scholarly journals How the Central American Seaway and an ancient northern passage affected flatfish diversification

2018 ◽  
Author(s):  
Lisa Byrne ◽  
François Chapleau ◽  
Stéphane Aris-Brosou
Keyword(s):  
Molecular Data ◽  
Central American ◽  
Molecular Clocks ◽  
Data Set ◽  
As Species ◽  
Central American Seaway ◽  
History Of ◽  
Clock Models ◽  
Current Species ◽  
Northern Species

AbstractWhile the natural history of flatfish has been debated for decades, the mode of diversification of this biologically and economically important group has never been elucidated. To address this question, we assembled the largest molecular data set to date, covering > 300 species (out of ca. 800 extant), from 13 of the 14 known families over nine genes, and employed relaxed molecular clocks to uncover their patterns of diversification. As the fossil record of flatfish is contentious, we used sister species distributed on both sides of the American continent to calibrate clock models based on the closure of the Central American Seaway (CAS), and on their current species range. We show that flatfish diversified in two bouts, as species that are today distributed around the Equator diverged during the closure of CAS, while those with a northern range diverged after this, hereby suggesting the existence of a post-CAS closure dispersal for these northern species, most likely along a trans-Arctic northern route, a hypothesis fully compatible with paleogeographic reconstructions.

scholarly journals Systematic relationships of five newly sequenced cervid species

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2307 ◽  
Author(s):  
Nicola S. Heckeberg ◽  
Dirk Erpenbeck ◽  
Gert Wörheide ◽  
Gertrud E. Rössner
Keyword(s):  
Comparative Anatomy ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Data Set ◽  
Systematic Uncertainties ◽  
Mitochondrial Cytochrome B ◽  
In The Wild ◽  
History Of ◽  
Systematic Relationships ◽  
Partial Consensus

Cervid phylogenetics has been puzzling researchers for over 150 years. In recent decades, molecular systematics has provided new input for both the support and revision of the previous results from comparative anatomy but has led to only partial consensus. Despite all of the efforts to reach taxon-wide species sampling over the last two decades, a number of cervid species still lack molecular data because they are difficult to access in the wild. By extracting ancient DNA from museum specimens, in this study, we obtained partial mitochondrial cytochrome b gene sequences forMazama bricenii,Mazama chunyi,Muntiacus atherodes,Pudu mephistophiles, andRusa marianna, including three holotypes. These new sequences were used to enrich the existing mitochondrial DNA alignments and yielded the most taxonomically complete data set for cervids to date. Phylogenetic analyses provide new insights into the evolutionary history of these five species. However, systematic uncertainties withinMuntiacuspersist and resolving phylogenetic relationships withinPuduandMazamaremain challenging.

scholarly journals Testing the reliability of standard and complementary DNA barcodes for the monocot subfamily Alooideae from South Africa

Genome ◽  
2017 ◽  
Vol 60 (4) ◽  
pp. 337-347 ◽  
Author(s):  
Barnabas H. Daru ◽  
Michelle van der Bank ◽  
Abubakar Bello ◽  
Kowiyou Yessoufou
Keyword(s):  
Dna Barcode ◽  
Poor Performance ◽  
Species Level ◽  
Discriminatory Power ◽  
Species Boundaries ◽  
Species Discrimination ◽  
Data Set ◽  
As Species ◽  
History Of ◽  
Combined Data

Although a standard DNA barcode has been identified for plants, it does not always provide species-level specimen identifications for investigating important ecological questions. In this study, we assessed the species-level discriminatory power of standard (rbcLa + matK) and complementary barcodes (ITS1 and trnH-psbA) within the subfamily Alooideae (Asphodelaceae), a large and recent plant radiation, whose species are important in horticulture yet are threatened. Alooideae has its centre of endemism in southern Africa, with some outlier species occurring elsewhere in Africa and Madagascar. We sampled 360 specimens representing 235 species within all 11 genera of the subfamily. With three distance-based methods, all markers performed poorly for our combined data set, with the highest proportion of correct species-level specimen identifications (30%) found for ITS1. However, when performance was assessed across genera, the discriminatory power varied from 0% for all single markers and combinations in Gasteria to 63% in Haworthiopsis, again for ITS1, suggesting that DNA barcoding success may be related to the evolutionary history of the lineage considered. Although ITS1 could be a good barcode for Haworthiopsis, the generally poor performance of all markers suggests that Alooideae remains a challenge. As species boundaries within Alooideae remain controversial, we call for continued search for suitable markers or the use of genomics approaches to further explore species discrimination in the group.

