Whale Evolution.

Saturnine Pariah

Saturnine Pariah

Hell is other people
Valued Senior Member
In a paper published in Nature Genetics, researchers from Korea Institute of Ocean Science and Technology, Korea Genome Research Foundation, BGI, and other institutes presented the first in-depth minke whale genome and their new findings on how whales successfully adapted to ocean environment. The data yielded in this study will contribute to future studies of marine mammal diseases, conservation and evolution.
Whales roam throughout all of the world's oceans, living in the water but breathing air like humans. At the top of the food chain, whales are vital to the health of the marine environment, whereas 7 out of the 13 great whale species are endangered or vulnerable. The minke whale is the most abundant baleen whale. Its wide distribution makes it an ideal candidate for whole reference genome sequencing.
In this study, researchers conducted de novo sequencing on a minke whale with 128x average depth of coverage, and re-sequenced three minke whales, a fin whale (Balaenoptera physalus), a bottlenose dolphin, and a finless porpoise (Neophocaena phocaenoides). The yielded data may help to improve scientists' understanding of the evolutionary changes adapted to ocean environment from whole genome level.
The adaptation of whale to ocean life was notably marked by resistance to physiological stresses caused by a lack of oxygen, increased reactive oxygen species, and high salt level. In this study, researchers investigated a number of whale-specific genes that were strongly associated with stress resistance, such as the peroxiredoxin (PRDX) family, O-linked N-acetylglucosaminylation (O-GlcNAcylation). The results revealed that the gene families associated with stress-responsive proteins and anaerobic metabolism were expanded.
Perhaps the most dramatic environmental adaptation for a whale is deep diving, which can induce hypoxia. Under the hypoxic conditions, the body might produce more reactive oxygen species (ROS), harmful compounds that can damage DNA. Glutathione is a well-known antioxidant that prevents damage to important cellular components by ROS. In this study, researchers provided evidence to support that there is an increased ratio of reduced glutathione/glutathione disulfide when suffering hypoxic or oxidative stress.
Minke whales and other Mysticeti whale species grow baleen instead of teeth. It's previously reported that the genes ENAM, MMP, and AMEL might play a role in tooth enamel formation and biomineralization. This study showed that these genes may be pseudogenes with early stop codons in the baleen whales. In addition, researchers found that the gene families related to whale's body hair and sensory receptors were contracted, such as Keratin-related gene families associated with hair formation, several Hox genes that play an important role in the body plan and embryonic development.
Xuanmin Guang, project manager from BGI, said, "Minke whale is the first marine mammal that has been sequenced with such high-depth genome coverage. The genome data not only can help us know much more about the adaption mechanisms underlying minke whale, but also provides invaluable resource for marine mammal's future studies such as diseases control and prevention, species conservation,and protection."
Story Source:
The above story is based on materials provided by BGI Shenzhen, via EurekAlert!, a service of AAAS.

Journal References:
Hyung-Soon Yim, Yun Sung Cho, Xuanmin Guang, Sung Gyun Kang, Jae-Yeon Jeong, Sun-Shin Cha, Hyun-Myung Oh, Jae-Hak Lee, Eun Chan Yang, Kae Kyoung Kwon, Yun Jae Kim, Tae Wan Kim, Wonduck Kim, Jeong Ho Jeon, Sang-Jin Kim, Dong Han Choi, Sungwoong Jho, Hak-Min Kim, Junsu Ko, Hyunmin Kim, Young-Ah Shin, Hyun-Ju Jung, Yuan Zheng, Zhuo Wang, Yan Chen, Ming Chen, Awei Jiang, Erli Li, Shu Zhang, Haolong Hou, Tae Hyung Kim, Lili Yu, Sha Liu, Kung Ahn, Jesse Cooper, Sin-Gi Park, Chang Pyo Hong, Wook Jin, Heui-Soo Kim, Chankyu Park, Kyooyeol Lee, Sung Chun, Phillip A Morin, Stephen J O'Brien, Hang Lee, Jumpei Kimura, Dae Yeon Moon, Andrea Manica, Jeremy Edwards, Byung Chul Kim, Sangsoo Kim, Jun Wang, Jong Bhak, Hyun Sook Lee, Jung-Hyun Lee. Minke whale genome and aquatic adaptation in cetaceans. Nature Genetics, 2013; DOI:http://dx.doi.org/10.1038/ng.2835
 
Saturnine Pariah said:
In a paper published in Nature Genetics, researchers from Korea Institute of Ocean Science and Technology, Korea Genome Research Foundation, BGI, and other institutes presented the first in-depth minke whale genome and their new findings on how whales successfully adapted to ocean environment. The data yielded in this study will contribute to future studies of marine mammal diseases, conservation and evolution.
Whales roam throughout all of the world's oceans, living in the water but breathing air like humans. At the top of the food chain, whales are vital to the health of the marine environment, whereas 7 out of the 13 great whale species are endangered or vulnerable. The minke whale is the most abundant baleen whale. Its wide distribution makes it an ideal candidate for whole reference genome sequencing.
In this study, researchers conducted de novo sequencing on a minke whale with 128x average depth of coverage, and re-sequenced three minke whales, a fin whale (Balaenoptera physalus), a bottlenose dolphin, and a finless porpoise (Neophocaena phocaenoides). The yielded data may help to improve scientists' understanding of the evolutionary changes adapted to ocean environment from whole genome level.
The adaptation of whale to ocean life was notably marked by resistance to physiological stresses caused by a lack of oxygen, increased reactive oxygen species, and high salt level. In this study, researchers investigated a number of whale-specific genes that were strongly associated with stress resistance, such as the peroxiredoxin (PRDX) family, O-linked N-acetylglucosaminylation (O-GlcNAcylation). The results revealed that the gene families associated with stress-responsive proteins and anaerobic metabolism were expanded.
Perhaps the most dramatic environmental adaptation for a whale is deep diving, which can induce hypoxia. Under the hypoxic conditions, the body might produce more reactive oxygen species (ROS), harmful compounds that can damage DNA. Glutathione is a well-known antioxidant that prevents damage to important cellular components by ROS. In this study, researchers provided evidence to support that there is an increased ratio of reduced glutathione/glutathione disulfide when suffering hypoxic or oxidative stress.
Minke whales and other Mysticeti whale species grow baleen instead of teeth. It's previously reported that the genes ENAM, MMP, and AMEL might play a role in tooth enamel formation and biomineralization. This study showed that these genes may be pseudogenes with early stop codons in the baleen whales. In addition, researchers found that the gene families related to whale's body hair and sensory receptors were contracted, such as Keratin-related gene families associated with hair formation, several Hox genes that play an important role in the body plan and embryonic development.
Xuanmin Guang, project manager from BGI, said, "Minke whale is the first marine mammal that has been sequenced with such high-depth genome coverage. The genome data not only can help us know much more about the adaption mechanisms underlying minke whale, but also provides invaluable resource for marine mammal's future studies such as diseases control and prevention, species conservation,and protection."
Story Source:
The above story is based on materials provided by BGI Shenzhen, via EurekAlert!, a service of AAAS.

