Comparative host–parasite population genetic structures: obligate fly ectoparasites on Galapagos seabirds

Parasitology ◽  
2013 ◽  
Vol 140 (9) ◽  
pp. 1061-1069 ◽  
Author(s):  
IRIS I. LEVIN ◽  
PATRICIA G. PARKER
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Population Genetic ◽  
Sequence Data ◽  
Population Genetic Study ◽  
Haemosporidian Parasite ◽  
Dna Sequence Data ◽  
Sula Granti ◽  
Breeding Attempt ◽  
Genetic Structures

SUMMARYParasites often have shorter generation times and, in some cases, faster mutation rates than their hosts, which can lead to greater population differentiation in the parasite relative to the host. Here we present a population genetic study of two ectoparasitic flies, Olfersia spinifera and Olfersia aenescens compared with their respective bird hosts, great frigatebirds (Fregata minor) and Nazca boobies (Sula granti). Olfersia spinifera is the vector of a haemosporidian parasite, Haemoproteus iwa, which infects frigatebirds throughout their range. Interestingly, there is no genetic differentiation in the haemosporidian parasite across this range despite strong genetic differentiation between Galapagos frigatebirds and their non-Galapagos conspecifics. It is possible that the broad distribution of this one H. iwa lineage could be facilitated by movement of infected O. spinifera. Therefore, we predicted more gene flow in both fly species compared with the bird hosts. Mitochondrial DNA sequence data from three genes per species indicated that despite marked differences in the genetic structure of the bird hosts, gene flow was very high in both fly species. A likely explanation involves non-breeding movements of hosts, including movement of juveniles, and movement by adult birds whose breeding attempt has failed, although we cannot rule out the possibility that closely related host species may be involved.

scholarly journals Patterns of spatial genetic structures in Aedes albopictus (Diptera: Culicidae) populations in China

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Yong Wei ◽  
Jiatian Wang ◽  
Zhangyao Song ◽  
Yulan He ◽  
Zihao Zheng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Population Genetic ◽  
Spatial Genetic Structure ◽  
Vector Borne Diseases ◽  
Vector Borne ◽  
Genetic Structures

Abstract Background The Asian tiger mosquito, Aedes albopictus, is one of the 100 worst invasive species in the world and the vector for several arboviruses including dengue, Zika and chikungunya viruses. Understanding the population spatial genetic structure, migration, and gene flow of vector species is critical to effectively preventing and controlling vector-borne diseases. Little is known about the population structure and genetic differentiation of native Ae. albopictus in China. The aim of this study was to examine the patterns of the spatial genetic structures of native Ae. albopictus populations, and their relationship to dengue incidence, on a large geographical scale. Methods During 2016–2018, adult female Ae. albopictus mosquitoes were collected by human landing catch (HLC) or human-bait sweep-net collections in 34 localities across China. Thirteen microsatellite markers were used to examine the patterns of genetic diversity, population structure, and gene flow among native Ae. albopictus populations. The correlation between population genetic indices and dengue incidence was also examined. Results A total of 153 distinct alleles were identified at the 13 microsatellite loci in the tested populations. All loci were polymorphic, with the number of distinct alleles ranging from eight to sixteen. Genetic parameters such as PIC, heterozygosity, allelic richness and fixation index (FST) revealed highly polymorphic markers, high genetic diversity, and low population genetic differentiation. In addition, Bayesian analysis of population structure showed two distinct genetic groups in southern-western and eastern-central-northern China. The Mantel test indicated a positive correlation between genetic distance and geographical distance (R2 = 0.245, P = 0.01). STRUCTURE analysis, PCoA and GLS interpolation analysis indicated that Ae. albopictus populations in China were regionally clustered. Gene flow and relatedness estimates were generally high between populations. We observed no correlation between population genetic indices of microsatellite loci in Ae. albopictus populations and dengue incidence. Conclusion Strong gene flow probably assisted by human activities inhibited population differentiation and promoted genetic diversity among populations of Ae. albopictus. This may represent a potential risk of rapid spread of mosquito-borne diseases. The spatial genetic structure, coupled with the association between genetic indices and dengue incidence, may have important implications for understanding the epidemiology, prevention, and control of vector-borne diseases.

