scholarly journals Local persistence of Mann’s soft-haired mouse Abrothrix manni (Rodentia, Sigmodontinae) during Quaternary glaciations in southern Chile

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e6130 ◽  
Author(s):  
Lourdes Valdez ◽  
Guilermo D’Elía
Keyword(s):  
Demographic History ◽  
Mitochondrial Gene ◽  
Ice Sheets ◽  
Secondary Contact ◽  
Southern Chile ◽  
Geographic Scale ◽  
Climatic Oscillations ◽  
Population Decrease ◽  
History Of ◽  
Valdivian Forest

Quaternary climatic oscillations have impacted Patagonian sigmodontine fauna, leaving traceable genetic footprints. In southern Chile, changes in the landscape included transitions to different vegetation formations as well as the extension of ice sheets. In this study, we focus on the Valdivian forest endemic and recently described sigmodontine species Abrothrix manni. We aim to assess the genetic structure of this species, testing for the existence of intraspecific lineages, and inferring the recent demographic history of the species. Analyses were based on the first 801 bp of the mitochondrial gene Cytocrhome-b from 49 individuals of A. manni collected at 10 localities that covers most part of its geographic distribution. Genealogical analyses recovered two main intraspecific lineages that are geographically segregated and present an intermediate site of secondary contact. Historical demography shows signal of recent population decrease. Based on these results, we proposed that current genetic diversity of A. manni differentiated in at least two distinct refugial areas in southern Chile. This scenario, in addition to be unique among those uncovered for the so far studied Valdivian forest rodents, is noteworthy because of the reduced geographic scale inhabited by the species.

Connection, isolation and reconnection: Quaternary climatic oscillations and the Andes shaped the phylogeographical patterns of the Patagonian bee Centris cineraria (Apidae)

2020 ◽  
Vol 131 (2) ◽  
pp. 396-416 ◽  
Author(s):  
María Sosa-Pivatto ◽  
Gonzalo A Camps ◽  
Matías C Baranzelli ◽  
Anahí Espíndola ◽  
Alicia N Sérsic ◽  
...  
Keyword(s):  
Demographic History ◽  
Joint Effect ◽  
Secondary Contact ◽  
Glacial Refugium ◽  
Distribution Models ◽  
Climatic Oscillations ◽  
The Andes ◽  
History Of ◽  
Spatio Temporal ◽  
Approximate Bayesian

Abstract The joint effect of the Andes as a geographical barrier and the Quaternary glaciations as promoters of genetic divergence remains virtually unexplored in southern South America. To help fill this knowledge gap, in this study we investigated the demographic history of Centris cineraria, a solitary bee mainly distributed in Patagonia. We used mitochondrial and nuclear markers and performed phylogeographical and dating analyses, adjusted spatio-temporal diffusion and species distribution models, and used Approximate Bayesian Computation to identify likely historical demographic scenarios. Our results revealed that during glacial periods the Andes represented a barrier due to the extent of the ice-sheets and the occurrence of unsuitable habitats, while interglacials allowed for gene flow across the Andes. Secondary contact between previously isolated lineages was evident across at least two low-altitude Andean areas, the northern one being a putative glacial refugium. Our findings also suggest that C. cineraria has persisted in situ in four periglacial refugia located along a north–south transect, congruent with the maximum extent of the ice sheet during the Greatest Patagonian Glaciation. As the first phylogeographical study of Patagonian insects, our work reveals that the interaction between Quaternary climatic oscillations and the Andes as a barrier was the main driver of the spatial and demographic history of C. cineraria.

scholarly journals Blockwise Site Frequency Spectra for Inferring Complex Population Histories and Recombination

2016 ◽  
Author(s):  
Champak R. Beeravolu ◽  
Michael J. Hickerson ◽  
Laurent A.F. Frantz ◽  
Konrad Lohse
Keyword(s):  
Demographic History ◽  
Composite Likelihood ◽  
Model Organisms ◽  
Secondary Contact ◽  
Parameter Estimates ◽  
Genome Sequences ◽  
Frequency Spectra ◽  
Genome Wide ◽  
Complex Population ◽  
History Of

AbstractWe introduce ABLE (Approximate Blockwise Likelihood Estimation), a novel composite likelihood framework based on a recently introduced summary of sequence variation: the blockwise site frequency spectrum (bSFS). This simulation-based framework uses the the frequencies of bSFS configurations to jointly model demographic history and recombination and is explicitly designed to make inference using multiple whole genomes or genome-wide multi-locus data (e.g. RADSeq) catering to the needs of researchers studying model or non-model organisms respectively. The flexible nature of our method further allows for arbitrarily complex population histories using unphased and unpolarized whole genome sequences. In silico experiments demonstrate accurate parameter estimates across a range of divergence models with increasing complexity, and as a proof of principle, we infer the demographic history of the two species of orangutan from multiple genome sequences (over 160 Mbp in length) from each species. Our results indicate that the two orangutan species split approximately 650-950 thousand years ago but experienced a pulse of secondary contact much more recently, most likely during a period of low sea-level South East Asia (∼300,000 years ago). Unlike previous analyses we can reject a history of continuous gene flow and co-estimate genome-wide recombination. ABLE is available for download at https://github.com/champost/ABLE.

