scholarly journals Phylogeography and population differentiation in Hepatozoon canis (Apicomplexa: Hepatozoidae) reveal expansion and gene flow in world populations

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Antonio Acini Vásquez-Aguilar ◽  
Arturo Barbachano-Guerrero ◽  
Diego F. Angulo ◽  
Víctor Hugo Jarquín-Díaz
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Population Expansion ◽  
Fixation Index ◽  
Hepatozoon Canis ◽  
Pairwise Comparisons ◽  
Distribution Analysis ◽  
Population Genetic Analysis ◽  
Molecular Variance ◽  
The World

Abstract Background Hepatozoon canis is a protozoan transmitted to dogs and other wild carnivores by the ingestion of ticks containing mature oocysts and is considered the principal cause of canine hepatozoonosis in the world. Here, we examined ribosomal RNA 18S gene sequence variation to determine the genetic differences and phylogeographic diversity of H. canis from various geographical areas around the world. Methods We used 550 publicly available sequences of H. canis from 46 countries to assess haplotype relationships, geographical structure, genetic diversity indices, and relationships among populations. We performed neutrality tests and pairwise comparisons of fixation index (FST) values between groups and pairwise comparisons of FST values between populations. To determine whether populations are structured, analyses of molecular variance (AMOVAs) and spatial analysis of molecular variance (SAMOVA) were performed. Results The dataset of H. canis yielded 76 haplotypes. Differentiation among populations indicated that there is no phylogeographical structure (GST = 0.302 ± 0.0475). Moreover, when samples were grouped by continents a significant FST was obtained, meaning that populations were genetically differentiated. The AMOVA showed that 57.4% of the genetic variation was explained by differences within populations when all locations were treated as a single group and revealed that there is no population structure when populations are grouped into two, three, and four groups (FCT, p > 0.05), suggesting that dispersal between populations is high. SAMOVA revealed significant FCT values for groups K = 5. The Tajima’s D and Fu’s Fs show that populations have undergone recent expansion, and the mismatch distribution analysis showed population expansion (multimodal distribution). Conclusions The current molecular data confirmed that H. canis does not show phylogeographic or population structure. The haplotypes exhibit low genetic differentiation, suggesting a recent expansion due to gene flow among populations. These results provide pivotal information required for future detailed population genetic analysis or to establish control strategies of this parasite. Graphical abstract

scholarly journals Population genetics of Aedes albopictus (Diptera: Culicidae) in its native range in Lao People’s Democratic Republic

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Maysa Tiemi Motoki ◽  
Dina Madera Fonseca ◽  
Elliott Frederic Miot ◽  
Bruna Demari-Silva ◽  
Phoutmany Thammavong ◽  
...  
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Aedes Albopictus ◽  
Isolation By Distance ◽  
Genetic Locus ◽  
Lao Pdr ◽  
Phylogenetic Network ◽  
Population Expansion ◽  
Recent Population Expansion ◽  
The Usa

Abstract Background The Asian tiger mosquito, Aedes (Stegomyia) albopictus (Skuse) is an important worldwide invasive species and can be a locally important vector of chikungunya, dengue and, potentially, Zika. This species is native to Southeast Asia where populations thrive in both temperate and tropical climates. A better understanding of the population structure of Ae. albopictus in Lao PDR is very important in order to support the implementation of strategies for diseases prevention and vector control. In the present study, we investigated the genetic variability of Ae. albopictus across a north-south transect in Lao PDR. Methods We used variability in a 1337-bp fragment of the mitochondrial cytochrome c oxidase subunit 1 gene (cox1), to assess the population structure of Ae. albopictus in Lao PDR. For context, we also examined variability at the same genetic locus in samples of Ae. albopictus from Thailand, China, Taiwan, Japan, Singapore, Italy and the USA. Results We observed very high levels of genetic polymorphism with 46 novel haplotypes in Ae. albopictus from 9 localities in Lao PDR and Thailand populations. Significant differences were observed between the Luangnamtha population and other locations in Lao PDR. However, we found no evidence of isolation by distance. There was overall little genetic structure indicating ongoing and frequent gene flow among populations or a recent population expansion. Indeed, the neutrality test supported population expansion in Laotian Ae. albopictus and mismatch distribution analyses showed a lack of low frequency alleles, a pattern often seen in bottlenecked populations. When samples from Lao PDR were analyzed together with samples from Thailand, China, Taiwan, Japan, Singapore, Italy and the USA, phylogenetic network and Bayesian cluster analysis showed that most populations from tropical/subtropical regions are more genetically related to each other, than populations from temperate regions. Similarly, most populations from temperate regions are more genetically related to each other, than those from tropical/subtropical regions. Conclusions Aedes albopictus in Lao PDR are genetically related to populations from tropical/subtropical regions (i.e. Thailand, Singapore, and California and Texas in the USA). The extensive gene flow among locations in Lao PDR indicates that local control is undermined by repeated introductions from untreated sites.

