scholarly journals Four new species, DNA barcode library and pre-Pliocene speciation of the euedaphic Afromontane Clivinini genera Trilophidius and Antireicheia (Coleoptera: Carabidae, Scaritinae)

2017 ◽  
Vol 49 (1) ◽  
pp. 1 ◽  
Author(s):  
Vasily V. Grebennikov ◽  
Petr Bulirsch ◽  
Paolo Magrini
Keyword(s):  
New Species ◽  
South African ◽  
Dna Barcode ◽  
Divergence Time ◽  
Time Estimation ◽  
Equatorial Guinea ◽  
Cytochrome Oxidase Subunit ◽  
Divergence Time Estimation ◽  
Maximum Likelihood Approach ◽  
Likelihood Approach

We describe and extensively illustrate four new species of euedaphic (= dwelling in the soil) Clivinini ground beetles: <em>Trilophidius</em> <em>acastus</em> sp. nov. and <em>T. argus</em> sp. nov. (both from Bioko, Equatorial Guinea), as well as <em>Antireicheia</em> <em>calais</em> sp. nov. and <em>A. zetes</em> sp. nov. (both from the South Pare Mountains, Tanzania). We generate and report all currently available DNA barcode (= cytochrome oxidase subunit I) data for euedaphic Afromontane Clivinini of the genera <em>Trilophidius</em> (2 species, four records) and <em>Antireicheia</em> (13 species, 43 records). We infer a phylogeny for these beetles using a Maximum Likelihood approach based upon a matrix of 53 sequenced specimens (dx.doi.org/10.5883/DS-ANTIREI) with 658 aligned positions. All nominative species represented by two or more sequences are recovered as monophyletic. Both new species of <em>Trilophidius</em> form a weakly supported clade, while all seven species of South African Antireicheia form a moderately supported clade. The genus <em>Antireicheia</em> and the geographical assemblage of its six Tanzanian species are not monophyletic. We perform divergence time estimation in Afrotropical <em>Antireicheia</em>, and our analysis indicates that these lineages diverged predominantly in the middle or late Miocene. We highlight the notable lack of phylogenetic hypothesis linked with the vaguely and variably defined taxon “subfamily Scaritinae” and its subordinated taxa.

Discovery of a new species of Anolis lizards from Brazil and its implications for the historical biogeography of montane Atlantic Forest endemics

2020 ◽  
Vol 41 (1) ◽  
pp. 87-103 ◽  
Author(s):  
Ivan Prates ◽  
Paulo Roberto Melo-Sampaio ◽  
Kevin de Queiroz ◽  
Ana Carolina Carnaval ◽  
Miguel Trefaut Rodrigues ◽  
...  
Keyword(s):  
New Species ◽  
Atlantic Forest ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Time Estimation ◽  
Molecular Data ◽  
Morphological Data ◽  
Lizard Species ◽  
Divergence Time Estimation ◽  
The City

Abstract Recent biological discoveries have changed our understanding of the distribution and evolution of neotropical biotas. In the Brazilian Atlantic Forest, the discovery of closely related species isolated on distant mountains has led to the hypothesis that the ancestors of montane species occupied and dispersed through lowland regions during colder periods. This process may explain the distribution of an undescribed Anolis lizard species that we recently discovered at a montane site in the Serra dos Órgãos National Park, a popular tourist destination close to the city of Rio de Janeiro. To investigate whether this species is closely related to other Atlantic Forest montane anoles, we implement phylogenetic analyses and divergence time estimation based on molecular data. We infer the new species nested within the Dactyloa clade of Anolis, forming a clade with A. nasofrontalis and A. pseudotigrinus, two species restricted to montane sites about 400 km northeast of Serra dos Órgãos. The new species diverged from its sister A. nasofrontalis around 5.24 mya, suggesting a cold-adapted lowland ancestor during the early Pliocene. Based on the phylogenetic results, we emend the definitions of the series taxa within Dactyloa, recognizing a clade containing the new species and several of its relatives as the nasofrontalis series. Lastly, we provide morphological data supporting the recognition of the new species and give it a formal scientific name. Future studies are necessary to assess how park visitors, pollutants, and shrinking montane habitats due to climate change will affect this previously overlooked anole species.

