01800nas a2200325 4500008004100000245007800041210006900119260001500188300000800203490000600211520078700217100002001004700002001024700001901044700002701063700002001090700002201110700001901132700002401151700002101175700002201196700002001218700001901238700002101257700001701278700001801295700002301313700002001336856011801356 2019 eng d00aYam genomics supports West Africa as a major cradle of crop domestication0 aYam genomics supports West Africa as a major cradle of crop dome c1 May 2019 a1-80 v53 a

While there has been progress in our understanding of the origin and history of agriculture in sub-Saharan Africa,
a unified perspective is still lacking on where and how major crops were domesticated in the region. Here, we
investigated the domestication of African yam (Dioscorea rotundata), a key crop in early African agriculture. Using
whole-genome resequencing and statistical models, we show that cultivated yam was domesticated from a forest
species. We infer that the expansion of African yam agriculture started in the Niger River basin. This result, alongside
with the origins of African rice and pearl millet, supports the hypothesis that the vicinity of the Niger River
was a major cradle of African agriculture.

1 aScarcelli, Nora1 aCubry, Philippe1 aAkakpo, Roland1 aThuillet, Anne-Céline1 aObidiegwu, Jude1 aBaco, Mohamed, N.1 aOtoo, Emmanuel1 aSonké, Bonaventure1 aDansi, Alexandre1 aDjedatin, Gustave1 aMariac, Cédric1 aCouderc, Marie1 aCausse, Sandrine1 aAlix, Karine1 aChaïr, Hâna1 aFrançois, Olivier1 aVigouroux, Yves uhttps://rubiaceae-africa.myspecies.info/content/yam-genomics-supports-west-africa-major-cradle-crop-domestication02610nas a2200157 4500008004100000245009900041210006900140520195900209100001602168700002902184700002702213700002002240700002402260700002802284856014002312 2016 eng d00aPhylogenetics and diversification history of African rattans (Calamoideae, Ancistrophyllinae).0 aPhylogenetics and diversification history of African rattans Cal3 a

Even though African rain forests display high levels of local species diversity and endemism, their lower
continental species diversity when compared with the Neotropics and Asia is paradoxical. This disparity is
mainly thought to be linked to either important extinction events during the Pleistocene or at the Eocene–
Oligocene boundary. African rattans or climbing palms are one of the most diverse clades of palms in Africa,
representing one-third of all known species. Here, we reconstruct the phylogeny and temporal evolution of
African rattans (Arecaceae: Calamoideae: Lepidocaryeae: Ancistrophyllinae) to test the two main hypotheses of
palm evolution in Africa. We constructed a near-complete, dated species-level phylogenetic tree for subtribe
Ancistrophyllinae using plastid and nuclear markers. The generic relationships between Ancistrophyllinae were
fully resolved and species-level relationships are well to weakly supported. Ancistrophyllinae diversified during
the Eocene with most species originating during the late Miocene after 10 Mya. This result is in agreement with
several other studies suggesting a pre–Pleistocene origin of the extant African flora. Ancistrophyllinae display an
anti-sigmoidal lineage-through-time plot with a moderate overall extinction fraction. Our simulations suggest
important roles for an ancient extinction event at the Oligocene–Eocene boundary. In contrast, the hypothesis of
an important extinction event in palms during the late Pliocene at 3 Mya is not supported. We suggest that the
evolutionary history of African rattans has undergone a constant diversification rate punctuated by one or
several important extinction events during the first part of the Cenozoic with most species diversity accumulating
during the late Miocene and Pliocene.

1 aFaye, Adama1 aPintaud, Jean-Christophe1 aFls, William, J. Baker1 aVigouroux, Yves1 aSonké, Bonaventure1 aCouvreur, Thomas, L. P. uhttps://rubiaceae-africa.myspecies.info/content/phylogenetics-and-diversification-history-african-rattans-calamoideae-ancistrophyllinae02084nas a2200169 4500008004100000245011800041210006900159520138700228100002801615700002301643700002401666700001901690700002001709700002701729700002001756856013801776 2018 eng d00aGuinea yam (Dioscorea spp., Dioscoreaceae) wild relatives identified using whole plastome phylogenetic analyses. 0 aGuinea yam Dioscorea spp Dioscoreaceae wild relatives identified3 a

The genus Dioscorea (Dioscoreaceae) contains several economically important species for human consumption,
medical and pharmaceutical uses. The phylogeny of this genus is not yet fully resolved. As a result, the relationships between
cultivated yams and their wild relatives are not well understood and this negatively affects the understanding of the evolution
of cultivated yams. Here, we reconstructed the phylogenetic relationships of the main African cultivated species with all West
African species in order to better circumscribe the crop wild relatives of African yams. Complete plastomes of 57 individuals
representing all 17 known Dioscorea species from West Africa were reconstructed. Tree topologies generated using maximum
parsimony and maximum likelihood approaches were highly congruent. Six monophyletic groups were obtained. All the
species were distinct except within the cultivated clade, where it was not possible to separate the two main cultivated species
(D. cayenensis, D. rotundata) from their closest West African wild relatives (D. abyssinica, D. praehensilis, D. sagittifolia).
Dioscorea baya formed a monophyletic group closely related to the cultivated clade. We therefore suggest it is included within
the yam crop–wild relative complex.

1 aMagwé-Tindo, acqueline1 aJ, Jan, J. Wiering1 aSonké, Bonaventure1 aZapfack, Louis1 aVigouroux, Yves1 aCouvreur, Thomas, L.P.1 aScarcelli, Nora uhttps://rubiaceae-africa.myspecies.info/content/guinea-yam-dioscorea-spp-dioscoreaceae-wild-relatives-identified-using-whole-plastome00623nas a2200157 4500008004100000245007600041210006900117100002900186700002200215700002400237700001900261700002000280700002800300700002000328856011700348 2019 eng d00aComplete plastome sequences of 14 African yam species (Dioscorea spp.).0 aComplete plastome sequences of 14 African yam species Dioscorea 1 aMagwé-Tindo, Jacqueline1 aWieringa, Jan, J.1 aSonké, Bonaventure1 aZapfack, Louis1 aVigouroux, Yves1 aCouvreur, Thomas, L. P.1 aScarcelli, Nora uhttps://rubiaceae-africa.myspecies.info/content/complete-plastome-sequences-14-african-yam-species-dioscorea-spp