Phylogeography of walnut pest Atrijuglans hetaohei (Lepidoptera: Gelechioidea) reveals comprehensive influence of geographic barriers and human activities

Qiqi Wang,Shaheen Tayyab,Rong Li,Guanghui Tang 한국응용곤충학회 2022 Journal of Asia-Pacific Entomology Vol.25 No.3

Phylogeographic patterns of some extant species have been well documented; however, the evolutionary patterns of plant pests were poorly understood. This study investigated the evolutionary patterns and historical demog raphy of Atrijuglans hetaohei using mitochondrial DNA (cox1 and cox2) and nuclear EF-1α. Networks and other statistical analyses concordantly revealed four genetic lineages (L1-L4), indicating varying influences of moun tains and rivers. Two shared ancestral haplotypes and strong gene flow in refugia (Mt. Qinling and Daba Shan) indicated that the evolutionary patterns of A. hetaohei coincided with its plant hosts, and A. hetaohei experienced long-term vicariance and secondary contact in these areas. The demographic analysis (EBSP) clearly showed that A. hetaohei underwent two sustained population expansions 4000 years ago, and its population size was affected by the size and quality of its plant hosts resulting from human agricultural activities. All the evidence suggests that physical barriers (mountains and rivers) and human agricultural activities have affected this insect’s pop ulation structure and distribution to varying degrees. Together, our study contributes to a growing understanding of the origin and population structure of A. hetaohei and provides an important framework for exploring the evolution patterns of the pest and its hosts.

Phylogeography of the economic seaweeds Chondrus (Gigartinales, Rhodophyta) in the northwest Pacific based on rbcL and COI-5P genes

Yang, Mi Yeon,Kim, Myung Sook The Korean Society of Phycology 2022 ALGAE Vol.37 No.2

The red algal genus Chondrus have long been used as raw materials for carrageenan and dietary fiber in health foods. Despite the importance of genetic information in safeguarding natural seaweed resources, knowledge of the population genetics of Chondrus in the northwest Pacific is limited. In this study, genetic diversity and phylogeographic structure of 45 populations (777 specimens) of Chondrus from Korea, China, and Japan were evaluated based on mitochondrial COI-5P gene sequences, and phylogenetic relationships were confirmed based on plastid rbcL gene sequences. Molecular analyses assigned the specimens in this study to three Chondrus species: C. nipponicus, C. ocellatus, and C. giganteus; phenotype-based species classification was impossible owing to their high morphological plasticity. We found moderate intraspecific genetic diversity and a shallow phylogeographic structure in both for C. nipponicus and C. ocellatus, and low intraspecific genetic diversity in C. giganteus. Each of the three species exhibited high-level intraspecific gene flow among regions based on the most common haplotypes (CN1 for C. nipponicus, CO1 for C. ocellatus, and CG1 for C. giganteus). Our comprehensive genetic information provides insights into the phylogeographic patterns and intraspecific diversity of the economically important Chondrus species. It also highlights the need to conserve existing natural Chondrus resources through continuous monitoring of genetic diversity and phylogeographic pattern.

Phylogeography and Population Genetic Structure of Amur Grayling Thymallus grubii in the Amur Basin

Ma, Bo,Lui, Tingting,Zhang, Ying,Chen, Jinping Asian Australasian Association of Animal Productio 2012 Animal Bioscience Vol.25 No.7

Amur grayling, Thymallus grubii, is an important economic cold freshwater fish originally found in the Amur basin. Currently, suffering from loss of habitat and shrinking population size, T. grubii is restricted to the mountain river branches of the Amur basin. In order to assess the genetic diversity, population genetic structure and infer the evolutionary history within the species, we analysised the whole mitochondrial DNA control region (CR) of 95 individuals from 10 rivers in China, as well as 12 individuals from Ingoda/Onon and Bureya River throughout its distribution area. A total of 64 variable sites were observed and 45 haplotypes were identified excluding sites with gaps/missing data. Phylogenetic analysis was able to confidently predict two subclade topologies well supported by maximum-parsimony and Bayesian methods. However, basal branching patterns cannot be unambiguously estimated. Haplotypes from the mitochondrial clades displayed local homogeneity, implying a strong population structure within T. grubii. Analysis of molecular variance detected significant differences among the different geographical rivers, suggesting that T. grubii in each river should be managed and conserved separately.

