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Šumbera R, Uhrová M, Montoya-Sanhueza G, Bryjová A, Bennett NC, Mikula O. Genetic diversity of the largest African mole-rat genus, Bathyergus. One, two or four species? Mol Phylogenet Evol 2024; 199:108157. [PMID: 39029550 DOI: 10.1016/j.ympev.2024.108157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 07/01/2024] [Accepted: 07/14/2024] [Indexed: 07/21/2024]
Abstract
Recent advances in sequencing technology and phylogenetic methods allow us to solve puzzling taxonomic questions using detailed analyses of genetic diversity of populations and gene flow between them. The genus of solitary-living dune mole-rat, Bathyergus, is quite unique among six genera of African mole-rats. The animals are by far the largest and the only scratch digging mole-rat genus possessing a skull less adapted to digging, grooved upper incisors, and more surface locomotor activity. Most authors recognize two species of dune mole-rats, B. suillus and B. janetta, but according to others, the genus is monotypic. In addition, recent molecular studies have revealed cryptic genetic diversity and suggested the existence of up to four species. In our study, we used mitochondrial and genome-wide nuclear data collected throughout the distribution of the genus to investigate the number of species. In agreement with previous studies, we found Bathyergus to be differentiated into several distinct lineages, but we also found evidence for a degree of gene flow between some of them. Furthermore, we confirmed that B. janetta is nested within B. suillus, making the latter paraphyletic and we documented an instance of local mitochondrial introgression between these two nominal species. Phylogeographic structure of the genus was found to be very shallow. Although traditionally dated to the Miocene, we found the first split within the genus to be much younger estimated to 0.82 Ma before present. Genealogical distinctiveness of some lineages was very low, and the coancestry matrix showed extensive sharing of closely related haplotypes throughout the genus. Accordingly, Infomap clustering on the matrix showed all populations to form a single cluster. Overall, our study tends to support the existence of only one species of Bathyergus namely, B. suillus. Environmental niche modelling confirmed its dependence on sandy soils and the preference for soils with relatively high carbon content. Bayesian skyline plots indicate recent population decline in the janetta lineage, probably related to global environmental change.
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Affiliation(s)
- R Šumbera
- Department of Zoology, Faculty of Sciences, University of South Bohemia in České Budějovice, Czech Republic.
| | - M Uhrová
- Department of Zoology, Faculty of Sciences, University of South Bohemia in České Budějovice, Czech Republic
| | - G Montoya-Sanhueza
- Department of Zoology, Faculty of Sciences, University of South Bohemia in České Budějovice, Czech Republic; Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile (UACh), Valdivia, Chile
| | - A Bryjová
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - N C Bennett
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, South Africa
| | - O Mikula
- Department of Zoology, Faculty of Sciences, University of South Bohemia in České Budějovice, Czech Republic; Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
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2
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Luo G, Pu T, Wang J, Ran W, Zhao Y, Dietrich CH, Li C, Song Y. Genetic differentiation and phylogeography of Erythroneurini (Hemiptera, Cicadellidae, Typhlocybinae) in the southwestern karst area of China. Ecol Evol 2024; 14:e11264. [PMID: 38606344 PMCID: PMC11007260 DOI: 10.1002/ece3.11264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 03/22/2024] [Accepted: 03/27/2024] [Indexed: 04/13/2024] Open
Abstract
Erythroneurini is the largest tribe of the microleafhopper subfamily Typhlocybinae. Most prior research on this tribe has focused on traditional classification, phylogeny, and control of agricultural pests, and the phylogeography of the group remains poorly understood. In this study, the mitochondrial genomes of 10 erythroneurine species were sequenced, and sequences of four genes were obtained for 12 geographical populations of Seriana bacilla. The new sequence data were combined with previously available mitochondrial DNA sequence data and analyzed using Bayesian and Maximum-Likelihood-based phylogenetic methods to elucidate relationships among genera and species and estimate divergence times. Seriana was shown to be derived from within Empoascanara. Phylogeographic and population genetic analysis of the endemic Chinese species Seriana bacilla suggest that the species diverged about 54.85 Mya (95% HPD: 20.76-66.23 million years) in the Paleogene period and that population divergence occurred within the last 14 million years. Ancestral area reconstruction indicates that Seriana bacilla may have originated in the central region of Guizhou, and geographical barriers are the main factors affecting gene flow among populations. Ecological niche modeling using the MaxEnt model suggests that the distribution of the species was more restricted in the past but is likely to expand in the future years 2050 and 2070.
