scholarly journals Population structure of Apodemus flavicollis and comparison to Apodemus sylvaticus in northern Poland based on RAD-seq

2019 ◽  
Author(s):  
Maria Luisa Martin Cerezo ◽  
Marek Kucka ◽  
Karol Zub ◽  
Yingguang Frank Chan ◽  
Jarosław Bryk
Keyword(s):  
Population Structure ◽  
Restriction Site ◽  
Population Genomics ◽  
Large Degree ◽  
Apodemus Flavicollis ◽  
Ecological Genomics ◽  
Genome Data ◽  
Northern Poland ◽  
Show Evidence ◽  
History Of

AbstractBackgroundMice of the genus Apodemus are one the most common mammals in the Palaearctic region. Despite their broad range and long history of ecological observations, there are no whole-genome data available for Apodemus, hindering our ability to further exploit the genus in evolutionary and ecological genomics context.ResultsHere we present results from the double-digest restriction site-associated DNA sequencing (ddRAD-seq) on 72 individuals of A. flavicollis and 10 A. sylvaticus from four populations, sampled across 500 km distance in northern Poland. Our data present clear genetic divergence of the two species, with average p-distance, based on 21377 common loci, of 1.51% and a mutation rate of 0.0011 - 0.0019 substitutions per site per million years. We provide a catalogue of 117 highly divergent loci that enable genetic differentiation of the two species in Poland and to a large degree of 20 unrelated samples from several European countries and Tunisia. We also show evidence of admixture between the three A. flavicollis populations but demonstrate that they have negligible average population structure, with largest pairwise FST < 0.086.ConclusionOur study demonstrates the feasibility of ddRAD-seq in Apodemus and provides the first insights into the population genomics of the species.

scholarly journals Understanding population structure in an evolutionary context: population-specific FST and pairwise FST

2020 ◽  
Author(s):  
Shuichi Kitada ◽  
Reiichiro Nakamichi ◽  
Hirohisa Kishino
Keyword(s):  
Population Structure ◽  
Evolutionary History ◽  
Population Genomics ◽  
Ancestral Population ◽  
Source Population ◽  
Moment Estimators ◽  
Current Population ◽  
Evolutionary Context ◽  
History Of ◽  
Representation Method

AbstractPopulations are shaped by their history. Therefore, it is crucial to interpret population structure in an evolutionary context. Wright’s FST measures current population structure, whereas population-specific FST measures deviation from the ancestral population. To understand current population structure and a population’s history of range expansion, we propose a novel representation method that overlays population-specific FST estimates on an unrooted neighbor-joining tree inferred from a pairwise FST distance matrix and on a map of sampling locations. We examined the usefulness of our procedure by conducting simulations that mimicked population colonization from an ancestral population and analyzing published human, Atlantic cod, and wild poplar genotype data sets. Our results demonstrated that population-specific FST values identify the source population and trace the evolutionary history of its derived populations based on genetic diversity. In contrast, pairwise FST values represent the current population structure. By integrating results of both estimators, we obtained a new picture of current population structure that incorporates evolutionary history. The generalized least squares of genome-wide population-specific FST indicated that the wild poplar population expanded its distribution to the north where it adapted to longer day lengths, to seashores where it adapted to abundant rainfall, and to the south where it adapted to dry summers. Genomic data highlight the power of the bias-corrected moment estimators of FST. All FST moment estimators described in this paper have reasonable CPU times and are useful in population genomics studies. The R codes for our representation method and simulations are available in the Supporting Information.

scholarly journals The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing

2013 ◽  
Vol 22 (11) ◽  
pp. 2864-2883 ◽  
Author(s):  
Julian Catchen ◽  
Susan Bassham ◽  
Taylor Wilson ◽  
Mark Currey ◽  
Conor O'Brien ◽  
...  
Keyword(s):  
Population Structure ◽  
Dna Sequencing ◽  
Restriction Site ◽  
Threespine Stickleback ◽  
Colonization History ◽  
History Of

scholarly journals Population structure of Apodemus flavicollis and comparison to Apodemus sylvaticus in northern Poland based on RAD-seq

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Maria Luisa Martin Cerezo ◽  
Marek Kucka ◽  
Karol Zub ◽  
Yingguang Frank Chan ◽  
Jarosław Bryk
Keyword(s):  
Population Structure ◽  
Apodemus Sylvaticus ◽  
Apodemus Flavicollis ◽  
Northern Poland

scholarly journals Understanding population structure in an evolutionary context: population-specific FST and pairwise FST

