Phylogenomics of Anguis and Pseudopus (Squamata, Anguidae) indicates Balkan-Apennine mitochondrial capture associated with the Messinian event.

A dated phylogenetic hypothesis on the evolutionary history of the extant taxa of the Western Palearctic lizards Anguis and Pseudopus is revised using genome-wide nuclear DNA and mitogenomes. We found overall concordance between nuclear and mitochondrial DNA phylogenies, with one significant exception - the Apennine A. veronensis. In mitochondrial DNA, this species forms a common clade with the earliest diverging lineage, the southern Balkan endemic A. cephallonica, while it clusters together with A. fragilis in nuclear DNA. The nuclear phylogeny conforms to the morphology, which is relatively similar between A. veronensis and A. fragilis. The most plausible explanation for the mitonuclear discordance is ancient mitochondrial capture from the Balkan ancestor of A. cephallonica to the Apennine population of the A. fragilis-veronensis ancestor. We hypothesize that this capture occurred only in a geographically restricted population. The dating of this presumed mitochondrial introgression and capture coincides with the Messinian event, when the Balkan and Apennine Peninsulas were presumably largely connected. The dated nuclear phylogenomic reconstruction estimated the divergence of A. cephallonica around 12 Mya, while the sister clade representing the A. fragilis species complex consisting of the sister species A. fragilis-A. veronensis and A. colchica-A. graeca further diversified around 7 Mya. The depth of nuclear divergence among the evolutionary lineages of Pseudopus (0.5-1.2 Mya) supports their subspecies status.

Systematic position of the Clicking Frog (Kassinula Laurent, 1940), the problem of chimeric sequences and the revised classification of the family Hyperoliidae.

The systematics of the African frog family Hyperoliidae has undergone turbulent changes in last decades. Representatives of several genera have not been genetically investigated or with only limited data, and their phylogenetic positions are thus still not reliably known. This is the case of the De Witte's Clicking Frog (Kassinula wittei) which belongs to a monotypic genus. This miniature frog occurs in a poorly studied region, southeastern Democratic Republic of the Congo, northern Zambia, Angola. So far it is not settled whether this genus belongs to the subfamily Kassininae as a relative of the genus Kassina, or to the subfamily Hyperoliinae as a relative of the genus Afrixalus. Here we present for the first time a multilocus phylogenetic reconstruction (using five nuclear and one mitochondrial marker) of the family Hyperoliidae, including Kassinula. We demonstrate with high confidence that Kassinula is a member of Hyperoliinae belonging to a clade also containing Afrixalus (sub-Saharan Africa), Heterixalus (Madagascar) and Tachycnemis (Seychelles). We find that Kassinula represents a divergent lineage (17-25 Mya), which supports its separate genus-level status, but its exact systematic position remains uncertain. We propose to name the clade to which the above four genera belong as the tribe Tachycnemini Channing, 1989. A new taxonomy of the family Hyperoliidae was recently proposed by Dubois et al. (2021: Megataxa 5, 1-738). We demonstrate here that the new taxonomy was based on a partially erroneous phylogenetic reconstruction resulting from a supermatrix analysis of chimeric DNA sequences combining data from two families, Hyperoliidae and Arthroleptidae (the case of Cryptothylax). We therefore correct the erroneous part and propose a new, revised suprageneric taxonomy of the family Hyperoliidae. We also emphasize the importance of inspecting individual genetic markers before their concatenation or coalescent-based tree reconstructions to avoid analyses of chimeric DNA sequences producing incorrect phylogenetic reconstructions. Especially when phylogenetic reconstructions are used to propose taxonomies and systematic classifications.

Gene flow in phylogenomics: Sequence capture resolves species limits and biogeography of Afromontane forest endemic frogs from the Cameroon Highlands.

