Radiation history of Asian Asarum (sect. Heterotropa, Aristolochiaceae) resolved using a phylogenomic approach based on double-digested RAD-seq data

Abstract Background and Aims The genus Asarum sect. Heterotropa (Aristolochiaceae) probably experienced rapid diversification into 62 species centred on the Japanese Archipelago and Taiwan, providing an ideal model for studying island adaptive radiation. However, resolving the phylogeny of this plant group using Sanger sequencing-based approaches has been challenging. To uncover the radiation history of Heterotropa, we employed a phylogenomic approach using double-digested RAD-seq (ddRAD-seq) to yield a sufficient number of phylogenetic signals and compared its utility with that of the Sanger sequencing-based approach. Methods We first compared the performance of phylogenetic analysis based on the plastid matK and trnL–F regions and nuclear ribosomal internal transcribed spacer (nrITS), and phylogenomic analysis based on ddRAD-seq using a reduced set of the plant materials (83 plant accessions consisting of 50 species, one subspecies and six varieties). We also conducted more thorough phylogenomic analyses including the reconstruction of biogeographic history using comprehensive samples of 135 plant accessions consisting of 54 species, one subspecies, nine varieties of Heterotropa and six outgroup species. Key Results Phylogenomic analyses of Heterotropa based on ddRAD-seq were superior to Sanger sequencing-based approaches and resulted in a fully resolved phylogenetic tree with strong support for 72.0–84.8 % (depending on the tree reconstruction methods) of the branches. We clarified the history of Heterotropa radiation and found that A. forbesii, the only deciduous Heterotropa species native to mainland China, is sister to the evergreen species (core Heterotropa) mostly distributed across the Japanese Archipelago and Taiwan. Conclusions The core Heterotropa group was divided into nine subclades, each of which had a narrow geographic distribution. Moreover, most estimated dispersal events (22 out of 24) were between adjacent areas, indicating that the range expansion has been geographically restricted throughout the radiation history. The findings enhance our understanding of the remarkable diversification of plant lineages in the Japanese Archipelago and Taiwan.

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Plastome Phylogenomic and Biogeographical Study on Thuja (Cupressaceae)

BioMed Research International ◽

10.1155/2020/8426287 ◽

2020 ◽

Vol 2020 ◽

pp. 1-13

Author(s):

Kole F. Adelalu ◽

Xu Zhang ◽

Xiaojian Qu ◽

Jacob B. Landis ◽

Jun Shen ◽

...

Keyword(s):

North America ◽

East Asia ◽

Potential Effect ◽

Molecular Dating ◽

Disjunct Distribution ◽

Land Bridge ◽

Biogeographic History ◽

Extant Species ◽

History Of ◽

Phylogenomic Analyses

Investigating the biogeographical disjunction of East Asian and North American flora is key to understanding the formation and dynamics of biodiversity in the Northern Hemisphere. The small Cupressaceae genus Thuja, comprising five species, exhibits a typical disjunct distribution in East Asia and North America. Owing to obscure relationships, the biogeographical history of the genus remains controversial. Here, complete plastomes were employed to investigate the plastome evolution, phylogenetic relationships, and biogeographic history of Thuja. All plastomes of Thuja share the same gene content arranged in the same order. The loss of an IR was evident in all Thuja plastomes, and the B-arrangement as previously recognized was detected. Phylogenomic analyses resolved two sister pairs, T. standishii-T. koraiensis and T. occidentalis-T. sutchuenensis, with T. plicata sister to T. occidentalis-T. sutchuenensis. Molecular dating and biogeographic results suggest the diversification of Thuja occurred in the Middle Miocene, and the ancestral area of extant species was located in northern East Asia. Incorporating the fossil record, we inferred that Thuja likely originated from the high-latitude areas of North America in the Paleocene with a second diversification center in northern East Asia. The current geographical distribution of Thuja was likely shaped by dispersal events attributed to the Bering Land Bridge in the Miocene and subsequent vicariance events accompanying climate cooling. The potential effect of extinction may have profound influence on the biogeographical history of Thuja.

