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Crossman CA, Fontaine MC, Frasier TR. A comparison of genomic diversity and demographic history of the North Atlantic and Southwest Atlantic southern right whales. Mol Ecol 2023. [PMID: 37577945 DOI: 10.1111/mec.17099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 07/25/2023] [Accepted: 07/31/2023] [Indexed: 08/15/2023]
Abstract
Right whales (genus Eubalaena) were among the first, and most extensively pursued, targets of commercial whaling. However, understanding the impacts of this persecution requires knowledge of the demographic histories of these species prior to exploitation. We used deep whole genome sequencing (~40×) of 12 North Atlantic (E. glacialis) and 10 Southwest Atlantic southern (E. australis) right whales to quantify contemporary levels of genetic diversity and infer their demographic histories over time. Using coalescent- and identity-by-descent-based modelling to estimate ancestral effective population sizes from genomic data, we demonstrate that North Atlantic right whales have lived with smaller effective population sizes (Ne ) than southern right whales in the Southwest Atlantic since their divergence and describe the decline in both populations around the time of whaling. North Atlantic right whales exhibit reduced genetic diversity and longer runs of homozygosity leading to higher inbreeding coefficients compared to the sampled population of southern right whales. This study represents the first comprehensive assessment of genome-wide diversity of right whales in the western Atlantic and underscores the benefits of high coverage, genome-wide datasets to help resolve long-standing questions about how historical changes in effective population size over different time scales shape contemporary diversity estimates. This knowledge is crucial to improve our understanding of the right whales' history and inform our approaches to address contemporary conservation issues. Understanding and quantifying the cumulative impact of long-term small Ne , low levels of diversity and recent inbreeding on North Atlantic right whale recovery will be important next steps.
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Affiliation(s)
- Carla A Crossman
- Biology Department, Saint Mary's University, Halifax, Nova Scotia, Canada
| | - Michael C Fontaine
- Laboratoire MIVEGEC (Université de Montpellier, CNRS 5290, IRD 224), Montpellier, France
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Timothy R Frasier
- Biology Department, Saint Mary's University, Halifax, Nova Scotia, Canada
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Hamilton PK, Frasier BA, Conger LA, George RC, Jackson KA, Frasier TR. Genetic identifications challenge our assumptions of physical development and mother–calf associations and separation times: a case study of the North Atlantic right whale (Eubalaena glacialis). Mamm Biol 2022. [DOI: 10.1007/s42991-021-00177-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AbstractWhile photo-identification is an effective tool to monitor individuals in wild populations, it has limitations. Specifically, it cannot be applied to very young animals before their identifying features have stabilized or to dead, decomposed animals. These shortfalls leave gaps in our understanding of survival, parentage, age structure, physical development, and behavioral variability. Here we report on 13 case studies of North Atlantic right whale, Eubalaena glacialis, calves that required genetics to track their life history data. These case studies revealed unexpected variations in mother–calf associations and separation times, as well as calf physical development. Prior to this study, calves were assumed to have died if their mothers were always alone on the feeding ground in the calf’s birth year. Using genetics and photo-identification, four such calves were discovered to be alive; two of the four possibly weaned earlier than expected at 7.5–8.0 months. To put these early separations in context, photo-identification data were queried and revealed that mothers and calves are seen apart from each other on the feeding grounds in 10–40% of all spring/summer sightings; previously, there were no published data on how often pairs are seen apart in the calf’s birth year. Two dead whales initially logged as calves of the year were discovered to be juveniles, thus allowing skewed survival estimates for calves of the year to be corrected. Genetically sampling animals early in their lives before they disperse or separate from their mothers provides an important means of individual identification at a time when photo-identification is not reliable.
