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<p>Sri Lanka, a biodiversity hotspot in South Asia, is home to 9–10 species of the genus <i>Piper</i>. Although previous studies have investigated the overall phylogenetics and biogeography of this genus, Sri Lankan species have largely been overlooked. In this study, we employed restriction-site-associated DNA sequencing (RADseq) to explore the phylogenetics, divergence times, and evolutionary relationships of Sri Lankan <i>Piper</i> species. We analyzed 27 <i>Piper</i> accessions, representing endemic, native, and introduced species, yielding 284,013 high-quality single nucleotide polymorphisms. Our results revealed two well-supported clades of <i>Piper</i> species: a, which includes the Sri Lankan endemics <i>P. zeylanicum</i> and <i>P. trineuron</i> along with native <i>P. hymenophyllum</i> and exotic <i>P. nigrum</i>, and b, comprising the Southeast Asian taxa <i>P. longum</i> and <i>P. sarmentosum</i> (the latter often considered a synonym of <i>P. longum</i>), and Sri Lankan <i>P. fallax</i> and <i>P. walkeri</i>. A time-calibrated analysis estimated that divergence of these two clades occurred at the Oligocene–Miocene boundary (~ 25.9&#xa0;Ma), with most speciation events occurring during the Miocene. The divergence of <i>P. zeylanicum</i> and <i>P. hymenophyllum</i> around 6.1&#xa0;Ma suggests a relatively recent speciation event in Sri Lanka. Notably, the positioning of <i>P. walkeri</i> among Southeast Asian taxa and close relationship between <i>P. nigrum</i> and <i>P. trineuron</i> challenge existing assumptions about their evolutionary origins. Furthermore, our findings indicate that Sri Lankan <i>Piper</i> species underwent repeated colonization episodes followed by in situ diversification, likely driven by Sri Lankan geological and ecological processes. This study provides insights in the biogeography and evolutionary history of <i>Piper</i> in South Asia, highlighting the complex evolutionary patterns that have shaped the diversity of this genus on the island.</p>

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Phylogenomics and age estimation for Sri Lankan Piper (Piperaceae) species using genotyping-by-sequencing

  • 期刊论文

  • 发表日期：

    2025年9月8日

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  • Bhathiya Gopallawa,
  • Dominik Metschina,
  • Anushka M. Wickramasuriya,
  • Luiz A. Cauz-Santos,
  • Nilni A. Wimalarathna,
  • Gudasalamani Ravikanth,
  • Mark W. Chase,
  • Rosabelle Samuel,
  • Deepthi Yakandawala

摘要

Sri Lanka, a biodiversity hotspot in South Asia, is home to 9–10 species of the genus Piper. Although previous studies have investigated the overall phylogenetics and biogeography of this genus, Sri Lankan species have largely been overlooked. In this study, we employed restriction-site-associated DNA sequencing (RADseq) to explore the phylogenetics, divergence times, and evolutionary relationships of Sri Lankan Piper species. We analyzed 27 Piper accessions, representing endemic, native, and introduced species, yielding 284,013 high-quality single nucleotide polymorphisms. Our results revealed two well-supported clades of Piper species: a, which includes the Sri Lankan endemics P. zeylanicum and P. trineuron along with native P. hymenophyllum and exotic P. nigrum, and b, comprising the Southeast Asian taxa P. longum and P. sarmentosum (the latter often considered a synonym of P. longum), and Sri Lankan P. fallax and P. walkeri. A time-calibrated analysis estimated that divergence of these two clades occurred at the Oligocene–Miocene boundary (~ 25.9 Ma), with most speciation events occurring during the Miocene. The divergence of P. zeylanicum and P. hymenophyllum around 6.1 Ma suggests a relatively recent speciation event in Sri Lanka. Notably, the positioning of P. walkeri among Southeast Asian taxa and close relationship between P. nigrum and P. trineuron challenge existing assumptions about their evolutionary origins. Furthermore, our findings indicate that Sri Lankan Piper species underwent repeated colonization episodes followed by in situ diversification, likely driven by Sri Lankan geological and ecological processes. This study provides insights in the biogeography and evolutionary history of Piper in South Asia, highlighting the complex evolutionary patterns that have shaped the diversity of this genus on the island.