Reduced genetic diversity and increased reproductive isolation follow population-level loss of larval dispersal in a marine gastropod

AbstractUnderstanding population genetic structure can help us to infer dispersal patterns, predict population resilience and design effective management strategies. For sessile species with limited dispersal, this is especially pertinent because genetic diversity and connectivity are key aspects of their resilience to environmental stressors. Here, we describe the population structure of Ircinia campana, a common Caribbean sponge subject to mass mortalities and disease. Microsatellites were used to genotype 440 individuals from 19 sites throughout the Greater Caribbean. We found strong genetic structure across the region, and significant isolation by distance across the Lesser Antilles, highlighting the influence of limited larval dispersal. We also observed spatial genetic structure patterns congruent with oceanography. This includes evidence of connectivity between sponges in the Florida Keys and the southeast coast of the United States (>700 km away) where the oceanographic environment is dominated by the strong Florida Current. Conversely, the population in southern Belize was strongly differentiated from all other sites, consistent with the presence of dispersal-limiting oceanographic features, including the Gulf of Honduras gyre. At smaller spatial scales (<100 km), sites showed heterogeneous patterns of low-level but significant genetic differentiation (chaotic genetic patchiness), indicative of temporal variability in recruitment or local selective pressures. Genetic diversity was similar across sites, but there was evidence of a genetic bottleneck at one site in Florida where past mass mortalities have occurred. These findings underscore the relationship between regional oceanography and weak larval dispersal in explaining population genetic patterns, and could inform conservation management of the species.

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Abundance and genetic diversity responses of a lizard (Eulamprus heatwolei) to logging disturbance

Australian Journal of Zoology ◽

10.1071/zo17051 ◽

2017 ◽

Vol 65 (6) ◽

pp. 362

Author(s):

Francesca Lyndon-Gee ◽

Joanna Sumner ◽

Yang Hu ◽

Claudio Ciofi ◽

Tim S. Jessop

Keyword(s):

Genetic Diversity ◽

Forest Management ◽

Management Practices ◽

Forest Disturbance ◽

Population Level ◽

Landscape Scale ◽

Population Abundance ◽

Animal Populations ◽

Eastern Australia ◽

Logging Disturbance

Rotational logging practices are used with the goal of reducing forest disturbance impacts on biodiversity. However, it is poorly understood whether such forest management practices conserve the demographic and genetic composition of animal populations across logged landscapes. Here we investigated whether rotational logging practices alter patterns of landscape-scale population abundance and genetic diversity of a forest-dwelling lizard (Eulamprus heatwolei) in south-eastern Australia. We sampled lizards (n = 407) at up to 48 sites across a chronosequence of logging disturbance intervals (<10 to >60 years after logging) to assess site-specific population changes and genetic diversity parameters. Lizard abundances exhibited a significant curvilinear response to time since logging, with decreased numbers following logging (<10 years), increased abundance as the forest regenerated (10–20 years), before decreasing again in older regenerated forest sites (>30 years). Lizard genetic diversity parameters were not significantly influenced by logging disturbance. These results suggest that logging practices, whilst inducing short-term changes to population abundance, had no measurable effects on the landscape-scale genetic diversity of E. heatwolei. These results are important as they demonstrate the value of monitoring for evaluating forest management efficacy, and the use of different population-level markers to make stronger inference about the potential impacts of logging activities.