An unusual disjunction in Loasaceae: Central American Chichicaste grandis is nested in Brazilian Aosa

Phytotaxa ◽  
2018 ◽  
Vol 365 (3) ◽  
pp. 273 ◽  
Author(s):  
RAFAEL ACUÑA ◽  
ISLER F. CHINCHILLA ◽  
MAXIMILIAN WEIGEND
Keyword(s):  
Costa Rica ◽  
Single Species ◽  
Molecular Data ◽  
Central American ◽  
Morphological Data ◽  
New Combination ◽  
Nuclear Marker ◽  
Data Set ◽  
Plastid Markers ◽  
Morphological Differences

The highly distinctive genus Chichicaste is restricted to the Costa Rica-Chocó Biogeographic Hotspsot from Costa Rica to northwestern Colombia and comprises a single species, C. grandis. Relationships of this taxon have been doubtful in the absence of critical morphological analyses (particularly of living plants) and convincing molecular data. The present study aims at identifying the phylogenetic relationships of C. grandis using molecular and morphological data to establish its relationships. Our molecular data set includes four plastid markers (trnL–trnF, matK, trnS–trnG and rps16) and the nuclear marker ITS for 38 in-group taxa, including all of the currently recognized genera of the Loasoideae clade, and six out-group taxa from non Loasoideae Loasaceae and Hydrangeaceae. The dataset was analyzed using Maximum Likelihood and Bayesian Inference approaches. The plastid and nuclear trees were mostly congruent, with their respective ML best and BI strict consensus trees showing no significant differences in their topologies. Chichicaste is nested in Aosa series Parviflorae and sister to A. plumieri from Hispaniola, thus representing northern and western outliers of this otherwise strictly Brazilian genus. A critical morphological re-examination indicates that considering C. grandis as part of Aosa is plausible, in spite of the ecological and morphological differences between the two taxa. Based on these results the genus Chichicaste is synonymized with Aosa and the required new combination is provided. An amended key for an expanded Aosa, is also presented.

Dissecting the major African snake radiation: a molecular phylogeny of the Lamprophiidae Fitzinger (Serpentes, Caenophidia)

Zootaxa ◽  
2008 ◽  
Vol 1945 (1) ◽  
pp. 51-66 ◽  
Author(s):  
NICOLAS VIDAL ◽  
WILLIAM R. BRANCH ◽  
OLIVIER S. G. PAUWELS ◽  
S. BLAIR HEDGES ◽  
DONALD G. BROADLEY ◽  
...  
Keyword(s):  
Mitochondrial Protein ◽  
Sister Group ◽  
Molecular Data ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Data Set ◽  
Protein Coding ◽  
Mitochondrial Rrna ◽  
Protein Coding Genes ◽  
History Of

The Elapoidea includes the Elapidae and a large (~60 genera, 280 sp.) and mostly African (including Madagascar) radiation termed Lamprophiidae by Vidal et al. (2007), that includes at least four major groups: the psammophiines, atractaspidines, lamprophiines and pseudoxyrhophiines. In this work, we reviewed the recent taxonomic history of the lamprophiids, and built a data set including two nuclear protein-coding genes (c-mos and RAG2), two mitochondrial rRNA genes (12S and 16S rRNA) and two mitochondrial protein-coding genes (cytochrome b and ND4) for 85 species belonging to 45 genera (thus representing about 75% of the generic diversity and 30% of the specific diversity of the radiation), in order to clarify the phylogenetic relationships of this large and neglected group at the subfamilial and generic levels. To this aim, 480 new sequences were produced. The vast majority of the investigated genera fall into four main monophyletic clusters, that correspond to the four subfamilies mentioned above, although the content of atractaspidines, lamprophiines and pseudoxyrhophiines is revised. We confirm the polyphyly of the genus Stenophis, and the relegation of the genus name Dromophis to the synonymy of the genus name Psammophis. Gonionotophis brussauxi is nested within Mehelya. The genus Lamprophis Fitzinger, 1843 is paraphyletic with respect to Lycodonomorphus Fitzinger, 1843. Lamprophis swazicus is the sister-group to Hormonotus modestus, and may warrant generic recognition. Molecular data do not support the traditional placement of Micrelaps within the Atractaspidinae, but its phylogenetic position, along with that of Oxyrhabdium (previously considered to belong to the Xenodermatidae), requires additional molecular data and they are both treated as Elapoidea incertae sedis. The interrelationships of Psammophiinae, Atractaspidinae, Lamprophiinae, Pseudoxyrhophiinae, Prosymna (13 sp.), Pseudaspis (1 sp.) and Pythonodipsas (1 sp.), Buhoma (2 species), and Psammodynastes (1 sp.) remain unresolved. Finally, the genus Lycognathophis, endemic to the Seychelles, does not belong to the African radiation, but to the Natricidae.