2021 ◽  
Author(s):  
Shuichi Kitada ◽  
Reiichiro Nakamichi ◽  
Hirohisa Kishino
Keyword(s):  
Population Structure ◽  
Evolutionary History ◽  
Population Genomics ◽  
Atlantic Cod ◽  
Ancestral Population ◽  
Source Population ◽  
Moment Estimators ◽  
Current Population ◽  
Evolutionary Context ◽  
History Of

Abstract Populations are shaped by their history. It is crucial to interpret population structure in an evolutionary context. Pairwise FST measures population structure, whereas population-specific FST measures deviation from the ancestral population. To understand the current population structure and a population’s history of range expansion, we propose a representation method that overlays population-specific FST estimates on a sampling location map, and on an unrooted neighbor-joining tree and a multi-dimensional scaling plot inferred from a pairwise FST distance matrix. We examined the usefulness of our procedure using simulations that mimicked population colonization from an ancestral population and by analyzing published human, Atlantic cod, and wild poplar data. Our results demonstrated that population-specific FST values identify the source population and trace the evolutionary history of its derived populations. Conversely, pairwise FST values represent the current population structure. By integrating the results of both estimators, we obtained a new picture of the population structure that incorporates evolutionary history. The generalized least squares estimate of genome-wide population-specific FST indicated that the wild poplar population expanded its distribution to the north, where daylight hours are long in summer, to coastal areas with abundant rainfall, and to the south where summers are dry. Genomic data highlight the power of the bias-corrected moment estimators of FST, whether global, pairwise, or population-specific, that provide unbiased estimates of FST. All FST moment estimators described in this paper have reasonable processing times and are useful in population genomics studies.

Identifying hidden biocomplexity and genomic diversity in Chinook salmon, an imperiled species with a history of anthropogenic influence

2020 ◽  
Vol 77 (3) ◽  
pp. 534-547
Author(s):  
Mariah H. Meek ◽  
Molly R. Stephens ◽  
Alisha Goodbla ◽  
Bernie May ◽  
Melinda R. Baerwald
Keyword(s):  
Chinook Salmon ◽  
Management Practices ◽  
Restriction Site ◽  
Central Valley ◽  
Genomic Diversity ◽  
Genomic Study ◽  
Show Evidence ◽  
History Of ◽  
Population Resilience ◽  
Imperiled Species

Biocomplexity is an important mechanism for population resilience in changing environments. However, we are just beginning to understand how to identify biocomplexity so that species management efforts promote resilience and stability. Genomic techniques are emerging as an important method for identifying biocomplexity. Central Valley (CV) Chinook salmon are an example of a species at risk of extinction if better methods for identifying and protecting biocomplexity are not employed. To address this knowledge gap, we employed restriction site associated DNA sequencing to conduct the first genomic study of all major populations of CV Chinook salmon. We found greater population structure across the Central Valley than previously documented. Additionally, we show evidence for differentiation and adaptation within migratory phenotypes despite high levels of gene flow. We also determined that genomic data can vastly improve our ability to assign individuals to their natal populations, even as they mix during migration, a finding that will assist management practices. These results demonstrate how genomic study can greatly improve our ability to identify and conserve biocomplexity.

RECENT INVESTIGATIONS AT TULA CHICO, TULA, HIDALGO

2021 ◽  
Vol 32 (1) ◽  
pp. 41-55
Author(s):  
Robert H. Cobean ◽  
Dan M. Healan ◽  
María Elena Suárez
Keyword(s):  
Classic Period ◽  
Cultural Continuity ◽  
Direct Control ◽  
Early Postclassic ◽  
Initial Settlement ◽  
Show Evidence ◽  
History Of

AbstractRecent excavations at Tula Chico, the monumental center for Tula's earliest settlement, revealed a long and complex history of occupation, beginning with its initial settlement in the Middle Classic period by Coyotlatelco peoples, when much of the region was under Teotihuacan's direct control. During the Epiclassic period, a program of monumental construction began that developed the monumental complex seen today over a period of about 200 years. Although Tula Chico was superseded by Tula Grande, the monumental center for the Early Postclassic city, it continued to be occupied and maintained until its destruction by fire. Tula Chico and Tula Grande show evidence of clear cultural continuity in ceramics, architecture, and sculpture, including “Toltec style” sculpture characteristic of Tula Grande that is present in temporally early contexts at Tula Chico.

scholarly journals Paracoccidioides brasiliensis Isolated from Nine-Banded Armadillos (Dasypus novemcinctus) Reveal Population Structure and Admixture in the Amazon Basin

