Absence Of Spatial Genetic Structure Research Articles

Mitochondrial cytochrome c oxidase subunit I gene analysis of the yellowfin snapper, Lutjanus xanthopinnis in the Indo-Pacific region and a note on Lutjanus lutjanus population structure

The yellowfin snapper, Lutjanus xanthopinnis, was recorded as a newly described species in the Indo-Pacific region in 2015. However, the knowledge of its biology, biogeography and ecology is scarcely understood, and, hence, its current conservation status is categorized as Data Deficient. The mitochondrial cytochrome c oxidase subunit I (COI) gene was examined to confirm species identification. We also examined the COI gene haplotypes of L. xanthopinnis in Brunei Darussalam and Malaysia together with other waters, i.e., Bangladesh, Indonesia, Japan, Singapore, Sri Lanka and Taiwan. Our molecular analyses found that Brunei Darussalam and eastern Peninsular Malaysia samples were genetically similar. However, the former showed higher genetic diversity than the latter. The samples from these two sites also showed signatures of population expansion. Furthermore, identical haplotypes could be found in different locations, suggesting the absence of spatial genetic structure. On the other hand, Lutjanus lutjanus showed a population structure associated with geographical locations, i.e., western Pacific Ocean, Indian Ocean and Maluku in Indonesia.

Would tropical climatic variations impact the genetic variability of triatomines: Rhodnius ecuadoriensis, principal vector of Chagas disease in Ecuador?

Rhodnius ecuadoriensis is one of the most important vector species of Chagas disease in Ecuador. This species is distributed in the Central coast region and in the south Andean region, and an incipient speciation process between these geographical populations was previously proposed. The current population genetics study only focused on the Central coast region and analyzed 96 sylvatic specimens of R. ecuadoriensis associated with Phytelephas aequatorialis palm trees. We used Cytb and 16S-rRNA sequences and a Cytb-16S-rRNA concatenated set to explore (i) the genetic variability, spatial structuring, and demographic history of R. ecuadoriensis, and to determine (ii) the relationship between the genetic and climatic variabilities. A particularly high genetic variability was observed without detectable general genetic structure; only some terminal genetic clusters were observed. We did not observe isolation by geographical distance (IBD), and it is likely that ancient expansion occurred, according to Fs index and mismatch distribution for Cytb-16S-rRNA concatenated sequences. Hierarchical clustering showed that the current locality origins of the bugs were grouped into four bioclimatic clusters. Genetic and bioclimatic distances were not correlated, but some genetic clusters were associated with bioclimatic ones. The results showed an ancient evolution of the species in the region with a possible old expansion. The absence of spatial genetic structure could be due to climatic conditions (possible selection of singular genotypes) and to passive transportation of palms tree materials where R. ecuadoriensis are living.

Lasting through the ice age: The role of the proglacial refugia in the maintenance of genetic diversity, population growth, and high dispersal rate in a widespread freshwater crustacean

Abstract The severe climatic changes during the Pleistocene ice ages have shaped the genetic structure and distribution of biota in Europe. We aimed to reveal in detail the genetic diversity, geographical population structure, historical and present demography, migration patterns, and the presence of possible glacial refugia within the nominative subspecies Asellus aquaticus aquaticus. We analysed DNA sequences of the mitochondrial cytochrome c oxidase subunit I gene and nuclear noncoding internal transcribed spacer II region, from populations inhabiting post‐glacial Europe (from the British Isles and Scandinavia to the northern Mediterranean and Black Sea coasts). The origin of the taxon, including establishment in the Dinaric Western Balkans, dates to the Middle/Late Pliocene, but most of its genetic diversity emerged during the Middle/Late Pleistocene before the Last Glacial Maximum. Despite the general absence of spatial genetic structure with population growth, we discovered two different phylogeographic stories across 11 clusters revealed by a coalescent approach. Firstly, the periglacial cluster group—spatially restricted mainly to the northern Balkans, Pannonian Basin, and Pontic Region—is older and more divergent. It apparently retained a relatively stable population size during the glacial‐interglacial cycles. Conversely, the proglacial cluster group—widely distributed in areas close to the glacier margins (north of the Alps, Sudetes, Carpathians) and in the Pannonian Basin—is younger and composed of closely related individuals. It originated in Pleistocene and lasted continuously through the Last Glacial Maximum in numerous high latitude refugia. This was probably due to the vast network of proglacial lakes and rivers, which played a crucial role in the maintenance of genetic diversity, population growth, and high dispersal rate. The evolutionary history of A. a. aquaticus reveals unexpected patterns and is an important lesson when making predictions for other aquatic taxa. Our results suggest that we should stop perceiving the proglacial habitats as lifeless ice desert.

