Distribution of two chromosome races of the common shrew (Sorex araneus L.) in the hybrid zone: may a change of the dispersal mode maintain independent gene frequencies?

Combination of different dispersal modes may itself, without external obstacles, lead to the appearance of subdivided populations and maintain the existence of independent population systems. The common shrew, a mammal convenient for studying different levels of intraspecific differentiation, was the object of the study. Empirical data have been used for simulation taking into account the change of dispersal modes in the population area. The obtained results agree with empirical data on the distribution of races and hybrids in the hybrid zone of chromosome races Moscow and Seliger. Change of the dispersal mode may maintain independent population dynamics and, in the case of chromosome races, prevent the migration of parental individuals into the territory of the other race.     

Sex-chromosome differentiation and ‘sex races’ in the common frog (Rana temporaria)

Sex-chromosome differentiation was recently shown to vary among common frog populations in Fennoscandia, suggesting a trend of increased differentiation with latitude. By rearing families from two contrasted populations (respectively, from northern and southern Sweden), we show this disparity to stem from differences in sex-determination mechanisms rather than in XY-recombination patterns. Offspring from the northern population display equal sex ratios at metamorphosis, with phenotypic sexes that correlate strongly with paternal LG₂ haplotypes (the sex chromosome); accordingly, Y haplotypes are markedly differentiated, with male-specific alleles and depressed diversity testifying to their smaller effective population size. In the southern population, by contrast, a majority of juveniles present ovaries at metamorphosis; only later in development do sex ratios return to equilibrium. Even at these later stages, phenotypic sexes correlate only mildly with paternal LG₂ haplotypes; accordingly, there are no recognizable Y haplotypes. These distinct patterns of gonadal development fit the concept of ‘sex races’ proposed in the 1930s, with our two populations assigned to the ‘differentiated’ and ‘semi-differentiated’ races, respectively. Our results support the suggestion that ‘sex races’ differ in the genetic versus epigenetic components of sex determination. Analysing populations from the ‘undifferentiated race’ with high-density genetic maps should help to further test this hypothesis.     

Beyond the point of no return? A comparison of genetic diversity in captive and wild populations of two nearly extinct species of Goodeid fish reveals that one is inbred in the wild

The relative importance of genetic and non-genetic factors in extinction liability has been extensively debated. Here, we examine the levels of genetic variability at 13 (seven informative) loci in wild and captive populations of two endangered species of Mexican Goodeid fish, Ameca splendens and Zoogoneticus tequila. Allelic diversity was higher in the wild populations, and F(IS) lower. Values of theta (=4Nemu) were estimated using a coalescent approach. These implied that the effective population size of all captive populations of A. splendens were smaller than that of the wild population; qualitatively similar results were obtained using an analytical method based on within-population gene identity disequilibrium. However, the wild population of Z. tequila did not show a significantly greater estimate of theta. We used the Beaumont approach to infer population declines, and found that both species showed clear evidence of a decline in effective population size, although this was stronger and probably occurred over a longer period of time in Z. tequila than in A. splendens. The decline in Z. tequila probably occurred before captive populations were established. We discuss implications for the conservation of critically endangered populations.     

Association between two genetic variants of CD226 gene and Cervical Squamous Cell Carcinoma: A case–control study

Cervical carcinoma is a common gynecologic tumor severely influencing the health and life quality of women worldwide. CD226, a costimulatory molecule, is mainly participated in the activation and differentiation of T cells. Recent studies have investigated the association between two genetic variants (rs763361 and rs727088) of CD226 gene and many diseases. In order to evaluate whether these two variants are associated with Cervical Squamous Cell Carcinoma (CSCC), a case–control study including 349 CSCC patients and 380 unrelated healthy controls was carried out to determine the genotypes of these two variants by using the methods of polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) and DNA sequencing methods. Significantly increased CSCC risk was observed to be associated with G allele of rs727088 locus (OR = 1.422, 95% CI = 1.129–1.792). We have also observed that increased CSCC risk was statistically associated with rs727088 polymorphism in a dominant model (OR = 1.41, 95% CI = 1.05–1.89). Results of stratified analysis revealed that both rs763361 and rs727088 polymorphisms were not associated with clinical characters. Collectively, this study supports that rs727088 polymorphism may contribute to increased CSCC susceptibility.     

