scholarly journals Phylogeny and Biogeography of the Amazonian Pachyptera (Bignonieae, Bignoniaceae)

2020 ◽  
Vol 45 (2) ◽  
pp. 361-374
Author(s):  
Jessica Nayara Carvalho Francisco ◽  
Lúcia G. Lohmann
Keyword(s):  
Species Complex ◽  
Middle Eocene ◽  
Morphological Data ◽  
Species Limits ◽  
Test Species ◽  
Multispecies Coalescent ◽  
Biogeographic History ◽  
Coalescent Approach ◽  
History Of ◽  
Migration Pathways

Abstract—The Amazon houses a large proportion of the overall biodiversity currently found on Earth. Despite that, our knowledge of Amazonian biodiversity is still limited. In this study, we reconstruct the phylogeny of Pachyptera (Bignoniaceae), a genus of neotropical lianas that is centered in the Amazon. We then use this phylogenetic framework to re-evaluate species limits and study the biogeographic history of the genus. We sampled three molecular markers (i.e. ndhF, rpl32-trnL, and PepC) and 51 individuals representing the breadth of morphological variation and geographic distribution of all species recognized in the genus. We used this information to reconstruct phylogenetic relationships among individuals of Pachyptera using Bayesian and maximum likelihood approaches. The resulting molecular phylogeny was used as a basis to test species limits within the P. kerere species complex using a cpDNA coalescent approach (GMYC). GMYC identified five potential species within the P. kerere species complex that were subsequently evaluated in the light of morphology. Morphological data supported the recognition of four of the five potential species suggested by GMYC, all of which were also supported by a multispecies coalescent model in a Bayesian framework. The phylogeny of Pachyptera was time-calibrated and used to reconstruct the biogeographical history of the genus. We identified historically important migration pathways using our comprehensive cpDNA dataset and a Bayesian stochastic search variable selection (BSSVS) framework. Our results indicate that the genus originated in lowland Amazonia during the Middle Eocene, and subsequently occupied Central America and the Andes. Most of the diversification of Pachyptera occurred in the Miocene, a period of intense perturbations in South America.

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.

scholarly journals Genetic and morphological analyses indicate that the Australian endemic scorpion Urodacus yaschenkoi (Scorpiones: Urodacidae) is a species complex

2016 ◽  
Author(s):  
Karen Luna-Ramirez ◽  
Adam D Miller ◽  
Gordana Rašić
Keyword(s):  
Species Complex ◽  
Evolutionary History ◽  
Morphological Data ◽  
Arid Zones ◽  
Evolutionary Potential ◽  
Linear Discriminant ◽  
Putative Species ◽  
History Of ◽  
Nuclear Locus ◽  
Mitochondrial Loci

Background. Australian scorpions have received far less attention from researchers than their overseas counterparts. Here we provide the first insight into the molecular variation and evolutionary history of the endemic Australian scorpion Urodacus yaschenkoi. Also known as the inland robust scorpion, it is widely distributed throughout arid zones of the continent and is emerging as a model organism in biomedical research due to the chemical nature of its venom. Methods. We employed Bayesian Inference (BI) methods for the phylogenetic reconstructions and divergence dating among lineages, using unique haplotype sequences from two mitochondrial loci (COXI, 16S) and one nuclear locus (28S). We also implemented two DNA taxonomy approaches (GMYC and PTP/dPTP) to evaluate the presence of cryptic species. Linear Discriminant Analysis was used to test whether the linear combination of 21 variables (ratios of morphological measurements) can predict individual’s membership to a putative species. Results. Genetic and morphological data suggest that U. yaschenkoi is a species complex. High statistical support for the monophyly of several divergent lineages was found both at the mitochondrial loci and at a nuclear locus. The extent of mitochondrial divergence between these lineages exceeds estimates of interspecific divergence reported for other scorpion groups. The GMYC model and the PTP/bPTP approach identified major lineages and several sub-lineages as putative species. Ratios of several traits that approximate body shape had a strong predictive power (83–100%) in discriminating two major molecular lineages. A time-calibrated phylogeny dates the early divergence at the onset of continental-wide aridification in late Miocene and Pliocene, with finer-scale phylogeographic patterns emerging during the Pleistocene. This structuring dynamics is congruent with the diversification history of other fauna of the Australian arid zones. Discussion. Our results indicate that the taxonomic status of U. yaschenkoi requires revision, and we provide recommendations for such future efforts. A complex evolutionary history and extensive diversity highlights the importance of conserving U. yaschenkoi populations from different Australian arid zones in order to preserve patterns of endemism and evolutionary potential.

