Chloroplast DNA sequence utility for the lowest phylogenetic and phylogeographic inferences in angiosperms: The tortoise and the hare IV

Shaw, Joey; Shafer, Hayden L.; Leonard, O. Rayne; Kovach, Margaret J.; Schorr, Mark S.; Morris, Ashley B.

doi:10.3732/ajb.1400398

Cited by 229 publications

(257 citation statements)

References 107 publications

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“…Similar result is obtained in safflower (Carthamus tinctorincus) revealing no polymorphic sequences of IGS atpB -rbcL among 76 populations (Chapman et al, 2010). This is in contrast to several previous references revealing that such a marker is suitable for lower-level phylogenetic studies, especially in photosynthetic angiosperm systematics Shaw et al, 2014). Along with other noncoding regions, i.e.…”

Section: Resultscontrasting

confidence: 49%

High Connectivity Among Synedrella nodiflora Populations in Java Island Based on Intergenic Spacer atpB-rbcL

2018

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The genus Synedrella remains monotypic in spite of its wide range of distribution, in which S. nodiflora (L.) Gaertn has taxonomically been the only member of the genus so far. This leads to assumption of the very low genetic difference among S. nodiflora populations worldwide. It may also be the case in Java Island, though rapid changes in ecosystem condition occurs. Here we report our study on S. nodiflora population genetics in Java Island using intergenic spacer (IGS) atpB-rbcL as a molecular marker, since it has been well known as one of the most variable chloroplast genome regions in a wide range of plant species so far. As many as 58 individuals were collected randomly from ten different locations in the island. Based on IGS atpBrbcL sequences of 860 bp length, only two haplotypes were observed. Both show only one polymorphic site (0.12%) as well as low haplotype diversity (0.0345) and low nucleotide diversity (0.000040). In addition, the very low fixation index (FST = 0.02645; p = 1.00000) proves low genetic difference, or in other words, indicates high connectivity among populations of S. nodiflora in Java Island. At the same time provides a fact of nearly no variation among the IGS atpB -rbcL sequences. (Chiang & Schaal, 2000a, 2000bFujii et al., 1997;Small et al., 2005;Taberlet et al., 1991). How to CiteThe purpose of this study is to know genetic diversity and the level of connectivity among S. nodiflora populations in Java Island based on IGS atpB -rbcL. It is expected from the study that molecular data can be obtained to compare with the existing taxonomical status of the species as the only member of genus Synedrella, which has been based merely on phenotypical characters. METHODSS. nodiflora samples were collected randomly from ten different locations in Java Island, i.e. Bogor (n = 5), Tasikmalaya (n = 5), Ciamis (n = 5), Banyumas (n = 10), Yogyakarta (n = 5), Mojokerto (n = 5), Probolinggo (n = 6), Malang (n = 6), Lumajang (n = 5) and Jember (n = 6) ( Figure 1). The plants were taken with their roots and were put into plastic bottles previously filled with a little water prior to be planted in pots in a glass house. Genomic DNAs were isolated from uppermost leaves following CTAB method (Doyle & Doyle, 1990). The quality and quantity of the isolated DNAs were measured using genequant. Amplification of IGS atpB -rbcL was performed using universal primers, i.e. 5'-ACA TCK ART ACK GGA CCA ATA A-3' as forward primer and 5' -AAC ACC AGC TTT RAA TCC AA-3' as reverse primer (Chiang et al., 1998). A total volume of 11.5 µl PCR mixture consisting of 2 µl template DNA, 5 µl KapaTaq DNA polymerase, 4.25 µl nuclease free water (NFW) and 0.125 µl of individual primer was subjected to PCR condition as follows: pre-denaturation of 94

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Section: Resultscontrasting

confidence: 49%

High Connectivity Among Synedrella nodiflora Populations in Java Island Based on Intergenic Spacer atpB-rbcL

2018

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“…For herbarium samples, genomic DNA was extracted using the protocol of CTAB + Wizard DNA Clean-Up System (42). SI Text details the process of DNA marker selection; chloroplast ndhFrpl32 intergenic spacer was chosen for its high variability (33) and ease of PCR amplification. Primer sequences and PCR conditions followed Shaw et al (33), with herbarium materials amplified using internal primers designed for short (ca.…”

Section: Methodsmentioning

confidence: 99%

“…To increase our understanding of the prehistoric Austronesian expansion and migrations, we tracked geographic origins of Oceanic paper mulberry, the only Polynesian commensal plant likely originating in East Asia, using DNA sequence variation of the maternally inherited (32) and hypervariable (SI Text) chloroplast ndhF-rpl32 intergenic spacer (33). We sampled broadly in East Asia (Taiwan, S China, and Japan) and SE Asia (Indochina, the Philippines, and Sulawesi) as well as Oceanic islands where traditional tapa making is still practiced.…”

