Genetic structure of the benthic amphipod Diporeia (Amphipoda: Pontoporeiidae) and its relationship to abundance in Lake Superior

2009 ◽  
Vol 66 (8) ◽  
pp. 1318-1327 ◽  
Author(s):  
Erik M. Pilgrim ◽  
Jill V. Scharold ◽  
John A. Darling ◽  
John R. Kelly
Keyword(s):  
Great Lakes ◽  
Dreissena Polymorpha ◽  
Sequence Data ◽  
Lake Superior ◽  
The Other ◽  
Dna Sequence Data ◽  
Population Structuring ◽  
History Of ◽  
Potential Population ◽  
Distinct Lineage

The freshwater amphipod Diporeia is a crucial part of the food web in the Laurentian Great Lakes, but has faced serious declines correlated with the invasion of zebra mussels ( Dreissena polymorpha ), except in Lake Superior, which has seen an increase in Diporeia abundance. Speculation on the mechanisms causing changes in Diporeia densities has not included the possibility of evolutionarily distinct lineages of Diporeia within the Great Lakes. In this study, we use cytochrome c oxidase subunit I (COI) DNA sequence data to investigate the evolutionary history of Lake Superior Diporeia relative to the other Great Lakes and consider potential population structuring within Lake Superior based upon depth or geography. Our analyses reveal that Lake Superior Diporeia represent a distinct lineage that diverged from populations of the other lakes at least several hundred thousand years ago. F statistics show that two localities within Lake Superior were significantly differentiated from all other locales, but analysis of molecular variance did not find significant structure based on depth or geography. Genetic diversity within Lake Superior was not correlated with depth, although abundance was significantly negatively correlated with increasing depth.

scholarly journals Phylogeography of two Andean frogs: Test of vicariance versus elevational gradient models of diversification

2019 ◽  
Author(s):  
Daria Koscinski ◽  
Paul Handford ◽  
Pablo L. Tubaro ◽  
Peiwen Li ◽  
Stephen C. Lougheed
Keyword(s):  
Sequence Data ◽  
Environmental Gradients ◽  
Spatial Scales ◽  
Elevational Gradient ◽  
Northwestern Argentina ◽  
Dna Sequence Data ◽  
The Andes ◽  
Common Causes ◽  
History Of ◽  
Historical Range

ABSTRACTThe tropical and subtropical Andes have among the highest levels of biodiversity in the world. Understanding the forces that underlie speciation and diversification in the Andes is a major focus of research. Here we tested two hypotheses of species origins in the Andes: 1. Vicariance mediated by orogenesis or shifting habitat distribution. 2. Parapatric diversification along elevational environmental gradients. We also sought insights on the factors that impacted the phylogeography of co-distributed taxa, and the influences of divergent species ecology on population genetic structure. We used phylogeographic and coalescent analyses of nuclear and mitochondrial DNA sequence data to compare genetic diversity and evolutionary history of two frog species: Pleurodema borellii (Family: Leiuperidae, 130 individuals; 20 sites), and Hypsiboas riojanus (Family: Hyllidae, 258 individuals; 23 sites) across their shared range in northwestern Argentina. The two showed concordant phylogeographic structuring, and our analyses support the vicariance model over the elevational gradient model. However, Pleurodema borellii exhibited markedly deeper temporal divergence (≥4 Ma) than H. riojanus (1-2 Ma). The three main mtDNA lineages of P. borellii were nearly allopatric and diverged between 4-10 Ma. At similar spatial scales, differentiation was less in the putatively more habitat-specialized H. riojanus than in the more generalist P. borellii. Similar allopatric distributions of major lineages for both species implies common causes of historical range fragmentation and vicariance. However, different divergence times among clades presumably reflect different demographic histories, permeability of different historical barriers at different times, and/or difference in life history attributes and sensitivities to historical environmental change. Our research enriches our understanding of the phylogeography of the Andes in northwestern Argentina.

scholarly journals Genome-scale DNA sequence data and the evolutionary history of placental mammals

Data in Brief ◽  
2018 ◽  
Vol 18 ◽  
pp. 1972-1975 ◽  
Author(s):  
Shaoyuan Wu ◽  
Scott Edwards ◽  
Liang Liu
Keyword(s):  
Dna Sequence ◽  
Evolutionary History ◽  
Sequence Data ◽  
Dna Sequence Data ◽  
History Of ◽  
Genome Scale

The invasive coconut mite Aceria guerreronis (Acari: Eriophyidae): origin and invasion sources inferred from mitochondrial (16S) and nuclear (ITS) sequences

2005 ◽  
Vol 95 (6) ◽  
pp. 505-516 ◽  
Author(s):  
D. Navia ◽  
G.J. de Moraes ◽  
G. Roderick ◽  
M. Navajas
Keyword(s):  
Sequence Data ◽  
Common Source ◽  
Aceria Guerreronis ◽  
Dna Sequence Data ◽  
Coconut Mite ◽  
Ocean Region ◽  
Invasion Routes ◽  
History Of ◽  
Nuclear Its ◽  
Production Areas

