scholarly journals Population structure in a continuously distributed coastal marine species, the harbor porpoise, based on microhaplotypes derived from poor‐quality samples

2021 ◽  
Vol 30 (6) ◽  
pp. 1457-1476
Author(s):  
Phillip A. Morin ◽  
Brenna R. Forester ◽  
Karin A. Forney ◽  
Carla A. Crossman ◽  
Brittany L. Hancock‐Hanser ◽  
...  
Keyword(s):  
Population Structure ◽  
Marine Species ◽  
Poor Quality ◽  
Harbor Porpoise ◽  
Coastal Marine

scholarly journals Population genetics and connectivity in Paphies subtriangulata and Paphies australis (Bivalvia: Mesodesmatidae)

2021 ◽  
Author(s):  
◽  
Danielle Amelia Hannan
Keyword(s):  
Population Structure ◽  
New Zealand ◽  
Marine Environment ◽  
Environmental Variables ◽  
Marine Species ◽  
Genetic Population Structure ◽  
Small Scale ◽  
Genetic Population ◽  
Geographic Patterns ◽  
Coastal Marine

<p>Understanding the different types of genetic population structure that characterise marine species, and the processes driving such patterns, is crucial for establishing links between the ecology and evolution of a species. This knowledge is vital for management and conservation of marine species. Genetic approaches are a powerful tool for revealing ecologically relevant insights to marine population dynamics. Geographic patterns of genetic population structure are largely determined by the rate at which individuals are exchanged among populations (termed ‘population connectivity’), which in turn is influenced by conditions in the physical environment. The complexity of the New Zealand marine environment makes it difficult to predict how physical oceanographic and environmental processes will influence connectivity in coastal marine organisms and hence the type of genetic structure that will form. This complexity presents a challenge for management of marine resources but also makes the New Zealand region an interesting model system to investigate how and why population structure develops and evolves over time. Paphies subtriangulata (tuatua) and P. australis (pipi) are endemic bivalve ‘surf clams’ commonly found on New Zealand surf beaches and harbour/estuary environments, respectively. They form important recreational, customary and commercial fisheries, yet little is known about the stock structure of these species. This study aimed to use genetic techniques to determine population structure, levels of connectivity and ‘seascape’ genetic patterns in P. subtriangulata and P. australis, and to gain further knowledge of common population genetic processes operating in the New Zealand coastal marine environment. Eleven and 14 novel microsatellite markers were developed for P. subtriangulata and P. australis, respectively. Samples were collected from 10 locations for P. subtriangulata and 13 locations for P. australis (35-57 samples per location; total sample size of 517 for P. subtriangulata and 674 for P. australis). Geographic patterns of genetic variation were measured and rates of migration among locations were estimated on recent and historic time scales. Both species were characterised by genetic population structure that was consistent with their habitat. For P. subtriangulata, the Chatham Island population was strongly differentiated from the rest of the sampled locations. The majority of mainland locations were undifferentiated and estimated rates of migration among locations were high on both time scales investigated, although differentiation among some populations was observed. For P. australis, an overall isolation by distance (IBD) pattern was likely to be driven by distance between discrete estuary habitats. However, it was difficult to distinguish IBD from hierarchical structure as populations could be further subdivided into three significantly differentiated groups (Northern, South Eastern and South Western), providing evidence for barriers to dispersal. Further small scale patterns of genetic differentiation were observed in some locations, suggesting that complex current patterns and high self-recruitment drive small scale genetic population structure in both P. subtriangulata and P. australis. These patterns of genetic variation were used in seascape genetic analyses to test for associations with environmental variables, with the purpose of understanding the processes that might shape genetic population structure in these two species. Although genetic population structure varied between the two species, common physical and environmental variables (geographic distance, sea surface temperature, bed slope, tidal currents) are likely to be involved in the structuring of populations. Results suggest that local adaptation, in combination with restricted dispersal, could play a role in driving the small scale patterns of genetic differentiation seen among some localities. Overall, the outcomes of this research fill a gap in our knowledge about the rates and routes by which populations are connected and the environmental factors influencing such patterns in the New Zealand marine environment. Other studies have highlighted the importance of using multi-faceted approaches to understand complex processes operating in the marine environment. The present study is an important first step in this direction as these methods are yet to be widely applied to New Zealand marine species. Importantly, this study used a comparative approach, applying standardised methodology to compare genetic population structure and migration across species. Such an approach is necessary if we wish to build a robust understanding of the spatial and temporal complexities of population dynamics in the New Zealand coastal marine environment, and to develop effective management strategies for our unique marine species.</p>

scholarly journals Population genetics and connectivity in Paphies subtriangulata and Paphies australis (Bivalvia: Mesodesmatidae)

2021 ◽  
Author(s):  
◽  
Danielle Amelia Hannan
Keyword(s):  
Population Structure ◽  
New Zealand ◽  
Marine Environment ◽  
Environmental Variables ◽  
Marine Species ◽  
Genetic Population Structure ◽  
Small Scale ◽  
Genetic Population ◽  
Geographic Patterns ◽  
Coastal Marine