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Affiliation(s)
- Guimei Luo
- School of Karst ScienceGuizhou Norml University/State Engineering Technology Institute for Karst Desertification ControlGuiyangGuizhouChina
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous RegionGuiyang UniversityGuiyangGuizhouChina
- Illinois Natural History Survey, Prairie Research InstituteUniversity of IllinoisChampaignIllinoisUSA
| | - Tianyi Pu
- School of Karst ScienceGuizhou Norml University/State Engineering Technology Institute for Karst Desertification ControlGuiyangGuizhouChina
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous RegionGuiyang UniversityGuiyangGuizhouChina
| | - Jinqiu Wang
- School of Karst ScienceGuizhou Norml University/State Engineering Technology Institute for Karst Desertification ControlGuiyangGuizhouChina
| | - Weiwei Ran
- School of Karst ScienceGuizhou Norml University/State Engineering Technology Institute for Karst Desertification ControlGuiyangGuizhouChina
| | - Yuanqi Zhao
- School of Karst ScienceGuizhou Norml University/State Engineering Technology Institute for Karst Desertification ControlGuiyangGuizhouChina
| | - Christopher H. Dietrich
- School of Karst ScienceGuizhou Norml University/State Engineering Technology Institute for Karst Desertification ControlGuiyangGuizhouChina
- Illinois Natural History Survey, Prairie Research InstituteUniversity of IllinoisChampaignIllinoisUSA
| | - Can Li
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous RegionGuiyang UniversityGuiyangGuizhouChina
| | - Yuehua Song
- School of Karst ScienceGuizhou Norml University/State Engineering Technology Institute for Karst Desertification ControlGuiyangGuizhouChina
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Daniels SR, Peer N, Myburgh AM, Barnes A, Klaus S. Let's get high: Cladogenesis in freshwater crabs (Decapoda: Potamonautidae: Potamonautes) supports the mountain gradient speciation hypothesis in the Cape Fold and Drakensberg Mountains, South Africa. Ecol Evol 2024; 14:e10960. [PMID: 38450318 PMCID: PMC10915499 DOI: 10.1002/ece3.10960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 12/13/2023] [Indexed: 03/08/2024] Open
Abstract
During the present study, the evolutionary relationship within a clade of mountain clade of freshwater crabs (Potamonautes) was examined using mtDNA sequence data for species from the Cape Fold Mountain (CFM) and Great Escarpment (Drakensberg Mountain range). We undertook phylogenetic analyses, divergence time estimation, and an ancestral area reconstruction to explore the period of cladogenesis and understand the biogeographic history in this high-altitude clade. Furthermore, we applied four species delimitation methods using ASAP, bPTP, bGMYC, and STACEY on the latter clade. Bayesian phylogenetic analyses retrieved a monophyletic freshwater crab clade comprised of two major sister clades, one comprised of the Cape Fold (clade A) and two comprised of Drakensberg Mountains (clade B) species. Divergence time estimation indicated that the two clades underwent Mio/Pliocene cladogenesis. Within the CFM clade (A), P. amathole (Amathola Mountains) was sister to P. parvispina (Cederberg and Kouebokkeveld Mountains) and the latter species were sister to P. parvicorpus (Cape Peninsula, Jonkershoek, and Helderberg Mountains) sister to P. tuerkayi (Overberg Mountains) and P. brincki (Hottentots Holland Mountains). Within the Drakensberg Mountain clade (B), we observed in situ diversification. Specimens from the southcentral Drakensberg Mountains (Dargle Forest, Injasuti, Karkloof, and Impendle) represent a new undescribed lineage Potamonautes sp. nov. 1. The second clade from the northern Drakensberg, representing P. clarus, was sister to a central Drakensberg Mountain clade that comprised P. depressus that was in turn sister to P. baziya from the Eastern Cape Province. The application of species delimitation methods generally overestimated the number of species. The biogeographic analyses indicated that the Eastern Cape Province is the most likely ancestral range area. Ecological niche modelling of representative species in clades A (Cape Fold Mountains) and B (Drakensberg Mountains) demonstrated that temperature and rainfall were the major abiotic drivers that differentiated the two clades. Our data favours the mountain gradient speciation hypothesis.
