scholarly journals Population genetic structure of raccoons as a consequence of multiple introductions and range expansion in the Boso Peninsula, Japan

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Miki Hirose ◽  
Kazuya Yoshida ◽  
Eiji Inoue ◽  
Masami Hasegawa
Keyword(s):  
Range Expansion ◽  
Population Control ◽  
Genetic Admixture ◽  
Effective Population ◽  
Multiple Introductions ◽  
Boso Peninsula ◽  
Genetic Groups ◽  
D Loop ◽  
Nuclear Microsatellite ◽  
Two Populations

AbstractThe raccoon (Procyon lotor) is an invasive carnivore that invaded various areas of the world. Although controlling feral raccoon populations is important to reduce serious threats to local ecosystems, raccoons are not under rigid population control in Europe and Japan. We examined the D-loop and nuclear microsatellite regions to identify spatially explicit and feasible management units for effective population control and further range expansion retardation. Through the identification of five mitochondrial DNA haplotypes and three nuclear genetic groups, we identified at least three independent introductions, range expansion, and subsequent genetic admixture in the Boso Peninsula. The management unit considered that two were appropriate because two populations have already genetic exchange. Furthermore, when taking management, we think that it is important to monitor DNA at the same time as capture measures for feasible management. This makes it possible to determine whether there is a invasion that has a significant impact on population growth from out of the unit, and enables adaptive management.

scholarly journals Population Genetic Structure of Raccoons as a Consequence of Multiple Introductions and Range Expansion in the Boso Peninsula, Japan

2021 ◽  
Author(s):  
Miki Hirose ◽  
Kazuya Yoshida ◽  
Eiji Inoue ◽  
Masami Hasegawa
Keyword(s):  
Range Expansion ◽  
Population Control ◽  
Large Population ◽  
Genetic Admixture ◽  
Effective Population ◽  
Genetic Barrier ◽  
Management Units ◽  
Multiple Introductions ◽  
Boso Peninsula ◽  
Chiba Prefecture

Abstract Raccoon (Procyon lotor) is a globally introduced invasive carnivore. Although controlling feral raccoon populations is important to reduce serious threats to local ecosystems, raccoons are not under rigid population control in Europe and Japan. We examined the D-loop and nuclear microsatellite regions to identify spatially explicit and feasible management units for effective population control and further range expansion retardation. Through the identification of five mitochondrial DNA haplotypes and three nuclear genetic groups, we identified at least three independent introductions, range expansion, and subsequent genetic admixture in the Boso Peninsula. Admitting that the currently recognizable two genetic clusters can be treated as different management units, these management units will soon fuse to a single but large population to which the effective population control will no longer be applicable due to the absence of a genetic barrier between southern and northern Chiba Prefecture.

scholarly journals Phylogeography of high Andean killifishes Orestias (Teleostei: Cyprinodontidae) in Caquena and Lauca sub-basins of the Altiplano (Chile): mitochondrial and nuclear analysis of an endangered fish

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11917
Author(s):  
Violeta Cárcamo-Tejer ◽  
Irma Vila ◽  
Francisco Llanquín-Rosas ◽  
Alberto Sáez-Arteaga ◽  
Claudia Guerrero-Jiménez
Keyword(s):  
Evolutionary History ◽  
Andes Mountains ◽  
Endangered Fish ◽  
The Andes ◽  
Genetic Groups ◽  
Biogeographic History ◽  
D Loop ◽  
History Of ◽  
Nuclear Microsatellite ◽  
Genic Diversity

From the early Miocene, the uplift of the Andes Mountains, intense volcanic activity and the occurrence of successive periods of dryness and humidity would have differentially influenced the modification of Altiplano watersheds, and consequently the evolutionary history of the taxa that live there. We analyzed Orestias populations from the Caquena and Lauca Altiplanic sub-basins of northern Chile to determine their genetic differentiation and relationship to their geographical distribution using mitochondrial (D-loop) and nuclear (microsatellite) molecular markers and to reconstruct its biogeographic history on these sub-basins. The results allowed reconstructing and reevaluating the evolutionary history of the genus in the area; genic diversity and differentiation together with different founding genetic groups suggest that Orestias have been spread homogeneously in the study area and would have experienced local disturbances that promoted isolation and diversification in restricted zones of their distribution.