scholarly journals Identification of Main Oyster Species and Comparison of Their Genetic Diversity in Zhejiang Coast, South of Yangtze River Estuary

2021 ◽  
Vol 8 ◽  
Author(s):  
Sheng Liu ◽  
Qinggang Xue ◽  
Hongqiang Xu ◽  
Zhihua Lin
Keyword(s):  
Genetic Diversity ◽  
River Estuary ◽  
Population Expansion ◽  
Fixation Index ◽  
Yangtze River Estuary ◽  
Indigenous Species ◽  
Molecular Variance ◽  
Introduction History ◽  
Oyster Species ◽  
C Subunit

Oysters are an important aquaculture species distributed worldwide, including in Zhejiang Province, located on the east coast of China. Because of the high diversity and complicated introduction history of oysters and their seedlings, there has been much disagreement regarding the origin of each species, and the dominant and indigenous species remain unclear. We sampled 16 batches of oysters from seven sites in three aquaculture bays and found two main oyster species, Crassostrea sikamea and Crassostrea angulata. The former occupied the higher intertidal zone and comprised more than 70% of the cultured oysters. Based on the cytochrome oxidase C subunit I (COI) and mitochondrial noncoding region (MNR), C. sikamea showed higher genetic diversity than C. angulata. The analysis of molecular variance among COI sequences of these species from the Xiangshan Bay populations were comparable to those of other populations and showed that most of the molecular variance was within groups, which was consistent with the low pairwise fixation index FST values. The neutrality test revealed that C. sikamea experienced population expansion events, whereas for C. angulata, the significant Fu’s Fs and non-significant Tajima’s D test results may indicate a possible population expansion event, implying that C. sikamea is likely an indigenous species. The method established based on internal transcribed spacer 1 digestion by the HindIII restriction enzyme is useful for identifying C. sikamea and C. angulata in the local region. The specific primers on the MNR sequence show potential for distinguishing C. sikamea from four other important Crassostrea oysters. These results highlight the abundance of C. sikamea on the Zhejiang coast and lay the foundation for protecting and utilizing the local oyster germplasm resources and for the sustainable development of the oyster industry.

scholarly journals cpDNA-Gene-Sequence-Based Genetic Diversity, Population Structure, and Gene Flow Analysis of Ethiopian Lowland Bamboo (Bambusinea: Oxytenanthera abyssinica (A. Rich.) Munro)

2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Oumer Abdie Oumer ◽  
Kassahun Tesfaye ◽  
Tileye Feyissa ◽  
Dagnew Yibeyen ◽  
Jayaraman Durai ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Gc Content ◽  
Wood Products ◽  
Population Structure Analysis ◽  
The World ◽  
Oxytenanthera Abyssinica ◽  
Metekel Zone

