Museomics for reconstructing historical floristic exchanges: Divergence of stone oaks across Wallacea

Natural history collections and tropical tree diversity are both treasure troves of biological and evolutionary information, but their accessibility for scientific study is impeded by a number of properties. DNA in historical specimens is generally highly fragmented, complicating the recovery of hig...

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Huvudupphovsmän:	Joeri S. Strijk, Hoàng, Thị Bình, Nguyễn, Văn Ngọc, Joan T. Pereira, J. W. Ferry Slik, Rahayu S Sukri, Yoshihisa Suyama, Shuichiro Tagane, Jan J. Wieringa, Tetsukazu Yahara, Damien D. Hinsinger
Materialtyp:	Journal article
Språk:	English
Publicerad:	2021
Länkar:	http://scholar.dlu.edu.vn/handle/123456789/526
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spelling	oai:scholar.dlu.edu.vn:123456789-5262022-08-03T23:41:08Z Museomics for reconstructing historical floristic exchanges: Divergence of stone oaks across Wallacea Joeri S. Strijk Hoàng, Thị Bình Nguyễn, Văn Ngọc Joan T. Pereira J. W. Ferry Slik Rahayu S Sukri Yoshihisa Suyama Shuichiro Tagane Jan J. Wieringa Tetsukazu Yahara Damien D. Hinsinger Natural history collections and tropical tree diversity are both treasure troves of biological and evolutionary information, but their accessibility for scientific study is impeded by a number of properties. DNA in historical specimens is generally highly fragmented, complicating the recovery of high-grade genetic material. Furthermore, our understanding of hyperdiverse, wide-spread tree assemblages is obstructed by extensive species ranges, fragmented knowledge of tropical tree diversity and phenology, and a widespread lack of species-level diagnostic characters, prohibiting the collecting of readily identifiable specimens which can be used to build, revise or strengthen taxonomic frameworks. This, in turn, delays the application of downstream conservation action. A sizable component of botanical collections are sterile—thus eluding identification and are slowing down progress in systematic treatments of tropical biodiversity. With rapid advances in genomics and bioinformatic approaches to biodiversity research, museomics is emerging as a new field breathing life into natural collections that have been built up over centuries. Using MIGseq (multiplexed ISSR genotyping by sequencing), we generated 10,000s of short loci, for both freshly collected materials and museum specimens (aged >100 years) of Lithocarpus—a widespread tropical tree genus endemic to the Asian tropics. Loci recovery from historical and recently collected samples was not affected by sample age and preservation history of the study material, underscoring the reliability and flexibility of the MIGseq approach. Phylogenomic inference and biogeographic reconstruction across insular Asia, highlights repeated migration and diversification patterns between continental regions and islands. Results indicate that co-occurring insular species at the extremity of the distribution range are not monophyletic, raising the possibility of multiple independent dispersals along the outer edge of Wallacea. This suggests that dispersal of large seeded tree genera throughout Malesia and across Wallacea may have been less affected by large geographic distances and the presence of marine barriers than generally assumed. We demonstrate the utility of MIGseq in museomic studies using non-model taxa, presenting the first range-wide genomic assessment of Lithocarpus and tropical Fagaceae as a proof-of-concept. Our study shows the potential for developing innovative genomic approaches to improve the capture of novel evolutionary signals using valuable natural history collections of hyperdiverse taxa. 15 5 2021-08-27T09:54:00Z 2021-08-27T09:54:00Z 2020-05 Journal article Bài báo đăng trên tạp chí thuộc ISI, bao gồm book chapter http://scholar.dlu.edu.vn/handle/123456789/526 10.1371/journal.pone.0232936 en PLoS ONE 10.1371/journal.pone.0232936 1932-6203
institution	Thư viện Trường Đại học Đà Lạt
collection	Thư viện số
language	English
