Rosenbaum, H. C.,Kershaw, F.,Mendez, M.,Pomilla, C.,Leslie, M. S.,Findlay, K. P.,Best, P. B.,Collins, T.,Vely, M.,Engel, M. H.,Baldwin, R.,Minton, G.,Meÿer, M.,Flórez-González, L.,Poole, M. M.,Hauser, N.,Garrigue, C.,Brasseur, M.,Bannister, J.,Anderson, M.,Olavarría, C.,Baker, C. S.
First circumglobal assessment of Southern Hemisphere humpback whale mitochondrial genetic variation and implications for management Journal Article
In: Endangered Species Research, vol. 32, no. 213, pp. 551-567, 2017.
Abstract | Links | BibTeX | Tags: Arabian Sea, breeding grounds, Genetic differentiation, Humpback Whale, megaptera novaeangliae, mtDNA, population structure, Stock assessment
@article{,
title = {First circumglobal assessment of Southern Hemisphere humpback whale mitochondrial genetic variation and implications for management},
author = {Rosenbaum, H. C.,Kershaw, F.,Mendez, M.,Pomilla, C.,Leslie, M. S.,Findlay, K. P.,Best, P. B.,Collins, T.,Vely, M.,Engel, M. H.,Baldwin, R.,Minton, G.,Meÿer, M.,Flórez-González, L.,Poole, M. M.,Hauser, N.,Garrigue, C.,Brasseur, M.,Bannister, J.,Anderson, M.,Olavarría, C.,Baker, C. S.},
url = {http://www.int-res.com/abstracts/esr/v32/p551-567/},
year = {2017},
date = {2017-01-01},
journal = {Endangered Species Research},
volume = {32},
number = {213},
pages = {551-567},
abstract = {ABSTRACT: 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 demographically discrete populations for the humpback whale \textit{Megaptera novaeangliae} is not fully known, hampering the definition of appropriate management units. Here, we present the first circumglobal assessment of mitochondrial genetic population structure across the species range in the Southern Hemisphere and Arabian Sea. We combine new and existing data from the mitochondrial (mt)DNA control region that resulted in a 311 bp consensus sequence of the mtDNA control region for 3009 individuals sampled across 14 breeding stocks and subpopulations currently recognized by the International Whaling Commission. We assess genetic diversity and test for genetic differentiation and also estimate the magnitude and directionality of historic matrilineal gene flow between putative populations. Our results indicate that maternally directed site fidelity drives significant genetic population structure between breeding stocks within ocean basins. However, patterns of connectivity differ across the circumpolar range, possibly as a result of differences in the extent of longitudinal movements on feeding areas. The number of population comparisons observed to be significantly differentiated were found to diminish at the subpopulation scale when nucleotide differences were examined, indicating that more complex processes underlie genetic structure at this scale. It is crucial that these complexities and uncertainties are afforded greater consideration in management and regulatory efforts.},
keywords = {Arabian Sea, breeding grounds, Genetic differentiation, Humpback Whale, megaptera novaeangliae, mtDNA, population structure, Stock assessment},
pubstate = {published},
tppubtype = {article}
}
ABSTRACT: 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 demographically discrete populations for the humpback whale Megaptera novaeangliae is not fully known, hampering the definition of appropriate management units. Here, we present the first circumglobal assessment of mitochondrial genetic population structure across the species range in the Southern Hemisphere and Arabian Sea. We combine new and existing data from the mitochondrial (mt)DNA control region that resulted in a 311 bp consensus sequence of the mtDNA control region for 3009 individuals sampled across 14 breeding stocks and subpopulations currently recognized by the International Whaling Commission. We assess genetic diversity and test for genetic differentiation and also estimate the magnitude and directionality of historic matrilineal gene flow between putative populations. Our results indicate that maternally directed site fidelity drives significant genetic population structure between breeding stocks within ocean basins. However, patterns of connectivity differ across the circumpolar range, possibly as a result of differences in the extent of longitudinal movements on feeding areas. The number of population comparisons observed to be significantly differentiated were found to diminish at the subpopulation scale when nucleotide differences were examined, indicating that more complex processes underlie genetic structure at this scale. It is crucial that these complexities and uncertainties are afforded greater consideration in management and regulatory efforts.
