Assortative mating and differential male mating success in an ash hybrid zone population

Background  

The structure and evolution of hybrid zones depend mainly on the relative importance of dispersal and local adaptation, and on the strength of assortative mating. Here, we study the influence of dispersal, temporal isolation, variability in phenotypic traits and parasite attacks on the male mating success of two parental species and hybrids by real-time pollen flow analysis. We focus on a hybrid zone population between the two closely related ash species Fraxinus excelsior L. (common ash) and F. angustifolia Vahl (narrow-leaved ash), which is composed of individuals of the two species and several hybrid types. This population is structured by flowering time: the F. excelsior individuals flower later than the F. angustifolia individuals, and the hybrid types flower in-between. Hybrids are scattered throughout the population, suggesting favorable conditions for their local adaptation. We estimate jointly the best-fitting dispersal kernel, the differences in male fecundity due to variation in phenotypic traits and level of parasite attack, and the strength of assortative mating due to differences in flowering phenology. In addition, we assess the effect of accounting for genotyping error on these estimations.     

The extent of population genetic subdivision differs among four co-distributed shark species in the Indo-Australian archipelago

Background  

The territorial fishing zones of Australia and Indonesia are contiguous to the north of Australia in the Timor and Arafura Seas and in the Indian Ocean to the north of Christmas Island. The area surrounding the shared boundary consists of a variety of bio-diverse marine habitats including shallow continental shelf waters, oceanic trenches and numerous offshore islands. Both countries exploit a variety of fisheries species, including whaler (Carcharhinus spp.) and hammerhead sharks (Sphyrna spp.). Despite their differences in social and financial arrangements, the two countries are motivated to develop complementary co-management practices to achieve resource sustainability. An essential starting point is knowledge of the degree of population subdivision, and hence fisheries stock status, in exploited species.     

Effect of plant secondary compounds on in vitro methane,ammonia production and ruminal protozoa population

Aims

The objective of this study was to evaluate the potential of secondary plant metabolites from 38 sources to serve as antimethanogenic additives in ruminant diets. The effect of leaf tannins from these different plant sources on rumen fermentation, protozoal populations and methanogenesis was also studied.

Methods and Results

Samples (200 mg dry matter, DM) were incubated without and with polyethylene glycol (PEG)‐6000 (400 mg DM) as a tannin binder during 24‐h incubation in the in vitro Hohenheim gas system. In the leaf samples, total phenol (g kg^?1 DM) was maximum in Pimenta officinalis (312) followed by Oenothera lamarckiana (185) and Lawsonia inermis (105). Of the 38 samples, condensed tannins exceeded 4·0 g kg^?1 in only Alpinia galanga (7·50), Cinnamomum verum (4·58), Pelargonium graveolens (18·7) and Pimenta officinalis (23·2) and were not detected in seven samples. When the bioactivity of the leaf samples was assessed using the tannin bioassay, the percentage increase in the amount of gas produced during incubation of samples with the tannin‐binding agent PEG‐6000 over the amount produced during incubation without the tannin binder ranged from nil (zero) to 367%, with the highest being recorded with A. galanga leaves. The ratio of methane reduction per ml of total gas reduction was maximum with Rauvolfia serpentina (131·8) leaves, followed by Indigofera tinctoria (16·8) and Withania somnifera (10·2) leaves. Total and differential protozoal counts increased with added PEG in twenty‐two samples, maximum being in Pimenta officinalis. Increased accumulation of total volatile fatty acids during incubation with added PEG‐6000 was recorded, and the values ranged from zero to 61%. However, the increase was significant in only 11 of the 38 tannin sources tested indicating noninterference of tannin on in vitro fermentation of carbohydrates by the majority of samples tested. Conversely, in 26 of 38 plant sources, the leaf tannins reduced N‐digestibility as evidenced by increased accumulation of NH₃‐N with added PEG.

Conclusions

Our study unequivocally demonstrated that plants containing secondary metabolites such as Rauvolfia serpentine, Indigofera tinctoria and Withania somnifera have great potential to suppress methanogenesis with minimal adverse effect of feedstuff fermentation.