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Pollen-mediated gene flow ensures connectivity among spatially discrete sub-populations of Phalaenopsis pulcherrima, a tropical food-deceptive orchid

BMC Plant Biology ◽

10.1186/s12870-019-2179-y ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 2

Author(s):

Zhe Zhang ◽

Stephan W. Gale ◽

Ji-Hong Li ◽

Gunter A. Fischer ◽

Ming-Xun Ren ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Polynomial Regression ◽

Genetic Erosion ◽

Population Level ◽

Hainan Island ◽

Paternity Analysis ◽

Genetic Structuring ◽

Long Distance ◽

High Genetic Diversity

Abstract Background Gene flow in plants via pollen and seeds is asymmetrical at different geographic scales. Orchid seeds are adapted to long-distance wind dispersal but pollinium transfer is often influenced by pollinator behavior. We combined field studies with an analysis of genetic diversity among 155 physically mapped adults and 1105 F1 seedlings to evaluate the relative contribution of pollen and seed dispersal to overall gene flow among three sub-populations of the food-deceptive orchid Phalaenopsis pulcherrima on Hainan Island, China. Results Phalaenopsis pulcherrima is self-sterile and predominantly outcrossing, resulting in high population-level genetic diversity, but plants are clumped and exhibit fine-scale genetic structuring. Even so, we detected low differentiation among sub-populations, with polynomial regression analysis suggesting gene flow via seed to be more restricted than that via pollen. Paternity analysis confirmed capsules of P. pulcherrima to each be sired by a single pollen donor, probably in part facilitated by post-pollination stigma obfuscation, with a mean pollen flow distance of 272.7 m. Despite limited sampling, we detected no loss of genetic diversity from one generation to the next. Conclusions Outcrossing mediated by deceptive pollination and self-sterility promote high genetic diversity in P. pulcherrima. Long-range pollinia transfer ensures connectivity among sub-populations, offsetting the risk of genetic erosion at local scales.

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Bayesian inference of reassortment networks reveals fitness benefits of reassortment in human influenza viruses

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1918304117 ◽

2020 ◽

Vol 117 (29) ◽

pp. 17104-17111

Author(s):

Nicola F. Müller ◽

Ugnė Stolz ◽

Gytis Dudas ◽

Tanja Stadler ◽

Timothy G. Vaughan

Keyword(s):

Genetic Diversity ◽

Phylogenetic Trees ◽

Sequence Data ◽

Population Level ◽

Influenza Viruses ◽

Monte Carlo Algorithm ◽

Full Genome Sequence ◽

Full Genome ◽

Human Influenza ◽

Fitness Benefits

Reassortment is an important source of genetic diversity in segmented viruses and is the main source of novel pathogenic influenza viruses. Despite this, studying the reassortment process has been constrained by the lack of a coherent, model-based inference framework. Here, we introduce a coalescent-based model that allows us to explicitly model the joint coalescent and reassortment process. In order to perform inference under this model, we present an efficient Markov chain Monte Carlo algorithm to sample rooted networks and the embedding of phylogenetic trees within networks. This algorithm provides the means to jointly infer coalescent and reassortment rates with the reassortment network and the embedding of segments in that network from full-genome sequence data. Studying reassortment patterns of different human influenza datasets, we find large differences in reassortment rates across different human influenza viruses. Additionally, we find that reassortment events predominantly occur on selectively fitter parts of reassortment networks showing that on a population level, reassortment positively contributes to the fitness of human influenza viruses.

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Associative Overdominance and Negative Epistasis Shape Genome-Wide Ancestry Landscape in Supplemented Fish Populations

Genes ◽

10.3390/genes12040524 ◽

2021 ◽

Vol 12 (4) ◽

pp. 524

Author(s):

Maeva Leitwein ◽

Hugo Cayuela ◽

Louis Bernatchez

Keyword(s):

