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Main DC, Taft JM, Geneva AJ, Jansenvan Vuuren B, Tolley KA. The efficacy of single mitochondrial genes at reconciling the complete mitogenome phylogeny-a case study on dwarf chameleons. PeerJ 2024; 12:e17076. [PMID: 38708350 PMCID: PMC11067893 DOI: 10.7717/peerj.17076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/19/2024] [Indexed: 05/07/2024] Open
Abstract
Although genome-scale data generation is becoming more tractable for phylogenetics, there are large quantities of single gene fragment data in public repositories and such data are still being generated. We therefore investigated whether single mitochondrial genes are suitable proxies for phylogenetic reconstruction as compared to the application of full mitogenomes. With near complete taxon sampling for the southern African dwarf chameleons (Bradypodion), we estimated and compared phylogenies for the complete mitogenome with topologies generated from individual mitochondrial genes and various combinations of these genes. Our results show that the topologies produced by single genes (ND2, ND4, ND5, COI, and COIII) were analogous to the complete mitogenome, suggesting that these genes may be reliable markers for generating mitochondrial phylogenies in lieu of generating entire mitogenomes. In contrast, the short fragment of 16S commonly used in herpetological systematics, produced a topology quite dissimilar to the complete mitogenome and its concatenation with ND2 weakened the resolution of ND2. We therefore recommend the avoidance of this 16S fragment in future phylogenetic work.
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Affiliation(s)
- Devon C. Main
- Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Johannesburg, Gauteng, South Africa
| | - Jody M. Taft
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Claremont, South Africa
| | - Anthony J. Geneva
- Department of Biology, Center for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, NJ, United States of America
| | - Bettine Jansenvan Vuuren
- Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Johannesburg, Gauteng, South Africa
| | - Krystal A. Tolley
- Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Johannesburg, Gauteng, South Africa
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Claremont, South Africa
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Keren-Rotem T, Main DC, Barocas A, Donaire-Barroso D, Haddas-Sasson M, Vila C, Shaharabany T, Wolf L, Tolley KA, Geffen E. Genetic and behavioural factors affecting interpopulation colour pattern variation in two congeneric chameleon species. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231554. [PMID: 38234439 PMCID: PMC10792394 DOI: 10.1098/rsos.231554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 12/19/2023] [Indexed: 01/19/2024]
Abstract
We conducted a study on interpopulation variation of colour patterns in two congeneric chameleon species, which have an analogous life history. Both species are able to rapidly change colour pattern, and their context-dependent colour patterns often vary across a wide geographical range. Specifically, we tested four hypotheses that can explain the observed interpopulation variation of colour patterns by a series of behavioural field trials where the colour patterns of individuals were recorded and later analysed by a deep neural network algorithm. We used redundancy analysis to relate genetic, spectral and behavioural predictors to interpopulation colour pattern distance. Our results showed that both isolation by distance (IBD) and alternative mating tactics were significant predictors for interpopulation colour pattern variation in Chamaeleo chamaeleon males. By contrast, in Chamaeleo dilepis, the interpopulation colour pattern variation was largely explained by IBD, and evidence for alternative mating tactics was absent. In both chameleon species, the environmental colours showed no evidence of influencing chameleon interpopulation colour pattern variation, regardless of sex or behavioural context. This contrasting finding suggests that interpopulation context-dependent colour pattern variations in each species are maintained under a different set of selective pressures or circumstances.
