Time calibrated tree of Dioscorea (Dioscoreaceae) indicates four origins of yams in the Neotropics since the Eocene

Couto, Ricardo Sousa; Martins, Aline C.; Bolson, Mônica; Lopes, Rosana Conrado; Smidt, Eric C.; Braga, João Marcelo Alvarenga

doi:10.1093/botlinnean/boy052

Cited by 24 publications

(21 citation statements)

References 55 publications

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“…We included taxa from all of the major Dioscorea lineages identified in previous studies (Viruel et al., , ), as well as several groups of more closely related taxa, to assess whether we could recover different levels of relationships that remained unresolved or poorly supported in previous studies. The composition of major clades and their interrelationships mostly agreed with published findings (Wilkin et al., ; Hsu et al., ; Maurin et al., ; Viruel et al., , ; Couto et al., ) but were consistently better supported across both coalescent‐based and ML analyses here. The tree inferred by Viruel et al.…”

Section: Discussionsupporting

confidence: 90%

“…(), and two additional conflicts between our study and findings from Couto et al. () considering Bayesian posterior probability values in their studies (support for these three branches from ML bootstrap analyses in those studies was moderate and low, respectively). The tree inferred from combined analysis of one nuclear gene and five plastid markers by Viruel et al.…”

Section: Discussioncontrasting

confidence: 82%

“…(, ), and Couto et al. (). There was one strongly supported conflict concerning relationships among major clades between our study and that of Viruel et al.…”

Section: Discussionmentioning

confidence: 98%

“…Yam lineages with perennial tubers and rhizomes have also been used as a main source of steroidal precursors (De Luca et al., ; Hua et al., ) and traditional medicines (Lebot, ). Our understanding of Dioscorea evolution has benefited greatly from previous studies using two to six plastid markers (Wilkin et al., ; Hsu et al., ; Maurin et al., ; Viruel et al., ; Couto et al., ) or a single nuclear gene (Viruel et al., ); these studies provide a baseline phylogenetic outline for the genus. However, relationships among most major clades and species remain highly uncertain, in part due to relatively limited taxon and gene sampling, coupled with low levels of molecular variation in sampled markers.…”

mentioning

confidence: 99%

“…(), who suggested that the two plastid markers they used were not sufficiently informative for inferring those relationships. The studies with the densest sampling to date included representatives of the approximately 10 major Dioscorea clades (Wilkin et al., ; Viruel et al., , ; Couto et al., ), but only 8–22% of the species in the genus. Sampling of crops and possible crop wild relatives (CWRs) has also remained relatively limited (e.g., Terauchi et al., ; Malapa et al., ; Mignouna et al., ; Mukherjee and Bhat, ; Girma et al., , ; Chaïr et al., ), and their inter‐relationships have yet to be resolved (e.g., confirming the identity of CWRs of D. alata ; Chaïr et al., ).…”

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confidence: 99%

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A customized nuclear target enrichment approach for developing a phylogenomic baseline for Dioscorea yams (Dioscoreaceae)

Gomez

Pokorny

Kantar³

et al. 2019

Appl Plant Sci

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Premise We developed a target enrichment panel for phylogenomic studies of Dioscorea , an economically important genus with incompletely resolved relationships. Methods Our bait panel comprises 260 low‐ to single‐copy nuclear genes targeted to work in Dioscorea , assessed here using a preliminary taxon sampling that includes both distantly and closely related taxa, including several yam crops and potential crop wild relatives. We applied coalescent‐based and maximum likelihood phylogenomic inference approaches to the pilot taxon set, incorporating new and published transcriptome data from additional species. Results The custom panel retrieved ~94% of targets and >80% of full gene length from 88% and 68% of samples, respectively. It has minimal gene overlap with existing panels designed for angiosperm‐wide studies and generally recovers longer and more variable targets. Pilot phylogenomic analyses consistently resolve most deep and recent relationships with strong support across analyses and point to revised relationships between the crop species D. alata and candidate crop wild relatives. Discussion Our customized panel reliably retrieves targeted loci from Dioscorea , is informative for resolving relationships in denser samplings, and is suitable for refining our understanding of the independent origins of cultivated yam species; the panel likely has broader promise for phylogenomic studies across Dioscoreales.

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Section: Discussionsupporting

confidence: 90%

Section: Discussioncontrasting

confidence: 82%

“…(, ), and Couto et al. (). There was one strongly supported conflict concerning relationships among major clades between our study and that of Viruel et al.…”

Section: Discussionmentioning

confidence: 98%

mentioning

confidence: 99%

mentioning

confidence: 99%

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A customized nuclear target enrichment approach for developing a phylogenomic baseline for Dioscorea yams (Dioscoreaceae)

Gomez

Pokorny

Kantar³

et al. 2019

Appl Plant Sci

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Population Genomics of Yams: Evolution and Domestication of Dioscorea Species

Sugihara

Kudoh

Oli

et al. 2021

Population Genomics

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Yam is a collective name of tuber crops belonging to the genus Dioscorea. Yam is important not only as a staple food crop but also as an integral component of society and culture of the millions of people who depend on it. However, due to its regional importance, yam has long been regarded as an “orphan crop” lacking a due global attention. Although this perception is changing with recent advances in genomics technologies, domestication processes of most yam species are still ambiguous. This is mainly due to the complicated evolutionary history of Dioscorea species caused by frequent hybridization and polyploidization, which is possibly caused by dioecy that imposed obligate outcrossing to the species of Dioscorea. In this chapter, we provide an overview of the evolution of Dioscorea and address the domestication of yam from population genomics perspectives by focusing on the processes of hybridization and polyploidization. A review is given to the recent population genomics studies on the hybrid origin of D. rotundata in West and Central Africa, the global dispersion of D. alata through human migrations, and the whole-genome duplication of the South America species of D. trifida. In the end, we give a summary of current understanding of sex-determination system in Dioscorea.

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Bioactive Compounds and Biological Activities of Edible Yam (Dioscorea sp.) in Thailand

Hongsprabhas,

Srivichai,

Israkarn

et al. 2023

Reference Series in Phytochemistry

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Time calibrated tree of Dioscorea (Dioscoreaceae) indicates four origins of yams in the Neotropics since the Eocene

Cited by 24 publications

References 55 publications

A customized nuclear target enrichment approach for developing a phylogenomic baseline for Dioscorea yams (Dioscoreaceae)

A customized nuclear target enrichment approach for developing a phylogenomic baseline for Dioscorea yams (Dioscoreaceae)

Population Genomics of Yams: Evolution and Domestication of Dioscorea Species

Bioactive Compounds and Biological Activities of Edible Yam (Dioscorea sp.) in Thailand

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