Significance and Impact of the Study

It was established that methanogenesis was not essentially related to the density of protozoa population in vitro. The tannins contained in these plants could be of interest in the development of new additives in ruminant nutrition.     

Selection dramatically reduces effective population size in HIV-1 infection

Background  

In HIV-1 evolution, a 100–100,000 fold discrepancy between census size and effective population size (N _e ) has been noted. Although it is well known that selection can reduce N _e , high in vivo mutation and recombination rates complicate attempts to quantify the effects of selection on HIV-1 effective size.     

Association of common polymorphisms in known susceptibility genes with rheumatoid arthritis in a Slovak population using osteoarthritis patients as controls

Introduction  

Both genetic and environmental factors contribute to rheumatoid arthritis (RA), a common and complex autoimmune disease. As well as the major susceptibility gene HLA-DRB1, recent genome-wide and candidate-gene studies reported additional evidence for association of single nucleotide polymorphism (SNP) markers in the PTPN22, STAT4, OLIG3/TNFAIP3 and TRAF1/C5 loci with RA. This study was initiated to investigate the association between defined genetic markers and RA in a Slovak population. In contrast to recent studies, we included intensively-characterized osteoarthritis (OA) patients as controls.     

Reconstruction of cell population dynamics using CFSE

Background  

Quantifying cell division and death is central to many studies in the biological sciences. The fluorescent dye CFSE allows the tracking of cell division in vitro and in vivo and provides a rich source of information with which to test models of cell kinetics. Cell division and death have a stochastic component at the single-cell level, and the probabilities of these occurring in any given time interval may also undergo systematic variation at a population level. This gives rise to heterogeneity in proliferating cell populations. Branching processes provide a natural means of describing this behaviour.     

The impact of early Quaternary climate change on the diversification and population dynamics of a South American cactus species

Aim

Climatic oscillations have been suggested to promote speciation and changes in species distributions, mostly in connection with the Last Glacial Maximum (LGM). However, the LGM is just the most recent of the 20+ glacial‐interglacial periods that characterise the Quaternary. Here, we investigate the role of climatic changes and geomorphological features in shaping the evolution, distribution and population dynamics of the South American cactus Cereus hildmannianus.

Location

South‐eastern South America.

Methods

We built a large fossil‐calibrated phylogeny for cacti (family Cactaceae), comprising 128 species distributed in all subfamilies, using a Bayesian relaxed clock. We used the results to derive a secondary calibration for a population‐level phylogeny in C. hildmannianus. We amplified two plastid (trnQ‐5′rps16 and psbJ‐petA) and one nuclear marker (PhyC) for 24 populations. We estimated population dynamics, ancestral areas, and species distribution models to infer the clade's evolutionary history in time and space.

Results

Our results show a major population divergence of C. hildmannianus at c. 2.60 Ma, which is strikingly coincident with the transition of the Pliocene–Pleistocene and onset of Quaternary glaciations. This was followed by a complex phylogeographic scenario involving population expansions across ecologically diverse regions.

Main conclusions

Contrary to the dominant research focus on the LGM, our study indicates a major impact of the first Quaternary glaciation on the distribution and population divergence of a South American plant species. Further intraspecific events seem related to successive climatic changes and geomorphology, including the development of the coastal plain and its peculiar diversity. We propose that the first Quaternary glaciation acted as a major evolutionary bottleneck, whereby many warm‐adapted lineages succumbed, while those that survived could diversify and better cope with subsequent climatic oscillations.     

Seroprevalence of Helicobacter pylori in Korea: A multicenter,nationwide study conducted in 2015 and 2016

Background

The Korean College of Helicobacter and Upper Gastrointestinal Research has studied Helicobacter pylori (H. pylori) prevalence since 1998 and found a dynamic change in its prevalence in Korea. The aim of this study was to determine the recent H. pylori prevalence rate and compare it with that of previous studies according to socioeconomic variables.

