Limits...
Biogeographic history and cryptic diversity of saxicolous Tropiduridae lizards endemic to the semiarid Caatinga.

Werneck FP, Leite RN, Geurgas SR, Rodrigues MT - BMC Evol. Biol. (2015)

Bottom Line: The phylogenetic and population structures are intrinsically associated with stable rock surfaces and landscape rearrangements, such as the establishment of drainage basins located to the northern and southern distribution ranges.The T. semitaeniatus complex preserved high genetic diversity during range expansion, possibly as a result of frequent long-distance dispersal events.Our results indicate that both the current course of the São Francisco River and its paleo-courses had an important role in promoting diversification of the Caatinga endemic T. semitaeniatus species group.

View Article: PubMed Central - PubMed

Affiliation: Programa de Coleções Científicas Biológicas, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo 2936, 69060-000, Manaus, AM, Brazil. fewerneck@gmail.com.

ABSTRACT

Background: Phylogeographic research has advanced in South America, with increasing efforts on taxa from the dry diagonal biomes. However, the diversification of endemic fauna from the semiarid Caatinga biome in northeastern Brazil is still poorly known. Here we targeted saxicolous lizards of the Tropidurus semitaeniatus species group to better understand the evolutionary history of these endemic taxa and the Caatinga. We estimated a time-calibrated phylogeny for the species group based on two mitochondrial and two nuclear genes and jointly estimated the species limits and species tree within the group. We also devoted a denser phylogeographic sampling of the T. semitaeniatus complex to explore migration patterns, and the spatiotemporal diffusion history to verify a possible role of the São Francisco River as a promoter of differentiation in this saxicolous group of lizards.

Results: Phylogenetic analysis detected high cryptic genetic diversity, occurrence of unique microendemic lineages associated with older highlands, and a speciation history that took place during the Pliocene-Pleistocene transition. Species delimitation detected five evolutionary entities within the T. semitaeniatus species group, albeit with low support. Thus, additional data are needed for a more accurate definition of species limits and interspecific relationships within this group. Spatiotemporal analyses reconstructed the geographic origin of the T. semitaeniatus species complex to be located north of the present-day course of the São Francisco River, followed by dispersal that expanded its distribution towards the northwest and south. Gene flow estimates showed higher migration rates into the lineages located north of the São Francisco River.

Conclusions: The phylogenetic and population structures are intrinsically associated with stable rock surfaces and landscape rearrangements, such as the establishment of drainage basins located to the northern and southern distribution ranges. The T. semitaeniatus complex preserved high genetic diversity during range expansion, possibly as a result of frequent long-distance dispersal events. Our results indicate that both the current course of the São Francisco River and its paleo-courses had an important role in promoting diversification of the Caatinga endemic T. semitaeniatus species group.

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Species delimitation based on the Generalized Mixed Yule Coalescent model. Summary of species delimitation analyses using maximum likelihood and Bayesian implementations of the Generalized Mixed Yule Coalescent model for saxicolous lizards of the Tropidurus semitaeniatus species group. The phylogeny is the maximum clade credibility tree from BEAST. The five ML entities identified by the GMYC method are outlined with continuous contours and microendemic lineages (expect for Seridó) are depicted with dashed lines. Numbers are the posterior probability of species identities calculated from a posterior distribution of trees generated in BEAST. The histogram represents uncertainty in coalescent units recovered in bGMYC analysis and grayscale plot is a sequence-by-sequence matrix colored by pair-wise posterior probabilities of conspecificity, where off-diagonal patterns indicate uncertainty of species limits owing to topological variation of phylogenetic tree.
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Fig3: Species delimitation based on the Generalized Mixed Yule Coalescent model. Summary of species delimitation analyses using maximum likelihood and Bayesian implementations of the Generalized Mixed Yule Coalescent model for saxicolous lizards of the Tropidurus semitaeniatus species group. The phylogeny is the maximum clade credibility tree from BEAST. The five ML entities identified by the GMYC method are outlined with continuous contours and microendemic lineages (expect for Seridó) are depicted with dashed lines. Numbers are the posterior probability of species identities calculated from a posterior distribution of trees generated in BEAST. The histogram represents uncertainty in coalescent units recovered in bGMYC analysis and grayscale plot is a sequence-by-sequence matrix colored by pair-wise posterior probabilities of conspecificity, where off-diagonal patterns indicate uncertainty of species limits owing to topological variation of phylogenetic tree.

Mentions: The GMYC maximum likelihood analysis recovered five evolutionary entities (Figure 3) with a confidence interval of 1–17 genetic clusters and a non-significant model of species delimitation (P = 0.41). Nodal support for delimited species, defined as the sum of Akaike weights of candidate delimitation models in which the node is included, was less than 0.5 within a 95% confidence set of 47 out of 98 models compared. The mean number of evolutionary entities delimited by the bGMYC analysis was 5.91 (mode = 5), with a 95% HPD probability interval of 2–10 species clusters. Four of the five maximum likelihood entities match those coalescent units with the highest marginal probabilities, whereas microendemics from Serra das Confusões showed higher marginal probability than the genetic cluster including all microendemic lineages but Seridó. However, none of the most frequently recovered species limits was found in greater than or equal to 95% of the posterior distribution (Figure 3).Figure 3


Biogeographic history and cryptic diversity of saxicolous Tropiduridae lizards endemic to the semiarid Caatinga.