Evolutionary history of the tribe Astereae in the Flora Iranica area: Systematic implications

Phytotaxa ◽  
2018 ◽  
Vol 379 (1) ◽  
pp. 95
Author(s):  
TAYYEBEH FARHANI ◽  
SHAHROKH KAZEMPOUR-OSALOO ◽  
HASSAN ZARE-MAIVAN ◽  
VALIOLLAH MOZAFFARIAN
Keyword(s):  
Morphological Characteristics ◽  
Intergenic Spacer ◽  
Molecular Data ◽  
Late Eocene ◽  
Molecular Dating ◽  
Trnl Intron ◽  
As Species ◽  
Beast Analysis ◽  
History Of ◽  
Nuclear Its

The present study reconstructs the phylogenetic relationships of the tribe with emphasis on Psychrogeton using both nuclear (ITS, ETS) and chloroplast (trnL intron and trnL-trnF intergenic spacer) markers. Divergence times for main lineages were estimated using BEAST analysis. Based on results of molecular analyses, tribe Astereae is circumscribed here as containing 16 genera and 38 species and comprising strongly supported five major clades: Aster, Chamaegeron, Erigeron, Galatella and Psychrogeton. Among the Eurasian asteroid taxa, Aster bachtiaricus formed the basal most diverging lineage far distantly from the Aster s.str. clade. Lachnophllum and Chamaegeron are sister taxa in nuclear tree, although weakly united in plastid topology. Galatella with the inclusion of Crinitina (= Crinitaria) constitutes a well-supported clade, which along with Tripolium forms the Galatella group. Eurasian Erigeron species were derived within the Erigeron clade. Erigeron uniflorus subsp. daenensis and subsp. elborsensis are distinct from the type subspecies and are resurrected here as species in their own right. Our analyses of the datasets revealed that all examined species of Psychrogeton, except P. obovatus, emerged in a single clade comprising four distinct subclades. Molecular dating analyses indicate that tribe Astereae originated in the Late Eocene at 38.6 Ma. The most genera of Astereae diverged during the Middle Miocene whereas the diversification of lineages began mostly through the Pliocene and Pleistocene. On the basis of the molecular data as well as the morphological characteristics, Aster bachtiaricus was elevated to the generic rank and this new monospecific genus was named Iranoaster. Psychrogeton obovatus was treated as a member of the recently established genus Neobrachyactis. The conflicting position of some taxa including Lachnophyllum gossypinum, Dichrocephala, Myriactis and Asterothamnus in nuclear and plastid trees might be the result of ancient hybridization/introgression events.

scholarly journals Phylogeographic Estimates of Colonization of The Deep Atlantic by The Protobranch Bivalve Nucula Atacellana

2014 ◽  
Vol 35 (2) ◽  
pp. 261-278 ◽  
Author(s):  
Robert M. Jennings ◽  
Ron J. Etter
Keyword(s):  
North Atlantic ◽  
Evolutionary History ◽  
Central American ◽  
Central Pacific ◽  
Mitochondrial Markers ◽  
Invertebrate Species ◽  
Central American Seaway ◽  
History Of ◽  
North And South ◽  
Population Genetic Analyses

AbstractThe Pleistocene and post-Pleistocene evolutionary history of many North Atlantic intertidal invertebrate species is well known, but the evolutionary history of the deep North Atlantic fauna is poorly understood, specifically whether colonization of the deep North Atlantic paralleled the patterns observed in shallow water. Contemporary pan-Atlantic species distributions could result from several colonization pathways that connected different regions of the Atlantic at different times (e.g. Arctic, Antarctic or Panamanian pathways). To test potential colonization pathways we quantified geographic variation in nuclear and mitochondrial markers from Atlantic samples ofNucula atacellana, a pan-Atlantic deep-sea protobranch bivalve, usingN. profundorumin the eastern central Pacific as an outgroup. We combined existing 16S data from North and South Atlantic populations ofN. atacellanawith new sequences of 16S, COI, and an intron of calmodulin from those populations, and newly sampled populations near Iceland. Population genetic analyses indicated a subtropical expansion via the Central American Seaway. We found no evidence for Transarctic migration to the Atlantic inN. atacellana, which suggests that colonization pathways may differ significantly between shallow- and deep-water fauna.