Methods

We planned to enroll 4920 asymptomatic Korean adults from 21 centers according to the population distribution of seven geographic areas (Seoul, Gyeonggi, Gangwon, Chungcheong, Kyungsang, Cholla, and Jeju). We centrally collected serum and tested H. pylori serum IgG using a chemiluminescent enzyme immunoassay.

Results

We analyzed 4917 samples (4917/4920 = 99.9%) from January 2015 to December 2016. After excluding equivocal serologic results, the H. pylori seropositivity rate was 51.0% (2414/4734). We verified a decrease in H. pylori seroprevalence compared with previous studies performed in 1998, 2005, and 2011 (P < .0001). The H. pylori seroprevalence rate differed by area: Cholla (59.5%), Chungcheong (59.2%), Kyungsang (55.1%), Jeju (54.4%), Gangwon (49.1%), Seoul (47.4%), and Gyeonggi (44.6%). The rate was higher in those older than 40 years (38.1% in those aged 30‐39 years and 57.7% in those aged 40‐49 years) and was lower in city residents than in noncity residents at all ages.

Conclusions

Helicobacter pylori seroprevalence in Korea is decreasing and may vary according to population characteristics. This trend should be considered to inform H. pylori‐related policies.     

Genetic population structure of sympatric and allopatric populations of Baltic ciscoes (<Emphasis Type="Italic">Coregonus albula</Emphasis>complex,Teleostei, Coregonidae)

Background  

Teleost fishes of the Coregonidae are good model systems for studying postglacial evolution, adaptive radiation and ecological speciation. Of particular interest is whether the repeated occurrence of sympatric species pairs results from in-situ divergence from a single lineage or from multiple invasions of one or more different lineages. Here, we analysed the genetic structure of Baltic ciscoes (Coregonus albula complex), examining 271 individuals from 8 lakes in northern Germany using 1244 polymorphic AFLP loci. Six lakes had only one population of C. albula while the remaining two lakes had C. albula as well as a sympatric species (C. lucinensis or C. fontanae).     

Helicobacter pylori antimicrobial resistance in a pediatric population

Background

The increasing prevalence of Helicobacter pylori (H. pylori) antimicrobial resistance, primarily for clarithromycin decreases the success of treatment. The aim of this study is to determine the local pattern of first‐line antimicrobials resistance and the eradication rate.

Material and Methods

Prospective cohort study of H. pylori infected patients (positive histological or cultural exams) treated at Centro Materno‐Infantil do Norte from January of 2013 to October of 2017. Susceptibility to 4 antibiotics: amoxicilin, metronidazole, clarithromycin, and levofloxacin were analyzed by E‐test (phenotypic resistance). The E‐test was chosen because it is simple and cost‐effective for routine susceptibility testing. Point mutations that confer clarithromycin resistance were surveyed (genotypic resistance). Eradication of H. pylori infection was defined by a negative urea breath test or fecal antigen 6‐8 weeks after the end of treatment.

Results

Of a total of 74 H. pylori infected patients, 16 were excluded because they had previous H. pylori treatment or severe systemic disease. Median age of infection cases was 15 years (3‐17 years). Eradication regimen used in all patients combined the use of 3 antibiotics (amoxicillin and metronidazole or clarithromycin) and proton pump inibhitor for 14 days and was tailored according antimicrobial susceptibility. 79.5% of the patients completed the treatment. The resistance rate for metronidazole and clarithromycin was 3.3% and 23.3%, respectively. There was no resistance for amoxicilin and levofloxacin. The rate of genotypic resistance to clarithromycin was 37.2%. The eradication rate was 97.8%.

Conclusions

The authors found a high resistance rate of H. pylori for clarithromycin in this northern portuguese pediatric center. This factor should determine a change in local current treatment, contraindicating the use of clarithromycin as a first‐line treatment for H. pylori infection in children. The high eradication rate maybe explained for the eradication treatment tailored according antimicrobial susceptibility.     

