Photo by Sandeep Sen

Researchers at University of Tsukuba have developed a novel analytical framework to reconstruct species distributional shifts from the past to the present while explicitly incorporating within-population genetic diversity. Using this approach, they resolved the high-resolution distributional history of wild black pepper (Piper nigrum)—the world's most valuable spice—which originated in the Western Ghats of India and traced its range dynamics from the Last Glacial Maximum (LGM) to the present.

Tsukuba, Japan—Historical climatic fluctuations have profoundly influenced species distributions and genetic structures. Traditionally, past distributional patterns have been inferred using paleoecological, vegetation, population-genetic, and phylogeographic evidence. Over the past 15 years, species distribution models (SDMs) have become widely used to estimate suitable habitats based on contemporary occurrences and climatic variables (e.g., temperature, precipitation). However, conventional SDMs often overlook dynamic processes such as actual migration pathways. Moreover, when SDMs are used alongside population genetic or phylogeographic analyses, these components are usually conducted independently, introducing uncertainty into historical reconstructions.

In this study, the research team introduced a "genetically informed dynamic species distribution model" by enhancing previously developed dynamic SDMs (DSDMs) and integrating genetic diversity data directly into the modeling framework. They applied this approach to wild Piper nigrum, native to the Western Ghats of India, one of the world's eight 'hottest hotspots' of biodiversity, to reconstruct its distributional history from the LGM (~21,000 years ago) to the present. The model identified glacial refugia in the southern Western Ghats and revealed subsequent patterns of range contraction, expansion, and fragmentation following the LGM.

The findings provide substantial contributions to population genetics, phylogeography, biogeography, vegetation science, palaeoecology, conservation genetics, and bioresource management. In addition to informing conservation strategies for the genetically rare wild black pepper, the framework offers a robust and transferable approach for reconstructing species' historical dynamics under changing climatic conditions. This research was carried out through international collaboration, primarily with the Swiss Federal Research Institute WSL and the Ashoka Trust for Research in Ecology and the Environment (ATREE), India.

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This work was supported by JSPS Postdoctoral Fellowships for Research in Japan (Fellowship ID P20403), JSPS Kakenhi Grant-in-Aid for JSPS Fellows (22F20403), JSPS Kakenhi Grant in Aid for Scientific Research B (25K02056), JSPS Core to Core program: Asia-Africa Science Platforms B (JPJSCCB20220007), Grants from Yamazaki Spice Promotion Foundation in 2018, International Association for Plant Taxonomy (IAPT) and Department of Science and Technology (DST), India (YSS/2015/000234.Dated02/08/2018).

The distribution of the pepper plant from the last Ice Age to the present day.
Dark green: simulated distribution area; light green: climatically suitable but uncolonised area
(Video: Michael Nobis, Swiss Federal Research Institute WSL)

Original Paper

Title of original paper:

Direct Integration of Population Genetics and Dynamic Species Distribution Modelling Improves Predictions of Post-Glacial History of Piper nigrum

Journal:

Diversity and Distributions

DOI:

10.1111/ddi.70070

Correspondence

Associate Professor TSUDA Yoshiaki
Institute of Life and Environmental Sciences, University of Tsukuba

Related Link

Institute of Life and Environmental Sciences

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