scholarly journals Stochasticity in space, persistence in time: genetic heterogeneity in harbour populations of the introduced ascidianStyela plicata

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2158 ◽  
Author(s):  
Mari-Carmen Pineda ◽  
Beatriz Lorente ◽  
Susanna López-Legentil ◽  
Creu Palacín ◽  
Xavier Turon
Keyword(s):  
Genetic Structure ◽  
Gene Diversity ◽  
Mitochondrial Gene ◽  
Geographic Distance ◽  
Marine Species ◽  
Mediterranean Coast ◽  
Medium Size ◽  
Indigenous Species ◽  
Spatial And Temporal Scales ◽  
Nw Mediterranean

Spatio-temporal changes in genetic structure among populations provide crucial information on the dynamics of secondary spread for introduced marine species. However, temporal components have rarely been taken into consideration when studying the population genetics of non-indigenous species. This study analysed the genetic structure ofStyela plicata,a solitary ascidian introduced in harbours and marinas of tropical and temperate waters, across spatial and temporal scales. A fragment of the mitochondrial gene Cytochrome Oxidase subunit I (COI) was sequenced from 395 individuals collected at 9 harbours along the NW Mediterranean coast and adjacent Atlantic waters (> 1,200 km range) at two time points 5 years apart (2009 and 2014). The levels of gene diversity were relatively low for all 9 locations in both years. Analyses of genetic differentiation and distribution of molecular variance revealed strong genetic structure, with significant differences among many populations, but no significant differences among years. A weak and marginally significant correlation between geographic distance and gene differentiation was found. Our results revealed spatial structure and temporal genetic homogeneity inS. plicata, suggesting a limited role of recurrent, vessel-mediated transport of organisms among small to medium-size harbours. Our study area is representative of many highly urbanized coasts with dense harbours. In these environments, the episodic chance arrival of colonisers appears to determine the genetic structure of harbour populations and the genetic composition of these early colonising individuals persists in the respective harbours, at least over moderate time frames (five years) that encompass ca. 20 generations ofS. plicata.

scholarly journals Genetic Structure of Rhynchosporium secalis in Australia

1999 ◽  
Vol 89 (8) ◽  
pp. 639-645 ◽  
Author(s):  
B. A. McDonald ◽  
J. Zhan ◽  
J. J. Burdon
Keyword(s):  
Genetic Structure ◽  
Gene Diversity ◽  
Sampling Site ◽  
Geographic Distance ◽  
South Australia ◽  
Rflp Markers ◽  
Rhynchosporium Secalis ◽  
Fungal Isolates ◽  
Fungal Populations ◽  
Average Gene

Restriction fragment length polymorphism (RFLP) markers were used to determine the genetic structure of Australian field populations of the barley scald pathogen Rhynchosporium secalis. Fungal isolates were collected by hierarchical sampling from five naturally infected barley fields in different geographic locations during a single growing season. Genetic variation was high in Australian R. secalis populations. Among the 265 fungal isolates analyzed, 214 distinct genotypes were identified. Average genotype diversity within a field population was 65% of its theoretical maximum. Nei's average gene diversity across seven RFLP loci was 0.54. The majority (76%) of gene diversity was distributed within sampling site areas measuring ≈1 m2; 19% of gene diversity was distributed among sampling sites within fields; and 5% of gene diversity was distributed among fields. Fungal populations from different locations differed significantly both in allele frequencies and genotype diversities. The degree of genetic differentiation was significantly correlated with geographic distance between populations. Our results suggest that the R. secalis population in Western Australia has a different genetic structure than populations in Victoria and South Australia.

scholarly journals Spatial and temporal genetic structure of the New Zealand scallop Pecten novaezelandiae: A multidisciplinary perspective

2021 ◽  
Author(s):  
◽  
Catarina Nunes Soares Silva
Keyword(s):  
Population Structure ◽  
Genetic Variation ◽  
New Zealand ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Marine Species ◽  
Effective Management ◽  
Spatial And Temporal Scales ◽  
Marine Connectivity ◽  
Management And Conservation

