Paving the way to the systematic understanding of a challenging clade of lepidote African Croton (Euphorbiaceae)

Although tropical rain forests represent the most species-rich terrestrial ecosystem on the planet, the three main rain forest regions (Neotropics, South-East Asia and continental Africa) are not equally diverse. Africa has been labeled the “odd man out” because of its perceived lower species diversity when compared to the Neotropics or South-East Asia. Understanding why, within a biome, certain regions have higher or lower species diversity provides important insights into the evolution of biodiversity. I review the evidence in favor of an “odd man out” pattern and the different hypotheses that have been advanced to explain and test this pattern using recent ecological, biogeographical and diversification studies. The “odd man out” pattern has yet to be formally tested using extensive inventory plot data (including non woody species) between all three major rain forest regions based on appropriate statistics in an area controlled manner. The lower species diversity is not the result of a single cause, but is probably linked to numerous intricate causes related to present and past events. Future comparative studies should combine numerous variables including novel ones such at plant functional diversity. Finally, though more extinction in Africa is apparent from the fossil record, it is still hard to precisely quantify to what degree extinction varied between the three major regions. Diversification studies of important tropical plant lineages tend to support higher speciation rates in the Neotropics and South-East Asia instead of higher extinction in Africa as the main cause explaining the differences in species diversity. The lower species diversity of African rain forests remains an understudied question with numerous preconceived and largely untested ideas for which we are still far from having a synthetic explanation. This review highlights that there are still very little intercontinental rain forest comparisons of plant species diversity hindering any solid conclusions. To better address this, an integrative approach involving archeologists, climatologists and biologists coupled with data from all three regions should be privileged.

Africa has the most tropical and subtropical land of any continent, yet has relatively low species richness in several taxa. This depauperate nature of the African tropical fauna and flora has led some to call Africa the “odd man out.” One exception to this pattern is velvet ants (Hymenoptera: Mutillidae), wingless wasps that are known for Müllerian mimicry. While North American velvet ants form one of the world’s largest mimicry complexes, mimicry in African species has not been investigated. Here we ask do African velvet ant Müllerian mimicry rings exist, and how do they compare to the North American complex. We then explore what factors might contribute to the differences in mimetic diversity between continents. To investigate this we compared the color patterns of 304 African velvet ant taxa using nonmetric multidimensional scaling (NMDS). We then investigated distributions of each distinct mimicry ring. Finally, we compared lizard diversity and ecoregion diversity on the two continents. We found that African female velvet ants form four Müllerian rings, which is half the number of North American rings. This lower mimetic diversity could be related to the relatively lower diversity of insectivorous lizard species or to the lower number of distinct ecoregions in Africa compared to North America.

Premise of research. Africa was declared the “odd man out” by P. W. Richards because its tropical forests have low species diversity and endemism relative to the Neotropics and Southeast Asia. A va...

In the face of the decline of many insects, there is an increasing demand for contemporary, fast and cost-effective approaches to monitor the development of populations and species. Numerous scientists favor molecular methods, especially those involving barcoding of the CO1 gene, as an alternative to classical, morphology-based species identification. Moreover, DNA barcoding is also discussed as a suitable method to support species delimitations in complexes of closely related taxa. We used the available sequences of ground beetles from North and Central Europe with additional ones we generated from Southern Europe and the Middle East to draw conclusion about the practicability of such approach for ground beetles. In general, while strong intraspecific differentiations within the CO1 fragment seem to characterize some wingless species (e.g. Graphipterus serrator, Siagona longula, Carabus problematicus, some Platycarabus species), others do not display much intraspecific variability (e.g. Graphipterus multiguttatus and G. sharonae within the “G. serrator clade”). These results certainly complicate the application of a metabarcoding approach without a larger database to delimitate these ground beetles. Furthermore, these results limit the applicability of the well-known barcoding gap, in ecological studies. With regards to taxonomic problems, mitochondrial and nuclear DNA sequences can provide support for taxonomic decisions. For example, the two taxa Carabus variolosus and nodulosus are characterized predominantely by K2P values lower than the barcoding gap. In view of the otherwise strong intraspecific differentiation within the genus Carabus, these two taxa should be regarded as subspecies. In contrast, DNA barcoding can also help to identify "good" species. Mitochondrial and nuclear data suggest, for example, that an Oreonebria taxon and a Platycarabus taxon from the South-western Alps represent "good species", although they were usually considered as synonyms or subspecies. In another case, two tiger beetle taxa, which until a few months ago were considered to belong to the same species, show such strong differentiation that only two species can be postulated (Calomera aulicoides and C. littoralis winkleri). In summary, we can state that DNA sequences and the barcoding gap can help to define species delimitations in ground beetles. However, several species, including widespread sister species, cannot be identified by DNA barcoding for various reasons (e.g. young species or horizontal gene flow). Consequently, until an automated, fast, and reliable method to identify species from samples emerges, ecological investigations have to rely on classical, morphology-based identifications.