Werneck FP, Leite RN, Geurgas SR, Rodrigues MT - BMC Evol. Biol. (2015)

Species delimitation based on the Generalized Mixed Yule Coalescent model. Summary of species delimitation analyses using maximum likelihood and Bayesian implementations of the Generalized Mixed Yule Coalescent model for saxicolous lizards of the Tropidurus semitaeniatus species group. The phylogeny is the maximum clade credibility tree from BEAST. The five ML entities identified by the GMYC method are outlined with continuous contours and microendemic lineages (expect for Seridó) are depicted with dashed lines. Numbers are the posterior probability of species identities calculated from a posterior distribution of trees generated in BEAST. The histogram represents uncertainty in coalescent units recovered in bGMYC analysis and grayscale plot is a sequence-by-sequence matrix colored by pair-wise posterior probabilities of conspecificity, where off-diagonal patterns indicate uncertainty of species limits owing to topological variation of phylogenetic tree.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4494643&req=5

Fig3: Species delimitation based on the Generalized Mixed Yule Coalescent model. Summary of species delimitation analyses using maximum likelihood and Bayesian implementations of the Generalized Mixed Yule Coalescent model for saxicolous lizards of the Tropidurus semitaeniatus species group. The phylogeny is the maximum clade credibility tree from BEAST. The five ML entities identified by the GMYC method are outlined with continuous contours and microendemic lineages (expect for Seridó) are depicted with dashed lines. Numbers are the posterior probability of species identities calculated from a posterior distribution of trees generated in BEAST. The histogram represents uncertainty in coalescent units recovered in bGMYC analysis and grayscale plot is a sequence-by-sequence matrix colored by pair-wise posterior probabilities of conspecificity, where off-diagonal patterns indicate uncertainty of species limits owing to topological variation of phylogenetic tree.
Mentions: The GMYC maximum likelihood analysis recovered five evolutionary entities (Figure 3) with a confidence interval of 1–17 genetic clusters and a non-significant model of species delimitation (P = 0.41). Nodal support for delimited species, defined as the sum of Akaike weights of candidate delimitation models in which the node is included, was less than 0.5 within a 95% confidence set of 47 out of 98 models compared. The mean number of evolutionary entities delimited by the bGMYC analysis was 5.91 (mode = 5), with a 95% HPD probability interval of 2–10 species clusters. Four of the five maximum likelihood entities match those coalescent units with the highest marginal probabilities, whereas microendemics from Serra das Confusões showed higher marginal probability than the genetic cluster including all microendemic lineages but Seridó. However, none of the most frequently recovered species limits was found in greater than or equal to 95% of the posterior distribution (Figure 3).Figure 3

Bottom Line: The phylogenetic and population structures are intrinsically associated with stable rock surfaces and landscape rearrangements, such as the establishment of drainage basins located to the northern and southern distribution ranges.The T. semitaeniatus complex preserved high genetic diversity during range expansion, possibly as a result of frequent long-distance dispersal events.Our results indicate that both the current course of the São Francisco River and its paleo-courses had an important role in promoting diversification of the Caatinga endemic T. semitaeniatus species group.

View Article: PubMed Central - PubMed

Affiliation: Programa de Coleções Científicas Biológicas, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo 2936, 69060-000, Manaus, AM, Brazil. fewerneck@gmail.com.

ABSTRACT

Background: Phylogeographic research has advanced in South America, with increasing efforts on taxa from the dry diagonal biomes. However, the diversification of endemic fauna from the semiarid Caatinga biome in northeastern Brazil is still poorly known. Here we targeted saxicolous lizards of the Tropidurus semitaeniatus species group to better understand the evolutionary history of these endemic taxa and the Caatinga. We estimated a time-calibrated phylogeny for the species group based on two mitochondrial and two nuclear genes and jointly estimated the species limits and species tree within the group. We also devoted a denser phylogeographic sampling of the T. semitaeniatus complex to explore migration patterns, and the spatiotemporal diffusion history to verify a possible role of the São Francisco River as a promoter of differentiation in this saxicolous group of lizards.

Results: Phylogenetic analysis detected high cryptic genetic diversity, occurrence of unique microendemic lineages associated with older highlands, and a speciation history that took place during the Pliocene-Pleistocene transition. Species delimitation detected five evolutionary entities within the T. semitaeniatus species group, albeit with low support. Thus, additional data are needed for a more accurate definition of species limits and interspecific relationships within this group. Spatiotemporal analyses reconstructed the geographic origin of the T. semitaeniatus species complex to be located north of the present-day course of the São Francisco River, followed by dispersal that expanded its distribution towards the northwest and south. Gene flow estimates showed higher migration rates into the lineages located north of the São Francisco River.

Conclusions: The phylogenetic and population structures are intrinsically associated with stable rock surfaces and landscape rearrangements, such as the establishment of drainage basins located to the northern and southern distribution ranges. The T. semitaeniatus complex preserved high genetic diversity during range expansion, possibly as a result of frequent long-distance dispersal events. Our results indicate that both the current course of the São Francisco River and its paleo-courses had an important role in promoting diversification of the Caatinga endemic T. semitaeniatus species group.

Show MeSH