Characterization of polymorphic microsatellite markers for the endangered Malagasy radiated tortoise (<i>Geochelone radiata</i>)

Paquette, Sébastien Rioux; Shore, Gary D.; Behncke, Sandra M.; Lapointe, François‐Joseph; Louis, Edward E.

doi:10.1111/j.1471-8286.2005.00979.x

Cited by 10 publications

(5 citation statements)

References 9 publications

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“…Extracted genomic DNA was used as template DNA in the PCR. Twenty two microsatellite DNA loci, which were successful in previous testudines population genetics studies [115][116][117][118][119][120][121] were tested. They were tested on the target animal using PCR, with all forward primers labelled fluorescently with different dye probes (primer details and optimal annealing temperatures are given in Additional file 7: Table S14).…”

Section: Microsatellite Dna Genotypingmentioning

confidence: 99%

Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa

et al. 2020

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Background Climatic and topographic changes function as key drivers in shaping genetic structure and cladogenic radiation in many organisms. Southern Africa has an exceptionally diverse tortoise fauna, harbouring one-third of the world’s tortoise genera. The distribution of Psammobates tentorius (Kuhl, 1820) covers two of the 25 biodiversity hotspots in the world, the Succulent Karoo and Cape Floristic Region. The highly diverged P. tentorius represents an excellent model species for exploring biogeographic and radiation patterns of reptiles in Southern Africa. Results We investigated genetic structure and radiation patterns against temporal and spatial dimensions since the Miocene in the Psammobates tentorius species complex, using multiple types of DNA markers and niche modelling analyses. Cladogenesis in P. tentorius started in the late Miocene (11.63–5.33 Ma) when populations dispersed from north to south to form two geographically isolated groups. The northern group diverged into a clade north of the Orange River (OR), followed by the splitting of the group south of the OR into a western and an interior clade. The latter divergence corresponded to the intensification of the cold Benguela current, which caused western aridification and rainfall seasonality. In the south, tectonic uplift and subsequent exhumation, together with climatic fluctuations seemed responsible for radiations among the four southern clades since the late Miocene. We found that each clade occurred in a habitat shaped by different climatic parameters, and that the niches differed substantially among the clades of the northern group but were similar among clades of the southern group. Conclusion Climatic shifts, and biome and geographic changes were possibly the three major driving forces shaping cladogenesis and genetic structure in Southern African tortoise species. Our results revealed that the cladogenesis of the P. tentorius species complex was probably shaped by environmental cooling, biome shifts and topographic uplift in Southern Africa since the late Miocene. The Last Glacial Maximum (LGM) may have impacted the distribution of P. tentorius substantially. We found the taxonomic diversify of the P. tentorius species complex to be highest in the Greater Cape Floristic Region. All seven clades discovered warrant conservation attention, particularly Ptt-B–Ptr, Ptt-A and Pv-A.

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Section: Microsatellite Dna Genotypingmentioning

confidence: 99%

Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa

et al. 2020

View full text Add to dashboard Cite

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“…Extracted genomic DNA was used as template DNA in the PCR. Twenty two microsatellite DNA loci, which were successful in previous testudines population genetics studies [114,115,116,117,118,119,120) were tested. They were tested on the target animal using PCR, with all forward primers labelled uorescently with different dye probes (primer details and optimal annealing temperatures are given in Supplementary Table S14).…”

Section: Microsatellite Dna Genotypingmentioning

confidence: 99%

Climatic and topographic changes since the Miocene influenced the diversification and biogeography of tent tortoise (Psammobates tentorius) species complex in Southern Africa