scholarly journals Hyainailourine and teratodontine cranial material from the late Eocene of Egypt and the application of parsimony and Bayesian methods to the phylogeny and biogeography of Hyaenodonta (Placentalia, Mammalia)

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2639 ◽  
Author(s):  
Matthew R. Borths ◽  
Patricia A. Holroyd ◽  
Erik R. Seiffert
Keyword(s):  
North America ◽  
Bayesian Methods ◽  
Middle Eocene ◽  
Phylogenetic Analyses ◽  
Late Eocene ◽  
Biogeographic History ◽  
Close Relationship ◽  
History Of ◽  
New Material ◽  
Latest Eocene

Hyaenodonta is a diverse, extinct group of carnivorous mammals that included weasel- to rhinoceros-sized species. The oldest-known hyaenodont fossils are from the middle Paleocene of North Africa and the antiquity of the group in Afro-Arabia led to the hypothesis that it originated there and dispersed to Asia, Europe, and North America. Here we describe two new hyaenodont species based on the oldest hyaenodont cranial specimens known from Afro-Arabia. The material was collected from the latest Eocene Locality 41 (L-41, ∼34 Ma) in the Fayum Depression, Egypt.Akhnatenavus nefertiticyonsp. nov. has specialized, hypercarnivorous molars and an elongate cranial vault. InA. nefertiticyonthe tallest, piercing cusp on M1–M2is the paracone.Brychotherium ephalmosgen. et sp. nov. has more generalized molars that retain the metacone and complex talonids. InB. ephalmosthe tallest, piercing cusp on M1–M2is the metacone. We incorporate this new material into a series of phylogenetic analyses using a character-taxon matrix that includes novel dental, cranial, and postcranial characters, and samples extensively from the global record of the group. The phylogenetic analysis includes the first application of Bayesian methods to hyaenodont relationships.B. ephalmosis consistently placed within Teratodontinae, an Afro-Arabian clade with several generalist and hypercarnivorous forms, andAkhnatenavusis consistently recovered in Hyainailourinae as part of an Afro-Arabian radiation. The phylogenetic results suggest that hypercarnivory evolved independently three times within Hyaenodonta: in Teratodontinae, in Hyainailourinae, and in Hyaenodontinae. Teratodontines are consistently placed in a close relationship with Hyainailouridae (Hyainailourinae + Apterodontinae) to the exclusion of “proviverrines,” hyaenodontines, and several North American clades, and we propose that the superfamily Hyainailouroidea be used to describe this relationship. Using the topologies recovered from each phylogenetic method, we reconstructed the biogeographic history of Hyaenodonta using parsimony optimization (PO), likelihood optimization (LO), and Bayesian Binary Markov chain Monte Carlo (MCMC) to examine support for the Afro-Arabian origin of Hyaenodonta. Across all analyses, we found that Hyaenodonta most likely originated in Europe, rather than Afro-Arabia. The clade is estimated by tip-dating analysis to have undergone a rapid radiation in the Late Cretaceous and Paleocene; a radiation currently not documented by fossil evidence. During the Paleocene, lineages are reconstructed as dispersing to Asia, Afro-Arabia, and North America. The place of origin of Hyainailouroidea is likely Afro-Arabia according to the Bayesian topologies but it is ambiguous using parsimony. All topologies support the constituent clades–Hyainailourinae, Apterodontinae, and Teratodontinae–as Afro-Arabian and tip-dating estimates that each clade is established in Afro-Arabia by the middle Eocene.