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Sharp SM, McLellan WA, Rotstein DS, Costidis AM, Barco SG, Durham K, Pitchford TD, Jackson KA, Daoust PY, Wimmer T, Couture EL, Bourque L, Frasier T, Frasier B, Fauquier D, Rowles TK, Hamilton PK, Pettis H, Moore MJ. Gross and histopathologic diagnoses from North Atlantic right whale Eubalaena glacialis mortalities between 2003 and 2018. DISEASES OF AQUATIC ORGANISMS 2019; 135:1-31. [PMID: 31219432 DOI: 10.3354/dao03376] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Seventy mortalities of North Atlantic right whales Eubalaena glacialis (NARW) were documented between 2003 and 2018 from Florida, USA, to the Gulf of St. Lawrence, Canada. These included 29 adults, 14 juveniles, 10 calves, and 17 of unknown age class. Females represented 65.5% (19/29) of known-sex adults. Fourteen cases had photos only; 56 carcasses received external examinations, 44 of which were also necropsied. Cause of death was determined in 43 cases, of which 38 (88.4%) were due to anthropogenic trauma: 22 (57.9%) from entanglement, and 16 (42.1%) from vessel strike. Gross and histopathologic lesions associated with entanglement were often severe and included deep lacerations caused by constricting line wraps around the flippers, flukes, and head/mouth; baleen plate mutilation; chronic extensive bone lesions from impinging line, and traumatic scoliosis resulting in compromised mobility in a calf. Chronically entangled whales were often in poor body condition and had increased cyamid burden, reflecting compromised health. Vessel strike blunt force injuries included skull and vertebral fractures, blubber and muscle contusions, and large blood clots. Propeller-induced wounds often caused extensive damage to blubber, muscle, viscera, and bone. Overall prevalence of NARW entanglement mortalities increased from 21% (1970-2002) to 51% during this study period. This demonstrates that despite mitigation efforts, entanglements and vessel strikes continue to inflict profound physical trauma and suffering on individual NARWs. These cumulative mortalities are also unsustainable at the population level, so urgent and aggressive intervention is needed to end anthropogenic mortality in this critically endangered species.
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Affiliation(s)
- S M Sharp
- International Fund for Animal Welfare, Yarmouth Port, MA 02675, USA Addresses for other authors are given in the supplements at www.int-res.com/articles/suppl/d135p001_supp.pdf
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Monsarrat S, Pennino MG, Smith TD, Reeves RR, Meynard CN, Kaplan DM, Rodrigues ASL. A spatially explicit estimate of the prewhaling abundance of the endangered North Atlantic right whale. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2016; 30:783-791. [PMID: 26632250 DOI: 10.1111/cobi.12664] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 10/26/2015] [Accepted: 11/25/2015] [Indexed: 06/05/2023]
Abstract
The North Atlantic right whale (NARW) (Eubalaena glacialis) is one of the world's most threatened whales. It came close to extinction after nearly a millennium of exploitation and currently persists as a population of only approximately 500 individuals. Setting appropriate conservation targets for this species requires an understanding of its historical population size, as a baseline for measuring levels of depletion and progress toward recovery. This is made difficult by the scarcity of records over this species' long whaling history. We sought to estimate the preexploitation population size of the North Atlantic right whale and understand how this species was distributed across its range. We used a spatially explicit data set on historical catches of North Pacific right whales (NPRWs) (Eubalaena japonica) to model the relationship between right whale relative density and the environment during the summer feeding season. Assuming the 2 right whale species select similar environments, we projected this model to the North Atlantic to predict how the relative abundance of NARWs varied across their range. We calibrated these relative abundances with estimates of the NPRW total prewhaling population size to obtain high and low estimates for the overall NARW population size prior to exploitation. The model predicted 9,075-21,328 right whales in the North Atlantic. The current NARW population is thus <6% of the historical North Atlantic carrying capacity and has enormous potential for recovery. According to the model, in June-September NARWs concentrated in 2 main feeding areas: east of the Grand Banks of Newfoundland and in the Norwegian Sea. These 2 areas may become important in the future as feeding grounds and may already be used more regularly by this endangered species than is thought.
