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

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Zhongning Zhao ◽  
Neil Heideman ◽  
Phillip Bester ◽  
Adriaan Jordaan ◽  
Margaretha D. Hofmeyr
Keyword(s):  
Genetic Structure ◽  
Southern Africa ◽  
Late Miocene ◽  
Species Complex ◽  
Driving Forces ◽  
Cape Floristic Region ◽  
Radiation Patterns ◽  
Niche Modelling ◽  
Climatic Fluctuations ◽  
Northern Group

Abstract 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.

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

2020 ◽  
Author(s):  
Zhongning Zhao ◽  
Neil Heideman ◽  
Phillip Bester ◽  
Adriaan Jordaan ◽  
Margaretha D. Hofmeyr
Keyword(s):  
Genetic Structure ◽  
Southern Africa ◽  
Late Miocene ◽  
Species Complex ◽  
Driving Forces ◽  
Cape Floristic Region ◽  
Radiation Patterns ◽  
Niche Modelling ◽  
Climatic Fluctuations ◽  
Northern Group

Abstract 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 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.

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

2020 ◽  
Author(s):  
Zhongning Zhao ◽  
Neil Heideman ◽  
Phillip Bester ◽  
Adriaan Jordaan ◽  
Margaretha D. Hofmeyr
Keyword(s):  
Genetic Structure ◽  
Southern Africa ◽  
Late Miocene ◽  
Species Complex ◽  
Driving Forces ◽  
Cape Floristic Region ◽  
Radiation Patterns ◽  
Niche Modelling ◽  
Climatic Fluctuations ◽  
Northern Group

Abstract 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.

scholarly journals Climatic and topographic changes since the Miocene influenced the radiation and biogeography of tent tortoises (Psammobates tentorius) species complex in southern Africa as inferred from mitochondrial and nuclear genes, microsatellite markers as well as ecological niche modelling

2020 ◽  
Author(s):  
Zhongning Zhao ◽  
Neil Heideman ◽  
Phillip Bester ◽  
Adriaan Jordaan ◽  
Margaretha D. Hofmeyr
Keyword(s):  
Population Dynamics ◽  
Genetic Structure ◽  
Southern Africa ◽  
Late Miocene ◽  
Species Complex ◽  
Cape Floristic Region ◽  
Radiation Patterns ◽  
Niche Modelling ◽  
Climatic Fluctuations ◽  
Northern Group

Abstract 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 covers two of the 25 biodiversity hotspots of southern Africa, 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 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 possibly functioned as major driving forces in shaping cladogenesis, population dynamics and genetic structure in southern African tortoise species. Our results revealed that the cryptic cladogenic radiation 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 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.

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

2020 ◽  
Author(s):  
Zhongning Zhao ◽  
Neil Heideman ◽  
Phillip Bester ◽  
Adriaan Jordaan ◽  
Margaretha D. Hofmeyr
Keyword(s):  
Population Dynamics ◽  
Genetic Structure ◽  
Southern Africa ◽  
Late Miocene ◽  
Species Complex ◽  
Driving Forces ◽  
Cape Floristic Region ◽  
Radiation Patterns ◽  
Climatic Fluctuations ◽  
Northern Group

Abstract 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.

Population genetic structure and species delimitation in the Cryptanthus zonatus complex (Bromeliaceae)

2020 ◽  
Author(s):  
Débora Maria Cavalcanti Ferreira ◽  
Clarisse Palma-Silva ◽  
Jordana Néri ◽  
Maria Cláudia Melo Pacheco de Medeiros ◽  
Diego Sotero Pinangé ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Population Genetic Structure ◽  
Species Delimitation ◽  
Population Genetic ◽  
Species Complex ◽  
Conservation Status ◽  
Niche Modelling ◽  
Morphological Comparison ◽  
Morphological Variations ◽  
Genetic Clusters

Abstract Morphological variations of individuals and populations of plants have hampered taxonomists from understanding whether such variations are intra- or interspecific. In this research, we study Cryptanthus burle-marxii and C. zonatus, the morphological variations of which overlap, making it difficult to identify them. Both taxa are restricted to the north of the Brazilian Atlantic Forest and are included in the C. zonatus species complex. We applied different methods such as morphological comparison, population genetics using ten nuclear microsatellite markers and ecological niche modelling to study population genetic structure and species delimitation of this species complex. Our analysis revealed that the two genetic clusters were formed possibly because of the presence of a historical geographical barrier in a region called ‘depressão do Abiaí’. The two genetic clusters were concordant with the northern and southern distribution of the complex but incongruent with a morphological variation or current taxonomic delimitation. Thus, we synonymize C. burle-marxii with C. zonatus and re-evaluate its conservation status as endangered.

scholarly journals Host-symbiont coevolution, cryptic structure, and bleaching susceptibility, in a coral species complex (Scleractinia; Poritidae)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Z. H. Forsman ◽  
R. Ritson-Williams ◽  
K.H. Tisthammer ◽  
I. S. S. Knapp ◽  
R. J. Toonen
Keyword(s):  
Genetic Structure ◽  
Evolutionary Biology ◽  
Species Complex ◽  
Coral Species ◽  
Genetic Relationships ◽  
Level Variation ◽  
Reduced Representation ◽  
The Pacific ◽  
Rapid Diversification ◽  
Candidate Loci