Can we continue to neglect genomic variation in introgression rates when inferring the history of speciation? A case study in a Mytilus hybrid zone

The use of molecular data to reconstruct the history of divergence and gene flow between populations of closely related taxa represents a challenging problem. It has been proposed that the long‐standing debate about the geography of speciation can be resolved by comparing the likelihoods of a model of isolation with migration and a model of secondary contact. However, data are commonly only fit to a model of isolation with migration and rarely tested against the secondary contact alternative. Furthermore, most demographic inference methods have neglected variation in introgression rates and assume that the gene flow parameter (Nm) is similar among loci. Here, we show that neglecting this source of variation can give misleading results. We analysed DNA sequences sampled from populations of the marine mussels, Mytilus edulis and M. galloprovincialis, across a well‐studied mosaic hybrid zone in Europe and evaluated various scenarios of speciation, with or without variation in introgression rates, using an Approximate Bayesian Computation (ABC) approach. Models with heterogeneous gene flow across loci always outperformed models assuming equal migration rates irrespective of the history of gene flow being considered. By incorporating this heterogeneity, the best‐supported scenario was a long period of allopatric isolation during the first three‐quarters of the time since divergence followed by secondary contact and introgression during the last quarter. By contrast, constraining migration to be homogeneous failed to discriminate among any of the different models of gene flow tested. Our simulations thus provide statistical support for the secondary contact scenario in the European Mytilus hybrid zone that the standard coalescent approach failed to confirm. Our results demonstrate that genomic variation in introgression rates can have profound impacts on the biological conclusions drawn from inference methods and needs to be incorporated in future studies.     

Adventitious roots as a source of information in reconstructing the activity of modern aeolian processes in the temperate climate zone: A case study from the Kozłów sandy area (SW Poland)

This paper presents a spatial-temporal reconstruction of inland dune movements at an anthropogenic active sandy area known as the Kozłów Desert, SW Poland. This unique sandy area, with assemblages of aeolian forms typical of “true” deserts, is an inactive military training ground (decommissioned in 1992) where military activity led to the initiation of geomorphic processes. The reconstruction was carried out based on the growth reaction characteristics of Scots pine (Pinus sylvestris L.) and downy birch (Betula pubescens L.) trees. 14 increment cores were collected from 12 trees and analysed with standard dendrochronological techniques. Samples of adventitious roots from all the trees examined were collected and prepared to extend the analyses and check their usefulness in dating modern geomorphic processes. The adventitious roots of pine and birch were found to react differently to burial, in terms of both reaction time and the shape of the root system. Growth-ring widths and wood anatomy were indicative of sudden or multi-stage sand movement, thus confirming the usefulness of adventitious roots as an additional source of information about aeolian process activity. More broadly, the study shows that the dynamics of landforming processes can be assessed more accurately and reliably by using such a combination of methods, comparing data from roots to data from tree trunks.     

What drives variation in the corticosterone stress response between subspecies? A common garden experiment of swamp sparrows (Melospiza georgiana)

Although differences in the corticosterone stress response have frequently been reported between populations or closely related subspecies, their origin remains unclear. These differences may appear because individuals adjust their corticosterone stress response to the environmental conditions they are experiencing. However, they may also result from selection that has favoured individuals with specific corticosterone stress response or from environmental factors that have affected the development of the corticosterone stress response during early life. We investigated these hypotheses by studying the corticosterone stress response of two closely related subspecies of swamp sparrows (Melospiza sp.). We showed for the first time that two closely related subspecies can differ in their corticosterone stress response when raised at the laboratory and held in similar conditions for a year. Thus, we demonstrated that selection, developmental processes or a conjunction of both of these processes can account for variation in the stress response between closely related subspecies.     

How much genetic variation is stored in the seed bank? A study of Atriplex tatarica (Chenopodiaceae)

We investigated to what extent the soil seed bank differed genetically and spatially in comparison to three consecutive life history stages (seedlings, mature plants, and fruiting plants) in a natural population of Atriplex tatarica. Representatives of particular life history stages from twenty subunits within a large population were randomly collected and subjected to allozyme analysis. Comparison of population polymorphism among various life history stages showed significant differences in observed heterozygosity (H(O)) and F statistics (F(IS) and F(ST)), but nonsignificant ones in the cases of number of alleles per polymorphic locus (A) and gene diversity (H(S)). These results indicate an increasing number of heterozygotes, a decreasing level of inbreeding and an increase of the partitioning genetic diversity among populations with increasing population age. Spatial autocorrelation was used to calculate f, the average co-ancestry coefficient between individuals within distance intervals of two meters along a 39 m long transect. Significant positive fine scale genetic structure was detected in mature and fruiting plants but not in soil seeds and seedlings stages. The results of the presented study on A. tatarica indicated that significant differences exist in genetic differentiation, differentiation in allele frequencies and spatial autocorrelation among early (soil seeds and seedlings) and late (mature and fruiting plants) life history stages but not within early and late ones. This pattern suggests that, rather than storing genetic variability in the soil or germination and establishment success, self-thinning might be the major microselective force in populations of A. tatarica.     