scholarly journals Genetic and morphological analyses indicate that the Australian endemic scorpionUrodacus yaschenkoi(Scorpiones: Urodacidae) is a species complex

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2759 ◽  
Author(s):  
Karen Luna-Ramirez ◽  
Adam D. Miller ◽  
Gordana Rašić
Keyword(s):  
Species Complex ◽  
Evolutionary History ◽  
Morphological Data ◽  
Arid Zones ◽  
Evolutionary Potential ◽  
Linear Discriminant ◽  
Putative Species ◽  
History Of ◽  
Nuclear Locus ◽  
Mitochondrial Loci

BackgroundAustralian scorpions have received far less attention from researchers than their overseas counterparts. Here we provide the first insight into the molecular variation and evolutionary history of the endemic Australian scorpionUrodacus yaschenkoi. Also known as the inland robust scorpion, it is widely distributed throughout arid zones of the continent and is emerging as a model organism in biomedical research due to the chemical nature of its venom.MethodsWe employed Bayesian Inference (BI) methods for the phylogenetic reconstructions and divergence dating among lineages, using unique haplotype sequences from two mitochondrial loci (COXI, 16S) and one nuclear locus (28S). We also implemented two DNA taxonomy approaches (GMYC and PTP/dPTP) to evaluate the presence of cryptic species. Linear Discriminant Analysis was used to test whether the linear combination of 21 variables (ratios of morphological measurements) can predict individual’s membership to a putative species.ResultsGenetic and morphological data suggest thatU. yaschenkoiis a species complex. High statistical support for the monophyly of several divergent lineages was found both at the mitochondrial loci and at a nuclear locus. The extent of mitochondrial divergence between these lineages exceeds estimates of interspecific divergence reported for other scorpion groups. The GMYC model and the PTP/bPTP approach identified major lineages and several sub-lineages as putative species. Ratios of several traits that approximate body shape had a strong predictive power (83–100%) in discriminating two major molecular lineages. A time-calibrated phylogeny dates the early divergence at the onset of continental-wide aridification in late Miocene and Pliocene, with finer-scale phylogeographic patterns emerging during the Pleistocene. This structuring dynamics is congruent with the diversification history of other fauna of the Australian arid zones.DiscussionOur results indicate that the taxonomic status ofU. yaschenkoirequires revision, and we provide recommendations for such future efforts. A complex evolutionary history and extensive diversity highlights the importance of conservingU. yaschenkoipopulations from different Australian arid zones in order to preserve patterns of endemism and evolutionary potential.

scholarly journals Phylogenetic analysis of a new morphological dataset elucidates the evolutionary history of Crocodylia and resolves the long-standing gharial problem

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12094
Author(s):  
Jonathan P. Rio ◽  
Philip D. Mannion
Keyword(s):  
Molecular Data ◽  
Morphological Data ◽  
Sister Taxon ◽  
Last Common Ancestor ◽  
South American ◽  
Biogeographic History ◽  
History Of ◽  
Gavialis Gangeticus ◽  
Divergence Timing ◽  
Early Paleogene