Biogeography and divergence time estimation of the relict Cape dragonfly genus Syncordulia: global significance and implications for conservation

Zootaxa ◽  
2009 ◽  
Vol 2216 (1) ◽  
pp. 22-36 ◽  
Author(s):  
JESSICA L. WARE ◽  
JOHN P. SIMAIKA ◽  
MICHAEL J. SAMWAYS
Keyword(s):  
South Africa ◽  
New Species ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Time Estimation ◽  
Cape Floristic Region ◽  
Conservation Action ◽  
Divergence Time Estimation ◽  
Divergence Time Estimates ◽  
Two New Species

Syncordulia (Odonata: Anisoptera: Libelluloidea) inhabits mostly cool mountainous streams in the Cape Floristic Region of South Africa. It is found at low densities in geographically restricted areas. Syncordulia is endemic to South Africa and, until recently, only two species were known, S. venator (Barnard, 1933) and S. gracilis (Burmeister 1839), both considered Vulnerable by the World Conservation Union (IUCN). Two new species, S. serendipator Dijsktra, Samways & Simaika 2007 and S. legator Dijsktra, Samways & Simaika 2007, were described from previously unrecognized museum specimens and new field collections. Here we corroborate the validity of these two new species using multiple genes and propose intergeneric relationships within Syncordulia. Molecular data from two independent gene fragments (nuclear 28S and ribosomal and cytochrome oxidase subunit I mitochondrial data) were sequenced and/or downloaded from GenBank for 7 libelluloid families, including 12 Syncordulia specimens (2 Syncordulia gracilis, 4 S. serendipator, 2 S. legator and 4 S. venator). The lower libelluloid group GSI (sensu Ware et al. 2007), a diverse group of non– corduliine taxa, is strongly supported as monophyletic. Syncordulia is well supported by both methods of phylogenetic analyses as a monophyletic group deeply nested within the GSI clade. A DIVA biogeographical analysis suggests that the ancestor to the genus Syncordulia may have arisen consequent to the break–up of Gondwana (>120 Mya). Divergence time estimates suggest that Syncordulia diverged well after the breakup of Gondwana, approximately 60 million years ago (Mya), which coincides with the divergence of several Cape fynbos taxa, between 86 – 60 Mya. DIVA analyses suggest that the present distributions of Syncordulia may be the result of dispersal events. We relate these phylogenetic data to the historical biogeography of the genus and to the importance of conservation action.

Two new species of freshwater crabs of the genus Potamonautes MacLeay, 1838 (Decapoda: Brachyura: Potamonautidae) from the forests of KwaZulu-Natal, South Africa

2019 ◽  
Vol 39 (4) ◽  
pp. 426-435 ◽  
Author(s):  
Savel R Daniels ◽  
Theo Busschau ◽  
Neil Cumberlidge
Keyword(s):  
South Africa ◽  
New Species ◽  
Divergence Time ◽  
Time Estimation ◽  
12S Rrna ◽  
Divergence Time Estimation ◽  
Freshwater Crabs ◽  
Kwazulu Natal ◽  
Two New Species ◽  
Indigenous Forest

ABSTRACTRecent taxonomic studies of forest habitats in South Africa have revealed the presence of three new species of freshwater crabs, suggesting that decapod diversity within the indigenous forest biome remain poorly documented. Surveys of the freshwater crabs of north eastern KwaZulu-Natal province produced a number of specimens from Ntendeka Wilderness Area (Ngome forest) and Nkandla and Ngoye forests that proved to belong to two new species following morphological and molecular analysis (mtDNA sequencing of three loci, 12S rRNA, 16S rRNA and COI). Two undescribed species, P. ntendekaensis sp. nov. and P. ngoyensis sp. nov. are described. The divergence time estimation of the new phylogeny for eastern and southern African freshwater crabs is discussed to illuminate biogeographic patterning and to understand factors responsible for cladogenesis.

scholarly journals Out of the Qinghai-Tibetan Plateau (QTP) and rapid radiation across Eurasia for Allium section Daghestanica (Amaryllidaceae)

AoB Plants ◽  
2021 ◽  
Author(s):  
Min-Jie Li ◽  
Huan-Xi Yu ◽  
Xian-Lin Guo ◽  
Xing-Jin He
Keyword(s):  
Evolutionary History ◽  
Divergence Time ◽  
Time Estimation ◽  
Adjacent Region ◽  
Rapid Radiation ◽  
Divergence Time Estimation ◽  
Species Diversification ◽  
The Third ◽  
Evolutionary Line ◽  
History Of

