scholarly journals Population Genomics of an Anadromous Hilsa Shad Tenualosa ilisha Species across Its Diverse Migratory Habitats: Discrimination by Fine-Scale Local Adaptation

Genes ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 46
Author(s):  
Md Asaduzzaman ◽  
Yoji Igarashi ◽  
Md Abdul Wahab ◽  
Md Nahiduzzaman ◽  
Md Jalilur Rahman ◽  
...  
Keyword(s):  
Local Adaptation ◽  
Genetic Divergence ◽  
Population Genomics ◽  
Large Population ◽  
Anadromous Fish ◽  
Fine Scale ◽  
Genetic Cluster ◽  
The North ◽  
Tenualosa Ilisha ◽  
Collection Sites

The migration of anadromous fish in heterogenic environments unceasingly imposes a selective pressure that results in genetic variation for local adaptation. However, discrimination of anadromous fish populations by fine-scale local adaptation is challenging because of their high rate of gene flow, highly connected divergent population, and large population size. Recent advances in next-generation sequencing (NGS) have expanded the prospects of defining the weakly structured population of anadromous fish. Therefore, we used NGS-based restriction site-associated DNA (NextRAD) techniques on 300 individuals of an anadromous Hilsa shad (Tenualosa ilisha) species, collected from nine strategic habitats, across their diverse migratory habitats, which include sea, estuary, and different freshwater rivers. The NextRAD technique successfully identified 15,453 single nucleotide polymorphism (SNP) loci. Outlier tests using the FST OutFLANK and pcadapt approaches identified 74 and 449 SNPs (49 SNPs being common), respectively, as putative adaptive loci under a divergent selection process. Our results, based on the different cluster analyses of these putatively adaptive loci, suggested that local adaptation has divided the Hilsa shad population into two genetically structured clusters, in which marine and estuarine collection sites were dominated by individuals of one genetic cluster and different riverine collection sites were dominated by individuals of another genetic cluster. The phylogenetic analysis revealed that all the riverine populations of Hilsa shad were further subdivided into the north-western riverine (turbid freshwater) and the north-eastern riverine (clear freshwater) ecotypes. Among all of the putatively adaptive loci, only 36 loci were observed to be in the coding region, and the encoded genes might be associated with important biological functions related to the local adaptation of Hilsa shad. In summary, our study provides both neutral and adaptive contexts for the observed genetic divergence of Hilsa shad and, consequently, resolves the previous inconclusive findings on their population genetic structure across their diverse migratory habitats. Moreover, the study has clearly demonstrated that NextRAD sequencing is an innovative approach to explore how dispersal and local adaptation can shape genetic divergence of non-model anadromous fish that intersect diverse migratory habitats during their life-history stages.

Lack of genetic divergence in capelin (Mallotus villosus) spawning at beach versus subtidal habitats in coastal embayments of Newfoundland

2014 ◽  
Vol 92 (5) ◽  
pp. 377-382 ◽  
Author(s):  
Paulette M. Penton ◽  
Craig T. McFarlane ◽  
Erin K. Spice ◽  
Margaret F. Docker ◽  
Gail K. Davoren
Keyword(s):  
Local Adaptation ◽  
Genetic Divergence ◽  
Geographic Area ◽  
Mallotus Villosus ◽  
The North ◽  
Coastal Embayments ◽  
Fish Spawning ◽  
Capelin Mallotus Villosus ◽  
Unpredictable Environment ◽  
Spawning Sites

Capelin (Mallotus villosus (Müller, 1776)), a focal forage fish in the north Atlantic, spawn on both beach and demersal (deep-water) sites throughout their circumpolar distribution. Although these habitats rarely occur in close proximity, demersal spawning sites within 4 km of beach spawning sites (subtidal) have recently been discovered in two coastal embayments in Newfoundland, Canada. The physical environment differs considerably between beach and subtidal spawning sites, creating the potential for local adaptation and genetic divergence of capelin from the two habitats, but this has never been investigated on a fine spatial scale. We use eight microsatellite loci to test for genetic divergence between capelin spawning at beach and subtidal sites within these two coastal regions in Newfoundland. We found no genetic differentiation between fish spawning at beach and subtidal sites or between the two regions. The results from this fine-scale study are in agreement with the lack of habitat-based structure reported in other studies examining beach and demersal sites separated by a larger geographic area. We suggest that instead of showing site fidelity and local adaptation, the facultative use of alternate spawning habitats may be a more successful strategy in an unpredictable environment.

GENETIC DIVERGENCE OF RED MOMBIN IN THE NORTH OF ESPÍRITO SANTO STATE, BRAZIL

Nucleus ◽  
2016 ◽  
Vol 13 (1) ◽  
pp. 143-152
Author(s):  
Anna Caroline Brinco Rocha ◽  
Layane Segantini Oliari ◽  
Letícia Abreu Simão ◽  
Juliany Morosini França ◽  
João Antônio Dutra Giles ◽  
...  
Keyword(s):  
Genetic Divergence ◽  
Espírito Santo ◽  
The North ◽  
Espirito Santo

scholarly journals RAD sequencing of common whelk, Buccinum undatum, reveals fine‐scale population structuring in Europe and cryptic speciation within the North Atlantic

2021 ◽  
Vol 11 (6) ◽  
pp. 2616-2629
Author(s):  
Jake Goodall ◽  
Kristen Marie Westfall ◽  
Hildur Magnúsdóttir ◽  
Snæbjörn Pálsson ◽  
Erla Björk Örnólfsdóttir ◽  
...  
Keyword(s):  
North Atlantic ◽  
Cryptic Speciation ◽  
Rad Sequencing ◽  
Fine Scale ◽  
Buccinum Undatum ◽  
The North ◽  
Scale Population ◽  
Population Structuring ◽  
The North Atlantic

scholarly journals Local adaptation of Mycobacterium tuberculosis on the Tibetan Plateau