<p>Knowledge about the population genetic structure of species and the factors shaping such patterns is crucial for effective management and conservation. The complexity of New Zealand’s marine environment presents a challenge for management and the classification of its marine biogeographic areas. As such, it is an interesting system to investigate marine connectivity dynamics and the evolutionary processes shaping the population structure of marine species. An accurate description of spatial and temporal patterns of dispersal and population structure requires the use of tools capable of incorporating the variability of the mechanisms involved. However, these techniques are yet to be broadly applied to New Zealand marine organisms.  This study used genetic markers to assess the genetic variation of the endemic New Zealand scallop, Pecten novaezelandiae, at different spatial and temporal scales. A multidisciplinary approach was used integrating genetic with environmental data (seascape genetics) and hydrodynamic modelling tools. P. novaezelandiae supports important commercial, recreational and customary fisheries but there is no previous information about its genetic structure. Therefore, twelve microsatellite markers were developed for this study (Chapter 2).  Samples (n=952) were collected from 15 locations to determine the genetic structure across the distribution range of P. novaezelandiae. The low genetic structure detected in this study is expected given the recent evolutionary history, the large reproductive potential and the pelagic larval duration of the species (approximately 3 weeks). A significant isolation by distance signal and a degree of differentiation from north to south was apparent, but this structure conflicted with some evidence of panmixia. A latitudinal genetic diversity gradient was observed that might reflect the colonisation and extinction events and insufficient time to reach migration-drift equilibrium during a recent range expansion (Chapter 3).  A seascape genetic approach was used to test for associations between patterns of genetic variation in P. novaezelandiae and environmental variables (three geospatial and six environmental variables). Although the geographic distance between populations was an important variable explaining the genetic variation among populations, it appears that levels of genetic differentiation are not a simple function of distance. Evidence suggests that some environmental factors such as freshwater discharge and suspended particulate matter can be contributing to the patterns of genetic differentiation of P. novaezelandiae in New Zealand (Chapter 4).  Dispersal of P. novaezelandiae was investigated at a small spatial and temporal scale in the Coromandel fishery using genetic markers integrated with hydrodynamic modelling. For the spatial analysis, samples (n=402) were collected in 2012 from 5 locations and for the temporal analysis samples (n=383) were collected in 2012 and 2014 from 3 locations. Results showed small but significant spatial and temporal genetic differentiation, suggesting that the Coromandel fishery does not form a single panmictic unit with free gene flow and supporting a model of source-sink population dynamics (Chapter 5).  The importance of using multidisciplinary approaches at different spatial and temporal scales is widely recognized as a means to better understand the complex processes affecting marine connectivity. The outcomes of this study highlight the importance of incorporating these different approaches, provide vital information to assist in effective management and conservation of P. novaezelandiae and contribute to our understanding of evolutionary processes shaping population structure of marine species.</p>

Bottlenose dolphin communities from the southern Brazilian coast: do they exchange genes or are they just neighbours?

2015 ◽  
Vol 66 (12) ◽  
pp. 1201 ◽  
Author(s):  
Ana Paula Borges Costa ◽  
Pedro Fruet ◽  
Fábio Gonçalves Daura-Jorge ◽  
Paulo César Simões-Lopes ◽  
Paulo Henrique Ott ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Bottlenose Dolphin ◽  
Gene Diversity ◽  
Mitochondrial Gene ◽  
Distinct Group ◽  
Unknown Origin ◽  
Brazilian Coast ◽  
Tissue Samples ◽  
Scale Population ◽  
Free Ranging

The genetic structure of bottlenose dolphin communities found along the southern Brazilian coast is reported in this study. Genetic structure analysis using biopsy samples from free ranging dolphins and tissue samples from stranded dolphins revealed a fine-scale population structure among three distinct groups. The first genetically distinct group was composed of resident dolphins of Laguna with a high degree of site fidelity. The second group was composed of one photo-identified dolphin, previously recognised by its interaction with fishermen, and dolphins that stranded near the mouth of Tramandaí Lagoon. Moderate nuclear and low mitochondrial gene diversity was found in dolphins of those coastal communities, whereas most of the dolphins stranded along the coast showed markedly higher levels of gene diversity at both markers. These stranded dolphins of unknown origin formed the third distinct group, which may be part of a larger offshore community. These results demonstrate the presence of at least three bottlenose dolphin clusters along this portion of the Brazilian coast, with the coastal specimens appearing to be only neighbours of a larger offshore community that eventually strands along the coast, highlighting the importance of the establishment of management and conservation measures for the species at a local scale.

scholarly journals Spatial and temporal genetic structure of the New Zealand scallop Pecten novaezelandiae: A multidisciplinary perspective

2021 ◽  
Author(s):  
◽  
Catarina Nunes Soares Silva
Keyword(s):  
Population Structure ◽  
Genetic Variation ◽  
New Zealand ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Marine Species ◽  
Effective Management ◽  
Spatial And Temporal Scales ◽  
Marine Connectivity ◽  
Management And Conservation

