scholarly journals A Biogeographic Barrier Test Reveals a Strong Genetic Structure for a Canopy-Emergent Amazon Tree Species

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Alison G. Nazareno ◽  
Christopher W. Dick ◽  
Lúcia G. Lohmann
Keyword(s):  
Genetic Structure ◽  
Life Histories ◽  
Genomic Data ◽  
Snp Markers ◽  
Genetic Barrier ◽  
Future Studies ◽  
Population Genomic ◽  
Rio Negro ◽  
Flooded Forests ◽  
Biogeographic Barrier

AbstractWallace’s (1854) Riverine Barrier hypothesis is one of the earliest explanations for Amazon biotic diversification. Despite the importance of this hypothesis for explaining speciation in some animal groups, it has not been studied extensively for plant species. In this study we use a prominent Amazon tree, Buchenavia oxycarpa (Mart.) Eichler (Combretaceae), to evaluate Wallace’s hypothesis along the Rio Negro, a major Amazon tributary that has driven allopatric speciation for several animal taxa. We sampled six individuals from sixteen localities along both river banks, and used a modified ddRADseq protocol to identify SNP markers. Our population genomic data revealed strong genetic structure for B. oxycarpa sampled across banks of the Rio Negro (ϕCT = 0.576, P < 0.001), supporting the hypothesis that the Rio Negro acted as a significant genetic barrier for B. oxycarpa. Our study shows that gene flow for this large and well-dispersed Amazon tree is impeded by riverine barriers, though this has not yet resulted in speciation. Future studies focused on species with different life histories, including species restricted to non-flooded forests, are needed to further advance our understanding of Amazon rivers as drivers of biotic diversification.

scholarly journals Genomic data reveal similar genetic differentiation in aquifer species with different dispersal capabilities and life histories

2019 ◽  
Vol 129 (2) ◽  
pp. 315-322
Author(s):  
Steve Jordan ◽  
Brian K Hand ◽  
Scott Hotaling ◽  
Amanda G Delvecchia ◽  
Rachel Malison ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Genetic Differentiation ◽  
Life Histories ◽  
Genomic Structure ◽  
Life Stage ◽  
Shallow Groundwater ◽  
Population Connectivity ◽  
North West ◽  
Population Genomic ◽  
Generation Sequencing

Abstract Little is known about the life histories, genetic structure and population connectivity of shallow groundwater organisms. We used next-generation sequencing (RAD-seq) to analyse population genomic structure in two aquifer species: Paraperla frontalis (Banks, 1902), a stonefly with groundwater larvae and aerial (winged) adults; and Stygobromus sp., a groundwater-obligate amphipod. We found similar genetic differentiation in each species between floodplains separated by ~70 river km in the Flathead River basin of north-west Montana, USA. Given that Stygobromus lacks the above-ground life stage of P. frontalis, our findings suggest that connectivity and the magnitude of genetic structure cannot be definitively assumed from life history differences.

scholarly journals Population genomic data in spider mites point to a role for local adaptation in shaping range shifts

2020 ◽  
Vol 13 (10) ◽  
pp. 2821-2835
Author(s):  
Lei Chen ◽  
Jing‐Tao Sun ◽  
Peng‐Yu Jin ◽  
Ary A. Hoffmann ◽  
Xiao‐Li Bing ◽  
...  
Keyword(s):  
Local Adaptation ◽  
Genomic Data ◽  
Spider Mites ◽  
Range Shifts ◽  
Population Genomic

scholarly journals Use of the flooded forest by fish assemblages in lakes of the National Park of Anavilhanas (Amazonas, Brazil)

2012 ◽  
Vol 42 (4) ◽  
pp. 561-566 ◽  
Author(s):  
Janette Noveras ◽  
Kedma C. Yamamoto ◽  
Carlos E.C. Freitas
Keyword(s):  
Species Diversity ◽  
Correspondence Analysis ◽  
National Park ◽  
Fish Assemblages ◽  
Open Water ◽  
Flooded Forest ◽  
Rio Negro ◽  
Flooded Forests ◽  
Filter Feeders ◽  
Distribution Of Fish

We evaluated diversity and distribution of fish species in two habitats: flooded forest and open water of lakes of Rio Negro. Each of four lakes within the Anavilhanas Archipelago was sampled three times from 2009-2010. Species diversity generally was higher in flooded forests and at night, according to correspondence analysis. Predators were most active at night, but showed no preference between the flooded forest and open water habitats. Omnivores, filter feeders, and detritivores were most active during the day.

scholarly journals Inferring Adaptive Introgression Using Hidden Markov Models

2020 ◽  
Author(s):  
Jesper Svedberg ◽  
Vladimir Shchur ◽  
Solomon Reinman ◽  
Rasmus Nielsen ◽  
Russell Corbett-Detig
Keyword(s):  
Markov Models ◽  
Hidden Markov ◽  
Genomic Data ◽  
Diverse Populations ◽  
Powerful Method ◽  
Adaptive Genetic Variation ◽  
Adaptive Introgression ◽  
Population Genomic ◽  
Significant Interest ◽  
Selection Parameters

