Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks

Farré,, Marta,Kim, Jaebum,Proskuryakova, Anastasia A.,Zhang, Yang,Kulemzina, Anastasia I.,Li, Qiye,Zhou, Yang,Xiong, Yingqi,Johnson, Jennifer L.,Perelman, Polina L.,Johnson, Warren E.,Warren, We Cold Spring Harbor Laboratory Press 2019 Genome research Vol.29 No.4

<P>The role of chromosome rearrangements in driving evolution has been a long-standing question of evolutionary biology. Here we focused on ruminants as a model to assess how rearrangements may have contributed to the evolution of gene regulation. Using reconstructed ancestral karyotypes of Cetartiodactyls, Ruminants, Pecorans, and Bovids, we traced patterns of gross chromosome changes. We found that the lineage leading to the ruminant ancestor after the split from other cetartiodactyls was characterized by mostly intrachromosomal changes, whereas the lineage leading to the pecoran ancestor (including all livestock ruminants) included multiple interchromosomal changes. We observed that the liver cell putative enhancers in the ruminant evolutionary breakpoint regions are highly enriched for DNA sequences under selective constraint acting on lineage-specific transposable elements (TEs) and a set of 25 specific transcription factor (TF) binding motifs associated with recently active TEs. Coupled with gene expression data, we found that genes near ruminant breakpoint regions exhibit more divergent expression profiles among species, particularly in cattle, which is consistent with the phylogenetic origin of these breakpoint regions. This divergence was significantly greater in genes with enhancers that contain at least one of the 25 specific TF binding motifs and located near bovidae-to-cattle lineage breakpoint regions. Taken together, by combining ancestral karyotype reconstructions with analysis of <I>cis</I> regulatory element and gene expression evolution, our work demonstrated that lineage-specific regulatory elements colocalized with gross chromosome rearrangements may have provided valuable functional modifications that helped to shape ruminant evolution.</P>

Subspecific Status of the Korean Tiger Inferred by Ancient DNA Analysis

Mu-Yeong Lee,Jee Yun Hyun,Seo-Jin Lee,Junghwa An,Eunok Lee,Mi-Sook Min,Junpei Kimura,Shin-ichiro Kawada,Nozomi Kurihara,Shu-Jin Luo,Stephen J. O’Brien,Warren E. Johnson,Hang Lee 한국동물분류학회 2012 Animal Systematics, Evolution and Diversity Vol.28 No.1

The tiger population that once inhabited the Korean peninsula was initially considered a unique subspecies (Panthera tigris coreensis), distinct from the Amur tiger of the Russian Far East (P. t. altaica). However, in the following decades, the population of P. t. coreensis was classified as P. t. altaica and hence forth the two populations have been considered the same subspecies. From an ecological point of view, the classification of the Korean tiger population as P. t. altaica is a plausible conclusion. Historically, there were no major dispersal barriers between the Korean peninsula and the habitat of Amur tigers in Far Eastern Russia and northeastern China that might prevent gene flow, especially for a large carnivore with long-distance dispersal abilities. However, there has yet to be a genetic study to confirm the subspecific status of the Korean tiger. Bone samples from four tigers originally caught in the Korean peninsula were collected from two museums in Japan and the United States. Eight mitochondrial gene fragments were sequenced and compared to previously published tiger subspecies’ mtDNA sequences to assess the phylogenetic relationship of the Korean tiger. Three individuals shared an identical haplotype with the Amur tigers. One specimen grouped with Malayan tigers, perhaps due to misidentification or mislabeling of the sample. Our results support the conclusion that the Korean tiger should be classified as P. t. altaica, which has important implications for the conservation and reintroduction of Korean tigers.