description	Natural history collections and tropical tree diversity are both treasure troves of biological and evolutionary information, but their accessibility for scientific study is impeded by a number of properties. DNA in historical specimens is generally highly fragmented, complicating the recovery of high-grade genetic material. Furthermore, our understanding of hyperdiverse, wide-spread tree assemblages is obstructed by extensive species ranges, fragmented knowledge of tropical tree diversity and phenology, and a widespread lack of species-level diagnostic characters, prohibiting the collecting of readily identifiable specimens which can be used to build, revise or strengthen taxonomic frameworks. This, in turn, delays the application of downstream conservation action. A sizable component of botanical collections are sterile—thus eluding identification and are slowing down progress in systematic treatments of tropical biodiversity. With rapid advances in genomics and bioinformatic approaches to biodiversity research, museomics is emerging as a new field breathing life into natural collections that have been built up over centuries. Using MIGseq (multiplexed ISSR genotyping by sequencing), we generated 10,000s of short loci, for both freshly collected materials and museum specimens (aged >100 years) of Lithocarpus—a widespread tropical tree genus endemic to the Asian tropics. Loci recovery from historical and recently collected samples was not affected by sample age and preservation history of the study material, underscoring the reliability and flexibility of the MIGseq approach. Phylogenomic inference and biogeographic reconstruction across insular Asia, highlights repeated migration and diversification patterns between continental regions and islands. Results indicate that co-occurring insular species at the extremity of the distribution range are not monophyletic, raising the possibility of multiple independent dispersals along the outer edge of Wallacea. This suggests that dispersal of large seeded tree genera throughout Malesia and across Wallacea may have been less affected by large geographic distances and the presence of marine barriers than generally assumed. We demonstrate the utility of MIGseq in museomic studies using non-model taxa, presenting the first range-wide genomic assessment of Lithocarpus and tropical Fagaceae as a proof-of-concept. Our study shows the potential for developing innovative genomic approaches to improve the capture of novel evolutionary signals using valuable natural history collections of hyperdiverse taxa.
format	Journal article
author	Joeri S. Strijk Hoàng, Thị Bình Nguyễn, Văn Ngọc Joan T. Pereira J. W. Ferry Slik Rahayu S Sukri Yoshihisa Suyama Shuichiro Tagane Jan J. Wieringa Tetsukazu Yahara Damien D. Hinsinger
spellingShingle	Joeri S. Strijk Hoàng, Thị Bình Nguyễn, Văn Ngọc Joan T. Pereira J. W. Ferry Slik Rahayu S Sukri Yoshihisa Suyama Shuichiro Tagane Jan J. Wieringa Tetsukazu Yahara Damien D. Hinsinger Museomics for reconstructing historical floristic exchanges: Divergence of stone oaks across Wallacea
author_facet	Joeri S. Strijk Hoàng, Thị Bình Nguyễn, Văn Ngọc Joan T. Pereira J. W. Ferry Slik Rahayu S Sukri Yoshihisa Suyama Shuichiro Tagane Jan J. Wieringa Tetsukazu Yahara Damien D. Hinsinger
author_sort	Joeri S. Strijk
title	Museomics for reconstructing historical floristic exchanges: Divergence of stone oaks across Wallacea
title_short	Museomics for reconstructing historical floristic exchanges: Divergence of stone oaks across Wallacea
title_full	Museomics for reconstructing historical floristic exchanges: Divergence of stone oaks across Wallacea
title_fullStr	Museomics for reconstructing historical floristic exchanges: Divergence of stone oaks across Wallacea
title_full_unstemmed	Museomics for reconstructing historical floristic exchanges: Divergence of stone oaks across Wallacea
title_sort	museomics for reconstructing historical floristic exchanges: divergence of stone oaks across wallacea
publishDate	2021
url	http://scholar.dlu.edu.vn/handle/123456789/526
_version_	1768305778780798976

Museomics for reconstructing historical floristic exchanges: Divergence of stone oaks across Wallacea

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