Background. As a member of Poaceae and subfamily Bambusoideae, Ethiopian lowland bamboo (Oxytenanthera abyssinica) is one of the most important nontimber forest resources or a potential alternative to wood and wood products. Ethiopia contributes 86% of the total area of bamboo on the continent, Africa, and 7% of the world. O. abyssinica in Ethiopia accounts for 85% of the total national coverage of bamboo. Several studies have been performed on the genetic diversity and population structure analysis of various bamboo species throughout the world but almost nothing in Ethiopia and O. abyssinica. Methods. Young fresh leaves of O. abyssinica from thirteen natural lowland bamboo growing areas across the country were collected. DNA was isolated using a modified CTAB DNA isolation method. Three cpDNA gene sequences (matK, ndhF3, and rps16) were used for the study. PCR products were analyzed, purified, and pair-end sequenced to calculate AC/GC content, average number of nucleotide differences (k), nucleotide diversity (π) and population mutation rates per 100 sites ( θ w ), InDel (Insertion-Deletion), DNA divergence, gene flow, and genetic differentiation. Results. Metekel Zone was found to have extremely higher k, π, and θ w . Higher frequency of genetic differentiation was found between Metekel Zone vs. the distant populations. Higher frequency of gene flow was found between Assosa Zone vs. Oromia populations. Kurmuk haplotype from gaps or missing data considered and Bambasi haplotype from not considered has descendants around them. Conclusion. Using sequences of cpDNA genes, populations of O. abyssinica collected in Ethiopia show clear diversity based on their geographic location. Metekel Zone was found to have the most diverse population, Assosa Zone has been found to be the source of evolution of O. abyssinica, and Gambella population shows a difference from other O. abyssinica populations.

scholarly journals Limited gene flow and partial isolation phylogeography of Himalayan snowcock Tetraogallus himalayensis based on part mitochondrial D-loop sequences

2011 ◽  
Vol 57 (6) ◽  
pp. 758-767 ◽  
Author(s):  
Xiaoli Wang ◽  
Jiangyong Qu ◽  
Naifa Liu ◽  
Xinkang Bao ◽  
Sen Song
Keyword(s):  
Mitochondrial Dna ◽  
Gene Flow ◽  
Control Region ◽  
Divergence Time ◽  
Population Expansion ◽  
Middle Pleistocene ◽  
Distribution Analysis ◽  
D Loop ◽  
Limited Gene Flow ◽  
Partial Isolation

Abstract Himalayan snowcock Tetraogallus himalayensis are distributed in alpine and subalpine areas in China. We used mitochondrial DNA control-region data to investigate the origin and past demographic change in sixty-seven Himalayan snowcock T. himalayensis. The fragments of 1155 nucleotides from the control region of mitochondrial DNA were sequenced, and 57 polymorphic positions defined 37 haplotypes. A high level of genetic diversity was detected in all populations sampled and may be associated isolation of the mountains and habitat fragmentation and deterioration from Quaternary glaciations. In the phylogenetic tree, all haplotypes grouped into four groups: clade A (Kunlun Mountains clade), clade B (Northern Qinghai-Tibetan Plateau clade), clade C (Tianshan Mountains clade) and clade D (Kalakunlun Mountains clade). We found a low level of gene flow and significant genetic differentiation among all populations. Based on divergence time we suggest that the divergence of Himalayan snowcock occurred in the middle Pleistocene inter-glaciation, and expansion occurred in the glaciation. Analysis of mtDNA D-loop sequences confirmed demographic population expansion, as did our non-significant mismatch distribution analysis. In conclusion, limited gene flow and a pattern of partial isolation phylogeographic was found in geographic populations of T. himalayansis based on the analysis on mtDNA D-loop sequences.

scholarly journals Population Genetic Analysis of Mountain Plover Using Mitochondrial DNA Sequence Data

The Condor ◽  
2005 ◽  
Vol 107 (2) ◽  
pp. 353-362 ◽  
Author(s):  
Sara J. Oyler-McCance ◽  
Judy St. John ◽  
Fritz L. Knopf ◽  
Tom W. Quinn
Keyword(s):  
Gene Flow ◽  
Control Region ◽  
Sequence Data ◽  
Population Expansion ◽  
Gene Pools ◽  
Population Genetic Analysis ◽  
Breeding Populations ◽  
Breeding Grounds ◽  
Charadrius Montanus ◽  
Atpase 6