scholarly journals Reconstructing the demographic history of divergence between European river and brook lampreys using approximate Bayesian computations

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1910 ◽  
Author(s):  
Quentin Rougemont ◽  
Camille Roux ◽  
Samuel Neuenschwander ◽  
Jerome Goudet ◽  
Sophie Launey ◽  
...  
Keyword(s):  
Gene Flow ◽  
Life Histories ◽  
Evolutionary Biology ◽  
Demographic History ◽  
Secondary Contact ◽  
Isolation With Migration ◽  
Genome Wide Data ◽  
History Of ◽  
Parameterized Model ◽  
Approximate Bayesian

Inferring the history of isolation and gene flow during species divergence is a central question in evolutionary biology. The European river lamprey (Lampetra fluviatilis) and brook lamprey(L. planeri)show a low reproductive isolation but have highly distinct life histories, the former being parasitic-anadromous and the latter non-parasitic and freshwater resident. Here we used microsatellite data from six replicated population pairs to reconstruct their history of divergence using an approximate Bayesian computation framework combined with a random forest model. In most population pairs, scenarios of divergence with recent isolation were outcompeted by scenarios proposing ongoing gene flow, namely the Secondary Contact (SC) and Isolation with Migration (IM) models. The estimation of demographic parameters under the SC model indicated a time of secondary contact close to the time of speciation, explaining why SC and IM models could not be discriminated. In case of an ancient secondary contact, the historical signal of divergence is lost and neutral markers converge to the same equilibrium as under the less parameterized model allowing ongoing gene flow. Our results imply that models of secondary contacts should be systematically compared to models of divergence with gene flow; given the difficulty to discriminate among these models, we suggest that genome-wide data are needed to adequately reconstruct divergence history.

Numts help to reconstruct the demographic history of the ocellated lizard (Lacerta lepida) in a secondary contact zone

2012 ◽  
Vol 21 (4) ◽  
pp. 1005-1018 ◽  
Author(s):  
ANDREIA MIRALDO ◽  
GODFREY M. HEWITT ◽  
PAUL H. DEAR ◽  
OCTAVIO S. PAULO ◽  
BRENT C. EMERSON
Keyword(s):  
Contact Zone ◽  
Demographic History ◽  
Secondary Contact ◽  
History Of ◽  
Secondary Contact Zone

First insights into the phylogeography and demographic history of the common hermit crab Pagurus bernhardus (Linnaeus, 1758) (Decapoda: Anomura: Paguridae) across the Eastern Atlantic and North Sea

2020 ◽  
Vol 40 (4) ◽  
pp. 435-449
Author(s):  
Sven Rossel ◽  
Temim Deli ◽  
Michael J Raupach
Keyword(s):  
Hermit Crab ◽  
Demographic History ◽  
Mitochondrial Gene ◽  
Demographic Trend ◽  
Significant Genetic Structure ◽  
History Of ◽  
Benthic Crustacean ◽  
The Common ◽  
Pagurus Bernhardus ◽  
First Time

Abstract The common hermit crab Pagurus bernhardus (Linnaeus, 1758) is an abundant and ecologically important benthic crustacean in the northeastern Atlantic Ocean. While this species has been intensively studied in terms of its ecology, physiology, behavior, and larval development, knowledge about its population structure and demographic history is still lacking. We examined, for the first time, the genetic variability of P. bernhardus by analyzing two mitochondrial gene fragments (CO1 and 16S) from more than 150 specimens collected from various locations from the Iberian Peninsula to Norway. Our results provide evidence for a significant genetic structure according to the sampled regions for both genetic markers. Furthermore, a comprehensive demographic history reconstruction, mainly based on neutrality tests and a Bayesian Skyline Plot (CO1), revealed a recent demographic expansion of P. bernhardus that preceded the Last Glacial Maximum. Such pattern of retrieved demographic trend could have been likely a successive process to historical contraction of the species into potential climate refugia within the surveyed geographic spectrum.

Systematic revision of the South American genus Praocis Eschscholtz, 1829 (Coleoptera: Tenebrionidae). Part 1: Introduction and subgenus Praocis s. str.

Zootaxa ◽  
2012 ◽  
Vol 3336 (1) ◽  
pp. 1 ◽  
Author(s):  
GUSTAVO E. FLORES ◽  
JAIME PIZARRO-ARAYA
Keyword(s):  
South American ◽  
Scanning Electron Micrographs ◽  
Southern Chile ◽  
Systematic Revision ◽  
Distribution Maps ◽  
Representative Species ◽  
Taxonomic Research ◽  
History Of ◽  
Valdivian Forest ◽  
Coleoptera Tenebrionidae