FLOW REVERSAL IN THE CENTRAL AMERICAN SEAWAY DURING OR AFTER THE OLIGOCENE MIOCENE TRANSITION

2017 ◽  
Author(s):  
Andrew Jeffrey Fraass ◽  
◽  
R. Mark Leckie ◽  
Christopher M. Lowery ◽  
Robert DeConto
Keyword(s):  
Flow Reversal ◽  
Central American ◽  
Central American Seaway

A Fierce Green Fire

2016 ◽  
Author(s):  
Marybeth Lorbiecki
Keyword(s):  
Life Story ◽  
Environmental Literature ◽  
Aldo Leopold ◽  
Paradigm Shifts ◽  
Ripple Effects ◽  
Ecological Vision ◽  
As Species ◽  
Wilderness Areas ◽  
The Face ◽  
History Of

For anyone interested in wildlife, birds, wilderness areas, parks, ecology, conservation, environmental literature, and ethics, the name Aldo Leopold is sure to pop up. Since first publication, Aldo Leopold: A Fierce Green Fire has remained the classic short, inspiring biography of Leopold--the perfect companion to reading his ever popular A Sand County Almanac. Winning numerous awards, this comprehensive account of his life story is dynamic and readable, written in the context of the history of American conservation and illustrated with historic photographs. Marybeth Lorbiecki has now enriched A Fierce Green Fire in a way no other biography on Leopold has, adding numerous chapters on the ripple effects of his ideas, books, ecological vision, land ethic, and Shack, as well as of the ecological contributions of his children, graduate students, contemporary scholars, and organizations--and the wilderness lands he helped preserve. Lorbiecki weaves these stories and factual information into the biography in a compelling way that keeps both lay and academic readers engaged. In the introduction to this edition, Lorbiecki makes it clear how much better our lives are because Leopold lived and why today we so radically need what he left us to bring about paradigm shifts in our ethical, economic, and cultural thinking. Instead of losing relevance, Leopold's legacy has gained ever more necessity and traction in the face of contemporary national and world challenges, such as species loss and climate change. Even the phenological studies he started at as a hobby are proving valuable, showing the climatic shifts that have occurred at the Shack lands since the 1930s, recognized by the plants and animals.

scholarly journals Linking morphological and molecular sources to disentangle the case of Xylodon australis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Javier Fernández-López ◽  
M. Teresa Telleria ◽  
Margarita Dueñas ◽  
Mara Laguna-Castro ◽  
Klaus Schliep ◽  
...  
Keyword(s):  
New Zealand ◽  
Phylogenetic Analyses ◽  
Single Species ◽  
R Package ◽  
Molecular Data ◽  
Historical Collections ◽  
Close Relationship ◽  
Kinship Relations ◽  
History Of ◽  
Different Sources

AbstractThe use of different sources of evidence has been recommended in order to conduct species delimitation analyses to solve taxonomic issues. In this study, we use a maximum likelihood framework to combine morphological and molecular traits to study the case of Xylodon australis (Hymenochaetales, Basidiomycota) using the locate.yeti function from the phytools R package. Xylodon australis has been considered a single species distributed across Australia, New Zealand and Patagonia. Multi-locus phylogenetic analyses were conducted to unmask the actual diversity under X. australis as well as the kinship relations respect their relatives. To assess the taxonomic position of each clade, locate.yeti function was used to locate in a molecular phylogeny the X. australis type material for which no molecular data was available using morphological continuous traits. Two different species were distinguished under the X. australis name, one from Australia–New Zealand and other from Patagonia. In addition, a close relationship with Xylodon lenis, a species from the South East of Asia, was confirmed for the Patagonian clade. We discuss the implications of our results for the biogeographical history of this genus and we evaluate the potential of this method to be used with historical collections for which molecular data is not available.

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