<p>Understanding the different types of genetic population structure that characterise marine species, and the processes driving such patterns, is crucial for establishing links between the ecology and evolution of a species. This knowledge is vital for management and conservation of marine species. Genetic approaches are a powerful tool for revealing ecologically relevant insights to marine population dynamics. Geographic patterns of genetic population structure are largely determined by the rate at which individuals are exchanged among populations (termed ‘population connectivity’), which in turn is influenced by conditions in the physical environment. The complexity of the New Zealand marine environment makes it difficult to predict how physical oceanographic and environmental processes will influence connectivity in coastal marine organisms and hence the type of genetic structure that will form. This complexity presents a challenge for management of marine resources but also makes the New Zealand region an interesting model system to investigate how and why population structure develops and evolves over time. Paphies subtriangulata (tuatua) and P. australis (pipi) are endemic bivalve ‘surf clams’ commonly found on New Zealand surf beaches and harbour/estuary environments, respectively. They form important recreational, customary and commercial fisheries, yet little is known about the stock structure of these species. This study aimed to use genetic techniques to determine population structure, levels of connectivity and ‘seascape’ genetic patterns in P. subtriangulata and P. australis, and to gain further knowledge of common population genetic processes operating in the New Zealand coastal marine environment. Eleven and 14 novel microsatellite markers were developed for P. subtriangulata and P. australis, respectively. Samples were collected from 10 locations for P. subtriangulata and 13 locations for P. australis (35-57 samples per location; total sample size of 517 for P. subtriangulata and 674 for P. australis). Geographic patterns of genetic variation were measured and rates of migration among locations were estimated on recent and historic time scales. Both species were characterised by genetic population structure that was consistent with their habitat. For P. subtriangulata, the Chatham Island population was strongly differentiated from the rest of the sampled locations. The majority of mainland locations were undifferentiated and estimated rates of migration among locations were high on both time scales investigated, although differentiation among some populations was observed. For P. australis, an overall isolation by distance (IBD) pattern was likely to be driven by distance between discrete estuary habitats. However, it was difficult to distinguish IBD from hierarchical structure as populations could be further subdivided into three significantly differentiated groups (Northern, South Eastern and South Western), providing evidence for barriers to dispersal. Further small scale patterns of genetic differentiation were observed in some locations, suggesting that complex current patterns and high self-recruitment drive small scale genetic population structure in both P. subtriangulata and P. australis. These patterns of genetic variation were used in seascape genetic analyses to test for associations with environmental variables, with the purpose of understanding the processes that might shape genetic population structure in these two species. Although genetic population structure varied between the two species, common physical and environmental variables (geographic distance, sea surface temperature, bed slope, tidal currents) are likely to be involved in the structuring of populations. Results suggest that local adaptation, in combination with restricted dispersal, could play a role in driving the small scale patterns of genetic differentiation seen among some localities. Overall, the outcomes of this research fill a gap in our knowledge about the rates and routes by which populations are connected and the environmental factors influencing such patterns in the New Zealand marine environment. Other studies have highlighted the importance of using multi-faceted approaches to understand complex processes operating in the marine environment. The present study is an important first step in this direction as these methods are yet to be widely applied to New Zealand marine species. Importantly, this study used a comparative approach, applying standardised methodology to compare genetic population structure and migration across species. Such an approach is necessary if we wish to build a robust understanding of the spatial and temporal complexities of population dynamics in the New Zealand coastal marine environment, and to develop effective management strategies for our unique marine species.</p>

scholarly journals Population structure in the native range predicts the spread of introduced marine species

2013 ◽  
Vol 280 (1760) ◽  
pp. 20130409 ◽  
Author(s):  
Michelle R. Gaither ◽  
Brian W. Bowen ◽  
Robert J. Toonen
Keyword(s):  
Population Structure ◽  
Marine Species ◽  
Native Range

scholarly journals Empowering conservation practice with efficient and economical genotyping from poor quality samples

2018 ◽  
Author(s):  
Meghana Natesh ◽  
Ryan W. Taylor ◽  
Nathan Truelove ◽  
Elizabeth A. Hadly ◽  
Stephen Palumbi ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Material ◽  
Cost Effective ◽  
Poor Quality ◽  
Wildlife Trade ◽  
List Type ◽  
High Quality ◽  
Conservation Practice ◽  
Queen Conch ◽  
Close Relatives

AbstractModerate to high density genotyping (100+ SNPs) is widely used to determine and measure individual identity, relatedness, fitness, population structure and migration in wild populations.However, these important tools are difficult to apply when high-quality genetic material is unavailable. Most genomic tools are developed for high quality DNA sources from labor medical settings. As a result, most genetic data from market or field settings is limited to easily amplified mitochondrial DNA or a few microsatellites.To enable genotyping in conservation contexts, we used next-generation sequencing of multiplex PCR products from very low-quality DNA extracted from feces, hair, and cooked samples. We demonstrated utility and wide-ranging potential application in endangered wild tigers and tracking commercial trade in Caribbean queen conch.We genotyped 100 SNPs from degraded tiger samples to identify individuals, discern close relatives, and detect population differentiation. Co-occurring carnivores do not amplify (e.g. Indian wild dog/Dhole) or are monomorphic (e.g. leopard). 62 SNPs from conch fritters and field-collected samples were used to test relatedness and detect population structure.We provide proof-of-concept for a rapid, simple, cost-effective, and scalable method (for both samples and number of loci), a framework that can be applied to other conservation scenarios previously limited by low quality DNA samples. These approaches provide a critical advance for wildlife monitoring and forensics, open the door to field-ready testing, and will strengthen the use of science in policy decisions and wildlife trade.