2021 ◽  
Vol 7 (1) ◽  
pp. 54
Author(s):  
Eduardo Bagagli ◽  
Daniel Ricardo Matute ◽  
Hans Garcia Garces ◽  
Bernardo Guerra Tenório ◽  
Adalberto Garcia Garces ◽  
...  
Keyword(s):  
Population Structure ◽  
Latin America ◽  
Endemic Area ◽  
Amazon Basin ◽  
Paracoccidioides Brasiliensis ◽  
Pathogenic Fungi ◽  
Sensu Stricto ◽  
Species Level ◽  
Dasypus Novemcinctus ◽  
Show Evidence

Paracoccidioidomycosis is an endemic fungal disease to Latin America caused by at least five species-level genotypes of Paracoccidioides, named P. lutzii, P. brasiliensis (S1a and S1b populations), P. americana, P. restrepiensis, and P. venezuelensis. In this manuscript, we report on Paracoccidioides sp. sampling efforts in armadillos from two different areas in Brazil. We sequenced the genomes of seven Paracoccidioides isolates and used phylogenomics and populations genetics for genotyping. We found that P. brasiliensis and P. lutzii are both present in the Amazon region. Additionally, we identified two Paracoccidioides isolates that seem to be the result of admixture between divergent populations within P. brasiliensis sensu stricto. Both of these isolates were recovered from armadillos in a P. lutzii endemic area in Midwestern Brazil. Additionally, two isolates from human patients also show evidence of resulting from admixture. Our results suggest that the populations of P. brasiliensis sensu stricto exchange genes in nature. More generally, they suggest that population structure and admixture within species is an important source of variation for pathogenic fungi.

scholarly journals Were they really laughed at? That much? Gelotophobes and their history of perceived derisibility

2009 ◽  
Vol 22 (1-2) ◽  
Author(s):  
René T. Proyer ◽  
Christian F. Hempelmann ◽  
Willibald Ruch
Keyword(s):  
Empirical Study ◽  
Large Degree ◽  
Time Span ◽  
Corpus Study ◽  
The Past ◽  
History Of ◽  
University Of Zurich

AbstractThe List of Derisible Situations (LDS; Proyer, Hempelmann and Ruch, List of Derisible Situations (LDS), University of Zurich, 2008) consists of 102 different occasions for being laughed at. They were retrieved in a corpus study and compiled into the LDS. Based on this list, information on the frequency and the intensity with which people recall being laughed at during a given time-span (12 months in this study) can be collected. An empirical study (N = 114) examined the relations between the LDS and the fear of being laughed at (gelotophobia), the joy of being laughed at (gelotophilia), and the joy of laughing at others (katagelasticism; Ruch and Proyer this issue). More than 92% of the participants recalled having been laughed at at least once over the past 12 months. Highest scores were found for experiencing an embarrassing situation, chauvinism of others or being laughed at for doing something awkward or clumsy. Gelotophobia, gelotophilia, and katagelasticism were related about equally to the recalled frequency of events of being laughed at (with the lowest relation to katagelasticism). Gelotophobia, gelotophilia, and katagelasticism yielded a distinct and plausible pattern of correlations to the frequency of events of being laughed at. Gelotophobes recalled the situations of being laughed at with a higher intensity than others. Thus, the fear of being laughed at exists to a large degree independently from actual experiences of being laughed at, but is related to a higher intensity with which these events are experienced.

Key Insights and Research Prospects at the Dawn of the Population Genomics Era for Verticillium dahliae

2021 ◽  
Vol 59 (1) ◽  
Author(s):  
Jie-Yin Chen ◽  
Steven J. Klosterman ◽  
Xiao-Ping Hu ◽  
Xiao-Feng Dai ◽  
Krishna V. Subbarao
Keyword(s):  
Population Structure ◽  
Verticillium Dahliae ◽  
Plant Pathogens ◽  
Population Genomics ◽  
Population Divergence ◽  
Annual Review ◽  
Publication Date ◽  
Disease Symptoms ◽  
Historical Perspectives ◽  
Characteristic Features

The genomics era has ushered in exciting possibilities to examine the genetic bases that undergird the characteristic features of Verticillium dahliae and other plant pathogens. In this review, we provide historical perspectives on some of the salient biological characteristics of V. dahliae, including its morphology, microsclerotia formation, host range, disease symptoms, vascular niche, reproduction, and population structure. The kaleidoscopic population structure of this pathogen is summarized, including different races of the pathogen, defoliating and nondefoliating phenotypes, vegetative compatibility groupings, and clonal populations. Where possible, we place the characteristic differences in the context of comparative and functional genomics analyses that have offered insights into population divergence within V. dahliae and the related species. Current challenges are highlighted along with some suggested future population genomics studies that will contribute to advancing our understanding of the population divergence in V. dahliae. Expected final online publication date for the Annual Review of Phytopathology, Volume 59 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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