Genetic and demographic aspects of Varronia curassavica Jacq. in a heterogeneous coastal ecosystem.

The restinga is a threatened Brazilian ecosystem and a highly heterogeneous environment. This work aimed to evaluate demographic and genetic aspects of Varronia curassavica and whether environmental heterogeneity can influence the studied population parameters. Three annual evaluations were carried out in an area of restinga in Florianópolis-SC, Brazil. Demographic data were analyzed using descriptive statistics, and the spatial distribution pattern was calculated by Ripley's K-function and correlated with environmental characteristics. To characterize diversity and genetic structure, eight microsatellite markers were used. This work demonstrated that variations in the distribution of individuals and genotypes can be related to specific environments. Dry lowlands were environments favorable to population development, and flooded lowland and mobile dunes were unfavorable. The fixation indices were distinct between environments, evidencing a tendency toward preferential crosses in favor of heterozygotes. We found absence of spatial genetic structure, indicating that genotypes are randomly distributed and that gene flow may be related to such genetic factors as the presence of autoincompatibility mechanisms. This diversity of environments contributed to the aggregate distribution and is relevant for the maintenance of demographic and genetic processes of the species in restingas, and this aspect should be considered for in situ conservation.

Absence of spatial genetic structure in common dentex (Dentex dentex Linnaeus, 1758) in the Mediterranean Sea as evidenced by nuclear and mitochondrial molecular markers.

The common dentex, Dentex dentex, is a fish species which inhabits marine environments in the Mediterranean and Northeast Atlantic regions. This is an important species from an ecological, economic and conservation perspective, however critical information on its population genetic structure is lacking. Most samples were obtained from the Mediterranean Sea (17 sites) with an emphasis around Corsica (5 sites), plus one Atlantic Ocean site. This provided an opportunity to examine genetic structuring at local and broader scales to provide science based data for the management of fishing stocks in the region. Two mitochondrial regions were examined (D-loop and COI) along with eight microsatellite loci. The COI data was combined with publicly available sequences and demonstrated past misidentification of common dentex. All markers indicated the absence of population genetic structure from the Bay of Biscay to the eastern Mediterranean Sea. Bayesian approaches, as well as the statistical tests performed on the allelic frequencies from microsatellite loci, indicated low differentiation between samples; there was only a slight (p = 0.05) indication of isolation by distance. Common dentex is a marine fish species with a unique panmictic population in the Mediterranean and likely in the Atlantic Ocean as well.

Are road verges corridors for weed invasion? Insights from the fine‐scale spatial genetic structure of Raphanus raphanistrum

SummaryRaphanus raphanistrum (Brassicaceae) is considered amongst the world's worst agricultural weeds. We address critical issues in its management by studying the pathway of colonisation at local scales. For this, we assessed the small‐scale spatial genetic structure of 231 samples collected from three different sites across the Cape Floristic Region, South Africa, using 11 nuclear microsatellite markers. Although natural pollen and seed dispersal were expected to be restricted, we found no significant relationship between genetic and geographical distance within sites. Instead, our results suggest that R. raphanistrum had colonised new habitats via jump dispersal, rather than through natural diffusive dispersal at local scales. We did not find evidence for road verges as dispersal corridors, as evidenced by a lack of isolation‐by‐distance at local scales. Instead, the absence of spatial genetic structure suggests that R. raphanistrum had rapidly spread throughout its current range, possibly facilitated by human‐mediated actions. Management plans addressing containment or suppression of the weedy species R. raphanistrum (and possibly other weedy species) should take the high degree of connectivity between distant geographical localities into account.

A pilot genetic study reveals the absence of spatial genetic structure in Norway lobster (Nephrops norvegicus) on fishing grounds in Icelandic waters

AbstractPampoulie, C., Skirnisdottir, S., Hauksdottir, S., Olafsson, K., Eiríksson, H., Chosson, V., Hreggvidsson, G. O., Gunnarsson, G. H., and Hjorleifsdottir, S. 2011. A pilot genetic study reveals the absence of spatial genetic structure in Norway lobster (Nephrops norvegicus) on fishing grounds in Icelandic waters. – ICES Journal of Marine Science, 68: 20–25. Stock structure of Norway lobster off southern Iceland was investigated using 12 microsatellite loci. No genetic method detected significant genetic differentiation among the locations sampled, even among Icelandic samples and an out-group from Scotland. Testing the power of resolution of microsatellite loci, the loci and sample sizes used were sufficient to detect significant genetic differentiation with confidence. The lack of genetic structure is discussed in terms of the level of gene flow, recent isolation of populations, and the statistical power of the experimental design.