2021 ◽  
Vol 118 (17) ◽  
pp. e2017831118
Author(s):  
Qingyun Liu ◽  
Haican Liu ◽  
Li Shi ◽  
Mingyu Gan ◽  
Xiuqin Zhao ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Local Adaptation ◽  
Population Genomics ◽  
Genetic Evidence ◽  
The Tibetan Plateau ◽  
Lower Altitude ◽  
Local Environments ◽  
Plausible Model ◽  
Genes Encoding

During its global dispersal, Mycobacterium tuberculosis (Mtb) has encountered varied geographic environments and host populations. Although local adaptation seems to be a plausible model for describing long-term host–pathogen interactions, genetic evidence for this model is lacking. Here, we analyzed 576 whole-genome sequences of Mtb strains sampled from different regions of high-altitude Tibet. Our results show that, after sequential introduction of a few ancestral strains, the Tibetan Mtb population diversified locally while maintaining strict separation from the Mtb populations on the lower altitude plain regions of China. The current population structure and estimated past population dynamics suggest that the modern Beijing sublineage strains, which expanded over most of China and other global regions, did not show an expansion advantage in Tibet. The mutations in the Tibetan strains showed a higher proportion of A > G/T > C transitions than strains from the plain regions, and genes encoding DNA repair enzymes showed evidence of positive selection. Moreover, the long-term Tibetan exclusive selection for truncating mutations in the thiol-oxidoreductase encoding sseA gene suggests that Mtb was subjected to local selective pressures associated with oxidative stress. Collectively, the population genomics of Mtb strains in the relatively isolated population of Tibet provides genetic evidence that Mtb has adapted to local environments.

scholarly journals Population genomics in two cave-obligate invertebrates confirms extremely limited dispersal between caves

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Andras Balogh ◽  
Lam Ngo ◽  
Kirk S. Zigler ◽  
Groves Dixon
Keyword(s):  
Genetic Divergence ◽  
Population Genomics ◽  
Sample Sizes ◽  
Dense Region ◽  
Evolutionary Processes ◽  
Cumberland Plateau ◽  
Selective Pressures ◽  
Genome Wide ◽  
Good Sample ◽  
Limited Dispersal

Abstract Caves offer selective pressures that are distinct from the surface. Organisms that have evolved to exist under these pressures typically exhibit a suite of convergent characteristics, including a loss or reduction of eyes and pigmentation. As a result, cave-obligate taxa, termed troglobionts, are no longer viable on the surface. This circumstance has led to an understanding of highly constrained dispersal capabilities, and the prediction that, in the absence of subterranean connections, extreme genetic divergence between cave populations. An effective test of this model would involve (1) common troglobionts from (2) nearby caves in a cave-dense region, (3) good sample sizes per cave, (4) multiple taxa, and (5) genome-wide characterization. With these criteria in mind, we used RAD-seq to genotype an average of ten individuals of the troglobiotic spider Nesticus barri and the troglobiotic beetle Ptomaphagus hatchi, each from four closely located caves (ranging from 3 to 13 km apart) in the cave-rich southern Cumberland Plateau of Tennessee, USA. Consistent with the hypothesis of highly restricted dispersal, we find that populations from separate caves are indeed highly genetically isolated. Our results support the idea of caves as natural laboratories for the study of parallel evolutionary processes.

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.

scholarly journals Fine-scale geographic variation in photosynthetic-related traits ofPicea glaucaseedlings indicates local adaptation to climate

2015 ◽  
Vol 35 (8) ◽  
pp. 864-878 ◽  
Author(s):  
Lahcen Benomar ◽  
Mohammed S. Lamhamedi ◽  
Isabelle Villeneuve ◽  
André Rainville ◽  
Jean Beaulieu ◽  
...  
Keyword(s):  
Geographic Variation ◽  
Local Adaptation ◽  
Fine Scale

Prey switching by killer whales in the north-east Atlantic: observational evidence and experimental insights

2013 ◽  
Vol 94 (6) ◽  
pp. 1357-1365 ◽  
Author(s):  
Dag Vongraven ◽  
Anna Bisther
Keyword(s):  
Killer Whale ◽  
Large Population ◽  
Tooth Wear ◽  
Killer Whales ◽  
Prey Switching ◽  
Photo Identification ◽  
North East ◽  
The North ◽  
Spawning Stock

Studies in the Pacific have identified distinct killer whale ecotypes that are either specialized mammal- or fish-eaters. The different types have developed hunting strategies that would suggest specialization could be more advantageous than generalism. However, it has been suggested, based on long-term dietary markers of tooth wear and stable isotope values, that lineages in the North Atlantic are generalist, but with individual variation in the proportion of prey types consumed. Here, we present the results of ten years of observational and photo-identification data of a population of killer whales that follows the Norwegian spring-spawning stock of Atlantic herring. Although the whales were predominantly observed while feeding upon herring, one pod of herring-eating whales was also observed interacting with seals. This supports the hypothesis based on the long-term markers, of a degree of specialization, with a small number of groups persistently feeding upon mammals, but switching between herring and seals. We further investigated this prey switching by conducting playbacks of herring-eating killer whale sounds to harbour seals at haul-out sites on the herring spawning grounds. We recorded changes in behaviour consistent with an anti-predator response, suggesting the seals perceived the herring-eating killer whales as a potential predatory threat and had not habituated to their calls. This could be due to the risk of herring-eating killer whales switching to mammalian prey, or the difficulty of discriminating between killer whale pods due to the large population size and number of killer whale call dialects in this population, or a combination of both.

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