Nanayakkara, Ranil P.,Herath, H. M. J. C. B.,Mel, Ruvinda K. de,Kusuminda, T. G. Tharaka
Molecular Genetic Identification of Beached Whales in Sri Lanka from Mitochondrial DNA Sequence Data Journal Article
In: Ceylon Journal of Science, vol. 43, no. 179, pp. 73, 2015.
Abstract | BibTeX | Tags: Arabian Sea, balaenoptera musculus, Blue whale, genetics, Indian Ocean, mtDNA, Sri Lanka
@article{,
title = {Molecular Genetic Identification of Beached Whales in Sri Lanka from Mitochondrial DNA Sequence Data},
author = {Nanayakkara, Ranil P.,Herath, H. M. J. C. B.,Mel, Ruvinda K. de,Kusuminda, T. G. Tharaka},
year = {2015},
date = {2015-01-01},
journal = {Ceylon Journal of Science},
volume = {43},
number = {179},
pages = {73},
abstract = {In the current study we attempt to identify eight baleen whale carcasses that were washed ashore to the Western, Northwestern and Southern coasts of Sri Lanka in 2010, using molecular phylogenetic techniques. Initial physical examination suggested that these carcasses belonged to blue whales ( Balaenoptera musculus ). Analysis of sequences of the mitochondrial control region from baleen whales confirmed that the samples belonged to blue whales ( Balaenoptera musculus ). However, it was impossible to identify the population of blue whales the individuals belonged to, due to the lack of strong population genetic signals in the mitochondrial control region sequences.},
keywords = {Arabian Sea, balaenoptera musculus, Blue whale, genetics, Indian Ocean, mtDNA, Sri Lanka},
pubstate = {published},
tppubtype = {article}
}
In the current study we attempt to identify eight baleen whale carcasses that were washed ashore to the Western, Northwestern and Southern coasts of Sri Lanka in 2010, using molecular phylogenetic techniques. Initial physical examination suggested that these carcasses belonged to blue whales ( Balaenoptera musculus ). Analysis of sequences of the mitochondrial control region from baleen whales confirmed that the samples belonged to blue whales ( Balaenoptera musculus ). However, it was impossible to identify the population of blue whales the individuals belonged to, due to the lack of strong population genetic signals in the mitochondrial control region sequences.
Rosenbaum, H.C.,Pomilla, C.,Mendez, M.C.,Leslie, M.,Best, P.,Findlay, K.,Minton, G.,Ersts, P.J.,Collins, T.,Engel, M.H.,Bonatto, S.,Kotze, D.,Meyer, M.,Barendse, J.,Thornton, M.,Razafindrakoto, Y.,Ngouessono, S,Vely, M.,Kiszka, J.
Population Structure of Humpback Whales from Their Breeding Grounds in the South Atlantic and Indian Oceans Journal Article
In: PLoS ONE, vol. 4, no. 460, pp. e7318. doi:10.1371/journal.pone.0007318, 2009.
Abstract | Links | BibTeX | Tags: Arabian Sea, Humpback Whale, Indian Ocean, megaptera novaeangliae, migration, mtDNA, Oman, population identity, population structure, Population X, Southern Hemisphere
@article{,
title = {Population Structure of Humpback Whales from Their Breeding Grounds in the South Atlantic and Indian Oceans},
author = {Rosenbaum, H.C.,Pomilla, C.,Mendez, M.C.,Leslie, M.,Best, P.,Findlay, K.,Minton, G.,Ersts, P.J.,Collins, T.,Engel, M.H.,Bonatto, S.,Kotze, D.,Meyer, M.,Barendse, J.,Thornton, M.,Razafindrakoto, Y.,Ngouessono, S,Vely, M.,Kiszka, J.},
url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0007318},
year = {2009},
date = {2009-01-01},
journal = {PLoS ONE},
volume = {4},
number = {460},
pages = {e7318. doi:10.1371/journal.pone.0007318},
abstract = {Although humpback whales are among the best-studied of the large whales, population boundaries in the Southern
Hemisphere (SH) have remained largely untested. We assess population structure of SH humpback whales using 1,527
samples collected from whales at fourteen sampling sites within the Southwestern and Southeastern Atlantic, the
Southwestern Indian Ocean, and Northern Indian Ocean (Breeding Stocks A, B, C and X, respectively). Evaluation of mtDNA
population structure and migration rates was carried out under different statistical frameworks. Using all genetic evidence,
the results suggest significant degrees of population structure between all ocean basins, with the Southwestern and
Northern Indian Ocean most differentiated from each other. Effective migration rates were highest between the
