scholarly journals Fine-scale population structure and ecotypes of anadromous Hilsa shad (Tenualosa ilisha) across complex aquatic ecosystems revealed by NextRAD genotyping

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Md Asaduzzaman ◽  
Md A. Wahab ◽  
Md J. Rahman ◽  
Md Nahiduzzzaman ◽  
Malcom W. Dickson ◽  
...  
Keyword(s):  
Aquatic Ecosystems ◽  
Population Genomics ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Local Adaptations ◽  
Life History Stages ◽  
Marine Habitats ◽  
Scale Population ◽  
Tenualosa Ilisha ◽  
Conservation And Management

Abstract The anadromous Hilsa shad (Tenualosa ilisha) live in the Bay of Bengal and migrate to the estuaries and freshwater rivers for spawning and nursing of the juveniles. This has led to two pertinent questions: (i) do all Hilsa shad that migrate from marine to freshwater rivers come from the same population? and (ii) is there any relationship between adults and juveniles of a particular habitat? To address these questions, NextRAD sequencing was applied to genotype 31,276 single nucleotide polymorphism (SNP) loci for 180 individuals collected from six strategic locations of riverine, estuarine and marine habitats. FST OutFLANK approach identified 14,815 SNP loci as putatively neutral and 79 SNP loci as putatively adaptive. We observed that divergent local adaptations in differing environmental habitats have divided Hilsa shad into three genetically structured ecotypes: turbid freshwater (Western Riverine), clear freshwater (Eastern Riverine) and brackish-saline (Southern Estuarine-Marine). Our results also revealed that genes involved in neuronal activity may have facilitated the juveniles’ Hilsa shad in returning to their respective natal rivers for spawning. This study emphasized the application of fundamental population genomics information in strategizing conservation and management of anadromous fish such as Hilsa shad that intersect diverse ecotypes during their life-history stages.

Summer emigration and resource acquisition within a shared nursery lake by sockeye salmon (Oncorhynchus nerka) from historically discrete rearing environments

2013 ◽  
Vol 70 (1) ◽  
pp. 57-63 ◽  
Author(s):  
Ryan K. Simmons ◽  
Thomas P. Quinn ◽  
Lisa W. Seeb ◽  
Daniel E. Schindler ◽  
Ray Hilborn
Keyword(s):  
Sockeye Salmon ◽  
Oncorhynchus Nerka ◽  
Genetic Composition ◽  
Nucleotide Polymorphism ◽  
Sympatric Populations ◽  
Single Nucleotide ◽  
Life History Stages ◽  
Variable Environments ◽  
Rearing Conditions ◽  
And Performance

Many fish species disperse broadly during juvenile life history stages. While this may enable persistence in variable environments, it may also produce novel competitive interactions in recipient habitats that contain conspecifics from other populations. Here we used genetics techniques to study the stock-specific movement and performance of juvenile sockeye salmon (Oncorhynchus nerka) between July and August of 2008 in an ecosystem characterized by extensive juvenile migration and environmental change: the Chignik Lake system, Alaska. Genetic composition of juvenile sockeye salmon in the lower nursery lake based on 45 single nucleotide polymorphism markers indicated that 2008 was characterized by earlier timing and larger magnitude of emigrations from the upper lake, where rearing conditions have become increasingly unstable in recent decades. However, the larger size of emigrants did not confer a clear advantage in foraging based on comparisons of growth and body condition with juveniles native to the lower lake. These results highlight how shifting environmental conditions may exert pressures on evolved behavior patterns and increase interactions between sympatric populations, a theme of increasing importance where ecological uncertainty is high.

scholarly journals DiscoSnp-RAD: de novo detection of small variants for RAD-Seq population genomics

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9291
Author(s):  
Jérémy Gauthier ◽  
Charlotte Mouden ◽  
Tomasz Suchan ◽  
Nadir Alvarez ◽  
Nils Arrigo ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
Restriction Site ◽  
Population Genomics ◽  
De Novo ◽  
State Of The Art ◽  
Phylogenetic Reconstruction ◽  
Original Method ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Require Time

Restriction site Associated DNA Sequencing (RAD-Seq) is a technique characterized by the sequencing of specific loci along the genome that is widely employed in the field of evolutionary biology since it allows to exploit variants (mainly Single Nucleotide Polymorphism—SNPs) information from entire populations at a reduced cost. Common RAD dedicated tools, such as STACKS or IPyRAD, are based on all-vs-all read alignments, which require consequent time and computing resources. We present an original method, DiscoSnp-RAD, that avoids this pitfall since variants are detected by exploiting specific parts of the assembly graph built from the reads, hence preventing all-vs-all read alignments. We tested the implementation on simulated datasets of increasing size, up to 1,000 samples, and on real RAD-Seq data from 259 specimens of Chiastocheta flies, morphologically assigned to seven species. All individuals were successfully assigned to their species using both STRUCTURE and Maximum Likelihood phylogenetic reconstruction. Moreover, identified variants succeeded to reveal a within-species genetic structure linked to the geographic distribution. Furthermore, our results show that DiscoSnp-RAD is significantly faster than state-of-the-art tools. The overall results show that DiscoSnp-RAD is suitable to identify variants from RAD-Seq data, it does not require time-consuming parameterization steps and it stands out from other tools due to its completely different principle, making it substantially faster, in particular on large datasets.

Evidence for a large-scale population structure of Arabidopsis thaliana from genome-wide single nucleotide polymorphism markers

2006 ◽  
Vol 112 (6) ◽  
pp. 1104-1114 ◽  
Author(s):  
Karl J. Schmid ◽  
Ottó Törjék ◽  
Rhonda Meyer ◽  
Heike Schmuths ◽  
Matthias H. Hoffmann ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Single Nucleotide Polymorphism ◽  
Population Structure ◽  
Large Scale ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Scale Population

UTILIZATION OF DNA MARKERS FOR EVALUATING AMYLOSE CONTENT OF GRAIN IN RICE

2013 ◽  
Vol 83 (5) ◽  
Author(s):  
Dương Thanh Thủy ◽  
Taiichiro Ookawa
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Amylose Content ◽  
Waxy Gene ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Branching Enzymes ◽  
Wx Gene ◽  
High Amylose ◽  
Suitable Marker ◽  
Granule Bound Starch Synthase

The sensory and functional properties of rice are predominantly associated with its amylose content. Granule-bound starch synthase (GBSS) encoded by the Waxy (Wx) gene determines the synthesis of amylose, while starch branching enzymes encoded by Sbe genes are involved in the formation of amylopectin. Some studies have demonstrated that Wx gene is the major controller of amylose content but there are one or more modifying genes affecting the amylose content. Three markers,  microsatellite, Single – nucleotide – polymorphism (G/T SNP) in Wx gene and Single – nucleotide – polymorphism (T/C SNP) in Sbe1 gene, were tested for their association with amylose content using sixty-nine  rice accessions from twenty countries. Of the three markers, two markers in Wx gene are significantly associated with amylose content. The combination of two markers in Wx gene (haplotypes) explained 83.8% of the variation in amylose content and discriminated the three market classes of glutinous, low, intermediate and high amylose content of rice from each other. And T/C SNP in Sbe1 locus was not a suitable marker for amylose content. Keywords: marker, amylose content, Waxy gene.

Sign in / Sign up

Export Citation Format

Share Document