Summary The taxonomic value and the typification of some species closely related to Ctenitis pretensa, particularly Ctenitis fraterna and Ctenitis speciosa, has been investigated. The study of the types and other collections in various European herbaria has led the author to recognize the following species and subspecies: Ctenitis pretensa (Afz. ex Swartz) Ching, typified by a specimen from Sierra Leone collected by Afzelius (S), widely distributed in West Tropical Africa. Ctenitis fraterna (Mett. ex Kuhn) Tardieu, lectotypified by a specimen from Madagascar collected by Boivin (W). The species is subdivided in two subspecies: subsp. fraterna confined to Madagascar and subsp. biokoensis Pic. Ser., subsp. nova, typified by Vogel 121 from Bioko (K) and distributed with certainty only in Sierra Leone, Bioko (Fernando Po), Angola and Tanzania, but probably present in other regions of continental tropical Africa. Ctenitis attenuata Pic. Ser., sp. nova, typified by a specimen collected by Mann in Principe Is. (...

Temporal and spatial patterns in flowering phenology were assessed for eight tropical African tree species. Specifically, the frequency and seasonality of flowering at seven sites in central Africa were determined using field data, graphical analysis and circular statistics. Additionally, spatial variation in the timing of flowering across species range was investigated using herbarium data, analysing the relative influence of latitude, longitude and timing of the dry season with a Bayesian circular generalized linear model. Annual flowering was found for 20 out of the 25 populations studied. For 21 populations located at the north of the climatic hinge flowering was occurring during the dry season. The analysis of herbarium collections revealed a significant shift in the timing of flowering with latitude forE. suaveolens, and with the timing of the dry season forM. excelsa(and to a lesser extentL. alata), with the coexistence of two flowering peaks near the equator where the distribution of monthly rainfall is bimodal. For the other species, none of latitude, longitude or timing of the dry season had an effect on the timing of flowering. Our study highlights the need to identify the drivers of the flowering phenology of economically important African tree species.

The genus Amanita is well represented in tropical Africa, but most previous taxonomic studies were largely based only on morphology. In this study, we used both morphological and molecular data (nLSU sequences) to infer the phylogenetic relationships of ten species of Amanita sect. Vaginatae s.l. from tropical Africa. It was found that all five species with both an annulus and commonly present clamp connections in the basidioma were clustered in the sect. Caesareae. One species with neither an annulus nor clamp connections was placed in sect. Vaginatae s.s. The remaining four taxa with an annulus, but without clamp connections were interestingly also grouped into sect. Vaginatae s.s. with strong statistical support. Consequently, the section Vaginatae s.s. should be slightly modified to include tropical species with an annulus. As a new species, A. madagascariensis was described and illustrated. Amanita tanzanica was treated as a synonym of A. mafingensis.

Although revised in the past 20 years for the two major centers of its range, the southern African winter-rainfall zone and the eastern southern African Drakensberg, the sub-Saharan African genus Hesperantha remains inadequately understood. Continuing botanical exploration in southern Africa has resulted in the discovery of several new species and of populations of species known only from the type or very few collections. Species are listed here in a revised taxonomic order together with keys for the genus in the southern African winter-rainfall zone and in eastern southern Africa and tropical Africa that have a summer-rainfall climate. Included here are 11 new species, a shift in the application of the name H. candida to plants called H. vernalis, recognition of H. leucantha for plants previously called H. candida, and a series of novel observations relating to species delimitation, biology, geography, and taxonomy. Important range extensions are also noted for poorly known species, among them H. ciliolata, H. flava, H. quadrangula, and H. teretifolia. Including the novelties described in this account, 79 species of Hesperantha are now recognized, 4 in tropical Africa, 37 in summer-rainfall southern Africa, mostly of the Drakensberg, and 42 in winter-rainfall southern Africa. Hesperantha longicollis and H. coccinea are shared between tropical and eastern southern Africa, and H. rediote and H. bachmannii between the winter- and summer-rainfall zones of southern Africa. The new species from the southern African winter-rainfall zone are: H. decipiens, from Narnaqualand, allied to H. radiata; H. glabrescens, from the Roggeveld Escarpment, closely related to H. pilosa; H. malvina, also related to H. pilosa, from cliffs on the Anysberg in the Little Karoo; H. rupicola, a lithophyle from western Bushmanland, possibly most closely related to H. acuta; and H. sufflava, a member of section Hesperantha from Malmesbury in Western Cape Province. New species from the southern African summer-rainfall zone are: H. altimontana, a spring-blooming, white-flowered species of the high Drakensberg of Lesotho and KwaZulu-Natal; H. brevistyla, a dwarf plant from Free State and adjacent KwaZulu-Natal; H. debilis, evidently allied to the widespread H. bachmannii, from the Albany Distriet of Eastern Cape Province; H. exiliflora, from Lesotho, which has small, purple flowers; H. saxicola, of rocky outcrops in Mpumalanga, South Africa, which has large white flowers with short anthers; and H. stenosiphon, a long-tubed, pink-flowered species with blackish anthers from Eastern Cape, South Africa.