Southeastern Atlantic and the Southwestern Indian Ocean, followed by rates within the Southeastern Atlantic, and the
lowest between the Southwestern and Northern Indian Ocean. At finer scales, very low gene flow was detected between
the two neighbouring sub-regions in the Southeastern Atlantic, compared to high gene flow for whales within the
Southwestern Indian Ocean. Our genetic results support the current management designations proposed by the
International Whaling Commission of Breeding Stocks A, B, C, and X as four strongly structured populations. The population
structure patterns found in this study are likely to have been influenced by a combination of long-term maternally directed
fidelity of migratory destinations, along with other ecological and oceanographic features in the region.},
keywords = {Arabian Sea, Humpback Whale, Indian Ocean, megaptera novaeangliae, migration, mtDNA, Oman, population identity, population structure, Population X, Southern Hemisphere},
pubstate = {published},
tppubtype = {article}
}
Although humpback whales are among the best-studied of the large whales, population boundaries in the Southern
Hemisphere (SH) have remained largely untested. We assess population structure of SH humpback whales using 1,527
samples collected from whales at fourteen sampling sites within the Southwestern and Southeastern Atlantic, the
Southwestern Indian Ocean, and Northern Indian Ocean (Breeding Stocks A, B, C and X, respectively). Evaluation of mtDNA
population structure and migration rates was carried out under different statistical frameworks. Using all genetic evidence,
the results suggest significant degrees of population structure between all ocean basins, with the Southwestern and
Northern Indian Ocean most differentiated from each other. Effective migration rates were highest between the
Southeastern Atlantic and the Southwestern Indian Ocean, followed by rates within the Southeastern Atlantic, and the
lowest between the Southwestern and Northern Indian Ocean. At finer scales, very low gene flow was detected between
the two neighbouring sub-regions in the Southeastern Atlantic, compared to high gene flow for whales within the
Southwestern Indian Ocean. Our genetic results support the current management designations proposed by the
International Whaling Commission of Breeding Stocks A, B, C, and X as four strongly structured populations. The population
structure patterns found in this study are likely to have been influenced by a combination of long-term maternally directed
fidelity of migratory destinations, along with other ecological and oceanographic features in the region.
Hemisphere (SH) have remained largely untested. We assess population structure of SH humpback whales using 1,527
samples collected from whales at fourteen sampling sites within the Southwestern and Southeastern Atlantic, the
Southwestern Indian Ocean, and Northern Indian Ocean (Breeding Stocks A, B, C and X, respectively). Evaluation of mtDNA
population structure and migration rates was carried out under different statistical frameworks. Using all genetic evidence,
the results suggest significant degrees of population structure between all ocean basins, with the Southwestern and
Northern Indian Ocean most differentiated from each other. Effective migration rates were highest between the
Southeastern Atlantic and the Southwestern Indian Ocean, followed by rates within the Southeastern Atlantic, and the
lowest between the Southwestern and Northern Indian Ocean. At finer scales, very low gene flow was detected between
the two neighbouring sub-regions in the Southeastern Atlantic, compared to high gene flow for whales within the
Southwestern Indian Ocean. Our genetic results support the current management designations proposed by the
International Whaling Commission of Breeding Stocks A, B, C, and X as four strongly structured populations. The population
structure patterns found in this study are likely to have been influenced by a combination of long-term maternally directed
fidelity of migratory destinations, along with other ecological and oceanographic features in the region.
Rosenbaum,H.C.,Glaberman,S.,Jefferson,T.,Collins,T.,Minton,G.,Peddemors,V.,Baldwin,R.M.
Phylogenetic relationships and population structure among humpback dolphins based on mtDNA variation Technical Report
no. 459, 2002, ISBN: SC/54/SM34.