Zhao

Heideman

Bester

et al. 2020

Preprint

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Background Climatic and topographic changes function as key drivers in shaping genetic structure and cladogenic radiation in many organisms. Southern Africa has an exceptionally diverse tortoise fauna, harbouring one-third of the world’s tortoise genera. The distribution of Psammobates tentorius (Kuhl, 1820) covers two of the 25 biodiversity hotspots of in the world, the Succulent Karoo and Cape Floristic Region. The highly diverged P. tentorius represents an excellent model species for exploring biogeographic and radiation patterns of reptiles in Southern Africa.Results We investigated genetic structure, population dynamics, and radiation patterns against temporal and spatial dimensions since the Miocene in the Psammobates tentorius species complex, using multiple types of DNA markers and niche modelling analyses. Cladogenesis in P. tentorius started in the late Miocene (11.63–5.33 Ma) when populations dispersed from north to south to form two geographically isolated groups. The northern group diverged into a clade north of the Orange River (OR), followed by the splitting of the group south of the OR into a western and an interior clade. The latter divergence corresponded to the intensification of the cold Benguela current, which caused western aridification and rainfall seasonality. In the south, tectonic uplift and subsequent exhumation, together with climatic fluctuations seemed responsible for radiations among the four southern clades since the late Miocene. We found that each clade occurred in a habitat shaped by different climatic parameters, and that the niches differed substantially among the clades of the northern group but were similar among clades of the southern group. Conclusion Climatic shifts, and biome and geographic changes were possibly the three major driving forces shaping cladogenesis, population dynamics, and genetic structure in Southern African tortoise species. Our results revealed that the cladogenesis of the P. tentorius species complex was probably shaped by environmental cooling, biome shifts and topographic uplift in Southern Africa since the late Miocene. The Last Glacial Maximum (LGM) may have impacted the population dynamics of P. tentorius substantially. We found the taxonomic diversify of the P. tentorius species complex to be highest in the Greater Cape Floristic Region. All seven clades discovered warrant conservation attention, particularly C1–C3, C5 and C6.

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“…Extracted genomic DNA was used as template DNA in the PCR. Twenty-two microsatellite DNA loci, which were successful in previous testudines population genetics studies (Vamberger et al, 2001; Ciofi et al, 2002; Schwartz et al, 2003; Forlani et al, 2005; Paquette et al, 2005; Mandimbihasina et al, 2009; Orozco-terWengel et al, 2013), were used. They were tested on our target animal using PCR, with all forward primers labelled fluorescently with different dye probes (primer details and optimal annealing temperatures are given in Supporting Information Table S3).…”

Section: Methodsmentioning

confidence: 99%

Testing alternative phylogenetic hypotheses for the tent tortoise species complex (Reptilia, Testudinidae) using multiple data types and methods

Zhao¹,

Heideman²,

Oosthuizen³

et al. 2020

Preprint

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We examined genetic differentiation in the highly polymorphic and taxonomically confusing tent tortoise (Psammobates tentorius) species complex in southern Africa, using three types of molecular markers (nDNA, mtDNA and microsatellite DNA) and morphological data. The Approximate Bayesian Computation based simulation analyses advocated an alternative phylogenetic hypothesis for the tent tortoise species complex, which was better and more inclusive in explaining its genealogical history. Based on the evidence derived from the sequence, microsatellite and morphology data, a four species scheme (among the seven mtDNA clades) appears to be the best taxonomic solution for the systematic puzzle of the P. tentorius species complex, namely, (C1+C4+C5+C7), (C3), (C2) and (C6). The microsatellite datasets yielded similar genetic structure and gene flow patterns among the seven mtDNA clades in comparison to the sequence DNA. Evidence was found of possible hybridization between C1 and C2 in their intergradation zone, but not between C2 and C4. Results of the inbreeding analyses provided strong evidence of inbreeding in the eastern population of C1 and the southern population of C2, which may be indicative of a bottleneck effect.

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Characterization of polymorphic microsatellite markers for the endangered Malagasy radiated tortoise (Geochelone radiata)

Cited by 10 publications

References 9 publications

Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa

Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa

Climatic and topographic changes since the Miocene influenced the diversification and biogeography of tent tortoise (Psammobates tentorius) species complex in Southern Africa

Testing alternative phylogenetic hypotheses for the tent tortoise species complex (Reptilia, Testudinidae) using multiple data types and methods

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