Genetic characterization and interspecies gene flow among the Oreochromis species in the Lake Victoria and Kyoga basins, Uganda: Implications for conservation

Journal of Great Lakes Research, Journal Year: 2025, Volume and Issue: unknown, P. 102535 - 102535

Published: Feb. 1, 2025

Language: Английский

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Unexpected landscape-scale contemporary gene flow and fine-scale genetic diversity in rural hedgehogs

Conservation Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 25, 2025

Language: Английский

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Application of a SSR‐GBS marker system on investigation of European Hedgehog species and their hybrid zone dynamics

Ecology and Evolution, Journal Year: 2019, Volume and Issue: 9(5), P. 2814 - 2832

Published: Feb. 14, 2019

By applying second-generation sequencing technologies to microsatellite genotyping, sequence information is produced which can result in high-resolution population genetics analysis populations and increased replicability between runs laboratories. In the present study, we establish an approach study genetic structure patterns of two European hedgehog species Erinaceaus europaeus E. roumanicus. These are usually associated with human settlements good models anthropogenic impacts on diversity wild populations. The short repeats genotyping by (SSR-GBS) method presented uses amplicon sequences determine genotypes for allelic variants be defined according both length single nucleotide polymorphisms (SNPs). To evaluate whether complete improved definition, compared this datasets based solely information. We identified a total 42 markers were successfully amplified species. Overall, resulted higher number alleles, as well greater differentiation Additionally, slightly clearer division some potential hybrids. There was degree within species, although only roumanicus related geographical distance. statistically significant results obtained SSR-GBS demonstrate that it superior electrophoresis-based methods SSR genotyping. Moreover, reproducibility throughput lower effort possibility include degraded DNA into analysis, allow continued relevance during genomic era.

Language: Английский

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Metabarcoding Analyses of Gut Microbiota of Nile Tilapia (Oreochromis niloticus) from Lake Awassa and Lake Chamo, Ethiopia

Microorganisms, Journal Year: 2020, Volume and Issue: 8(7), P. 1040 - 1040

Published: July 13, 2020

The Nile tilapia (Oreochromis niloticus) gut harbors a diverse microbial community; however, their variation across regions, lumen and mucosa is not fully elucidated. In this study, microbiota of all samples regions sample types (luminal content mucosa) were analyzed compared from two Ethiopian lakes. Microbiota characterized using 16S rRNA Illumina MiSeq platform sequencing. A total 2061 operational taxonomic units (OTUs) obtained the results indicated that Lake Chamo harbored much more diversified than Awassa. addition, diversity varied significantly region based on Chao1, Shannon Simpson index. microbiome analyses in midgut showed higher values for alpha (Chao 1, Simpson). Beta analysis revealed clear separation according to sampling areas regions. most abundant genera Clostridium_sensu_stricto Clostridium_XI samples. Between lakes, phyla, Phylum Fusobacteria Cyanobacteria, found be different. On other hand, six phyla (Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria Cyanobacteria) different we shared large core microbiota, comprising relatively number OTUs, which was dominated by Proteobacteria, Actinobacteria. This study has established bases future large-scale investigations fishes

Language: Английский

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The Impact of Sampling Season and Catching Site (Wild and Aquaculture) on Gut Microbiota Composition and Diversity of Nile Tilapia (Oreochromis niloticus)

Biology, Journal Year: 2021, Volume and Issue: 10(3), P. 180 - 180

Published: March 1, 2021

The gut microbiota of fishes is known to play an essential role in diverse aspects host biology. fish affected by various environmental parameters, including temperature changes, salinity and diet. Studies effect environment on enables have a further understanding what comprises healthy under different conditions. However, there insufficient regarding the effects sampling season catching site (wild aquaculture) Nile tilapia. This study characterised microbial composition diversity from samples collected Lake Tana Bahir Dar aquaculture facility centre using 16S rDNA Illumina MiSeq platform sequencing. Firmicutes Fusobacteria were most dominant phyla samples, while Proteobacteria was samples. results differential abundance testing clearly indicated significant differences for Firmicutes, Fusobacteria, Bacteroidetes Cyanobacteria across months. Proteobacteria, Chloroflexi, significantly enriched comparison centre. Significant observed months between wild captive alpha showed that (captive) had higher than tilapia Tana. core all used our comprised Fusobacteria. impact bacterial communities associated with Overall, this first Ethiopia. Future work recommended precisely explain causes these changes large representative lakes farms.

