Spatial and temporal genetic variation in an exploited reef fish: The effects of exploitation on cohort genetic structure

The European eel ( Anguilla anguilla L.) has been a prime example of the panmixia paradigm because of its extraordinary adaptation to the North Atlantic gyral system, semelparous spawning in the Sargasso Sea and long trans-oceanic migration. Recently, this view was challenged by the suggestion of a genetic structure characterized by an isolation-by-distance (IBD) pattern. This is only likely if spawning subpopulations are spatially and/or temporally separated, followed by non-random larval dispersal. A limitation of previous genetic work on eels is the lack of replication over time to test for temporal stability of genetic structure. Here, we hypothesize that temporal genetic variation plays a significant role in explaining the spatial structure reported earlier for this species. We tested this by increasing the texture of geographical sampling and by including temporal replicates. Overall genetic differentiation among samples was low, highly significant and comparable with earlier studies ( F ST =0.0014; p <0.01). On the other hand, and in sharp contrast with current understandings, hierarchical analyses revealed no significant inter-location genetic heterogeneity and hence no IBD. Instead, genetic variation among temporal samples within sites clearly exceeded the geographical component. Our results provide support for the panmixia hypothesis and emphasize the importance of temporal replication when assessing population structure of marine fish species.

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Genomic variation in the American pika: signatures of geographic isolation and implications for conservation

BMC Ecology and Evolution ◽

10.1186/s12862-020-01739-9 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Kelly B. Klingler ◽

Joshua P. Jahner ◽

Thomas L. Parchman ◽

Chris Ray ◽

Mary M. Peacock

Keyword(s):

Genetic Variation ◽

Genetic Structure ◽

Sierra Nevada ◽

Spatial Genetic Structure ◽

Spatial Scales ◽

Thermal Sensitivity ◽

Genomic Variation ◽

Genome Wide ◽

A Genome ◽

American Pika

Abstract Background Distributional responses by alpine taxa to repeated, glacial-interglacial cycles throughout the last two million years have significantly influenced the spatial genetic structure of populations. These effects have been exacerbated for the American pika (Ochotona princeps), a small alpine lagomorph constrained by thermal sensitivity and a limited dispersal capacity. As a species of conservation concern, long-term lack of gene flow has important consequences for landscape genetic structure and levels of diversity within populations. Here, we use reduced representation sequencing (ddRADseq) to provide a genome-wide perspective on patterns of genetic variation across pika populations representing distinct subspecies. To investigate how landscape and environmental features shape genetic variation, we collected genetic samples from distinct geographic regions as well as across finer spatial scales in two geographically proximate mountain ranges of eastern Nevada. Results Our genome-wide analyses corroborate range-wide, mitochondrial subspecific designations and reveal pronounced fine-scale population structure between the Ruby Mountains and East Humboldt Range of eastern Nevada. Populations in Nevada were characterized by low genetic diversity (π = 0.0006–0.0009; θW = 0.0005–0.0007) relative to populations in California (π = 0.0014–0.0019; θW = 0.0011–0.0017) and the Rocky Mountains (π = 0.0025–0.0027; θW = 0.0021–0.0024), indicating substantial genetic drift in these isolated populations. Tajima’s D was positive for all sites (D = 0.240–0.811), consistent with recent contraction in population sizes range-wide. Conclusions Substantial influences of geography, elevation and climate variables on genetic differentiation were also detected and may interact with the regional effects of anthropogenic climate change to force the loss of unique genetic lineages through continued population extirpations in the Great Basin and Sierra Nevada.

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Impact of cyclones on hard coral and metapopulation structure, connectivity and genetic diversity of coral reef fish

Coral Reefs ◽

10.1007/s00338-021-02096-9 ◽

2021 ◽

Author(s):

Gabriele Gerlach ◽

Philipp Kraemer ◽

Peggy Weist ◽

Laura Eickelmann ◽

Michael J. Kingsford

Keyword(s):

