scholarly journals Comparative transcriptomics reveal that adaptive evolution in immune genes drives the local adaptation and speciation of schizothoracine fish

2019 ◽  
Author(s):  
Delin Qi ◽  
Rongrong Wu ◽  
Yan Chao ◽  
Mingzhe Xia ◽  
Qichang Chen ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Local Adaptation ◽  
Adaptive Evolution ◽  
Fish Species ◽  
Ecological Niches ◽  
Orthologous Genes ◽  
Immune Genes ◽  
Species Specific ◽  
Schizothoracine Fish ◽  
Ecological Differences

ABSTRACTTranscriptomic information can increase our understanding of the molecular processes underlying speciation. The schizothoracine fish, the largest and most diverse taxon within the Qinghai-Tibetan Plateau (QTP) ichthyofauna, are widespread in drainages throughout the QTP. These fish thus serve as an ideal model group with which to investigate how molecular evolution drives local adaptation during speciation. Here, we performed an interspecific comparative analysis of the transcriptomes of 13 schizothoracine fish species, and identified the key positively selected genes (PSGs) associated with significantly enriched functions and metabolite pathway acting on the specific lineages (or species) in the schizothoracine fish. We generated 64,637,602–83,968,472 sequence reads per schizothoracine fish species using Illumina sequencing, yielding 95,251–145,805 unigenes per species. We identified 52 out of 2,064 orthologous genes as candidate genes, which have probably been subject to positive selection along the whole schizothoracine fish lineage. Nine of these candidate genes were significantly enriched in key GO functions and metabolite pathways, all of which were associated with the immune system. The lineage-specific evolution test showed species-specific differences among the nine candidate PSGs, probably due to ecological differences among drainages, as well as among micro-habitats in the same drainage (e.g., benthic and pelagic). Here, we provide evidence that the adaptive evolution of immune genes, along with the uplift of the QTP, allowed new schizothoracine species to colonize ecologically novel environments or to exploit vacant ecological niches during speciation.Supplemental material available at FigShare: https://doi.org/10.25387/.

scholarly journals Genetic differentiation of mainland-island sheep of Greece: Implications for identifying candidate genes for long-term local adaptation

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0257461
Author(s):  
Antonios Kominakis ◽  
Eirini Tarsani ◽  
Ariadne L. Hager-Theodorides ◽  
Ioannis Mastranestasis ◽  
Dimitra Gkelia ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Candidate Genes ◽  
Local Adaptation ◽  
Ecological Niches ◽  
P Value ◽  
Positional Candidate ◽  
Island Populations ◽  
Significant Marker ◽  
Genome Wide ◽  
Wide Range

In Greece, a number of local sheep breeds are raised in a wide range of ecological niches across the country. These breeds can be used for the identification of genetic variants that contribute to local adaptation. To this end, 50k genotypes of 90 local sheep from mainland Greece (Epirus, n = 35 and Peloponnesus, n = 55) were used, as well as 147 genotypes of sheep from insular Greece (Skyros, n = 21), Lemnos, n = 36 and Lesvos, n = 90). Principal components and phylogenetic analysis along with admixture and spatial point patterns analyses suggested genetic differentiation of ‘mainland-island’ populations. Genome scans for signatures of selection and genome-wide association analysis (GWAS) pointed to one highly differentiating marker on OAR4 (FST = 0.39, FLK = 21.93, FDR p-value = 0.10) that also displayed genome wide significance (FDR p-value = 0.002) during GWAS. A total number of 6 positional candidate genes (LOC106990429, ZNF804B, TEX47, STEAP4, SRI and ADAM22) were identified within 500 kb flanking regions around the significant marker. In addition, two QTLs related to fat tail deposition are reported in genomic regions 800 kb downstream the significant marker. Based on gene ontology analysis and literature evidence, the identified candidate genes possess biological functions relevant to local adaptation that worth further investigation.