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Reassessing the concept of the ‘Neolithic’ in the Jomon of Western Japan

Documenta Praehistorica ◽

10.4312/dp.34.1 ◽

2007 ◽

Vol 34 ◽

pp. 1-7 ◽

Cited By ~ 1

Author(s):

Simon Kaner ◽

Takeshi Ishikawa

Keyword(s):

Large Scale ◽

Population Densities ◽

Neolithic Transition ◽

Japanese Archipelago ◽

History Of ◽

Western Japan ◽

The Japanese Archipelago ◽

Lower Population ◽

Late Palaeolithic

The concept of the Mesolithic/Neolithic transition is difficult to apply in the Japanese archipelago. The earliest pottery usage occurs in late Palaeolithic contexts. Holocene foragers lived in stable, permanent village settlements and constructed large scale monuments, and the first real ‘agriculture’ arrived as part of a cultural package which also included metallurgy. This paper will examine the use of the term ‘Neolithic’ in the history of Japanese archaeology, with particular emphasis on what happened in the western part of the archipelago in the latter part of the Jomon period (c. 5000 BC – c. 500 BC). Recent investigations in Kyushu and Western Honshu are leading to a re-assessment of the nature of Jomon culture and society in this region, traditionally considered to have ‘lagged behind’ the more developed societies of the eastern part of the archipelago, expressed in part through much lower population densities.

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Phylogenomic analysis of the Chilean clade ofLiolaemuslizards (Squamata: Liolaemidae) based on sequence capture data

PeerJ ◽

10.7717/peerj.3941 ◽

2017 ◽

Vol 5 ◽

pp. e3941 ◽

Cited By ~ 7

Author(s):

Alejandra Panzera ◽

Adam D. Leaché ◽

Guillermo D’Elía ◽

Pedro F. Victoriano

Keyword(s):

Incomplete Lineage Sorting ◽

Phylogenetic Analyses ◽

Strong Support ◽

Taxon Sampling ◽

Phylogenomic Analysis ◽

Molecular Systematic ◽

Data Set ◽

Protein Coding ◽

Protein Coding Genes ◽

Phylogenomic Analyses

The genusLiolaemusis one of the most ecologically diverse and species-rich genera of lizards worldwide. It currently includes more than 250 recognized species, which have been subject to many ecological and evolutionary studies. Nevertheless,Liolaemuslizards have a complex taxonomic history, mainly due to the incongruence between morphological and genetic data, incomplete taxon sampling, incomplete lineage sorting and hybridization. In addition, as many species have restricted and remote distributions, this has hampered their examination and inclusion in molecular systematic studies. The aims of this study are to infer a robust phylogeny for a subsample of lizards representing the Chilean clade (subgenusLiolaemus sensu stricto), and to test the monophyly of several of the major species groups. We use a phylogenomic approach, targeting 541 ultra-conserved elements (UCEs) and 44 protein-coding genes for 16 taxa. We conduct a comparison of phylogenetic analyses using maximum-likelihood and several species tree inference methods. The UCEs provide stronger support for phylogenetic relationships compared to the protein-coding genes; however, the UCEs outnumber the protein-coding genes by 10-fold. On average, the protein-coding genes contain over twice the number of informative sites. Based on our phylogenomic analyses, all the groups sampled are polyphyletic.Liolaemus tenuis tenuisis difficult to place in the phylogeny, because only a few loci (nine) were recovered for this species. Topologies or support values did not change dramatically upon exclusion ofL. t. tenuisfrom analyses, suggesting that missing data did not had a significant impact on phylogenetic inference in this data set. The phylogenomic analyses provide strong support for sister group relationships betweenL. fuscus,L. monticola,L. nigroviridisandL. nitidus, andL. plateiandL. velosoi. Despite our limited taxon sampling, we have provided a reliable starting hypothesis for the relationships among many major groups of the Chilean clade ofLiolaemusthat will help future work aimed at resolving theLiolaemusphylogeny.