<p>Knowledge about the population genetic structure of species and the factors shaping such patterns is crucial for effective management and conservation. The complexity of New Zealand’s marine environment presents a challenge for management and the classification of its marine biogeographic areas. As such, it is an interesting system to investigate marine connectivity dynamics and the evolutionary processes shaping the population structure of marine species. An accurate description of spatial and temporal patterns of dispersal and population structure requires the use of tools capable of incorporating the variability of the mechanisms involved. However, these techniques are yet to be broadly applied to New Zealand marine organisms.  This study used genetic markers to assess the genetic variation of the endemic New Zealand scallop, Pecten novaezelandiae, at different spatial and temporal scales. A multidisciplinary approach was used integrating genetic with environmental data (seascape genetics) and hydrodynamic modelling tools. P. novaezelandiae supports important commercial, recreational and customary fisheries but there is no previous information about its genetic structure. Therefore, twelve microsatellite markers were developed for this study (Chapter 2).  Samples (n=952) were collected from 15 locations to determine the genetic structure across the distribution range of P. novaezelandiae. The low genetic structure detected in this study is expected given the recent evolutionary history, the large reproductive potential and the pelagic larval duration of the species (approximately 3 weeks). A significant isolation by distance signal and a degree of differentiation from north to south was apparent, but this structure conflicted with some evidence of panmixia. A latitudinal genetic diversity gradient was observed that might reflect the colonisation and extinction events and insufficient time to reach migration-drift equilibrium during a recent range expansion (Chapter 3).  A seascape genetic approach was used to test for associations between patterns of genetic variation in P. novaezelandiae and environmental variables (three geospatial and six environmental variables). Although the geographic distance between populations was an important variable explaining the genetic variation among populations, it appears that levels of genetic differentiation are not a simple function of distance. Evidence suggests that some environmental factors such as freshwater discharge and suspended particulate matter can be contributing to the patterns of genetic differentiation of P. novaezelandiae in New Zealand (Chapter 4).  Dispersal of P. novaezelandiae was investigated at a small spatial and temporal scale in the Coromandel fishery using genetic markers integrated with hydrodynamic modelling. For the spatial analysis, samples (n=402) were collected in 2012 from 5 locations and for the temporal analysis samples (n=383) were collected in 2012 and 2014 from 3 locations. Results showed small but significant spatial and temporal genetic differentiation, suggesting that the Coromandel fishery does not form a single panmictic unit with free gene flow and supporting a model of source-sink population dynamics (Chapter 5).  The importance of using multidisciplinary approaches at different spatial and temporal scales is widely recognized as a means to better understand the complex processes affecting marine connectivity. The outcomes of this study highlight the importance of incorporating these different approaches, provide vital information to assist in effective management and conservation of P. novaezelandiae and contribute to our understanding of evolutionary processes shaping population structure of marine species.</p>

scholarly journals Genetic Structure of Natural Populations of Wild Sunflowers (Helianthus annuus L.) in Australia

1986 ◽  
Vol 39 (3) ◽  
pp. 255 ◽  
Author(s):  
PJ Dry ◽  
JJ Burdon
Keyword(s):  
Genetic Structure ◽  
Gene Diversity ◽  
New South ◽  
Geographic Distance ◽  
Natural Populations ◽  
Wild Populations ◽  
South Wales ◽  
Fixation Indices ◽  
O 19 ◽  
Isozyme Diversity

The genetic structure of 11 wild populations of H. annuus occurring in New South Wales and Queensland was determined by isozyme analysis. Considerable isozyme diversity was found among loci within and between populations, with three to five alleles being identified at each of 10 loci. Mean levels of heterozygosity ranged from o� 19 to O� 38 and gene diversity values from 0�29 to O� 52. In all populations Wright's fixation indices were positive (0�09-0� 51) suggesting a degree of inbreeding. Differences in the level of genetic differentiation between populations were not correlated with geographic distance. Indeed, notable genetic diversity was detected between six sites occurring within a 2-km radius of Gunnedah, N.S.W., where the genetic distance relationships were D = 0�13 � 0'08, the same as those between popUlations throughout the region.

scholarly journals DNA BARCODING OF FISH SPECIES FROM THE MEDITERRANEAN COAST OF ISRAEL

2016 ◽  
Vol 17 (2) ◽  
pp. 459 ◽  
Author(s):  
A. SHIRAK ◽  
LIOR DOR ◽  
E. SEROUSSI ◽  
M. RON ◽  
G. HULATA ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Classification Tree ◽  
Mitochondrial Gene ◽  
Mediterranean Coast ◽  
Composite Likelihood ◽  
Marine Biodiversity ◽  
Indigenous Species ◽  
Phylogeny Analysis ◽  
Geographic Origins ◽  
The Mediterranean

