Arthur François Boom

Biome conservatism is prevalent during the evolution of plant lineages. However, studies assessing biome lability, i.e. the capacity to shift biomes and its impact on tropical tree species diversification is currently limited. To address this, we analysed an endemic lineage of African tropical trees to investigate phylogenetic patterns of biome conservatism and lability and their impact on speciation and extinction rates. We reconstructed a time-calibrated phylogeny of the Berlinia clade (16 genera, 201 species) using 140 nuclear genes, 75% of its extant species and two fossil calibrations. We found the forest biome as the ancestral habitat and we inferred nine independent shifts from forest to savanna with no reversals. The forest biome is mostly conserved within the Berlinia clade, while the ability to shift to the savanna biome is randomly distributed across the group. We found five palaeoendemic genera that have persisted solely in the forest biome since the Oligocene. However, the ability to shift among biomes does not seem to influence speciation or extinction rates. Our results suggest that palaeoendemic and forest-restricted lineages are more susceptible to habitat alterations and climate change than lineages with biome lability, due perhaps to an innate limitation to adapt to new habitat types.

Summary: Niche conservatism is prevalent during the evolution of plant lineages. However, inferring biome niche lability and its impact on tropical tree species diversification is currently limited. To better understand biome niche lability and its effect on diversification rates, we analyzed an endemic lineage of African tropical trees, testing whether biome niche type (forest vs savanna) and biome lability are non-randomly distributed. We reconstructed a time-calibrated phylogeny of the Berlinia clade (16 genera, ca 201 species) using 140 nuclear genes, 75% of its extant species, and eight fossil calibrations. We also analyzed the phylogenetic signal of biome shifts across the group and its effect on diversification and extinction rates. We found the forest biome as the ancestral condition and a directional shift from forest to savanna (no reversals). The forest biome type is conserved in the Berlinia clade, but the lability to shift biomes is randomly distributed in the group. We did not find evidence that biome shift was associated with higher diversification or lower extinction rates. Our analyses identified five paleoendemic genera that have persisted solely in the forest biome since the Eocene. These paleoendemic and forest-restricted lineages are potentially more susceptible to habitat alterations of human related activities and future climate change, due to perhaps an innate limitation to adapt to new habitat types.

Characterizing the feeding ecology of threatened species is essential to establish appropriate conservation strategies. We focused our study on the proboscis monkey (Nasalis larvatus), an endangered primate species which is endemic to the island of Borneo. Our survey was conducted in the Lower Kinabatangan Wildlife Sanctuary (LKWS), a riverine protected area that is surrounded by oil palm plantations. We aimed to determine the diet of multiple proboscis monkey groups by using two methods. First, we conducted boat-based direct observations (scan and ad libitum sampling) and identified 67 plant species consumed by the monkeys at their sleeping sites in early mornings and late afternoons. Secondly, we used the DNA metabarcoding approach, based on next-generation sequencing (NGS, MiSeq Illumina) of faecal samples (n = 155), using the short chloroplast sequence, the trnL (UAA) P6 loop. In addition, we built a DNA reference database with the local plants available in the LKWS. When combining feeding data from both methods, we reported a diverse dietary ecology in proboscis monkeys, with at least 89 consumed plant taxa, belonging to 76 genera and 45 families. Moreover, we were able to add 22 new genera as part of the diet of this endangered colobine primate in the LKWS. The two methods provided congruent and complementary results, both having their advantages and limitations. This study contributed to enhance the knowledge on the feeding ecology of proboscis monkeys, highlighting the significance of several plant species that should further be considered in habitat restoration plans or corridor establishment.

