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

Kulenkampff, Kyle Sieghard; Zyl, Francois Van; Klaus, Sebastian; Daniels, Savel R.

doi:10.3897/zookeys.838.32022

Cited by 7 publications

(13 citation statements)

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“…A study on the semiterrestrial swamp forest crab, Potamonautes lividus, revealed Pleistocene divergence of two reciprocally monophyletic mtDNA clades that coincide with specimens from the two provinces in the present study (Daniels et al, 2020). Other phylogenetic and phylogeographic studies on snakes (Kulenkampff et al, 2019), velvet worms (Daniels et al, 2016) and chameleons (Tolley et al, 2008) in the MPA have also revealed similar latitudinal structuring.…”

Section: Other Studies In the Mpa Biodiversity Hotspotsupporting

confidence: 80%

Pseudocongruent phylogeography reflects unique responses to environmental perturbations in a biodiversity hotspot

Busschau

Jordaan

Conradie

et al. 2022

Journal of Biogeography

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Aim: Comparative phylogeographic studies provide important insights into the biogeographic processes shaping regional patterns of diversity. Yet, comparative studies are lacking for southern African herpetofauna, despite their high diversity. We statistically compare phylogeographic structure and divergence-time estimates among five co-distributed forest-living herpetofaunal taxa to assess rivers, climatic refugia and climatic gradients as congruent drivers of phylogeographic diversity.Location: Maputoland-Pondoland-Albany biodiversity hotspot, Southern Africa. Taxon: herpetofauna (reptiles and amphibians).Methods: Phylogeographic structure and divergence-times within species were estimated from mitochondrial and nuclear DNA sequence data. Phylogeographic concordance factors were used to estimate the degree of phylogeographic congruence among sympatric localities. Full-likelihood Bayesian comparisons were used to estimate synchronous divergence between phylogeographic regions and across a putative river barrier. Palaeoclimatic niche models were compared among taxa to identify congruent climatic refugia. Nonparametric statistics were used to identify climatic differences between regions and among populations within each species. Finally, redundancy analyses were used to assess geographic distance, climate and the putative river barrier as explanatory variables to genetic diversity. Results: There is comprehensive phylogeographic structuring within each species, comprising distinct northerly and southerly clades. Phylogeographic concordance factors generally support co-diversification in a north/south axis. Yet, analyses of the divergence-time estimates through the Mio/Plio/Pleistocene indicate asynchronous phylogeographic histories. Climatic niche models identified idiosyncratic responses to palaeoclimatic change. Climatic variables are significantly different among populations in all species and correlated with latitude. A combined model of distance, climate and rivers explained the greatest proportion of genetical diversity in most taxa, of which climate explained the highest variance. Main Conclusions: Ancient and recent species-specific responses to climatic and geological processes resulted in pseudo congruent phylogeographic histories among the five co-distributed species. The presence of a congruent north/south pattern in multiple taxonomic groups occupying different forested microhabitats, from fossorial to arboreal, supports latitudinal gradients as global drivers of phylogeographic diversity along the east coast of South Africa.

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Section: Other Studies In the Mpa Biodiversity Hotspotsupporting

confidence: 80%

Pseudocongruent phylogeography reflects unique responses to environmental perturbations in a biodiversity hotspot

Busschau

Jordaan

Conradie

et al. 2022

Journal of Biogeography

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“…The two mtDNA loci selected were cytochrome b ( cyt b ) and nicotinamide adenine dinucleotide dehydrogenase subunit 4 ( ND4 ). The latter two mtDNA loci are widely used in reptile phylogeographic studies (Vidal et al, 2008; Makhubo, Tolley, & Bates, 2015; Medina et al, 2016; Blair & Bryson, 2017; Díaz et al, 2017; Portillo et al, 2018; Kullenkampff et al, 2019). The primer pairs ND4 (5′‐ACC TAT GAC TAC CAA AAG CTC ATG TAG‐3′) (Arévalo, Davis, & Sites, 1994) and H12763V (5′‐TTC TAT CAC TTG GAT TTG CAC CA‐3′) (Barlow et al, 2013) were used to amplify ± 890 base pairs (bp) of the ND4 locus, while ± 650 bp were amplified for the cyt b region using the primer pairs WWF (5′‐AAA YCA YCG TTG TWA TTC AAC TAC‐3′) and R2 (5′‐GGG TGR AAK GGR ATT TTA TC‐3′) (Whiting, Bauer, & Sites, 2003).…”