A candidate gene study reveals association between a variant of the Peroxisome Proliferator-Activated Receptor Gamma (PPAR-γ) gene and systemic sclerosis

IntroductionThe multifunctional nuclear receptor peroxisome proliferator-activated receptor gamma (PPAR-γ) has potent anti-fibrotic effects, and its expression and activity are impaired in patients with systemic sclerosis (SSc). We investigated PPAR-γ gene (PPARG) single nucleotide polymorphisms (SNPs) associated with SSc.MethodsTag SNPs spanning PPARG were genotyped in a European ancestry US discovery cohort comprising 152 SSc patients and 450 controls, with replication of our top signal in a European cohort (1031 SSc patients and 1014 controls from France). Clinical parameters and disease severity were analyzed to evaluate clinical associations with PPARG variants.ResultsIn the discovery cohort, a single PPARG intronic SNP (rs10865710) was associated with SSc (p = 0.010; odds ratio = 1.52 per C allele, 95% confidence interval 1.10-2.08). This association was replicated in the French validation cohort (p = 0.052; odds ratio = 1.16 per C allele, 95% confidence interval 1.00-1.35). Meta-analysis of both cohorts indicated stronger evidence for association (p = 0.002; odds ratio = 1.22 per C allele, 95% confidence interval 1.07-1.40). The rs10865710 C allele was also associated with pulmonary arterial hypertension in the French SSc cohort (p = 0.002; odds ratio = 2.33 per C allele, 95% confidence interval 1.34-4.03).ConclusionsA PPARG variant is associated with susceptibility to SSc, consistent with a role of PPAR-γ in the pathogenesis of SSc.

Electronic supplementary material

The online version of this article (doi:10.1186/s13075-015-0641-2) contains supplementary material, which is available to authorized users.     

How much of the invader's genetic variability can slip between our fingers? A case study of secondary dispersal of Poa annua on King George Island (Antarctica)

We studied an invasion of Poa annua on King George Island (Maritime Antarctic). The remoteness of this location, its geographic isolation, and its limited human traffic provided an opportunity to trace the history of an invasion of the species. Poa annua was recorded for the first time at H. Arctowski Polish Antarctic Station in the austral summer of 1985/6. In 2008/9, the species was observed in a new locality at the Ecology Glacier Forefield (1.5 km from “Arctowski”). We used AFLP to analyze the genetic differences among three populations of P. annua: the two mentioned above (Station and Forefield) and the putative origin of the introduction, Warsaw (Poland). There was 38% genetic variance among the populations. Pairwise Ф_PT was 0.498 between the Forefield and Warsaw populations and 0.283 between Warsaw and Station. There were 15 unique bands in the Warsaw population (frequency from 6% to 100%) and one in the Station/Forefield populations (which appears in all analyzed individuals from both populations). The Δ(K) parameter indicated two groups of samples: Warsaw/Station and Forefield. As indicated by Fu's Fs statistics and an analysis of mismatch distribution, the Forefield population underwent a bottleneck and/or founder effect. The Forefield population was likely introduced by secondary dispersal from the Station population.     

A preliminary study in the use of RAPD markers in detecting genetic differences in hatching patterns of Chirocephalus diaphanus Prévost, 1803 (Crustacea: Anostraca)

Randomly amplified polymorphic DNA (RAPD) was used to detect intra-clutch genetic differences of the anostracan Chirocephalus diaphanus Prévost, 1803. Thirty primers were tested on 130 nauplii from three different clutches. Two primers produced five repeatable and well-defined amplification products, that were used as genotype markers. Nauplii hatched after three successive dehydration and rehydration cycles. Consistent genetic differentiation was observed among nauplii from the same clutch. Significant association between presence or absence of three polymorphic amplification products and hatching after different stimuli was observed. These results suggest that RAPD markers might be related to the difference in nauplii hatching and provide reasonable support to the hypothesis that the source of the observed variation in hatching phenology are genetic as well as epigenetic.     

