Jayasankar, P.,Anoop, B.,Vivekanandan, E.,Rajagopalan, M.,Yousuf, K.M.M.,Reynolds, P.,Krishnakumar, P.K.,Kumaran, PL.,Afsal, V.V.,Krishnan, A.A.
Molecular identification of delphinids and finless porpoise (Cetacea) from the Arabian Sea and Bay of Bengal Journal Article
In: Zootaxa, vol. 1853, no. 125, pp. 57-67, 2008.
Abstract | BibTeX | Tags: bottlenose dolphin, Common dolphin, D.capensis, DNA, Finless Porpoise, India, Neophocaena phocaenoides, sousa, species identification, Spinner dolphin, Stenella longirostris, taxonomy, tursiops aduncus
@article{,
title = {Molecular identification of delphinids and finless porpoise (Cetacea) from the Arabian Sea and Bay of Bengal},
author = {Jayasankar, P.,Anoop, B.,Vivekanandan, E.,Rajagopalan, M.,Yousuf, K.M.M.,Reynolds, P.,Krishnakumar, P.K.,Kumaran, PL.,Afsal, V.V.,Krishnan, A.A.},
year = {2008},
date = {2008-01-01},
journal = {Zootaxa},
volume = {1853},
number = {125},
pages = {57-67},
abstract = {The exact number of extant delphinid species from seas around India is still debated and the lack of adequate field keys
and reliable inventory has resulted in misidentification of several species. As a part of a project to develop a molecular
taxonomy of cetaceans from this region, partial sequences of mtDNA cytochrome b were generated from accidentally
caught/stranded delphinids and finless porpoise. Species were identified by phylogenetic reconstruction of sample
sequences with the reference sequences available in portals GenBank (NCBI) and the web-based program DNA Surveillance.
A comparison was made with the homologous sequences of corresponding species from other seas of the world.
Our molecular investigations allowed us to identify five species of cetaceans from Indian coasts, including Delphinus
capensis, previously reported as D. delphis. We detected unique haplotypes in Indo pacific humpbacked dolphin (Sousa
chinensis; n = 2) and finless porpoise (Neophocaena phocaenoides; n = 12) from Indian coast. On the other hand, some
haplotypes were shared with other regional populations in spinner dolphin (Stenella longirostris; n = 16) and bottlenose
dolphin (Tursiops aduncus; n = 3). Common dolphins (Delphinus capensis; n = 2) had both unique and shared haplotypes
including one highly divergent sequence.},
keywords = {bottlenose dolphin, Common dolphin, D.capensis, DNA, Finless Porpoise, India, Neophocaena phocaenoides, sousa, species identification, Spinner dolphin, Stenella longirostris, taxonomy, tursiops aduncus},
pubstate = {published},
tppubtype = {article}
}
The exact number of extant delphinid species from seas around India is still debated and the lack of adequate field keys
and reliable inventory has resulted in misidentification of several species. As a part of a project to develop a molecular
taxonomy of cetaceans from this region, partial sequences of mtDNA cytochrome b were generated from accidentally
caught/stranded delphinids and finless porpoise. Species were identified by phylogenetic reconstruction of sample
sequences with the reference sequences available in portals GenBank (NCBI) and the web-based program DNA Surveillance.
A comparison was made with the homologous sequences of corresponding species from other seas of the world.
Our molecular investigations allowed us to identify five species of cetaceans from Indian coasts, including Delphinus
capensis, previously reported as D. delphis. We detected unique haplotypes in Indo pacific humpbacked dolphin (Sousa
chinensis; n = 2) and finless porpoise (Neophocaena phocaenoides; n = 12) from Indian coast. On the other hand, some
haplotypes were shared with other regional populations in spinner dolphin (Stenella longirostris; n = 16) and bottlenose
dolphin (Tursiops aduncus; n = 3). Common dolphins (Delphinus capensis; n = 2) had both unique and shared haplotypes
including one highly divergent sequence.
and reliable inventory has resulted in misidentification of several species. As a part of a project to develop a molecular
taxonomy of cetaceans from this region, partial sequences of mtDNA cytochrome b were generated from accidentally
caught/stranded delphinids and finless porpoise. Species were identified by phylogenetic reconstruction of sample
sequences with the reference sequences available in portals GenBank (NCBI) and the web-based program DNA Surveillance.
A comparison was made with the homologous sequences of corresponding species from other seas of the world.
Our molecular investigations allowed us to identify five species of cetaceans from Indian coasts, including Delphinus
capensis, previously reported as D. delphis. We detected unique haplotypes in Indo pacific humpbacked dolphin (Sousa
chinensis; n = 2) and finless porpoise (Neophocaena phocaenoides; n = 12) from Indian coast. On the other hand, some
haplotypes were shared with other regional populations in spinner dolphin (Stenella longirostris; n = 16) and bottlenose
dolphin (Tursiops aduncus; n = 3). Common dolphins (Delphinus capensis; n = 2) had both unique and shared haplotypes
including one highly divergent sequence.
Rosenbaum,H.C.,Pomilla,C.,Olavarria,C.,Baker,C.S.,Leslie,M.,Mendez,M.C.,Caballero,S.,Brasseur,M,Bannister,J.L,Best,P.B.,Bonatto,S.,Collins,T.J.Q.,Engel,M.H.,Ersts,P.J.,Findlay,K.P.,Florez-Gonzalez,L.,Garrigue,C.,Hauser,N.,Jenner,C.,Meyer,M.,Minton,G.,Poole,M.M.,Razafindrakoto,Y.
A first and preliminary analysis of mtDNA sequences from humpback whales for breeding stocks A-G and X Technical Report
no. 461, 2006, ISBN: SC/A06/HW59.
