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.

The results of the first molecular phylogenetic study of Pseudephebe are presented; a three-locus phylogeny. The genus is confirmed as monophyletic within the alectorioid clade of Parmeliaceae. Two major clades were recovered, which can be assigned to the two traditional taxa, P. minuscula and P. pubescens, with modifications of the species delimitation, especially the variable P. minuscula. These species are cryptic and cannot be confidently distinguished morphologically due to phenotypic convergence. Therefore, the use of P. pubescens aggr. is recommended for samples not molecularly analyzed. Contrary to previous studies, specimens of both species might have indistinct pseudocyphellae and also contain lichen substances; norstictic acid was detected in c. 60% of specimens tested. An SSU 1516 Group I intron is usually present in P. minuscula but always absent in P. pubescens. The species-level nomenclature is summarized and sequenced reference specimens (RefSpec) for both Pseudephebe species are selected. Sequences from Bryoria mariensis established that this name was a synonym of P. minuscula.

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.

Previous phylogenetic studies have demonstrated that the Manilkarinae are a monophyletic subtribe if Northia is excluded. The subtribe consists of four genera: Faucherea, Labourdonnaisia, Labramia and Manilkara. However, the same phylogenetic studies also raised taxonomic issues concerning unclear generic delimitations and unresolved relationships. The current study's aims are: to resolve these taxonomic issues using a molecular phylogeny based on hundreds of nuclear markers sequenced from a representative sampling of taxa across the four genera; to find relevant morphological characters allowing the distinction of the clades retrieved with the phylogeny; and finally to understand the evolutionary history of the subtribe by conducting a divergence time estimation and ancestral state reconstructions. Our phylogeny shows a well‐resolved backbone with four main lineages: the Labramia clade, the main clade of Manilkara, a clade in which all species of Labourdonnaisia and Faucherea are mixed, and a clade of three Pacific Manilkara species. The main clade of Manilkara is retrieved as sister to Labramia, and the Labourdonnaisia‐Faucherea clade is clearly assessed as sister to the three Pacific Manilkara species. As a consequence, Faucherea is synonymized with Labourdonnaisia, and the three Pacific Manilkara are considered to be a separate genus, for which the name Abebaia is resurrected. We provide emended descriptions for Labourdonnaisia and Abebaia as well as the necessary new combinations. The ancestral state reconstruction of flower characters shows that ancestral Manilkarinae were characterized by a hexamerous corolla, well‐developed dorsal appendages and staminodes, and a pubescent ovary. These character states have been retained in the main Manilkara clade, but surprisingly also in Abebaia, which appears as a cryptic genus. The lack of dorsal appendages and the reduction of staminodes observed in Labourdonnaisia appeared after the split from Abebaia. The increase in corolla merism observed mainly in the Mascarene Labourdonnaisia, which was used to separate it from Faucherea, appears to be a derived state, which evolved separately in a few species during the radiation of Labourdonnaisia on Madagascar and the Mascarenes. The glabrous ovary state observed in Labramia also constitutes a derived synapomorphic state in the genus.

In order to confirm and investigate the extent of reported mismatches between chemotypes and molecular sequence data in Bryoria fuscescens s. lat., we examined 15 morphologically similar thalli from each of three Pinus forest sites in the Sistema Central of central Spain. Three thalli were rejected due to infections by Phacopsis huuskonenii (not previously published from Spain). The remaining 42 thalli represented nine ITS rDNA haplotypes and four chemotypes (by TLC): fumarprotocetraric and protocetraric acids; norstictic and connorstictic acids; psoromic acid; and fumarprotocetraric, protocetraric and psoromic acids. The molecular phylogenetic tree was characterized by extremely short branch lengths, often only with a single mutational difference, and a single haplotype could have different chemical products. In some cases, adjacent specimens represented different chemotypes, and three thalli appeared to be mixed individuals. Consistency of both molecular and chemical data within individual specimens was demonstrated by examining four different parts of each thallus, which showed only a difference in the location of psoromic acid in some. This is the first population-level study of this taxon, and so it is premature to propose taxonomic changes at this time. Further populations in different parts of the geographical range of this widespread complex now need to be analyzed, and more sensitive chemical analyses conducted, in order to understand the basis of the variability and determine the appropriate taxonomic treatment.