scholarly journals Population Genomic Signatures of Genetic Structure and Environmental Selection in the Catadromous Roughskin Sculpin Trachidermus fasciatus

2019 ◽  
Vol 11 (7) ◽  
pp. 1751-1764 ◽  
Author(s):  
Yu-Long Li ◽  
Dong-Xiu Xue ◽  
Bai-Dong Zhang ◽  
Jin-Xian Liu
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Anthropogenic Activities ◽  
Aquatic Animal ◽  
Genetic Structuring ◽  
Frequency Spectra ◽  
Environmental Selection ◽  
Population Genomic ◽  
Trachidermus Fasciatus ◽  
Roughskin Sculpin

Abstract Understanding the patterns of genetic diversity and adaptation across species’ range is crucial to assess its long-term persistence and determine appropriate conservation measures. The impacts of human activities on the genetic diversity and genetic adaptation to heterogeneous environments remain poorly understood in the marine realm. The roughskin sculpin (Trachidermus fasciatus) is a small catadromous fish, and has been listed as a second-class state protected aquatic animal since 1988 in China. To elucidate the underlying mechanism of population genetic structuring and genetic adaptations to local environments, RAD tags were sequenced for 202 individuals in nine populations across the range of T. fasciatus in China. The pairwise FST values over 9,271 filtered SNPs were significant except that between Dongying and Weifang. All the genetic clustering analysis revealed significant population structure with high support for eight distinct genetic clusters. Both the minor allele frequency spectra and Ne estimations suggested extremely small Ne in some populations (e.g., Qinhuangdao, Rongcheng, Wendeng, and Qingdao), which might result from recent population bottleneck. The strong genetic structure can be partly attributed to genetic drift and habitat fragmentation, likely due to the anthropogenic activities. Annotations of candidate adaptive loci suggested that genes involved in metabolism, development, and osmoregulation were critical for adaptation to spatially heterogenous environment of local populations. In the context of anthropogenic activities and environmental change, results of the present population genomic work provided important contributions to the understanding of genetic differentiation and adaptation to changing environments.

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

2019 ◽  
Author(s):  
Papius Dias Tibihika ◽  
Manuel Curto ◽  
Esayas Alemayehu ◽  
Herwig Waidbacher ◽  
Charles Masembe ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
East Africa ◽  
Oreochromis Niloticus ◽  
Nile Tilapia ◽  
Anthropogenic Activities ◽  
Genetic Erosion ◽  
Gene Pools ◽  
East African ◽  
Nile Tilapia Oreochromis Niloticus

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

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

2019 ◽  
Author(s):  
Papius Dias Tibihika ◽  
Manuel Curto ◽  
Esayas Alemayehu ◽  
Herwig Waidbacher ◽  
Charles Masembe ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
East Africa ◽  
Oreochromis Niloticus ◽  
Nile Tilapia ◽  
Anthropogenic Activities ◽  
Genetic Erosion ◽  
Gene Pools ◽  
East African ◽  
Nile Tilapia Oreochromis Niloticus

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

scholarly journals Evidence of rapid change in genetic structure and diversity during range expansion in a recovering large terrestrial carnivore

2015 ◽  
Vol 282 (1807) ◽  
pp. 20150092 ◽  
Author(s):  
Snorre B. Hagen ◽  
Alexander Kopatz ◽  
Jouni Aspi ◽  
Ilpo Kojola ◽  
Hans Geir Eiken
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Range Expansion ◽  
Ursus Arctos ◽  
Rapid Change ◽  
Natural Populations ◽  
Brown Bear ◽  
Genetic Structuring ◽  
Genetic Theory ◽  
Animal Populations