BibTeX | Tags: Atlantic, Atlantic Ocean, breeding grounds, DNA, dolphin, Humpback Whale, humpback whales, Indian Ocean, mitochondrial DNA, Oman, population, South Atlantic, Southern Hemisphere, stocks, whale, whales
@techreport{,
title = {A first and preliminary analysis of mtDNA sequences from humpback whales for breeding stocks A-G and X},
author = {Rosenbaum,H.C.,Pomilla,C.,Olavarria,C.,Baker,C.S.,Leslie,M.,Mendez,M.C.,Caballero,S.,Brasseur,M,Bannister,J.L,Best,P.B.,Bonatto,S.,Collins,T.J.Q.,Engel,M.H.,Ersts,P.J.,Findlay,K.P.,Florez-Gonzalez,L.,Garrigue,C.,Hauser,N.,Jenner,C.,Meyer,M.,Minton,G.,Poole,M.M.,Razafindrakoto,Y.},
issn = {SC/A06/HW59},
year = {2006},
date = {2006-01-01},
journal = {Report presented to the Comprehensive Assessment of Southern Hemisphere Humpback Whales, Hobart, Tasmania},
volume = {SC/A06/HW59},
number = {461},
keywords = {Atlantic, Atlantic Ocean, breeding grounds, DNA, dolphin, Humpback Whale, humpback whales, Indian Ocean, mitochondrial DNA, Oman, population, South Atlantic, Southern Hemisphere, stocks, whale, whales},
pubstate = {published},
tppubtype = {techreport}
}
Riemann,L.,Steward,G.F.,Fandino,L.B.,Campbell,L.,Landry,M.R.,Azam,F.
Bacterial community composition during two consecutive NE Monsoon periods in the Arabian Sea studied by denaturing gradient gel electrophoresis (DGGE) of rRNA genes Journal Article
In: Deep-Sea Research Part II, vol. 46, no. 205, pp. 1791-1811, 1999.
Abstract | BibTeX | Tags: Arabian Sea, depth, DNA, dominance, Oceanic, PCR
@article{,
title = {Bacterial community composition during two consecutive NE Monsoon periods in the Arabian Sea studied by denaturing gradient gel electrophoresis (DGGE) of rRNA genes},
author = {Riemann,L.,Steward,G.F.,Fandino,L.B.,Campbell,L.,Landry,M.R.,Azam,F.},
year = {1999},
date = {1999-01-01},
journal = {Deep-Sea Research Part II},
volume = {46},
number = {205},
pages = {1791-1811},
abstract = {Horizontal and vertical variations in bacterial community composition were examined in samples collected during two Joint Global Ocean Flux Study (JGOFS) Arabian Sea cruises in 1995. The cruises, 11 months apart, took place during two consecutive NE Monsoon periods (January and December). Bacteria were harvested by filtration from samples collected in the mixed layer, mid-water, and deep sea at stations across the study area. Total bacterial community genomic DNA was analyzed by PCR amplification of 16S rRNA gene fragments, followed by denaturing gradient gel electrophoresis (DGGE). In total, 20 DGGE bands reflecting unique or varying phylotypes were excised, cloned and sequenced. Amplicons were dominated by bacterial groups commonly found in oceanic waters (e.g., the SAR11 cluster of a-Proteobacteria and cyanobacteria), but surprisingly none of the sequenced amplicons were related to c-Proteobacteria or to members of the Cytophaga-Flavobacter-Bacteroides phylum. Amplicons related to magnetotactic bacteria were found for the first time in pelagic oceanic waters. The DGGE banding patterns revealed a dominance of ÷ 15 distinguishable amplicons in all samples. In the mixed layer the bacterial community was dominated by the same ÷ 15 phylotypes at all stations, but unique phylotypes were found with increasing depth. Except for cyanobacteria, comparison of the bacterial community composition in surface waters from January and December 1995 showed only minor differences, despite significant differences in environmental parameters. These data suggest a horizontal homogeneity and some degree of seasonal predictability of bacterial community composition in the Arabian Sea.},
keywords = {Arabian Sea, depth, DNA, dominance, Oceanic, PCR},
pubstate = {published},
tppubtype = {article}
}
Horizontal and vertical variations in bacterial community composition were examined in samples collected during two Joint Global Ocean Flux Study (JGOFS) Arabian Sea cruises in 1995. The cruises, 11 months apart, took place during two consecutive NE Monsoon periods (January and December). Bacteria were harvested by filtration from samples collected in the mixed layer, mid-water, and deep sea at stations across the study area. Total bacterial community genomic DNA was analyzed by PCR amplification of 16S rRNA gene fragments, followed by denaturing gradient gel electrophoresis (DGGE). In total, 20 DGGE bands reflecting unique or varying phylotypes were excised, cloned and sequenced. Amplicons were dominated by bacterial groups commonly found in oceanic waters (e.g., the SAR11 cluster of a-Proteobacteria and cyanobacteria), but surprisingly none of the sequenced amplicons were related to c-Proteobacteria or to members of the Cytophaga-Flavobacter-Bacteroides phylum. Amplicons related to magnetotactic bacteria were found for the first time in pelagic oceanic waters. The DGGE banding patterns revealed a dominance of ÷ 15 distinguishable amplicons in all samples. In the mixed layer the bacterial community was dominated by the same ÷ 15 phylotypes at all stations, but unique phylotypes were found with increasing depth. Except for cyanobacteria, comparison of the bacterial community composition in surface waters from January and December 1995 showed only minor differences, despite significant differences in environmental parameters. These data suggest a horizontal homogeneity and some degree of seasonal predictability of bacterial community composition in the Arabian Sea.
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.