Population genomics of the widespread African savannah trees Afzelia africana and Afzelia quanzensis (Caesalpinioideae, Fabaceae) reveals no significant past fragmentation of their distribution ranges

ABSTRACTFew studies have addressed the evolutionary history of tree species from African savannahs at large geographic scales, particularly in the southern hemisphere (Zambezian region). Afzelia (Fabaceae: Caesalpinioideae) contains economically important timber species, including two species widely distributed in African savannahs: A. africana in the Sudanian region and A. quanzensis in the Zambezian region. To characterize the population genetic diversity and structure of these two species across their distribution ranges, we used nuclear microsatellites (simple sequence repeats, SSRs) and genotyping-by-sequencing (GBS) markers. Six SSR loci were genotyped in 241 A. africana and 113 A. quanzensis individuals, while 2,800 and 3,841 high-quality single nucleotide polymorphisms (SNPs) were identified in 30 A. africana and 12 A. quanzensis individuals, respectively. Both species appeared to be outcrossing (selfing rate ~ 0%). The spatial genetic structure was consistent with isolation-by-distance expectations based on both SSR and SNP data, suggesting that gene dispersal is spatially restricted in both species (bLd (SSR)= −0.005 and −0.007 and bLd (SNP)= −0.008 and −0.006 for A. africana and A. quanzensis, respectively). Bayesian clustering of SSR genotypes failed to identify genetic structure within species. In contrast, SNP data resolved intraspecific genetic clusters in both species, illustrating the higher resolving power of GBS at shallow levels of divergence. However, the clusters identified by SNPs revealed low levels of differentiation and no clear geographical entities. These results suggest that, although gene flow has been restricted over short distances in both species, populations have remained connected throughout the large, continuous Savannah landscapes. The absence of clear phylogeographic discontinuities, also found in a few other African savannah trees, indicates that their distribution ranges have not been significantly fragmented during past climate changes, in contrast to patterns commonly found in African rainforest trees.

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Spatial population genomics of a recent mosquito invasion

10.1101/2020.11.30.405191 ◽

2020 ◽

Author(s):

Thomas L Schmidt ◽

T. Swan ◽

Jessica Chung ◽

Stephan Karl ◽

Samuel Demok ◽

...

Keyword(s):

Gene Flow ◽

Population Genomics ◽

Isolation By Distance ◽

Spatial Genetic Structure ◽

Nucleotide Polymorphisms ◽

Discrete Events ◽

Long Distance ◽

Population Genomic ◽

Asian Tiger ◽

Study Designs

AbstractPopulation genomic approaches can characterise dispersal across a single generation through to many generations in the past, bridging the gap between individual movement and intergenerational gene flow. These approaches are particularly useful when investigating dispersal in recently altered systems, where they provide a way of inferring long-distance dispersal between newly established populations and their interactions with existing populations. Human-mediated biological invasions represent such altered systems which can be investigated with appropriate study designs and analyses. Here we apply temporally-restricted sampling and a range of population genomic approaches to investigate dispersal in a 2004 invasion of Aedes albopictus (the Asian tiger mosquito) in the Torres Strait Islands (TSI) of Australia. We sampled mosquitoes from 13 TSI villages simultaneously and genotyped 373 mosquitoes at genome-wide single nucleotide polymorphisms (SNPs): 331 from the TSI, 36 from Papua New Guinea (PNG), and 4 incursive mosquitoes detected in uninvaded regions. Within villages, spatial genetic structure varied substantially but overall displayed isolation by distance and a neighbourhood size of 232–577. Close kin dyads revealed recent movement between islands 31–203 km apart, and deep learning inferences showed incursive Ae. albopictus had travelled to uninvaded regions from both adjacent and non-adjacent islands. Private alleles and a coancestry matrix indicated direct gene flow from PNG into nearby islands. Outlier analyses also detected four linked alleles introgressed from PNG, with the alleles surrounding 12 resistance-associated cytochrome P450 genes. By treating dispersal as both an intergenerational process and a set of discrete events, we describe a highly interconnected invasive system.