AbstractAdaptive introgression - the flow of adaptive genetic variation between species or populations - has attracted significant interest in recent years and it has been implicated in a number of cases of adaptation, from pesticide resistance and immunity, to local adaptation. Despite this, methods for identification of adaptive introgression from population genomic data are lacking. Here, we present Ancestry_HMM-S, a Hidden Markov Model based method for identifying genes undergoing adaptive introgression and quantifying the strength of selection acting on them. Through extensive validation, we show that this method performs well on moderately sized datasets for realistic population and selection parameters. We apply Ancestry_HMM-S to a dataset of an admixed Drosophila melanogaster population from South Africa and we identify 17 loci which show signatures of adaptive introgression, four of which have previously been shown to confer resistance to insecticides. Ancestry_HMM-S provides a powerful method for inferring adaptive introgression in datasets that are typically collected when studying admixed populations. This method will enable powerful insights into the genetic consequences of admixture across diverse populations. Ancestry_HMM-S can be downloaded from https://github.com/jesvedberg/Ancestry_HMM-S/.

scholarly journals Level of Inbreeding in Norik of Muran Horse: Pedigree vs. Genomic Data

2019 ◽  
Vol 67 (6) ◽  
pp. 1457-1463 ◽  
Author(s):  
Radovan Kasarda ◽  
Nina Moravčíková ◽  
Ondrej Kadlečík ◽  
Anna Trakovická ◽  
Marko Halo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Quality Control ◽  
Genomic Analysis ◽  
Genomic Data ◽  
Reference Population ◽  
Pedigree Analysis ◽  
Snp Markers ◽  
Runs Of Homozygosity ◽  
Current Generation ◽  
Genomic Inbreeding

The objective of this study was to analyse the level of pedigree and genomic inbreeding in a herd of the Norik of Muran horses. The pedigree file included 1374 animals (603 stallions and 771 mares), while the reference population consisted of animals that were genotyped by using 70k SNP platform (n = 25). The trend of pedigree inbreeding was expressed as the probability that an animal has two identical alleles by descent according to classical formulas. The trend of genomic inbreeding was derived from the distribution of runs of homozygosity (ROHs) with various length in the genome based on the assumption that these regions reflect the autozygosity originated from past generations of ancestors. A maximum of 19 generations was found in pedigree file. As expected, the highest level of pedigree completeness was found in first five generations. Subsequent quality control of genomic data resulted in totally 54432 SNP markers covering 2.242 Mb of the autosomal genome. The pedigree analysis showed that in current generation can be expected the pedigree inbreeding at level 0.23% (ΔFPEDi = 0.19 ± 1.17%). Comparable results was obtained also by the genomic analysis, when the inbreeding in current generation reached level 0.11%. Thus, in term of genetic diversity both analyses reflected sufficient level of variability across analysed population of Norik of Muran horses.

scholarly journals Estimating Seven Coefficients of Pairwise Relatedness Using Population-Genomic Data

Genetics ◽  
2017 ◽  
Vol 206 (1) ◽  
pp. 105-118 ◽  
Author(s):  
Matthew S. Ackerman ◽  
Parul Johri ◽  
Ken Spitze ◽  
Sen Xu ◽  
Thomas G. Doak ◽  
...  
Keyword(s):  
Genomic Data ◽  
Population Genomic

scholarly journals Diverging Genetic Structure of Coexisting Populations of the Black Storm-Petrel and the Least Storm-Petrel in the Gulf of California

2020 ◽  
Vol 13 ◽  
pp. 194008292094917
Author(s):  
Misael D. Mancilla-Morales ◽  
Santiago Romero-Fernández ◽  
Araceli Contreras-Rodríguez ◽  
José J. Flores-Martínez ◽  
Víctor Sánchez-Cordero ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Population Genetic Structure ◽  
Mate Selection ◽  
Gulf Of California ◽  
Population Genetic ◽  
Life Histories ◽  
Gene Diversity ◽  
Isolation By Distance ◽  
Storm Petrel

Estimations on the influence of evolutionary and ecological forces as drivers of population gene diversity and genetic structure have been performed on a growing number of colonial seabirds, but many remain poorly studied. In particular, the population genetic structure of storm-petrels (Hydrobatidae) has been evaluated in only a few of the 24 recognized species. We assessed the genetic diversity and population structure of the Black Storm-Petrel ( Hydrobates melania) and the Least Storm-Petrel ( Hydrobates microsoma) in the Gulf of California. The two species were selected because they are pelagic seabirds with comparable ecological traits and breeding grounds. Recent threats such as introduced species of predators and human disturbance have resulted in a decline of many insular vertebrate populations in this region and affected many different aspects of their life histories (ranging from reproductive success to mate selection), with a concomitant loss of genetic diversity. To elucidate to what extent the population genetic structure occurs in H. melania and H. microsoma, we used 719 base pairs from the mitochondrial cytochrome oxidase c subunit I gene. The evaluation of their molecular diversity, genetic structure, and gene flow were performed through diversity indices, analyses of molecular and spatial variance, and isolation by distance (IBD) across sampling sites, respectively. The population genetic structure (via AMOVA and SAMOVA) and isolation by distance (pairwise p-distances and FST/1– FST (using ΦST) were inferred for H. microsoma. However, for H. melania evidence was inconclusive. We discuss explanations leading to divergent population genetic structure signatures in these species, and the consequences for their conservation.

scholarly journals Equitable Expanded Carrier Screening Needs Indigenous Clinical and Population Genomic Data

2020 ◽  
Vol 107 (2) ◽  
pp. 175-182
Author(s):  
Simon Easteal ◽  
Ruth M. Arkell ◽  
Renzo F. Balboa ◽  
Shayne A. Bellingham ◽  
Alex D. Brown ◽  
...  
Keyword(s):  
Genomic Data ◽  
Carrier Screening ◽  
Expanded Carrier Screening ◽  
Population Genomic
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