Regional population structuring and conservation units in the platypus (Ornithorhynchus anatinus)

2013 ◽  
Vol 61 (5) ◽  
pp. 378 ◽  
Author(s):  
Stephen H. Kolomyjec ◽  
Tom R. Grant ◽  
Christopher N. Johnson ◽  
David Blair
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Large Scale ◽  
Wide Distribution ◽  
Conservation Units ◽  
Genetic Structuring ◽  
The North ◽  
Contemporary Gene Flow ◽  
Ornithorhynchus Anatinus ◽  
Southern Island

The platypus (Ornithorhynchus anatinus) has a wide distribution in Australia, encompassing the southern island of Tasmania and a broad latitudinal range of the mainland from the temperate south to the tropical north. We used 12 microsatellite markers from 235 individuals sampled from 13 river systems to examine patterns of genetic differentiation and gene flow throughout the species’ range. Using a Bayesian approach we identified three large-scale groupings that correspond closely to geographically distinct regions of the species’ distribution: the tropical northern mainland, the subtropical and temperate southern mainland, and Tasmania. Six additional clusters were found within the regional groups, three in the northern, two in the southern mainland regions, and the last in Tasmania. These clusters coincided with major river drainages. Genetic differentiation was generally high, with pairwise Fst values ranging from 0.065 to 0.368 for regions and 0.037 to 0.479 for clusters. We found no evidence of contemporary gene flow among the three clusters in the north, but some migration may occur between the larger clusters in the south. Due to the high genetic structuring and lack of gene flow between these three regional populations of the platypus we recommend their treatment as evolutionarily significant units (ESUs) within the platypus species. We have also detailed several smaller management units (MUs) existing within our study area based on subregional clusters and geographically significant features.

scholarly journals Large-scale geographic survey provides insights into the colonization history of a major aphid pest on its cultivated apple host in Europe, North America and North Africa

2020 ◽  
Author(s):  
S.G. Olvera-Vazquez ◽  
C. Remoue ◽  
A. Venon ◽  
A. Rousselet ◽  
O. Grandcolas ◽  
...  
Keyword(s):  
Gene Flow ◽  
North America ◽  
Genetic Differentiation ◽  
North Africa ◽  
Large Scale ◽  
Demographic History ◽  
High Genetic Diversity ◽  
The North ◽  
The Us ◽  
History Of

With frequent host shifts involving the colonization of new hosts across large geographical ranges, crop pests are good models for examining the mechanisms of rapid colonization. The microbial partners of pest insects may be involved or affected by colonization, which has been little studied so far. We investigated the demographic history of the rosy apple aphid, Dysaphis plantaginea, a major pest of the cultivated apple (Malus domestica) in Europe, North Africa and North America, as well as the diversity of its endosymbiotic bacterial community. We genotyped a comprehensive sample of 714 colonies from Europe, Morocco and the US using mitochondrial (CytB and CO1), bacterial (16s rRNA and TrnpB), and 30 microsatellite markers. We detected five populations spread across the US, Morocco, Western and Eastern Europe, and Spain. Populations showed weak genetic differentiation and high genetic diversity, except the Moroccan and the North American that are likely the result of recent colonization events. Coalescent-based inferences releaved high levels of gene flow among populations during the colonization, but did not allow determining the sequence of colonization of Europe, America and Morroco by D. plantaginea, likely because of the weak genetic differentiation and the occurrence of gene flow among populations. Finally, we found that D. plantaginea rarely hosts any other endosymbiotic bacteria than its obligate nutritional symbiont Buchnera aphidicola. This suggests that secondary endosymbionts did not play any role in the rapid spread of the rosy apple aphid. These findings have fundamental importance for understanding pest colonization processes and implications for sustainable pest control programs.