Abstract Mountain Plover (Charadrius montanus) distribution and abundance have been reduced drastically in the past 30 years and the conversion of shortgrass prairie to agriculture has caused breeding populations to become geographically isolated. This, coupled with the fact that Mountain Plovers are thought to show fidelity to breeding grounds, leads to the prediction that the isolated breeding populations would be genetically distinct. This pattern, if observed, would have important management implications for a species at risk of extinction. Our study examined genetic variation at two mitochondrial regions for 20–30 individuals from each of four breeding sites. We found no evidence of significant population differentiation in the data from the control region or the ATPase 6/8 region. Nested-clade analysis revealed no relationship between haplotype phylogeny, and geography among the 47 control region haplotypes. In the ATPase 6/8 region, however, one of the two clades provided information suggesting that, historically, there has been continuous range expansion. Analysis of mismatch distributions and Tajima's D suggest that the Mountain Plover underwent a population expansion, following the Pleistocene glacial period. To explain the lack of detectable genetic differentiation among populations, despite their geographic isolation and fidelity to breeding locations, we speculate that there is sufficient female-mediated gene flow to homogenize gene pools among populations. Such gene flow might ensue if pair bonds are formed in mixed flocks on wintering grounds rather than on the summer breeding grounds. Análisis Genéticos de Poblaciones de Charadrius montanus Usando Secuencias de ADN Mitocondrial Resumen. La distribución y la abundancia de Charadrius montanus se han reducido drásticamente desde hace 30 años y las poblaciones han quedado más aisladas geográficamente debido a la transformación de las praderas de pastos cortos a tierras agrícolas. Estos cambios, combinados con el hecho de que se cree que C. montanus presenta fidelidad a sus áreas de nidificación, sugieren que las poblaciones reproductivas aisladas podrían ser distintas genéticamente. De observarse este patrón, tendría consecuencias importantes para el manejo de esta especie en peligro de extinción. En nuestro estudio, investigamos el patrón de variación genética en dos regiones mitocondriales en 20–30 individuos de C. montanus provenientes de cuatro sitios de nidificación. No encontramos evidencia de diferencias poblacionales significativas en los datos de la región de control, ni en la región de ATPasa 6/ 8. Un análisis de clados anidados reveló que no hay ninguna relación entre haplotipos filogenia y geografía entre los 47 haplotipos de la región de control. Sin embargo, en la región ATPasa 6/8, uno de los dos clados proveyó información que sugiere que la especie ha aumentado históricamente su rango de distribución. Análisis de distribuciones “mismatch” y de la D de Tajima sugieren que la población se expandió después del período glacial del Pleistoceno. Para explicar la falta de diferenciación genética entre las poblaciones, a pesar de su aislamiento geográfico y de la fidelidad a sus sitios de nidificación, especulamos que el flujo de genes es controlado por las hembras de la población de tal modo que los acervos génicos son bastante homogéneos entre las poblaciones. Dicho flujo de genes podría ocurrir si se formaran las parejas en las bandadas mixtas en el invierno, no en el verano cuando están en sus áreas de nidificación.

scholarly journals Population Structure of Rhizoctonia oryzae-sativae in California Rice Fields

2010 ◽  
Vol 100 (5) ◽  
pp. 502-510 ◽  
Author(s):  
Patcharavipa Chaijuckam ◽  
Jong-Min Baek ◽  
Christopher A. Greer ◽  
Robert K. Webster ◽  
R. Michael Davis
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Genotypic Diversity ◽  
Fixation Index ◽  
Population Subdivision ◽  
Microsatellite Primers ◽  
Rhizoctonia Oryzae ◽  
Sexual Recombination ◽  
Hierarchical Levels ◽  
High Level

