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1.
Ying Yong Sheng Tai Xue Bao ; 31(2): 634-642, 2020 Feb.
Artigo em Chinês | MEDLINE | ID: mdl-32476358

RESUMO

A total of 64 haplotypes were obtained from the complete Cytochrome b gene (Cyt b) of 77 Sorex isodon collected from three populations (Daxing'anling, Xiaoxing'anling, and Changbai Mountains) in Northeast China. The haplotype diversity was 0.9920 and the nucleotide diversity was 0.0105, indicating high genetic diversity. The genetic diversity of Changbai Mountains population was significantly higher than that of Daxing'anling and Xiaoxing'anling populations. The F-statistics, the number of migrants per generation and the genetic distance results showed that the genetic distances among the populations and among the sampling sites were generally consistent with geographical distance. Analysis of molecular variance showed that the differentiation among populations, among sampling sites, and within sampling site accounted for 33.4%, 10.2% and 56.4% of total variation, respectively. The analysis of population history showed that S. isodon in Northeast China experienced no population expansion. The reported complete sequence of Cyt b gene of S. isodon (GenBank) of Europe and other parts of Asia was downloaded to examine the genetic structure of S. isodon. The phylogenetic tree was divided into two large branches. One branch consisted mainly of Daxing'anling and Xiaoxing'anling samples. The other branch was departed into two sub-branches. Median-joining network analysis showed that there were three lineages: one lineage mainly consisted of haplotypes from Daxing'anling and Xiaoxing'anling, and also four haplotypes of Changbai Mountains, while the other lineage included a few haplotypes of three populations in Northeast China, and those from Baikal Lake, Russia and Finland. The last lineage was entirely composed of haplotypes from Changbai Mountains. The results of genetic diversity, phylogenetic tree and median-joining network all suggested that the Changbai Mountains was the refuge for S. isodon during last glacial.


Assuntos
Isodon , Ásia , China , DNA Mitocondrial , Europa (Continente) , Estruturas Genéticas , Variação Genética , Genética Populacional , Haplótipos , Filogenia , Filogeografia
2.
Hum Genet ; 139(8): 1091-1105, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32266522

RESUMO

Unlike other European countries, the human population genetics and demographic history of Metropolitan France is surprisingly understudied. In this work, we combined newly genotyped samples from various zones in France with publicly available data and applied both allele frequency and haplotype-based methods to describe the internal structure of this country, using genome-wide single nucleotide polymorphism (SNP) array genotypes. We found out that French Basques, already known for their linguistic uniqueness, are genetically distinct from all other groups and that the populations from southwest France (namely the Gascony region) share a large proportion of their ancestry with Basques. Otherwise, the genetic makeup of the French population is relatively homogeneous and mostly related to Southern and Central European groups. However, a fine-grained, haplotype-based analysis revealed that Bretons slightly separated from the rest of the groups, due mostly to gene flow from the British Isles in a time frame that coincides both historically attested Celtic population movements to this area between the 3th and the ninth centuries CE, but also with a more ancient genetic continuity between Brittany and the British Isles related to the shared drift with hunter-gatherer populations. Haplotype-based methods also unveiled subtle internal structures and connections with the surrounding modern populations, particularly in the periphery of the country.


Assuntos
Fluxo Gênico , Frequência do Gene , Variação Genética/genética , Genética Populacional , Genoma/genética , Haplótipos , Europa (Continente) , França , Estruturas Genéticas , Genômica , Genótipo , Geografia , Humanos
3.
Mitochondrial DNA A DNA Mapp Seq Anal ; 31(3): 98-107, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-32186219

RESUMO

South China presents an excellent opportunity to build a phylogeographic paradigm for complex geological history, including mountain lifting, climate change, and river capture/reversal events. The phylogeography of cyprinids, particularly Opsariichthys hainanensis, an endemic species restricted to South China, was examined to explore the relationship between the populations in Red River, Hainan Island and its adjacent mainland China. A total of 37 haplotypes were genotyped for the mitochondrial cytochrome b (Cyt b) gene in 115 specimens from 11 river systems. Relatively high levels of haplotype diversity (h = 0.946) and low levels of nucleotide diversity (π = 0.014) were detected in O. hainanensis. Four major phylogenetic haplotype groups revealed a relationship between phylogeny and geography. Our results found that (i) the ancestral populations of O. hainanensis were distributed south of the Wuzhishan and Yinggeling mountains, including the Changhua River on Hainan Island, and then spread to the surrounding areas, (ii) the admixtures within lineages occurred between the Red River in North Vietnam and the Changhua River in western Hainan Island and (iii) indicated that the exposure of straits and shelves under water retreat, provides opportunities for population dispersion during glaciations.