AbstractOver the past 30 years the coconut mite Aceria guerreronis Keifer has emerged as one of the most important pests of coconut and has recently spread to most coconut production areas worldwide. The mite has not been recorded in the Indo-Pacific region, the area of origin of coconut, suggesting that it has infested coconut only recently. To investigate the geographical origin, ancestral host associations, and colonization history of the mite, DNA sequence data from two mitochondrial and one nuclear region were obtained from samples of 29 populations from the Americas, Africa and the Indo-ocean region. Mitochondrial DNA 16S ribosomal sequences were most diverse in Brazil, which contained six of a total of seven haplotypes. A single haplotype was shared by non-American mites. Patterns of nuclear ribosomal internal transcribed spacer (ITS) variation were similar, again with the highest nucleotide diversity found in Brazil. These results suggest an American origin of the mite and lend evidence to a previous hypothesis that the original host of the mite is a non-coconut palm. In contrast to the diversity in the Americas, all samples from Africa and Asia were identical or very similar, consistent with the hypothesis that the mite invaded these regions recently from a common source. Although the invasion routes of this mite are still only partially reconstructed, the study rules out coconut as the ancestral host of A. guerreronis, thus prompting a reassessment of efforts using quarantine and biological control to check the spread of the pest.

Cryptic species, biogeographic complexity and the evolutionary history of theEctemnorhinusgroup in the sub-Antarctic, including a description ofBothrometopus huntleyi, n. sp.

2011 ◽  
Vol 23 (3) ◽  
pp. 211-224 ◽  
Author(s):  
G.C. Grobler ◽  
A.D.S. Bastos ◽  
A.M. Treasure ◽  
S.L. Chown
Keyword(s):  
Sequence Data ◽  
Morphological Data ◽  
Early Pleistocene ◽  
Dna Sequence Data ◽  
Prince Edward Islands ◽  
South Indian ◽  
Prevailing Wind Direction ◽  
Previous Hypothesis ◽  
Molecular Phylogenetic ◽  
History Of

AbstractThe biogeography of the South Indian Ocean Province (SIP) biotas has long been controversial. Much of the discussion has been based on interpretation of species distributions, based on morphological or anatomical delimitations. However, molecular phylogenetic approaches elsewhere have recently shown that interpretations based solely on morphological data may be misleading. Nonetheless, few studies have employed molecular phylogenetic approaches to understand the biogeography of the SIP biotas. We do so here for theEctemnorhinusgroup of genera, a monophyletic unit of weevils endemic to the region. We use mitochondrial cytochrome oxidase I DNA sequence data to reconstruct relationships among 13 species and 22 populations in the generaPalirhoeus,BothrometopusandEctemnorhinus. On the basis of this analysis we find little support for separating the genusPalirhoeusfromBothrometopus, and little support for the morphologically-based species groups currently recognized withinBothrometopus. Using a molecular clock we show that dispersal among islands probably took place against the prevailing wind direction. These data also support a previous hypothesis of radiation of the epilithic generaBothrometopusandPalirhoeusduring the Pliocene/early Pleistocene, but reject the hypothesis that the genusEctemnorhinusradiated following the last glacial maximum. We show thatBothrometopus parvulus(C.O. Waterhouse) on the Prince Edward Islands comprises two species that are not sister taxa. We name the second speciesBothrometopus huntleyin. sp. and provide a description thereof.

scholarly journals Complex Evolutionary History of the Aeromonas veronii Group Revealed by Host Interaction and DNA Sequence Data

PLoS ONE ◽  
2011 ◽  
Vol 6 (2) ◽  
pp. e16751 ◽  
Author(s):  
Adam C. Silver ◽  
David Williams ◽  
Joshua Faucher ◽  
Amy J. Horneman ◽  
J. Peter Gogarten ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Evolutionary History ◽  
Sequence Data ◽  
Dna Sequence Data ◽  
Aeromonas Veronii ◽  
Host Interaction ◽  
History Of ◽  
Complex Evolutionary History

From 18S ribosomal sequence data to evolution of morphology among the fungi

1995 ◽  
Vol 73 (S1) ◽  
pp. 677-683 ◽  
Author(s):  
Mary L. Berbee ◽  
John W. Taylor
Keyword(s):  
Sequence Data ◽  
Morphological Evolution ◽  
Strong Support ◽  
Morphological Characters ◽  
Geological Time ◽  
Data Set ◽  
Dna Sequence Data ◽  
Sequence Of Events ◽  
History Of ◽  
Time Of Divergence

From ribosomal DNA sequence data we can estimate ascomycete relationships, the time of divergence of major ascomycete lineages, and the history of morphological evolutionary change. Groups long accepted by mycologists such as the filamentous ascomycetes with fruiting bodies, (the plectomycetes and pyrenomycetes) are supported by 18S rDNA sequence data. After generating a phylogenetic tree showing relationships, the geological time of divergence of major fungal lineages may be estimated, inferring elapsed time using the calibrated percent substitutions between sequences. Determining the pathway of evolution of morphological characters is more difficult than inferring the relationships among these taxa. To establish the history of morphological evolution, we need accurate trees receiving strong support from our data set. We also need taxa with the intermediate characters to reveal the sequence of events in morphological evolution. Soon, however, we may be able to take a more direct approach to evolution of morphological characters, sequencing the genes that code for the character. Key words: fungus evolution, ascomycete phylogeny.