AimPalms (Arecaceae/Palmae) are a model group for evolutionary studies in the tropics. In two companion papers, we aim to establish a general framework of palm evolution, exploring the geographical distribution of palm lineages and species diversity patterns at global and regional levels. In this, the second paper, we analyse the biogeographical events underlying regional palm assemblages and diversification processes across the family. We investigate the timing and location of diversification rate shifts and test the ‘odd man out’ pattern of low species diversity observed in the African palm flora.LocationGlobal.MethodsA complete, dated phylogeny of palm genera and ancestral area reconstructions were used to infer the biogeographical history of regional palm assemblages. Diversification rates for all genera were estimated and significant shifts in diversification rates across the family were identified under a maximum likelihood model.ResultsFollowing their early diversification in Laurasia around 100 Ma, palms dispersed southwards before the end of the Cretaceous. Few dispersal events into Africa, North America and South America were inferred, whereas numerous lineages migrated between Eurasia, the Pacific and the Indian Ocean. Thirteen diversification rate increases were identified. High diversification rates were found only in lineages from Asia, the Americas, the Pacific and the Indian Ocean, but not in any African groups. Diversification decreases were not identified in any lineage.Main conclusionsDispersal of palms into their present‐day distribution started during the Late Cretaceous, consistent with the first fossil records for rain forests in Africa and South America. The few dispersal events into South America and Africa emphasize the isolated position of these continents for most of the Cenozoic. In contrast, high dispersal between Eurasia, the Pacific and the Indian Ocean, notably during the Miocene, can be attributed to geological activity in the region, especially in Malesia. Low species diversity in Africa relative to other regions is explained here by increased in situ diversification in Asia, the Americas, the Pacific and the Indian Ocean, rather than by diversification rate decreases in Africa. This may prove to be a general pattern in other organisms showing a similar disparity in richness in Africa.

Notoriously slow rates of molecular evolution and convergent evolution among some morphological characters have limited phylogenetic resolution for the palm family (Arecaceae). This study adds nuclear DNA (18S SSU rRNA) and chloroplast DNA (cpDNA; atpB and rbcL) sequence data for 65 genera of palms and characterizes molecular variation for each molecule. Phylogenetic relationships were estimated with maximum likelihood and maximum parsimony techniques for the new data and for previously published molecular data for 45 palm genera. Maximum parsimony analysis was also used to compare molecular and morphological data for 33 palm genera. Incongruence among datasets was detected between cpDNA and 18S data and between molecular and morphological data. Most conflict between nuclear and cpDNA data was associated with the genus Nypa. Several taxa showed relatively long branches with 18S data, but phylogenetic resolution of these taxa was essentially the same for 18S and cpDNA data. Base composition bias for 18S that contributed to erroneous phylogenetic resolution in other taxa did not seem to be present in Palmae. Morphological data were incongruent with all molecular data due to apparent morphological homoplasy for Caryoteae, Ceroxyloideae, Iriarteae, and Thrinacinae. Both cpDNA and nuclear 18S data firmly resolved Caryoteae with Borasseae of Coryphoideae, suggesting that at least some morphological characters used to place Caryoteae in Arecoideae are homoplastic. In this study, increased character sampling seems to be more important than increased taxon sampling; a comparison of the full (65-taxon) and reduced (45- and 33-taxon) datasets suggests little difference in core topology but considerably more nodal support with the increased character sample sizes. These results indicate a general trend toward a stable estimate of phylogenetic relationships for the Palmae. Although the 33-taxon topologies are even better resolved, they lack several critical taxa and are affected by incongruence between molecular and morphological data. As such, a comparison of results from the 45- and 33-taxon trees offers the best available reference for phylogenetic inference on palms.