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Affiliation(s)
- Savel R. Daniels
- Department of Botany and ZoologyUniversity of StellenboschStellenboschSouth Africa
| | - Nasreen Peer
- Department of Botany and ZoologyUniversity of StellenboschStellenboschSouth Africa
| | | | - Aaron Barnes
- Department of Botany and ZoologyUniversity of StellenboschStellenboschSouth Africa
| | - Sebastian Klaus
- Department of Ecology and EvolutionJ. W. Goethe‐University, BiologicumFrankfurt am MainGermany
- ERM GmbHNeu‐IsenburgGermany
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4
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Daniels SR, Busschau T, Gullacksen G, Marais H, Gouws G, Barnes A. Cryptic and widespread: a recipe for taxonomic misidentification in a freshwater crab species (Decapoda: Potamonautidae: Potamonautes sidneyi) as evident from species delimitation methods. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
AbstractWe examined the systematics of a ubiquitously distributed southern African freshwater crab, Potamonautes sidneyi s.l. species complex. Specimens were subjected to DNA sequence analyses of two mitochondrial loci (16S rRNA + COI). We applied three species delimitations methods (ASAP, bGMYC and bPTP) to test their utility in delineating species boundaries in Potamonautes and three additional Afrotropical genera (Liberonautes, Nesonautes and Seychellum). The combined mtDNA dataset retrieved five clades. Clade 1 comprised of P. barbarai, clade 2 comprised of specimens from the interior of the Great Karoo Basin, sister to P. sidneyi s.s. in clade 3. Clade 4 was confined to Eswatini and the Mpumalanga Province of South Africa, and sister to clade 5 that comprised P. danielsi. The three species delimitation methods either over- or underestimated the number of species. Phylogenetically, specimens from the Great Karoo Basin (clade 2) were equidistant to P. sidneyi s.s. and P. perlatus, while the Eswatini and Mpumalanga specimens (clade 4) were sister to P. danielsi. Clades 2 and 4 are herein described as P. karooensis sp. nov. and P. valles sp. nov., respectively.
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Affiliation(s)
- Savel R Daniels
- Department of Botany and Zoology, University of Stellenbosch , Private Bag X1, Matieland, 7602 , South Africa
| | - Theo Busschau
- Department of Botany and Zoology, University of Stellenbosch , Private Bag X1, Matieland, 7602 , South Africa
| | | | - Hannes Marais
- Mpumalanga Tourism and Parks Agency, Aquatic Unit , Lydenburg, 1120 , South Africa
| | - Gavin Gouws
- National Research Foundation - South African Institute for Aquatic Biodiversity , Private Bag 1015, Makhanda, 6140 , South Africa
| | - Aaron Barnes
- Department of Botany and Zoology, University of Stellenbosch , Private Bag X1, Matieland, 7602 , South Africa
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5
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Matamba E, Richards LR, Cherry MI, Rambau RV. Phylogeography of the mesic-adapted striped mouse, Rhabdomys dilectus chakae (Rodentia: Muridae) in forest margins of the Eastern Cape and southern KwaZulu-Natal provinces of South Africa. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Rhabdomys is a genus that occupies a variety of habitats, including forest margins. Among the Rhabdomys taxa, Rhabdomys dilectus chakae has a distribution that covers the eastern seaboard of South Africa, with a poorly defined divergence date from its sister taxon Rhabdomys dilectus dilectus. Here, we study three mitochondrial markers (cytochrome b, cytochrome c oxidase I and partial control region) of R. d. chakae across the Eastern Cape and KwaZulu-Natal forests of South Africa, aiming to determine the cladogenesis (molecular dating) and effective population size of this subspecies through time, in addition to its cladogenesis in relationship to other species within the genus. A phylogenetic analysis revealed six clades within Rhabdomys, confirming that our study area is occupied solely by R. d. chakae, to the exclusion of other recognized sibling species. A fossil-calibrated Bayesian relaxed molecular clock estimated a recent split between R. d. chakae and R. d. dilectus ~1.4 ± 0.35 Mya and between two Rhabdomys pumilio groups, coastal A and B, at 1.16 ± 0.44 Mya. Coalescent Bayesian skyline plots revealed a stable population of R. d. chakae in the study area that was in slow decline until 2500 years ago, when there was an expansion in the late Holocene. Radiation within Rhabdomys dates as far back as 4.27 Mya, and subsequent demographic fluctuations primarily reflect palaeoclimatic changes.