In spite of the global barcoding effort, there is still a lack of genetic data on African freshwater fishes. We aimed to contribute to bridging this gap by providing molecular data on commercially important catfish species from the north-western part of Lake Tanganyika. We collected 215 catfish specimens and sequenced the standard vertebrate barcoding gene (COI) for 41 specimens. Additionally, we sequenced 20 specimens for the mitochondrial Cyt-b gene to make the link to previously published datasets. We identified 11 species using morphology, compared DNA sequences with those available on GenBank, and employed Automatic Barcode Gap Discovery (ABGD) and phylogenetic approaches. The dataset includes the first molecular data (COI and Cyt-b) for Chrysichthys acsiorum, as well as the first-ever COI sequences for Dinotopterus cunningtoni and Malapterurus tanganyikaensis. Our findings extend the known distribution of C. acsiorum by approximately 100 km. Additionally, we demonstrated the difficulty in delineating species of Chrysichthys and Synodontis from Lake Tanganyika with molecular tools. For Chrysichthys, automated methods, such as ABGD, failed to delineate species. However, barcoding does seem promising as all the individual species are resolved as clades. Within Synodontis, the study found a strong similarity between S. grandiops and S. multipunctatus, highlighting a need for revision. Our findings emphasize the necessity for integrative taxonomy in the study of catfishes from Lake Tanganyika.

Premise: Phylogenetic approaches can provide valuable insights on how and when a biome emerged and developed using its structuring species. In this context, Brachystegia Benth, a dominant genus of trees in miombo woodlands, appears as a key witness of the history of the largest woodland and savanna biome of Africa.Methods: We reconstructed the evolutionary history of the genus using targeted‐enrichment sequencing on 60 Brachystegia specimens for a nearly complete species sampling. Phylogenomic inferences used supermatrix (RAxML‐NG) and summary‐method (ASTRAL‐III) approaches. Conflicts between species and gene trees were assessed, and the phylogeny was time‐calibrated in BEAST. Introgression between species was explored using Phylonet.Results: The phylogenies were globally congruent regardless of the method used. Most of the species were recovered as monophyletic, unlike previous plastid phylogenetic reconstructions where lineages were shared among geographically close individuals independently of species identity. Still, most of the individual gene trees had low levels of phylogenetic information and, when informative, were mostly in conflict with the reconstructed species trees. These results suggest incomplete lineage sorting and/or reticulate evolution, which was supported by network analyses. The BEAST analysis supported a Pliocene origin for current Brachystegia lineages, with most of the diversification events dated to the Pliocene‐Pleistocene.Conclusions: These results suggest a recent origin of species of the miombo, congruently with their spatial expansion documented from plastid data. Brachystegia species appear to behave potentially as a syngameon, a group of interfertile but still relatively well‐delineated species, an aspect that deserves further investigations.

Background and aims – Brachystegia is a species-rich tree genus found in tropical Africa and a typical element of Miombo woodlands, a widely distributed subtype of the Zambezian savanna. Plastid DNA was shown to be largely uninformative to assess species phylogenetic relationships due to widespread chloroplast capture among species. Here, we aim to assess the capacity of nuclear ribosomal DNA (rDNA) to clarify the phylogeny of Brachystegia species while accounting for intra-individual site polymorphisms (2ISPs), which are often present in rDNA and potentially phylogenetically informative. Material and methods – Genome skimming sequencing on 47 samples representing 27 of the 29 currently recognized Brachystegia species, allowed us to retrieve complete nuclear ribosomal cistrons encoding for 18S, 5.8S, and 25S rRNA genes (35S rDNA). We reconstructed the Brachystegia phylogeny using Maximum Likelihood methods based on the standard substitution model or integrating 2ISPs (GENOTYPE implementation in RAxML-NG). We additionally tested the effect of partitioning the data (one partition for rDNA genes and one for the ITS1+ITS2). We also conducted network inferences (Neighbor-Net splits graph), as a strict bifurcative approach might not properly model topological uncertainty at shallow phylogenetic depth. Key results – 2ISPs-aware and standard phylogenetic reconstructions are largely congruent. We identified several well-supported main clades clarifying the species relationships, including two clades of Miombo woodlands species. Miombo Group A includes species with ovoid to globose axillary dormant buds, while Miombo Group B species have flattened ones. Two morphologically close Brachystegia species (B. kennedyi and B. leonensis) found in Guineo-Congolian rain forests form also a robustly supported clade. 2ISPs coding allowed to identify an additional Guineo-Congolian clade (B. eurycoma and B. nigerica). Ribosomal DNA therefore proves more useful to explore the generic phylogeny than plastid DNA but the species relationships within and among the main clades remain poorly resolved, probably due to recent diversification and/or recurrent hybridization, so that the diversification of Brachystegia remains to be more properly characterised. Conclusion – Nuclear and plastid phylogenetic reconstructions of Brachystegia species are discordant. Even if not well-resolved, rDNA phylograms and networks are characterized by taxonomic sorting, while we observe a strictly geographic sorting in the plastid dataset. Most of the species’ relationships remain to be characterized using additional nuclear markers combined with in-depth morphological investigations.