Contemporary gene flow and weak genetic structuring in Rococo toad (Rhinella schneideri) populations in habitats fragmented by agricultural activities

2011 ◽  
Vol 32 (3) ◽  
pp. 399-411 ◽  
Author(s):  
Artur Silva ◽  
Evonnildo C. Gonçalves ◽  
Eliana Morielle-Versute ◽  
Maurício P. Arruda ◽  
Maria Paula C. Schneider
Keyword(s):  
Gene Flow ◽  
Isolation By Distance ◽  
Agricultural Practices ◽  
Genetic Structuring ◽  
Genetic Stock ◽  
Homogeneous Population ◽  
The North ◽  
Contemporary Gene Flow ◽  
Rhinella Schneideri ◽  
Two Populations

AbstractThe reduced vagility and philopatric behaviour of most amphibians make them especially vulnerable to the effects of habitat fragmentation, in particular the loss of genetic variation. However, almost no data are available on the effects of agricultural practices on populations of Neotropical amphibians. Here, the genetic diversity of Rococo toad (Rhinella schneideri) populations in the highly disturbed landscape of the north-western region of the Brazilian state of São Paulo was analysed using microsatellite markers. Two areas were sampled – one dominated by open pastures (four populations) and the other by sugar cane plantations (two populations) – in an attempt to evaluate the possible influence of the type of anthropogenic matrix on genetic variability and gene flow (dispersion). The populations presented a relatively uniform genetic stock, with low levels of inbreeding (Fis) and high levels of admixture between localities (Fst, Rst, STRUCTURE) indicating no genetic subdivision. The results indicated relatively high levels of recent migration among sites (m) and no isolation by distance. The analyses also found that historical and contemporary rates of migration among populations were broadly similar. Overall, then, neither type of matrix appeared to have an effect on the connectivity of the Rococo toad populations. This suggests that the species has a considerable capacity for dispersal, allowing it to maintain a relatively homogeneous population, even under intense human pressure.

scholarly journals Genome-wide SNPs redefines species boundaries and conservation units in the freshwater mussel genus Cyprogenia of North America

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kyung Seok Kim ◽  
Kevin J. Roe
Keyword(s):  
Phylogenetic Analyses ◽  
Freshwater Mussel ◽  
Conservation Strategies ◽  
Nucleotide Polymorphisms ◽  
Conservation Units ◽  
Genetic Structuring ◽  
The North ◽  
Snp Data ◽  
Genome Wide ◽  
Significant Difference

AbstractDetailed information on species delineation and population genetic structure is a prerequisite for designing effective restoration and conservation strategies for imperiled organisms. Phylogenomic and population genomic analyses based on genome-wide double digest restriction-site associated DNA sequencing (ddRAD-Seq) data has identified three allopatric lineages in the North American freshwater mussel genus Cyprogenia. Cyprogenia stegaria is restricted to the Eastern Highlands and displays little genetic structuring within this region. However, two allopatric lineages of C. aberti in the Ozark and Ouachita highlands exhibit substantial levels (mean uncorrected FST = 0.368) of genetic differentiation and each warrants recognition as a distinct evolutionary lineage. Lineages of Cyprogenia in the Ouachita and Ozark highlands are further subdivided reflecting structuring at the level of river systems. Species tree inference and species delimitation in a Bayesian framework using single nucleotide polymorphisms (SNP) data supported results from phylogenetic analyses, and supports three species of Cyprogenia over the currently recognized two species. A comparison of SNPs generated from both destructively and non-destructively collected samples revealed no significant difference in the SNP error rate, quality and amount of ddRAD sequence reads, indicating that nondestructive or trace samples can be effectively utilized to generate SNP data for organisms for which destructive sampling is not permitted.

scholarly journals Landscape, colonization, and life history: their effects on genetic diversity in four sympatric species inhabiting a dendritic system

2019 ◽  
Vol 76 (12) ◽  
pp. 2288-2302 ◽  
Author(s):  
Daniel E. Ruzzante ◽  
Gregory R. McCracken ◽  
Sarah J. Salisbury ◽  
Hilary T. Brewis ◽  
Donald Keefe ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Lake Trout ◽  
Sympatric Species ◽  
Genetic Structuring ◽  
Colonization History ◽  
Diversity Patterns ◽  
Contemporary Gene Flow ◽  
Approximate Bayesian ◽  
Longnose Sucker