Microsatellites reveal substantial among-population genetic differentiation and strong inbreeding in the relict fern Dryopteris aemula

A previous study detected no allozyme diversity in Iberian populations of the buckler-fern Dryopteris aemula. The use of a more sensitive marker, such as microsatellites, was thus needed to reveal the genetic diversity, breeding system and spatial genetic structure of this species in natural populations. Eight microsatellite loci for D. aemula were developed and their cross-amplification with other ferns was tested. Five polymorphic loci were used to characterize the amount and distribution of genetic diversity of D. aemula in three populations from the Iberian Peninsula and one population from the Azores. Most microsatellite markers developed were transferable to taxa close to D. aemula. Overall genetic variation was low (H(T) = 0.447), but was higher in the Azorean population than in the Iberian populations of this species. Among-population genetic differentiation was high (F(ST) = 0.520). All loci strongly departed from Hardy-Weinberg equilibrium. In the population where genetic structure was studied, no spatial autocorrelation was found in any distance class. The higher genetic diversity observed in the Azorean population studied suggested a possible refugium in this region from which mainland Europe has been recolonized after the Pleistocene glaciations. High among-population genetic differentiation indicated restricted gene flow (i.e. lack of spore exchange) across the highly fragmented area occupied by D. aemula. The deviations from Hardy-Weinberg equilibrium reflected strong inbreeding in D. aemula, a trait rarely observed in homosporous ferns. The absence of spatial genetic structure indicated effective spore dispersal over short distances. Additionally, the cross-amplification of some D. aemula microsatellites makes them suitable for use in other Dryopteris taxa.

Evidence of wolf dispersal in anthropogenic habitats of the Polish Carpathian Mountains

In the course of their maturation, most young wolves leave their natal pack and disperse in search for mating partners, improved food availability and new territories. We investigated whether this dispersal is affected by anthropogenic infrastructure in a 5,000 km² area of the eastern region of the Polish Carpathian Mountains occupied by wolves. A radio-collared male wolf covered 230 km while dispersing through forested hills and densely populated valleys. To test if such dispersal is common in the population we analysed by microsatellite genotyping 39 samples taken from live-trapped wolves or wolves found dead in the study area. Although the obtained genotypes were assigned to different clusters in Bayesian tests, we could not ascribe this structure to landscape features, but rather to shared ancestry of wolf individuals found in distant locations. Moreover, we could not detect a spatial genetic structure in the wolf population, indicating a random occurrence of genotypes within the study area. Observation of the dispersing wolf and the absence of spatial genetic structure imply that wolves are still able to roam the entire area despite high densities of roads and a dense human population. Thus, we concluded that the existing anthropogenic infrastructure does not restrict wolf dispersal in the area and the studied wolves represent a coherent part of the Polish Carpathian wolf population.

Spatial genetic structure links between soil seed banks and above‐ground populations of Primula modesta in subalpine grassland

Summary The spatial genetic structure of soil seed banks establishes the initial template for development of spatial genetic structure in above‐ground plants, but is rarely evaluated. We used kinship coefficients to analyse the fine‐scale spatial genetic autocorrelation of plants and of seed banks from different soil depths for Primula modesta at a subalpine fen site on Mt Asama, central Japan. The spatial genetic structure of surface seeds (0–1 cm depth) was significant, while deeper seeds (1–5 cm depth) had no significant genetic structure. We also detected a more pronounced spatial genetic association between the surface seeds and flowering genets than between the deeper seeds and flowering genets. These results suggest that the surface seed bank accounts for a large proportion of the previous season's seed dispersal and therefore represents the transient seed bank, whereas the deeper (persistent) seed bank pools the reproductive output of multiple generations. Directional analysis indicated that secondary dispersal by running water modifies the spatial genetic structure and extends dispersal distances. Over time, this may impact on the spatial pattern of soil seeds, possibly accounting for the absence of spatial genetic structure in deeper seeds. Emerging seedlings and flowering ramets were strongly clustered together at distances up to 20 cm. Surviving seedlings were aggregated at short distances because of the patchy spatial distribution of safe sites for establishment, allowing development and strengthening of the marked fine‐scale spatial genetic structure.