​Discrimination of Five Gobid Species (Family: Gobiidae) based on Otolith Morphometry

2021 ◽  
Author(s):  
Vikas Pathak ◽  
Rinchen N. Bhutia ◽  
Shashi Bhushan ◽  
Geetanjali Deshmukhe ◽  
A.K. Jaiswar
Keyword(s):  
Fish Species ◽  
Discriminant Function Analysis ◽  
Function Analysis ◽  
Allometric Growth ◽  
Fish Size ◽  
Sagittal Otolith ◽  
Shape Indices ◽  
Glossogobius Giuris ◽  
Species Specific ◽  
Boleophthalmus Dussumieri

Background: The fishes of family Gobiidae are one of the least studied fishes, especially for otolith structure. The otoliths were possess species specific features. Hence, traits of sagittal otolith of gobid species studied. Methods: Five gobid species Odontamblyopus roseus (Valenciennes, 1837), Trypauchen vagina (Bloch and Schneider, 1801), Glossogobius giuris (Hamilton, 1822), Parachaeturichthys polynema (Bleeker, 1853) and Boleophthalmus dussumieri (Valenciennes, 1837) were investigated by three methods including morphological, shape indices and step wise discriminant function analysis (SDFA). Result: Interrelationship between shape indices investigated, at 95% level of confidence (P less than 0.05), revealed that perimeter of P. polynema and area of T. vagina have isometric growth with their length (b = 3.0071, 2.90, respectively) and otolith area of B. dussumieri have positive allometric growth (b = 4.23077). SDFA, based on otolith morphometry, discriminated species up with 97.18% accuracy. Hence, the results of present investigation can be used for discrimination of the species and as a tool in predicting fish size from the otoliths and in calculating the biomass of these less studied fish species.

scholarly journals Individual Serum Triiodothyronine and Thyroxine Levels in Seven Freshwater Fish Species

2021 ◽  
Vol 23 (1) ◽  
pp. 59-66
Author(s):  
Alexander Atanasoff ◽  
Dimitrinka Zapryanova ◽  
Cigdem Urku ◽  
Galin Nikolov
Keyword(s):  
Serum Concentration ◽  
Thyroid Hormones ◽  
Fresh Water ◽  
Fish Species ◽  
Reference Intervals ◽  
Specific Reference ◽  
Fresh Water Fish ◽  
Water Fish ◽  
Total Thyroxine ◽  
Species Specific

Abstract The thyroid hormones (THs) play an important role in the regulation of the rate of metabolism, affect the growth and function of different systems in the organism. The aim of this study was to assess serum concentration of total triiodothyronine (T3), total thyroxine (T4) as well as T3/T4 ratio in serum from healthy fresh water fish from Salmonidae, Acipenseridae, Cyprinidae, and Clariidae families to determine species-specific reference intervals. Mean concentrations of T3 and T4 levels varied significantly among fish. Finally, the test results show clear differences in the serum concentration of the T3 and T4 and give new insight into the thyroid hormones reference values in some commercial fresh water fish species.

scholarly journals Polygenic local adaptation in metapopulations: a stochastic eco-evolutionary model

2020 ◽  
Author(s):  
Enikő Szép ◽  
Himani Sachdeva ◽  
Nick Barton
Keyword(s):  
Population Size ◽  
Local Adaptation ◽  
Genetic Drift ◽  
Diffusion Approximation ◽  
Joint Distribution ◽  
Evolutionary Model ◽  
Ecological Niches ◽  
Demographic Stochasticity ◽  
Linkage Disequilibria ◽  
Population Sizes

AbstractThis paper analyses the conditions for local adaptation in a metapopulation with infinitely many islands under a model of hard selection, where population size depends on local fitness. Each island belongs to one of two distinct ecological niches or habitats. Fitness is influenced by an additive trait which is under habitat-dependent directional selection. Our analysis is based on the diffusion approximation and accounts for both genetic drift and demographic stochasticity. By neglecting linkage disequilibria, it yields the joint distribution of allele frequencies and population size on each island. We find that under hard selection, the conditions for local adaptation in a rare habitat are more restrictive for more polygenic traits: even moderate migration load per locus at very many loci is sufficient for population sizes to decline. This further reduces the efficacy of selection at individual loci due to increased drift and because smaller populations are more prone to swamping due to migration, causing a positive feedback between increasing maladaptation and declining population sizes. Our analysis also highlights the importance of demographic stochasticity, which exacerbates the decline in numbers of maladapted populations, leading to population collapse in the rare habitat at significantly lower migration than predicted by deterministic arguments.