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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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Can We Compare Effect Size of Spatial Genetic Structure Between Studies and Species Using Moran Eigenvector Maps?

Frontiers in Ecology and Evolution ◽

10.3389/fevo.2021.612718 ◽

2021 ◽

Vol 9 ◽

Author(s):

Celia Hein ◽

Hossam E. Abdel Moniem ◽

Helene H. Wagner

Keyword(s):

Genetic Structure ◽

Effect Size ◽

Stationary Process ◽

Isolation By Distance ◽

Spatial Genetic Structure ◽

Meta Analysis ◽

Empirical Studies ◽

Sampling Locations ◽

Number Of Individuals ◽

Moran Eigenvector Maps

As the field of landscape genetics is progressing toward comparative empirical studies and meta-analysis, it is important to know how best to compare the strength of spatial genetic structure between studies and species. Moran’s Eigenvector Maps are a promising method that does not make an assumption of isolation-by-distance in a homogeneous environment but can discern cryptic structure that may result from multiple processes operating in heterogeneous landscapes. MEMgene uses spatial filters from Moran’s Eigenvector Maps as predictor variables to explain variation in a genetic distance matrix, and it returns adjusted R2 as a measure of the amount of genetic variation that is spatially structured. However, it is unclear whether, and under which conditions, this value can be used to compare the degree of spatial genetic structure (effect size) between studies. This study addresses the fundamental question of comparability at two levels: between independent studies (meta-analysis mode) and between species sampled at the same locations (comparative mode). We used published datasets containing 9,900 haploid, biallelic, neutral loci simulated on a quasi-continuous, square landscape under four demographic scenarios (island model, isolation-by-distance, expansion from one or two refugia). We varied the genetic resolution (number of individuals and loci) and the number of random sampling locations. We considered two measures of effect size, the MEMgene adjusted R2 and multivariate Moran’s I, which is related to Moran’s Eigenvector Maps. Both metrics were highly sensitive to the number of locations, even when using standardized effect sizes, SES, and the number of individuals sampled per location, but not to the number of loci. In comparative mode, using the same Moran Eigenvector Maps for all species, even those with missing values at some sampling locations, reduced bias due to the number of locations under isolation-by-distance (stationary process) but increased it under expansion from one or two refugia (non-stationary process). More robust measures of effect size need to be developed before the strength of spatial genetic structure can be accurately compared, either in a meta-analysis of independent empirical studies or within a comparative, multispecies landscape genetic study.

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Genotyping-by-sequencing reveals genomic homogeneity among overwintering Pacific Dunlin (Calidris alpina pacifica) aggregations along the Pacific coast of North America

The Condor ◽

10.1093/condor/duz036 ◽

2019 ◽

Vol 121 (3) ◽

Cited By ~ 1

Author(s):

Iva Popovic ◽

David P L Toews ◽

Carson C Keever ◽

C Toby St. Clair ◽

Blake A Barbaree ◽

...

Keyword(s):

Genetic Structure ◽

Isolation By Distance ◽

Spatial Scales ◽

River Estuary ◽

Genotyping By Sequencing ◽

Genomic Diversity ◽

Nucleotide Polymorphisms ◽

Migratory Connectivity ◽

Calidris Alpina ◽

The Pacific

Abstract Information on how migratory populations are genetically structured during the overwintering season of the annual cycle can improve our understanding of the strength of migratory connectivity and help identify populations as units for management. Here, we use a genotype-by-sequencing approach to investigate whether population genetic structure exists among overwintering aggregations of the Pacific Dunlin subspecies (Calidris alpina pacifica) sampled at 2 spatial scales (within and among overwintering sites) in the eastern Pacific Flyway. Genome-wide analyses of 874 single nucleotide polymorphisms across 80 sampled individuals revealed no evidence for genetic differentiation among aggregations overwintering at 3 locations within the Fraser River Estuary (FRE) of British Columbia. Similarly, comparisons of aggregations in the FRE and those overwintering in southern sites in California and Mexico indicated no genetic segregation between northern and southern overwintering areas. These results suggest that Pacific Dunlin within the FRE, Sacramento Valley (California), and Guerrero Negro (Mexico) are genetically homogeneous, with no evident genetic structure between sampled sites or regions across the overwintering range. Despite no evidence for differentiation among aggregations, we identified a significant effect of geographical distance between sites on the distribution of individual genotypes in a redundancy analysis. A small proportion of the total genotypic variance (R2 =0.036, P = 0.011) was explained by the combined effect of latitude and longitude, suggesting weak genomic patterns of isolation-by-distance that are consistent with chain-like migratory connectivity between breeding and overwintering areas. Our study represents the first genome-scale investigation of population structure for a Dunlin subspecies and provides essential baseline estimates of genomic diversity and differentiation within the Pacific Dunlin.