Phylogeographic analyses provide valuable insights for species delimitation and taxonomic decision-making. The family Adelgidae (infraorder: Aphidomorpha) exhibits relatively low species diversity, comprising approximately 63 species primarily distributed across temperate regions. However, the taxonomy of this family remains debatable because of its complex life cycle and high morphological plasticity. The DELINEATE program offers a statistical framework that integrates multiple species concepts and prior taxonomic knowledge to improve species delimitation. In this study, we validated the taxonomic status of 3 newly discovered Adelges species—Adelges breviacus sp. nov., Adelges baborinisanensis sp. nov., and Adelges xueshanensis sp. nov.—and elucidated their phylogeographic characteristics. Our findings indicated that the most recent common ancestor of these 3 species diverged from their North American sister—Adelges lariciatus—approximately 4.6 million years ago and persisted in the coastal mountain regions of southeast China. Subsequently, these 3 adelgids migrated to Taiwan with Picea morrisonicola 1–3 million years ago, when environments became favorable for both Adelges and their host Picea. Ancestral area reconstruction revealed that the origins of the crown groups of Adelges and Picea were associated with the biogeographic connection between East Asia and North America, corresponding to dispersal of Picea from North America to East Asia via the Bering Land Bridge. Although transoceanic dispersal might have contributed to the origin of the crown group of Pineus, current data sets are insufficient to test this biogeographic hypothesis. Overall, long-distance dispersal appears to have facilitated the disjunct distribution and current biogeographic patterns of Adelgidae.

Background: The phylogenetic resolution within the Gloydius halys-intermedius Complex remains debatable due to the following reasons: loci selection in previous studies varied between authors; limited dataset (1-5 mitochondrial or nuclear gene fragments); lack of sampling density; and nodal supports at specific nodes remain weak, specifically within Gloydius cognatus, G. halys, and G. stejnegeri. Objectives: To revise the taxonomic and phylogenetic relationships within the G. halys-intermedius Complex, we reconstructed the molecular phylogeny and performed species delimitation based on the complete mitochondrial genomes. Methods: In this study, twelve nomenclatural groups of Gloydius species were involved in the computation of Bayesian phylogenomic inference, five of the twelve nomenclature groups were newly sequenced, while the rest were acquired from the National Center for Biotechnology Information (NCBI). The Bayesian phylogenomic inference was constructed based on 13 mitochondrial protein-coding genes. Species delimitation was performed by two distance-based methods (ABGD and ASAP) and two tree-based methods (GMYC and bPTP). Results: This research resolved the systematic relationship within the G. intermedius Complex with the support of mitogenome-based phylogenomics, while indicating cryptic diversity within the Gloydius halys-intermedius Complex: G. intermedius samples from South Korea show as paraphyletic to the cluster of the samples from northeastern China. Species delimitation results based on four models resemble each other, supporting Gloydius caucasicus, G. cognatus, G. halys, and G. stejnegeri, each representing full species. The species delimitation results of this research also resemble the nomenclatural species based on previous morphometrical results. This research indicates that species delimitation efforts based on the phylogenomic approach would likely resolve complex evolutionary relationships.

Species delimitation and phylogenomics of economically important African Pterocarpus trees, with an implication for the development of DNA-based species identification tools.

Special care is needed in the delimitation and identification of halictid bee species, which are renowned for being morphologically monotonous. Corynura Spinola and Halictillus Moure (Halictidae: Augochlorini) contain species that are key elements in southern South American ecosystems. These bees are very difficult to identify due to close morphological similarity among species and high sexual dimorphism. We analyzed 170 barcode-compliant COI sequences from 19 species. DNA barcodes were useful to confirm gender associations and to detect two new cryptic species. Interspecific distances were significantly higher than those reported for other bees. Maximum intraspecific divergence was less than 1% in 14 species. Barcode index numbers (BINs) were useful to identify putative species that need further study. More than one BIN was assigned to five species. The name Corynura patagonica (Cockerell) probably refers to two cryptic species. The results suggest that Corynura and Halictillus species can be identified using DNA barcodes. The sequences of the species included in this study can be used as a reference to assess the identification of unknown specimens. This study provides additional support for the use of DNA barcodes in bee taxonomy and the identification of specimens, which is particularly relevant in insects of ecological importance such as pollinators.

Species delimitation is challenging in lineages that exhibit both high plasticity and introgression. This challenge can be compounded by collection biases, which may downweight specimens morphologically intermediate between traditional species. Additionally, mismatch between named species and observable phenotypes can compromise species conservation. We studied the species boundaries of Quercus acerifolia, a tree endemic to Arkansas, U.S. We performed morphometric analyses of leaves and acorns from 527 field and 138 herbarium samples of Q. acerifolia and its close relatives, Q. shumardii and Q. rubra. We employed two novel approaches: sampling ex situ collections to detect phenotypic plasticity caused by environmental variation and comparing random field samples with historical herbarium samples to identify collection biases that might undermine species delimitation. To provide genetic evidence, we also performed molecular analyses on genome-wide SNPs. Quercus acerifolia shows distinctive morphological, ecological, and genomic characteristics, rejecting the hypothesis that Q. acerifolia is a phenotypic variant of Q. shumardii. We found mismatches between traditional taxonomy and phenotypic clusters. We detected underrepresentation of morphological intermediates in herbarium collections, which may bias species discovery and recognition. Rare species conservation requires considering and addressing taxonomic problems related to phenotypic plasticity, mismatch between taxonomy and morphological clusters, and collection biases.