scholarly journals Nanopore amplicon sequencing reveals molecular convergence and local adaptation of opsin genes

2020 ◽  
Author(s):  
Katherine M. Eaton ◽  
Moisés A. Bernal ◽  
Nathan J.C. Backenstose ◽  
Trevor J. Krabbenhoft
Keyword(s):  
Local Adaptation ◽  
Environmental Gradients ◽  
Parallel Evolution ◽  
Amplicon Sequencing ◽  
Species Flock ◽  
Closely Related Species ◽  
Oxford Nanopore ◽  
Opsin Genes ◽  
Potential Case ◽  
Species Specific

AbstractLocal adaptation can drive diversification of closely related species across environmental gradients and promote convergence of distantly related taxa that experience similar conditions. We examined a potential case of adaptation to novel visual environments in a species flock (Great Lakes salmonids, genus Coregonus) using a new amplicon genotyping protocol on the Oxford Nanopore Flongle. Five visual opsin genes were amplified for individuals of C. artedi, C. hoyi, C. kiyi, and C. zenithicus. Comparisons revealed species-specific differences in the coding sequence of rhodopsin (Tyr261Phe substitution), suggesting local adaptation by C. kiyi to the blue-shifted depths of Lake Superior. Parallel evolution and “toggling” at this amino acid residue has occurred several times across the fish tree of life, resulting in identical changes to the visual systems of distantly related taxa across replicated environmental gradients. Our results suggest that ecological differences and local adaptation to distinct visual environments are strong drivers of both evolutionary parallelism and diversification.

scholarly journals The Role of Plasticity and Adaptation in the Incipient Speciation of a Fire Salamander Population

Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 875
Author(s):  
Joana Sabino-Pinto ◽  
Daniel J. Goedbloed ◽  
Eugenia Sanchez ◽  
Till Czypionka ◽  
Arne W. Nolte ◽  
...  
Keyword(s):  
Gene Expression ◽  
Phenotypic Plasticity ◽  
Local Adaptation ◽  
Habitat Preferences ◽  
Genetic Change ◽  
Incipient Speciation ◽  
Expression Of Genes ◽  
Species Specific ◽  
Reciprocal Transfer ◽  
High Degree

Phenotypic plasticity and local adaptation via genetic change are two major mechanisms of response to dynamic environmental conditions. These mechanisms are not mutually exclusive, since genetic change can establish similar phenotypes to plasticity. This connection between both mechanisms raises the question of how much of the variation observed between species or populations is plastic and how much of it is genetic. In this study, we used a structured population of fire salamanders (Salamandra salamandra), in which two subpopulations differ in terms of physiology, genetics, mate-, and habitat preferences. Our goal was to identify candidate genes for differential habitat adaptation in this system, and to explore the degree of plasticity compared to local adaptation. We therefore performed a reciprocal transfer experiment of stream- and pond-originated salamander larvae and analyzed changes in morphology and transcriptomic profile (using species-specific microarrays). We observed that stream- and pond-originated individuals diverge in morphology and gene expression. For instance, pond-originated larvae have larger gills, likely to cope with oxygen-poor ponds. When transferred to streams, pond-originated larvae showed a high degree of plasticity, resembling the morphology and gene expression of stream-originated larvae (reversion); however the same was not found for stream-originated larvae when transferred to ponds, where the expression of genes related to reduction-oxidation processes was increased, possibly to cope with environmental stress. The lack of symmetrical responses between transplanted animals highlights the fact that the adaptations are not fully plastic and that some level of local adaptation has already occurred in this population. This study illuminates the process by which phenotypic plasticity allows local adaptation to new environments and its potential role in the pathway of incipient speciation.