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Population genetic structure of the Gulf of St. Lawrence aster, Symphyotrichum laurentianum (Asteraceae), a threatened coastal endemic

Botany ◽

10.1139/b09-068 ◽

2009 ◽

Vol 87 (11) ◽

pp. 1089-1095 ◽

Cited By ~ 5

Author(s):

Stephen B. Heard ◽

Linley K. Jesson ◽

Kirby Tulk

Keyword(s):

Genetic Variation ◽

Genetic Structure ◽

Threatened Species ◽

Population Genetic Structure ◽

Population Genetic ◽

Isolation By Distance ◽

Spatial Genetic Structure ◽

Population Decline ◽

Allelic Diversity ◽

Magdalen Islands

The Gulf of St. Lawrence aster ( Symphyotrichum laurentianum (Fernald) G.L. Nesom) is an endemic annual of saline habitats in the southern Gulf of St. Lawrence. It is listed as a threatened species, and has recently experienced population declines in much of its range. We used 11 allozyme markers to assay population genetic variation in six wild populations of S. laurentianum from the Magdalen Islands, Quebec (QC), the only remaining wild population from Prince Edward Island National Park (PEI), and a greenhouse population founded in 1999 with seed collected from PEI. Symphyotrichum laurentianum harbours moderate genetic diversity (Ps = 0.36, As = 1.54), with only modest spatial genetic structure (pairwise FST < 0.15) and no significant isolation by distance. The PEI population had greatly reduced allelic diversity compared with the populations from the Magdalen Islands, which likely act as a reservoir of genetic variation in S. laurentianum. Recent loss of alleles during population decline in PEI is suggested by the retention of greater allelic diversity in the greenhouse population. Estimates of breeding structure suggest small but nonzero rates of outcross pollination (FIS = 0.73, 95% CI = 0.48–0.97; outcrossing rate ∼16%). Population genetic structure in S. laurentianum can inform those forming and carrying out conservation and recovery plans for this threatened species.

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Temporal patterns of spatial genetic structure and effective population size in European plaice (Pleuronectes platessa) along the west coast of Scotland and in the Irish Sea

ICES Journal of Marine Science ◽

10.1093/icesjms/fsp274 ◽

2009 ◽

Vol 67 (4) ◽

pp. 607-616 ◽

Cited By ~ 8

Author(s):

Phillip C. Watts ◽

Suzanne M. Kay ◽

Drew Wolfenden ◽

Clive J. Fox ◽

Audrey J. Geffen ◽

...

Keyword(s):

Genetic Structure ◽

Population Size ◽

Effective Population Size ◽

West Coast ◽

Isolation By Distance ◽

Spatial Genetic Structure ◽

Irish Sea ◽

Effective Population ◽

The West ◽

Pleuronectes Platessa

Abstract Watts, P. C., Kay, S. M., Wolfenden, D., Fox, C. J., Geffen, A. J., Kemp, S. J., and Nash, R. D. M. 2010. Temporal patterns of spatial genetic structure and effective population size in European plaice (Pleuronectes platessa) along the west coast of Scotland and in the Irish Sea. – ICES Journal of Marine Science, 67: 607–616. The European plaice (Pleuronectes platessa) is a relatively mobile flatfish species, and previous studies have reported broad-scale genetic homogeneity among samples distributed throughout much of its northern European range, with no evidence for isolation-by-distance (IBD) population structure. Using microsatellite loci, the pattern of spatial genetic structure and effective population size is characterized for >800 plaice collected from locations off the west coast of Great Britain over a 3-year period (2001–2003). The plaice populations are characterized by weak spatial genetic structure, consistent with tagging data, and relatively low effective population sizes. In contrast to previous work, a pattern of isolation by distance is present among pairs of plaice from within each sampling period. However, IBD spatial structure was not observed for comparisons of plaice from different sampling years or using the entire dataset, indicating a patchy temporal genetic structure. Therefore, pooling the data from several years can mask subtle patterns of population structure and potentially confound estimation of other important demographic parameters, such as effective population size.