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Affiliation(s)
- Emmanuel Matamba
- Department of Botany and Zoology, Stellenbosch University , Matieland , South Africa
| | | | - Michael I Cherry
- Department of Botany and Zoology, Stellenbosch University , Matieland , South Africa
| | - Ramugondo V Rambau
- Department of Botany and Zoology, Stellenbosch University , Matieland , South Africa
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6
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Aguado S, Clusella-Trullas S. Intra-specific variation of thermal performance, skin reflectance and body size partially co-vary with climate in a lizard. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Thermal adaptation theory posits that variation of thermal traits such as those affecting thermal budgets and the performance of ectotherms should be associated with climate gradients. Under a simple scenario, thermal traits should also co-vary to shape optimal thermal phenotypes under a particular climate. However, geographical variation and covariation of thermal traits can result from other sources of selection and a wide range of other mechanisms. Here, we explore variation and covariation of skin reflectance (melanization), body size and thermal performance traits among three populations of the lizard Cordylus cordylus, a species endemic to South Africa. We also examine relationships between skin reflectance and substrate reflectance, body size and crevice size to test alternative hypotheses. We found partial support for predictions of thermal adaptation to climate regimes for body size, melanization and chill-coma recovery time. Darker lizards also performed optimally at higher temperatures than lighter coloured lizards but there was limited individual covariation between morphological and performance traits. Despite partial support for thermal adaptation, the complex interactions between sex and body size and between substrate reflectance and size underlying skin reflectance emphasized the importance of testing multiple hypotheses when exploring drivers of thermal trait variation within species.
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Affiliation(s)
- Sara Aguado
- Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo, and Unidad Mixta de Investigación en Biodiversidad (UMIB, CSIC-UO-PA), Oviedo, Spain
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7
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Busschau T, Conradie W, Daniels SR. One species hides many: Molecular and morphological evidence for cryptic speciation in a thread snake (Leptotyphlopidae:
Leptotyphlops sylvicolus
Broadley & Wallach, 1997). J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12401] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Theo Busschau
- Department of Botany & Zoology University of Stellenbosch Matieland South Africa
| | - Werner Conradie
- Port Elizabeth Museum Humewood South Africa
- School of Natural Resource Management, George Campus Nelson Mandela University George South Africa
| | - Savel R. Daniels
- Department of Botany & Zoology University of Stellenbosch Matieland South Africa
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8
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Kushata JNT, Conradie W, Cherry MI, Daniels SR. Comparison of the mitochondrial phylogeographical structure of a generalist and two specialist frog species reveals contrasting patterns in the Eastern and Western Cape provinces of South Africa. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
AbstractIn this study, we examined the phylogeographical structure of three frog species (Anhydrophryne rattrayi, Arthroleptis wageri and Cacosternum nanum) in the Eastern and Western Cape provinces of South Africa. The first two species are forest dwelling and exhibit direct development, whereas the last species is a habitat generalist, breeding in open freshwater bodies and exhibiting rapid metamorphosis. Evolutionary relationships were inferred using combined mitochondrial DNA (mtDNA) sequence data [16S rRNA and cytochrome b (Cytb)]. Divergence times were estimated for each species using the combined mtDNA dataset, and population genetic structuring was inferred using haplotype networks and analysis of molecular variance using the rapidly evolving Cytb locus. The two forest-dwelling species (Anhydrophryne rattrayi and Arthroleptis wageri) each revealed two statistically well-supported clades and were characterized by marked genetic differentiation and the general absence of shared maternal haplotypes, indicating no maternal gene flow between conspecific populations; a result corroborated by moderate values of pairwise genetic distance. In contrast, for the generalist species C. nanum, two shallow clades were observed and several haplotypes were shared between localities, indicating moderate maternal gene flow. Diversification in the two forest-dwelling species occurred during the Plio-Pleistocene climatic oscillations and was associated with increased xeric conditions, whereas in C. nanum a recent, Holocene divergence was inferred. Ancient climatic factors thought to be causal in the divergences within each of the three species are discussed. The marked mtDNA differentiation in the two forest specialist species suggests the presence of distinct management units that should be considered in future conservation management decisions.
