Molecular data from contemporary and historical collections reveal a complex story of cryptic diversification in the Varanus (Polydaedalus) niloticus Species Group

Abstract

Previous studies of color pattern, tongue pigmentation, and scale counts have been used to distinguish two species of semiaquatic varanids in Africa, but these findings have yet to be tested with molecular data. The Varanus (Polydaedalus) niloticus Species Group is comprised of the Nile monitor (V. niloticus) and the Ornate monitor (V. ornatus). Due to the high rate of exploitation of both species for bushmeat, the leather industry, and the pet trade, a clear understanding of the taxonomy and genetic partitioning is necessary for effective management. Here we utilize a multilocus approach, consisting of mitochondrial and nuclear markers, totaling 4251 bp, as well as microsatellite loci to assess the taxonomic validity and intraspecific evolutionary patterns within the V. niloticus Species Group. By incorporating historical specimens from museum collections as well as contemporary samples, we obtained range-wide coverage for both species across Africa. Concordant results from various approaches all suggest that V. ornatus does not represent a distinct monophyletic group. Our analyses recovered three genetic clades within V. niloticus, representing western, northern, and southern lineages. The western clade was found to diverge first, around 7.7 mya (95% HPD: 4.6-11.0 mya) and exhibits 8.4% and 8.7% uncorrected sequence divergence between the northern and southern V. niloticus clades, respectively. This geographically separate lineage corresponds to previous descriptions of Tupinambis stellatusDaudin (1802). These findings not only call for taxonomic revision of this species group, but also shed light on the biogeographic history of Africa as well as aid in the management planning of varanids and other co-distributed African species.

Molecular phylogeny of Panaspis and Afroablepharus skinks (Squamata: Scincidae) in the savannas of sub-Saharan Africa

“…Similar patterns and timing of diversification have been demonstrated in other vertebrate groups with non-forest distributions, including African clawed frogs (Furman et al, 2015), cobras (Trape et al, 2009), and lizards (Makokha et al, 2007; Diedericks and Daniels, 2014; Dowell et al, 2016), which have all been shown to form complexes of divergent populations correlated with the expansion of C 4 grasslands during the Miocene. Subsequent aridification in the Pliocene and Pleistocene likely explain the more recent cladogenic events in our analyses (Fig.…”

Evaluating mechanisms of diversification in a Guineo‐Congolian tropical forest frog using demographic model selection

“…Other studies with a larger geographic scope (that include Upper Guinea) have detected genetic breaks between populations in western Cameroon and those located in Nigeria, but west of the Niger River. The large sampling gap between the Niger and Cross Rivers in Nigeria leaves population boundaries unresolved, and whether these breaks coincide with the Cross River remains unknown (Dowell et al., ; Fuchs & Bowie, ; Fuchs, Fjeldså, & Bowie, ; Nicolas et al., , ). These patterns could also be the result of postulated sea incursions, which may have been the proximate cause of divergence (Penner, Wegmann, Hillers, Schmidt, & Rödel, ).…”

Fine scale patterns of genetic partitioning in the rediscovered African crocodile,Crocodylus suchus(Saint-Hilaire 1807)

“…Until recently, widespread taxa including such high profile species as giraffe, lion, cheetah, and even elephant were managed primarily as panmictic populations throughout Africa. Over the past decade, however, molecular tools have uncovered deep divergence between West African and other lineages in these ( Bertola et al, 2015 ; Brown et al, 2007 ; Charruau et al, 2011 ; Dowell et al, 2015b ; Eaton et al, 2009 ; Shirley et al, 2014 ; Smolensky, Hurtado & Fitzgerald, 2014 ) and many other taxa, including the Nile crocodile ( Hekkala et al, 2011 ).…”