Accurately-classified genomic data in the Barcode of Life Data System (BOLD) database is vital to the protection and conservation of marine biodiversity in the Mediterranean Sea. The taxonomic classifications of 468 fish of 50 Mediterranean species were analyzed using the BOLD Identifier tool for variation in the cytochrome oxidase subunit I (COI) mitochondrial gene. Within species, nucleotide maximum composite likelihood was low with a mean of 0.0044±0.0008. Three presumptive species had significantly higher values e.g., Arnoglossus spp. (0.07), Torquigener flavimaculosus (0.013) and Boops boops (0.028). However, samples of Arnoglossus species were sub-classified into two groups that were finally identified as two different species e.g., Arnoglossus laterna and Arnoglossus thori. For the different species, BLAST searches against the BOLD database using our DNA barcoding data as the query sequences designated the most similar targets into groups. For each analyzed species, the similarity of the first and second threshold groups ranged from 95 to 99% and from 83 to 98%, respectively. Sequence based classification for the first threshold group was concordant with morphology-based identification. However, for 34 analyzed species (68%) overlaps of species between the two threshold groups hampered classification. Tree-based phylogeny analysis detected more than one cluster in the first threshold group for 22 out of 50 species, representing genetic subgroups and geographic origins. There was a tendency for higher conservation and lower number of clusters in the Lessepsian (Red Sea) migrant versus indigenous species.

scholarly journals Science in support of ecologically sound decommissioning strategies for offshore man-made structures: taking stock of current knowledge and considering future challenges

2020 ◽  
Vol 77 (3) ◽  
pp. 1075-1078 ◽  
Author(s):  
Silvana N R Birchenough ◽  
Steven Degraer
Keyword(s):  
Oil And Gas ◽  
Current Knowledge ◽  
Wind Farms ◽  
Marine Species ◽  
Offshore Wind ◽  
Marine Biodiversity ◽  
Indigenous Species ◽  
Stepping Stones ◽  
Offshore Wind Farms ◽  
Spatial And Temporal Scales

Abstract The blue growth agenda has spurred an accelerating exploitation and continued development of the coastal and marine environment. This is also driven by the increasing need to generate renewable energy. In most cases, this has resulted in a large number of man-made structures (MMSs) across several soft sediment environments. The nature of these structures ranges from oil and gas installations to harbour walls, anchored buoys, pipelines and offshore wind farms. These structures host fouling communities that are often new to offshore regions, potentially serving as stepping stones for range-expanding (non-indigenous) species and providing habitat and shelter for a variety of marine species. The altered local biodiversity also affects biological and biogeochemical processes from the water column to the seafloor, either directly (e.g. scouring, organic matter export from piles) or indirectly (e.g. closure or displacement of fisheries) and, hence, ecosystem functioning at various spatial and temporal scales. A proper understanding of the effects of artificial hard substrate and the consequences of its removal (e.g. through decommissioning) to marine biodiversity has yet to develop to maturity. This themed article set contributes to the scientific knowledge base on the impacts of MMSs on marine ecosystems with the specific aim to fertilize and facilitate an evidence-based debate over decommissioning. This discussion will become ever more vital to inform marine spatial planning and future policy decisions on the use and protection of marine resources.

Spatial analysis of microgeographic genetic structure in Richardson's ground squirrels

1996 ◽  
Vol 74 (7) ◽  
pp. 1187-1195 ◽  
Author(s):  
Moira J. van Staaden ◽  
Gail R. Michener ◽  
Ronald K. Chesser
Keyword(s):  
Genetic Structure ◽  
Gene Diversity ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
Ground Squirrels ◽  
Breeding Systems ◽  
Population Subdivision ◽  
Genetic Structuring ◽  
Candidate Species ◽  
Empirical Demonstration

Local genetic structure has a sound theoretical basis, yet empirical demonstration in animal species has proved elusive, even in apparently ideal candidate species. Techniques based on the distribution of individual genotypes may offer a more complete picture of population structure than traditional measures focusing on isolation by distance and dispersal behavior. We used spatial autocorrelation and contiguous clustering to identify structure in a population of Richardson's ground squirrel (Spermophilus richardsonii) for which deviation from Hardy–Weinberg expectations indicated population subdivision. Nonrandom aggregates of genotypes were detected at five of six enzyme loci examined and selection at one locus. Genetic structuring was highly sex-dependent, being prominent only among females. Isolation by distance cannot account for the patterns of gene diversity observed, but Mantel matrix procedures of inter-individual distance based on demographic–behavioral characteristics and geographic distance were significantly associated. Social and breeding systems of S. richardsonii lead to significant local substructure. While philopatry alone may not account for fine-scale genetic structure in small mammals with sex-biased dispersal, nonrandom aggregates will be detected if appropriate social models and rigorous sampling criteria are adopted. Identification of such localized structure remains fundamental to understanding evolutionary models of population genetic structure and sociality.

