variation in killer whale (Orcinus o...
Article
Full-text available
ABSTRACT Southern right whales (SRW) are capital breeders that use stored energy reserves to sustain themselves and their calves on nursery areas. With successful calving events declining in some SRW populations, it has been hypothesized that nutritional stress in adult females causes reproductive failure or death of calves shortly after birth. Her...
Preprint
Runs of homozygosity (ROH) occur when offspring inherit haplotypes that are identical by descent from each parent. Length distributions of ROH are informative about population history; specifically the probability of inbreeding mediated by mating system and/or population demography. Here, we investigate whether variation in killer whale (Orcinus or...
Article
Full-text available
Introduction DNA methylation data facilitate the development of accurate molecular estimators of chronological age, or ‘epigenetic clocks.’ We present a robust epigenetic clock for the beluga whale, Delphinapterus leucas, developed for an endangered population in Cook Inlet, Alaska, USA. Methods and Results We used a custom methylation array to me...
Preprint
Full-text available
Introduction DNA methylation data facilitate the development of accurate molecular estimators of chronological age, or ‘epigenetic clocks.’ We present a robust epigenetic clock for the beluga whale, Delphinapterus leucas, developed for an endangered population in Cook Inlet, Alaska, USA. Methods and Results We used a custom methylation array to me...
Article
Full-text available
Humpback whales Megaptera novaeangliae were severely depleted by commercial whaling. Understanding key factors in their recovery is a crucial step for their conservation world- wide. In Oceania, the Chesterfield-Bellona archipelago was a primary whaling site in the 19th cen- tury, yet has been left almost unaffected by anthropogenic activities sinc...
Article
Full-text available
Southern right whales (Eubalaena australis) migrate between Austral-winter calving and socialising grounds to offshore mid- to high latitude Austral-summer feeding grounds. In Australasia, winter calving grounds used by southern right whales extend from Western Australia across southern Australia to the New Zealand sub-Antarctic Islands. During the...
Article
Full-text available
As species recover from exploitation, continued assessments of connectivity and population structure are warranted to provide information for conservation and management. This is particularly true in species with high dispersal capacity, such as migratory whales, where patterns of connectivity could change rapidly. Here we build on a previous long-...
Conference Paper
Here we present results of a pilot project to simultaneously collect photographs, acoustic call records, and tissue biopsy sample of a blue whale from the eastern North Pacific, with the goal to assign the individual to a population of origin based on acoustic call records and genetic profile. On 17 October 2018, a pair of blue whales was located ~...
Presentation
These are the Abstracts of the 2019 annual meeting of SNVB, WA TWS, and NW PARC. I have two abstracts in this compilation: Olson et al., Density Management and Riparian Buffer Study update, pp 154-155; Weil and Olson, NW PARC update, pp 162-163.
Article
Reconstruction of the demographic and evolutionary history of populations assuming a consensus tree‐like relationship can mask more complex scenarios, which are prevalent in nature. An emerging genomic toolset, which has been most comprehensively harnessed in the reconstruction of human evolutionary history, enables molecular ecologists to elucidat...
Article
Full-text available
Genomic phylogeography plays an important role in describing evolutionary processes and their geographic, ecological, or cultural drivers. These drivers are often poorly understood in marine environments, which have fewer obvious barriers to mixing than terrestrial environments. Taxonomic uncertainty of some taxa (e.g. cetaceans), due to the diffic...
Article
Full-text available
In the context of a changing climate, understanding the environmental drivers of marine megafauna distribution is important for conservation success. The extent of humpback whale breeding habitats and the impact of temperature variation on their availability are both unknown. We used 19 years of dedicated survey data from seven countries and territ...
Article
Full-text available
Coastal and freshwater cetaceans are particularly vulnerable due to their proximity to human activity, localized distributions and small home ranges. These species include Sotalia guianensis, found in the Atlantic and Caribbean coastal areas of central and South America, and Sotalia fluviatilis, distributed in the Amazon River and tributaries. We i...
Article
Strong balancing selection on the Major Histocompatibility Complex (MHC) can lead to different patterns in gene frequencies and neutral genomic variation within species. We investigated diversity and geographic structure of MHC genes DQA and DQB, as well as their inferred functional haplotypes, from two regional populations (East and West Coast) of...
Article
Understanding how dispersal and gene flow link geographically separated the populations over evolutionary history is challenging, particularly in migratory marine species. In southern right whales (SRWs, Eubalaena australis), patterns of genetic diversity are likely influenced by the glacial climate cycle and recent history of whaling. Here we use...
Article
Full-text available
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...
Article
Full-text available
Species conservation depends on robust population assessment. Data on population abundance, distribution, and connectivity are critical for effective management, especially as baseline information for newly documented populations. We describe a pygmy blue whale Balaen - optera musculus brevicauda population in New Zealand waters with year-round pre...
Article
Full-text available
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 sp...
Article
Full-text available
Humpback whales (Megaptera novaeangliae) congregate to breed during the austral winter near tropical islands of the South Pacific (Oceania). It has long been assumed that humpback whales from Oceania migrate primarily to Antarctic feeding grounds directly south (International Whaling Commission Management Areas V and VI); however, there are few rec...
Article
Mitochondrial DNA has been heavily utilized in phylogeography studies for several decades. However, underlying patterns of demography and phylogeography may be misrepresented due to coalescence stochasticity, selection, variation in mutation rates, and cultural hitchhiking (linkage of genetic variation to culturally transmitted traits affecting fit...
Article
Obtaining direct measurements to characterise ecosystem function can be hindered by remote or inaccessible regions. Next-generation satellite tags that inform increasingly sophisticated movement models, and the min-iaturisation of animal-borne loggers, have enabled the use of animals as tools to collect habitat data in remote environments, such as...
