Conservation genetics of an endangered Catalonian cattle breed ("Alberes")

We biochemically analyzed and characterized the genetic structure of a population in danger of extinction ,"Alberes", a local cattle breed of the Catalonian Pyrenees (Spain and France). Ninety-two individuals were analyzed for five polymorphic genetic loci (Hb, Alb, Tf, Gc and Ptf2). The animals were grouped according to coat color: Fagina Alberes variety (N = 39) and Black Alberes variety (N = 53). The genetic structures and relationships between these subpopulations and one "outgroup" breed ("Bruna dels Pirineus") were analyzed and compared by using F-statistics. We determined that inbreeding in the Alberes breed is not significant, since negative and nonsignificant FIT and FIS values were obtained. The average genetic differentiation between subpopulations within the Alberes breed was 1.5% (FST = 0.015; P < 0.05), with an effective number of 4.1 individuals exchanged between subpopulations per generation (gene flow). The results obtained in this study corroborate the potential danger of extinction of the breed. The Black Alberes variety is proposed as the principal nucleus of genetic conservation for this breed, as it seems to show a higher degree of genetic isolation from other foreign populations.

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

Parasites & Vectors ◽

10.1186/s13071-019-3801-4 ◽

2019 ◽

Vol 12 (1) ◽

Cited By ~ 2

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.

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A differential expression of pyrethroid resistance genes in the malaria vector Anopheles funestus across Uganda is associated with patterns of gene flow

PLoS ONE ◽

10.1371/journal.pone.0240743 ◽

2020 ◽

Vol 15 (11) ◽

pp. e0240743

Author(s):

Maurice Marcel Sandeu ◽

Charles Mulamba ◽

Gareth D. Weedall ◽

Charles S. Wondji

Keyword(s):

Population Structure ◽

Gene Flow ◽

Genetic Structure ◽

Genetic Differentiation ◽

Insecticide Resistance ◽

Pyrethroid Resistance ◽

Anopheles Funestus ◽

Metabolic Resistance ◽

Transcription Analysis ◽

Genome Wide

Background Insecticide resistance is challenging the effectiveness of insecticide-based control interventions to reduce malaria burden in Africa. Understanding the molecular basis of insecticides resistance and patterns of gene flow in major malaria vectors such as Anopheles funestus are important steps for designing effective resistance management strategies. Here, we investigated the association between patterns of genetic structure and expression profiles of genes involved in the pyrethroid resistance in An. funestus across Uganda and neighboring Kenya. Methods Blood-fed mosquitoes An. funestus were collected across the four localities in Uganda and neighboring Kenya. A Microarray-based genome-wide transcription analysis was performed to identify the set of genes associated with permethrin resistance. 17 microsatellites markers were genotyped and used to establish patterns of genetic differentiation. Results Microarray-based genome-wide transcription profiling of pyrethroid resistance in four locations across Uganda (Arua, Bulambuli, Lira, and Tororo) and Kenya (Kisumu) revealed that resistance was mainly driven by metabolic resistance. The most commonly up-regulated genes in pyrethroid resistance mosquitoes include cytochrome P450s (CYP9K1, CYP6M7, CYP4H18, CYP4H17, CYP4C36). However, expression levels of key genes vary geographically such as the P450 CYP6M7 [Fold-change (FC) = 115.8 (Arua) vs 24.05 (Tororo) and 16.9 (Kisumu)]. In addition, several genes from other families were also over-expressed including Glutathione S-transferases (GSTs), carboxylesterases, trypsin, glycogenin, and nucleotide binding protein which probably contribute to insecticide resistance across Uganda and Kenya. Genotyping of 17 microsatellite loci in the five locations provided evidence that a geographical shift in the resistance mechanisms could be associated with patterns of population structure throughout East Africa. Genetic and population structure analyses indicated significant genetic differentiation between Arua and other localities (FST>0.03) and revealed a barrier to gene flow between Arua and other areas, possibly associated with Rift Valley. Conclusion The correlation between patterns of genetic structure and variation in gene expression could be used to inform future interventions especially as new insecticides are gradually introduced.

