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•First study on the phylogenetics of the freshwater crabs of São Tomé and Príncipe island.•Documents the transoceanic dispersal from two distinct biogeographic regions in the ...Afrotropical region.•Reveals cryptic speciation in the São Tomé freshwater crab species.
We examined the colonization history and phylogeographic structure of the two endemic freshwater crab species (Potamonautes margaritarius and P. principe) inhabiting the volcanic islands of São Tomé and Príncipe, respectively, using mitochondrial and nuclear DNA sequence data. All samples were sequenced for the mtDNA COI locus and used in the phylogeographic analyses, while a single specimen per lineage was sequenced for the two remaining loci (16S rRNA and histone 3) and used in the phylogenetic reconstruction. Phylogenetic results reveal that P. principe diverged early within a clade of East/Southern African Potamonautes during the Miocene, while P. margaritarius diverged between the Late Eocene to Early Miocene. Furthermore, the two species are not sister taxa and are distantly related. These results corroborate previously hypothesised independent transoceanic dispersal events that resulted in the establishment of the endemic freshwater crab fauna of the two islands. Within P. margaritarius, we observed two reciprocally monophyletic clades on São Tomé Island. Clade one occurred in the southeast and southwest of the island, while clade two occurred in the northeast and the northwest; the divergence between the latter two clades was estimated to be of Pleistocene age. The two clades within P. margartarius are genetically highly structured and characterised by the absence of shared maternal haplotypes, suggesting possible speciation within P. margartarius. In contrast P. principe exhibits a shallow population genetic structure. Possible mechanisms of colonization and cladogenesis in the two freshwater crabs are discussed.
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•First RADseq paper for velvet worms.•Combined sanger and RADseq data were generally congruent.•RADseq provided finer scale resolution.•Both analytical methods revealed marked cryptic ...differentiation.
In the present study, first generation DNA sequencing (mitochondrial cytochrome c oxidase subunit one, COI) and reduced-representative genomic RADseq data were used to understand the patterns and processes of diversification of the velvet worm, Peripatopsis sedgwicki species complex across its distribution range in South Africa. For the RADseq data, three datasets (two primary and one supplementary) were generated corresponding to 1,259–11,468 SNPs, in order to assess the diversity and phylogeography of the species complex. Tree topologies for the two primary datasets were inferred using maximum likelihood and Bayesian inferences methods. Phylogenetic analyses using the COI datasets retrieved four distinct, well-supported clades within the species complex. Five species delimitation methods applied to the COI data (ASAP, bPTP, bGMYC, STACEY and iBPP) all showed support for the distinction of the Fort Fordyce Nature Reserve specimens. In the main P. sedgwicki species complex, the species delimitation methods revealed a variable number of operational taxonomic units and overestimated the number of putative taxa. Divergence time estimates coupled with the geographic exclusivity of species and phylogeographic results suggest recent cladogenesis during the Plio/Pleistocene. The RADseq data were subjected to a principal components analysis and a discriminant analysis of principal components, under a maximum-likelihood framework. The latter results corroborate the four main clades observed using the COI data, however, applying additional filtering revealed additional diversity. The high overall congruence observed between the RADseq data and COI data suggest that first generation sequence data remain a cheap and effective method for evolutionary studies, although RADseq does provide a far greater resolution of contemporary temporo-spatial patterns.
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.
We investigate the phylogeographic structure of a fossorial forest‐living snake species, the forest thread snake, Leptotyphlopssylvicolus 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.
We investigated the phylogeographic structure of a fossorial forest‐living snake species, Leptotyphlops sylvicolus. Phylogenetic and population genetic analyses suggest the presence of phylogeographic breaks broadly congruent to those exhibited by other forest‐living taxa. Divergence‐time estimates suggest that cladogenesis was driven by habitat fragmentation during the late Miocene climatic shifts. The species delimitation methods retrieved 10–12 putative species nested within L. sylvicolus. Morphological analyses exhibit large overlap among putative species but indicate differences between grassland and forest species.
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► Examines the colonisation of a freshwater crab species in the Seychelles. ► Demonstrates transoceanic dispersal as the only causal mechanisms. ► Discovers the presence of three ...allospecies on the islands in the Seychelles.
The endemic, monotypic freshwater crab species
Seychellum alluaudi was used as a template to examine the initial colonisation and evolutionary history among the major islands in the Seychelles Archipelago. Five of the “inner” islands in the Seychelles Archipelago including Mahé, Praslin, Silhouette, La Digue and Frégate were sampled. Two partial mtDNA fragments, 16S rRNA and cytochrome oxidase subunit I (COI) was sequenced for 83 specimens of
S. alluaudi. Evolutionary relationships between populations were inferred from the combined mtDNA dataset using maximum parsimony, maximum likelihood and Bayesian inferences. Analyses of molecular variance (AMOVA) were used to examine genetic variation among and within clades. A haplotype network was constructed using TCS while BEAST was employed to date the colonisation and divergence of lineages on the islands. Phylogenetic analyses of the combined mtDNA data set of 1103 base pairs retrieved a monophyletic
S. alluaudi group comprised three statistically well-supported monophyletic clades. Clade one was exclusive to Silhouette; clade two included samples from Praslin sister to La Digue, while clade three comprised samples from Mahé sister to Frégate. The haplotype network corresponded to the three clades. Within Mahé, substantial phylogeographic substructure was evident. AMOVA results revealed limited genetic variation within localities with most variation occurring among localities. Divergence time estimations predated the Holocene sea level regressions and indicated a Pliocene/Pleistocene divergence between the three clades evident within
S. alluaudi. The monophyly of each clade suggests that transoceanic dispersal is rare. The absence of shared haplotypes between the three clades, coupled with marked sequence divergence values suggests the presence of three allospecies within
S. alluaudi.
A living fossil tale of Pangaean biogeography Murienne, Jerome; Daniels, Savel R.; Buckley, Thomas R. ...