Assuntos
Cyprinidae/genética , Citocromos b/genética , Animais , China , DNA Mitocondrial/genética , Peixes/genética , Genes Mitocondriais/genética , Estruturas Genéticas/genética , Variação Genética/genética , Genética Populacional/métodos , Genoma Mitocondrial/genética , Haplótipos/genética , Mitocôndrias/genética , Filogenia , Filogeografia , Rios , Análise de Sequência de DNA/métodos
4.
Mol Ecol ; 29(5): 859-861, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-32045058

RESUMO

Does the structure and connectivity of host populations influence the dynamics and evolution of their pathogens? This topical question is the essence of research investigating the ecology of a Pteropus fruit bat and its zoonotic Nipah virus (NiV) published by Olival et al. in this issue of Molecular Ecology. Questioned less overtly, but nonetheless implicit to the study, is "what are the mechanisms underpinning intraspecific host-pathogen congruence (IHPC) of genetic structure?". Olival et al. investigated the phylogeographical structure of Pteropus medius and NiV isolates across Bangladesh, from areas inside and outside of the Nipah belt-an area where most human spillover events occur. A high degree of host panmixia was discovered, with some population differentiation east of the Nipah belt. NiV genetic structure was congruent with the host. The authors attributed the panmixia and structuring, respectively, to (a) the highly vagile nature of P. medius, and (b) possible differences between bioregions within and outside the Nipah belt. Other potential explanatory mechanisms were acknowledged, including hybridization and transmission mode. This study makes a valuable contribution to a growing body of literature examining IHPC. This has implications not only for pathogen spillover to humans and domestic animals, but more generally for thinking about the mechanisms that underlie patterns of host and pathogen genetic associations.


Assuntos
Quirópteros , Infecções por Henipavirus , Vírus Nipah/genética , Animais , Estruturas Genéticas , Genética Populacional , Humanos
5.
Pak J Biol Sci ; 23(1): 45-54, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31930882

RESUMO

BACKGROUND AND OBJECTIVE: Visceral leishmaniasis (VL) remains a major concern in many parts of Sudan. The disease is transmitted by Phlebotomus orientalis. The objective of this study was to determine genetic structure of Phlebotomus orientalis population from 5 geographical regions in Sudan. MATERIALS AND METHODS: A total of 194 individual sand flies were collected from 5 geographic regions in Sudan. The field collected sand flies were analyzed by Random Amplified Polymorphic DNA (RAPD) using 30 primers. RESULTS: Eight hundred and 65 bands from 4 RAPD primers were analyzed for genetic variation. A higher level of intrapopulational variability was detected in populations of P. orientalis from eastern Sudan compared to those populations from central and northern Sudan. Diagnostic bands were detected in populations of P. orientalis central Sudan. Hieratical clustering analysis showed clear clustering into 2 main populations with 1 population subdivided into 4 subpopulations. However, these populations did not show any correlation with their geographical origins. Furthermore, the low genetic differentiation among subpopulations was supported by fixation index (FST) estimated by analysis of molecular variance (AMOVA). CONCLUSION: It is concluded that the populations of P. orientalis from the selected areas in Sudan have a low genetic differentiation. However, assessment of genetic structure of P. orientalis populations is important for understanding the patterns of transmission of VL in different endemic areas.