Language: Английский

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Molecular genetic diversity and differentiation of Nile tilapia (Oreochromis niloticus, L. 1758) in East African natural and stocked populations

BMC Evolutionary Biology, Journal Year: 2020, Volume and Issue: 20(1)

Published: Jan. 30, 2020

Abstract Background The need for enhancing the productivity of fisheries in Africa triggered introduction non-native fish, causing dramatic changes to local species. In East Africa, extensive translocation Nile tilapia ( Oreochromis niloticus ) is one major factors this respect. Using 40 microsatellite loci with SSR-GBS techniques, we amplified a total 664 individuals investigate genetic structure O. from comparison Ethiopian and Burkina Faso populations. Results All three African regions were characterized by independent gene-pools, however, population Lake Tana was genetically more divergent (F st = 2.1) than expected suggesting that it might be different sub-species. congruent both geographical location anthropogenic activities (Isolation By Distance R 2 0.67 Uganda, 0.24). Turkana (Kenya) isolated, while despite populations being rather similar each other, two main natural catchments able defined. We show these groups contributed gene-pool Moreover, admixture possible hybridization other tilapiine species may have divergence found some such as Victoria. detected affecting variation. For example, most gone through reduction diversity, which can consequence bottleneck (G-W, < 0.5) caused overfishing, erosion due fragmentation or founder effect resulting stocking activities. Conclusions particularly translocations, promoted artificial among Tilapia Translocations also native congenerics, needs further studied. These events contribute outbreeding depression hence compromising sustainability region.

Language: Английский

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Fast sequence-based microsatellite genotyping development workflow

PeerJ, Journal Year: 2020, Volume and Issue: 8, P. e9085 - e9085

Published: May 4, 2020

Application of high-throughput sequencing technologies to microsatellite genotyping (SSRseq) has been shown remove many the limitations electrophoresis-based methods and refine inference population genetic diversity structure. We present here a streamlined SSRseq development workflow that includes development, multiplexed marker amplification sequencing, automated bioinformatics data analysis. illustrate its application five groups species across phyla (fungi, plant, insect fish) with different levels genomic resource availability. found relying on previously developed assay is not optimal leads resulting low number reliable locus being genotyped. In contrast, de novo ad hoc primer designs gives highly assays can be sequenced produce high quality genotypes for 20–40 loci. highlight critical upfront factors consider effective setup in wide range situations. Sequence analysis accounting all linked polymorphisms along sequence quickly generates powerful multi-allelic haplotype-based genotypic dataset, calling new theoretical analytical frameworks extract more information from multi-nucleotide polymorphism systems.

Language: Английский

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How Is Wildlife Affected by the COVID-19 Pandemic? Lockdown Effect on the Road Mortality of Hedgehogs

Animals, Journal Year: 2021, Volume and Issue: 11(3), P. 868 - 868

Published: March 18, 2021

Globally, wildlife is affected by unprecedented changes related to the COVID-19 pandemic. In this paper, lockdown effect on traffic-related mortality in hedgehogs an urban area was studied. Comparing pre-pandemic (2018 and 2019) pandemic (2020) years, we showed that hedgehog roadkill levels during period were over 50% lower (which means a decrease greater than road traffic same measured number of accidents or average vehicles per day). Based literature data, may mean at least tens thousands have survived national scale. We report need start intensive research possible demographic genetic effects unique phenomenon. also ask how stable will be whether anthropause) reverse negative trends decline wild species, including hedgehogs.

Language: Английский

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Introgressive hybridization levels of Tilapiine species in Lake Victoria basin, Kenya inferred from microsatellite and mitochondrial DNA genotyping based on next-generation sequencing

Conservation Genetics, Journal Year: 2023, Volume and Issue: 25(2), P. 305 - 318

Published: Sept. 27, 2023

Abstract Despite their high abundance and species richness, tilapiines have been compromised by various factors especially overfishing, climate change, uncontrolled fish transfers introductions. Fish introductions negatively impacted native tilapiine populations through competition, predation, hybridization, introgression compromising genetic integrity. The hybridization levels of different in the Lake Victoria basin remain relatively understudied. study utilized nuclear microsatellite mitochondrial DNA (mtDNA) markers to investigate signals compare diversity Victoria, Kenya, using next-generation sequencing. Low from Oreochromis niloticus into other were detected Bayesian clustering analysis principal coordinate (PCoA). results contribute need for conservation measures these species.

Language: Английский

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Evidence for High Levels of Gene Flow in Hedgehogs (Erinaceus europaeus) Across South Wales, UK, Despite Potential Anthropogenic and Natural Barriers to Dispersal

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(4)

Published: April 1, 2025

ABSTRACT Understanding how landscape connectivity affects gene flow can help to guide the management of animal species conservation concern. One such is West European hedgehog ( Erinaceus europaeus ), which has seen significant declines across its distribution, with highest rate being reported in rural areas UK. The drivers these are not well understood, but anthropogenic changes as modified agricultural practices and increased road traffic have been proposed play a part. These impacts likely fragment populations into smaller sub‐populations, leading genetic differentiation depletion. Here, we used (microsatellite) data investigate impact habitat resistance features (roads waterways) on structure hedgehogs 5800 km 2 area South Wales, We found evidence weak structuring, four clusters present study area, many individuals were admixed. no that this was related roads, waterways, resistance, or geographic distance, suggesting may be able disperse potential barriers frequently enough minimise fragmentation. This demonstrates importance understanding interactions between wider inform management.

Language: Английский

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