Genomic evidence of demographic fluctuations and lack of genetic structure across flyways in a long distance migrant, the European turtle dove

AbstractMicrosatellite markers were used to investigate the genetic structure among invasive L. decolor populations from Australia and a single international population from Kansas, USA to determine patterns of dispersal. Six variable microsatellites displayed an average of 2.5–4.2 alleles per locus per population. Observed (HO) heterozygosity ranged from 0.12–0.65 per locus within populations; but, in 13 of 36 tests, HO was less than expected. Despite low levels of allelic diversity, genetic structure estimated as θ was significant for all pairwise comparisons between populations (θ=0.05–0.23). Due to suspected null alleles at four loci, ENA (excluding null alleles) corrected FST estimates were calculated overall and for pairwise population comparisons. The ENA-corrected FST values (0.02–0.10) revealed significant overall genetic structure, but none of the pairwise values were significantly different from zero. A Mantel test of isolation by distance indicated no relationship between genetic structure and geographic distance among all populations (r2=0.12, P=0.18) and for Australian populations only (r2=0.19, P=0.44), suggesting that IBD does not describe the pattern of gene flow among populations. This study supports a hypothesis of long distance dispersal by L. decolor at moderate to potentially high levels.

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Cryptic Lineages and a Population Dammed to Incipient Extinction? Insights into the Genetic Structure of a Mekong River Catfish

Journal of Heredity ◽

10.1093/jhered/esz016 ◽

2019 ◽

Vol 110 (5) ◽

pp. 535-547 ◽

Cited By ~ 2

Author(s):

Amanda S Ackiss ◽

Binh T Dang ◽

Christopher E Bird ◽

Ellen E Biesack ◽

Phen Chheng ◽

...

Keyword(s):

Genetic Structure ◽

Natural Populations ◽

Principal Component ◽

Flood Pulse ◽

Mekong River ◽

Effective Population ◽

Long Distance ◽

Genetic Lineages ◽

Low Genetic Diversity ◽

Population Size Estimates

Abstract An understanding of the genetic composition of populations across management boundaries is vital to developing successful strategies for sustaining biodiversity and food resources. This is especially important in ecosystems where habitat fragmentation has altered baseline patterns of gene flow, dividing natural populations into smaller subpopulations and increasing potential loss of genetic variation through genetic drift. River systems can be highly fragmented by dams built for flow regulation and hydropower. We used reduced-representation sequencing to examine genomic patterns in an exploited catfish, Hemibagrus spilopterus, in a hotspot of biodiversity and hydropower development—the Mekong River basin. Our results revealed the presence of 2 highly divergent coexisting genetic lineages which may be cryptic species. Within the lineage with the greatest sample sizes, pairwise FST values, principal component analysis, and a STRUCTURE analysis all suggest that long-distance migration is not common across the Lower Mekong Basin, even in areas where flood-pulse hydrology has limited genetic divergence. In tributaries, effective population size estimates were at least an order of magnitude lower than in the Mekong mainstream indicating these populations may be more vulnerable to perturbations such as human-induced fragmentation. Fish isolated upstream of several dams in one tributary exhibited particularly low genetic diversity, high amounts of relatedness, and a level of inbreeding (GIS = 0.51) that has been associated with inbreeding depression in other outcrossing species. Our results highlight the importance of assessing genetic structure and diversity in riverine fisheries populations across proposed dam development sites for the preservation of these critically important resources.

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Assessment of local genetic structure and connectivity of the common eelgrass Zostera marina for seagrass restoration in northern Europe

Marine Ecology Progress Series ◽

10.3354/meps13658 ◽

2021 ◽

Vol 664 ◽

pp. 103-116

Author(s):

L Martínez-García ◽

B Hansson ◽

J Hollander

Keyword(s):