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Genome-Wide SNP Analysis Reveals Population Structure and Demographic History of the Ryukyu Islanders in the Southern Part of the Japanese Archipelago

Molecular Biology and Evolution ◽

10.1093/molbev/msu230 ◽

2014 ◽

Vol 31 (11) ◽

pp. 2929-2940 ◽

Cited By ~ 30

Author(s):

Takehiro Sato ◽

Shigeki Nakagome ◽

Chiaki Watanabe ◽

Kyoko Yamaguchi ◽

Akira Kawaguchi ◽

...

Keyword(s):

Population Structure ◽

Demographic History ◽

Snp Analysis ◽

Japanese Archipelago ◽

Genome Wide ◽

History Of ◽

The Japanese Archipelago

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Multiple waves of freshwater colonization of the three-spined stickleback in the Japanese Archipelago

BMC Evolutionary Biology ◽

10.1186/s12862-020-01713-5 ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Ryo Kakioka ◽

Seiichi Mori ◽

Tomoyuki Kokita ◽

Takuya K. Hosoki ◽

Atsushi J. Nagano ◽

...

Keyword(s):

North America ◽

Pacific Northwest ◽

Gasterosteus Aculeatus ◽

Parallel Evolution ◽

Divergence Time ◽

Northern Europe ◽

Phylogenomic Analysis ◽

Japanese Archipelago ◽

The Pacific ◽

The Japanese Archipelago

Abstract Background The three-spined stickleback (Gasterosteus aculeatus) is a remarkable system to study the genetic mechanisms underlying parallel evolution during the transition from marine to freshwater habitats. Although the majority of previous studies on the parallel evolution of sticklebacks have mainly focused on postglacial freshwater populations in the Pacific Northwest of North America and northern Europe, we recently use Japanese stickleback populations for investigating shared and unique features of adaptation and speciation between geographically distant populations. However, we currently lack a comprehensive phylogeny of the Japanese three-spined sticklebacks, despite the fact that a good phylogeny is essential for any evolutionary and ecological studies. Here, we conducted a phylogenomic analysis of the three-spined stickleback in the Japanese Archipelago. Results We found that freshwater colonization occurred in multiple waves, each of which may reflect different interglacial isolations. Some of the oldest freshwater populations from the central regions of the mainland of Japan (hariyo populations) were estimated to colonize freshwater approximately 170,000 years ago. The next wave of colonization likely occurred approximately 100,000 years ago. The inferred origins of several human-introduced populations showed that introduction occurred mainly from nearby habitats. We also found a new habitat of the three-spined stickleback sympatric with the Japan Sea stickleback (Gasterosteus nipponicus). Conclusions These Japanese stickleback systems differ from those in the Pacific Northwest of North America and northern Europe in terms of divergence time and history. Stickleback populations in the Japanese Archipelago offer valuable opportunities to study diverse evolutionary processes in historical and contemporary timescales.

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Population dynamics in the Japanese Archipelago since the Pleistocene revealed by the complete mitochondrial genome sequences

Scientific Reports ◽

10.1038/s41598-021-91357-2 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Fuzuki Mizuno ◽

Jun Gojobori ◽

Masahiko Kumagai ◽

Hisao Baba ◽

Yasuhiro Taniguchi ◽

...

Keyword(s):

Mitochondrial Genome ◽

Demographic History ◽

Complete Mitochondrial Genome ◽

Cultural Transition ◽

Rice Agriculture ◽

Japanese Archipelago ◽

Mitogenome Sequence ◽

Basal Group ◽

History Of ◽

The Japanese Archipelago

AbstractThe Japanese Archipelago is widely covered with acidic soil made of volcanic ash, an environment which is detrimental to the preservation of ancient biomolecules. More than 10,000 Palaeolithic and Neolithic sites have been discovered nationwide, but few skeletal remains exist and preservation of DNA is poor. Despite these challenging circumstances, we succeeded in obtaining a complete mitogenome (mitochondrial genome) sequence from Palaeolithic human remains. We also obtained those of Neolithic (the hunting-gathering Jomon and the farming Yayoi cultures) remains, and over 2,000 present-day Japanese. The Palaeolithic mitogenome sequence was not found to be a direct ancestor of any of Jomon, Yayoi, and present-day Japanese people. However, it was an ancestral type of haplogroup M, a basal group of the haplogroup M. Therefore, our results indicate continuity in the maternal gene pool from the Palaeolithic to present-day Japanese. We also found that a vast increase of population size happened and has continued since the Yayoi period, characterized with paddy rice farming. It means that the cultural transition, i.e. rice agriculture, had significant impact on the demographic history of Japanese population.