Upper thermal limits and warming safety margins of coastal marine species – Indicator baseline for future reference

2019 ◽  
Vol 102 ◽  
pp. 644-649 ◽  
Author(s):  
Catarina Vinagre ◽  
Marta Dias ◽  
Rui Cereja ◽  
Francisca Abreu-Afonso ◽  
Augusto A.V. Flores ◽  
...  
Keyword(s):  
Marine Species ◽  
Thermal Limits ◽  
Coastal Marine ◽  
Safety Margins ◽  
Future Reference

Biocomplexity in a demersal exploited fish, white hake (Urophycis tenuis): depth-related structure and inadequacy of current management approaches

2012 ◽  
Vol 69 (3) ◽  
pp. 415-429 ◽  
Author(s):  
Denis Roy ◽  
Thomas R. Hurlbut ◽  
Daniel E. Ruzzante
Keyword(s):  
Population Structure ◽  
Fisheries Management ◽  
Management Strategies ◽  
Marine Species ◽  
Current Management ◽  
Recovery Strategies ◽  
Management Schemes ◽  
Management Approaches ◽  
Management Priorities ◽  
Conservation And Management

Understanding the factors generating patterns of genetic diversity is critical to implementing robust conservation and management strategies for exploited marine species. Yet, often too little is known about population structure to properly tailor management schemes. Here we report evidence of substantial population structure in white hake ( Urophycis tenuis ) in the Northwest Atlantic, perhaps among the highest levels of population structure exhibited by a highly exploited, widely dispersed, long-lived marine fish. We show that depth plays a role in this extensive and temporally stable structure, which does not conform to previously established fisheries management units. Three genetically distinguishable populations were identified, where all straddle several management divisions and two (Southern Gulf of St. Lawrence and Scotian Shelf) overlap in their range, coexisting within a single division. The most highly exploited population in the Southern Gulf of St. Lawrence was also the most isolated and likely the smallest (genetically effective). This work shows that conservation and management priorities must include population structure and stability in establishing effective species recovery strategies.

scholarly journals Hierarchical genetic structure in an evolving species complex: Insights from genome wide ddRAD data in Sebastes mentella

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0251976
Author(s):  
Atal Saha ◽  
Matthew Kent ◽  
Lorenz Hauser ◽  
Daniel P. Drinan ◽  
Einar E. Nielsen ◽  
...  
Keyword(s):  
Population Structure ◽  
Life History ◽  
Learning Algorithm ◽  
Marine Species ◽  
Intraspecific Diversity ◽  
Genetic Population Structure ◽  
Microsatellite Data ◽  
Adaptive Genetic Variation ◽  
Genetic Population ◽  
Sebastes Mentella

The diverse biology and ecology of marine organisms may lead to complex patterns of intraspecific diversity for both neutral and adaptive genetic variation. Sebastes mentella displays a particular life-history as livebearers, for which existence of multiple ecotypes has been suspected to complicate the genetic population structure of the species. Double digest restriction-site associated DNA was used to investigate genetic population structure in S. mentella and to scan for evidence of selection. In total, 42,288 SNPs were detected in 277 fish, and 1,943 neutral and 97 tentatively adaptive loci were selected following stringent filtration. Unprecedented levels of genetic differentiation were found among the previously defined ‘shallow pelagic’, ‘deep pelagic’ and ‘demersal slope’ ecotypes, with overall mean FST = 0.05 and 0.24 in neutral and outlier SNPs, respectively. Bayesian computation estimated a concurrent and historical divergence among these three ecotypes and evidence of local adaptation was found in the S. mentella genome. Overall, these findings imply that the depth-defined habitat divergence of S. mentella has led to reproductive isolation and possibly adaptive radiation among these ecotypes. Additional sub-structuring was detected within the ‘shallow’ and ‘deep’ pelagic ecotypes. Population assignment of individual fish showed more than 94% agreement between results based on SNP and previously generated microsatellite data, but the SNP data provided a lower estimate of hybridization among the ecotypes than that by microsatellite data. We identified a SNP panel with only 21 loci to discriminate populations in mixed samples based on a machine-learning algorithm. This first SNP based investigation clarifies the population structure of S. mentella, and provides novel and high-resolution genomic tools for future investigations. The insights and tools provided here can readily be incorporated into the management of S. mentella and serve as a template for other exploited marine species exhibiting similar complex life history traits.

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>

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