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

Parasitology ◽

10.1017/s0031182013000437 ◽

2013 ◽

Vol 140 (9) ◽

pp. 1061-1069 ◽

Cited By ~ 23

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.

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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 Journal of Biological Diversity ◽

10.13057/biodiv/d180427 ◽

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.

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Isozyme and RAPD studies in Prosopis glandulosa and P. Velutina (Leguminosae, Mimosoideae)

Genetics and Molecular Biology ◽

10.1590/s1415-47572000000300024 ◽

2000 ◽

Vol 23 (3) ◽

pp. 639-648 ◽

Cited By ~ 12

Author(s):

Cecilia Bessega ◽

Beatriz O. Saidman ◽

Juan C. Vilardi

Keyword(s):

Gene Flow ◽

Genetic Structure ◽

Genetic Variability ◽

Genetic Differentiation ◽

Rapd Markers ◽

Random Amplified Polymorphic Dna ◽

Mantel Test ◽

Prosopis Glandulosa ◽

Geographical Distance ◽

Taxonomic Studies

Allozyme and random amplified polymorphic DNA (RAPD) techniques have been compared for their usefulness for genetic and taxonomic studies in Prosopis glandulosa and P. velutina populations. Isozymes and RAPDs yielded similarly high estimates of genetic variability. Genetic structure and differentiation were analyzed through non-hierarchical Wright's F DT. For all populations considered, both markers produced low gene flow (Nm < 1) estimates. When only P. glandulosa populations were analyzed, isozyme data yielded higher gene flow estimates (Nm > 1), in agreement with that expected for conspecific populations. However, in RAPD data the expected reduction in F DT and the increase in Nm were not observed. Correlation between F DT and geographical distance matrices (Mantel test) for all populations was significant (P = 0.02) when based on isozymes, but not so (P = 0.33) when based on RAPDs. No significant associations among genetic and geographical or climatic variables were observed. Two isoenzyme systems (GOT and PRX) enabled us to distinguish between P. glandulosa and P. velutina, but no diagnostic band for recognition of populations or species studied here were detected by RAPD. However, RAPD markers showed higher values for genetic differentiation among conspecific populations of P. glandulosa and a lower coefficient of variation than those obtained from isozymes.

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Comparing the genetic structure of codling moth Cydia pomonella (L.) from Greece and France: long distance gene-flow in a sedentary pest species

Bulletin of Entomological Research ◽

10.1017/s0007485311000563 ◽

2011 ◽

Vol 102 (2) ◽

pp. 185-198 ◽

Cited By ~ 15

Author(s):

C.Ch. Voudouris ◽

P. Franck ◽

J. Olivares ◽

B. Sauphanor ◽

Z. Mamuris ◽

...

Keyword(s):

Gene Flow ◽

Genetic Structure ◽

Genetic Differentiation ◽

Insect Pest ◽

Cydia Pomonella ◽

Codling Moth ◽

Pest Species ◽

Long Distance ◽

Control Programs ◽

Genetic Clusters

AbstractCodling moth Cydia pomonella L. (Lepidoptera: Tortricidae) is the most important insect pest of apple production in Europe. Despite the economic importance of this pest, there is not information about the genetic structure of its population in Greece and the patterns of gene-flow which might affect the success of control programs. In this study, we analysed nine samples from apple, pear and walnut from various regions of mainland Greece using 11 microsatellite loci. Six samples from the aforementioned hosts from southern France were also examined for comparison. Bayesian clustering and genetic distance analyses separated the codling moth samples in two genetic clusters. The first cluster consisted mainly of the individuals from Greece, and the second of those from France, although admixture and miss-classified individuals were also observed. The low genetic differentiation among samples within each country was also revealed by FST statistics (0.009 among Greek samples and 0.0150 among French samples compared to 0.050 global value among all samples and 0.032 the mean of the pair-wise values between the two countries). These FST values suggest little structuring at large geographical scales in agreement with previous published studies. The host species and local factors (climatic conditions, topography, pest control programs) did not affect the genetic structure of codling moth populations within each country. The results are discussed in relation to human-made activities that promote gene-flow even at large geographic distances. Possible factors for the genetic differentiation between the two genetic clusters are also discussed.