Phylogeography of the Korean endemic Coreoleuciscus (Cypriniformes: Gobionidae): the genetic evidence of colonization through Eurasian continent to the Korean Peninsula during Late Plio-Pleistocene

Jeon Hyung-Bae,Song Ha Youn,Suk Ho Young,Bang In-Chul 한국유전학회 2022 Genes & Genomics Vol.44 No.6

Background: Freshwater endemism is thought to have been formed through the vicariance of connected water systems or the process by which ancestral populations colonized specific areas. The Korean Peninsula is well recognized for its high level of freshwater endemism with about 40% of freshwater fish species being endemic. Objective: In this study, we attempted to reconstruct the process of speciation and phylogenetic dispersal of Coreoleuciscus species, which is endemic in the Korean Peninsula. Methods: We used fossil-calibrated divergence time estimation and ancestral distributional reconstruction to infer phylogeographic reconstruction of Coreoleuciscus based on mitochondrial cytochrome c oxidate subunit I (COI) sequences (1551 bp). Results: Our phylogeographic analysis based on a total of 626 individuals revealed that the two Coreoleuciscus species have originated from the independent colonization of different lineages in the ancestral populations, probably during the Late Plio-Pleistocene. The full-scale expansion of Coreoleuciscus populations appears to have taken place after major river structures were completed on the Korean Peninsula. We also provided evidence that the common ancestors of Coreoleuciscus was distributed in Eastern Eurasian continent and subsequently dispersed into the tip of East Asia. High genetic diversity was mainly concentrated in large drainage populations, while small populations showed an monomorphism, which could give important implications for planning the conservation and management of Coreoleuciscus. Conclusions: The phylogenetic background of the rheophilic Coreoleuciscus species can be explained by the colonizer hypothesis that the endemic freshwater fish originated from the common ancestor in continental region.

Phylogeography of Wolbachia and Its Lytic Phage Shows Incongruent Infection history in Vollenhovia emeryi (Hymenoptera: Myrmicinae)

Soyeon Park,Pureum Noh,Jae Chun Choe,Gilsang Jeong 한국응용곤충학회 2014 한국응용곤충학회 학술대회논문집 Vol.2014 No.04

The phylogenetic analysis the queen polymorphic Vollenhovia emeryi ant reveals derivation of the Wolbachia- free short-winged from the Wolbachia-infected long-winged. However, intriguingly, some Japanese short-winged colonies harbor Wolbachia. Wolbachia specific bacteriophage (WO) is also detected in more than half of the infected colonies with no clear distribution pattern across the host insect lineage. We hypothesized that 1) the infected Japanese short-winged is in the intermediate stage to complete loss of Wolbachia and 2) the phage invaded the host after the host insect diverged. To test the hypotheses, we studied the strain diversity using the multi-locus sequence typing (MLST) of five ant colonies; three longwinged colonies from Korea and one long-winged colony and one short-winged colony from Japan. Both Korean and Japanese V. emeryi colonies show unexpectedly high level of Wolbachia strain diversity. However, the diversity is not significantly different between the long-winged and the short-winged against our first hypothesis. Phylogenies of Wolbachia show Korean strains and Japanese strains are largely monophyletic indicating prior infection before the host divergence. The strain diversity of the phage is also surprisingly high. Phylogenies of orf2 and orf7 genes are incongruent to that of Wolbachia and geographically distinct. This indicates that the phage is spatially static and the current infection pattern may be the consequence of local repeated gain and loss of the phage.

Phylogeography of the current rabies viruses in Indonesia

I Nyoman Dibia,Bambang Sumiarto,Heru Susetya,Anak Agung Gde Putra,Helen Scott-Orr,Gusti Ngurah Mahardika 대한수의학회 2015 Journal of Veterinary Science Vol.16 No.4

Rabies is a major fatal zoonotic disease in Indonesia. This study was conducted to determine the recent dynamics of rabies virus (RABV) in various areas and animal species throughout Indonesia. A total of 27 brain samples collected from rabid animals of various species in Bali, Sumatra, Kalimantan, Sulawesi, Java, and Flores in 2008 to 2010 were investigated. The cDNA of the nucleoprotein gene from each sample was generated and amplified by one-step reverse transcription-PCR, after which the products were sequenced and analyzed. The symmetric substitution model of a Bayesian stochastic search variable selection extension of the discrete phylogeographic model of the social network was applied in BEAST ver. 1.7.5 software. The spatial dispersal was visualized in Cartographica using Spatial Phylogenetic Reconstruction of Evolutionary Dynamics. We demonstrated inter-island introduction and reintroduction, and dog was found to be the only source of infection of other animals. Ancestors of Indonesian RABVs originated in Java and its descendants were transmitted to Kalimantan, then further to Sumatra, Flores, and Bali. The Flores descendent was subsequently transmitted to Sulawesi and back to Kalimantan. The viruses found in various animal species were transmitted by the dog.