Journal References:
Hyung-Soon Yim, Yun Sung Cho, Xuanmin Guang, Sung Gyun Kang, Jae-Yeon Jeong, Sun-Shin Cha, Hyun-Myung Oh, Jae-Hak Lee, Eun Chan Yang, Kae Kyoung Kwon, Yun Jae Kim, Tae Wan Kim, Wonduck Kim, Jeong Ho Jeon, Sang-Jin Kim, Dong Han Choi, Sungwoong Jho, Hak-Min Kim, Junsu Ko, Hyunmin Kim, Young-Ah Shin, Hyun-Ju Jung, Yuan Zheng, Zhuo Wang, Yan Chen, Ming Chen, Awei Jiang, Erli Li, Shu Zhang, Haolong Hou, Tae Hyung Kim, Lili Yu, Sha Liu, Kung Ahn, Jesse Cooper, Sin-Gi Park, Chang Pyo Hong, Wook Jin, Heui-Soo Kim, Chankyu Park, Kyooyeol Lee, Sung Chun, Phillip A Morin, Stephen J O'Brien, Hang Lee, Jumpei Kimura, Dae Yeon Moon, Andrea Manica, Jeremy Edwards, Byung Chul Kim, Sangsoo Kim, Jun Wang, Jong Bhak, Hyun Sook Lee, Jung-Hyun Lee. Minke whale genome and aquatic adaptation in cetaceans. Nature Genetics, 2013; DOI:http://dx.doi.org/10.1038/ng.2835
Click to expand...

Interesting. Does this DNA work shed any further light - or confirm any previous findings - on the kinship of whales to terrestrial mammals, such as hippos? I ask because it's a good one for dealing with creationists, as we all have to do from time to time.
 
exchemist said:
Interesting. Does this DNA work shed any further light - or confirm any previous findings - on the kinship of whales to terrestrial mammals, such as hippos? I ask because it's a good one for dealing with creationists, as we all have to do from time to time.
Click to expand...
It does add further evidence to the well observed transition of terrestrial to aquatic. Before genetic studies we relied on taxonomy and skeletal remains. Many creationist often cringe when new evidence is found for evolution, then again i wouldn't expect a creationist to be a good choice for discussing anything rational.
 
exchemist said:
Interesting. Does this DNA work shed any further light - or confirm any previous findings - on the kinship of whales to terrestrial mammals, such as hippos? I ask because it's a good one for dealing with creationists, as we all have to do from time to time.
Click to expand...
From what I've read, there's no controversy about the cetaceans evolving from primitive hippopotamuses. Presumably some of the adventurous hippos swam down the river all the way to the sea and liked what they found there, since mammals with our air-breathing lungs and warm-blooded circulation absolutely rule in aquatic environments, once they've adapted to the locomotion.

The latest update to the Wikipedia article not only continues the merging of Cetacea with Artiodactyla, but specifically with Hippopotamidae.
  • Superorder: Laurasiatheria
  • Order: Cetartiodactyla
  • Suborder: Tylopoda
  • Infraorder: Artiofabula
  • Superfamily: Cetruminantia
  • Family: Cetancodonta
  • 2 subfamilies: Hippopotamidae and Cetacea.
I may have the terminology for some of those classification levels wrong (such as infraorder vs. superfamily), but the rankings are right.
 
Fraggle Rocker said:
From what I've read, there's no controversy about the cetaceans evolving from primitive hippopotamuses. Presumably some of the adventurous hippos swam down the river all the way to the sea and liked what they found there, since mammals with our air-breathing lungs and warm-blooded circulation absolutely rule in aquatic environments, once they've adapted to the locomotion.

The latest update to the Wikipedia article not only continues the merging of Cetacea with Artiodactyla, but specifically with Hippopotamidae.
  • Superorder: Laurasiatheria
  • Order: Cetartiodactyla
  • Suborder: Tylopoda
  • Infraorder: Artiofabula
  • Superfamily: Cetruminantia
  • Family: Cetancodonta
  • 2 subfamilies: Hippopotamidae and Cetacea.
I may have the terminology for some of those classification levels wrong (such as infraorder vs. superfamily), but the rankings are right.
Click to expand...

Thanks for this. It all looks a pretty rock-solid attribution. But I see the divergence was 50m years ago, back in the Eocene, apparently before any aquatic adaptations had occurred, which is curious in view of what happened to both branches subsequently.
 
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