Assuntos
Estruturas Genéticas , Leishmaniose , Phlebotomus/genética , Animais , Humanos , Insetos Vetores/genética , Psychodidae/genética , Sudão
6.
Plant Dis ; 104(4): 1019-1025, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-31994983

RESUMO

Bacterial wilt-causing Ralstonia threaten numerous crops throughout the world. We studied the population structure of 196 isolates of Ralstonia solanacearum and 39 isolates of Ralstonia pseudosolanacearum, which were collected from potato- and tomato-growing areas in 19 states of Brazil. Regardless of the species, three groups of isolates were identified. One group encompassed R. pseudosolanacearum isolates. The other two groups comprise isolates of R. solanacearum (phylotype II) split according to geographic regions, one made of isolates from the North and Northeast and the other made of isolates from the Central, Southeast, and South regions (CSS). Among the isolates collected in CSS, those from tomato were genetically distinct from the potato isolates. The genetic variability in the population of R. pseudosolanacearum was lower than that of R. solanacearum, suggesting that the former was introduced in Brazil. Conversely, the high genetic variability of R. solanacearum in all regions, hosts, and times supports the hypothesis that this species is autochthonous in South America, more precisely in Brazil and Peru. For R. solanacearum, higher variability and lower migration rates were observed when tomato isolates were analyzed, indicating that the variability is caused mainly by the differences of the local, native soil population. The North subpopulation was distinct from all others, possibly because of differences in environmental features of this region. The proximity of some geographic regions and the movement of potato tubers could have facilitated migration and therefore low genetic differentiation between geographic regions. Finally, geography, which also influences host distribution, affects the structure of the population of R. solanacearum in Brazil. Despite quarantine procedures in Brazil, increasing levels of trade are a threat to biosecurity, and these results emphasize the need for improving our regional efforts to prevent the dispersal of pathogens.


Assuntos
Ralstonia solanacearum , Brasil , Estruturas Genéticas , Peru , Filogenia , Doenças das Plantas , Ralstonia
7.
Mol Phylogenet Evol ; 143: 106661, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-31644958

RESUMO

Knowledge of how contemporary and historical factors drive patterns of genetic structure across geographic space can shed light on the processes underlying diversification. This approach is especially fruitful in studies of widespread species or species clades that occur across multiple environmental conditions and biomes. In the Neotropics, specifically, molecular data from widespread vertebrate species have revealed high levels of lineage diversity and spatial genetic structure - yet studies that explore the possible correlates of local structure patterns are lacking. We investigate the distribution of lineage diversity within two widespread South American skink species complexes of the genus Mabuya. We characterize genetic structure and diversity in these widely ranged lizards, and identify potential geographic and environmental correlates, to shed light on the processes that promote lineage diversification across the heterogeneous landscapes which they occupy. In both groups, we found mitochondrial lineages to be spatially structured along the coastal forests and the savannas of Brazil. These mtDNA patterns are, however, not shared with those inferred from nuclear DNA markers. The geographic location of major mitochondrial genetic breaks is consistent with those of other taxa, suggesting common responses to former landscape change in eastern South America, particularly along geological faults. Genetic differentiation is correlated with environmental turnover and geographic separation in one, but not in the other, group of skinks. Compared to other studies of similarly widely distributed organisms, the link between spatial environmental gradients and genetic differentiation is not as strong or consistent, suggesting a more complex history underlying current phylogeographic patterns. Our genetic data indicate the existence of yet undescribed diversity in wide-ranging lizards, and the value of phylogenetic and phylogeographic studies of similarly understudied species.


Assuntos
Lagartos/classificação , Lagartos/genética , Animais , Brasil , Núcleo Celular/genética , DNA Mitocondrial/química , Ecossistema , Florestas , Estruturas Genéticas , Variação Genética , Pradaria , Filogenia , Filogeografia , Clima Tropical
8.
Genes Dev ; 33(23-24): 1688-1701, 2019 12 01.
Artigo em Inglês | MEDLINE | ID: mdl-31727772