Genetic Diversity ◽

Coral Reef ◽

Genetic Structure ◽

Reef Fish ◽

Coral Reef Fish ◽

Population Genetic Study ◽

Hard Coral ◽

Great Loss ◽

Metapopulation Structure ◽

The Impact

AbstractCyclones have one of the greatest effects on the biodiversity of coral reefs and the associated species. But it is unknown how stochastic alterations in habitat structure influence metapopulation structure, connectivity and genetic diversity. From 1993 to 2018, the reefs of the Capricorn Bunker Reef group in the southern part of the Great Barrier Reef were impacted by three tropical cyclones including cyclone Hamish (2009, category 5). This resulted in substantial loss of live habitat-forming coral and coral reef fish communities. Within 6–8 years after cyclones had devastated, live hard corals recovered by 50–60%. We show the relationship between hard coral cover and the abundance of the neon damselfish (Pomacentrus coelestis), the first fish colonizing destroyed reefs. We present the first long-term (2008–2015 years corresponding to 16–24 generations of P. coelestis) population genetic study to understand the impact of cyclones on the meta-population structure, connectivity and genetic diversity of the neon damselfish. After the cyclone, we observed the largest change in the genetic structure at reef populations compared to other years. Simultaneously, allelic richness of genetic microsatellite markers dropped indicating a great loss of genetic diversity, which increased again in subsequent years. Over years, metapopulation dynamics were characterized by high connectivity among fish populations associated with the Capricorn Bunker reefs (2200 km2); however, despite high exchange, genetic patchiness was observed with annual strong genetic divergence between populations among reefs. Some broad similarities in the genetic structure in 2015 could be explained by dispersal from a source reef and the related expansion of local populations. This study has shown that alternating cyclone-driven changes and subsequent recovery phases of coral habitat can greatly influence patterns of reef fish connectivity. The frequency of disturbances determines abundance of fish and genetic diversity within species.

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Genetic Relationships of Cory's Shearwater: Parentage, Mating Assortment, and Geographic Differentiation Revealed by DNA Fingerprinting

The Auk ◽

10.1093/auk/117.3.651 ◽

2000 ◽

Vol 117 (3) ◽

pp. 651-662 ◽

Cited By ~ 1

Author(s):

Corinne Rabouam ◽

Vincent Bretagnolle ◽

Yves Bigot ◽

Georges Periquet

Keyword(s):

Genetic Variation ◽

Genetic Structure ◽

Dna Fingerprinting ◽

Genetic Relatedness ◽

Isolation By Distance ◽

Genetic Relationships ◽

Cory’S Shearwater ◽

Genetic Structure Of Populations ◽

The Social ◽

Calonectris Diomedea

Abstract We used DNA fingerprinting to assess genetic structure of populations in Cory's Shearwater (Calonectris diomedea). We analyzed mates and parent-offspring relationships, as well as the amount and distribution of genetic variation within and among populations, from the level of subcolony to subspecies. We found no evidence of extrapair fertilization, confirming that the genetic breeding system matches the social system that has been observed in the species. Mates were closely related, and the level of genetic relatedness within populations was within the range usually found in inbred populations. In contrast to previous studies based on allozymes and mtDNA polymorphism, DNA fingerprinting using microsatellites revealed consistent levels of genetic differentiation among populations. However, analyzing the two subspecies separately revealed that the pattern of genetic variation among populations did not support the model of isolation by distance. Natal dispersal, as well as historic and/or demographic events, probably contributed to shape the genetic structure of populations in the species.

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Significant genetic differences among Heterodera schachtii populations within and among sugar beet production areas

Nematology ◽

10.1163/15685411-00003297 ◽

2020 ◽

Vol 22 (2) ◽

pp. 165-177 ◽

Cited By ~ 1

Author(s):

Rasha Haj Nuaima ◽

Johannes Roeb ◽

Johannes Hallmann ◽

Matthias Daub ◽

Holger Heuer

Keyword(s):

Genetic Variation ◽

Genetic Structure ◽

Population Genetic Structure ◽

Population Genetic ◽

Spatial Scales ◽

Geographic Distance ◽

Heterodera Schachtii ◽

Parasitic Nematodes ◽

Neutral Genetic Variation ◽

Production Areas

Summary Characterising the non-neutral genetic variation within and among populations of plant-parasitic nematodes is essential to determine factors shaping the population genetic structure. This study describes the genetic variation of the parasitism gene vap1 within and among geographic populations of the beet cyst nematode Heterodera schachtii. Forty populations of H. schachtii were sampled at four spatial scales: 695 km, 49 km, 3.1 km and 0.24 km. DGGE fingerprinting showed significant differences in vap1 patterns among populations. High similarity of vap1 patterns appeared between geographically close populations, and occasionally among distant populations. Analysis of spatially sampled populations within fields revealed an effect of tillage direction on the vap1 similarity for two of four studied fields. Overall, geographic distance and similarity of vap1 patterns of H. schachtii populations were negatively correlated. In conclusion, the population genetic structure was shaped by the interplay between the genetic adaptation and the passive transport of this nematode.