The first part of a revision of the species comprising the genus Praocis Eschscholtz, 1829 (Pimeliinae: Praociini) is present-ed. The history of taxonomic research on Praocis is reviewed. The subgeneric classification is outlined. The subgenusPraocis s. str., distributed in Central and Southern Chile, is revised. Species occur from 26º South to 42º South in the bio-geographic provinces of Atacama, Coquimbo, Santiago, Maule and Valdivian Forest. Included is a redescription of the sub-genus Praocis s. str., redescription of its species, an identification key, habitus photographs of the most representative species,illustrations of external morphology and genital features, scanning electron micrographs of pronotum, head and antenna, as well as distribution maps. Praocis s. str. comprises 18 species, two of which are new: Praocis (Praocis) bicentenario sp.nov. and P. (P.) medvedevi sp. nov. Other species include: Praocis (Praocis) aenea Gay & Solier 1840, P. (P.) costata Gay& Solier 1840, P. (P.) curta Solier 1840, P. (P.) elliptica Philippi & Philippi 1864, P. (P.) hirtella Kulzer 1958, P. (P.) mar-ginata Germain 1855, P. (P.) parva Gay & Solier 1840, P. (P.) quadrisulcata Germain 1855, P. (P.) rufipes Eschscholtz1829 (type species), P. (P.) sanquinolenta Gay & Solier 1840, P. (P.) spinolai Gay & Solier 1840, P. (P.) subaenea Erichson1834, P. (P.) subsulcata Gay & Solier 1840, P. (P.) sulcata Eschscholtz 1829 and P. (P.) tibialis Gay & Solier 1840. Thestatus of P. (P.) bicostata Philippi & Philippi 1864, currently considered a valid name, is discussed. A lectotype is desig-nated for Praocis (P.) laevicosta Curtis 1845 (synonym of P. (P.) subaenea). The subgenus Praocis (Parapraocis) Kulzer 1958 is excluded from Praocis.

Allopatric divergence and secondary contact with gene flow: a recurring theme in rattlesnake speciation

2019 ◽  
Vol 128 (1) ◽  
pp. 149-169 ◽  
Author(s):  
Drew R Schield ◽  
Blair W Perry ◽  
Richard H Adams ◽  
Daren C Card ◽  
Tereza Jezkova ◽  
...  
Keyword(s):  
Gene Flow ◽  
Demographic History ◽  
Secondary Contact ◽  
Tree Model ◽  
Crotalus Viridis ◽  
Species Complexes ◽  
Isolating Mechanisms ◽  
Allopatric Divergence ◽  
History Of ◽  
Study Population

Abstract The study of recently diverged lineages whose geographical ranges come into contact can provide insight into the early stages of speciation and the potential roles of reproductive isolation in generating and maintaining species. Such insight can also be important for understanding the strategies and challenges for delimiting species within recently diverged species complexes. Here, we use mitochondrial and nuclear genetic data to study population structure, gene flow and demographic history across a geographically widespread rattlesnake clade, the western rattlesnake species complex (Crotalus cerberus, Crotalus viridis, Crotalus oreganus and relatives), which contains multiple lineages with ranges that overlap geographically or contact one another. We find evidence that the evolutionary history of this group does not conform to a bifurcating tree model and that pervasive gene flow has broadly influenced patterns of present-day genetic diversity. Our results suggest that lineage diversity has been shaped largely by drift and divergent selection in isolation, followed by secondary contact, in which reproductive isolating mechanisms appear weak and insufficient to prevent introgression, even between anciently diverged lineages. The complexity of divergence and secondary contact with gene flow among lineages also provides new context for why delimiting species within this complex has been difficult and contentious historically.

scholarly journals Reconstructing the demographic history of Atlantic Salmon (Salmo salar) across its distribution range using Approximate Bayesian Computations

2017 ◽  
Author(s):  
Quentin Rougemont ◽  
Louis Bernatchez
Keyword(s):  
North America ◽  
Atlantic Salmon ◽  
Northern Hemisphere ◽  
Demographic History ◽  
Secondary Contact ◽  
Population Divergence ◽  
Isolated Populations ◽  
Quaternary Period ◽  
History Of ◽  
Approximate Bayesian

AbstractUnderstanding the dual roles of demographic and selective processes in the buildup of population divergence is one of the most challenging tasks in evolutionary biology. In the Northern hemisphere in particular, species genetic makeup has been largely influenced by severe climatic oscillations of the Quaternary Period. Here, we investigated the demographic history of Atlantic Salmon across the entire species range using 2035 anadromous individuals from 77 sampling sites from North America and Eurasia genotyped at 4,656 SNPs. By combining results from admixture graphs, geogenetic maps and an approximate Bayesian computation framework, we validate previous hypotheses pertaining to secondary contact between European and Northern American populations, but also demonstrate that European populations from different glacial refugia have been exchanging alleles in contemporary times. We further identify the major sources of admixture from the southern range of North America to more northern populations along with a strong signal of secondary gene flow between genetic regional groups. We hypothesize that these patterns reflects the spatial redistribution of ancestral variation across the entire American range. Results also point to a role for linked selection in the form of background selection and or positive hitchhiking. Altogether, differential introgression and linked selective effects likely played an underappreciated role in shaping the genomic landscape of species in the Northern hemisphere Therefore we conclude that such heterogeneity among loci should be systematically integrated into demographic inferences of the divergence process, even between incompletely reproductively isolated populations.

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