Background and objectives—Podocarpus latifolius (synonym of P. milanjianus) is a key tree representative of Afromontane forests where it is highly threatened by climate and land-use changes. While large populations occur in East Africa, only a few isolated and usually small populations remain in western Central Africa (Cameroon to Angola). Studying the evolutionary history of such relictual populations can thus be relevant to understand their resilience under changing environments. Materials and Methods—we developed nine polymorphic nuclear microsatellites (nSSRs) to estimate genetic variability, (historical) gene flow, and demographic changes among natural populations from Central to East Africa. Results—despite the extended distribution range of P. latifolius, a strong isolation-by-distance pattern emerges at the intra-population scale, indicating low seed and pollen dispersal capacities. Central African populations display a lower genetic diversity (He = 0.34 to 0.61) and are more differentiated from each other (F_ST = 0.28) than are East African populations (He = 0.65 to 0.71; F_ST = 0.10), suggesting high genetic drift in the Central African populations. Spatial genetic structure reveals past connections between East and West Africa but also a gene flow barrier across the equator in western Central Africa. Demographic modelling anchors the history of current lineages in the Pleistocene and supports a strong demographic decline in most western populations during the last glacial period. By contrast, no signature of demographic change was detected in East African populations. Conclusions—in Cameroon, our results exclude a recent (re)colonization from one source population of all mountain ranges, but rather indicate long-term persistence of populations in each mountain with fluctuating sizes. A higher impact of genetic drift and further loss of diversity can be expected by survival through climatically unfavorable periods in such small refugial populations. Tracking the Quaternary legacy of podocarp populations is thus essential for their conservation since there is a temporal gap between environment crises and an ecological/genetic answer at the population level.

Soil‐feeding termites are abundant in tropical regions and play an important role in soil bioturbation and in the organic matter cycle. The Apicotermitinae are arguably the most diverse lineage of soil‐feeding termites, but they are also the most understudied, probably because many species are soldierless, which makes identification difficult. Although the backbone of the termite phylogenetic tree is now well‐resolved, the relationships among representatives of Apicotermitinae are still largely unknown. Here, we present phylogenetic trees inferred from 113 mitochondrial genomes of Apicotermitinae representative of the group diversity. Our analyses confirm the monophyly of the Apicotermitinae and the basal position of soldiered taxa, within which two lineages of soldierless species are nested. We describe two new monotypic genera, whose phylogenetic position appeared of special interest: Koutabatermes gen. n. , lies on a long branch among soldiered taxa, and Apolemotermes gen. n. , is sister to Adaiphrotermes . We resolved, with high support, the position of Asian genera as sister group of a clade comprising the monophyletic neotropical Anoplotermes ‐group and the small African clade including Adaiphrotermes and Apolemotermes gen. n. . Our trees cast light on the intergeneric and interspecific relationships within Apicotermitinae and reveal the polyphyly of several genera, including Ruptitermes , Astalotermes and Anoplotermes . Biogeographic reconstructions revealed two dispersal events out of Africa, one to the Oriental realm and one to the Neotropical realm. Overall, the timing of Apicotermitinae diversification and dispersal, following the Eocene–Oligocene boundary, matches that found for other groups of Neoisoptera. Nomenclatural acts are registered in ZooBank: http://zoobank.org/urn:lsid:zoobank.org:pub:CA1A21B6‐573E‐4855‐8C88‐372453C922F7 .