Region-Specific Genetic Diversity of Black Rats (Rattus rattus Complex) in Southeast and East Asia Shaped by Rapid Population Expansion Events
Among the six mitochondrial DNA lineages of the black rat (Rattus rattus Complex; RrC), lineages II and IV are widespread in Southeast and East Asia. This study explored their demographic history using 17 new sequences from the Miyako Islands in the Ryukyu archipelago, together with 178 publicly ava...
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ftbioone:10.2108/zs230065 2024-05-12T08:10:21+00:00 Region-Specific Genetic Diversity of Black Rats (Rattus rattus Complex) in Southeast and East Asia Shaped by Rapid Population Expansion Events Hajime Kai Nobuhiro Takada Vicki Thomson Hitoshi Suzuki Hajime Kai Nobuhiro Takada Vicki Thomson Hitoshi Suzuki world 2024-04-08 text/HTML https://doi.org/10.2108/zs230065 en eng Zoological Society of Japan doi:10.2108/zs230065 All rights reserved. https://doi.org/10.2108/zs230065 Black Rats prehistoric farmer rapid population expansion time dependent evolutionary rate Text 2024 ftbioone https://doi.org/10.2108/zs230065 2024-04-16T01:59:13Z Among the six mitochondrial DNA lineages of the black rat (Rattus rattus Complex; RrC), lineages II and IV are widespread in Southeast and East Asia. This study explored their demographic history using 17 new sequences from the Miyako Islands in the Ryukyu archipelago, together with 178 publicly available cytochrome b sequences. We defined six and two haplotype groups showing rapid population expansion signals in Lineages II and IV, respectively. The six haplotype groups of Lineage II were represented by haplotypes from 1) Myanmar/Bangladesh/Northeast India, 2) Laos, 3) Thailand, 4) Indonesia/Philippines, 5) Vietnam/southern China, and 6) the Ryukyu archipelago. These expansion times were estimated using time-dependent evolutionary rates to be 115,300 years ago (ya), 128,500 ya, 9600 ya, 10,600 ya, 7200 ya, and 1400 ya, respectively, although all had large confidence intervals. The two groups of Lineage IV were recovered from the mainland and islands of Southeast Asia with predicted expansion times of 197,000 ya and 5800 ya, respectively. These results suggest that climatic fluctuations during the last 200,000 years of the Quaternary, affected the population dynamics in subtropical areas at different times. Furthermore, the results of the younger rapid expansion events of RrC suggest the possibility of agricultural advancement and dispersal of Neolithic farmers to different areas within the mainland and islands of Southeast Asia during the Holocene. A subset of rats from the Miyako Islands were found to have the same lineage IV haplotypes as those in Southeast Asia, suggesting a recent introduction of these new lineages. Text Rattus rattus BioOne Online Journals Zoological Science 41 3 |
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English |
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Black Rats prehistoric farmer rapid population expansion time dependent evolutionary rate |
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Black Rats prehistoric farmer rapid population expansion time dependent evolutionary rate Hajime Kai Nobuhiro Takada Vicki Thomson Hitoshi Suzuki Region-Specific Genetic Diversity of Black Rats (Rattus rattus Complex) in Southeast and East Asia Shaped by Rapid Population Expansion Events |
topic_facet |
Black Rats prehistoric farmer rapid population expansion time dependent evolutionary rate |
description |
Among the six mitochondrial DNA lineages of the black rat (Rattus rattus Complex; RrC), lineages II and IV are widespread in Southeast and East Asia. This study explored their demographic history using 17 new sequences from the Miyako Islands in the Ryukyu archipelago, together with 178 publicly available cytochrome b sequences. We defined six and two haplotype groups showing rapid population expansion signals in Lineages II and IV, respectively. The six haplotype groups of Lineage II were represented by haplotypes from 1) Myanmar/Bangladesh/Northeast India, 2) Laos, 3) Thailand, 4) Indonesia/Philippines, 5) Vietnam/southern China, and 6) the Ryukyu archipelago. These expansion times were estimated using time-dependent evolutionary rates to be 115,300 years ago (ya), 128,500 ya, 9600 ya, 10,600 ya, 7200 ya, and 1400 ya, respectively, although all had large confidence intervals. The two groups of Lineage IV were recovered from the mainland and islands of Southeast Asia with predicted expansion times of 197,000 ya and 5800 ya, respectively. These results suggest that climatic fluctuations during the last 200,000 years of the Quaternary, affected the population dynamics in subtropical areas at different times. Furthermore, the results of the younger rapid expansion events of RrC suggest the possibility of agricultural advancement and dispersal of Neolithic farmers to different areas within the mainland and islands of Southeast Asia during the Holocene. A subset of rats from the Miyako Islands were found to have the same lineage IV haplotypes as those in Southeast Asia, suggesting a recent introduction of these new lineages. |
author2 |
Hajime Kai Nobuhiro Takada Vicki Thomson Hitoshi Suzuki |
format |
Text |
author |
Hajime Kai Nobuhiro Takada Vicki Thomson Hitoshi Suzuki |
author_facet |
Hajime Kai Nobuhiro Takada Vicki Thomson Hitoshi Suzuki |
author_sort |
Hajime Kai |
title |
Region-Specific Genetic Diversity of Black Rats (Rattus rattus Complex) in Southeast and East Asia Shaped by Rapid Population Expansion Events |
title_short |
Region-Specific Genetic Diversity of Black Rats (Rattus rattus Complex) in Southeast and East Asia Shaped by Rapid Population Expansion Events |
title_full |
Region-Specific Genetic Diversity of Black Rats (Rattus rattus Complex) in Southeast and East Asia Shaped by Rapid Population Expansion Events |
title_fullStr |
Region-Specific Genetic Diversity of Black Rats (Rattus rattus Complex) in Southeast and East Asia Shaped by Rapid Population Expansion Events |
title_full_unstemmed |
Region-Specific Genetic Diversity of Black Rats (Rattus rattus Complex) in Southeast and East Asia Shaped by Rapid Population Expansion Events |
title_sort |
region-specific genetic diversity of black rats (rattus rattus complex) in southeast and east asia shaped by rapid population expansion events |
publisher |
Zoological Society of Japan |
publishDate |
2024 |
url |
https://doi.org/10.2108/zs230065 |
op_coverage |
world |
genre |
Rattus rattus |
genre_facet |
Rattus rattus |
op_source |
https://doi.org/10.2108/zs230065 |
op_relation |
doi:10.2108/zs230065 |
op_rights |
All rights reserved. |
op_doi |
https://doi.org/10.2108/zs230065 |
container_title |
Zoological Science |
container_volume |
41 |
container_issue |
3 |
_version_ |
1798853791236227072 |