Contrasting the population genetic structure of two velvet worm taxa (Onychophora : Peripatopsidae : Peripatopsis) in forest fragments along the south-eastern Cape, South Africa

2017 ◽  
Vol 31 (6) ◽  
pp. 781 ◽  
Author(s):  
Savel R. Daniels ◽  
Megan Dreyer ◽  
Prashant P. Sharma
Keyword(s):  
South Africa ◽  
Population Genetic ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Forest Fragments ◽  
Eastern Cape ◽  
Dna Sequence Data ◽  
Mtdna Coi ◽  
Haplotype Networks ◽  
Velvet Worm

During the present study, we examined the phylogeography and systematics of two species of velvet worm (Peripatopsis Pocock, 1894) in the forested region of the southern Cape of South Africa. A total of 89 P. moseleyi (Wood-Mason, 1879) and 65 P. sedgwicki (Purcell, 1899) specimens were collected and sequenced for the cytochrome c oxidase subunit I mtDNA (COI). In addition, a single P. sedgwicki specimen per sample locality was sequenced for the 18S rRNA locus. Furthermore, morphological variation among P. sedgwicki sample localities were explored using traditional alpha taxonomic characters. DNA sequence data were subjected to phylogenetic analyses using Bayesian inference and population genetic analyses using haplotype networks and analyses of molecular variance (AMOVAs). Phylogenetic results revealed the presence of four and three clades within P. moseleyi and P. sedgwicki respectively. Haplotype networks were characterised by the absence of shared haplotypes between clades, suggesting genetic isolation, a result corroborated by the AMOVA and highly significant FST values. Specimens from Fort Fordyce Nature Reserve were both genetically and morphologically distinct from the two remaining P. sedgwicki clades. The latter result suggests the presence of a novel lineage nested within P. sedgwicki and suggests that species boundaries within this taxon require re-examination.

scholarly journals Geography is more important than life history in the recent diversification of the tiger salamander complex

2021 ◽  
Vol 118 (17) ◽  
pp. e2014719118
Author(s):  
Kathryn M. Everson ◽  
Levi N. Gray ◽  
Angela G. Jones ◽  
Nicolette M. Lawrence ◽  
Mary E. Foley ◽  
...  
Keyword(s):  
Life History ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Population Genetic ◽  
Tiger Salamander ◽  
Life History Variation ◽  
Mexican Axolotl ◽  
Population Genetic Differentiation ◽  
Wide Range ◽  
Lineage Divergence

The North American tiger salamander species complex, including its best-known species, the Mexican axolotl, has long been a source of biological fascination. The complex exhibits a wide range of variation in developmental life history strategies, including populations and individuals that undergo metamorphosis; those able to forego metamorphosis and retain a larval, aquatic lifestyle (i.e., paedomorphosis); and those that do both. The evolution of a paedomorphic life history state is thought to lead to increased population genetic differentiation and ultimately reproductive isolation and speciation, but the degree to which it has shaped population- and species-level divergence is poorly understood. Using a large multilocus dataset from hundreds of samples across North America, we identified genetic clusters across the geographic range of the tiger salamander complex. These clusters often contain a mixture of paedomorphic and metamorphic taxa, indicating that geographic isolation has played a larger role in lineage divergence than paedomorphosis in this system. This conclusion is bolstered by geography-informed analyses indicating no effect of life history strategy on population genetic differentiation and by model-based population genetic analyses demonstrating gene flow between adjacent metamorphic and paedomorphic populations. This fine-scale genetic perspective on life history variation establishes a framework for understanding how plasticity, local adaptation, and gene flow contribute to lineage divergence. Many members of the tiger salamander complex are endangered, and the Mexican axolotl is an important model system in regenerative and biomedical research. Our results chart a course for more informed use of these taxa in experimental, ecological, and conservation research.

scholarly journals Disentangling selection on genetically correlated polygenic traits using whole-genome genealogies

2020 ◽  
Author(s):  
Aaron J. Stern ◽  
Leo Speidel ◽  
Noah A. Zaitlen ◽  
Rasmus Nielsen
Keyword(s):  
Dna Sequence ◽  
Population Genetic ◽  
Sequence Data ◽  
Directional Selection ◽  
Likelihood Method ◽  
Correlated Response ◽  
Correlated Traits ◽  
Dna Sequence Data ◽  
Polygenic Traits ◽  
Polygenic Trait

AbstractWe present a full-likelihood method to estimate and quantify polygenic adaptation from contemporary DNA sequence data. The method combines population genetic DNA sequence data and GWAS summary statistics from up to thousands of nucleotide sites in a joint likelihood function to estimate the strength of transient directional selection acting on a polygenic trait. Through population genetic simulations of polygenic trait architectures and GWAS, we show that the method substantially improves power over current methods. We examine the robustness of the method under uncorrected GWAS stratification, uncertainty and ascertainment bias in the GWAS estimates of SNP effects, uncertainty in the identification of causal SNPs, allelic heterogeneity, negative selection, and low GWAS sample size. The method can quantify selection acting on correlated traits, fully controlling for pleiotropy even among traits with strong genetic correlation (|rg| = 80%; c.f. schizophrenia and bipolar disorder) while retaining high power to attribute selection to the causal trait. We apply the method to study 56 human polygenic traits for signs of recent adaptation. We find signals of directional selection on pigmentation (tanning, sunburn, hair, P=5.5e-15, 1.1e-11, 2.2e-6, respectively), life history traits (age at first birth, EduYears, P=2.5e-4, 2.6e-4, respectively), glycated hemoglobin (HbA1c, P=1.2e-3), bone mineral density (P=1.1e-3), and neuroticism (P=5.5e-3). We also conduct joint testing of 137 pairs of genetically correlated traits. We find evidence of widespread correlated response acting on these traits (2.6-fold enrichment over the null expectation, P=1.5e-7). We find that for several traits previously reported as adaptive, such as educational attainment and hair color, a significant proportion of the signal of selection on these traits can be attributed to correlated response, vs direct selection (P=2.9e-6, 1.7e-4, respectively). Lastly, our joint test uncovers antagonistic selection that has acted to increase type 2 diabetes (T2D) risk and decrease HbA1c (P=1.5e-5).