Recovery of natural populations occurs often with simultaneous or subsequent range expansions. According to population genetic theory, genetic structuring emerges at the expansion front together with decreasing genetic diversity, owing to multiple founder events. Thereupon, as the expansion proceeds and connectivity among populations is established, homogenization and a resurgence of genetic diversity are to be expected. Few studies have used a fine temporal scale combined with genetic sampling to track range expansions as they proceed in wild animal populations. As a natural experiment, the historical eradication of large terrestrial carnivores followed by their recovery and recolonization may facilitate empirical tests of these ideas. Here, using brown bear ( Ursus arctos ) as model species, we tested predictions from genetic theory of range expansion. Individuals from all over Finland were genotyped for every year between 1996 and 2010 using 12 validated autosomal microsatellite markers. A latitudinal shift of about 110 km was observed in the distribution and delineation of genetic clusters during this period. As the range expansion proceeded, we found, as theory predicts, that the degree of genetic structure decreased, and that both genetic variation and admixture increased. The genetic consequences of range expansions may first be detected after multiple generations, but we found major changes in genetic composition after just 1.5 generations, accompanied by population growth and increased migration. These rapid genetic changes suggest an ongoing concerted action of geographical and demographic expansion combined with substantial immigration of bears from Russia during the recovery of brown bears within the large ecosystem of northern Europe.

scholarly journals High levels of genetic diversity and an absence of genetic structure among breeding populations of the endangered Rufous-backed Bunting in Inner Mongolia, China: implications for conservation

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Shi Li ◽  
Dan Li ◽  
Lishi Zhang ◽  
Weiping Shang ◽  
Bo Qin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Genetic Structure ◽  
Endangered Species ◽  
Habitat Loss ◽  
Inner Mongolia ◽  
Avian Species ◽  
Genetic Structuring ◽  
Breeding Populations ◽  
The Impact

Abstract Background The Rufous-backed Bunting, Emberiza jankowskii, is an endangered species that is primarily distributed in Inner Mongolia, China. The main threats to the continued persistence of this species are habitat loss and degradation. However, the impact of population loss on genetic diversity remains unclear. To support future conservation and management efforts, we assessed the genetic diversity and population structure of E. jankowskii using mitochondrial DNA and microsatellites. Methods Blood samples were collected from 7‒8-day-old nestlings in Inner Mongolia, China between May and August of 2012 and 2013. Mitochondrial DNA sequences and microsatellite markers were used to assess the genetic diversity, genetic structure and inbreeding of E. jankowskii. The results of genetic diversity and inbreeding were compared to other avian species. Results We found an unexpectedly high level of genetic diversity in terms of mitochondrial DNA and microsatellite compared to other avian species. However, there were high levels of gene flow and minimal genetic structuring, among the fragmented breeding populations of E. jankowskii in Inner Mongolia. These findings suggest that E. jankowskii in Inner Mongolia is a metapopulation. Despite the high genetic diversity of E. jankowskii, local populations in each small patch remain at risk of extinction due to habitat loss. In addition, the E. jankowskii population has a high risk of inbreeding. Conclusions To minimize further loss of genetic diversity of this endangered species, we suggest that the E. jankowskii in Inner Mongolia should be considered as a protected species for management purposes. Conservation efforts should concentrate on E. jankowskii habitat management. This may be most effectively achieved by protecting the current breeding habitats and prohibiting over-grazing.

scholarly journals Mitochondrial DNA sequence variations in populations of Sardinapilchardus(Walbaum 1792) along the Tunisian coasts

2019 ◽  
Vol 20 (2) ◽  
Author(s):  
ΚARIMA FADHLAOUI-ZID
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Genetic Structure ◽  
Dna Sequences ◽  
Population Distribution ◽  
Genetic Structuring ◽  
Efficient Management ◽  
Sequence Variations ◽  
Haplotypic Diversity ◽  
High Level

Sardine is a fish species of great economic importance to Tunisia. Knowledge of genetic diversity and population distribution is essential for an efficient management and sustainability of any regional fishery. This study aimed to assessing the genetic structure and to specify the stocks of the European sardine (Sardina pilchardus). To this end, 83 specimens were collected from three localities along the Tunisian coast and analysed using mitochondrial DNA sequences. The results of sequence analysis determined the existence of variations in 40 single nucleotide sites within the 307 bp fragment of the cytb gene examined and defined twenty different haplotypes. Genetic diversity, estimated by haplotypic diversity, was high in all samples. Tunisian S.pilchardus samples show some level of genetic structuring. First, genetic differentiation between localities (ΦST estimates) was significant for all comparison. Second, the analysis of molecular variance AMOVA indicates a high level of genetic variation (ΦST = 0.093; P<0.001). The structural patterns identified can be explained largely in relation to the regional oceanographic features. In conclusion, this study provided initial genetic data in making inference of the genetic structure of S. pilchardus along the Tunisian coasts. 