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Spatial and temporal genetic structure of Asclepias verticillata (whorled milkweed) among prairie patches in a forested landscape

Canadian Journal of Botany ◽

10.1139/b96-156 ◽

1996 ◽

Vol 74 (8) ◽

pp. 1289-1297 ◽

Cited By ~ 5

Author(s):

S. A. Foré ◽

S. I. Guttman

Keyword(s):

Genetic Structure ◽

Genetic Differentiation ◽

Genetic Data ◽

Suitable Habitat ◽

Conditional Allele ◽

Large Numbers ◽

Region Data ◽

Population Sizes ◽

Prairie Management ◽

F Statistics

We examined the spatial scale of genetic structure of Asclepias verticillata L. (whorled milkweed) populations in a landscape where suitable habitat is fragmented by woodlands to determine if the distance between patches influences genetic differentiation. In addition, we sampled over 2 years to determine if there are temporal genetic differences. This forb is found in prairie habitat in the Edge of Appalachia Preserve System, Ohio. Prairie patches have a clumped distribution with patches within a region located < 150 m apart and regions located > 1.5 km apart. Allozyme electrophoresis was used to collect genetic data from reproductive individuals in nine patches representing four regions. Observed heterozygosity was not significantly different among patches or between years, even though population sizes varied. Rogers' genetic distance and hierarchical F-statistics indicated that there was little genetic differentiation among patches within a region. Although genetic differentiation was greater among regions, it was relatively low. Between years, genetic differentiation within a patch was as great as genetic differentiation between patches. Conditional allele frequencies suggest that loss of one patch within a region will increase genetic differentiation within a region. Data suggest that prairie management could focus on a few regions with large numbers of patches. Keywords: habitat fragmentation, allozyme, genetic diversity, prairie management.

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High nuclear genetic differentiation, but low chloroplast diversity in a rare species, Aluta quadrata (Myrtaceae), with a disjunct distribution in the Pilbara, Western Australia

Australian Journal of Botany ◽

10.1071/bt16128 ◽

2016 ◽

Vol 64 (8) ◽

pp. 687 ◽

Cited By ~ 5

Author(s):

M. Byrne ◽

D. J. Coates ◽

B. M. Macdonald ◽

M. Hankinson ◽

S. M. McArthur ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Genetic Structure ◽

Genetic Differentiation ◽

Microsatellite Loci ◽

Disjunct Distribution ◽

Chloroplast Gene ◽

Seed Sources ◽

Chloroplast Haplotype ◽

Haplotype Variation

Geographically separated populations may show high levels of genetic differentiation, depending on the levels of current and historical isolation. In the ancient landscape of the Pilbara region, there are few plant species with restricted distributions, and one such species, Aluta quadrata Rye & Trudgen, is restricted to three separate locations on the southern edge of the Hamersley Range. We investigated genetic diversity and differentiation among geographically isolated locations of A. quadrata, using 10 microsatellite loci to assess contemporary genetic structure, and sequences of seven chloroplast gene regions to infer historical isolation. Nuclear genetic diversity was moderate, with moderate to high genetic differentiation among the three locations, and low differentiation among populations within locations. In contrast, there was no detected variation in the chloroplast genome. The high genetic differentiation is consistent with limited contemporary connectivity among the geographically separated locations, although lack of chloroplast haplotype variation indicates that limited connectivity has occurred more recently and is not due to historical isolation. The level of differentiation suggests use of local seed sources for augmentation or establishment of populations within gene flow distance of existing populations, whereas an experimental translocation established on more distant sites could use mixed seed sources to maximise genetic diversity.