RESUMO

Human nucleolar organizer regions (NORs), containing ribosomal gene (rDNA) arrays, are located on the p-arms of acrocentric chromosomes (HSA13-15, 21, and 22). Absence of these p-arms from genome references has hampered research on nucleolar formation. Previously, we assembled a distal junction (DJ) DNA sequence contig that abuts rDNA arrays on their telomeric side, revealing that it is shared among the acrocentrics and impacts nucleolar organization. To facilitate inclusion into genome references, we describe sequencing the DJ from all acrocentrics, including three versions of HSA21, ∼3 Mb of novel sequence. This was achieved by exploiting monochromosomal somatic cell hybrids containing single human acrocentric chromosomes with NORs that retain functional potential. Analyses revealed remarkable DJ sequence and functional conservation among human acrocentrics. Exploring chimpanzee acrocentrics, we show that "DJ-like" sequences and abutting rDNA arrays are inverted as a unit in comparison to humans. Thus, rDNA arrays and linked DJs represent a conserved functional locus. We provide direct evidence for exchanges between heterologous human acrocentric p-arms, and uncover extensive structural variation between chromosomes and among individuals. These findings lead us to revaluate the molecular definition of NORs, identify novel genomic structural variation, and provide a rationale for the distinctive chromosomal organization of NORs.


Assuntos
Cromossomos/química , Cromossomos/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Região Organizadora do Nucléolo/química , Região Organizadora do Nucléolo/genética , Animais , Sequência de Bases , Linhagem Celular , Sequência Conservada/genética , Estruturas Genéticas/genética , Variação Genética , Humanos , Células Híbridas , Camundongos , Pan troglodytes/genética
9.
BMC Evol Biol ; 19(1): 202, 2019 11 04.
Artigo em Inglês | MEDLINE | ID: mdl-31684859

RESUMO

BACKGROUND: Understanding the origin of genetic variation is the key to predict how species will respond to future climate change. The genus Quercus is a species-rich and ecologically diverse woody genus that dominates a wide range of forests and woodland communities of the Northern Hemisphere. Quercus thus offers a unique opportunity to investigate how adaptation to environmental changes has shaped the spatial genetic structure of closely related lineages. Furthermore, Quercus provides a deep insight into how tree species will respond to future climate change. This study investigated whether closely related Quercus lineages have similar spatial genetic structures and moreover, what roles have their geographic distribution, ecological tolerance, and historical environmental changes played in the similar or distinct genetic structures. RESULTS: Despite their close relationships, the three main oak lineages (Quercus sections Cyclobalanopsis, Ilex, and Quercus) have different spatial genetic patterns and occupy different climatic niches. The lowest level and most homogeneous pattern of genetic diversity was found in section Cyclobalanopsis, which is restricted to warm and humid climates. The highest genetic diversity and strongest geographic genetic structure were found in section Ilex, which is due to their long-term isolation and strong local adaptation. The widespread section Quercus is distributed across the most heterogeneous range of environments; however, it exhibited moderate haplotype diversity. This is likely due to regional extinction during Quaternary climatic fluctuation in Europe and North America. CONCLUSIONS: Genetic variations of sections Ilex and Quercus were significantly predicted by geographic and climate variations, while those of section Cyclobalanopsis were poorly predictable by geographic or climatic diversity. Apart from the different historical environmental changes experienced by different sections, variation of their ecological or climatic tolerances and physiological traits induced varying responses to similar environment changes, resulting in distinct spatial genetic patterns.


Assuntos
Cloroplastos/genética , Ilex/genética , Quercus/genética , Mudança Climática , Ecologia , Europa (Continente) , Florestas , Estruturas Genéticas , Variação Genética , Haplótipos , Ilex/citologia , Ilex/crescimento & desenvolvimento , América do Norte , Filogenia , Quercus/citologia , Quercus/crescimento & desenvolvimento
10.
PLoS One ; 14(10): e0223277, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31581227

RESUMO

Lutzomyia longipalpis is the main vector of Leishmania infantum, the causative agent of visceral leishmaniasis in the Neotropical realm. Its taxonomic status has been widely discussed once it encompasses a complex of species. The knowledge about the genetic structure of insect vector populations helps the elucidation of components and interactions of the disease ecoepidemiology. Thus, the objective of this study was to genotypically analyze populations of the Lu. longipalpis complex from a macrogeographic perspective using Next Generation Sequencing. Polymorphism analysis of three molecular markers was used to access the levels of population genetic structure among nine different populations of sand flies. Illumina Amplicon Sequencing Protocol® was used to identify possible polymorphic sites. The library was sequenced on paired-end Illumina MiSeq platform. Significant macrogeographical population differentiation was observed among Lu. longipalpis populations via PCA and DAPC analyses. Our results revealed that populations of Lu. longipalpis from the nine municipalities were grouped into three clusters. In addition, it was observed that the levels of Lu. longipalpis population structure could be associated with distance isolation. This new sequencing method allowed us to study different molecular markers after a single sequencing run, and to evaluate population and inter-species differences on a macrogeographic scale.