Genetic diversity and population structure of the Black-faced Spoonbill (<i>Platalea minor</i>) among its breeding sites in South Korea: Implication for conservation

Lee, Mu-Yeong,Kwon, In-Ki,Lee, Kisup,Choi, Sung Kyoung,Jeon, Hey Sook,Lee, Ji-Yeon,Eo, Kyung-yeon,Kim, Hwa-Jung,Kim, Jin-Han,Johnson, Warren E.,Yoo, Jeong-Chil,An, Junghwa Elsevier 2017 Biochemical systematics and ecology Vol.71 No.-

<P><B>Abstract</B></P> <P>The endangered Black-faced Spoonbill <I>Platalea minor</I> has experienced drastic reductions in population size, geographic distribution, and habitat availability throughout East Asia. In the present study, we examined population genetic structure and genetic diversity of Black-faced Spoonbills inhabiting five sites off the west coast of South Korea encompassing a few of its major breeding sites. Ten microsatellite loci and the mitochondrial sequence were used to assess patterns of genetic variation based on 63 individuals. Three ND2 haplotypes were found among 61 individuals; the remaining two were identified as Eurasian Spoonbills, revealing an unexpected hybridization between these two species having different ecological niches in South Korea—the Eurasian Spoonbill overwinters in inland areas, whereas the Black-faced Spoonbill inhabits coastal areas during the summer. Analyses of microsatellite variation revealed no discrete population structure among the five breeding sites but very weak genetic differentiation among geographically distant regions. Assignment tests identified several possible migrants among sites. Our findings suggested that Black-faced Spoonbills from the five breeding sites could be managed as a single population and highlighted the importance of conserving the populations from Maedo, Suhaam, and Namdong reservoir, which are geographically close and have retained high levels of genetic diversity and large populations.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Ten polymorphic microsatellite loci and the mitochondrial DNA sequence were used to assess genetic diversity and structure. </LI> <LI> No discrete population structure among the five breeding sites in South Korea but very weak genetic differentiation among geographically distant regions. </LI> <LI> Black-faced Spoonbill individuals from the five breeding sites could be managed as a single population in South Korea. </LI> <LI> Unexpected hybridization between the Eurasian Spoonbill and the Black-faced Spoonbill was observed in our genetic studies. </LI> </UL> </P>

Subspecific Status of the Korean Tiger Inferred by Ancient DNA Analysis

Lee, Mu-Yeong,Hyun, Jee-Yun,Lee, Seo-Jin,An, Jung-Hwa,Lee, Eun-Ok,Min, Mi-Sook,Kimura, Junpei,Kawada, Shin-Ichiro,Kurihara, Nozomi,Luo, Shu-Jin,O'Brien, Stephen J.,Johnson, Warren E.,Lee, Hang The Korean Society of Systematic Zoology 2012 Animal Systematics, Evolution and Diversity Vol.28 No.1

The tiger population that once inhabited the Korean peninsula was initially considered a unique subspecies (Panthera tigris coreensis), distinct from the Amur tiger of the Russian Far East (P. t. altaica). However, in the following decades, the population of P. t. coreensis was classified as P. t. altaica and hence forth the two populations have been considered the same subspecies. From an ecological point of view, the classification of the Korean tiger population as P. t. altaica is a plausible conclusion. Historically, there were no major dispersal barriers between the Korean peninsula and the habitat of Amur tigers in Far Eastern Russia and northeastern China that might prevent gene flow, especially for a large carnivore with long-distance dispersal abilities. However, there has yet to be a genetic study to confirm the subspecific status of the Korean tiger. Bone samples from four tigers originally caught in the Korean peninsula were collected from two museums in Japan and the United States. Eight mitochondrial gene fragments were sequenced and compared to previously published tiger subspecies' mtDNA sequences to assess the phylogenetic relationship of the Korean tiger. Three individuals shared an identical haplotype with the Amur tigers. One specimen grouped with Malayan tigers, perhaps due to misidentification or mislabeling of the sample. Our results support the conclusion that the Korean tiger should be classified as P. t. altaica, which has important implications for the conservation and reintroduction of Korean tigers.