To what degree are patterns of genetic structure in fragmented systems the result of contemporary landscape versus history? We examined the distribution of genetic diversity as a function of colonization history and contemporary landscape in four fish species inhabiting a hierarchically fragmented, unaltered system, the Kogaluk drainage (Labrador): lake trout (Salvelinus namaycush), longnose sucker (Catostomus catostomus), round whitefish (Prosopium cylindraceum), and lake chub (Couesius plumbeus). The footprint of colonization history was still observable in the three species where this issue was examined regardless of the generations since their arrival. Approximate Bayesian computation (ABC) analyses suggest colonization took place from the southwest. The species exhibit similar diversity patterns despite different [Formula: see text] values and generation intervals. Contemporary gene flow was largely negligible except for gene flow from a centrally located lake. These results suggest landscape has driven colonization history, which still has influence on genetic structuring. The species are widespread. Understanding how they behave in the pristine Kogaluk provides a baseline against which to evaluate how other anthropogenically perturbed systems are performing. Improved understanding of historical and contemporary processes is required to fully explain diversity patterns in complex metapopulations.

scholarly journals Genetic Consequences of Forest Fragmentation in a Widespread Forest Bat (Natalus mexicanus, Chiroptera: Natalidae)

Diversity ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 140
Author(s):  
Ricardo López-Wilchis ◽  
Aline Méndez-Rodríguez ◽  
Javier Juste ◽  
Alejandra Serrato-Díaz ◽  
Flor Rodríguez-Gómez ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Habitat Fragmentation ◽  
Natural Habitat ◽  
Mitochondrial Control Region ◽  
Genetic Structuring ◽  
Forest Connectivity ◽  
Contemporary Gene Flow ◽  
Multiple Species ◽  
Genetic Structure And Diversity

Recent historical and anthropogenic changes in the landscape causing habitat fragmentation can disrupt the connectivity of wild populations and pose a threat to the genetic diversity of multiple species. This study investigated the effect of habitat fragmentation on the structure and genetic diversity of the Mexican greater funnel-eared bat (Natalus mexicanus) throughout its distribution range in Mexico, whose natural habitat has decreased dramatically in recent years. Genetic structure and diversity were measured using the HVII hypervariable domain of the mitochondrial control region and ten nuclear microsatellite loci, to analyze historical and contemporary information, respectively. The mitochondrial and nuclear results pointed to a differential genetic structuring, derived mainly from philopatry in females. Our results also showed that genetic diversity was historically high and currently moderate; additionally, the contemporary gene flow between the groups observed was null. These findings confirm that the effects of habitat fragmentation have started to be expressed in populations and that forest loss is already building barriers to contemporary gene flow. The concern is that gene flow is a process essential to ensure that the genetic diversity of N. mexicanus populations (and probably of many other forest species) distributed in Mexico is preserved or increased in the long term by maintaining forest connectivity between locations.

scholarly journals High-Level Gene Flow Restricts Genetic Differentiation in Dairy Cattle Populations in Thailand: Insights from Large-Scale Mt D-Loop Sequencing

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1680
Author(s):  
Nattakan Ariyaraphong ◽  
Nararat Laopichienpong ◽  
Worapong Singchat ◽  
Thitipong Panthum ◽  
Syed Farhan Ahmad ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Dairy Cattle ◽  
Large Scale ◽  
Genetic Relationships ◽  
Extensive Study ◽  
Distribution Analysis ◽  
Cattle Breeds ◽  
D Loop

Domestication and artificial selection lead to the development of genetically divergent cattle breeds or hybrids that exhibit specific patterns of genetic diversity and population structure. Recently developed mitochondrial markers have allowed investigation of cattle diversity worldwide; however, an extensive study on the population-level genetic diversity and demography of dairy cattle in Thailand is still needed. Mitochondrial D-loop sequences were obtained from 179 individuals (hybrids of Bos taurus and B. indicus) sampled from nine different provinces. Fifty-one haplotypes, of which most were classified in haplogroup “I”, were found across all nine populations. All sampled populations showed severely reduced degrees of genetic differentiation, and low nucleotide diversity was observed in populations from central Thailand. Populations that originated from adjacent geographical areas tended to show high gene flow, as revealed by patterns of weak network structuring. Mismatch distribution analysis was suggestive of a stable population, with the recent occurrence of a slight expansion event. The results provide insights into the origins and the genetic relationships among local Thai cattle breeds and will be useful for guiding management of cattle breeding in Thailand.

