The phylogeny of the African wood mice (Muridae, Hylomyscus) based on complete mitochondrial genomes and five nuclear genes reveals their evolutionary history and undescribed diversity

Nicolas, Violaine; Fabre, Pierre‐Henri; Bryja, Josef; Denys, Christiane; Verheyen, Erik; Missoup, Alain Didier; Olayemi, Ayodeji; Katuala, Pionus; Dudu, A.; Colyn, Marc; Peterhans, Julian Kerbis; Demos, Terrence C.

doi:10.1016/j.ympev.2019.106703

Cited by 29 publications

(25 citation statements)

References 88 publications

(121 reference statements)

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“…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).…”

Section: Major Speciation Models Of Tropical African Biodiversitymentioning

confidence: 99%

“…For example, speciation in clawed frogs started during the Late Miocene, and high diversity in central Africa was linked to persistence of forest refugia that remain today (Evans et al ., 2015). Finally, Miocene and Pliocene speciation was suggested to explain diversification of several rodent clades (Demos et al ., 2014; Bryja et al ., 2017; Nicolas et al ., 2020) and within African colobines (Ting, 2008).…”

Section: Major Speciation Models Of Tropical African Biodiversitymentioning

confidence: 99%

“…The exceptional and unique biodiversity of the ancient Eastern Arc Mountains of Tanzania and Kenya (Burgess et al ., 2007) was suggested to be driven by long‐term persistence of montane forests together with recurrent connections and disconnections between montane isolates since the Oligocene–Miocene (Lovett, 1993; Lovett et al ., 2005; Fjeldså & Bowie, 2008; Voelker et al ., 2010; Loader et al ., 2014). This mechanism was inferred for several clades such as songbirds (Passeriformes) (Bowie et al ., 2004; Fjeldså & Bowie, 2008; Voelker et al ., 2010; Fjeldså, Bowie, & Rahbek, 2012), rodents (Mizerovská et al ., 2019; Nicolas et al ., 2020), forest‐restricted chameleons (Tolley et al ., 2011; Ceccarelli et al ., 2014), brevicipitid frogs (Loader et al ., 2014), various insect groups such as Orthoptera (Voje et al ., 2009; Hemp et al ., 2010) and weevils (Grebennikov, 2017), and plants (Dimitrov et al ., 2012). Evidence suggests that most montane sister species in the Eastern Arc Mountains are allopatric but located on different montane areas, refuting in situ speciation (Hemp et al ., 2010; Voelker et al ., 2010; Missoup et al ., 2012; Ceccarelli et al ., 2014; Taylor et al ., 2014).…”

Section: Major Speciation Models Of Tropical African Biodiversitymentioning

confidence: 99%

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

et al. 2020

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Tropical Africa is home to an astonishing biodiversity occurring in a variety of ecosystems. Past climatic change and geological events have impacted the evolution and diversification of this biodiversity. During the last two decades, around 90 dated molecular phylogenies of different clades across animals and plants have been published leading to an increased understanding of the diversification and speciation processes generating tropical African biodiversity. In parallel, extended geological and palaeoclimatic records together with detailed numerical simulations have refined our understanding of past geological and climatic changes in Africa. To date, these important advances have not been reviewed within a common framework. Here, we critically review and synthesize African climate, tectonics and terrestrial biodiversity evolution throughout the Cenozoic to the mid‐Pleistocene, drawing on recent advances in Earth and life sciences. We first review six major geo‐climatic periods defining tropical African biodiversity diversification by synthesizing 89 dated molecular phylogeny studies. Two major geo‐climatic factors impacting the diversification of the sub‐Saharan biota are highlighted. First, Africa underwent numerous climatic fluctuations at ancient and more recent timescales, with tectonic, greenhouse gas, and orbital forcing stimulating diversification. Second, increased aridification since the Late Eocene led to important extinction events, but also provided unique diversification opportunities shaping the current tropical African biodiversity landscape. We then review diversification studies of tropical terrestrial animal and plant clades and discuss three major models of speciation: (i) geographic speciation via vicariance (allopatry); (ii) ecological speciation impacted by climate and geological changes, and (iii) genomic speciation via genome duplication. Geographic speciation has been the most widely documented to date and is a common speciation model across tropical Africa. We conclude with four important challenges faced by tropical African biodiversity research: (i) to increase knowledge by gathering basic and fundamental biodiversity information; (ii) to improve modelling of African geophysical evolution throughout the Cenozoic via better constraints and downscaling approaches; (iii) to increase the precision of phylogenetic reconstruction and molecular dating of tropical African clades by using next generation sequencing approaches together with better fossil calibrations; (iv) finally, as done here, to integrate data better from Earth and life sciences by focusing on the interdisciplinary study of the evolution of tropical African biodiversity in a wider geodiversity context.