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Significant population genetic structure detected for a new and highly restricted species of Atriplex (Chenopodiaceae) from Western Australia, and implications for conservation management

Australian Journal of Botany ◽

10.1071/bt11223 ◽

2012 ◽

Vol 60 (1) ◽

pp. 32 ◽

Cited By ~ 15

Author(s):

Laurence J. Clarke ◽

Duncan I. Jardine ◽

Margaret Byrne ◽

Kelly Shepherd ◽

Andrew J. Lowe

Keyword(s):

Genetic Variation ◽

New Species ◽

Genetic Structure ◽

Western Australia ◽

Sequence Data ◽

Isolation By Distance ◽

Conservation Strategies ◽

New Taxon ◽

Near Surface ◽

Two Populations

Atriplex sp. Yeelirrie Station (L. Trotter & A. Douglas LCH 25025) is a highly restricted, potentially new species of saltbush, known from only two sites ~30 km apart in central Western Australia. Knowledge of genetic structure within the species is required to inform conservation strategies as both populations occur within a palaeovalley that contains significant near-surface uranium mineralisation. We investigate the structure of genetic variation within populations and subpopulations of this taxon using nuclear microsatellites. Internal transcribed spacer sequence data places this new taxon within a clade of polyploid Atriplex species, and the maximum number of alleles per locus suggests it is hexaploid. The two populations possessed similar levels of genetic diversity, but exhibited a surprising level of genetic differentiation given their proximity. Significant isolation by distance over scales of less than 5 km suggests dispersal is highly restricted. In addition, the proportion of variation between the populations (12%) is similar to that among A. nummularia populations sampled at a continent-wide scale (several thousand kilometres), and only marginally less than that between distinct A. nummularia subspecies. Additional work is required to further clarify the exact taxonomic status of the two populations. We propose management recommendations for this potentially new species in light of its highly structured genetic variation.

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Spatial genetic structure of the sea sandwort (<i>Honckenya peploides</i>) on Surtsey: an immigrant's journey

Biogeosciences ◽

10.5194/bg-11-6495-2014 ◽

2014 ◽

Vol 11 (22) ◽

pp. 6495-6507 ◽

Cited By ~ 3

Author(s):

S. H. Árnason ◽

Ǽ. Th. Thórsson ◽

B. Magnússon ◽

M. Philipp ◽

H. Adsersen ◽

...

Keyword(s):

Genetic Variation ◽

Genetic Structure ◽

Early Stage ◽

Isolation By Distance ◽

Spatial Genetic Structure ◽

Rapid Expansion ◽

Aflp Markers ◽

Plant Colonization ◽

Southern Coast ◽

Binary Matrix

Abstract. Sea sandwort (Honckenya peploides) was one of the first plants to successfully colonize and reproduce on the volcanic island Surtsey, formed in 1963 off the southern coast of Iceland. Using amplified fragment length polymorphic (AFLP) markers, we examined levels of genetic variation and differentiation among populations of H. peploides on Surtsey in relation to populations on the nearby island Heimaey and from the southern coast of Iceland. Selected populations from Denmark and Greenland were used for comparison. In addition, we tested whether the effects of isolation by distance could be seen in the Surtsey populations. Using two primer combinations, we obtained 173 AFLP markers from a total of 347 plant samples. The resulting binary matrix was then analysed statistically. The main results include the following: (i) Surtsey had the highest proportion of polymorphic markers as well as a comparatively high genetic diversity (55.5% proportion of polymorphic loci, PLP; 0.1974 HE) and Denmark the lowest (31.8% PLP; 0.132 HE), indicating rapid expansion during an early stage of population establishment on Surtsey and/or multiple origins of immigrants; (ii) the total genetic differentiation (FST) among Surtsey (0.0714) and Heimaey (0.055) populations was less than half of that found among the mainland populations in Iceland (0.1747), indicating substantial gene flow on the islands; (iii) most of the genetic variation (79%, p < 0.001) was found within localities, possibly due to the outcrossing and subdioecious nature of the species; (iv) a significant genetic distance was found within Surtsey, among sites, and this appeared to correlate with the age of plant colonization; and (v) the genetic structure analysis indicated multiple colonization episodes on Surtsey, whereby H. peploides most likely immigrated from the nearby island of Heimaey and directly from the southern coast of Iceland.

