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

Abstract

Puddle frogs of the Phrynobatrachus steindachneri species complex are a useful group for investigating speciation and phylogeography in Afromontane forests of the Cameroon Highlands (Cameroon Volcanic Line) in western Central Africa. The species complex is represented by six morphologically relatively cryptic mitochondrial DNA lineages, with only two of them distinguished at the species level – southern P. jimzimkusi and Lake Oku endemic P. njiomock, leaving the remaining four lineages with a pooled identification as ‘P. steindachneri’. In this study, the six mtDNA lineages are subjected to genomic sequence capture analyses to delimit species (together with morphology) and to study biogeography. Nuclear DNA data (387 loci; 571,936 aligned base pairs) distinguished all six mtDNA lineages, but the splitting pattern and depths of divergences supported only four main clades—besides P. jimzimkusi and P. njiomock, only two from the four ‘P. steindachneri’ mtDNA lineages. One is here described as a new species, P. 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 phylogenetic artefact – a ladder-like tree pattern. The presence of hybrids is undesirable in standard phylogenetic analyses, but is essential and beneficial in the network multispecies coalescent. This latter approach allowed us an 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 (warm interglacials) of montane forests. The genomic phylogeographic pattern supports the earliest division between 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). Mount Oku harboring three species is of particular conservation importance. 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. We therefore urge for conservation actions in the Cameroon Highlands to preserve their diversity before it is too late.

Exploring the distribution of phylogenetic networks generated under a birth-death-hybridization process

“…Methods that can directly investigate which type of reticulation occurs on phylogenetic networks (Hibbins and Hahn 2019;Flouri et al 2020) will be vital as we infer patterns of gene flow. Further, system-specific knowledge-factors like life history (Wolf et al 2001;Rumpho et al 2008;Wendel et al 2009;Schulte et al 2012;Montanari et al 2016;Meier et al 2019), geographic distributions (López-Caamal et al 2014;Ottenburghs et al 2017;Dolinay et al 2021), and genomic architecture (Wendel and Cronn 2003;Ottenburghs et al 2017;Edelman et al 2019)-should be incorporated to help inform how to model and interpret each type of reticulation. The specific reticulation types affect diversification and topology of phylogenetic networks, potentially violating assumptions of some methods or biasing diversification rate estimates if not taken into account.…”

“…Althoughfor eponymous consistency-events are denoted as hybridizations, the process does not make any mechanistic assumptions about gene flow; reticulate events on phylogenetic networks can model the many processes where genetic material is exchanged between lineages. Consequently, phylogenetic network inference has been used to describe histories of introgression (Thawornwattana et al 2018;Myers et al 2022), hybridization (Morales-Briones et al 2018;Dolinay et al 2021), and lateral gene transfer (Betat et al 2015). The specific biological interpretation of a given reticulation event is a challenge that depends largely on the system under investigation and is further complicated by how reticulation events are modeled on the phylogenetic network (Hibbins and Hahn 2022).…”

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

“…The measured values were subsequently statistically treated according to Mosimann 66 to filter out the effect of body size, see also Gvoždík et al 67 or Dolinay et al 68 . Principal component analysis (PCA) was performed in the programming language R v3.6.3 69 using R-package “vegan” v2.5–6 70 to explore the morphospace of the body shapes.…”