Tracking the impact of Pliocene/Pleistocene sea level and climatic oscillations on the cladogenesis of the Cape legless skink, Acontias meleagris species complex, in South Africa

Abstract

Aim To determine the geographical boundaries among cryptic lineages and examine the evolutionary drivers of cladogenesis within the Cape legless skink, Acontias meleagris species complex.Location Coastal plains and adjacent interior of the Eastern, Northern and Western Cape provinces of South Africa.Methods A total of 231 specimens from 55 localities were collected from the entire known distribution range of the A. meleagris complex. Partial sequence data were collected from two mitochondrial DNA loci, 16S rRNA and cytochrome c oxidase subunit I (COI), and one protein-coding nuclear DNA locus, exophilin 5 (EXPH5). Phylogenetic, phylogeographical and population genetic analyses, together with divergence time estimation, were conducted on the DNA sequence data to examine evolutionary history and diversification within the species complex.Results Marked genetic structure was observed within the A. meleagris complex, and five clades were retrieved, most of which were statistically well supported. These five clades were also evident within the haplotypic analyses and were characterized by demographic stability. Cladogenesis was induced during the Pliocene/Pleistocene epochs, most likely as a result of oscillations in climate and sea level, and Neogene geomorphic phenomena. The Breede River Valley is an area of high genetic diversity and is likely to have served as a refugium.Main conclusions Lineage diversification and the current biogeographical patterning reflect the impact of sea level oscillations on historical coastal habitat availability. Fine-scale differences between co-distributed subterranean and supraterranean herpetofaunal taxa can be attributed to differences in life-history traits amongst different habitat types. Historical evolutionary drivers within this subterranean species complex are inferred and discussed.

Molecular evidence for cryptic species in the common slug eating snake Duberria lutrix lutrix (Squamata, Lamprophiidae) from South Africa

“…The distribution of D.l.lutrix overlaps with several phylogeographic breaks for co-distributed lizard species (Fig. 1) (Daniels et al 2007; Engelbrecht et al 2013; Diedericks and Daniels 2014). A xeric biogeographic barrier known as the Bedford gap exists which separates the eastern and south-eastern part of the Cape Floristic Region (CFR) between East London and Port Elizabeth (Lawes 1990).…”

“…Climatic oscillations are thought to be responsible for inducing dramatic impacts on the habitat and eco-physiological characteristics promoting cladogenesis (Hewitt 2000, 2004; Daniels et al 2007, 2009; Barlow et al 2013; Engelbrecht et al 2013). The effects of climatic impacts on terrestrial biota vary considerably depending on latitude, longitude, habitat and the topographic heterogeneity of the environment (Hewitt 2000, 2004).…”

“…The distribution range of Duberrial.lutrix in South Africa is bisected by several large mountain ranges, including the Cape Fold Mountains and the Great Drakensberg escarpment (Partridge and Maud 1987, 2000; Partridge 1997) and low-lying xeric corridors. The habitat availability of the species in the Western Cape Province would have undergone significant climatic shifts from mesic conditions in the Miocene to enhanced arid conditions during the Pliocene/Pleistocene, possibly impacting habitat availability for this mesophylic species and the contraction of populations to high-lying mountainous refugia (Daniels et al 2007; Engelbrecht et al 2013; Diedericks and Daniels 2014). Xeric areas could potentially act as dispersal barriers for a small-bodied snake species with a preference for mesic environments (Hewitt 2004).…”

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

“…Several studies have revealed concealed genetic divergence in multiple lineages of skinks from different regions of the world (Daniels et al, 2009; Engelbrecht et al, 2013; Heideman et al, 2011; Portik et al, 2011; Siler et al, 2011). The family exhibits a wide variety of ecomorphs, but the fossorial/semi-fossorial forms typically have reduced vagility that can facilitate population fragmentation and divergence by historical climatic and geographic processes.…”

Unmasking alpha diversity, cladogenesis and biogeographical patterning in an ancient panarthropod lineage (Onychophora: Peripatopsidae: Opisthopatus cinctipes) with the description of five novel species

“…Evolutionary inferences derived from DNA sequences [particularly the mitochondrial cytochrome c oxidase subunit 1 ( COI ) data and to a lesser extent nuclear loci] are widely used to describe alpha diversity and identify cryptic species, and have gained recent momentum (albeit with considerable criticism) due to the advocacy of the “Barcoding of Life” initiative (Hebert et al., ,b, ,b; de Salle et al., ; Hickerson et al., ). Cryptic speciation has been discovered in several eumetazoan lineages (Hedin and Wood, ; Baker et al., ; Boyer et al., ; Daniels et al., ; Daniels, , ; McDonald and Daniels, ; Engelbrecht et al., ; Fernández and Giribet, ; Medina et al., ). Molecular systematic studies of cryptic species have revealed substantial hidden diversity and localized endemism, negating the traditional paradigm of species with cosmopolitan distributions and forcing a rethink of units for conservation priority (Bickford et al., ).…”