Six pairs of single-locus microsatellite primers were developed to study the population structure of Rhizoctonia oryzae-sativae, the cause of aggregate sheath spot disease of rice, among and within three rice-growing areas in California over a 3-year period. A high level of gene flow among growing areas was indicated by low population subdivision according to analysis of molecular variance and moderate to no population differentiation between pairs of populations based on the fixation index (FST). Gametic equilibrium of most pairs of microsatellite loci, high numbers of unique multilocus genotypes, and high genotypic diversity indicated extensive sexual recombination within growing areas. Because there was little differentiation among populations in all hierarchical levels, including among growing areas within sampling years, fields within growing areas, and corners within individual fields, a high level of gene flow was revealed in all levels. Basidiospores were likely the main vehicle of gene flow among populations, including short and long distances. Asexual inocula (sclerotia and mycelia) probably overwinter because a few clones were detected over a 2-year period within the same field. A few clones were shared among fields but were not commonly shared among growing areas.

scholarly journals Morphogenetic and population structure of two species marine bivalve (Ostreidae: Saccostrea cucullata and Crassostrea iredalei) in Aceh, Indonesia

2018 ◽  
Vol 19 (3) ◽  
pp. 978-988 ◽  
Author(s):  
MUTIA RAMADHANIATY ◽  
ISDRAJAD SETYOBUDIANDI ◽  
HAWIS H. MADDUPPA
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Genetic Distance ◽  
Haplotype Diversity ◽  
Fixation Index ◽  
Morphological Identification ◽  
Marine Bivalve ◽  
Geographical Distance ◽  
Environmental Complexity ◽  
Saccostrea Cucullata

Ramadhaniaty M, Setyobudiandi I, Madduppa HH. 2018. Morphogenetic and population structure of two species marine bivalve (Ostreidae: Saccostrea cucullata and Crassostrea iredalei) in Aceh, Indonesia. Biodiversitas 19: 978-988. Oysters (Family Ostreidae) are mollusks, with high levels of phenotypic plasticity and wide geographic distribution. Oysters are a challenging group for morphological identification and genetic populations study. Saccostrea cucullata and Crassostrea iredalei are oysters from bivalve class that lives in the intertidal area and mangrove ecosystem. To clarify the morphology, genetic diversity and population structure of the two forms of S. cucullata and C. iredalei, we collected and studied oysters from three locations along the coastal region of Aceh by using morphometric method and 16 S mtDNA sequences analysis. We also added more oysters sequences from China, Japan, and Thailand to determine the connectivity between all populations. Morphometric characteristics of the oyster showed a negative allometric growth pattern, which means the rate of length gain is faster than that of the weight gain. The genetic distance from S. cucullata was 0.0030.004 (Fst = 0.708) and C. iredalei was 0.000 (Fst = 0.971). The long genetic distance and high fixation index (Fst) in the oysters population are caused by the close geographical distance of the species in the three populations. The haplotype diversity value from S. cucullata and C. iredalei were 20 and 3, respectively. The haplotype showed the connectivity among the oyster populations which indicated by the gene flow pattern. The gene flow was affected by geographical distance and environmental complexity.

scholarly journals Comparative Genetic Analysis of Invasive Fall Armyworm Populations Provides Evidence for Population Expansion in India

2020 ◽  
Author(s):  
Nishtha Nayyar ◽  
Gracy Ramasamy ◽  
Ashika Thotambyl ◽  
Mohan Govindasamy ◽  
Mohan Muthugounder ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Fall Armyworm ◽  
Western Hemisphere ◽  
Coi Gene ◽  
Polymorphism Analysis ◽  
Distribution Analysis ◽  
Maize Production ◽  
The World