Section: Methodsmentioning

confidence: 99%

“…Climatic oscillations are thought to have driven cladogenesis and phylogeographic structuring in several southern African reptile taxa (Barlow et al, 2013; da Silva & Tolley, 2017; Diedericks & Daniels, 2013; Engelbrecht, vanNiekerk, Heideman, & Daniels, 2013; Stanley & Bates, 2014). In addition, divergence‐time estimates have demonstrated that cladogenesis among southern African reptile taxa closely mirror periods characterized by climatic ameliorations throughout the Mio/Plio/Pleistocene (Kullenkampff, Van Zyl, Klaus, & Daniels, 2019; Medina et al, 2016; Tolley, Chase, & Forest, 2008; Weinell & Bauer, 2018).…”

Section: Introductionmentioning

confidence: 99%

One species hides many: Molecular and morphological evidence for cryptic speciation in a thread snake (Leptotyphlopidae: Leptotyphlops sylvicolus Broadley & Wallach, 1997)

Busschau

Conradie

Daniels

2020

J. Zool. Syst. Evol. Res.

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We investigate the phylogeographic structure of a fossorial forest-living snake species, the forest thread snake, Leptotyphlops sylvicolus Broadley & Wallach, 1997 by sampling specimens from the Eastern Cape and KwaZulu-Natal provinces of South Africa. Phylogenetic results, using Bayesian inferences and maximum likelihood, from the combined mitochondrial sequence data (cyt b and ND4), along with population genetic analyses suggest the presence of phylogeographic breaks broadly congruent to those exhibited by other forest-living taxa. Divergence-time estimates indicate that cladogenesis within the study taxon occurred during the late Miocene climatic shifts, suggesting that cladogenesis was driven by habitat fragmentation. We further investigate the species-level divergence within L. sylvicolus by including two partial nuclear loci (PRLR and RAG1). The three species delimitation methods (ABGD, bGMYC, and STACEY), retrieved 10-12 putative species nested within the L. sylvicolus species complex. These results were corroborated by iBPP implementing molecular and morphological data in an integrative Bayesian framework. The morphological analyses exhibit large overlap among putative species but indicate differences between grassland and forest species. Due to the narrow distributions of these putative species, the results of the present study have further implications for the conservation status of the L. sylvicolus species complex and suggest that forest and grassland habitats along the east coast of South Africa may harbor significantly higher levels of diversity than currently recognized.

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“…However, this remains a challenge due to the existence of cryptic species and species complexes. This may be a result of the long and complex evolution of reptiles, which first appeared on Earth more than 250 million years ago 1 , 5 – 7 . Among the Gekkonids (geckos), which is a group of lizards (Sauria), the most diverse group of reptiles in the world, the taxonomy of numerous species, including Hemidactylus 8 – 10 , Hemiphyllodactylus 11 – 13 , and Cyrtodactylus 14 – 16 , is still controversial.…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic analyses of distantly related clades of bent-toed geckos (genus Cyrtodactylus) reveal an unprecedented amount of cryptic diversity in northern and western Thailand

Chomdej

Pradit

Suwannapoom

et al. 2021

Sci Rep

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Cyrtodactylus species are the most diverse of the geckos and are widely distributed in Southeast Asia, including Thailand. However, their patterns of distribution, especially in northern and western parts of Thailand, remain unknown because few Cyrtodactylus species in these regions have been described. Thus, a data set of mitochondrial NADH dehydrogenase 2 (ND2) gene and flanking tRNAs from Cyrtodactylus found in northern and western Thailand, including contiguous areas, was assembled to elucidate phylogenetic relationships and identify the distribution patterns of these geckos. The results showed four well-supported clades, a northwestern clade (A), a northern clade (B), a western clade (C), and a special clade characterized by specific morphological features (D). Clades A–C were grouped with strong support by the geography of their localities from northern Thailand (Mae Hong Son and Chiang Mai Provinces) along the Tenasserim mountain ranges to Phang-Nga Province, Thailand. Clade D is a distinct clade of Cyrtodactylus species characterized by a tuberculate and prehensile tail and distributed widely in mainland Southeast Asia. Overall, the results suggest a pattern of geographic separation and distribution of Cyrtodactylus in northern and western Thailand. Additionally, this study provides evidence of a hidden biodiversity of Cyrtodactylus in these regions.

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

Cited by 7 publications

References 53 publications

Pseudocongruent phylogeography reflects unique responses to environmental perturbations in a biodiversity hotspot

Pseudocongruent phylogeography reflects unique responses to environmental perturbations in a biodiversity hotspot

One species hides many: Molecular and morphological evidence for cryptic speciation in a thread snake (Leptotyphlopidae: Leptotyphlops sylvicolus Broadley & Wallach, 1997)

Phylogenetic analyses of distantly related clades of bent-toed geckos (genus Cyrtodactylus) reveal an unprecedented amount of cryptic diversity in northern and western Thailand

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