A hybrid zone defined by allozymes and ventral colour in Geocrinia rosea (Anura:Myobatrachidae)

2007 ◽  
Vol 55 (6) ◽  
pp. 371 ◽  
Author(s):  
Don A. Driscoll ◽  
J. Dale Roberts
Keyword(s):  
Hybrid Zone ◽  
Range Expansion ◽  
Taxonomic Revision ◽  
Hybrid Population ◽  
Genetic Groups ◽  
Colour Patterns ◽  
Allozyme Loci ◽  
Two Populations ◽  
Genetic Division

The frog Geocrinia rosea is highly genetically subdivided with a major genetic division between northern and southern populations. Previous research did not sample a region spanning 12 km between these two populations. We report the distribution of G. rosea in the unsampled area and identify a geographically restricted hybrid zone. Boundaries of genetic groups were defined using two allozyme loci in 13 populations and ventral colouration. G. rosea was not continuously distributed in the area of parapatry. At the only point where the northern and southern groups met, there was a single hybrid population with genotypes demonstrating substantial interbreeding. Colour patterns implied a slightly broader hybrid zone, with four populations showing ventral colour introgression. Northern populations tended to have pink bellies whereas southern populations generally had orange bellies. We conclude that the two groups have diverged in allopatry and have formed a very narrow hybrid zone after range expansion. The magnitude of allozyme divergence between the four currently recognised species in the G. rosea complex is similar to the divergence between northern and southern G. rosea and is much greater than the divergence between other intraspecific groups. Taxonomic revision may therefore be warranted.

scholarly journals Genetic Analysis of Invasive Populations of Ventenata Dubia (Poaceae)

2020 ◽  
Author(s):  
Inna Pervukhina-Smith
Keyword(s):  
Genetic Analysis ◽  
Range Expansion ◽  
Propagule Pressure ◽  
Genetic Admixture ◽  
Enzyme Electrophoresis ◽  
Evolutionary Potential ◽  
Multiple Introductions ◽  
Western Us ◽  
Invaluable Tool ◽  
Low Levels

Molecular markers prove to be an invaluable tool in assessing the introduction dynamics, pattern of range expansion, and population genetics of an invasive species. Ventenata dubia (Leers) Coss. (Aveneae; ventenata) is a diploid, primarily self-pollinating, annual grass native to Eurasia and Northern Africa. The grass has a detailed herbarium collection history in the western United States since its discovery in eastern Washington in 1952. Genetic analysis of 51 invasive populations (1636 individuals) of V. dubia, coupled with historical records, suggests moderate propagule pressure from multiple introductions, followed by local or regional range expansion. Enzyme electrophoresis detected nine multilocus genotypes (MLGs) across eight western US states. A single MLG, referred to as the most common genotype (MCG), was detected in 37 of 51 (72.5%) invasive populations across all states. The other eight MLGs were generally found in fewer populations, with limited geographic distributions. Despite multiple introductions, invasive populations exhibit low levels of genetic admixture, low levels of genetic diversity within populations (A = 1.03, %P = 2.94, Hexp = 0.007) and high genetic differentiation among populations (GST = 0.864). The apparent reduced evolutionary potential of most V. dubia populations did not preclude the initial establishment and rapid spread of this species across its new range in the western US.

scholarly journals Deciphering the Patterns of Genetic Admixture and Diversity in the Ecuadorian Creole Chicken

Animals ◽  
2019 ◽  
Vol 9 (9) ◽  
pp. 670 ◽  
Author(s):  
Paula Alexandra Toalombo Vargas ◽  
José Manuel León ◽  
Luis Rafael Fiallos Ortega ◽  
Amparo Martinez ◽  
Alex Arturo Villafuerte Gavilanes ◽  
...  
Keyword(s):  
Latin American ◽  
Reference Data ◽  
Genetic Relationships ◽  
Scientific Information ◽  
Genetic Admixture ◽  
Genetic Isolation ◽  
Genetic Groups ◽  
D Loop ◽  
Structure Assessment

Latin American Creole chickens are generally not characterized; this is the case in Ecuador, where the lack of scientific information is contributing to their extinction. Here, we developed a characterization of the genetic resources of Ecuadorian chickens located in three continental agroecosystems (Pacific coastal, Andean, and Amazonian). Blood samples of 234 unrelated animals were collected in six provinces across Ecuador: Bolívar, Chimborazo, Cotopaxi, Guayas, Morona Santiago, and Tungurahua, in order to perform a genetic characterization and population structure assessment using the AVIANDIV project microsatellites panel (30 loci) and D-loop sequences of mitochondrial DNA and comparing with reference data from other breeds or genetic lines. The results indicate that Ecuadorian Creole chickens are the result of the admixture of different genetic groups that occurred during the last five centuries. While the influence of South Spanish breeds is demonstrated in the colonial age, genetic relationships with other breeds (Leghorn, Spanish fighter cock) cannot be discarded. The geographical configuration of the country and extreme climate variability have influenced the genetic isolation of groups constituting a homogeneous genetic status into the whole population. This is not only a source of genetic variation, but also a critical point because genetic drift produces a loss of genetic variants.