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Affiliation(s)
- Judith N T Kushata
- Department of Botany and Zoology, University of Stellenbosch, Matieland, South Africa
| | - Werner Conradie
- Port Elizabeth (Bayworld) Museum, Humewood, South Africa
- School of Natural Resource Management, George Campus, Nelson Mandela University, George, South Africa
| | - Michael I Cherry
- Department of Botany and Zoology, University of Stellenbosch, Matieland, South Africa
| | - Savel R Daniels
- Department of Botany and Zoology, University of Stellenbosch, Matieland, South Africa
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9
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Evidence for cryptic diversification in a rupicolous forest-dwelling gecko (Gekkonidae: Afroedura pondolia) from a biodiversity hotspot. Mol Phylogenet Evol 2019; 139:106549. [DOI: 10.1016/j.ympev.2019.106549] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/25/2019] [Accepted: 06/28/2019] [Indexed: 11/22/2022]
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10
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Kulenkampff K, Van Zyl F, Klaus S, Daniels SR. Molecular evidence for cryptic species in the common slug eating snake Duberrialutrixlutrix (Squamata, Lamprophiidae) from South Africa. Zookeys 2019; 838:133-154. [PMID: 31048972 PMCID: PMC6477839 DOI: 10.3897/zookeys.838.32022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/09/2019] [Indexed: 11/28/2022] Open
Abstract
We examined the impact of climatic fluctuations on the phylogeographic structure of the common slug eating snake (Duberrialutrixlutrix) throughout its distribution in South Africa. The evolutionary history within the taxon was examined using partial DNA sequence data for two mitochondrial genes (ND4 + cyt b) in combination with a nuclear locus (SPTBN1). Phylogenetic relationships were investigated for both the combined mtDNA and total evidence DNA sequence data. In addition, population and demographic analyses together with divergence time estimations were conducted on the combined mtDNA data. Topologies derived from the combined mtDNA analyses and the total evidence analyses were congruent and retrieved five statistically well-supported clades, suggesting that Duberrial.lutrix represents a species complex. The five clades were generally allopatric, separated by altitudinal barriers and characterised by the absence of shared mtDNA haplotypes suggesting long term isolation. Divergence time estimations indicate that the diversification within the D.l.lutrix species complex occurred during the Plio/Pleistocene as a result of climatic fluctuations and habitat shifts for the species. A taxonomic revision of the D.l.lutrix species complex may be required to delineate possible species boundaries.
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Affiliation(s)
- Kyle Kulenkampff
- Department of Botany and Zoology, Private Bag X1, Stellenbosch University, Matieland, 7602, South AfricaStellenbosch UniversityStellenboschSouth Africa
| | - Francois Van Zyl
- Department of Botany and Zoology, Private Bag X1, Stellenbosch University, Matieland, 7602, South AfricaStellenbosch UniversityStellenboschSouth Africa
| | - Sebastian Klaus
- Department of Ecology and Evolution, J. W. Goethe-University, Biologicum, Frankfurt am Main, GermanyJ. W. Goethe-UniversityFrankfurtGermany
| | - Savel R. Daniels
- Department of Botany and Zoology, Private Bag X1, Stellenbosch University, Matieland, 7602, South AfricaStellenbosch UniversityStellenboschSouth Africa
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Zhao Z, Verdú‐Ricoy J, Mohlakoana S, Jordaan A, Conradie W, Heideman N. Unexpected phylogenetic relationships within the world's largest limbless skink species (
Acontias plumbeus
) highlight the need for a review of the taxonomic status of
Acontias poecilus. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Zhongning Zhao
- Department of Zoology & EntomologyUniversity of the Free State Bloemfontein South Africa
| | - Joaquín Verdú‐Ricoy
- Department of Zoology & EntomologyUniversity of the Free State Bloemfontein South Africa
| | - Setjhaba Mohlakoana
- Department of Zoology & EntomologyUniversity of the Free State Bloemfontein South Africa
| | - Adriaan Jordaan
- Department of Zoology & EntomologyUniversity of the Free State Bloemfontein South Africa
| | - Werner Conradie
- Port Elizabeth Museum (Bayworld) Port Elizabeth South Africa
- School of Natural Resource ManagementNelson Mandela University George South Africa
| | - Neil Heideman
- Department of Zoology & EntomologyUniversity of the Free State Bloemfontein South Africa
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12
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Phylogeography of the Japanese ratsnake, Elaphe climacophora (Serpentes: Colubridae): impacts of Pleistocene climatic oscillations and sea-level fluctuations on geographical range. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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13
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Matenaar D, Fingerle M, Heym E, Wirtz S, Hochkirch A. Phylogeography of the endemic grasshopper genus Betiscoides (Lentulidae) in the South African Cape Floristic Region. Mol Phylogenet Evol 2017; 118:318-329. [PMID: 28986236 DOI: 10.1016/j.ympev.2017.09.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 09/12/2017] [Accepted: 09/30/2017] [Indexed: 11/25/2022]