Puddle frogs of the Phrynobatrachus steindachneri species complex are a useful group for investigating speciation and phylogeography in Afromontane forests of the Cameroon Volcanic Line, western Central Africa. The species complex is represented by six morphologically relatively cryptic mitochondrial DNA lineages, only two of which are distinguished at the species level - southern P. jimzimkusi and Lake Oku endemic P. njiomock, leaving the remaining four lineages identified as 'P. steindachneri'. In this study, the six mtDNA lineages are subjected to genomic sequence capture analyses and morphological examination to delimit species and to study biogeography. The nuclear DNA data (387 loci; 571,936 aligned base pairs) distinguished all six mtDNA lineages, but the topological pattern and divergence depths supported only four main clades: P. jimzimkusi, P. njiomock, and only two divergent evolutionary lineages within the four 'P. steindachneri' mtDNA lineages. One of the two lineages is herein described as a new species, P. amieti sp. nov. Reticulate evolution (hybridization) was detected within the species complex with morphologically intermediate hybrid individuals placed between the parental species in phylogenomic analyses, forming a ladder-like phylogenetic pattern. The presence of hybrids is undesirable in standard phylogenetic analyses but is essential and beneficial in the network multispecies coalescent. This latter approach provided insight into the reticulate evolutionary history of these endemic frogs. Introgressions likely occurred during the Middle and Late Pleistocene climatic oscillations, due to the cyclic connections (likely dominating during cold glacials) and separations (during warm interglacials) of montane forests. The genomic phylogeographic pattern supports the separation of the southern (Mt. Manengouba to Mt. Oku) and northern mountains at the onset of the Pleistocene. Further subdivisions occurred in the Early Pleistocene, separating populations from the northernmost (Tchabal Mbabo, Gotel Mts.) and middle mountains (Mt. Mbam, Mt. Oku, Mambilla Plateau), as well as the microendemic lineage restricted to Lake Oku (Mt. Oku). This unique model system is highly threatened as all the species within the complex have exhibited severe population declines in the past decade, placing them on the brink of extinction. In addition, Mount Oku is identified to be of particular conservation importance because it harbors three species of this complex. We, therefore, urge for conservation actions in the Cameroon Highlands to preserve their diversity before it is too late.

Congolius, a new genus of African reed frog endemic to the central Congo: A potential case of convergent evolution.

The reed frog genus Hyperolius (Afrobatrachia, Hyperoliidae) is a speciose genus containing over 140 species of mostly small to medium-sized frogs distributed in sub-Saharan Africa. Its high level of colour polymorphism, together with in anurans relatively rare sexual dichromatism, make systematic studies more difficult. As a result, the knowledge of the diversity and taxonomy of this genus is still limited. Hyperolius robustus known only from a handful of localities in rain forests of the central Congo Basin is one of the least known species. Here, we have used molecular methods for the first time to study the phylogenetic position of this taxon, accompanied by an analysis of phenotype based on external (morphometric) and internal (osteological) morphological characters. Our phylogenetic results undoubtedly placed H. robustus out of Hyperolius into a common clade with sympatric Cryptothylax and West African Morerella. To prevent the uncovered paraphyly, we place H. robustus into a new genus, Congolius. The review of all available data suggests that the new genus is endemic to the central Congolian lowland rain forests. The analysis of phenotype underlined morphological similarity of the new genus to some Hyperolius species. This uniformity of body shape (including cranial shape) indicates that the two genera have either retained ancestral morphology or evolved through convergent evolution under similar ecological pressures in the African rain forests.

Evolutionary history of the Cameroon radiation of puddle frogs (Phrynobatrachidae: Phrynobatrachus), with descriptions of two critically endangered new species from the northern Cameroon Volcanic Line.

The Cameroon Volcanic Line, a mountain chain located between West and Central Africa, is a region of numerous endemic diversifications, including of puddle frogs (Phrynobatrachus). This study reviews the phylogeny and taxonomy of puddle frogs of the "Cameroon radiation," which is a clade containing mainly montane but also at least three lowland species. Molecular data revealed a novel evolutionary lineage from high altitudes in the northern part of the mountains. Puddle frogs from the new, minute-sized (SVL < 20 mm) lineage are identified using molecular, morphological and acoustic data and described as two new species, Phrynobatrachus arcanus sp. nov. (Gotel Mountains, Cameroon-Nigeria) and P. mbabo sp. nov. (Tchabal Mbabo, Cameroon). The tadpole of the first species is also described. Phylogenetic analyses placed the new lineage to the proximity of the recently described lowland small-sized taxa (P. horsti, P. ruthbeateae). Based on the inferred phylogeny, we propose five species groups within the Cameroon radiation: P. arcanus, P. chukuchuku, P. ruthbeateae, P. steindachneri, and P. werneri. The taxonomically enigmatic P. hylaios is proposed to be a member of the P. ruthbeateae species group. The basal radiation evolved during the late Miocene with subsequent diversifications occurring during the Pliocene, while closely related terminal taxa originated during the Pleistocene. We recommend that the newly described species are categorized as Critically Endangered due to their limited ranges and because recent surveys did not identify any individuals at the type localities. This further supports the need for conservation interventions in the mountains of Cameroon and Nigeria.