Abstract | BibTeX | Tags: control region, dolphin, dolphins, humpback dolphins, International Whaling Commission, mtDNA, Oman, Pacific Ocean, phylogenetic, population, population structure, South Africa, status, taxonomy, whaling
@techreport{,
title = {Phylogenetic relationships and population structure among humpback dolphins based on mtDNA variation},
author = {Rosenbaum,H.C.,Glaberman,S.,Jefferson,T.,Collins,T.,Minton,G.,Peddemors,V.,Baldwin,R.M.},
issn = {SC/54/SM34},
year = {2002},
date = {2002-01-01},
journal = {Document presented to the 54th meeting of the International Whaling Commission},
volume = {SC/54/SM34},
number = {459},
pages = {1-8},
abstract = {The taxonomy, systematic relationships, and population structure of humpback dolphins (genus Sousa) have been controversial. Various nominal species have been described or subsumed. Recent reports have suggested the division of Sousa into one to three distinct species or sub-species. However, many of these analyses have not been conducted in a proper systematics framework, did not include all representative putative taxa or were lacking specimens from parts of their geographic range, and have not been in published in peer-reviewed journals (typically necessary for revising taxonomy). In order to address relationships and taxonomic status among Sousa species, we present a preliminary genetic analysis of humpback dolphins primarily from Southeast Asia, the coast of Oman, and South Africa. A total of 110 samples were sequenced for 501 by of mtDNA control region and significant population structuring at the regional level was revealed. Population Aggregation and phylogenetic analyses of mtDNA control region lineages and a subset of lineages analyzed for a 358 by fragment of Cytochrome B revealed a series of complex relationships among humpback dolphins in the Indian and Pacific Oceans. These preliminary data are a critical first step to better understanding the taxonomy and systematics in the genus Sousa. Additional molecular character data from other mitochondria) and nuclear genes will be essential for resolving relationship and taxonomic status for humpback dolphins.},
keywords = {control region, dolphin, dolphins, humpback dolphins, International Whaling Commission, mtDNA, Oman, Pacific Ocean, phylogenetic, population, population structure, South Africa, status, taxonomy, whaling},
pubstate = {published},
tppubtype = {techreport}
}
The taxonomy, systematic relationships, and population structure of humpback dolphins (genus Sousa) have been controversial. Various nominal species have been described or subsumed. Recent reports have suggested the division of Sousa into one to three distinct species or sub-species. However, many of these analyses have not been conducted in a proper systematics framework, did not include all representative putative taxa or were lacking specimens from parts of their geographic range, and have not been in published in peer-reviewed journals (typically necessary for revising taxonomy). In order to address relationships and taxonomic status among Sousa species, we present a preliminary genetic analysis of humpback dolphins primarily from Southeast Asia, the coast of Oman, and South Africa. A total of 110 samples were sequenced for 501 by of mtDNA control region and significant population structuring at the regional level was revealed. Population Aggregation and phylogenetic analyses of mtDNA control region lineages and a subset of lineages analyzed for a 358 by fragment of Cytochrome B revealed a series of complex relationships among humpback dolphins in the Indian and Pacific Oceans. These preliminary data are a critical first step to better understanding the taxonomy and systematics in the genus Sousa. Additional molecular character data from other mitochondria) and nuclear genes will be essential for resolving relationship and taxonomic status for humpback dolphins.
Lento,G.M.,Dalebout,M.L.,Baker,C.S.
Species and individual identification of whale and dolphin products for sale in Japan by mtDNA sequences and nuclear microsatellite profiles Technical Report
no. 399, 1998.