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

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

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

scholarly journals Genetic Diversity and Population Structure in the Ryukyu Flying Fox Inferred from Remote Sampling in the Yaeyama Archipelago

2020 ◽  
Author(s):  
Yuto Taki ◽  
Christian E. Vincenot ◽  
Yu Sato ◽  
Miho Inoue-Murayama
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Haplotype Network ◽  
Iucn Red List ◽  
The Philippines ◽  
Conservation Units ◽  
Long Distance ◽  
Flying Fox

AbstractThe Ryukyu flying fox (Pteropus dasymallus) is distributed throughout the island chain spanning across southern Japan, Taiwan, and possibly the Philippines. Although P. dasymallus is listed as VU (vulnerable) in the IUCN Red List, only few genetic works have been conducted to support its conservation. In this study we analyzed 19 markers (mtDNA haplotypes and 18 microsatellite markers) to evaluate genetic diversity and investigate the genetic structure of this species.mtDNA analysis was conducted with 142 DNA remote samples, mostly from feces, and wing tissues collected on eight islands (Miyako, Ishigaki, Kohama, Kuroshima, Hateruma, Taketomi, Iriomote, Yonaguni). 39 haplotypes were identified in 526bp of the control region, and haplotype network showed no clear genetic structure.Microsatellite analysis was also conducted with 155 samples collected on six islands (Miyako, Ishigaki, Kohama, Taketomi, Iriomote, Yonaguni). It showed that the Yonaguni population exhibits low genetic diversity, high inbreeding, and clear genetic differentiation from other populations. Gene flow between Ishigaki and Miyako through small stepstone islands might be preventing inbreeding of the Miyako population.We provide for the first time indirect proof of long-distance inter-island dispersal in the Ryukyu flying fox and revealed genetic diversity, gene flow and genetic differentiation among populations of the archipelago. These results will be useful for delineating conservation units and designing specific conservation policies for each island based on metapopulation genetic structure.

Review of the genetics, dispersal and recruitment of crown-of-thorns starfish (Acanthaster planci)

1992 ◽  
Vol 43 (3) ◽  
pp. 597 ◽  
Author(s):  
JAH Benzie
Keyword(s):  
Gene Flow ◽  
Indian Ocean ◽  
Genetic Differentiation ◽  
Primary Source ◽  
Acanthaster Planci ◽  
Genetic Structuring ◽  
West Pacific ◽  
North West ◽  
The Pacific ◽  
Western Australian

The lack of genetic structuring reported for Acanthaster planci (L.) from major biogeographical zones (i.e. Indian Ocean versus Pacific) may reflect a lack of data rather than confirmation of a recent and rapid dispersal of the species worldwide. The low level of genetic variation among A. planci populations throughout the Pacific is evidence of high levels of gene flow throughout this region. However, gene flow among widely separated reef complexes (average number of migrants per generation, N/em, approximately 2) is an order of magnitude less than that occurring within highly connected reef systems like the Ryukyus and the Great Barrier Reef (GBR) (Nem approximately 20). The genetic similarity between North-west Pacific and Australian populations is likely to reflect gene flow to each place from the central Indo-West Pacific region. Populations peripheral to the species' main distribution show greater genetic differentiation, probably as a result of founder effect. Some, like the Hawaiian and western Australian populations, show reduced genetic diversity, implying colonization by a very small number of individuals or a recent severe bottleneck in population size. Western Australian populations appear to have been derived from eastern Australian populations in the Pacific rather than Indian Ocean sources. On the GBR, genetic differentiation is low among populations that are undergoing outbreaks but there is significant differentiation among populations that are not involved in outbreaks; this suggests that a single primary source is the origin of outbreaks on the GBR. The development of distinctive DNA markers may also allow the detailed tracking of dispersal routes of A. planci and of recruitment within reefs.

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