Anatomy and genetic diversity of two populations of Schinus terebinthifolius (Anacardiaceae) from the Tibagi River basin in Paraná, Brazil

Knowledge of the effects of flooding on plant survival is relevant for the efficiency of management and conservation programs. Schinus terebinthifolius is a tree of economic and ecological importance that is common in northeast Brazil. Flooding tolerance and genetic variation were investigated in two riparian populations of S. terebinthifolius distributed along two different ecological regions of the Tibagi River basin. Flooding tolerance was evaluated through the investigation of young plants, submitted to different flooding intensities to examine the morphological and anatomical responses to this stress. The growth rate of S. terebinthifolius was not affected by flooding, but total submersion proved to be lethal for 100% of the plants. Morphological alterations such as hypertrophied lenticels were observed in both populations and lenticel openings were significantly higher in plants from one population. Genetic analysis using DNA samples obtained from both populations showed a moderate degree of genetic variation between populations (13.7%); most of the variation was found within populations (86.3%). These results show that for conservation purposes and management of degraded areas, both populations should be preserved and could be used in programs that intend to recompose riparian forests.     

Stages in iron storage in the ferritin of Escherichia coli (EcFtnA): analysis of M?ssbauer spectra reveals a new intermediate.

Iron uptake into the nonheme ferritin of Escherichia coli (EcFtnA) and its site-directed variants have been investigated by M?ssbauer spectroscopy. EcFtnA, like recombinant human H chain ferritin (HuHF), oxidized Fe(II) at a dinuclear ferroxidase center situated at a central position within each subunit. As with HuHF, M?ssbauer subspectra observed between 1 min and 24 h after Fe(II) addition were assigned to Fe(III) monomers, "c", mu-oxo-bridged dimers, "b", and clusters, "a", the latter showing magnetically split spectra, "d", at 4.1 K. Like those of HuHF, the mu-oxo-bridged dimers were formed at the ferroxidase centers. However, the analysis also revealed the presence of a new type of dimer, "e" (QS1 = 0.38 mm/s, IS1 = 0.51 mm/s and QS2 = 0.72 mm/s, IS2 = 0.50 mm/s), and this was also assigned to the ferroxidase center. Dimers "b" appeared to be converted to dimers "e" over time. Subspectra "e" became markedly asymmetric at temperatures above 90 K, suggesting that the two Fe(III) atoms of dimers "e" were more weakly coupled than in the mu-oxo-bridged dimers "b", possibly due to OH- bridging. Monomeric Fe(III), giving relaxation spectra "c", was assigned to a unique site C that is near the dinuclear center. In EcFtnA all three iron atoms seemed to be oxidized together. In contrast to HuHF, no Fe(III) clusters were observed 24 h after the aerobic addition of 48 Fe(II) atoms/molecule in wild-type EcFtnA. This implies that iron is more evenly distributed between molecules in the bacterial ferritins, which may account for its greater accessibility.     

A century of genetic change and metapopulation dynamics in the Galápagos warbler finches (Certhidea)

Populations that are connected by immigrants play an important role in evolutionary and conservation biology, yet we have little direct evidence of how such metapopulations change genetically over evolutionary time. We compared historic (1894–1906) to modern (1988–2006) genetic variation in 11 populations of warbler finches at 14 microsatellite loci. Although several lines of evidence suggest that Darwin's finches may be in decline, we found that the genetic diversity of warbler finches has not generally declined, and broad‐scale patterns of variation remained similar over time. Contrary to expectations, inferred population sizes have generally increased over time (6–8%) as have immigration rates (8–16%), which may reflect a recent increase in the frequency and intensity of El Niño events. Individual island populations showed significant declines (18–19%) and also substantial gains (18–20%) in allelic richness over time. Changes in genetic diversity were correlated with changes in immigration rates, but did not correspond to population size or human disturbance. These results reflect the expected stabilizing properties of whole metapopulations over time. However, the dramatic and unpredictable changes observed in individual populations during this short time interval suggests that care should be taken when monitoring individual population fragments with snapshots of genetic variation.     