scholarly journals Limited geographic genetic structure detected in a widespread Palearctic corvid, Nucifraga caryocatactes

2014 ◽  
Author(s):  
Kimberly M Dohms ◽  
Theresa M Burg
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Sequence Data ◽  
Base Pairs ◽  
Mitochondrial Dna Control Region ◽  
Potential Barriers ◽  
Seed Crops ◽  
Wide Population

The Eurasian or spotted nutcracker (Nucifraga caryocatactes) is a widespread resident corvid found throughout the Palearctic from Central Europe to Japan. Characterized by periodic bouts of irruptive dispersal in search of Pinus seed crops, this species has potential for high levels of gene flow across its range. Previous analysis of 11 individuals did not find significant range-wide population genetic structure. We investigated population structure using 924 base pairs of mitochondrial DNA control region sequence data from 62 individuals from 12 populations distributed throughout the nutcracker’s range. We complemented this analysis by incorporating additional genetic data from previously published sequences. High levels of genetic diversity and limited population genetic structure were detected suggesting that potential barriers to dispersal do not restrict gene flow in nutcrackers.

scholarly journals Gene flow and selection evidence of sandalwood (Santalum album) under various population structures in Gunung Sewu (Java, Indonesia), and its effects on genetic differentiation

2017 ◽  
Vol 18 (4) ◽  
pp. 1493-1505
Author(s):  
YENI W.N. RATNANINGRUM ◽  
SAPTO INDRIOKO ◽  
ENY FARIDAH ◽  
ATUS SYAHBUDIN
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Population Diversity ◽  
Santalum Album ◽  
Isoenzyme Analysis ◽  
Genetic Base ◽  
Selection Processes ◽  
Population Structures ◽  
Genetic Structures ◽  
Genetic Drifts

Ratnaningrum YWN, Indrioko S, Faridah E, Syahbudin A. 2017. Gene flow and selection evidence of sandalwood (Santalum album) under various population structures in Gunung Sewu (Java, Indonesia), and its effects on genetic differentiation. Biodiversitas 18: 1493-1505. Field observations on population structures and isoenzyme analysis were conducted to determine gene flow and selection evidence of sandalwood under various population structures in Gunung Sewu, and its effects on genetic differentiation. Sandalwood (Santalum album Linn., Santalaceae) is origin to the south-eastern islands but recently emerged as new landraces in Java Island, Indonesia. Results suggested that (i) natural barriers contributed to habitat fragmentation and disrupted gene flow among populations; (ii) gene flow affected selection processes regarding bottleneck effects and genetic drifts, which determined allelic richness and population diversity; and (iii) variation on gene flow and selection processes affected genetic differentiation among populations. Gene flow restriction and genetic drift occurred when population had lower genetic base, highly clonalized, fragmented, and/or more inbreeding in mating. Genetic differentiation was highest between populations within Timor island, and between Gunung Sewu (Java Island) and Sumba-Timor islands. Populations were not clustered based on geographical sites, but more by the similarity of genetic structures. Genetic differentiations were the combined effect of the differences on genetical processes regarding gene flow and selection events. Both differences existed due to differences on (i) population structures including landscape, clonality and parental genetic composition, and (ii) the disturbance histories of population, which affected the equilibrium between gene flow and drift. These findings emphasized the importance of larger gene flow and genetic base to naturally maintain genetical processes of sandalwood population under various landscapes structures.