scholarly journals Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication

2021 ◽  
Vol 134 (5) ◽  
pp. 1343-1362
Author(s):  
Alex C. Ogbonna ◽  
Luciano Rogerio Braatz de Andrade ◽  
Lukas A. Mueller ◽  
Eder Jorge de Oliveira ◽  
Guillaume J. Bauchet
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Manihot Esculenta ◽  
Ex Situ ◽  
Germplasm Bank ◽  
Effective Population ◽  
Manihot Esculenta Crantz ◽  
Genetic Groups ◽  
Population Structure Analysis ◽  
Modern Breeding

Abstract Key message Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation. Abstract Cassava (Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonian region. In this study, 3354 cassava landraces and modern breeding lines from the Embrapa Cassava Germplasm Bank (CGB) were characterized. All individuals were subjected to genotyping-by-sequencing (GBS), identifying 27,045 single-nucleotide polymorphisms (SNPs). Identity-by-state and population structure analyses revealed a unique set of 1536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, a density of 1300–4700 SNP markers were selected for large-effect quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity $$({H}_{o})$$ ( H o ) , effective population size estimate $$\widehat{{(N}_{e}}$$ ( N e ^ ) and polymorphism information content (PIC). Selection footprints and introgressions of M. glaziovii were detected. Spatial population structure analysis revealed five ancestral populations related to distinct Brazilian ecoregions. Estimation of historical relationships among identified populations suggests an early population split from Amazonian to Atlantic forest and Caatinga ecoregions and active gene flows. This study provides a thorough genetic characterization of ex situ germplasm resources from cassava’s center of origin, South America, with results shedding light on Brazilian cassava characteristics and its biogeographical landscape. These findings support and facilitate the use of genetic resources in modern breeding programs including implementation of association mapping and genomic selection strategies.

scholarly journals Low genetic diversity in the endangered Taxus yunnanensis following a population bottleneck, a low effective population size and increased inbreeding

2016 ◽  
Vol 65 (1) ◽  
pp. 59-66 ◽  
Author(s):  
Y. C. Miao ◽  
Z. J. Zhang ◽  
J. R. Su
Keyword(s):  
Genetic Diversity ◽  
Habitat Fragmentation ◽  
Population Size ◽  
Effective Population Size ◽  
Spatial Genetic Structure ◽  
Population Bottleneck ◽  
Effective Population ◽  
Taxus Yunnanensis ◽  
Low Genetic Diversity ◽  
Two Populations

Abstract Taxus yunnanensis, which is an endangered tree that is considered valuable because it contains the effective natural anticancer metabolite taxol and heteropolysaccharides, has long suffered from severe habitat fragmentation. In this study, the levels of genetic diversity in two populations of 136 individuals were analyzed based on eleven polymorphic microsatellite loci. Our results suggested that these two populations were characterized by low genetic diversity (NE = 2.303/2.557; HO = 0.168/0.142; HE = 0.453/0.517), a population bottleneck, a low effective population size (Ne = 7/9), a high level of inbreeding (FIS = 0.596/0.702), and a weak, but significant spatial genetic structure (Sp = 0.001, b = −0.001*). Habitat fragmentation, seed shadow overlap and limited seed and pollen dispersal and potential selfing may have contributed to the observed gene tic structure. The results of the present study will enable development of practical conservation measures to effectively conserve the valuable genetic resources of this endangered plant.

scholarly journals Legacy of draught cattle breeds of South India: Insights into population structure, genetic admixture and maternal origin

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0246497
Author(s):  
Vandana Manomohan ◽  
Ramasamy Saravanan ◽  
Rudolf Pichler ◽  
Nagarajan Murali ◽  
Karuppusamy Sivakumar ◽  
...  
Keyword(s):  
Population Structure ◽  
Population Size ◽  
Effective Population Size ◽  
South India ◽  
Genetic Admixture ◽  
Zebu Cattle ◽  
Effective Population ◽  
Cattle Breeds ◽  
South Indian ◽  
Indian Cattle

The present study is the first comprehensive report on diversity, population structure, genetic admixture and mitochondrial DNA variation in South Indian draught type zebu cattle. The diversity of South Indian cattle was moderately high. A significantly strong negative correlation coefficient of -0.674 (P<0.05) was observed between the effective population size of different breeds and their estimated FIS. The genetic structure analysis revealed the distinctness of Kangayam, Vechur and Punganur cattle from the rest of the zebu breeds. The results showed the influence of Hallikar breed in the development of most Mysore type cattle breeds of South India with the exception of Kangayam. Bayesian clustering analysis was performed to assess the taurine admixture in South Indian zebu cattle using purebred Jersey and Holstein-Friesian as reference genotypes. Relatively high levels of taurine admixture (>6.25%) was observed in Punganur, Vechur, Umblachery and Pulikulam cattle breeds. Two major maternal haplogroups, I1 and I2, typical of zebu cattle were observed, with the former being predominant than the later. The pairwise differences among the I2 haplotypes of South Indian cattle were relatively higher than West Indian (Indus valley site) zebu cattle. The results indicated the need for additional sampling and comprehensive analysis of mtDNA control region variations to unravel the probable location of origin and domestication of I2 zebu lineage. The present study also revealed major concerns on South Indian zebu cattle (i) risk of endangerment due to small effective population size and high rate of inbreeding (ii) lack of sufficient purebred zebu bulls for breeding and (iii) increasing level of taurine admixture in zebu cattle. Availability of purebred semen for artificial insemination, incorporation of genomic/molecular information to identify purebred animals and increased awareness among farmers will help to maintain breed purity, conserve and improve these important draught cattle germplasms of South India.