Assuntos
Estruturas Genéticas , Genética Populacional , Genoma de Inseto , Genômica , Sequenciamento de Nucleotídeos em Larga Escala , Psychodidae/genética , Animais , Brasil , Genômica/métodos , Geografia
11.
PLoS One ; 14(8): e0205862, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31461452

RESUMO

Translocated saltwater crocodiles (Crocodylus porosus) in the Northern Territory (NT) of Australia often return to their original capture sites, which complicates management interventions aimed at reducing human-crocodile conflict. We examined the spatial events implicated in this homing ability, using ARGOS satellite tracking devices. Five large male C. porosus (3.03 m to 4.02 m TL) were shifted and released 100-320 km from their capture sites, and 3 additional ones (3.67 m to 4.23 m TL) were released at their site of capture as controls. Translocated crocodiles were more mobile than the controls, and moved at sea in the direction of their original capture site. However, they were unable or unwilling to swim around a geographic structure, Cobourg Peninsula, which prevented homing being achieved in all five cases. Two control crocodiles remained near their capture sites, but one, after the first year, made a 900km journey for six months, before returning to its original capture and release site. Genetic analysis of tissue samples from nests across the NT coast demonstrated significant genetic structure across the coast, and confirmed that Cobourg Peninsula contributes to genetic differentiation among populations along the NT coast. These results provide new insights into C. porosus movements, which have management significance for the maintenance of public safety.


Assuntos
Jacarés e Crocodilos/genética , Jacarés e Crocodilos/fisiologia , Distribuição Animal , Geografia , Comportamento de Retorno ao Território Vital , Movimento , Animais , Estruturas Genéticas , Masculino , Astronave
12.
J Phycol ; 55(6): 1319-1334, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31390066

RESUMO

The evolutionary and population demographic history of marine red algae in East Asia is poorly understood. Here, we reconstructed the phylogeographies of two upper intertidal species endemic to East Asia, Gelidiophycus divaricatus and G. freshwateri. Phylogenetic and phylogeographic inferences of 393 mitochondrial cox1, 128 plastid rbcL, and 342 nuclear ITS2 sequences were complemented with ecological niche models. Gelidiophycus divaricatus, a southern species adapted to warm water, is characterized by a high genetic diversity and a strong geographical population structure, characteristic of stable population sizes and sudden reduction to recent expansion. In contrast, G. freshwateri, a northern species adapted to cold temperate conditions, is genetically relatively homogeneous with a shallow population structure resulting from steady population growth and recent equilibrium. The overlap zone of the two species roughly matches summer and winter isotherms, indicating that surface seawater temperature is a key feature influencing species range. Unidirectional genetic introgression was detected at two sites on Jeju Island where G. divaricatus was rare while G. freshwateri was common, suggesting the occurrence of asymmetric natural hybrids, a rarely reported event for rhodophytes. Our results illustrate that Quaternary climate oscillations have left strong imprints on the current day genetic structure and highlight the importance of seawater temperature and sea level change in driving speciation in upper intertidal seaweed species.


