Multilocus phylogeny of the Crocidura poensis species complex (Mammalia, Eulipotyphla): Influences of the palaeoclimate on its diversification and evolution

Abstract

Aim This study aims to reconstruct the evolutionary history of the Crocidura poensis species complex and to identify factors driving diversification within it. We tested whether: (a) there is a pattern of allopatric differentiation coincident with the location of hypothesized Pleistocene forest refugia, (b) sister taxa are separated by broad rivers, (c) sister taxa occupy adjacent but distinct habitat. Location Sub‐Saharan African forests and adjacent savanna. Taxon Shrews. Methods Analyses were based on 247 specimens collected from across the distribution of the species complex. We reconstructed the phylogeny (Bayesian and maximum likelihood methods) and assessed historical biogeography of this taxonomic group using a combination of mitochondrial and nuclear markers. We mapped the genetic diversity and estimated the divergence times by a relaxed clock model. Informed by multilocus species delimitation methods, we discussed possible taxonomic implications. Results This complex is composed of nine major genetic lineages (proposed species). The earliest split within this complex occurred after 2.0–2.4 Ma, which corresponds to a period of increased aridity and/or extreme environmental variability. Most other divergence events occurred after the Early‐Middle Pleistocene Transition (1.2–0.8 Ma). Divergent selection across ecological gradients could explain diversification within the West African lineage. In Central Africa, the observed phylogeographic pattern fits the Pleistocene refuge hypothesis and supports the existence of multiple small rather than a few large forest refugia during glacial maxima. Large rivers, like the Congo and Sanaga Rivers, are important barriers to gene flow for several lineages but probably were not the primary cause of differentiation. Main conclusions Both geographic isolation in distinct forest refugia and divergent selection along ecological gradients could explain Pleistocene diversification within this complex.

Tectonics, climate and the diversification of the tropical African terrestrial flora and fauna

“…In West Africa, these changes are suggested to have triggered speciation in certain animal clades (e.g. mammals; Nicolas et al ., 2019) and also led to vicariant speciation between West and Central species as discussed above (see Section III.2 a ). Interestingly, these changes appear to have had little impact on mammal diversification in East Africa, with speciation and extinction rates estimated from the fossil record to have been generally continuous during the Plio‐Pleistocene (Bibi & Kiessling, 2015).…”

“…Estimated ages of vicariance, based on dated phylogenies between animal species on either side of West and Central Africa, span the Late Miocene and Plio‐Pleistocene (e.g. Nicolas et al ., 2006, 2019; Hassanin et al ., 2015; Huntley & Voelker, 2016; Gaubert et al ., 2018; Jongsma et al ., 2018). The late Pliocene–early Pleistocene, between 3 and 2 Ma, appears to concentrate most of these vicariance events across studies.…”

“…Species of the largely forest‐restricted guenons (tribe Cercopithecini), a diverse clade of African primates (63 species), were inferred to have diversified mainly via allopatric speciation during the Pleistocene, but also during the Late Miocene (Guschanski et al ., 2013). Other examples of allopatric speciation linked to isolation in refugia during the Pleistocene have been reported in mammals (Johnston & Anthony, 2012; Missoup et al ., 2012; Bohoussou et al ., 2015; Gaubert et al ., 2018; Nicolas et al ., 2019, 2020) and frogs (Bell et al ., 2017). In insects, this mechanism was suggested for the East African Coastal forests of Tanzania and Kenya, where the origin of 25 species of East African flightless grasshoppers ( Parepistaurus ) was dated to the Pleistocene and attributed to allopatric speciation linked to climatic fluctuations (Hemp et al ., 2015).…”

Molecular investigation of non-volant endemic mammals through mitochondrial cytochrome b gene from Andaman and Nicobar archipelago

“…Nevertheless, the odd distribution and ecology of any species induce uneven speciation in the Islands ecosystem, and extinction among groups (Upham et al 2019). Further, the multi-locus phylogeny has been tested to clarify the diversification and evolution of Crocidura species from mainland of Africa (Nicolas et al 2019), and the Island of Philippines and Taiwan (Esselstyn and Oliveros 2010;Giarla and Esselstyn 2015), Java (Esselstyn et al 2013), Sundaland , as well as from Sulawesi (Eldridge et al 2018). The genetic data is used to know the relationships between the higher taxonomic levels of Crocidura species (Dubey et al 2007;He et al 2010).…”

“…Further, with the advancement of molecular technique and its utility in systematics, the researchers have generated the genetic information of shrew and treeshrew species from different parts of the world to know their phylogeny and evolutionary pattern. The phylogeny, phylogeography, and geographical variation of shrew species, especially for the genus Crocidura were largely evaluated through mitochondrial cytochrome b (mtCytb) gene (Ruedi et al 1998;Ohdachi et al 2004;Querouil et al 2011;Stanley et al 2015) and multi-gene approaches (Nicolas et al 2019). Further, the mitochondrial 12S and 16S rRNA genes were also used to understand the molecular phylogeny of treeshrews and their timescale of diversification (Olson et al 2005;Roberts et al 2011).…”