Eritreo-Arabian Affinities of the Socotran Flora as Revealed from the Molecular Phylogeny of Aerva (Amaranthaceae)

2006 ◽  
Vol 31 (3) ◽  
pp. 560-570 ◽  
Author(s):  
Mike Thiv ◽  
Mats Thulin ◽  
Norbert Kilian ◽  
H. Peter Linder
Keyword(s):  
Indian Ocean ◽  
Sequence Data ◽  
Plastid Dna ◽  
Molecular Dating ◽  
Tropical Asia ◽  
Biogeographic Patterns ◽  
Dna Sequence Data ◽  
Biogeographic History ◽  
History Of ◽  
Taxonomic Groups

We investigated the colonization of the Indian Ocean archipelago of Socotra through phylogenetic analysis of Aerva (Amaranthaceae) based on nuclear and plastid DNA sequence data. The biogeographic history of the genus was tracked using ancestral area reconstructions and molecular dating. Three independent colonization lineages from the Eritreo-Arabian subregion of the Sudano-Zambesian Region were revealed: one endemic clade comprising Aerva revoluta / A. microphylla and once within A. lanata and A. javanica. Our results provide further support for the dominance of Eritreo-Arabian affinities in the flora of Socotra, in contrast to more rare affinities to Madagascar, the Mascarenes, southern Africa, and tropical Asia. Our data point towards colonization via dispersal, rather than a vicariance origin of the island elements. The overall biogeographic patterns of Aerva show only limited concordance with other taxonomic groups distributed on Indian Ocean islands.

scholarly journals Genomic Evidences Support an Independent History of Grapevine Domestication in the Levant

2020 ◽  
Author(s):  
Aviad Sivan ◽  
Oshrit Rahimi ◽  
Mail Salmon-Divon ◽  
Ehud Weiss ◽  
Elyashiv Drori ◽  
...  
Keyword(s):  
Sequence Data ◽  
Genetic Load ◽  
Whole Genome Sequence ◽  
Local Varieties ◽  
Caucasus Region ◽  
Demographic Models ◽  
Comprehensive Survey ◽  
History Of ◽  
Distinct Lineage ◽  
Pedigree Relationship

AbstractThe ancient grapevines of the Levant have inspired beliefs and rituals in human societies which are still practiced today in religious and traditional ceremonies around the world. Despite their importance, the original Levantine wine-grapes varieties were lost due to cultural turnovers commencing in the 7th century CE, which lead to the collapse of a flourishing winemaking industry in this region. Recently, a comprehensive survey of feral grapevines was conducted in Israel in an attempt to identify local varieties, yet the origin of these domesticated accessions is unclear. Here we study the origin of Levantine grapevines using whole-genome sequence data generated for a diversity panel of wild and cultivated accessions. Comparison between Levantine and Eurasian grapevines indicated that the Levantine varieties represent a distinct lineage from the Eurasian varieties. Demographic models further supported this observation designating that domestication in the Caucasus region predated the emergence of the Levantine samples in circa 5000 years and that authentic descendants of ancient varieties are represented among the Levantine samples. We further explore the pedigree relationship among cultivated grapevines, identify footprints of selective sweeps, and estimate the extent of genetic load in each group. We conclude that the Levantine varieties are distinct from the Eurasian varieties and that resistance to disease and abiotic stress are key traits in the development of both Eurasian and Levantine varieties.

scholarly journals Molecular phylogeny uncovers an overlooked species in the macrolichen family Parmeliaceae (Ascomycota) from India

2018 ◽  
Author(s):  
Pradeep K. Divakar ◽  
Ana Crespo
Keyword(s):  
Sequence Data ◽  
Molecular Data ◽  
Fungal Species ◽  
Species Boundaries ◽  
Data Set ◽  
Dna Sequence Data ◽  
Distinct Lineage ◽  
Phylogenetic Framework ◽  
Phenotypic Features ◽  
A New Species

Several obligately sexualy reproducing lichen-forming fungal species are disjunctly distributed in pantropical regions. Here, we aim to re-examine species boundaries within the sexually reproducing, disjunctly distributed species, Hypotrachyna intercalanda. We gathered a three-locus DNA sequence data set of Hypotrachyna subgen. Parmelinopsis, especially including the samples from India, and these data were analysed in a phylogenetic framework. Our results show that specimens of H. intercalanda, as currently circumscribed, do not form a monophyletic group but fall into two well-supported independent clades. Morphological and chemical features were re-evaluated. Corroborating with the phenotypic features, the sample recovered in clade 2 occurring in southern India are described as a new species, viz. Hypotrachyna upretii Divakar and A. Crespo sp. nov. Our study adds a further example of a previously overlooked, geographically distinct, lineage that was uncovered using molecular data. Additionally, our study underlines the need of critical reexamination of phenotypic features of samples falling into different clades.

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