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Fine-Scale Spatial Genetic Structure with Nonuniform Distribution of Individuals

Genetics ◽

10.1093/genetics/148.2.905 ◽

1998 ◽

Vol 148 (2) ◽

pp. 905-919

Author(s):

Agnès Doligez ◽

Claire Baril ◽

Hélène I Joly

Keyword(s):

Genetic Structure ◽

Local Density ◽

Isolation By Distance ◽

Spatial Genetic Structure ◽

Pollen Dispersal ◽

Continuous Distribution ◽

Fine Scale ◽

Independent Locus ◽

Continuous Plant ◽

Input Variables

Abstract This paper presents the first theoretical study of spatial genetic structure within nonuniformly distributed continuous plant populations. A novel individual-based model of isolation by distance was constructed to simulate genetic evolution within such populations. We found larger values of spatial genetic autocorrelations in highly clumped populations than in uniformly distributed populations. Most of this difference was caused by differences in mean dispersal distances, but aggregation probably also produced a slight increase in spatial genetic structure. Using an appropriate level of approximation of the continuous distribution of individuals in space, we assessed the potential effects of density, seed and pollen dispersal, generation overlapping, and overdominance selection at an independent locus, on fine-scale genetic structure, by varying them separately in a few particular cases with extreme clumping. When selfing was allowed, all these input variables influenced both aggregation and spatial genetic structure. Most variations in spatial genetic structure were closely linked to variations in clumping and/or local density. When selfing was not allowed, spatial genetic structure was lower in most cases.

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Spatial genetic structure in the very rare and species-rich Picea chihuahuana tree community (Mexico)

Silvae Genetica ◽

10.1515/sg-2014-0020 ◽

2014 ◽

Vol 63 (1-6) ◽

pp. 149-158 ◽

Cited By ~ 9

Author(s):

C. Z. Quiñones-Pérez ◽

S. L. Simental-Rodríguez ◽

C. Sáenz-Romero ◽

J. P. Jaramillo-Correa ◽

C. Wehenkel

Keyword(s):

Genetic Structure ◽

Populus Tremuloides ◽

Isolation By Distance ◽

Spatial Genetic Structure ◽

Strong Support ◽

Forest Tree ◽

Conservation Strategies ◽

Fine Scale ◽

Ecological Features ◽

Tree Community

Abstract In natural plant populations, the spatial genetic structure (SGS) is occasionally associated with evolutionary and ecological features such as the mating system, individual fitness, inbreeding depression and natural selection of the species of interest. The very rare Mexican P. chihuahuana tree community covers an area no more than 300 ha and has been the subject of several studies concerning its ecology and population genetics. The overall aim of most of these studies has been to obtain data to help design preservation and conservation strategies. However, analysis of the fine-scale SGS in this special forest tree community has not yet been conducted, which might help enrich the above mentioned conservation programs. In this study, we examined the SGS of this community, mostly formed by P. chihuahuana Martínez, Pinus strobiformis Ehrenberg ex Schlechtendah, Pseudotsuga menziesii (Mirb.) Franco, and Populus tremuloides Michx, in 14 localities at both the fine and large scales, with the aim of obtaining a better understanding of evolutionary processes. We observed a non-significant autocorrelation in fine-scale SGS, suggesting that the genetic variants of all four tree species are randomly distributed in space within each sampled plot of 50 x 50 m. At the larger scale, the autocorrelation was highly significant for P. chihuahuana and P. menziesii, probably as a result of insufficient gene flow due to the extreme population isolation and small sizes. For these two species our results provided strong support for the theory of isolation by distance.