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Section: Major Speciation Models Of Tropical African Biodiversitymentioning

confidence: 99%

Section: Major Speciation Models Of Tropical African Biodiversitymentioning

confidence: 99%

Section: Major Speciation Models Of Tropical African Biodiversitymentioning

confidence: 99%

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

et al. 2020

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“…The optimal partitioning scheme and substitution model was selected by PartitionFinder 2.1.1.2 (Lanfear et al, 2016). We followed Mackiewicz et al (2019) considering 3 codon positions for each individual protein coding gene and separate partitions for each of the RNA genes, but retained contiguous t-RNAs because individual t-RNA alignments would be too short to be informative (Nicolas et al, 2019). This reduced the number of initial partitions from 67 to 53.…”

Section: Phylogenetic Analyses and Haplotype Networkmentioning

confidence: 99%

Ancient Divergence Driven by Geographic Isolation and Ecological Adaptation in Forest Dependent Sundaland Tree Squirrels

et al. 2020

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A surprising amount of hidden phylogenetic diversity exists in the small to medium size, drab colored squirrels of the genus Sundasciurus. This genus is endemic to Sundaland and the Philippines, where it is widespread. An earlier revision of this genus found that the high elevation ‘populations’ of the widespread, lowland slender squirrel (S. tenuis) were different species. Previous phylogenies based on mitochondrial cytochrome b sequences also suggested that the widespread, lowland Low’s squirrel (S. lowii) and the narrow endemic Fraternal squirrel (S. fraterculus) are not reciprocally monophyletic. Additionally, deep divergences have been identified between lineages within Low’s squirrel that date to the early Pliocene. Here we focus on evaluating the relationships and differences within and between populations of these two nominal species using whole mitochondrial genome sequences, nuclear intron sequences, and morphology. We reassess the taxonomy of this group, revalidate the species status of Robinson’s squirrel (Sundasciurus robinsoniBonhote, 1903) support the species level recognition of the Natuna squirrel (Sundasciurus natunensisThomas, 1895) and identify three other lineages that require further study. We estimate times of divergence and integrate geologic history to find that most of the divergences are pre-Pleistocene, and thus predate the Pleistocene flooding of Sundaland. Biogeographic, and ecological factors may have played a more important role than climatic factors in generating these patterns. While divergence in allopatry seems to be the main process driving speciation in lowland Sundaland squirrels (Sundasciurus), ecomorphological and behavioral adaptations in this clade suggest an important role of niche divergence.

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“…The DNA sequences obtained were compared through a BLAST analysis to those available in the Genbank database. Recent molecular studies are available for the genera Hylomyscus (Nicolas et al 2012(Nicolas et al , 2020, Praomys (Nicolas et al 2012, Mikula et al 2020, Lemniscomys (Nicolas et al 2008, Denys et al 2020, Mastomys (Nicolas et al 2012) and Rattus (Lack et al 2012, Colangelo et al 2015, allowing accurate molecular species identification.…”

Section: Species Identificationmentioning

confidence: 99%

Small mammal inventory in the Lama forest reserve (south Benin), with new cytogenetical data

Nicolas

Gerbault‐Seureau

Delapré

et al. 2020

Journal of Vertebrate Biology

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The phylogeny of the African wood mice (Muridae, Hylomyscus) based on complete mitochondrial genomes and five nuclear genes reveals their evolutionary history and undescribed diversity

Cited by 29 publications

References 88 publications

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

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

Ancient Divergence Driven by Geographic Isolation and Ecological Adaptation in Forest Dependent Sundaland Tree Squirrels

Small mammal inventory in the Lama forest reserve (south Benin), with new cytogenetical data

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