Genetic Diversity and Structure of the Nile Soft-Shelled Turtle (Trionyx triunguis) Along the Mediterranean coast of Turkey

2020 ◽  
Vol 27 (6) ◽  
pp. 307-315
Author(s):  
Özgür Güçlü ◽  
Bülent Bozdoğan
Keyword(s):  
Microsatellite Loci ◽  
Geographic Distance ◽  
Iucn Red List ◽  
Genetic Variations ◽  
Mediterranean Coast ◽  
Critically Endangered ◽  
Mediterranean Populations ◽  
Genetic Diversity And Structure ◽  
Polymorphic Microsatellite ◽  
The Mediterranean

The Nile soft-shelled turtle (Trionyx triunguis) is distributed between Dalyan and Samandağ throughout the Mediterranean coast in Turkey. The Mediterranean subpopulation of the Nile soft-shelled turtle is listed as critically endangered in the IUCN Red List Categories. This investigation aimed to determinate levels of genetic variations and patterns of genetic structures among Mediterranean populations in Turkey by using T. triunguis-specific microsatellite primers. A total of 13 polymorphic microsatellite loci were studied among samples of 121 individuals collected from five populations in Turkey. Of 13 polymorphic microsatellite loci used, 3 new were identified in this study. The genetic differentiation among the 5 studied populations of T. triunguis was significant (p 0.001). The analysis of molecular variance (AMOVA) indicated that genetic variations occurred mainly within populations (89.7%) rather than among populations (10.3%). Structure analysis showed presence of two main groups among the Mediterranean T. triunguis populations. However genetic variations among populations were not correlated with geographic distance between the locations. Analysis of data showed that one of the populations (Dalyan) had undergone a bottleneck effect. Migration analysis indicates that T. triunguis migrates between five Mediterranean populations in Turkey. We concluded that based on our results the status of ‘critically endangered’ of T. triunguis should be maintained. Long term population genetic survey studies should be undertaken and changes in habitats of T. triunguis populations, as well as their population size and structure should be monitored for each population to be able to establish a clear strategy for protection of T. triunguis.

scholarly journals Advances in Egyptian Mediterranean Coast Climate Change Monitoring

Water ◽  
2021 ◽  
Vol 13 (13) ◽  
pp. 1870
Author(s):  
Matteo Gentilucci ◽  
Abdelraouf A. Moustafa ◽  
Fagr Kh. Abdel-Gawad ◽  
Samira R. Mansour ◽  
Maria Rosaria Coppola ◽  
...  
Keyword(s):  
Climate Change ◽  
Fish Species ◽  
Mitochondrial Gene ◽  
Mediterranean Coast ◽  
Sea Surface ◽  
Homogeneity Test ◽  
Sea Surface Temperatures ◽  
Climate Trends ◽  
Surface Temperatures ◽  
Lessepsian Species

This paper characterizes non-indigenous fish species (NIS) and analyses both atmospheric and sea surface temperatures for the Mediterranean coast of Egypt from 1991 to 2020, in relation to previous reports in the same areas. Taxonomical characterization depicts 47 NIS from the Suez Canal (Lessepsian/alien) and 5 from the Atlantic provenance. GenBank accession number of the NIS mitochondrial gene, cytochrome oxidase 1, reproductive and commercial biodata, and a schematic Inkscape drawing for the most harmful Lessepsian species were reported. For sea surface temperatures (SST), an increase of 1.2 °C to 1.6 °C was observed using GIS software. The lack of linear correlation between annual air temperature and annual SST at the same detection points (Pearson r) could suggest a difference in submarine currents, whereas the Pettitt homogeneity test highlights a temperature breakpoint in 2005–2006 that may have favoured the settlement of non-indigenous fauna in the coastal sites of Damiette, El Arish, El Hammam, Alexandria, El Alamain, and Mersa Matruh, while there seems to be a breakpoint present in 2001 for El Sallum. This assessment of climate trends is in good agreement with the previous sightings of non-native fish species. New insights into the assessment of Egyptian coastal climate change are discussed.

Sign in / Sign up

Export Citation Format

Share Document