scholarly journals Population Genetic Structure and Connectivity of the European Lobster Homarus gammarus in the Adriatic and Mediterranean Seas

2020 ◽  
Vol 11 ◽  
Author(s):  
Mišo Pavičić ◽  
Iva Žužul ◽  
Sanja Matić-Skoko ◽  
Alexandros Triantafyllidis ◽  
Fabio Grati ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Adriatic Sea ◽  
Habitat Degradation ◽  
Anthropogenic Activities ◽  
Population Connectivity ◽  
Mitochondrial Coi ◽  
European Lobster ◽  
The North

Highly selective fishing has the potential to permanently change the characteristics within a population and could drive the decline of genetic diversity. European lobster is an intensively fished crustacean species in the Adriatic Sea which reaches high market value. Since knowledge of population structure and dynamics is important for effective fisheries management, in this study, we used 14 neutral microsatellites loci and partial mitochondrial COI region sequencing to explore population connectivity and genetic structure by comparing samples from the Adriatic Sea and the adjacent basins of the Mediterranean Sea. The obtained results suggest that neutral genetic diversity has not been significantly affected by decrease in population size due to overfishing, habitat degradation and other anthropogenic activities. Global genetic differentiation across all populations was low (FST = 0.0062). Populations from the Adriatic Sea were panmictic, while genetic differentiation was found among populations from different Mediterranean basins. Observed gene flow for European lobster suggest that populations in the north eastern Adriatic act as a source for surrounding areas, emphasizing the need to protect these populations by establishing interconnected MPAs that will be beneficial for both fisheries and conservation management.

scholarly journals Gene Flow and Genetic Structure Reveal Reduced Diversity between Generations of a Tropical Tree, Manilkara multifida Penn., in Atlantic Forest Fragments

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 2025
Author(s):  
Zubaria Waqar ◽  
Ramiris César Souza Moraes ◽  
Maíra Benchimol ◽  
José Carlos Morante-Filho ◽  
Eduardo Mariano-Neto ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Atlantic Forest ◽  
Tree Species ◽  
Spatial Genetic Structure ◽  
Anthropogenic Activities ◽  
Forest Fragments ◽  
Human Disturbances ◽  
Large Tree

The Atlantic Forest remnants in southern Bahia, Brazil, contain large tree species that have suffered disturbances in recent decades. Anthropogenic activities have led to a decrease in the population of many tree species and a loss of alleles that can maintain the evolutionary fitness of their populations. This study assessed patterns of genetic diversity, spatial genetic structure, and genetic structure among Manilkara multifida Penn. populations, comparing the genetic parameters of adult and juvenile trees. In particular, we collected leaves from adults and juveniles of M. multifida in two protected areas, the Veracel Station (EVC) and the Una Biological Reserve (UBR), located in threatened Atlantic Forest fragments. We observed a substantial decay in genetic variability between generations in both areas i.e., adults’ HO values were higher (EVC = 0.720, UBR = 0.736) than juveniles’ (EVC = 0.463 and UBR = 0.560). Both juveniles and adults showed genetic structure between the two areas (θ = 0.017 for adults and θ = 0.109 for juveniles). Additionally, forest fragments indicated an unexpectedly short gene flow. Our results, therefore, highlight the pervasive effects of historical deforestation and other human disturbances on the genetic diversity of M. multifida populations within a key conservation region of the Atlantic Forest biodiversity hotspot.

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

2019 ◽  
Author(s):  
Papius Dias Tibihika ◽  
Manuel Curto ◽  
Esayas Alemayehu ◽  
Herwig Waidbacher ◽  
Charles Masembe ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
East Africa ◽  
Oreochromis Niloticus ◽  
Nile Tilapia ◽  
Anthropogenic Activities ◽  
Genetic Erosion ◽  
Gene Pools ◽  
East African ◽  
Nile Tilapia Oreochromis Niloticus

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

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

2020 ◽  
Author(s):  
Papius Dias Tibihika ◽  
Manuel Curto ◽  
Esayas Alemayehu ◽  
Herwig Waidbacher ◽  
Charles Masembe ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
East Africa ◽  
Oreochromis Niloticus ◽  
Nile Tilapia ◽  
Anthropogenic Activities ◽  
Genetic Erosion ◽  
Gene Pools ◽  
East African ◽  
Nile Tilapia Oreochromis Niloticus

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

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