Genetic Diversity ◽

Genetic Drift ◽

Recombination Rate ◽

Management Strategies ◽

Population Level ◽

Negative Effects ◽

Isolated Populations ◽

Positive Effects ◽

Genome Wide ◽

Negative Epistasis

The interplay between recombination rate, genetic drift and selection modulates variation in genome-wide ancestry. Understanding the selective processes at play is of prime importance toward predicting potential beneficial or negative effects of supplementation with domestic strains (i.e., human-introduced strains). In a system of lacustrine populations supplemented with a single domestic strain, we documented how population genetic diversity and stocking intensity produced lake-specific patterns of domestic ancestry by taking the species’ local recombination rate into consideration. We used 552 Brook Charr (Salvelinus fontinalis) from 22 small lacustrine populations, genotyped at ~32,400 mapped SNPs. We observed highly variable patterns of domestic ancestry between each of the 22 populations without any consistency in introgression patterns of the domestic ancestry. Our results suggest that such lake-specific ancestry patterns were mainly due to variable associative overdominance (AOD) effects among populations (i.e., potential positive effects due to the masking of possible deleterious alleles in low recombining regions). Signatures of AOD effects were also emphasized by highly variable patterns of genetic diversity among and within lakes, potentially driven by predominant genetic drift in those small isolated populations. Local negative effects such as negative epistasis (i.e., potential genetic incompatibilities between the native and the introduced population) potentially reflecting precursory signs of outbreeding depression were also observed at a chromosomal scale. Consequently, in order to improve conservation practices and management strategies, it became necessary to assess the consequences of supplementation at the population level by taking into account both genetic diversity and stocking intensity when available.

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The Systematics of Salmonid Fishes of Recently Glaciated Lakes

Journal of the Fisheries Research Board of Canada ◽

10.1139/f72-112 ◽

1972 ◽

Vol 29 (6) ◽

pp. 639-671 ◽

Cited By ~ 217

Author(s):

Robert J. Behnke

Keyword(s):

Genetic Diversity ◽

Reproductive Isolation ◽

Fisheries Management ◽

Common Ancestor ◽

Morphological Divergence ◽

Salmonid Fishes ◽

Sympatric Populations ◽

Homing Behavior ◽

Taxonomic Problem ◽

Fisheries Biology

The systematics of the subfamilies Salmoninae and Coregoninae of recently glaciated regions are reviewed. Interrelation between systematics and fisheries biology are stressed, pointing out the abundance of intraspecific genetic diversity of some salmonid fishes manifested in ecological and behavioral specializations, but not necessarily by morphological divergence. Innate, reproductive homing behavior of salmonid fishes may allow closely related populations to exist in sympatry and maintain reproductive isolation. Examples are cited to support the contention that many sympatric "sibling species" have evolved from a common ancestor in postglacial times. Closely related, sympatric populations are a major taxonomic problem, but this phenomenon which allows a species to consist of genetically discrete units with reproductive isolation between the stocks is of great significance for fisheries management. Postglacial salmonid communities are typically fragile and highly susceptible to disruption or destruction by introductions, eutrophication, and exploitation. Every effort should be made to protect the genetic diversity of a species.

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High-Level Genetic Diversity but No Population Structure Inferred from Nuclear and Mitochondrial Markers of the Peritrichous Ciliate Carchesium polypinum in the Grand River Basin (North America)

Applied and Environmental Microbiology ◽

10.1128/aem.00178-09 ◽

2009 ◽

Vol 75 (10) ◽

pp. 3187-3195 ◽

Cited By ~ 28

Author(s):

E. Gentekaki ◽

D. H. Lynn

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

River Basin ◽

Large Subunit ◽

Population Level ◽

Nuclear Markers ◽

Mitochondrial Markers ◽

Intraspecific Genetic Variation ◽

Grand River

ABSTRACT Studies that assess intraspecific genetic variation in ciliates are few and quite recent. Consequently, knowledge of the subject and understanding of the processes that underlie it are limited. We sought to assess the degree of intraspecific genetic variation in Carchesium polypinum (Ciliophora: Peritrichia), a cosmopolitan, freshwater ciliate. We isolated colonies of C. polypinum from locations in the Grand River basin in Southwestern Ontario, Canada. We then used the nuclear markers—ITS1, ITS2, and the hypervariable regions of the large subunit rRNA—and an 819-bp fragment of the mitochondrial cytochrome c oxidase I gene (cox-1) to investigate the intraspecific genetic variation of C. polypinum and the degree of resolution of the above-mentioned markers at the population level. We also sought to determine whether the organism demonstrated any population structure that mapped onto the geography of the region. Our study shows that there is a high degree of genetic diversity at the isolate level, revealed by the mitochondrial markers but not the nuclear markers. Furthermore, our results indicate that C. polypinum is likely not a single morphospecies as previously thought.