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Seascape Genomics of the Sugar Kelp Saccharina latissima along the North Eastern Atlantic Latitudinal Gradient

Genes ◽

10.3390/genes11121503 ◽

2020 ◽

Vol 11 (12) ◽

pp. 1503

Author(s):

Jaromir Guzinski ◽

Paolo Ruggeri ◽

Marion Ballenghien ◽

Stephane Mauger ◽

Bertrand Jacquemin ◽

...

Keyword(s):

Genetic Diversity ◽

Climatic Changes ◽

Statistical Correlation ◽

Limiting Factors ◽

Saccharina Latissima ◽

Nucleotide Polymorphisms ◽

Marker Allele ◽

The North ◽

Distribution Ranges ◽

Genetic Diversity And Structure

Temperature is one of the most important range-limiting factors for many seaweeds. Driven by the recent climatic changes, rapid northward shifts of species’ distribution ranges can potentially modify the phylogeographic signature of Last Glacial Maximum. We explored this question in detail in the cold-tolerant kelp species Saccharina latissima, using microsatellites and double digest restriction site-associated DNA sequencing ( ddRAD-seq) derived single nucleotide polymorphisms (SNPs) to analyze the genetic diversity and structure in 11 sites spanning the entire European Atlantic latitudinal range of this species. In addition, we checked for statistical correlation between genetic marker allele frequencies and three environmental proxies (sea surface temperature, salinity, and water turbidity). Our findings revealed that genetic diversity was significantly higher for the northernmost locality (Spitsbergen) compared to the southern ones (Northern Iberia), which we discuss in light of the current state of knowledge on phylogeography of S. latissima and the potential influence of the recent climatic changes on the population structure of this species. Seven SNPs and 12 microsatellite alleles were found to be significantly associated with at least one of the three environmental variables. We speculate on the putative adaptive functions of the genes associated with the outlier markers and the importance of these markers for successful conservation and aquaculture strategies for S. latissima in this age of rapid global change.

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Genome-Wide Screening of Aedes aegypti (Culicidae: Diptera) Populations From Northwestern Argentina: Active and Passive Dispersal Shape Genetic Structure

Journal of Medical Entomology ◽

10.1093/jme/tjaa125 ◽

2020 ◽

Vol 57 (6) ◽

pp. 1930-1941

Author(s):

Lucía Maffey ◽

Maximiliano J Garzón ◽

Viviana Confalonieri ◽

Mariana M Chanampa ◽

Esteban Hasson ◽

...

Keyword(s):

Genetic Structure ◽

Aedes Aegypti ◽

Isolation By Distance ◽

Spatial Genetic Structure ◽

Local Level ◽

Regional Level ◽

Northwestern Argentina ◽

Entomological Survey ◽

Genome Wide ◽

High Prevalence

Abstract Aedes aegypti is the primary vector of arboviruses of great impact on human health. Our goal was to assess the spatial genetic structure of Ae. aegypti at the regional and local levels in Northwestern Argentina, an area with high prevalence of dengue fever. We analyzed 59 Ae. aegypti individuals collected from six locations in Northwestern Argentina using nuclear genome-wide Single Nucleotide Polymorphisms (SNPs) generated with double digest Restriction-site Associated DNA Sequencing. We also performed an entomological survey in 70 households in the cities of Orán and Tartagal. An analysis at the regional level indicated that the populations of Ae. aegypti in Northwestern Argentina are spatially structured and present a significant IBD pattern. Our results suggest that passive transport of eggs/immature stages, in both northward and southward directions, plays an important role in structuring Ae. aegypti populations at a regional scale and also as a source for the introduction of novel genetic variants through migration events into established populations. At a local level, we found neither spatial genetic structure nor significant isolation by distance (IBD) in Tartagal, indicating high gene flow within the city and active dispersal. In contrast, samples from Orán formed two clusters with a significant IBD pattern, although weaker than that at a regional level. Both populations showed signs of recent bottleneck events, probably coincident with past eradication campaigns. The entomological survey revealed a high prevalence of Ae. aegypti in both cities, although significantly higher in Tartagal.

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