Assuntos
Rodófitas , Ásia , DNA Mitocondrial , Estruturas Genéticas , Variação Genética , Haplótipos , Filogenia , Filogeografia
13.
Harmful Algae ; 86: 46-54, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31358276

RESUMO

Paralytic Shellfish Poisoning (PSP) caused by the dinoflagellate Alexandrium catenella is a well-known global syndrome that negatively impacts human health and fishery economies. Understanding the population dynamics and ecology of this species is thus important for identifying determinants of blooms and associated PSP toxicity. Given reports of extensive genetic heterogeneity in the toxicity and physiology of Alexandrium species, knowledge of genetic population structure in harmful algal species such as A. catenella can also facilitate the understanding of toxic bloom development and ecological adaptation. In this study we employed microsatellite markers to analyze multiple A. catenella strains isolated from several sub-regions in the Gulf of Maine (GoM) during summer blooms, to gain insights into the sources and dynamics of this economically important phytoplankton species. At least three genetically distinct clusters of A. catenella were identified in the GoM. Each cluster contained representatives from different sub-regions, highlighting the extent of connectivity and dispersal throughout the region. This shared diversity could result from cyst beds created by previous coastal blooms, thereby preserving the overall diversity of the regional A. catenella population. Rapid spatiotemporal genetic differentiation of A. catenella populations was observed in local blooms, likely driven by natural selection through environmental conditions such as silicate and nitrate/nitrite concentrations, emphasizing the role of short-term water mass intrusions and biotic processes in determining the diversity and dynamics of marine phytoplankton populations. Given the wide-spread intraspecific diversity of A. catenella in GoM and potentially elsewhere, harmful algal blooms will likely persist in many regions despite global warming and changing environmental conditions in the future. Selection of different genetic lineages through variable hydrological conditions might impact toxin production and profiles of future blooms, challenging HAB control and prediction of PSP risk in the future.


Assuntos
Dinoflagelados , Intoxicação por Frutos do Mar , Estruturas Genéticas , Proliferação Nociva de Algas , Humanos , Maine
14.
Mol Phylogenet Evol ; 139: 106556, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31283982

RESUMO

Freshwater systems are naturally fragmented and heterogeneous habitats that promote genetic sub-division and speciation for aquatic biota. Here we provide a novel nuclear genetic perspective (49 allozyme loci) complimented with updated mitochondrial data for the eleotrid genus Philypnodon to investigate broad genetic sub-structure across south-eastern Australia as a foundation for management and conservation. The genus is nominally comprised of two small benthic fishes with contrasting physical and ecological traits, namely the Flathead Gudgeon P. grandiceps and the Dwarf Flathead Gudgeon P. macrostomus. Extensive sample coverage included 99 sites across 5 major drainage divisions and 48 river basins. Nuclear markers revealed strong, geographically-based divergence and sub-structure, contrasting with shallower but largely congruent patterns for mtDNA. The results flag that each nominal species represents a hyper-cryptic species complex, including both broadly distributed and narrow-range taxa, with complicated biogeographic patterns. Predictions on dispersal and genetic structure based on ecological traits were only partially supported and varied by region, with the potential signature of human-assisted translocation evident in several catchments. Further intensive sampling in an important area of high genetic diversity, coastal south-east Queensland, is recommended to better resolve species boundaries and conservation units. The findings provide new insights on regional ecology and biogeography, demonstrating that even supposedly common species can, in reality, have complex conservation and management needs.


Assuntos
Conservação dos Recursos Naturais , Água Doce , Estruturas Genéticas , Perciformes/genética , Animais , Núcleo Celular/genética , Citocromos b/genética , DNA Mitocondrial/genética , Ecossistema , Variação Genética , Funções Verossimilhança , Filogenia , Filogeografia , Análise de Componente Principal , Queensland , Especificidade da Espécie
15.
Methods Mol Biol ; 1910: 3-31, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31278660

RESUMO

Organisms display astonishing levels of cell and molecular diversity, including genome size, shape, and architecture. In this chapter, we review how the genome can be viewed as both a structural and an informational unit of biological diversity and explicitly define our intended meaning of genetic information. A brief overview of the characteristic features of bacterial, archaeal, and eukaryotic cell types and viruses sets the stage for a review of the differences in organization, size, and packaging strategies of their genomes. We include a detailed review of genetic elements found outside the primary chromosomal structures, as these provide insights into how genomes are sometimes viewed as incomplete informational entities. Lastly, we reassess the definition of the genome in light of recent advancements in our understanding of the diversity of genomic structures and the mechanisms by which genetic information is expressed within the cell. Collectively, these topics comprise a good introduction to genome biology for the newcomer to the field and provide a valuable reference for those developing new statistical or computation methods in genomics. This review also prepares the reader for anticipated transformations in thinking as the field of genome biology progresses.