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Affiliation(s)
- Sophie Monsarrat
- CEFE UMR 5175, CNRS - Université de Montpellier - Université Paul-Valéry Montpellier - EPHE - CNRS, 1919 route de Mende, 34293, Montpellier Cedex 5, France
- Institut de Recherche pour le Développement (IRD), UMR MARBEC 248, Marine Biodiversity, Exploitation and Conservation. Avenue Jean Monnet, CS 30171, 34203, Sète cedex, France
| | - M Grazia Pennino
- Universidade Federal do Rio Grande do Norte - UFRN. Depto. de Botânica, Ecologia e Zoologia - DBEZ, Campus Universitário s/n, Lagoa Nova. Cx postal 1524., CEP 59.098-970, Natal (RN), Brazil
| | | | | | - Christine N Meynard
- Virginia Institute of Marine Science, College of William & Mary, P.O. Box 1346, Gloucester Point, VA, 23062, U.S.A
| | - David M Kaplan
- Virginia Institute of Marine Science, College of William & Mary, P.O. Box 1346, Gloucester Point, VA, 23062, U.S.A
| | - Ana S L Rodrigues
- CEFE UMR 5175, CNRS - Université de Montpellier - Université Paul-Valéry Montpellier - EPHE - CNRS, 1919 route de Mende, 34293, Montpellier Cedex 5, France
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Gillett RM, Murray BW, White BN. Characterization of class I- and class II-like major histocompatibility complex loci in pedigrees of North Atlantic right whales. J Hered 2013; 105:188-202. [PMID: 24381183 DOI: 10.1093/jhered/est095] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
North Atlantic right whales have one of the lowest levels of genetic variation at minisatellite loci, microsatellite loci, and mitochondrial control region haplotypes among mammals. Here, adaptive variation at the peptide binding region of class I and class II DRB-like genes of the major histocompatibility complex was assessed. Amplification of a duplicated region in 222 individuals revealed at least 11 class II alleles. Six alleles were assigned to the locus Eugl-DRB1 and 5 alleles were assigned to the locus Eugl-DRB2 by assessing segregation patterns of alleles from 81 parent/offspring pedigrees. Pedigree analysis indicated that these alleles segregated into 12 distinct haplotypes. Genotyping a smaller subset of unrelated individuals (n = 5 and 10, respectively) using different primer sets revealed at least 2 class II pseudogenes (with ≥ 4 alleles) and at least 3 class I loci (with ≥ 6 alleles). Class II sequences were significantly different from neutrality at peptide binding sites suggesting loci may be under the influence of balancing selection. Trans-species sharing of alleles was apparent for class I and class II sequences. Characterization of class II loci represents the first step in determining the relationship between major histocompatibility complex variability and factors affecting health and reproduction in this species.
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Affiliation(s)
- Roxanne M Gillett
- the Natural Resources DNA Profiling and Forensic Centre, Department of Biology, Trent University, 2140 East Bank Drive, Peterborough, Ontario K9J 7B8, Canada
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Ancient DNA from marine mammals: studying long-lived species over ecological and evolutionary timescales. Ann Anat 2011; 194:112-20. [PMID: 21652193 DOI: 10.1016/j.aanat.2011.04.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 04/14/2011] [Accepted: 04/15/2011] [Indexed: 11/21/2022]
Abstract
Marine mammals have long generation times and broad, difficult to sample distributions, which makes inferring evolutionary and demographic changes using field studies of extant populations challenging. However, molecular analyses from sub-fossil or historical materials of marine mammals such as bone, tooth, baleen, skin, fur, whiskers and scrimshaw using ancient DNA (aDNA) approaches provide an opportunity for investigating such changes over evolutionary and ecological timescales. Here, we review the application of aDNA techniques to the study of marine mammals. Most of the studies have focused on detecting changes in genetic diversity following periods of exploitation and environmental change. To date, these studies have shown that even small sample sizes can provide useful information on historical genetic diversity. Ancient DNA has also been used in investigations of changes in distribution and range of marine mammal species; we review these studies and discuss the limitations of such 'presence only' studies. Combining aDNA data with stable isotopes can provide further insights into changes in ecology and we review past studies and suggest future potential applications. We also discuss studies reconstructing inter- and intra-specific phylogenies from aDNA sequences and discuss how aDNA sequences could be used to estimate mutation rates. Finally, we highlight some of the problems of aDNA studies on marine mammals, such as obtaining sufficient sample sizes and calibrating for the marine reservoir effect when radiocarbon-dating such wide-ranging species.
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