Phylogenomic Data Reveal Widespread Introgression Across the Range of an Alpine and Arctic Specialist

2020 ◽  
Author(s):  
Erik R Funk ◽  
Garth M Spellman ◽  
Kevin Winker ◽  
Jack J Withrow ◽  
Kristen C Ruegg ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genome Sequence ◽  
Population Genetic ◽  
Approximate Bayesian Computation ◽  
Sequence Data ◽  
Species Group ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Data ◽  
Approximate Bayesian

Abstract Understanding how gene flow affects population divergence and speciation remains challenging. Differentiating one evolutionary process from another can be difficult because multiple processes can produce similar patterns, and more than one process can occur simultaneously. Although simple population models produce predictable results, how these processes balance in taxa with patchy distributions and complicated natural histories is less certain. These types of populations might be highly connected through migration (gene flow), but can experience stronger effects of genetic drift and inbreeding, or localized selection. Although different signals can be difficult to separate, the application of high-throughput sequence data can provide the resolution necessary to distinguish many of these processes. We present whole-genome sequence data for an avian species group with an alpine and arctic tundra distribution to examine the role that different population genetic processes have played in their evolutionary history. Rosy-finches inhabit high elevation mountaintop sky islands and high-latitude island and continental tundra. They exhibit extensive plumage variation coupled with low levels of genetic variation. Additionally, the number of species within the complex is debated, making them excellent for studying the forces involved in the process of diversification, as well as an important species group in which to investigate species boundaries. Total genomic variation suggests a broadly continuous pattern of allele frequency changes across the mainland taxa of this group in North America. However, phylogenomic analyses recover multiple distinct, well supported, groups that coincide with previously described morphological variation and current species-level taxonomy. Tests of introgression using D-statistics and approximate Bayesian computation reveal significant levels of introgression between multiple North American taxa. These results provide insight into the balance between divergent and homogenizing population genetic processes and highlight remaining challenges in interpreting conflict between different types of analytical approaches with whole-genome sequence data. [ABBA-BABA; approximate Bayesian computation; gene flow; phylogenomics; speciation; whole-genome sequencing.]

POPULATION GENETIC ANALYSIS OF MOUNTAIN PLOVER USING MITOCHONDRIAL DNA SEQUENCE DATA

The Condor ◽  
10.1650/7594 ◽  
2005 ◽  
Vol 107 (2) ◽  
pp. 353 ◽  
Author(s):  
Sara J. Oyler-McCance ◽  
Judy St. John ◽  
Fritz L. Knopf ◽  
Tom W. Quinn
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Analysis ◽  
Dna Sequence ◽  
Population Genetic ◽  
Sequence Data ◽  
Population Genetic Analysis ◽  
Dna Sequence Data ◽  
Mitochondrial Dna Sequence

scholarly journals Ocean Currents Drove Genetic Structure of Seven Dominant Mangrove Species Along the Coastlines of Southern China

2021 ◽  
Vol 12 ◽  
Author(s):  
Qifang Geng ◽  
Zhongsheng Wang ◽  
Jianmin Tao ◽  
Megumi K. Kimura ◽  
Hong Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
South China ◽  
Population Genetic ◽  
Ocean Currents ◽  
Mangrove Species ◽  
Contemporary Gene Flow ◽  
Low Levels ◽  
Oceanic Currents

Mangrove forest ecosystems, which provide important ecological services for marine environments and human activities, are being destroyed worldwide at an alarming rate. The objective of our study was to use molecular data and analytical techniques to separate the effects of historical and contemporary processes on the distribution of mangroves and patterns of population genetic differentiation. Seven mangrove species (Acanthus ilicifolius, Aegiceras corniculatum, Avicennia marina, Bruguiera gymnorrhiza, Kandelia obovata, Lumnitzera racemosa, and Rhizophora stylosa), which are predominant along the coastlines of South China, were genotyped at nuclear (nSSR) and chloroplast (cpSSR) microsatellite markers. We estimated historical and contemporary gene flow, the genetic diversity and population structure of seven mangrove species in China. All of these seven species exhibited few haplotypes, low levels of genetic diversity (HE = 0.160–0.361, with the exception of K. obovata) and high levels of inbreeding (FIS = 0.104–0.637), which may be due to their marginal geographical distribution, human-driven and natural stressors on habitat loss and fragmentation. The distribution patterns of haplotypes and population genetic structures of seven mangrove species in China suggest historical connectivity between populations over a large geographic area. In contrast, significant genetic differentiation [FST = 0.165–0.629 (nSSR); GST = 0.173–0.923 (cpSSR)] indicates that populations of mangroves are isolated from one another with low levels of contemporary gene flow among populations. Our results suggest that populations of mangroves were historically more widely inter-connected and have recently been isolated, likely through a combination of ocean currents and human activities. In addition, genetic admixture in Beibu Gulf populations and populations surrounding Hainan Island and southern mainland China were attributed to asymmetric gene flow along prevailing oceanic currents in China in historical times. Even ocean currents promote genetic exchanges among mangrove populations, which are still unable to offset the effects of natural and anthropogenic fragmentation. The recent isolation and lack of gene flow among populations of mangroves may affect their long-term survival along the coastlines of South China. Our study enhances the understanding of oceanic currents contributing to population connectivity, and the effects of anthropogenic and natural habitat fragmentation on mangroves, thereby informing future conservation efforts and seascape genetics toward mangroves.

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