Archipelago colonization by ecologically dissimilar amphibians: Evaluating the expectation of common evolutionary history of geographical diffusion in co-distributed rainforest tree frogs in islands of Southeast Asia

Phylogeny is a statistical approach displaying the evolutionary history of a genetically related group of organisms with the fundamental prerequisite of the utilization of a significant sample size that could represent the whole population under investigation. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) phylogeny analyses are based on a single isolate of BatCoVs, which is not a sufficient representation of genetically related CoVs. For instance, the unique Bat-CoV RaTG13 sequence that is genetically associated with SARS-CoV-2 was isolated from Yunnan, China, in 2013. To date, no other RaTG13 sequence has been obtained in a different time (temporal), place (spatial), or other host condition. Data scarcity of Bat-CoVs sequences raises concern on the several fundamental experimental and biostatistical aspects, e.g. repeatability of the sequences and intraspecies variation of critical genes, such as the receptor-binding domain of Spike protein. Sunda pangolin has been proposed as the intermediate host and source of SARS-CoV-2, but no Pangolin-CoV isolates have been isolated in Southeast Asia, where Sunda pangolins inhabit. Most Pangolin-CoVs were isolated from deceased pangolins, that were captured during illegal animal trafficking into China, hence raising questions about the reliability and quality of such isolates. Pangolin-CoV sampling problems are also evident in the deposited sequences that are of sub-standard quality. Therefore, there is urgent need for survey the Bat-CoVs and possible intermediate hosts, such as pangolins and civets in Southeast Asia. These surveys are required to investigate the genomic source of SARS-CoV-2 and assess possible future risks for new outbreaks. The current SARS-CoV-2 phylogeny with unacceptably limited numbers of Bat-CoVs and Pangolin-CoVs sequences not sufficient and technically not appropriate for reliable phylogenic analysis.

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Out of Asia: Mitochondrial evolutionary history of the globally introduced supralittoral isopod Ligia exotica

10.7287/peerj.preprints.3497v1 ◽

2017 ◽

Author(s):

Luis A Hurtado ◽

Mariana Mateos ◽

Chang Wang ◽

Carlos A Santamaria ◽

Jongwoo Jung ◽

...

Keyword(s):

Southeast Asia ◽

16S Rdna ◽

Evolutionary History ◽

Phylogenetic Analyses ◽

Marine Species ◽

Genetic Lineages ◽

East And Southeast Asia ◽

History Of ◽

Marine Vessels ◽

Establishment Process

The native ranges and invasion histories of many marine species remain elusive due to a dynamic dispersal process via marine vessels. Molecular markers can aid in identification of native ranges and elucidation of the introduction and establishment process. The supralittoral isopod Ligia exotica has a wide tropical and subtropical distribution, frequently found in harbors and ports around the globe. This isopod is hypothesized to have an Old World origin, from where it was unintentionally introduced to other regions via wooden ships and solid ballast. Its native range, however, remains uncertain. Recent molecular studies uncovered the presence of two highly divergent lineages of L. exotica in East Asia, and suggest this region is a source of nonindigenous populations. In this study, we conducted phylogenetic analyses (Maximum Likelihood and Bayesian) of a fragment of the mitochondrial 16S ribosomal (r)DNA gene using a dataset of this isopod that greatly expanded previous representation from Asia and putative nonindigenous populations around the world. For a subset of samples, sequences of 12S rDNA and NaK were also obtained and analyzed together with 16S rDNA. Our results show that L. exotica is comprised of several highly divergent genetic lineages, which probably represent different species. Most of the 16S rDNA genetic diversity (48 haplotypes) was detected in East and Southeast Asia. Only seven haplotypes were observed outside this region (in the Americas, Hawai’i, Africa and India), which were identical or closely related to haplotypes found in East and Southeast Asia. Phylogenetic patterns indicate the L. exotica clade originated and diversified in East and Southeast Asia, and only members of one of the divergent lineages have spread out of this region, recently, suggesting the potential to become invasive is phylogenetically constrained.

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A traditional evolutionary history of foot-and-mouth disease viruses in Southeast Asia challenged by analyses of non-structural protein coding sequences

Scientific Reports ◽

10.1038/s41598-018-24870-6 ◽

2018 ◽

Vol 8 (1) ◽

Cited By ~ 13

Author(s):

Barbara Brito ◽

Steven J. Pauszek ◽

Ethan J. Hartwig ◽

George R. Smoliga ◽

Le T. Vu ◽

...

Keyword(s):

Southeast Asia ◽

Evolutionary History ◽

Foot And Mouth Disease ◽

Mouth Disease ◽

Structural Protein ◽

Protein Coding ◽

Coding Sequences ◽

Foot And Mouth ◽

History Of

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Late PlioceneSemnopithecusfossils from central Myanmar: rethinking of the evolutionary history of cercopithecid monkeys in Southeast Asia

Historical Biology ◽

10.1080/08912963.2015.1018018 ◽

2015 ◽

Vol 28 (1-2) ◽

pp. 172-188 ◽

Cited By ~ 3

Author(s):

Masanaru Takai ◽

Yuichiro Nishioka ◽

Thaung-Htike ◽

Maung Maung ◽

Kyaw Khaing ◽

...