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Temporal genetic variation in Aedes aegypti populations in Ho Chi Minh City (Vietnam)

Heredity ◽

10.1038/sj.hdy.6800086 ◽

2002 ◽

Vol 89 (1) ◽

pp. 7-14 ◽

Cited By ~ 33

Author(s):

K Huber ◽

Luu Le Loan ◽

Tran Huu Hoang ◽

Tran Khanh Tien ◽

F Rodhain ◽

...

Keyword(s):

Genetic Variation ◽

Aedes Aegypti ◽

Ho Chi Minh City ◽

Temporal Genetic Variation

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Temporal Genetic Variation in the Raccoon, Procyon lotor

Journal of Mammalogy ◽

10.2307/1383085 ◽

1998 ◽

Vol 79 (3) ◽

pp. 747 ◽

Cited By ~ 6

Author(s):

Susan E. White ◽

Phyllis K. Kennedy ◽

Michael L. Kennedy

Keyword(s):

Genetic Variation ◽

Procyon Lotor ◽

Temporal Genetic Variation

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Landscape permeability and individual variation in a dispersal-linked gene jointly determine genetic structure in the Glanville fritillary butterfly

10.1101/409003 ◽

2018 ◽

Author(s):

Michelle F. DiLeo ◽

Arild Husby ◽

Marjo Saastamoinen

Keyword(s):

Genetic Variation ◽

Gene Flow ◽

Genetic Structure ◽

Individual Variation ◽

Landscape Fragmentation ◽

Landscape Matrix ◽

Fragmented Landscapes ◽

Dispersal Traits ◽

Glanville Fritillary Butterfly ◽

Large Decline

AbstractThere is now clear evidence that species across a broad range of taxa harbour extensive heritable variation in dispersal. While studies suggest that this variation can facilitate demographic outcomes such as range expansion and invasions, few have considered the consequences of intraspecific variation in dispersal for the maintenance and distribution of genetic variation across fragmented landscapes. Here we examine how landscape characteristics and individual variation in dispersal combine to predict genetic structure using genomic and spatial data from the Glanville fritillary butterfly. We used linear and latent factor mixed models to identify the landscape features that best predict spatial sorting of alleles in the dispersal-related gene phosphoglucose isomerase (Pgi). We next used structural equation modeling to test if variation in Pgi mediated gene flow as measured by Fst at putatively neutral loci. In a year when the population was expanding following a large decline, individuals with a genotype associated with greater dispersal ability were found at significantly higher frequencies in populations isolated by water and forest, and these populations showed lower levels of genetic differentiation at neutral loci. These relationships disappeared in the next year when metapopulation density was high, suggesting that the effects of individual variation are context dependent. Together our results highlight that 1) more complex aspects of landscape structure beyond just the configuration of habitat can be important for maintaining spatial variation in dispersal traits, and 2) that individual variation in dispersal plays a key role in maintaining genetic variation across fragmented landscapes.Impact summaryUnderstanding how fragmentation affects dispersal and gene flow across human-modified landscapes has long been a goal in evolutionary biology. It is typically assumed that individuals of the same species respond to the landscape in the same way, however growing evidence suggests that individuals can vary considerably in their dispersal traits. While the effects of this individual dispersal variation on range expansions and invasions have been well-characterized, knowledge of how it might mediate genetic responses to landscape fragmentation are almost entirely lacking. Here we demonstrate that individual variation in dispersal is key to the maintenance of genetic variation during a population expansion following a large decline in a butterfly metapopulation. We further show that spatial variation in dispersal is not maintained by the configuration of habitat patches alone, but by a more complex genotype-environment interaction involving the landscape matrix (i.e. landscape features found between habitat patches). This challenges the simplified landscape representations typically used in studies of dispersal evolution that ignore heterogeneity in the landscape matrix. More broadly, our results highlight the interplay of adaptive and neutral processes across fragmented landscapes, suggesting that an understanding of species vulnerability to landscape fragmentation requires consideration of both.

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