Proceedings of the Royal Society. B, Biological sciences,
01/2014, Letnik:
281, Številka:
1775
Journal Article
Recenzirano
Odprti dostop
The current distributions of widespread groups of terrestrial animals and plants are supposedly the result of a mixture of either vicariance owing to continental split or more recent trans-oceanic ...dispersal. For organisms exhibiting a vicariant biogeographic pattern—achieving their current distribution by riding on the plates of former supercontinents—this view is largely inspired by the belief that Pangaea lacked geographical or ecological barriers, or that extinctions and dispersal would have erased any biogeographic signal since the early Mesozoic. We here present a time-calibrated molecular phylogeny of Onychophora (velvet worms), an ancient and exclusively terrestrial panarthropod group distributed throughout former Pangaean landmasses. Our data not only demonstrate that trans-oceanic dispersal does not need be invoked to explain contemporary distributions, but also reveal that the early diversification of the group pre-dates the break-up of Pangaea, maintaining regionalization even in landmasses that have remained contiguous throughout the history of the group. These results corroborate a growing body of evidence from palaeontology, palaeogeography and palaeoclimatic modelling depicting ancient biogeographic regionalization over the continuous landmass of Pangaea.
A new pearl white freshwater crab was collected in sympatry with Potamonautes sidneyi (Rathbun, 1904) in the Indian Ocean coastal belt forest at Mbotyi on the Wild Coast of the Eastern Cape Province, ...South Africa. Specimens of the two sympatric congeneric species were subjected to DNA sequencing of three partial mitochondrial loci (COI, 12S rRNA and 16S rRNA) together with morphological examination. Phylogenetic analyses of the new species were undertaken to determine its evolutionary relationship with the other east and southern African species of freshwater crabs. Results revealed that, Potamonautes mhlophe sp. nov. is sister to P. dentatus (Stewart & Cook, 1995) and distantly related to the sympatric P. sidneyi. The two congeneric sympatric species were characterised by the absence of shared COI haplotypes and marked sequence divergence value for the latter locus. Furthermore, Potamonautes mhlophe sp. nov. is morphologically distinct from P. sidneyi based on the structure of the first and second gonopods. Considering the congruence between the mtDNA and morphology, the new species is herein described.
In the present study, two new species of velvet worm, Opisthopatus, from the Eastern Cape province of South Africa are described. We used both mitochondrial and nuclear DNA sequence data (cytochrome ...oxidase subunit I COI and 18S rRNA subunit 18S) to explore the possibility that species boundaries in Opisthopatus have been underestimated. A previous fine‐scale phylogeographic study of the velvet worm Opisthopatus amaxhosa demonstrated the presence of two distinct clades, of which the first could be assigned to O. amaxhosa and the second represented a novel as yet undescribed species. In addition, specimens of Opisthopatus from the Valley of Desolation, Camdeboo Nature Reserve, Graaff‐Reinet, were not assigned to a new species in the most recent taxonomic revision because of the limited number of specimens. Following recent collection and scanning electron microscopy, we assigned the Graaff‐Reinet specimens to Opisthopatus camdebooi sp. nov. and the second lineage in sympatry with O. amaxhosa we described as Opisthopatus baziya sp. nov. The application of four species delimitation methods (Assemble Species by Automatic Partitioning ASAP, Poisson Tree Processes PTP, generalized mixed Yule‐coalescent model GMYC, and Species Tree and Classification Estimation, Yarely STACEY) generally revealed congruent groupings across clades, suggesting that the alpha taxonomic diversity in Opisthopatus has been underestimated. The continued discovery of new velvet worm species in poorly or unsampled areas suggests that several novel species might still be undescribed in South Africa. Collectively, our results suggest that fine‐scale sampling is critical to detect and describe the biodiversity of other saproxylic taxa.
Abstract We investigated the evolutionary patterns of two forest-dwelling endemic terrestrial snails (Gittenedouardia spadicea and Maizania wahlbergi) in the Maputaland–Pondoland–Albany biodiversity ...hotspot in South Africa to examine the degree of phylogeographical congruence between the two species. Phylogenetic relationships and divergence time estimations within each species were inferred using the combined mitochondrial DNA (mtDNA) sequence dataset for the cytochrome c oxidase subunit I (COI) and large subunit ribosomal RNA (16S rRNA). In addition, the rapidly evolving COI datasets were used to infer intraspecific genetic structure and population differentiation within both species. Phylogeographical concordance factor (PCF) analysis was used to statistically estimate the degree of congruence between the two species at localities where both species were sampled. Phylogenetically, G. spadicea exhibited two clades that diverged during the Plio/Pleistocene, while M. wahlbergi formed a single shallow clade that showed Pleistocene divergence. The haplotype networks for the COI locus demonstrated evidence of geographical and genetic isolation within both species. PCF analysis demonstrated partial phylogeographical concordance, suggesting that the two species may have been affected by similar ancient climatic events. Traits other than poor dispersal capabilities and limited gene flow may also influence how a species responds to fluctuating climate change.
Abstract
We 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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