Keyword(s):

Southeast Asia ◽

Evolutionary History ◽

History Of

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An integrative phylogenomic approach illuminates the evolutionary history of Old World tree frogs (Anura: Rhacophoridae)

Molecular Phylogenetics and Evolution ◽

10.1016/j.ympev.2019.106724 ◽

2020 ◽

Vol 145 ◽

pp. 106724 ◽

Cited By ~ 2

Author(s):

Jin-Min Chen ◽

Elizabeth Prendini ◽

Yun-He Wu ◽

Bao-Lin Zhang ◽

Chatmongkon Suwannapoom ◽

...

Keyword(s):

Evolutionary History ◽

Old World ◽

History Of ◽

Tree Frogs

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Evolutionary histories and antimicrobial resistance in Shigella flexneri and Shigella sonnei in Southeast Asia

Communications Biology ◽

10.1038/s42003-021-01905-9 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Hao Chung The ◽

Ladaporn Bodhidatta ◽

Duy Thanh Pham ◽

Carl J. Mason ◽

Tuyen Ha Thanh ◽

...

Keyword(s):

Southeast Asia ◽

Disease Surveillance ◽

Evolutionary History ◽

Shigella Flexneri ◽

Asian Countries ◽

Genome Sequences ◽

Evolutionary Trajectory ◽

History Of ◽

Susceptibility Patterns ◽

Clonal Replacement

AbstractConventional disease surveillance for shigellosis in developing country settings relies on serotyping and low-resolution molecular typing, which fails to contextualise the evolutionary history of the genus. Here, we interrogated a collection of 1,804 Shigella whole genome sequences from organisms isolated in four continental Southeast Asian countries (Thailand, Vietnam, Laos, and Cambodia) over three decades to characterise the evolution of both S. flexneri and S. sonnei. We show that S. sonnei and each major S. flexneri serotype are comprised of genetically diverse populations, the majority of which were likely introduced into Southeast Asia in the 1970s–1990s. Intranational and regional dissemination allowed widespread propagation of both species across the region. Our data indicate that the epidemiology of S. sonnei and the major S. flexneri serotypes were characterised by frequent clonal replacement events, coinciding with changing susceptibility patterns against contemporaneous antimicrobials. We conclude that adaptation to antimicrobial pressure was pivotal to the recent evolutionary trajectory of Shigella in Southeast Asia.

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Out of Asia: mitochondrial evolutionary history of the globally introduced supralittoral isopodLigia exotica

PeerJ ◽

10.7717/peerj.4337 ◽

2018 ◽

Vol 6 ◽

pp. e4337 ◽

Cited By ~ 3

Author(s):

Luis A. Hurtado ◽

Mariana Mateos ◽

Chang Wang ◽

Carlos A. Santamaria ◽

Jongwoo Jung ◽

...

Keyword(s):

Southeast Asia ◽

16S Rdna ◽

Evolutionary History ◽

Phylogenetic Analyses ◽

Marine Species ◽

Genetic Lineages ◽

East And Southeast Asia ◽

History Of ◽

Marine Vessels ◽

Establishment Process

The native ranges and invasion histories of many marine species remain elusive due to a dynamic dispersal process via marine vessels. Molecular markers can aid in identification of native ranges and elucidation of the introduction and establishment process. The supralittoral isopodLigia exoticahas a wide tropical and subtropical distribution, frequently found in harbors and ports around the globe. This isopod is hypothesized to have an Old World origin, from where it was unintentionally introduced to other regions via wooden ships and solid ballast. Its native range, however, remains uncertain. Recent molecular studies uncovered the presence of two highly divergent lineages ofL. exoticain East Asia, and suggest this region is a source of nonindigenous populations. In this study, we conducted phylogenetic analyses (Maximum Likelihood and Bayesian) of a fragment of the mitochondrial 16S ribosomal (r)DNA gene using a dataset of this isopod that greatly expanded previous representation from Asia and putative nonindigenous populations around the world. For a subset of samples, sequences of 12S rDNA and NaK were also obtained and analyzed together with 16S rDNA. Our results show thatL. exoticais comprised of several highly divergent genetic lineages, which probably represent different species. Most of the 16S rDNA genetic diversity (48 haplotypes) was detected in East and Southeast Asia. Only seven haplotypes were observed outside this region (in the Americas, Hawai’i, Africa and India), which were identical or closely related to haplotypes found in East and Southeast Asia. Phylogenetic patterns indicate theL. exoticaclade originated and diversified in East and Southeast Asia, and only members of one of the divergent lineages have spread out of this region, recently, suggesting the potential to become invasive is phylogenetically constrained.

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