scholarly journals Female philopatry and limited male-biased dispersal in the Ussuri tube-nosed bat, Murina ussuriensis

2016 ◽  
Vol 97 (2) ◽  
pp. 545-553 ◽  
Author(s):  
Jon Flanders ◽  
Miho Inoue-Murayama ◽  
Stephen J. Rossiter ◽  
David A. Hill
Keyword(s):  
Temperate Forest ◽  
Spatial Clustering ◽  
Social Groups ◽  
Movement Ecology ◽  
Female Philopatry ◽  
Sampling Locations ◽  
Behavioral Variables ◽  
D Loop ◽  
Nuclear Microsatellite ◽  
Forest Habitats

Abstract Male-biased dispersal and female philopatry are common traits among social mammals, often leading to elevated relatedness within social groups. However, exceptions do occur, with documented cases of female-biased dispersal, dispersal by both sexes, and philopatry of both sexes. In this study, we examined levels of dispersal and relatedness based on analyses of the mitochondrial D-loop and 12 nuclear microsatellite markers in the woodland specialist Ussuri tube-nosed bat ( Murina ussuriensis ), a relatively widespread, yet locally rare species that is thought to be threatened by loss of its forest habitats across its range. A total of 85 individuals were captured in lowland temperate forest on the island of Yakushima and 28 individuals in montane forest in Hokkaido, Japan. In the former, haplotypes showed extreme spatial clustering among females consistent with strong philopatry, but spatial mixing among males suggesting dispersal over short distances. These findings were broadly supported by microsatellite analyses, which indicated considerable genealogical structure within sampling locations but a lack of spatial structure, again indicating that some gene flow does occur in one or both sexes. The Hokkaido data, although limited, did not show these patterns and instead suggest that differences in environmental and behavioral variables may influence movement ecology of individuals at these 2 sites and consequently fine-scale genetic structure within this species.

scholarly journals Identification of a Natural Hybrid between Castanopsis sclerophylla and Castanopsis tibetana (Fagaceae) Based on Chloroplast and Nuclear DNA Sequences

Forests ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 873
Author(s):  
Xiaorong Zeng ◽  
Risheng Chen ◽  
Yunxin Bian ◽  
Xinsheng Qin ◽  
Zhuoxin Zhang ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Nuclear Dna ◽  
Genetic Admixture ◽  
Natural Hybrid ◽  
Hybrid Species ◽  
Chloroplast Haplotype ◽  
Flora Of China ◽  
Nuclear Microsatellite ◽  
Chloroplast Dna Sequences ◽  
Genetic Pools

Castanopsis × kuchugouzhui Huang et Y. T. Chang was recorded in Flora Reipublicae Popularis Sinicae (FRPS) as a hybrid species on Yuelushan mountain, but it is treated as a hybrid between Castanopsis sclerophylla (Lindl.) Schott. and Castanopsis tibetana Hance in Flora of China. After a thorough investigation on Yuelushan mountain, we found a population of C. sclerophylla and one individual of C. × kuchugouzhui, but no living individual of C. tibetana. We collected C. × kuchugouzhui, and we sampled 42 individuals of C. sclerophylla from Yuelushan and Xiushui and 43 individuals of C. tibetana from Liangyeshan and Xiushui. We used chloroplast DNA sequences and 29 nuclear microsatellite markers to investigate if C. × kuchugouzhui is a natural hybrid between C. sclerophylla and C. tibetana. The chloroplast haplotype analysis showed that C. × kuchugouzhui shared haplotype H2 with C. sclerophylla on Yuelushan. The STRUCTURE analysis identified two distinct genetic pools that corresponded well to C. sclerophylla and C. tibetana, revealing the genetic admixture of C. × kuchugouzhui. Furthermore, the NewHybrids analysis suggested that C. × kuchugouzhui is an F2 hybrid between C. sclerophylla and C. tibetana. Our results confirm that C. × kuchugouzhui recorded in FRPS is a rare hybrid between C. sclerophylla and C. tibetana.

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