First appearing in the latest Cretaceous, Crocodylia is a clade of semi-aquatic, predatory reptiles, defined by the last common ancestor of extant alligators, caimans, crocodiles, and gharials. Despite large strides in resolving crocodylian interrelationships over the last three decades, several outstanding problems persist in crocodylian systematics. Most notably, there has been persistent discordance between morphological and molecular datasets surrounding the affinities of the extant gharials, Gavialis gangeticus and Tomistoma schlegelii. Whereas molecular data consistently support a sister taxon relationship, in which they are more closely related to crocodylids than to alligatorids, morphological data indicate that Gavialis is the sister taxon to all other extant crocodylians. Here we present a new morphological dataset for Crocodylia based on a critical reappraisal of published crocodylian character data matrices and extensive firsthand observations of a global sample of crocodylians. This comprises the most taxonomically comprehensive crocodylian dataset to date (144 OTUs scored for 330 characters) and includes a new, illustrated character list with modifications to the construction and scoring of characters, and 46 novel characters. Under a maximum parsimony framework, our analyses robustly recover Gavialis as more closely related to Tomistoma than to other extant crocodylians for the first time based on morphology alone. This result is recovered regardless of the weighting strategy and treatment of quantitative characters. However, analyses using continuous characters and extended implied weighting (with high k-values) produced the most resolved, well-supported, and stratigraphically congruent topologies overall. Resolution of the gharial problem reveals that: (1) several gavialoids lack plesiomorphic features that formerly drew them towards the stem of Crocodylia; and (2) more widespread similarities occur between species traditionally divided into tomistomines and gavialoids, with these interpreted here as homology rather than homoplasy. There remains significant temporal incongruence regarding the inferred divergence timing of the extant gharials, indicating that several putative gavialids (‘thoracosaurs’) are incorrectly placed and require future re-appraisal. New alligatoroid interrelationships include: (1) support for a North American origin of Caimaninae in the latest Cretaceous; (2) the recovery of the early Paleogene South American taxon Eocaiman as a ‘basal’ alligatoroid; and (3) the paraphyly of the Cenozoic European taxon Diplocynodon. Among crocodyloids, notable results include modifications to the taxonomic content of Mekosuchinae, including biogeographic affinities of this clade with latest Cretaceous–early Paleogene Asian crocodyloids. In light of our new results, we provide a comprehensive review of the evolutionary and biogeographic history of Crocodylia, which included multiple instances of transoceanic and continental dispersal.

Species limits in Carpha (Schoeneae, Cyperaceae) based on phenetic analyses

2006 ◽  
Vol 19 (5) ◽  
pp. 437 ◽  
Author(s):  
Xiufu Zhang ◽  
Karen L. Wilson ◽  
Jeremy J. Bruhl
Keyword(s):  
Morphological Data ◽  
Species Limits ◽  
Number Of Species ◽  
Taxonomic History ◽  
History Of

We review the taxonomic history of Carpha. Recent estimates of the number of species in Carpha have varied from 4 to 15. The generic limits of Carpha and some species limits within Carpha have been uncertain. This study tests the limits of species in Carpha sensu lato by phenetic analyses of morphological data and identifies 16 species. Three of them (Carpha cf. bracteosa C.B.Clarke, C. discolor ms and C. ulugurensis ms) are new; the taxonomic ranks of C. angustissima Cherm., C. capitellata (Nees) Boeck. var. bracteosa (C.B.Clarke) Kük., C. nivicola F.Muell. and C. schoenoides Banks et Sol. ex Hook.f. are clarified; C. perrieri Cherm. is synonymised with C. capitellata (Nees) Boeck.; the definitions of C. schlechteri C.B.Clarke and C. glomerata (Thunb.) Nees are amended.

scholarly journals Topology Testing and Demographic Modeling Illuminate a Novel Speciation Pathway in the Greater Caribbean Sea Following the Formation of the Isthmus of Panama

2021 ◽  
Author(s):  
Benjamin M. Titus ◽  
H. Lisle Gibbs ◽  
Nuno Simões ◽  
Marymegan Daly
Keyword(s):  
Gene Flow ◽  
Species Complex ◽  
Phylogenetic Analyses ◽  
Secondary Contact ◽  
Test Species ◽  
Demographic Modeling ◽  
Isthmus Of Panama ◽  
Allopatric Divergence ◽  
History Of ◽  
Topology Testing

