Biology subjects

van Andel, T. R.

Publications and source records attributed to van Andel, T. R..

3 recordsLinked to original sources

bioRxiv2022

A TOMATO GENOME FROM THE ITALIAN RENAISSANCE PROVIDES INSIGHTS INTO COLUMBIAN AND PRE-COLUMBIAN EXCHANGE LINKS AND DOMESTICATION

AO_SCPLOWBSTRACTC_SCPLOWThe history of the tomatos interactions with humans spans both a pre-Columbian period of millennia of cultivation and domestication in South and Central America as well as the plants rise to becoming one of the worlds major cash crops following the arrival of Europeans in the Neotropics and the subsequent Columbian Exchange. In the process, the influence of successive regimes of artificial selection gave rise to an entangled species complex comprised of a wild ancestor and numerous cultivars exhibiting a great diversity of fruit phenotypes (often sorted in cherry and big types). Here, we provide a snapshot into these dynamics by presenting the ancient nuclear and plastid genomes of one of the oldest tomatoes still in existence: the almost half a millennium old En Tibi specimen from the Italian Renaissance. By placing the genome skimming data obtained from this specimen within the phylogenomic context of wild relatives and Neotropical tomato cultivars and land races, we are able to show that the most likely geographic origins of the specimens immediate ancestors, i.e. whence the exchange of this particular lineage originated, are around the Gulf of Mexico. We also show that this specimen was less inbred than present-day tomatoes, shedding light on the genomic signatures of historical domestication processes. Probing deeper into the ancestry that shaped extant genetic diversity within the complex, we reconstruct multiple ancestral populations with diffuse but distinct signatures in cherry and big tomatoes. The geographic structure of these ancestries within the nearest wild relative of tomatoes and the differential extent to which these ancestries are represented in domesticates points to early cultivation and human-assisted dispersal of tomatoes originating from the northern extreme of the natural range of the species. Our findings illustrate the inferences that can be drawn from ancient DNA extracted from herbarium specimens and historic plant collections. At the same time, we stress that our findings draw on multiple disciplines including ethnobotanical and historical research and on the (agri)cultural contributions of a variety of world cultures.

plant biology↗

bioRxiv2020

Methodological priorities in assessing wild edible plant knowledge and use: a case study among the Baka in Cameroon.

Freelisting and dietary recalls are frequently used methods in ethnobotany to assess wild edible plant (WEP) knowledge and use. Though these ex-situ interviewing methods are practical to perform and may yield large datasets in a short time, they are known to be limited by the informants memory and cognitive bias. Alternatively, the much more laborious walk-in-the-woods method may be used, in which informants point out edible plants in-situ. Few studies, however, examine quantitatively how these different methods influence results. In this study, we assessed how these methods capture the diversity of wild edible plant knowledge and use among the Baka, a group of forager-horticulturalists from southeastern Cameroon. We show that within a single population, and when data on consumption frequency are collected simultaneously, the walk-in-the-woods method results in more detailed information of WEP knowledge and use than do freelisting or dietary recalls. Our in-situ method yielded 91 species of WEP, much more than the ex-situ methods of freelisting (34 spp.) and dietary recalls (12 spp.). Our results imply that previous studies based only on ex situ surveys may have underestimated the importance of WEP for local communities. We propose that future studies on WEP knowledge and use frequency should rely on mixed methods, taking an in-situ method as the starting point of their approach.

plant biology↗

bioRxiv2018

Origins and geographic diversification of African rice (Oryza glaberrima)

Rice is a staple food for the majority of our worlds growing population. Whereas Asian rice (Oryza sativa L.) has been extensively studied, the exact origins of African rice (Oryza glaberrima Steud.) are still contested. Previous studies have supported either a centric or a non-centric origin of African rice domestication. Here we review the evidence for both scenarios through a critical reassessment of 206 whole genome sequences of domesticated and wild African rice. While genetic diversity analyses support a severe bottleneck caused by domestication, signatures of recent and strong positive selection do not unequivocally point to candidate domestication genes, suggesting that domestication proceeded differently than in Asian rice - either by selection on different alleles, or different modes of selection. Population structure analysis revealed five genetic clusters localising to different geographic regions. Isolation by distance was identified in the coastal populations, which could account for parallel adaptation in geographically separated demes. Although genome-wide phylogenetic relationships support an origin in the eastern cultivation range followed by diversification along the Atlantic coast, further analysis of domestication genes shows distinct haplotypes in the southwest - suggesting that at least one of several key domestication traits might have originated there. These findings shed new light on an old controversy concerning plant domestication in Africa by highlighting the divergent roots of African rice cultivation, including a separate centre of domestication activity in the Guinea Highlands. We thus suggest that the commonly accepted centric origin of African rice must be reconsidered in favour of a non-centric or polycentric view.

genomics↗