Keratinocyte-specific ablation of the NF-κB regulatory protein A20 (TNFAIP3) reveals a role in the control of epidermal homeostasis

The ubiquitin-editing enzyme A20 (tumor necrosis factor-α-induced protein 3) serves as a critical brake on nuclear factor κB (NF-κB) signaling. In humans, polymorphisms in or near the A20 gene are associated with several inflammatory disorders, including psoriasis. We show here that epidermis-specific A20-knockout mice (A20(EKO)) develop keratinocyte hyperproliferation, but no signs of skin inflammation, such as immune cell infiltration. However, A20(EKO) mice clearly developed ectodermal organ abnormalities, including disheveled hair, longer nails and sebocyte hyperplasia. This phenotype resembles that of mice overexpressing ectodysplasin-A1 (EDA-A1) or the ectodysplasin receptor (EDAR), suggesting that A20 negatively controls EDAR signaling. We found that A20 inhibited EDAR-induced NF-κB signaling independent from its de-ubiquitinating activity. In addition, A20 expression was induced by EDA-A1 in embryonic skin explants, in which its expression was confined to the hair placodes, known to be the site of EDAR expression. In summary, our data indicate that EDAR-induced NF-κB levels are controlled by A20, which functions as a negative feedback regulator, to assure proper skin homeostasis and epidermal appendage development.     

A genetic and functional analysis of the unusually large variable region in the M·Alu I DNA-(cytosine C5 )-methyltransferase

The M·AluI DNA-(cytosine C5)-methyltransferase (5mC methylase) acts on the sequence 5′-AGCT-3′. The amino acid sequences of known 5mC methylases contain ten conserved motifs, with a variable region between Motifs VIII and IX that contains one or more “target-recognizing domains” (TRDs) responsible for DNA sequence specificity. Monospecific 5mC methylases are believed to have only one TRD, while multispecific 5mC methylases have as many as five. M·AluI has the second-largest variable region of all known 5mC methylases, and sequence analysis reveals five candidate TRDs. In testing whether M·AluI is in fact monospecific it was found that AGCT methylation represents only 80–90% of the methylating activity of this enzyme, while control experiments with the enzyme M·HhaI gave no unexplained activity. Because individual TRDs can be deleted from multispecific methylases without general loss of activity, a series of insertion and deletion mutants of the M·AluI variable region were prepared. All deletions that removed more than single amino acids from the variable region caused significant loss of activity; a sensitive in vivo assay for methylase activity based on McrBC restriction suggested that the central portion of the variable region is particularly important. In some cases, multispecific methylases can accommodate a TRD from another multispecific methylase, thereby acquiring an additional specificity. When TRDs were moved from a multispecific methylase into two different locations in the variable region of M·AluI, all hybrid enzymes had greatly reduced activity and no new specificities. M·AluI thus behaves in most respects as a monospecific methylase despite the remarkable size of its variable region.     

Second-site mutation at M43 (Asn→Asp) compensates for the loss of two acidic residues in the QB site of the reaction center

Two acidic residues, L212Glu and L213Asp, in the Q_B binding sites of the photosynthetic reaction centers of Rhodobacter capsulatus and Rhodobacter sphaeroides are thought to play central roles in the transfer of protons to the quinone anion(s) generated by photoinduced electron transfer. We constructed the site-specific double mutant L212Ala-L213Ala in R. capsulatus, that is incapable of growth under photosynthetic conditions. A photocompetent derivative of that strain has been isolated that carries the original L212Ala-L213Ala double mutation and a second-site suppressor mutation at residue M43 (AsnAsp), outside of the Q_B binding site, that is solely responsible for restoring the photosynthetic phenotype. The Asp,Asn combination of residues at the L213 and M43 positions is conserved in the five species of photosynthetic bacteria whose reaction center sequences are known. In R. capsulatus and R. sphaeroides, the pair is L213Asp-M43Asn. But, the reaction centers of Rhodopseudomonas viridis, Rhodospirillum rubrum and Chloroflexus aurantiacus reverse the combination to L213Asn-M43Asp. In this respect, the Q_B site of the suppressor strain resembles that of the latter three species in that it couples an uncharged residue at L213 with an acidic residue at M43. These reaction centers, in which L213 is an amide, must employ an alternative proton transfer pathway. The observation that the M43AsnAsp mutation in R. capsulatus compensates for the loss of both acidic residues at L212 and L213 suggests that M43Asp is involved in a new proton transfer route in this species that resembles the one normally used in reaction centers of Rps. virddis, Rsp. rubrum and C. aurantiacus.