Abstract The disjunctive distribution (Europe-Caucasus-Asia) and species diversification across Eurasia for the genus Allium sect. Daghestanica has fascinating attractions for researchers aiming to understanding the development and history of the modern Eurasia flora. However, no any studies have been carried out to address the evolutionary history of this section. Based on the nrITS and cpDNA fragments (trnL-trnF and rpl32-trnL), the evolutionary history of the third evolutionary line (EL3) of the genus Allium was reconstructed and we further elucidate the evolutionary line of sect. Daghestanica under this background. Our molecular phylogeny recovered two highly supported clades in sect. Daghestanica: the Clade I includes Caucasian-European species and Asian A. maowenense, A. xinlongense and A. carolinianum collected in Qinghai; the Clade II comprises Asian yellowish tepal species, A. chrysanthum, A. chrysocephalum, A. herderianum, A. rude and A. xichuanense. The divergence time estimation and biogeography inference indicated that Asian ancestor located in the QTP and the adjacent region could have migrated to Caucasus and Europe distributions around the Late Miocene and resulted in further divergence and speciation; Asian ancestor underwent the rapid radiation in the QTP and the adjacent region most likely due to the heterogeneous ecology of the QTP resulted from the orogeneses around 4–3 Mya. Our study provides a picture to understand the origin and species diversification across Eurasia for sect. Daghestanica.

Taxonomy, phylogeny, and divergence time estimation for Apiosphaeria guaranitica, a Neotropical parasite on bignoniaceous hosts

Mycologia ◽  
2018 ◽  
Vol 110 (3) ◽  
pp. 526-545 ◽  
Author(s):  
Debora Cervieri Guterres ◽  
Samuel Galvão-Elias ◽  
Bruno Cézar Pereira de Souza ◽  
Danilo Batista Pinho ◽  
Maria do Desterro Mendes dos Santos ◽  
...  
Keyword(s):  
Divergence Time ◽  
Time Estimation ◽  
Divergence Time Estimation

scholarly journals Correction: Large-scale molecular phylogeny, morphology, divergence-time estimation, and the fossil record of advanced caenophidian snakes (Squamata: Serpentes)

PLoS ONE ◽  
2019 ◽  
Vol 14 (5) ◽  
pp. e0217959 ◽  
Author(s):  
Hussam Zaher ◽  
Robert W. Murphy ◽  
Juan Camilo Arredondo ◽  
Roberta Graboski ◽  
Paulo Roberto Machado-Filho ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
Fossil Record ◽  
Large Scale ◽  
Divergence Time ◽  
Time Estimation ◽  
Divergence Time Estimation

scholarly journals Uncertainty in divergence time estimation

2020 ◽  
Author(s):  
Tom Carruthers ◽  
Robert W Scotland
Keyword(s):  
Fossil Record ◽  
Academic Research ◽  
Divergence Time ◽  
Time Estimation ◽  
Divergence Time Estimation ◽  
Diversification Rates ◽  
Divergence Time Estimates ◽  
Use Of Time ◽  
Time Estimates ◽  
Highly Sensitive

Abstract Understanding and representing uncertainty is crucial in academic research, because it enables studies to build on the conclusions of previous studies, leading to robust advances in a particular field. Here, we evaluate the nature of uncertainty and the manner by which it is represented in divergence time estimation, a field that is fundamental to many aspects of macroevolutionary research, and where there is evidence that uncertainty has been seriously underestimated. We address this issue in the context of methods used in divergence time estimation, and with respect to the manner by which time-calibrated phylogenies are interpreted. With respect to methods, we discuss how the assumptions underlying different methods may not adequately reflect uncertainty about molecular evolution, the fossil record, or diversification rates. Therefore, divergence time estimates may not adequately reflect uncertainty, and may be directly contradicted by subsequent findings. For the interpretation of time-calibrated phylogenies, we discuss how the use of time-calibrated phylogenies for reconstructing general evolutionary timescales leads to inferences about macroevolution that are highly sensitive to methodological limitations in how uncertainty is accounted for. By contrast, we discuss how the use of time-calibrated phylogenies to test specific hypotheses leads to inferences about macroevolution that are less sensitive to methodological limitations. Given that many biologists wish to use time-calibrated phylogenies to reconstruct general evolutionary timescales, we conclude that the development of methods of divergence time estimation that adequately account for uncertainty is necessary.

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