Abstract
Vicariance and dispersal are two important processes shaping biodiversity patterns. The South African Cape Floristic Region (CFR) is known for its high biotic diversity and endemism. However, studies on the phylogeography of endemic invertebrates in this biodiversity hotspot are still scarce. Here, we present a phylogenetic study of the flightless grasshopper genus Betiscoides, which is endemic to the CFR and strongly associated with restio plants (Restionaceae). We hypothesized that the genus originated in the southwestern part of the CFR, that differentiation within the genus is mainly an effect of vicariance and that the three known species only represent a minor fraction of the real genetic diversity of the genus. We inferred the phylogeny based on sequences of three mitochondrial and two nuclear genes from 99 Betiscoides specimens collected across the CFR. Furthermore, we conducted a SDIVA analysis to detect distributions of ancestral nodes and the possible spatial origin of these lineages. Strong differentiation among genetic lineages was shown. The ancestor of this genus was most likely distributed in the southwestern CFR. Five major lineages were detected, three of which were ancestrally distributed in the southwestern CFR. The ancestors of the two other lineages were distributed in the northern and eastern margins of the CFR. A total of 24 divergent evolutionary lineages were found, reflecting the geographical isolation of restio-dominated fynbos habitats. Dispersal played a more prominent role than expected in differentiation of Betiscoides. While the five main lineages were separated during a first phase via dispersal, differentiation occurred later and on smaller spatial scale, predominantly driven by isolation in montane refugia (i.e. vicariance). Our study also suggests that flightless insect taxa likely show high levels of differentiation in biodiversity hotspots with their taxonomy often being incomplete.
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Affiliation(s)
- Daniela Matenaar
- Trier University, Department of Biogeography, D-54286 Trier, Germany; Stuttgart State Museum of Natural History, Department of Entomology, D-70191 Stuttgart, Germany; Hessisches Landesmuseum Darmstadt, Friedensplatz 1, D-64283 Darmstadt, Germany.
| | - Marcus Fingerle
- Trier University, Department of Biogeography, D-54286 Trier, Germany
| | - Eva Heym
- Trier University, Department of Biogeography, D-54286 Trier, Germany
| | - Sarah Wirtz
- Trier University, Department of Biogeography, D-54286 Trier, Germany
| | - Axel Hochkirch
- Trier University, Department of Biogeography, D-54286 Trier, Germany
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14
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Busschau T, Conradie W, Jordaan A, Daniels SR. Unmasking evolutionary diversity among two closely related South African legless skink species (Acontinae: Acontias ) using molecular data. ZOOLOGY 2017; 121:72-82. [DOI: 10.1016/j.zool.2016.11.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 09/07/2016] [Accepted: 11/29/2016] [Indexed: 10/20/2022]
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15
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Molecular phylogeny of Panaspis and Afroablepharus skinks (Squamata: Scincidae) in the savannas of sub-Saharan Africa. Mol Phylogenet Evol 2016; 100:409-423. [PMID: 27118179 DOI: 10.1016/j.ympev.2016.04.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 03/13/2016] [Accepted: 04/20/2016] [Indexed: 11/20/2022]
Abstract
African snake-eyed skinks are relatively small lizards of the genera Panaspis and Afroablepharus. Species allocation of these genera frequently changed during the 20th century based on morphology, ecology, and biogeography. Members of these genera occur primarily in savanna habitats throughout sub-Saharan Africa and include species whose highly conserved morphology poses challenges for taxonomic studies. We sequenced two mitochondrial (16S and cyt b) and two nuclear genes (PDC and RAG1) from 76 Panaspis and Afroablepharus samples from across eastern, central, and southern Africa. Concatenated gene-tree and divergence-dating analyses were conducted to infer phylogenies and biogeographic patterns. Molecular data sets revealed several cryptic lineages, with most radiations occurring during the mid-Miocene to Pliocene. We infer that rifting processes (including the formation of the East African Rift System) and climatic oscillations contributed to the expansion and contraction of savannas, and caused cladogenesis in snake-eyed skinks. Species in Panaspis and Afroablepharus used in this study, including type species for both genera, formed a monophyletic group. As a result, the latter genus should be synonymized with the former, which has priority. Conservatively, we continue to include the West African species P. breviceps and P. togoensis within an expanded Panaspis, but note that they occur in relatively divergent clades, and their taxonomic status may change with improved taxon sampling. Divergence estimates and cryptic speciation patterns of snake-eyed skinks were consistent with previous studies of other savanna vertebrate lineages from the same areas examined in this study.