Climate Change ◽

Genetic Variation ◽

Genetic Structure ◽

Genetic Differentiation ◽

Baltic Sea ◽

Zostera Marina ◽

Anthropogenic Impacts ◽

Ecosystem Functions ◽

Long Distance ◽

Seagrass Meadows

Seagrass meadows are one of the most important habitats in coastal regions since they constitute a multifunctional ecosystem providing high productivity and biodiversity. They play a key role in carbon sequestration capacity, mitigation against coastal erosion and as nursery grounds for many marine fish and invertebrates. However, despite these ecosystem functions and services, seagrass meadows are a threatened ecosystem worldwide. In the Baltic Sea, seagrass meadows have declined rapidly, mainly because of eutrophication, anthropogenic activities and climate change. This decline has the potential to erode the genetic variation and genetic structure of the species. In this study, we assessed how genetic variation and genetic differentiation vary among Zostera marina meadows and with a number of environmental characteristics in the county of Scania in southern Sweden. A total of 205 individuals sampled at 12 locations were analysed with 10 polymorphic microsatellite loci. Results showed that in spite of anthropogenic impacts and climate change pressures, locations of Z. marina possessed high genetic variation and weak genetic differentiation, with 3 major genetic clusters. Long-distance dispersal and/or stepping-stone dispersal was found among locations, with higher migration rates within the west coast. Organic matter, salinity and maximum depth appeared to be factors most strongly associated with the genetic structure and morphological variation of Z. marina. These findings contribute significantly in the identification of potential donor sites and the viability of impacted areas to recover from natural recruitment, for the development of effective transplantation measures of Z. marina in the southern Baltic Sea and temperate regions elsewhere.

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Phenological and molecular studies on the introduced seaweed Dictyota cyanoloma (Dictyotales, Phaeophyceae) along the Mediterranean coast of the Iberian Peninsula

Mediterranean Marine Science ◽

10.12681/mms.1872 ◽

2016 ◽

Vol 17 (3) ◽

pp. 766 ◽

Cited By ~ 5

Author(s):

J. ARAGAY ◽

D. VITALES ◽

A. GÓMEZ GARRETA ◽

M. A. RIBERA SIGUAN ◽

F. STEEN ◽

...

Keyword(s):

Genetic Structure ◽

Mediterranean Sea ◽

Algal Species ◽

Haplotype Diversity ◽

Morphological Plasticity ◽

Mediterranean Coast ◽

Long Distance ◽

Multiple Introductions ◽

Mitochondrial Haplotypes ◽

The Mediterranean

Dictyota cyanoloma, a distinctive brown algal species characterized by a blue-iridescent margin, was recently reported as an introduced species in the Mediterranean Sea (Steen et al., 2016) but little is known about its distribution dynamics, morphological plasticity and genetic structure. In the present integrative study, we evaluate its past and present occurrence along the Mediterranean Iberian coast, assess the species’ phenology in Palamós (Girona, Spain) and analyze the haplotype diversity by sequencing 49 individuals from nine sampling sites for different chloroplast and mitochondrial DNA regions. Although D. cyanoloma currently occurs along the Mediterranean Iberian coast (in 19 of 36 localities sampled between Algeciras and Llançà, mostly in marinas and harbour environments), we were not able to find any herbarium material of this species (at BCN-Phyc and MA) predating the year 1987. In Palamós, D. cyanoloma is present all through the year, with a maximum development in winter and a minimum in summer. Fertile specimens are absent during summer (July and August). Sporophytes are dominant from January to June and dioecious gametophytes were found only in February, March and June. Information about the antheridia, which has never been described before, is provided. Two chloroplast and three mitochondrial haplotypes were observed, indicating that multiple introductions of D. cyanoloma occurred in the study area. Additionally, the genetic structure suggests that spread did not occur through simple advancing wave fronts but by several long-distance dispersal events. Further studies employing microsatellite markers could potentially offer a better resolution to unravel expansion and colonisation dynamics of D. cyanoloma in the Mediterranean Sea.

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Restricted dispersal in a sea of gene flow

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2021.0458 ◽

2021 ◽

Vol 288 (1951) ◽

pp. 20210458

Author(s):

L. Benestan ◽

K. Fietz ◽

N. Loiseau ◽

P. E. Guerin ◽

E. Trofimenko ◽

...

Keyword(s):

Genetic Structure ◽

Population Genetic ◽

Spatial Scales ◽

Sampling Strategy ◽

Biophysical Model ◽

Long Distance Dispersal ◽

Long Distance ◽

Genetic Studies ◽

Large Spatial Scale ◽

Continuous Sampling

How far do marine larvae disperse in the ocean? Decades of population genetic studies have revealed generally low levels of genetic structure at large spatial scales (hundreds of kilometres). Yet this result, typically based on discrete sampling designs, does not necessarily imply extensive dispersal. Here, we adopt a continuous sampling strategy along 950 km of coast in the northwestern Mediterranean Sea to address this question in four species. In line with expectations, we observe weak genetic structure at a large spatial scale. Nevertheless, our continuous sampling strategy uncovers a pattern of isolation by distance at small spatial scales (few tens of kilometres) in two species. Individual-based simulations indicate that this signal is an expected signature of restricted dispersal. At the other extreme of the connectivity spectrum, two pairs of individuals that are closely related genetically were found more than 290 km apart, indicating long-distance dispersal. Such a combination of restricted dispersal with rare long-distance dispersal events is supported by a high-resolution biophysical model of larval dispersal in the study area, and we posit that it may be common in marine species. Our results bridge population genetic studies with direct dispersal studies and have implications for the design of marine reserve networks.