Phylogeography of Gloiopeltis furcata sensu lato (Gigartinales, Rhodophyta) provides the evidence of glacial refugia in Korea and Japan

Yang, Mi Yeon,Fujita, Daisuke,Kim, Myung Sook The Korean Society of Phycology 2021 ALGAE Vol.36 No.1

The present-day genetic structure of macroalgal species reflects both geographical history and oceanic circulation patterns as well as anthropogenic introduction across native ranges. To precisely understand the genetic diversity and how the factors shape the current population structure of Gloiopeltis furcata sensu lato, we determined the mitochondrial 5' end of cytochrome c oxidase subunit I (COI-5P) sequences for 677 individuals sampled from 67 sites spanning almost the entire distribution range in Korea and Japan. Results from the phylogenetic analysis and haplotype distribution revealed eleven distinct lineages within G. furcata s.l. along the Korea-Japan coastal areas and displayed divergent phylogeographic patterns among lineages. Despite the closely related lineages distributed in same habitats as high rocky intertidal zone, they display different phylogeographic patterns among lineages. The populations from the south of Korea-Japan harbored the highest genetic diversity and unique endemism in comparison with other populations in the distribution range. This could be the evidence of southern refugia for G. furcata s.l. in the Northwest (NW) Pacific and the recent migration from native to introduced region. The reason is that an exceptional distribution pattern was found high genetic diversity in Hakodate of Japan where is the northern location in the NW Pacific. Our results imply the contemporary influence on the distribution due to current circulation pattern and anthropogenic effects. These phylogeographic findings provide the important insight into cryptic species diversity and the detailed distribution pattern of Gloiopeltis in the NW Pacific.

Comparative Phylogeography of the Wood-Feeding Cockroach Cryptocercus spp. and Their Intracellular Endosymbionts: a Coevolutionary Approach to Historical Split Hypotheses of Asian and American Cryptocercus Lineages

Yung C. Park,Kiyoto Maekawa,Nathan Lo,Joo P. Kim,Won Kim,Jae C. Choe 한국응용곤충학회 2005 한국응용곤충학회 학술대회논문집 Vol.2005 No.05

East Asian Phylogeography of Diostracus (Diptera: Dolichopodidae), a Torrenticolous Genus ofLong-legged Flies

K. Masunaga,T. Saigusa 한국응용곤충학회 2005 한국응용곤충학회 학술대회논문집 Vol.2005 No.05

Intraspecific Molecular Phylogeny, Genetic Variation and Phylogeography of Reticulitermes speratus (Isoptera: Rhinotermitidae)

박영철,Osamu Kitade,Michael Schwarz,Joo Pil Kim,김원 한국분자세포생물학회 2006 Molecules and cells Vol.21 No.1

Population structure was investigated in Reticulitermes speratus populations in the Korean Peninsula and the Japanese Archipelago. All trees derived from analyses of the combined sequence dataset of two mitochondrial genes, COII and COIII, showed that R. speratus populations cluster into two major clades comprising the Korean/southern Japanese populations and the northern Japanese populations. Analysis of population genetic structure showed strong genetic partitioning between populations of the two clades. To understand historical migration routes and current distributions, the phylogeographic history of R. speratus was inferred from intra-/interspecific phylogeny and divergence times estimated between the clades of the phylogenetic tree. The estimated migration route and divergence time of ancestral R. speratus are congruent with recent paleogeographic hypotheses involving land-bridge connections between the Asian continent and the Japanese Archipelago. We suggest that ancestral R. speratus separated into northern and southern Japanese populations after its migration into the Japanese main islands from East China during the early Pleistocene via the East China Sea basin, which may have been exposed during that period. The Korean populations seem to have diverged recently from southern Japanese populations; this may explain the current distribution of R. speratus in the Japanese Arachipelago, and account for why it is restricted to northern areas of the Tokara Strait.