scholarly journals Vertebrate Alpha2,8-Sialyltransferases (ST8Sia): A Teleost Perspective

2020 ◽  
Vol 21 (2) ◽  
pp. 513 ◽  
Author(s):  
Marzia Tindara Venuto ◽  
Mathieu Decloquement ◽  
Joan Martorell Ribera ◽  
Maxence Noel ◽  
Alexander Rebl ◽  
...  
Keyword(s):  
Fish Species ◽  
Evolutionary History ◽  
Recombinant Enzymes ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments ◽  
Functional Studies ◽  
Genome Duplications ◽  
History Of ◽  
Species Specific

We identified and analyzed α2,8-sialyltransferases sequences among 71 ray-finned fish species to provide the first comprehensive view of the Teleost ST8Sia repertoire. This repertoire expanded over the course of Vertebrate evolution and was primarily shaped by the whole genome events R1 and R2, but not by the Teleost-specific R3. We showed that duplicated st8sia genes like st8sia7, st8sia8, and st8sia9 have disappeared from Tetrapods, whereas their orthologues were maintained in Teleosts. Furthermore, several fish species specific genome duplications account for the presence of multiple poly-α2,8-sialyltransferases in the Salmonidae (ST8Sia II-r1 and ST8Sia II-r2) and in Cyprinus carpio (ST8Sia IV-r1 and ST8Sia IV-r2). Paralogy and synteny analyses provided more relevant and solid information that enabled us to reconstruct the evolutionary history of st8sia genes in fish genomes. Our data also indicated that, while the mammalian ST8Sia family is comprised of six subfamilies forming di-, oligo-, or polymers of α2,8-linked sialic acids, the fish ST8Sia family, amounting to a total of 10 genes in fish, appears to be much more diverse and shows a patchy distribution among fish species. A focus on Salmonidae showed that (i) the two copies of st8sia2 genes have overall contrasted tissue-specific expressions, with noticeable changes when compared with human co-orthologue, and that (ii) st8sia4 is weakly expressed. Multiple sequence alignments enabled us to detect changes in the conserved polysialyltransferase domain (PSTD) of the fish sequences that could account for variable enzymatic activities. These data provide the bases for further functional studies using recombinant enzymes.

scholarly journals Differential evolution in 3′UTRs leads to specific gene expression in Staphylococcus

2020 ◽  
Vol 48 (5) ◽  
pp. 2544-2563 ◽  
Author(s):  
Pilar Menendez-Gil ◽  
Carlos J Caballero ◽  
Arancha Catalan-Moreno ◽  
Naiara Irurzun ◽  
Inigo Barrio-Hernandez ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Regulation ◽  
Bacterial Species ◽  
Regulatory Elements ◽  
Specific Gene ◽  
Species Differentiation ◽  
Orthologous Genes ◽  
Genome Wide ◽  
Sequence Variations ◽  
Species Specific

Abstract The evolution of gene expression regulation has contributed to species differentiation. The 3′ untranslated regions (3′UTRs) of mRNAs include regulatory elements that modulate gene expression; however, our knowledge of their implications in the divergence of bacterial species is currently limited. In this study, we performed genome-wide comparative analyses of mRNAs encoding orthologous proteins from the genus Staphylococcus and found that mRNA conservation was lost mostly downstream of the coding sequence (CDS), indicating the presence of high sequence diversity in the 3′UTRs of orthologous genes. Transcriptomic mapping of different staphylococcal species confirmed that 3′UTRs were also variable in length. We constructed chimeric mRNAs carrying the 3′UTR of orthologous genes and demonstrated that 3′UTR sequence variations affect protein production. This suggested that species-specific functional 3′UTRs might be specifically selected during evolution. 3′UTR variations may occur through different processes, including gene rearrangements, local nucleotide changes, and the transposition of insertion sequences. By extending the conservation analyses to specific 3′UTRs, as well as the entire set of Escherichia coli and Bacillus subtilis mRNAs, we showed that 3′UTR variability is widespread in bacteria. In summary, our work unveils an evolutionary bias within 3′UTRs that results in species-specific non-coding sequences that may contribute to bacterial diversity.