Abstract Fall Armyworm (FAW), Spodoptera frugiperda, is a polyphagous pest capable of feeding over 80 plant species and was indigenous to Western Hemisphere until recently. Within a span of four years, FAW has established itself throughout most of the regions in Africa and Asia incurring significant losses in maize production. Owing to its revamped distribution range, it would be prudent to analyse the ensuing genetic changes and study the emerging phylogeographic patterns across the world. In this regard, we would like to provide a current snapshot of genetic diversity of FAW in India after two years of the initial introduction and compare it with the worldwide diversity in order to trace the origins and evolutionary trajectories of FAW in India.We have investigated around 145 FAW samples from different regions in India for strain identity and polymorphism analysis on the basis of partial mitochondrial cytochrome oxidase I (COI) gene sequences. Apart from the ancestral rice and corn strain haplotype, our study demonstrates the presence of 19 more haplotypes unique to India at a haplotype diversity of 0.498. We were also able to record the occurrence of inter-strain hybrid haplotypes of rice and corn strain in India. Regional heterogeneity within Indian populations seems to be quite low representative of extensive migration of FAW within India. Distribution analysis of pairwise differences and rejection of neutrality tests suggest that the FAW population in India is undergoing expansion. However, the scenario is much different for rest of the invaded regions like Africa and other Asian countries where FAW still appear to evolve neutrally. Our data is consistent with the findings suggesting a recent and common origin for invasive FAW populations in Asia and Africa, with significant population structure observed in Indian populations.This study reports the highest genetic diversity for Indian FAW populations till date and identifies India as the emerging hotspot for expansion of COIA rice haplotypes across the world. The findings will be useful to track the subsequent evolution of FAW and would have important ramifications for FAW behaviour and composition throughout the world.

Differentiation and Interrelations of Two Representatives of Laudakia stellio Complex (Reptilia: Agamidae) in Israel

2011 ◽  
Vol 4 (2) ◽  
pp. 102-114 ◽  
Author(s):  
Evgenyi N. Panov ◽  
Larissa Yu. Zykova
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Habitat Preference ◽  
Additional Data ◽  
Near East ◽  
Field Studies ◽  
Subspecies Level ◽  
Limited Gene Flow ◽  
Study Sites ◽  
And Behavior

Field studies were conducted in Central Negev within the breeding range of Laudakia stellio brachydactyla and in NE Israel (Qyriat Shemona) in the range of an unnamed form (tentatively “Near-East Rock Agama”), during March – May 1996. Additional data have been collected in Jerusalem at a distance of ca. 110 km from the first and about 170 km from the second study sites. A total of 63 individuals were caught and examined. The animals were marked and their subsequent movements were followed. Social and signal behavior of both forms were described and compared. Lizards from Negev and Qyriat Shemona differ from each other sharply in external morphology, habitat preference, population structure, and behavior. The differences obviously exceed the subspecies level. At the same time, the lizards from Jerusalem tend to be intermediate morphologically between those from both above-named localities, which permits admitting the existence of a limited gene flow between lizard populations of Negev and northern Israel. The lizards from NE Israel apparently do not belong to the nominate subspecies of L. stellio and should be regarded as one more subspecies within the species.

Population Genetics ofCaenorhabditis elegans: The Paradox of Low Polymorphism in a Widespread Species

Genetics ◽  
2003 ◽  
Vol 163 (1) ◽  
pp. 147-157 ◽  
Author(s):  
Arjun Sivasundar ◽  
Jody Hey
Keyword(s):  
Genetic Variation ◽  
Microsatellite Loci ◽  
Population Expansion ◽  
Widespread Species ◽  
C Elegans ◽  
Model Research ◽  
The World ◽  
Natural Isolates ◽  
History Of ◽  
Low Levels

AbstractCaenorhabditis elegans has become one of the most widely used model research organisms, yet we have little information on evolutionary processes and recent evolutionary history of this widespread species. We examined patterns of variation at 20 microsatellite loci in a sample of 23 natural isolates of C. elegans from various parts of the world. One-half of the loci were monomorphic among all strains, and overall genetic variation at microsatellite loci was low, relative to most other species. Some population structure was detected, but there was no association between the genetic and geographic distances among different natural isolates. Thus, despite the nearly worldwide occurrence of C. elegans, little evidence was found for local adaptation in strains derived from different parts of the world. The low levels of genetic variation within and among populations suggest that recent colonization and population expansion might have occurred. However, the patterns of variation are not consistent with population expansion. A possible explanation for the observed patterns is the action of background selection to reduce polymorphism, coupled with ongoing gene flow among populations worldwide.

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