Abstract | BibTeX | Tags: Atlantic, baleen whale, baleen whales, beaked whales, developing, DNA, dolphin, dolphins, fin whale, Japan, Microsatellite, minke whale, mtDNA, North Atlantic, Oman, population, Porpoise, pygmy sperm whale, Southern Hemisphere, sperm whale, stocks, survey, whale, whales, whaling
@techreport{,
title = {Species and individual identification of whale and dolphin products for sale in Japan by mtDNA sequences and nuclear microsatellite profiles },
author = {Lento,G.M.,Dalebout,M.L.,Baker,C.S.},
year = {1998},
date = {1998-01-01},
volume = {SC/50/O8},
number = {399},
pages = {1-12},
abstract = {We report on species and individual identification of whale and dolphin products available on commercial markets of Japan in 1997/98 based on analysis of mitochondria) DNA (mtDNA) sequences and microsatellite variation. The total sample of 74 products included four species of baleen whales, the fin (n=4), sei (n=1), northern minke (n=15) and southern minke (n=39) whales. The remaining 15 samples included dolphins (n = 8; at least four species), Baird's beaked whales (n=5), a porpoise (n=1), and a pygmy sperm whale (n=1), all sold as "kujira" in Japan. It is noted that two new species, the sei whale, and the pygmy sperm whale, appeared for the first time in this series of market surveys. With the inclusion of the sei whale, a total of eight species of baleen whale have been found for sale in post-moratorium surveys of markets in Korea and Japan. Comparison of the sei whale mtDNA to reference sequences from the North Atlantic and Southern Hemisphere suggested that this product originated from the Southern Hemisphere. The last legal hunting of this population was in 1979-80. To investigate the stock origins of northern minke whale products sold in Japan, in 1997-98, the mtDNA haplotypes of these products were compared to those found previously in Korea, 1994-97 (Lento et al. 1998). This comparison revealed that four (33%) of the 12 haplotypes among the Japanese products were identical to those from Korea. This is not consistent with the hypothesis that northern minke whale products sold in Japan originate exclusively from the scientific hunting of a stock that is genetically distinct from the Korean coastal bycatch. Instead, these findings could suggest that whales from both stocks are being hunted illegally or that whale products are being smuggled between the two countries. To further investigate the possibility of smuggling and to estimate the total number of individual whales represented in commercial products, we are developing protocols for DNA profiling using microsatellite loci. Based on preliminary analysis of three loci, the four fin whale products, representing three mtDNA haplotypes, were shown to have originated from four individuals. The 15 northern minke whale products found in 1997-98, representing 12 mtDNA haplotypes, were shown to have originated from a minimum of 14 individuals. One of these products that shared a haplotype with a 1997 product, was also shown to be unique.},
keywords = {Atlantic, baleen whale, baleen whales, beaked whales, developing, DNA, dolphin, dolphins, fin whale, Japan, Microsatellite, minke whale, mtDNA, North Atlantic, Oman, population, Porpoise, pygmy sperm whale, Southern Hemisphere, sperm whale, stocks, survey, whale, whales, whaling},
pubstate = {published},
tppubtype = {techreport}
}
We report on species and individual identification of whale and dolphin products available on commercial markets of Japan in 1997/98 based on analysis of mitochondria) DNA (mtDNA) sequences and microsatellite variation. The total sample of 74 products included four species of baleen whales, the fin (n=4), sei (n=1), northern minke (n=15) and southern minke (n=39) whales. The remaining 15 samples included dolphins (n = 8; at least four species), Baird's beaked whales (n=5), a porpoise (n=1), and a pygmy sperm whale (n=1), all sold as "kujira" in Japan. It is noted that two new species, the sei whale, and the pygmy sperm whale, appeared for the first time in this series of market surveys. With the inclusion of the sei whale, a total of eight species of baleen whale have been found for sale in post-moratorium surveys of markets in Korea and Japan. Comparison of the sei whale mtDNA to reference sequences from the North Atlantic and Southern Hemisphere suggested that this product originated from the Southern Hemisphere. The last legal hunting of this population was in 1979-80. To investigate the stock origins of northern minke whale products sold in Japan, in 1997-98, the mtDNA haplotypes of these products were compared to those found previously in Korea, 1994-97 (Lento et al. 1998). This comparison revealed that four (33%) of the 12 haplotypes among the Japanese products were identical to those from Korea. This is not consistent with the hypothesis that northern minke whale products sold in Japan originate exclusively from the scientific hunting of a stock that is genetically distinct from the Korean coastal bycatch. Instead, these findings could suggest that whales from both stocks are being hunted illegally or that whale products are being smuggled between the two countries. To further investigate the possibility of smuggling and to estimate the total number of individual whales represented in commercial products, we are developing protocols for DNA profiling using microsatellite loci. Based on preliminary analysis of three loci, the four fin whale products, representing three mtDNA haplotypes, were shown to have originated from four individuals. The 15 northern minke whale products found in 1997-98, representing 12 mtDNA haplotypes, were shown to have originated from a minimum of 14 individuals. One of these products that shared a haplotype with a 1997 product, was also shown to be unique.