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Molecular phylogeny and diversification timing of the Nemouridae family (Insecta, Plecoptera) in the Japanese Archipelago

10.1101/440529 ◽

2018 ◽

Author(s):

Maribet Gamboa ◽

David Muranyi ◽

Shota Kanmori ◽

Kozo Watanabe

Keyword(s):

North America ◽

Nuclear Dna ◽

Mainland China ◽

Species Diversification ◽

Japanese Archipelago ◽

Late Neogene ◽

History Of ◽

Local Species ◽

Western Japan ◽

The Japanese Archipelago

AbstractThe generation of the high species diversity of insects in Japan was profoundly influenced by the formation of the Japanese Archipelago. We explored the species diversification and biogeographical history of the Nemouridae family in the Japanese Archipelago using mitochondrial DNA and nuclear DNA markers. We collected 49 species among four genera: Indonemoura, Protonemura, Amphinemura and Nemoura in Japan, China, South Korea and North America. We estimated their divergence times—based on three molecular clock node calibrations—using Bayesian phylogeography approaches. Our results suggested that Japanese Archipelago formation events resulted in diversification events in the middle of the Cretaceous (<120 Ma), speciation in the Paleogene (<50 Ma) and intra-species diversification segregated into eastern and western Japan of the Fossa Magna region at late Neogene (20 Ma). The Indonemoura samples were genetically separated into two clades—that of Mainland China and that of Japan. The Japanese clade clustered with the Nemouridae species from North America, suggesting the possibility of a colonisation event prior to the formation of the Japanese Archipelago. We believe that our results enhanced the understanding both of the origin of the species and of local species distribution in the Japanese Archipelago.

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Multiple waves of freshwater colonization of the three-spined stickleback in the Japanese Archipelago

10.21203/rs.3.rs-59443/v1 ◽

2020 ◽

Author(s):

Ryo Kakioka ◽

Seiichi Mori ◽

Tomoyuki Kokita ◽

Takuya K Hosoki ◽

Atsushi J Nagano ◽

...

Keyword(s):

North America ◽

Pacific Northwest ◽

Gasterosteus Aculeatus ◽

Parallel Evolution ◽

Divergence Time ◽

Northern Europe ◽

Phylogenomic Analysis ◽

Japanese Archipelago ◽

The Pacific ◽

The Japanese Archipelago

Abstract Background: The three-spined stickleback (Gasterosteus aculeatus) is a remarkable system to study the genetic mechanisms underlying parallel evolution during the transition from marine to freshwater habitats. Although the majority of previous studies on the parallel evolution of sticklebacks have mainly focused on postglacial freshwater populations in the Pacific Northwest of North America and northern Europe, we recently use Japanese stickleback populations for investigating shared and unique features of adaptation and speciation between geographically distant populations. However, we currently lack a comprehensive phylogeny of the Japanese three-spined sticklebacks, despite the fact that a good phylogeny is essential for any evolutionary and ecological studies. Here, we conducted a phylogenomic analysis of the three-spined stickleback in the Japanese Archipelago.Results: We found that freshwater colonization occurred in multiple waves, each of which may reflect different interglacial isolations. Some of the oldest freshwater populations from the central regions of the mainland of Japan (Hariyo populations) were estimated to colonize freshwater approximately 170,000 years ago. The next wave of colonization likely occurred approximately 100,000 years ago. The inferred origins of several human-introduced populations showed that introduction occurred mainly from nearby habitats. We also found a new habitat of the three-spined stickleback sympatric with the Japan Sea stickleback (Gasterosteus nipponicus).Conclusions: These Japanese stickleback systems differ from those in the Pacific Northwest of North America and northern Europe in terms of divergence time and history. Stickleback populations in the Japanese Archipelago offer valuable opportunities to study diverse evolutionary processes in historical and contemporary timescales.

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