Assuntos
Biodiversidade , Eucariotos/genética , Genoma , Genômica , Archaea/genética , Bactérias/genética , Biologia Computacional/métodos , Regulação da Expressão Gênica , Estruturas Genéticas , Genômica/métodos , Padrões de Herança , Vírus/genética
16.
Genes Genomics ; 41(10): 1127-1134, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31209767

RESUMO

BACKGROUND: The genetic structure of marine organisms in the East Asian region has long been a subject of interest. Two grapsid crab species, Hemigrapsus penicillatus (De Haan, 1835) and Hemigrapsus sanguineus (De Haan, 1835), are commonly found in the rocky intertidal zones around this region. They are known to spread via larval migration, which makes them an appropriate model species for observing the genetic structure of East Asian intertidal invertebrate animals. OBJECTIVE: We investigated the genetic structure of the East Asian crabs H. penicillatus and H. sanguineus. METHODS: We collected specimens of H. penicillatus from seven locations (42 individuals) and of H. sanguineus from ten locations (58 individuals) in Korea, Japan, and Taiwan. We investigated and compared the genetic diversity and structure of populations of these species using mitochondrial cytochrome oxidase subunit I (COI) sequences. RESULTS: Our results show that both species are genetically structured between South Korea and Japan, and that the Taiwan population forms a cluster that is separate from those of the other countries. Populations of H. penicillatus contain less genetic diversity than those of H. sanguineus. CONCLUSION: These results suggest that there is a genetic structure between the two species at present in East Asia.


Assuntos
Braquiúros/classificação , Braquiúros/genética , Estruturas Genéticas , Filogeografia , Animais , DNA Mitocondrial/genética , Complexo I de Transporte de Elétrons/genética , Extremo Oriente , Variação Genética , Japão , Filogenia , República da Coreia , Taiwan
17.
J Genet ; 98(2)2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31204711

RESUMO

Ceratitis capitata is one among the most destructive and economically important agricultural pests worldwide. Despite its economic significance, the population structures of this pest have remained relatively unexplored in the eastern Mediterranean basin. Using two mitochondrial markers, the present study aimed to examining the population genetic structure and diversity of C. capitata populations in Turkey, the region that covers a large part of the eastern Mediterranean area. Our results revealed that the Turkish Mediterranean fruit fly populations are characterized by low levels of genetic diversity and limited population differentiation. For comparison purposes, wemerged the sequences identified in the present study with the previously reported sequences from acrossthe world into the data matrix. The haplotype network showed that, unlike the African samples the Mediterranean samples and samples from the new world (America, Pacific region and Australia) did not show any clear pattern of geographical structuring, which indicates that the Mediterranean basin, particularly the eastern Mediterranean region populations, may have played a moreimportant role in the colonization of C. capitata populations to the new world. The results also revealed a close genetic relationship between the Turkish and Iranian populations, suggesting that the Iranian C. capitata populations probably originated from Turkey.


Assuntos
Ceratitis capitata/genética , DNA Mitocondrial , Genes de Insetos , Marcadores Genéticos , Estruturas Genéticas , Genética Populacional , Animais , Ceratitis capitata/classificação , Geografia , Haplótipos , Filogenia , Polimorfismo Genético , Análise de Sequência de DNA , Turquia
18.
Proc Biol Sci ; 286(1905): 20190983, 2019 06 26.
Artigo em Inglês | MEDLINE | ID: mdl-31213183

