reduced representation sequencing
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Author(s):  
Brandon T. Sinn ◽  
Sandra J. Simon ◽  
Mathilda V. Santee ◽  
Stephen P. DiFazio ◽  
Nicole M. Fama ◽  
...  

2021 ◽  
Author(s):  
Matt J. Thorstensen ◽  
Peter T. Euclide ◽  
Jennifer D. Jeffrey ◽  
Yue Shi ◽  
Jason R. Treberg ◽  
...  

AbstractGenomic architecture, such as chromosomal inversions, may play an important role in facilitating adaptation despite opportunities for gene flow. One system where chromosomal inversions may be important for eco-evolutionary dynamics are in freshwater fish, which often live in heterogenous environments characterized by varying levels of connectivity and varying opportunities for gene flow. In the present study, reduced representation sequencing was used to study possible adaptation in n=345 walleye (Sander vitreus) from three North American waterbodies: Cedar Bluff Reservoir (Kansas, USA), Lake Manitoba (Manitoba, Canada), and Lake Winnipeg (Manitoba, Canada). Haplotype and outlier-based tests revealed a putative chromosomal inversion that contained three expressed genes and was nearly fixed for alternate genotypes in each Canadian lake. These patterns exist despite several opportunities for gene flow between these proximate Canadian lakes, suggesting that the inversion may be important for facilitating adaptative divergence between the two lakes despite gene flow. Our study illuminates the importance of genomic architecture for facilitating local adaptation in freshwater fish and provides additional evidence that inversions may facilitate local adaptation in many organisms that inhabit connected but heterogenous environments.


BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Henrik Christiansen ◽  
Franz M. Heindler ◽  
Bart Hellemans ◽  
Quentin Jossart ◽  
Francesca Pasotti ◽  
...  

Abstract Background Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS. Results In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA. Conclusions Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.


2021 ◽  
Author(s):  
Lionel N Di Santo ◽  
Sean Hoban ◽  
Thomas L Parchman ◽  
Jessica W Wright ◽  
Jill A Hamilton

Understanding the contribution of neutral and adaptive evolutionary processes to population differences is often necessary for better informed management and conservation of rare species. In this study, we focused on Pinus torreyana Parry (Torrey pine), one of the world's rarest pines, endemic to one island and one mainland population in California. Small population size, low genetic diversity, and susceptibility to abiotic and biotic stresses suggest Torrey pine may benefit from inter-population genetic rescue to preserve the species' evolutionary potential. We leveraged reduced representation sequencing to tease apart the respective contributions of stochastic and deterministic evolutionary processes to population differentiation. We applied these data to model spatial and temporal demographic changes in effective population sizes and genetic connectivity, to assess loci possibly under selection, and evaluate genetic rescue as a potential conservation strategy. Overall, we observed exceedingly low standing variation reflecting consistently low effective population sizes across time and limited genetic differentiation suggesting maintenance of gene flow following divergence. However, genome scans identified more than 2000 SNPs candidates for divergent selection. Combined with previous observations indicating population phenotypic differentiation, this indicates that natural selection has likely contributed to population genetic differences. Thus, while reduced genetic diversity, small effective population size, and genetic connectivity between populations suggest genetic rescue could mitigate the adverse effect of rarity, divergent selection between populations indicates that genetic mixing could disrupt adaptation. Further work evaluating the fitness consequences of inter-population admixture is necessary to empirically evaluate the trade-offs associated with genetic rescue in Torrey pine.


Forests ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 520
Author(s):  
Heng Liang ◽  
Jiabin Deng ◽  
Gang Gao ◽  
Chunbang Ding ◽  
Li Zhang ◽  
...  

Clarifying the genetic relationship and divergence among Curcuma L. (Zingiberaceae) species around the world is intractable, especially among the species located in China. In this study, Reduced Representation Sequencing (RRS), as one of the next generation sequences, has been applied to infer large scale genotyping of major Chinese Curcuma species which present little differentiation of morphological characteristics and genetic traits. The 1295 high-quality SNPs (reduced-filtered SNPs) were chosen from 997,988 SNPs of which were detected from the cleaned 437,061 loci by RRS to investigate the phylogeny and divergence among eight major Curcuma species locate in the Hengduan Mountains of the Qinghai–Tibet Plateau (QTP) in China. The results showed that all the population individuals were clustered together within species, and species were obviously separated; the clustering results were recovered in PCA (Principal Component Analysis); the phylogeny was (((((C. Phaeocaulis, C. yunnanensis), C. kwangsiensis), (C. amarissima, C. sichuanensis)), C. longa), (C. wenyujin, C. aromatica)); Curcuma in China originated around ~7.45 Mya (Million years ago) in the Miocene, and interspecific divergence appeared at ca. 4–2 Mya, which might be sped up rapidly along with the third intense uplift of QTP.


2021 ◽  
Author(s):  
Henrik Christiansen ◽  
Franz M. Heindler ◽  
Bart Hellemans ◽  
Quentin Jossart ◽  
Francesca Pasotti ◽  
...  

Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS. In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA. Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.


2020 ◽  
Author(s):  
D. Selechnik ◽  
M.F. Richardson ◽  
M.K. Hess ◽  
A.S. Hess ◽  
K.G. Dodds ◽  
...  

AbstractAs technological advancements enhance our ability to study population genetics, we must understand how the intrinsic properties of our datasets influence the decisions we make when designing experiments. Filtering parameter thresholds, such as call rate and minimum minor allele frequency (MAF), are known to affect inferences of population structure in reduced representation sequencing (RRS) studies. However, it is unclear to what extent the impacts of these parameter choices vary across datasets. Here, we reviewed literature on filtering choices and levels of genetic differentiation across RRS studies on wild populations to highlight the diverse approaches that have been used. Next, we hypothesized that choices in filtering thresholds would have the greatest impact when analyzing datasets with low levels of genetic differentiation between populations. To test this hypothesis, we produced seven simulated RRS datasets with varying levels of population structure, and analyzed them using four different combinations of call rate and MAF. We performed the same analysis on two empirical RRS datasets (low or high population structure). Our simulated and empirical results suggest that the effects of filtering choices indeed vary based on inherent levels of differentiation: specifically, choosing stringent filtering choices was important to detect distinct populations that were slightly differentiated, but not those that were highly differentiated. As a result, experimental design and analysis choices need to consider attributes of each specific dataset. Based on our literature review and analyses, we recommend testing a range of filtering parameter choices, and presenting all results with clear justification for ultimate filtering decisions used in downstream analyses.


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