Some tropical plant families, such as the Sapotaceae, have a complex taxonomy, which can be resolved using Next Generation Sequencing (NGS). For most groups however, methodological protocols are still missing. Here we identified 531 monocopy genes and 227 Short Tandem Repeats (STR) markers and tested them on Sapotaceae using target capture and NGS. The probes were designed using two genome skimming samples from Capurodendron delphinense and Bemangidia lowryi, both from the Tseboneae tribe, as well as the published Manilkara zapota transcriptome from the Sapotoideae tribe. We combined our probes with 261 additional ones previously published and designed for the entire angiosperm group. On a total of 792 low-copy genes, 638 showed no signs of paralogy and were used to build a phylogeny of the family with 231 individuals from all main lineages. A highly supported topology was obtained at high taxonomic ranks but also at the species level. This phylogeny revealed the existence of more than 20 putative new species. Single nucleotide polymorphisms (SNPs) extracted from the 638 genes were able to distinguish lineages within a species complex and to highlight geographical structuration. STR were recovered efficiently for the species used as reference (C. delphinense) but the recovery rate decreased dramatically with the phylogenetic distance to the focal species. Altogether, the new loci will help reaching a sound taxonomic understanding of the family Sapotaceae for which many circumscriptions and relationships are still debated, at the species, genus and tribe levels.

Aim: Central America is largely covered by hyperdiverse, yet poorly understood, rain forests. Understorey palms are diverse components of these forests, but little is known about their historical assembly. It is not clear when palms in Central America reached present diversity levels and whether most species arrived from neighbouring regions or evolved locally. We addressed these questions using the most species‐rich American palm clades indicative of rain forests. We reconstructed and compared their phylogenomic and biogeographical history with the diversification of 54 other plant lineages, to gain a better understanding of the processes that shaped the assembly of Central American rain forests.Location: Central America.Time period: Cretaceous to present.Major taxa studied: Arecaceae: Arecoideae: Bactridinae, Chamaedoreeae, Geonomateae.Methods: We sampled 218 species through fieldwork and living collections. We sequenced their genomic DNA using target sequence‐capture procedures. Using 12 calibration points, we reconstructed dated phylogenies under three approaches (multispecies coalescent, maximum likelihood and Bayesian inference), conducted biogeographical analyses (dispersal–extinction–cladogenesis) and estimated phylogenetic diversity metrics.Results: Dated phylogenies revealed intense diversification in Central America from 12 Ma. Local diversification events were four times more frequent than dispersal events, and we found strong phylogenetic clustering in relationship to Central America.Main conclusions: Our results suggest that most understorey palm species that characterize the Central American rain forests today evolved locally after repeated dispersal events, mostly from South America. Understorey palms in Central American rain forests diversified primarily after closure of the Central American Seaway at c. 13 Ma, suggesting that the Great American Biotic Interchange was a major trigger for plant diversification in Central American rain forests. This recent diversification contrasts with the much earlier existence of rain forest palms in neighbouring South America since c. 58 Ma. We found similar timings of diversification in 54 other seed plant lineages, suggesting an unexpectedly recent assembly of the hyperdiverse Central American flora.

The Malagasy genusCapurodendroncurrently accommodates 26 described species and is the largest genus of the family Sapotaceae in Madagascar. These species are frequently logged because of their valued hardwood, which potentially puts them at risk of extinction. Species‐level identifications are often problematic, and this hinders both an accurate assessment of their conservation status and the development of effective protection measures. We sorted all the material (ca. 860 collections) available in the herbaria with significant collections for Madagascar into 47 putative species based on morphology. On 41 of these, for which we were able to retrieve suitable DNA, we conducted a phylogenetic reconstruction based on molecular sequences of 638 loci from 108Capurodendronspecimens, performing a target capture approach combined with next‐generation sequencing. Maximum likelihood (RAxML), pseudocoalescence (ASTRAL), and coalescence (STACEY) analyses showed thatCapurodendroncomprises two deeply divergent lineages. One, which includes a single species, is here newly described asC. subg.Reflexisepalabased on its distinctive morphology. The second lineage contains all remaining species, which seem to have resulted from a rapid radiation event. The phylogenetic tree provides good support for most of the species hypothesized based on morphology, with the exception of two species‐groups that we have named the Arid Complex and the Eastern Complex. As many as 20 species‐level lineages genetically distinct from any of the currently recognized species were identified, 17 of which were morphologically well‐characterized, representing strong candidates for new species. This would suggest thatCapurodendronis the most species‐rich endemic genus of plants in Madagascar. While 14 of these 20 clades are still under study, we here describe six species new to science:Capurodendron andrafiamenae(provisionally assessed as CR),C. aubrevillei(VU),C. birkinshawii(CR),C. naciriae(EN),C. randrianaivoi(CR), andC. sakarivorum(EN).Capurodendron oblongifoliumcomb. nov. (EN), previously regarded as a variety ofC. perrieri, represents a distinct lineage that is here recognized at the species level. The newly described species are illustrated by line drawings and photographs from the field, and a preliminary threat assessment is provided. We discuss the evolutionary history ofCapurodendronand also explore the question of node age estimates and their methodological limitations.