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Dowell SA, Portik DM, de Buffrénil V, Ineich I, Greenbaum E, Kolokotronis SO, Hekkala ER. Molecular data from contemporary and historical collections reveal a complex story of cryptic diversification in the Varanus (Polydaedalus) niloticus Species Group. Mol Phylogenet Evol 2016; 94:591-604. [DOI: 10.1016/j.ympev.2015.10.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 09/09/2015] [Accepted: 10/06/2015] [Indexed: 11/16/2022]
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Phiri EE, Daniels SR. Multilocus coalescent species delimitation reveals widespread cryptic differentiation among Drakensberg mountain-living freshwater crabs (Decapoda : Potamonautes). INVERTEBR SYST 2016. [DOI: 10.1071/is15035] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Cryptic lineages present major challenges for evolutionary and conservation studies, particularly where these lineages remain undiscovered. Freshwater crabs are known to harbour cryptic diversity, in most cases with limited morphological differences. During the present study, we used a multilocus (12S rRNA, 16S rRNA, COI, 28S rRNA, DecapANT and PEPCK) Bayesian species delimitation to examine cryptic diversity within a freshwater crab species complex (Potamonautes clarus/P. depressus). We sampled 25 highland rivers in the Tugela and uMkomazi River drainage systems of the Drakensberg Mountain range, in the KwaZulu–Natal province of South Africa. Our results showed there to be at least eight lineages: six novel potamonautid freshwater crabs, and two described taxa P. clarus and P. depressus. Divergence from the most recent common ancestor occurred between the mid- and late Miocene (12.1 Mya), while divergence within the species complex occurred ~10.3 Mya up until the Holocene (0.11 Mya). The discovery of six novel lineages of freshwater crabs from a seemingly restricted distribution range has conservation implications, but to date most conservation planning strategies have focussed on freshwater vertebrates. By conducting a fine-scale phylogenetic survey using invertebrates, this study provides a platform for the inclusion of freshwater invertebrates in future conservation assessments.
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Phylogeography of a Morphologically Cryptic Golden Mole Assemblage from South-Eastern Africa. PLoS One 2015; 10:e0144995. [PMID: 26683828 PMCID: PMC4684196 DOI: 10.1371/journal.pone.0144995] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 11/25/2015] [Indexed: 11/19/2022] Open
Abstract
The Greater Maputaland-Pondoland-Albany (GMPA) region of southern Africa was recently designated as a centre of vertebrate endemism. The phylogeography of the vertebrate taxa occupying this region may provide insights into the evolution of faunal endemism in south-eastern Africa. Here we investigate the phylogeographic patterns of an understudied small mammal species assemblage (Amblysomus) endemic to the GMPA, to test for cryptic diversity within the genus, and to better understand diversification across the region. We sampled specimens from 50 sites across the distributional range of Amblysomus, with emphasis on the widespread A. hottentotus, to analyse geographic patterns of genetic diversity using mitochondrial DNA (mtDNA) and nuclear intron data. Molecular dating was used to elucidate the evolutionary and phylogeographic history of Amblysomus. Our phylogenetic reconstructions show that A. hottentotus comprises several distinct lineages, or evolutionarily significant units (ESUs), some with restricted geographic ranges and thus worthy of conservation attention. Divergence of the major lineages dated to the early Pliocene, with later radiations in the GMPA during the late-Pliocene to early-Pleistocene. Evolutionary diversification within Amblysomus may have been driven by uplift of the Great Escarpment c. 5-3 million years ago (Ma), habitat changes associated with intensification of the east-west rainfall gradient across South Africa and the influence of subsequent global climatic cycles. These drivers possibly facilitated geographic spread of ancestral lineages, local adaptation and vicariant isolation. Our study adds to growing empirical evidence identifying East and southern Africa as cradles of vertebrate diversity.
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