Amelia Shepherd-Clowes

We investigated here speciation and diversification mechanisms in Turraea and allied genera (Meliaceae-Turraeeae) from Madagascar and continental Africa, as well as their generic delimitations. Our goal was to contribute to an improved understanding of the origin and diversification of the Malagasy and African floras. Using target-enrichment sequencing, we assembled a nuclear dataset comprising 64 taxa (75% of the group’s species diversity) to reconstruct phylogenetic relationships within the group. We estimated divergence times and diversification rate shifts and assessed the prevalence of incomplete lineage sorting and introgression/hybridization. The group appears to have originated in the Eocene, probably in southern Africa, with a diversification rate shift occurring in the Miocene coinciding with the colonization of Madagascar. This shift, associated with incomplete lineage sorting and introgression/hybridization, suggests a rapid diversification linked to the onset of the Indian Monsoon. We propose a revised generic classification, including a new key and synoptic descriptions of the genera, to accommodate the polyphyly of Turraea. In this context, we place the endemic Malagasy genera Humbertioturraea and Calodecaryia in synonymy under Turraea, and resurrect the South African genus Nurmonia and the Angolan and Indian genus Naregamia. We therefore publish the necessary new combinations in Nurmonia and Turraea.

The development and establishment of a broader range of coffee species and hybrids is likely to play a key role in coffee farming sustainability in an era of accelerated climate change. We investigated hybridization between Coffea liberica (Liberica) and C. dewevrei (excelsa) utilizing 7,618 SNPs from 113 accessions, sampled across three continents. Our analyses demonstrated that these two species have hybridized readily in cultivation and produced fertile progeny with a wide range of genomic admixture. We revealed extensive genomic admixture in farmed accessions from Sarawak. The identified hybrids exhibited intermediate characteristics and overlapping values for key agronomic traits, including seed size and parchment thickness. These traits, which influence yield, outturn and post-harvest processing, can be transferred via hybridization. The hybrids also have the potential to broaden the climate envelope for successful coffee cultivation and transfer disease resistance. Improved genotypes resulting from hybrids between C. liberica and C. dewevrei could be brought into production relatively quickly, as a means of developing both species. We propose the formal name Coffea × libex for the interspecies hybrid.

Androsace cantabrica (Losa & P. Monts.) Kress is a narrow endemic alpine plant restricted to a few high‐elevation localities in the Cantabrian Mountains of northern Spain. Although currently accepted as a distinct species, its close morphological and phylogenetic affinity to related taxa such as Androsace adfinis and Androsace halleri has led to historical uncertainty about its taxonomic status and evolutionary origin. Here, we use the universal Angiosperms353 target capture kit to generate nuclear and plastid data from A. cantabrica and closely related species in section Aretia . We employ phylogenomic analyses to clarify species boundaries and population genomic analyses to inform conservation management, as well as flow cytometry and sequence‐based analysis using allelic frequencies to estimate its ploidy level. Phylogenetic analyses based on nuclear loci support A. cantabrica as a monophyletic clade, distinct from both A. adfinis and the A. halleri and Androsace laggeri clades, although topological incongruence with plastid data suggests historical hybridization. Flow cytometry and allelic frequency‐based analysis indicate that A. cantabrica is tetraploid, differentiating it from A. halleri and A.  laggeri , which are diploid. Population structure analyses reveal a shallow genetic split between eastern and western groups ( F _ST = 0.04485), with higher genetic diversity observed in the east. We estimated the species' distribution, population sizes, and threats, and classified it as Vulnerable under IUCN criteria B1ab(ii,iii) + 2ab(ii,iii). We recommend targeted in situ management, ex situ seed conservation, and the establishment of a micro‐reserve. This study illustrates the utility of Angiosperms353 data for resolving both taxonomic questions and conservation strategies in polyploid, range‐restricted species.

Safeguarding the long-term future of the global coffee supply chain represents a major challenge, particularly in an era of accelerated climate change. Of particular concern are the millions of smallholder farmers across the tropical belt who rely on coffee as their major source of income. The world’s coffee farmers, and thus the global coffee supply chain, rely on two species: Arabica (Coffea arabica) and robusta (Coffea canephora)¹. A third species, Coffea liberica, including Liberica coffee (C. liberica var. liberica) and excelsa coffee (C. liberica var. dewevrei), represents a minor share of global production, although the cultivation of this species is steadily increasing owing to climate challenges affecting Arabica and robusta, coupled with an increasing market demand². In Southeast Asia, Liberica consumption has continued since its introduction in the late-nineteenth century and is now witnessing a renaissance, particularly in Malaysia, Indonesia and Fiji. In Uganda, South Sudan and Guinea, attention is focused on excelsa owing to its ability to grow and produce commercially viable crops under higher temperatures and extended periods of low rainfall compared with robusta^2,3. Excelsa production is also increasing in India in response to worsening climate conditions for Arabica and robusta, and in Vietnam and Indonesia to supplement robusta and diversify coffee production. Here we investigate species delimitation in C. liberica using genomic data in combination with morphology and geographical distribution, to understand the implications for coffee crop improvement and the conservation of coffee genetic resources.