Capurodendron is the largest endemic genus of plants from Madagascar, with around 76% of its species threatened by deforestation and illegal logging. However, some species are not well circumscribed and many of them remain undescribed, impeding a confident evaluation of their conservation status. Here we focus on taxa delimitation and conservation of two species complexes within Capurodendron: the Arid and Western complexes, each containing undescribed morphologies as well as intermediate specimens alongside well-delimited taxa. To solve these taxonomic issues, we studied 381 specimens morphologically and selected 85 of them to obtain intergenic, intronic, and exonic protein-coding sequences of 794 nuclear genes and 227 microsatellite loci. These data were used to test species limits and putative hybrid patterns using different approaches such as phylogenies, PCA, structure analyses, heterozygosity level, FST, and ABBA-BABA tests. The potential distributions were furthermore estimated for each inferred species. The results show that the Capurodendron Western Complex contains three well-delimited species, C. oblongifolium, C. perrieri, and C. pervillei, the first two hybridizing sporadically with the last and producing morphologies similar to, but genetically distinct from C. pervillei. The Arid Complex shows a more intricate situation, as it contains three species morphologically well-delimited but genetically intermixed. Capurodendron mikeorum nom. prov. is shown to be an undescribed species with a restricted distribution, while C. androyense and C. mandrarense have wider and mostly sympatric distributions. Each of the latter two species contains two major genetic pools, one showing interspecific admixture in areas where both taxa coexist, and the other being less admixed and comprising allopatric populations having fewer contacts with the other species. Only two specimens out of 172 showed clear genetic and morphological signals of recent hybridization, while all the others were morphologically well-delimited, independent of their degree of genetic admixture. Hybridization between Capurodendron androyense and C. microphyllum, the sister species of the Arid Complex, was additionally detected in areas where both species coexist, producing intermediate morphologies. Among the two complexes, species are well-defined morphologically with the exception of seven specimens (1.8%) displaying intermediate patterns and genetic signals compatible with a F1 hybridization. A provisional conservation assessment for each species is provided.

The alpine clematis (Clematis alpina L., Ranunculaceae) is a liana growing in mountain regions of northern Eurasia. In the European Alpine region, where the subspecies C. alpina subsp. alpina occurs, a few populations are isolated from the main range in the peripheral north-western Prealps, a relatively understudied but biogeographically important region. It has been shown that such edge populations could potentially contain a source of unique genetic variability that reflects past biogeographical and microevolutionary processes. We tested this hypothesis using sequence capture data and a large population sampling across the species range. We show that individuals from the north-western Prealps form a genetic cluster that is clearly distinct from the other individuals of the European subspecies C. alpina subsp. alpina. This cluster adds to two other geographically driven clusters with a larger spatial extent, that include populations from the rest of the Alps and from the Carpathians/Balkan Peninsula mountains, respectively. Genetic diversity indices such as inbreeding and nucleotide diversity are the highest and lowest, respectively, for the Prealps populations indicating a possible loss of diversity. Our results demonstrate the biogeographical importance of isolated, marginal populations as sources of distinctive lineages, and highlight the conservation value of the north-western Prealps populations of alpine clematis. They also point out the promising use of sequence capture of gene selected for studies at high phylogenetic level for studies at intraspecific level.

Trachycarpus fortunei(Arecaceae: Coryphoideae) is an Asian palm that was introduced during the nineteenth century in southern Switzerland and northern Italy as an ornamental plant. In the recent decades, the palm has become an aggressive invasive species in the region. Before this study, the genetic structure and diversity of the naturalised populations were unknown. We aimed at understanding the dynamics of invasion and at comparing the results obtained with two types of markers. This genetic approach aimed at tracing back as far as possible the source of invasive populations comparing historical information found in literature and invasive genetic patterns. The genetic diversity was analysed using eight microsatellites (five were developed for that purpose) and 31′000 SNPs identified through GBS analyses. Genetic analyses were carried out for 200 naturalised individuals sampled from 21 populations in the Canton Ticino (Switzerland) and the provinces of Lombardy and Piedmont (Italy). The observed general panmixia indicates that the expansion ofT. fortuneiis active in its naturalised areas. The genetic pattern found for both SNPs and microsatellites appears to be related to the colonisation process, with a lack of geographic structure and bottleneck signatures occurring at the colonisation front, distantly from historical sites. This study gives a better understanding of the expansion ofT. fortuneiand adds new insights to its ecology.