Article
Full-text available
Southern Hemisphere humpback whales breed in tropical waters and migrate to Antarctica to forage. While the breeding grounds are well defined, the population structure on Antarctic feeding grounds is poorly described. The Western Antarctic Peninsula (WAP) is of particular interest, where rapidly changing environmental conditions could alter prey di...
Poster
Full-text available
The status of humpback whale populations under the Endangered Species Act (ESA) was changed recently to remove the species level-listing of endangered and, instead, recognize 14 Distinct Populations Segments (DPS) with their own ESA status, including three in the central and eastern North Pacific with Hawaii delisted, Mexico threatened, and Central...
Presentation
Full-text available
A blue whale foraging ground was recently documented in the South Taranaki Bight (STB) region of New Zealand (NZ), yet blue whales remain listed as ‘Migrant’ under the NZ threat classification system due to minimal knowledge of their ecology and population. We collected relevant data to fill pressing knowledge gaps, leading us to hypothesize that b...
Research
Full-text available
Statement regarding the inadequacy of Japan's latest scientific whaling programs.
Article
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ABSTRACT: Bryde’s whales Balaenoptera edeni in New Zealand are classified as ‘nationally critical’ according to the New Zealand Threat Classification System. In the Hauraki Gulf, Bryde’s whales occur year round and are subject to ship-strike mortality events. Photo-identification surveys were conducted to estimate local abundance, apparent survival...
Article
Conservation and management decisions for wild populations are often based on demographic estimates of abundance ( ), and less frequently, on genetic estimates of effective population size ( e). We used genotype-based methods to estimate both parameters from the same set of biopsy samples, while also providing information on the geographic closure...
Article
Full-text available
The description of genetic population structure over a species’ geographic range can provide insights into its evolutionary history and also support effective management efforts. Assessments for globally distributed species are rare, however, requiring significant international coordination and collaboration. The global distribution of demographica...
Article
Obtaining the representative morphological data required for traditional taxonomy is difficult, and sometimes impossible, for cetaceans, especially large ones. As a result, three quarters of the 88 currently recognized extant species have no subspecies and 40 taxa likely have additional unnamed taxa. Conservation needs give urgency to improving tax...
Article
Taxonomy is an imprecise science that delimits the evolutionary continuum into discrete categories. For marine mammals, this science is complicated by the relative lack of morphological data for taxa that inhabit remote and often vast ranges. We provide guidelines to promote consistency in studies relying primarily on molecular genetic data to deli...
Technical Report
Full-text available
Since 2012, we have investigated a newly documented group of blue whales (Balaenoptera musculus sp.) in the New Zealand region. Field research has focused on multi-disciplinary data collection regarding the ecology of blue whales occurring in the South Taranaki Bight (STB) region of New Zealand (40.15 S, 173.30 W). The STB region incurs significant...
Article
Full-text available
Humpback whales wintering in tropical waters along the Atlantic and Pacific coasts of the South American continent are thought to represent distinct populations or “stocks.” Here we present the first analysis of genetic differentiation and estimates of gene flow between these breeding stocks, based on both mitochondrial DNA (mtDNA) control region s...
Article
Full-text available
Rough-toothed dolphins have a worldwide tropical and subtropical distribution, yet little is known about the population structure and social organization of this typically open-ocean species. Although it has been assumed that pelagic dolphins range widely due to the lack of apparent barriers and unpredictable prey distribution, recent evidence sugg...
Article
Full-text available
The rigorous program of monitoring humpback whales (Megaptera novaeangliae), implemented by Glacier Bay National Park and Preserve in 1985, augmented by additional data collected in southeastern Alaska since 1968, constitutes one of the longest studies of living whales in the world. This monitoring program, now a National Park Service (NPS) Invento...
Article
Full-text available
Since the decimation of the southern right whale Eubalaena australis population in New Zealand by whaling, research on its recovery has focused on the wintering ground at the Auckland Islands, neglecting potentially important wintering habitat at Campbell Island. For the first time in 20 years we conducted an expedition to sub-Antarctic Campbell Is...
Article
Full-text available
The complementarity of historical and contemporary processes contributes to understanding the genetic structure of continuously distributed marine species with high dispersal capabilities. Cephalorhynchus eutropia, has a continuous coastal distribution with strong genetic differentiation identified by nuclear DNA markers. We explored the historical...
Article
Full-text available
We provide new information on the scale at which fidelity and recruitment underlie observed increases in humpback whale Megaptera novaeangliae populations. We used photoidentification records and DNA profiles from whales in Glacier Bay and Icy Strait (GBIS), southeastern Alaska (SEAK) to investigate 3 sources of population increase over 33 yr (1973...
Article
There are two recognized species in the genus Berardius, Baird's and Arnoux's beaked whales. In Japan, whalers have traditionally recognized two forms of Baird's beaked whales, the common “slate-gray” form and a smaller, rare “black” form. Previous comparison of mtDNA control region sequences from three black specimens to gray specimens around Japa...
Article
Full-text available
Effective management of space-use conflicts with anthropogenic activities is contingent upon reliable knowledge of a species’ ecology. The Māui dolphin Cephalorhynchus hectori maui is endemic to New Zealand and is listed as Critically Endangered, mainly as a result of fisheries bycatch. Despite conservation efforts, the population was estimated at...
Conference Paper
Full-text available
Here we review the published records of mtDNA control region sequences of southern hemisphere humpback whales as a first step in developing a validated register of haplotypes for future analyses of interest to the Scientific Committee of the International Whaling Commission. We restricted our initial review to sequences submitted to GenBank as 'pop...