AbstractRecent genomic analyses have highlighted the prevalence of speciation with gene flow in many taxa and have underscored the importance of accounting for these reticulate evolutionary processes when constructing species trees and generating parameter estimates. This is especially important for deepening our understanding of speciation in the sea where fast moving ocean currents, expanses of deep water, and periodic episodes of sea level rise and fall act as soft and temporary allopatric barriers that facilitate both divergence and secondary contact. Under these conditions, gene flow is not expected to cease completely while contemporary distributions are expected to differ from historical ones. Here we conduct range-wide sampling for Pederson’s cleaner shrimp (Ancylomenes pedersoni), a species complex from the Greater Caribbean that contains three clearly delimited mitochondrial lineages with both allopatric and sympatric distributions. Using mtDNA barcodes and a genomic ddRADseq approach, we combine classic phylogenetic analyses with extensive topology testing and demographic modeling (10 site frequency replicates x 45 evolutionary models x 50 model simulations/replicate = 22,500 simulations) to test species boundaries and reconstruct the evolutionary history of what was expected to be a simple case study. Instead, our results indicate a history of allopatric divergence, secondary contact, introgression, and endemic hybrid speciation driven by the final closure of the Isthmus of Panama and the strengthening of the Gulf Stream Current ~3.5 million years ago. The history of this species complex recovered by model-based methods that allow reticulation differs from that recovered by standard phylogenetic analyses and is unexpected given contemporary distributions. The geologically and biologically meaningful insights gained by our model selection analyses illuminate a novel pathway of species formation that resulted from one of the most biogeographically significant events in Earth’s history.

scholarly journals Genetic and morphological analyses indicate that the Australian endemic scorpion Urodacus yaschenkoi (Scorpiones: Urodacidae) is a species complex

2016 ◽  
Author(s):  
Karen Luna-Ramirez ◽  
Adam D Miller ◽  
Gordana Rašić
Keyword(s):  
Species Complex ◽  
Evolutionary History ◽  
Morphological Data ◽  
Arid Zones ◽  
Evolutionary Potential ◽  
Linear Discriminant ◽  
Putative Species ◽  
History Of ◽  
Nuclear Locus ◽  
Mitochondrial Loci

Background. Australian scorpions have received far less attention from researchers than their overseas counterparts. Here we provide the first insight into the molecular variation and evolutionary history of the endemic Australian scorpion Urodacus yaschenkoi. Also known as the inland robust scorpion, it is widely distributed throughout arid zones of the continent and is emerging as a model organism in biomedical research due to the chemical nature of its venom. Methods. We employed Bayesian Inference (BI) methods for the phylogenetic reconstructions and divergence dating among lineages, using unique haplotype sequences from two mitochondrial loci (COXI, 16S) and one nuclear locus (28S). We also implemented two DNA taxonomy approaches (GMYC and PTP/dPTP) to evaluate the presence of cryptic species. Linear Discriminant Analysis was used to test whether the linear combination of 21 variables (ratios of morphological measurements) can predict individual’s membership to a putative species. Results. Genetic and morphological data suggest that U. yaschenkoi is a species complex. High statistical support for the monophyly of several divergent lineages was found both at the mitochondrial loci and at a nuclear locus. The extent of mitochondrial divergence between these lineages exceeds estimates of interspecific divergence reported for other scorpion groups. The GMYC model and the PTP/bPTP approach identified major lineages and several sub-lineages as putative species. Ratios of several traits that approximate body shape had a strong predictive power (83–100%) in discriminating two major molecular lineages. A time-calibrated phylogeny dates the early divergence at the onset of continental-wide aridification in late Miocene and Pliocene, with finer-scale phylogeographic patterns emerging during the Pleistocene. This structuring dynamics is congruent with the diversification history of other fauna of the Australian arid zones. Discussion. Our results indicate that the taxonomic status of U. yaschenkoi requires revision, and we provide recommendations for such future efforts. A complex evolutionary history and extensive diversity highlights the importance of conserving U. yaschenkoi populations from different Australian arid zones in order to preserve patterns of endemism and evolutionary potential.

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