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The Genomic Basis of the Genetic Differentiation and Local Adaptive Evolution of Pampus Echinogaster based on SLAF-seq

10.21203/rs.3.rs-640424/v1 ◽

2021 ◽

Author(s):

Yuan Li ◽

Fangrui Lou ◽

Hai Li ◽

Rui Wang ◽

Zizi Cai ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Genetic Differentiation ◽

Population Expansion ◽

Nucleotide Polymorphisms ◽

Stress Reactions ◽

Long Distance ◽

Evolutionary Mechanisms ◽

Inflammatory Reactions ◽

Genomic Study

Abstract Background: Factors such as climate change (especially ocean warming) and overfishing have led to a decline in the supply of Pampus echinogaster and a trend of decreasing age. Exploring the genetic structure and local adaptive evolutionary mechanisms is crucial for the management of P. echinogaster. Results: This population genomic study of nine geographical populations of P. echinogaster in China was conducted by specific-locus amplified fragment sequencing (SLAF-seq). A total of 935,215 SLAF tags were obtained, and the average sequencing depth of the SLAF tags was 20.80×. After filtering, a total of 46,187 high-consistency genome-wide single nucleotide polymorphisms (SNPs) were detected. Based on all SNPs, the overall genetic diversity among the nine P. echinogaster populations was high. The Shantou population had the lowest genetic diversity, and the Tianjin population had the highest. Meanwhile, the population genetic structure based on all SNPs revealed significant gene exchange and insignificant genetic differentiation between the nine P. echinogaster populations. Based on pairwise genetic differentiation (FST), we further screened 1,852 outlier SNPs that might have been affected by habitat selection and annotated SLAF tags containing these 1,852 outlier SNPs using Blast2GO. The annotation results showed that the genomic sequences at the outlier SNPs were mainly related to material metabolism, ion transport, breeding, stress response, and inflammatory reactions, which may be related to the adaptation of P. echinogaster to different environmental conditions (such as water temperature and salinity) in different sea areas.Conclusions: The high genetic similarity of nine P. echinogaster populations may have been caused by the population expansion after the last glacial period, the lack of balance between migration and genetic drift, and the long-distance diffusion of eggs and larvae. We suspected that variation of these genes associated with material metabolism, ion transfer, breeding, stress reactions, and inflammatory reactions were critical for adaptation to spatially heterogeneous temperatures in natural P. echinogaster populations.

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Genetic structure of the crown-of-thorns seastar in the Pacific Ocean, with focus on Guam

PeerJ ◽

10.7717/peerj.1970 ◽

2016 ◽

Vol 4 ◽

pp. e1970 ◽

Cited By ~ 3

Author(s):

Sergio Tusso ◽

Kerstin Morcinek ◽

Catherine Vogler ◽

Peter J. Schupp ◽

Ciemon F. Caballes ◽

...

Keyword(s):

Genetic Structure ◽

Pacific Ocean ◽

Long Distance ◽

The Past ◽

The Pacific ◽

Tropical Coral ◽

Population Outbreaks ◽

Geographical Regions ◽

The Pacific Ocean ◽

The Western Pacific

Population outbreaks of the corallivorous crown-of-thorns seastar (COTS),Acanthaster ‘planci’ L., are among the most important biological disturbances of tropical coral reefs. Over the past 50 years, several devastating outbreaks have been documented around Guam, an island in the western Pacific Ocean. Previous analyses have shown that in the Pacific Ocean, COTS larval dispersal may be geographically restricted to certain regions. Here, we assess the genetic structure of Pacific COTS populations and compared samples from around Guam with a number of distant localities in the Pacific Ocean, and focused on determining the degree of genetic structure among populations previously considered to be isolated. Using microsatellites, we document substantial genetic structure between 14 localities from different geographical regions in the Pacific Ocean. Populations from the 14 locations sampled were found to be structured in three significantly differentiated groups: (1) all locations immediately around Guam, as well as Kingman Reef and Swains Island; (2) Japan, Philippines, GBR and Vanuatu; and (3) Johnston Atoll, which was significantly different from all other localities. The lack of genetic differentiation between Guam and extremely distant populations from Kingman Reef and Swains Island suggests potential long-distance dispersal of COTS in the Pacific.

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