Abstract The ‘species’ is a key concept for conservation and evolutionary biology, yet the lines between population and species-level variation are often blurred, especially for corals. The ‘Porites lobata species complex’ consists of branching and mounding corals that form reefs across the Pacific. We used reduced representation meta-genomic sequencing to examine genetic relationships within this species complex and to identify candidate loci associated with colony morphology, cryptic genetic structure, and apparent bleaching susceptibility. We compared existing Porites data with bleached and unbleached colonies of the branching coral P. compressa collected in Kāneʻohe Bay Hawaiʻi during the 2015 coral bleaching event. Loci that mapped to coral, symbiont, and microbial references revealed genetic structure consistent with recent host-symbiont co-evolution. Cryptic genetic clades were resolved that previous work has associated with distance from shore, but no genetic structure was associated with bleaching. We identified many candidate loci associated with morphospecies, including candidate host and symbiont loci with fixed differences between branching and mounding corals. We also found many loci associated with cryptic genetic structure, yet relatively few loci associated with bleaching. Recent host-symbiont co-evolution and rapid diversification suggests that variation and therefore the capacity of these corals to adapt may be underappreciated.

scholarly journals The evolutionary history of the white wagtail species complex, (Passeriformes: Motacillidae: Motacilla alba)

2019 ◽  
Vol 88 (3) ◽  
pp. 257-276
Author(s):  
Maliheh Pirayesh Shirazinejad ◽  
Mansour Aliabadian ◽  
Omid Mirshamsi
Keyword(s):  
Species Complex ◽  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Considerable Effect ◽  
Niche Modelling ◽  
Complex Species ◽  
Ancestral Area ◽  
Genetic Lineages ◽  
Western Asia ◽  
Motacilla Alba

The white wagtail (Motacilla alba) species complex with its distinctive plumage in separate geographical areas can serve as a model to test evolutionary hypotheses. Its extensive variety in plumage, despite the genetic similarity between taxa, and the evolutionary events connected to this variety are poorly understood. Therefore we sampled in the breeding range of the white wagtail: 338 individuals were analyzed from 74 areas in the Palearctic and Mediterranean. We studied the white wagtail complex based on two mitochondrial DNA markers to make inferences about the evolutionary history. Our phylogenetic trees highlight mtDNA sequences (ND2, CR), and one nuclear marker (CHD1Z), which partly correspond to earlier described clades: the northern Palearctic (clade N); eastern and central Asia (clade SE); south-western Asia west to the British Isles (clade SW); and Morocco (clade M). The divergence of all clades occurred during the Pleistocene. We also used ecological niche modelling for three genetic lineages (excluding clade M); results showed congruence between niche and phylogenetic divergence in these clades. The results of the white wagtail ancestral area reconstruction showed the influence of dispersal on the distribution and divergence of this complex species. The most important vicariance event for the white wagtail complex may have been caused by the Gobi and Taklamakan deserts. We conclude that the ancestral area of the white wagtail complex was probably in the Mediterranean, with its geography having a considerable effect on speciation processes.

scholarly journals Genetic structure and biogeographic history of the Bicknell’s Thrush/ Gray-cheeked Thrush species complex

The Auk ◽  
2019 ◽  
Vol 137 (1) ◽  
Author(s):  
Alyssa M Fitzgerald ◽  
Jason Weir ◽  
Joel Ralston ◽  
Ian G Warkentin ◽  
Darroch M Whitaker ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Late Pleistocene ◽  
Species Complex ◽  
Extended Period ◽  
Genetic Data ◽  
Distribution Models ◽  
Biogeographic History ◽  
History Of ◽  
Low Levels ◽  
Bicknell's Thrush

Abstract We examined species limits, admixture, and genetic structure among populations in the Bicknell’s Thrush (Catharus bicknelli)–Gray-cheeked Thrush (C. minimus) species complex to establish the geographic and temporal context of speciation in this group, which is a model system in ecology and a high conservation priority. We obtained mitochondrial ND2 sequences from 186 Bicknell’s Thrushes, 77 Gray-cheeked Thrushes, and 55 individuals of their closest relative, the Veery (C. fuscescens), and genotyped a subset of individuals (n = 72) at 5,633 anonymous single nucleotide polymorphic (SNP) loci. Between-species sequence divergence was an order of magnitude greater than divergence within each species, divergence was dated to the late Pleistocene (420 kbp) based on Bayesian coalescence estimation, and a coalescent model (IMa) revealed almost no gene flow between species based on ND2. SNP data were consistent with mitochondrial results and revealed low levels of admixture among species (3 of 37 Bicknell’s Thrushes, no Gray-cheeked Thrushes, and no Veeries were >2% admixed). Species distribution models projected to the Last Glacial Maximum suggest that Bicknell’s Thrush and Gray-cheeked Thrush resided in primarily allopatric refugia in the late Pleistocene, consistent with the genetic data that support reproductive isolation over an extended period of time. Our genetic data suggest that both species underwent demographic expansions, possibly as they expanded out of Pleistocene refugia into their current ranges. We conclude that Bicknell’s Thrush and Gray-cheeked Thrush are 2 distinct species-level lineages despite low levels of Gray-cheeked Thrush introgression in Bicknell’s Thrushes, and divergence has been maintained by a long history of allopatry in subtly different habitats. Their unique phylogeography among boreal forest birds indicates that either cryptic species breaks in eastern North America are still undiscovered, or another factor, such as divergent natural selection, high migratory connectivity, or interspecific competition, played a role in their divergence.

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