scholarly journals Seascape context modifies how fish respond to restored oyster reef structures

2019 ◽  
Vol 76 (4) ◽  
pp. 1131-1139 ◽  
Author(s):  
Ben L Gilby ◽  
Andrew D Olds ◽  
Christopher J Henderson ◽  
Nicholas L Ortodossi ◽  
Rod M Connolly ◽  
...  
Keyword(s):  
Species Richness ◽  
Fish Species ◽  
Fish Assemblages ◽  
Oyster Reef ◽  
Pivotal Role ◽  
Oyster Reefs ◽  
Total Abundance ◽  
Fish Recruitment ◽  
Abundance And Diversity ◽  
Species Specific

Abstract The seascape context of coastal ecosystems plays a pivotal role in shaping patterns in fish recruitment, abundance, and diversity. It might also be a principal determinant in structuring the recruitment of fish assemblages to restored habitats, but the trajectories of these relationships require further testing. In this study, we surveyed fish assemblages from 14 restored oyster reefs and 14 control sites in the Noosa River, Queensland, Australia, that differed in the presence or absence of seagrass within 500 m, over four periods using baited cameras. Fish assemblages at oyster reefs differed from those at control sites, with higher species richness (1.4 times) and more individuals of taxa that are harvested by fishers (1.8 times). The presence or absence of seagrass nearby affected the abundance of a key harvestable fish species (yellowfin bream Acanthopagrus australis) on oyster reefs, but not the overall composition of fish assemblages, species richness, or the total abundance of harvestable fishes overall. These findings highlight the importance of considering species-specific patterns in seascape utilization when selecting restoration sites and setting restoration goals, and suggest that the effects of restoration on fish assemblages might be optimized by focusing efforts in prime positions in coastal seascapes.

scholarly journals Janthinobacterium CG23_2: Comparative Genome Analysis Reveals Enhanced Environmental Sensing and Transcriptional Regulation for Adaptation to Life in an Antarctic Supraglacial Stream

2019 ◽  
Vol 7 (10) ◽  
pp. 454
Author(s):  
Markus Dieser ◽  
Heidi J. Smith ◽  
Thiruvarangan Ramaraj ◽  
Christine M. Foreman
Keyword(s):  
Transcriptional Regulation ◽  
Extreme Environment ◽  
Ecological Niches ◽  
Genome Plasticity ◽  
Functional Categories ◽  
Environmental Sensing ◽  
Copy Numbers ◽  
Environmental Extremes ◽  
Species Specific ◽  
Extracellular Environment

As many bacteria detected in Antarctic environments are neither true psychrophiles nor endemic species, their proliferation in spite of environmental extremes gives rise to genome adaptations. Janthinobacterium sp. CG23_2 is a bacterial isolate from the Cotton Glacier stream, Antarctica. To understand how Janthinobacterium sp. CG23_2 has adapted to its environment, we investigated its genomic traits in comparison to genomes of 35 published Janthinobacterium species. While we hypothesized that genome shrinkage and specialization to narrow ecological niches would be energetically favorable for dwelling in an ephemeral Antarctic stream, the genome of Janthinobacterium sp. CG23_2 was on average 1.7 ± 0.6 Mb larger and predicted 1411 ± 499 more coding sequences compared to the other Janthinobacterium spp. Putatively identified horizontal gene transfer events contributed 0.92 Mb to the genome size expansion of Janthinobacterium sp. CG23_2. Genes with high copy numbers in the species-specific accessory genome of Janthinobacterium sp. CG23_2 were associated with environmental sensing, locomotion, response and transcriptional regulation, stress response, and mobile elements—functional categories which also showed molecular adaptation to cold. Our data suggest that genome plasticity and the abundant complementary genes for sensing and responding to the extracellular environment supported the adaptation of Janthinobacterium sp. CG23_2 to this extreme environment.

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