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Spatial genetic structure and asymmetrical gene flow within the Pacific walrus

Journal of Mammalogy ◽

10.1644/11-mamm-a-344.1 ◽

2012 ◽

Vol 93 (6) ◽

pp. 1512-1524 ◽

Cited By ~ 9

Author(s):

Sarah A. Sonsthagen ◽

Chadwick V. Jay ◽

Anthony S. Fischbach ◽

George K. Sage ◽

Sandra L. Talbot

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Genetic Structure ◽

Genetic Differentiation ◽

Spatial Genetic Structure ◽

Genetic Relationships ◽

Breeding Population ◽

Pacific Walrus ◽

Breeding Populations ◽

The Pacific

Abstract Pacific walruses (Odobenus rosmarus divergens) occupying shelf waters of Pacific Arctic seas migrate during spring and summer from 3 breeding areas in the Bering Sea to form sexually segregated nonbreeding aggregations. We assessed genetic relationships among 2 putative breeding populations and 6 nonbreeding aggregations. Analyses of mitochondrial DNA (mtDNA) control region sequence data suggest that males are distinct among breeding populations (ΦST = 0.051), and between the eastern Chukchi and other nonbreeding aggregations (ΦST = 0.336–0.449). Nonbreeding female aggregations were genetically distinct across marker types (microsatellite FST = 0.019; mtDNA ΦST = 0.313), as was eastern Chukchi and all other nonbreeding aggregations (microsatellite FST = 0.019–0.035; mtDNA ΦST = 0.386–0.389). Gene flow estimates are asymmetrical from St. Lawrence Island into the southeastern Bering breeding population for both sexes. Partitioning of haplotype frequencies among breeding populations suggests that individuals exhibit some degree of philopatry, although weak. High levels of genetic differentiation among eastern Chukchi and all other nonbreeding aggregations, but considerably lower genetic differentiation between breeding populations, suggest that at least 1 genetically distinct breeding population remained unsampled. Limited genetic structure at microsatellite loci between assayed breeding areas can emerge from several processes, including male-mediated gene flow, or population admixture following a decrease in census size (i.e., due to commercial harvest during 1880–1950s) and subsequent recovery. Nevertheless, high levels of genetic diversity in the Pacific walrus, which withstood prolonged decreases in census numbers with little impact on neutral genetic diversity, may reflect resiliency in the face of past environmental challenges.

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Patterns of genetic variation in leading-edge populations of Quercus robur: genetic patchiness due to family clusters

Tree Genetics & Genomes ◽

10.1007/s11295-020-01465-9 ◽

2020 ◽

Vol 16 (5) ◽

Author(s):

Pekka Vakkari ◽

Mari Rusanen ◽

Juha Heikkinen ◽

Tea Huotari ◽

Katri Kärkkäinen

Keyword(s):

Population Structure ◽

Genetic Structure ◽

Genetic Differentiation ◽

Population Genetic ◽

Quercus Robur ◽

Spatial Genetic Structure ◽

Medium Size ◽

Pedunculate Oak ◽

Genetic Structures ◽

Genetic Patchiness

Abstract The genetic structure of populations at the edge of species distribution is important for species adaptation to environmental changes. Small populations may experience non-random mating and differentiation due to genetic drift but larger populations, too, may have low effective size, e.g., due to the within-population structure. We studied spatial population structure of pedunculate oak, Quercus robur, at the northern edge of the species’ global distribution, where oak populations are experiencing rapid climatic and anthropogenic changes. Using 12 microsatellite markers, we analyzed genetic differentiation of seven small to medium size populations (census sizes 57–305 reproducing trees) and four populations for within-population genetic structures. Genetic differentiation among seven populations was low (Fst = 0.07). We found a strong spatial genetic structure in each of the four populations. Spatial autocorrelation was significant in all populations and its intensity (Sp) was higher than those reported in more southern oak populations. Significant genetic patchiness was revealed by Bayesian structuring and a high amount of spatially aggregated full and half sibs was detected by sibship reconstruction. Meta-analysis of isoenzyme and SSR data extracted from the (GD)2 database suggested northwards decreasing trend in the expected heterozygosity and an effective number of alleles, thus supporting the central-marginal hypothesis in oak populations. We suggest that the fragmented distribution and location of Finnish pedunculate oak populations at the species’ northern margin facilitate the formation of within-population genetic structures. Information on the existence of spatial genetic structures can help conservation managers to design gene conservation activities and to avoid too strong family structures in the sampling of seeds and cuttings for afforestation and tree improvement purposes.

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