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confidence: 99%

A holistic picture of Austronesian migrations revealed by phylogeography of Pacific paper mulberry

Chang

Liu

Moncada

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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The peopling of Remote Oceanic islands by Austronesian speakers is a fascinating and yet contentious part of human prehistory. Linguistic, archaeological, and genetic studies have shown the complex nature of the process in which different components that helped to shape Lapita culture in Near Oceania each have their own unique history. Important evidence points to Taiwan as an Austronesian ancestral homeland with a more distant origin in South China, whereas alternative models favor South China to North Vietnam or a Southeast Asian origin. We test these propositions by studying phylogeography of paper mulberry, a common East Asian tree species introduced and clonally propagated since prehistoric times across the Pacific for making barkcloth, a practical and symbolic component of Austronesian cultures. Using the hypervariable chloroplast ndhF-rpl32 sequences of 604 samples collected from East Asia, Southeast Asia, and Oceanic islands (including 19 historical herbarium specimens from Near and Remote Oceania), 48 haplotypes are detected and haplotype cp-17 is predominant in both Near and Remote Oceania. Because cp-17 has an unambiguous Taiwanese origin and cp-17–carrying Oceanic paper mulberries are clonally propagated, our data concur with expectations of Taiwan as the Austronesian homeland, providing circumstantial support for the “out of Taiwan” hypothesis. Our data also provide insights into the dispersal of paper mulberry from South China “into North Taiwan,” the “out of South China–Indochina” expansion to New Guinea, and the geographic origins of post-European introductions of paper mulberry into Oceania.

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“…2 in the companion data publication Welch et al, 2016), even between Stenogyne haliakalae and the most distant Stachys species. To conduct a more detailed investigation of chloroplast genome variation in this mint radiation, we compared variable positions, or potentially informative characters (PICs) (Shaw et al, 2007;Shaw et al, 2014), among six complete, high-quality chloroplast genome sequences (i.e. > 10X depth): Stenogyne haliakalae, Stenogyne bifida, Haplostachys haplostachya, Stachys chamissonis, Stachys coccinea, and Stachys sylvatica.…”

Section: Chloroplast Genome Sequence Variability Within a Mint Radiationmentioning

confidence: 99%

The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)

Welch

Collins

Drautz–Moses

et al. 2016

Molecular Phylogenetics and Evolution

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(2016) 'The quest to resolve recent radiations : plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae).', Molecular phylogenetics and evolution., 99 . pp. 16-33. Further information on publisher's website: Use policyThe full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-pro t purposes provided that:• a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders.Please consult the full DRO policy for further details. AbstractThe Hawaiian mints (Lamiaceae), one of the largest endemic plant lineages in the archipelago, provide an excellent system to study rapid diversification of a lineage with a remote, likely paleohybrid origin. Since their divergence from New World mints 4-5 million years ago the members of this lineage have diversified greatly and represent a remarkable array of vegetative and reproductive phenotypes. Today many members of this group are endangered or already extinct, and molecular phylogenetic work relies largely on herbarium samples collected during the last century. So far a gene-by-gene approach has been utilized, but the recent radiation of the Hawaiian mints has resulted in minimal sequence divergence and hence poor phylogenetic resolution. In our quest to trace the reticulate evolutionary history of the lineage, a resolved maternal phylogeny is necessary. We applied a high-throughput approach to sequence 12 complete or nearly complete plastid genomes from multiple Hawaiian mint species and relatives, including extinct and rare taxa. We also targeted 108 hypervariable regions from throughout the chloroplast genomes in nearly all of the remaining Hawaiian species, and relatives, using a nextgeneration amplicon sequencing approach. This procedure generated ~20Kb of sequence data for each taxon and considerably increased the total number of variable sites over previous analyses. Our results demonstrate the potential of high-throughput sequencing of historic material for evolutionary studies in rapidly evolving lineages. Our study, however, also highlights the challenges of resolving relationships within recent radiations even at the genomic level.

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Chloroplast DNA sequence utility for the lowest phylogenetic and phylogeographic inferences in angiosperms: The tortoise and the hare IV

Cited by 229 publications

References 107 publications

High Connectivity Among Synedrella nodiflora Populations in Java Island Based on Intergenic Spacer atpB-rbcL

High Connectivity Among Synedrella nodiflora Populations in Java Island Based on Intergenic Spacer atpB-rbcL

A holistic picture of Austronesian migrations revealed by phylogeography of Pacific paper mulberry

The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)

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