RESUMO

Disentangling the contemporary and historical factors underlying the spatial distributions of species is a central goal of biogeography. For species with broad distributions but little capacity to actively disperse, disconnected geographical distributions highlight the potential influence of passive, long-distance dispersal (LDD) on their evolutionary histories. However, dispersal alone cannot completely account for the biogeography of any species, and other factors-e.g. habitat suitability, life history-must also be considered. North American ice worms ( Mesenchytraeus solifugus) are ice-obligate annelids that inhabit coastal glaciers from Oregon to Alaska. Previous studies identified a complex biogeographic history for ice worms, with evidence for genetic isolation, unexpectedly close relationships among geographically disjunct lineages, and contemporary migration across large (e.g. greater than 1500 km) areas of unsuitable habitat. In this study, we analysed genome-scale sequence data for individuals from most of the known ice worm range. We found clear support for divergence between populations along the Pacific Coast and the inland flanks of the Coast Mountains (mean FST = 0.60), likely precipitated by episodic ice sheet expansion and contraction during the Pleistocene. We also found support for LDD of ice worms from Alaska to Vancouver Island, perhaps mediated by migrating birds. Our results highlight the power of genomic data for disentangling complex biogeographic patterns, including the presence of LDD.


Assuntos
Ecossistema , Camada de Gelo , Oligoquetos/genética , Alaska , Animais , Evolução Biológica , Estruturas Genéticas , Variação Genética , Oregon , Filogenia , Filogeografia
19.
Phytopathology ; 109(9): 1614-1627, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31066347

RESUMO

The oomycete Phytophthora infestans is an important plant pathogen on potato and tomato crops. We examined the genetic structure of extant 20th and 21st century U.S. lineages of P. infestans and compared them with populations from South America and Mexico to examine genetic relationships and potential sources of lineages. US-23, currently the most prevalent lineage detected in the United States, shared genetic similarity primarily with the BR-1 lineage identified in the 1990s from Bolivia and Brazil. Lineages US-8, US-14, and US-24, predominantly virulent on potato, formed a cluster distinct from other U.S. lineages. Many of the other U.S. lineages shared significant genetic similarity with Mexican populations. The US-1 lineage, dominant in the mid-20th century, clustered with US-1 lineages from Peru. A survey of the presence of RXLR effector PiAVR2 revealed that some lineages carried PiAVR2, its resistance-breaking variant PiAVR2-like, or both. Minimum spanning networks developed from simple sequence repeat genotype datasets from USABlight outbreaks clearly showed the expansion of US-23 over a 6-year time period and geographic substructuring of some lineages in the western United States. Many clonal lineages of P. infestans in the United States have come from introductions from Mexico, but the US-23 and US-1 lineages were most likely introduced from other sources.


Assuntos
Phytophthora infestans , Solanum tuberosum , Brasil , Estruturas Genéticas , México , Phytophthora infestans/fisiologia , Doenças das Plantas/estatística & dados numéricos , Estados Unidos
20.
ScientificWorldJournal ; 2019: 6507954, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31118874

RESUMO

The Astyanax scabripinnis complex is composed of a large number of almost morphological indistinguishable species, including Astyanax paranae and Astyanax rivularis, which exist in the Paraná and São Francisco Basins, respectively, and sometimes are considered subspecies of the A. scabripinnis group or even are cited just as A. scabripinnis. The two river basins are separated by the Upper Paranaíba Arc, likely the main cause of the isolation of these species. We used geometric morphometric tools and DNA analyses of populations of both species to identify the differences between them. Geometric morphometrics separated the two species into distinct groups, whose main difference was the body depth. This is generally related to the speed of the water flow in the river basins. The maximum likelihood phylogram based on mitochondrial DNA sequences formed two main clades: one composed of the population of A. rivularis and the other, of A. paranae. In the haplotype network, the species were similarly separated into two groups from the same ancestral haplotype, with A. rivularis dispersing into two lineages in the São Francisco River Basin. The distribution of A. paranae is a consequence of a secondary dispersion event in the Paraná River Basin. It forms two lineages from a haplotype derived from the ancestor. The vicariant effect of separate basins, through the elevation of the Upper Paranaíba Arc, led to the allopatric speciation of the populations originating the present species. The results of geometric morphometrics and molecular data of the fish show the importance of this geological event in the biogeography and evolutionary history of the ichthyofauna of the region and indicate that the isolation of these species seems to be effective.


Assuntos
Caraciformes/anatomia & histologia , Caraciformes/genética , Estudos de Associação Genética , Variação Genética , Fenótipo , Animais , Brasil , Caraciformes/classificação , Estruturas Genéticas , Haplótipos , Filogenia
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