Fine-scale genetic structure of the ringtail (Bassariscus astutus) in a Sky Island mountain range

Abstract Deciphering genetic structure and inferring migration routes of insects with high migratory ability have been challenging, due to weak genetic differentiation and limited resolution offered by traditional genotyping methods. Here, we tested the ability of double digest restriction-site associated DNA sequencing (ddRADseq)-based single nucleotide polymorphisms (SNPs) in revealing the population structure relative to 13 microsatellite markers by using four small brown planthopper populations as subjects. Using ddRADseq, we identified 230,000 RAD loci and 5,535 SNP sites, which were present in at least 80% of individuals across the four populations with a minimum sequencing depth of 10. Our results show that this large SNP panel is more powerful than traditional microsatellite markers in revealing fine-scale population structure among the small brown planthopper populations. In contrast to the mixed population structure suggested by microsatellites, discriminant analysis of principal components (DAPC) of the SNP dataset clearly separated the individuals into four geographic populations. Our results also suggest the DAPC analysis is more powerful than the principal component analysis (PCA) in resolving population genetic structure of high migratory taxa, probably due to the advantages of DAPC in using more genetic variation and the discriminant analysis function. Together, these results point to ddRADseq being a promising approach for population genetic and migration studies of small brown planthopper.

Download Full-text

Fine scale human genetic structure in three regions of Cameroon reveals episodic diversifying selection

Scientific Reports ◽

10.1038/s41598-020-79124-1 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Kevin K. Esoh ◽

Tobias O. Apinjoh ◽

Steven G. Nyanjom ◽

Ambroise Wonkam ◽

Emile R. Chimusa ◽

...

Keyword(s):

Genetic Structure ◽

Ethnic Groups ◽

Genetic Association ◽

Association Studies ◽

Genetic Association Studies ◽

Genomic Region ◽

Sub Saharan Africa ◽

Genome Wide Association Studies ◽

Fine Scale ◽

Sub Saharan

AbstractInferences from genetic association studies rely largely on the definition and description of the underlying populations that highlight their genetic similarities and differences. The clustering of human populations into subgroups (population structure) can significantly confound disease associations. This study investigated the fine-scale genetic structure within Cameroon that may underlie disparities observed with Cameroonian ethnicities in malaria genome-wide association studies in sub-Saharan Africa. Genotype data of 1073 individuals from three regions and three ethnic groups in Cameroon were analyzed using measures of genetic proximity to ascertain fine-scale genetic structure. Model-based clustering revealed distinct ancestral proportions among the Bantu, Semi-Bantu and Foulbe ethnic groups, while haplotype-based coancestry estimation revealed possible longstanding and ongoing sympatric differentiation among individuals of the Foulbe ethnic group, and their Bantu and Semi-Bantu counterparts. A genome scan found strong selection signatures in the HLA gene region, confirming longstanding knowledge of natural selection on this genomic region in African populations following immense disease pressure. Signatures of selection were also observed in the HBB gene cluster, a genomic region known to be under strong balancing selection in sub-Saharan Africa due to its co-evolution with malaria. This study further supports the role of evolution in shaping genomes of Cameroonian populations and reveals fine-scale hierarchical structure among and within Cameroonian ethnicities that may impact genetic association studies in the country.

Download Full-text

Fine‐scale genetic structure reflects limited and coordinated dispersal in the colonial monk parakeet, Myiopsitta monachus

Molecular Ecology ◽

10.1111/mec.15818 ◽

2021 ◽

Author(s):

Francesca S. E. Dawson Pell ◽

Juan Carlos Senar ◽

Daniel W. Franks ◽

Ben J. Hatchwell

Keyword(s):

Genetic Structure ◽

Fine Scale ◽

Monk Parakeet ◽

Myiopsitta Monachus

Download Full-text

Genotyping of Two Mediterranean Trout Populations in Central-Southern Italy for Conservation Purposes Using a Rainbow-Trout-Derived SNP Array

Animals ◽

10.3390/ani11061803 ◽

2021 ◽

Vol 11 (6) ◽

pp. 1803

Author(s):

Valentino Palombo ◽

Elena De Zio ◽

Giovanna Salvatore ◽

Stefano Esposito ◽

Nicolaia Iaffaldano ◽

...