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The Genetic Diversity and Geographic Differentiation of the Wild Soybean in Northeast China Based on Nuclear Microsatellite Variation

International Journal of Genomics ◽

10.1155/2018/8561458 ◽

2018 ◽

Vol 2018 ◽

pp. 1-9

Author(s):

Hongkun Zhao ◽

Yumin Wang ◽

Fu Xing ◽

Xiaodong Liu ◽

Cuiping Yuan ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Northeast China ◽

Wild Soybean ◽

Population Level ◽

Mantel Test ◽

Microsatellite Variation ◽

Information Index ◽

Ssr Loci ◽

The Mean

In this study, the genetic diversity and population structure of 205 wild soybean core collections in Northeast China from nine latitude populations and nine longitude populations were evaluated using SSR markers. A total of 973 alleles were detected by 43 SSR loci, and the average number of alleles per locus was 22.628. The mean Shannon information index (I) and the mean expected heterozygosity were 2.528 and 0.879, respectively. At the population level, the regions of 42°N and 124°E had the highest genetic diversity among all latitudes and longitudes. The greater the difference in latitude was, the greater the genetic distance was, whereas a similar trend was not found in longitude populations. Three main clusters (1N, <41°N-42°N; 2N, 43°N-44°N; and 3N, 45°N–>49°N) were assigned to populations. AMOVA analysis showed that the genetic differentiation among latitude and longitude populations was 0.088 and 0.058, respectively, and the majority of genetic variation occurred within populations. The Mantel test revealed that genetic distance was significantly correlated with geographical distance (r=0.207, p<0.05). Furthermore, spatial autocorrelation analysis showed that there was a spatial structure (ω=119.58, p<0.01) and the correlation coefficient (r) decreased as distance increased within a radius of 250 km.

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Genetic structure and diversity of a collection of Brassica rapa subsp. rapa L. revealed by simple sequence repeat markers

The Journal of Agricultural Science ◽

10.1017/s002185961100013x ◽

2011 ◽

Vol 149 (5) ◽

pp. 617-624 ◽

Cited By ~ 9

Author(s):

P. SOENGAS ◽

M. E. CARTEA ◽

M. FRANCISCO ◽

M. LEMA ◽

P. VELASCO

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Brassica Rapa ◽

Genetic Relationships ◽

Population Level ◽

Research Centre ◽

Breeding Programmes ◽

Western Spain ◽

Genetic Structure And Diversity ◽

Simple Sequence

SUMMARYBrassica rapa subsp. rapa L. includes three different crops: turnips (roots), turnip greens (leaves) and turnip tops (inflorescences). A collection of B. rapa subsp. rapa from north-western Spain is currently kept at ‘Misión Biológica de Galicia’ (a research centre of the Consejo Superior de Investigaciones Científicas (CSIC), Spain). This collection has been characterized based on morphological and agronomical traits. A better understanding of the genetic diversity present in the collection is necessary in order to optimize its use and maintenance. The objectives of the present work were to assess the genetic diversity present in the B. rapa subsp. rapa collection, to establish genetic relationships among populations and to study the genetic structure of the collection. Eighty populations were analysed based on 18 simple sequence repeats (SSRs). Populations showed a broad range of genetic diversity, thus offering good potential for further genetic improvement. Most of the variability was found within the population level, probably due to high rates of allogamy, to migration and/or interchange of seed among local growers. Populations showed a low level of differentiation, grouping in just one cluster, and therefore they can be considered as samples of a highly variable metapopulation that can be used for B. rapa breeding programmes.

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