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Affiliation(s)
- Tammy Keren-Rotem
- Ecology Department, Israel Nature and Parks Authority, Jerusalem, Israel
| | - Devon C. Main
- Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park Campus, Johannesburg, South Africa
| | - Adi Barocas
- San Diego Zoo Wildlife Alliance, Escondido, CA, USA
- Wildlife Conservation Research Unit, University of Oxford, Oxford, UK
| | | | | | - Carles Vila
- Doñana Biological Station (EBD-CSIC), Seville, Spain
| | - Tal Shaharabany
- The Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Lior Wolf
- School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Krystal A. Tolley
- Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park Campus, Johannesburg, South Africa
- Kirstenbosch Research Centre, South African National Biodiversity Institute, Cape Town, South Africa
| | - Eli Geffen
- School of Zoology, Tel Aviv University, Tel Aviv, Israel
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Main DC, van Vuuren BJ, Tilbury CR, Tolley KA. Out of southern Africa: Origins and cryptic speciation in Chamaeleo, the most widespread chameleon genus. Mol Phylogenet Evol 2022; 175:107578. [PMID: 35809854 DOI: 10.1016/j.ympev.2022.107578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 05/18/2022] [Accepted: 07/01/2022] [Indexed: 11/19/2022]
Abstract
Molecular phylogenetics and the application of species delimitation methods have proven useful in addressing limitations associated with morphology based taxonomy and have highlighted the inconsistencies in the current taxonomy for many groups. For example, the genus Chamaeleo, which comprises 14 species with large distributions across mainland Africa and parts of Eurasia, exhibits relatively minor phenotypic differentiation between species, leading to speculation regarding the presence of cryptic diversity in the genus. Therefore, the aims of the present study were to construct a robust and comprehensive phylogeny of the genus and highlight potential species-level cryptic diversity. Additionally, we sought to ascertain the most likely biogeographic origin of the genus and understand its spatio-temporal diversification. Accordingly, we made use of species delimitation methods (Bayesian and divergence based) to investigate the extent of cryptic diversity in Chamaeleo, and applied an ancestral area reconstruction to examine the biogeographic origin of the group. Our phylogenetic analyses suggested the presence of at least 18 taxa within Chamaeleo. Notably, three taxa could be recognised within C. dilepis, none of which are equivalent in context with any of the currently described subspecies. There were also three taxa within C. gracilis and two within C. anchietae. The single available tissue specimen identified as C. necasi was embedded within the C. gracilis clade. Our ancestral area reconstruction points to a southern African/Zambezian origin for Chamaeleo, with diversification beginning during the cooling and aridification of Africa that characterised the Oligocene Epoch, ca. 34-23 Mya (Million years ago). Species-level diversification began in the Miocene Epoch (ca. 23-5 Mya), possibly tracking the aridification that triggered the shift from forest to more open, mesic savanna for most clades, but with tectonic events influencing speciation in a Palearctic clade. These findings lay the foundation for a future integrative taxonomic re-evaluation of Chamaeleo, which will be supported with additional lines of evidence before implementing any taxonomic changes.
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Affiliation(s)
- Devon C Main
- Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park, 2006 Johannesburg, South Africa
| | - Bettine Jansen van Vuuren
- Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park, 2006 Johannesburg, South Africa
| | - Colin R Tilbury
- Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland, South Africa
| | - Krystal A Tolley
- Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park, 2006 Johannesburg, South Africa; South African National Biodiversity Institute, Kirstenbosch Research Centre, Private Bag X7 Claremont, Cape Town, South Africa.
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Clinging to survival: Critically Endangered Chapman's pygmy chameleon Rhampholeon chapmanorum persists in shrinking forest patches. ORYX 2021. [DOI: 10.1017/s0030605320000952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
AbstractThe Critically Endangered Chapman's pygmy chameleon Rhampholeon chapmanorum is endemic to the low elevation rainforest of the Malawi Hills in southern Malawi. Much of this forest has been converted to agriculture and it was uncertain whether chameleon populations have persisted. We used current and historical satellite imagery to identify remaining forest patches and assess deforestation. We then surveyed forest patches for the presence of this chameleon, and assessed its genetic diversity and structure. We estimated that 80% of the forest has been destroyed since 1984, although we found extant populations of the chameleon in each of the patches surveyed. Differentiation of genetic structure was strong between populations, suggesting that gene flow has been impaired. Genetic diversity was not low, but this could be the result of a temporal lag as well as lack of sensitivity in the mitochondrial marker used. Overall, the impact of forest loss is assumed to have led to a large demographic decline, with forest fragmentation preventing gene flow.
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O’Donoghue TL, Slater K, Brown LR. Seasonal habitat utilisation and morphological characteristics of Chamaeleo dilepis on Telperion Nature Reserve, Mpumalanga, South Africa. AFR J HERPETOL 2020. [DOI: 10.1080/21564574.2020.1798290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Trevor L O’Donoghue
- Applied Behavioural Ecology and Ecosystem Research Unit, Department of Environmental Sciences, University of South Africa, Florida, South Africa
| | - Kerry Slater
- Applied Behavioural Ecology and Ecosystem Research Unit, Department of Environmental Sciences, University of South Africa, Florida, South Africa
| | - Leslie R Brown
- Applied Behavioural Ecology and Ecosystem Research Unit, Department of Environmental Sciences, University of South Africa, Florida, South Africa
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Main D, Tensen L, Gihring K, Bronner G, Aboul-Hassan N, Blanckenberg M, van Vuuren BJ. Unravelling the taxonomy and distribution of two problematic small mammal genera in the Karoo biome. AFRICAN ZOOLOGY 2019. [DOI: 10.1080/15627020.2019.1628661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Devon Main
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, South Africa
| | - Laura Tensen
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, South Africa
| | - Katharina Gihring
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, South Africa
| | - Gary Bronner
- Department of Biological Sciences, University of Cape Town, Rondebosch, South Africa
| | - Nadine Aboul-Hassan
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, South Africa
| | - Michelle Blanckenberg
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, South Africa
| | - Bettine Jansen van Vuuren
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, South Africa
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