Keyword(s):

Rainbow Trout ◽

Genetic Structure ◽

Fishery Management ◽

Snp Array ◽

Fine Scale ◽

Principal Coordinates Analysis ◽

Data Set ◽

Management Actions ◽

Principal Coordinates ◽

Mediterranean Trout

Mediterranean trout is a freshwater fish of particular interest with economic significance for fishery management, aquaculture and conservation biology. Unfortunately, native trout populations’ abundance is significantly threatened by anthropogenic disturbance. The introduction of commercial hatchery strains for recreation activities has compromised the genetic integrity status of native populations. This work assessed the fine-scale genetic structure of Mediterranean trout in the two main rivers of Molise region (Italy) to support conservation actions. In total, 288 specimens were caught in 28 different sites (14 per basins) and genotyped using the Affymetrix 57 K rainbow-trout-derived SNP array. Population differentiation was analyzed using pairwise weighted FST and overall F-statistic estimated by locus-by-locus analysis of molecular variance. Furthermore, an SNP data set was processed through principal coordinates analysis, discriminant analysis of principal components and admixture Bayesian clustering analysis. Firstly, our results demonstrated that rainbow trout SNP array can be successfully used for Mediterranean trout genotyping. In fact, despite an overwhelming number of loci that resulted as monomorphic in our populations, it must be emphasized that the resulted number of polymorphic loci (i.e., ~900 SNPs) has been sufficient to reveal a fine-scale genetic structure in the investigated populations, which is useful in supporting conservation and management actions. In particular, our findings allowed us to select candidate sites for the collection of adults, needed for the production of genetically pure juvenile trout, and sites to carry out the eradication of alien trout and successive re-introduction of native trout.

Download Full-text

Distinctions in Fine-Scale Spatial Genetic Structure Between Growth Stages of Picea jezoensis Carr.

Frontiers in Genetics ◽

10.3389/fgene.2018.00490 ◽

2018 ◽

Vol 9 ◽

Cited By ~ 3

Author(s):

Keiko Kitamura ◽

Atsushi Nakanishi ◽

Chunlan Lian ◽

Susumu Goto

Keyword(s):

Genetic Structure ◽

Spatial Genetic Structure ◽

Growth Stages ◽

Fine Scale ◽

Picea Jezoensis

Download Full-text

Stirred but not shaken: population and recruitment genetics of the scallop (Pecten fumatus) in Bass Strait, Australia

ICES Journal of Marine Science ◽

10.1093/icesjms/fsw068 ◽

2016 ◽

Vol 73 (9) ◽

pp. 2333-2341 ◽

Cited By ~ 2

Author(s):

Jennifer R. Ovenden ◽

Bree J. Tillett ◽

Michael Macbeth ◽

Damien Broderick ◽

Fiona Filardo ◽

...

Keyword(s):

Genetic Structure ◽

Population Genetic Structure ◽

Population Genetic ◽

Allelic Variation ◽

Open Water ◽

Marine Species ◽

Population Connectivity ◽

Valuable Insight ◽

Fine Scale ◽

Scale Population

Abstract We report population genetic structure and fine-scale recruitment processes for the scallop beds (Pecten fumatus) in Bass Strait and the eastern coastline of Tasmania in southern Australia. Conventional population pairwise FST analyses are compared with novel discriminant analysis of principal components (DAPC) to assess population genetic structure using allelic variation in 11 microsatellite loci. Fine-scale population connectivity was compared with oceanic features of the sampled area. Disjunct scallop beds were genetically distinct, but there was little population genetic structure between beds connected by tides and oceanic currents. To identify recruitment patterns among and within beds, pedigree analyses determined the distribution of parent–offspring and sibling relationships in the sampled populations. Beds in northeastern Bass Strait were genetically distinct to adjacent beds (FST 0.003–0.005) and may not contribute to wider recruitment based on biophysical models of larval movement. Unfortunately, pedigree analyses lacked power to further dissect fine-scale recruitment processes including self-recruitment. Our results support the management of disjunct populations as separate stocks and the protection of source populations among open water beds. The application of DAPC and parentage analyses in the current study provided valuable insight into their potential power to determine population connectivity in marine species with larval dispersal.

Download Full-text