Population structure of Helicobacter pylori among ethnic groups in Malaysia: recent acquisition of the bacterium by the Malay population

Background  

Helicobacter pylori is a major gastric bacterial pathogen. This pathogen has been shown to follow the routes of human migration by their geographical origin and currently the global H. pylori population has been divided into six ancestral populations, three from Africa, two from Asia and one from Europe. Malaysia is made up of three major ethnic populations, Malay, Chinese and Indian, providing a good population for studying recent H. pylori migration and admixture.     

Single-nucleotide polymorphisms and haplotype of <Emphasis Type="Italic">CYP2E1</Emphasis>gene associated with systemic lupus erythematosus in Chinese population

Introduction  

Cytochrome P-450 2E1 (CYP2E1) is an important member of the CYP superfamily, which is involved in the metabolism and activation of many low molecular weight toxic compounds. We tried to investigate the possible association of CYP2E1 tag single nucleotide polymorphisms (SNPs) with susceptibility to systemic lupus erythematosus (SLE) in a Chinese Han population.     

Polymorphism at the apical membrane antigen 1 locus reflects the world population history of <Emphasis Type="Italic">Plasmodium vivax</Emphasis>

Background  

In malaria parasites (genus Plasmodium), ama-1 is a highly polymorphic locus encoding the Apical Membrane Protein-1, and there is evidence that the polymorphism at this locus is selectively maintained. We tested the hypothesis that polymorphism at the ama-1 locus reflects population history in Plasmodium vivax, which is believed to have originated in Southeast Asia and is widely geographically distributed. In particular, we tested for a signature of the introduction of P. vivax into the New World at the time of the European conquest and African slave trade and subsequent population expansion.     

CTLA4 gene polymorphisms are associated with, and linked to, insulin-dependent diabetes mellitus in a Russian population

Background  

The association between the human cytotoxic T lymphocyte-associated antigen-4 (CTLA4) gene and insulin-dependent diabetes mellitus (IDDM) is unclear in populations. We therefore investigated whether the gene conferred susceptibility to IDDM in a Russian population. We studied two polymorphic regions of the CTLA4 gene, the codon 17 dimorphism and the (AT)_n microsatellite marker in the 3' untranslated region in 56 discordant sibling pairs and in 33 identical by descent (IBD) affected sibships.     

High climate velocity and population fragmentation may constrain climate‐driven range shift of the key habitat former Fucus vesiculosus

Aim

The Baltic Sea forms a unique regional sea with its salinity gradient ranging from marine to nearly freshwater conditions. It is one of the most environmentally impacted brackish seas worldwide, and the low biodiversity makes it particularly sensitive to anthropogenic pressures including climate change. We applied a novel combination of models to predict the fate of one of the dominant foundation species in the Baltic Sea, the bladder wrack Fucus vesiculosus.

Location

The Baltic Sea.

Methods

We used a species distribution model to predict climate change‐induced displacement of F. vesiculosus and combined these projections with a biophysical model of dispersal and connectivity to explore whether the dispersal rate of locally adapted genotypes may match estimated climate velocities to recolonize the receding salinity gradient. In addition, we used a population dynamic model to assess possible effects of habitat fragmentation.

Results

The species distribution model showed that the habitat of F. vesiculosus is expected to dramatically shrink, mainly caused by the predicted reduction of salinity. In addition, the dispersal rate of locally adapted genotypes may not keep pace with estimated climate velocities rendering the recolonization of the receding salinity gradient more difficult. A simplistic model of population dynamics also indicated that the risk of local extinction may increase due to future habitat fragmentation.

Main conclusions

Results point to a significant risk of locally adapted genotypes being unable to shift their ranges sufficiently fast considering the restricted dispersal and long generation time. The worst scenario is that F. vesiculosus may disappear from large parts of the Baltic Sea before the end of this century with large effects on the biodiversity and ecosystem functioning. We finally discuss how to reduce this risk through conservation actions, including assisted colonization and assisted evolution.     

Global drivers of population density in terrestrial vertebrates

Aim

Although the effects of life history traits on population density have been investigated widely, how spatial environmental variation influences population density for a large range of organisms and at a broad spatial scale is poorly known. Filling this knowledge gap is crucial for global species management and conservation planning and to understand the potential impact of environmental changes on multiple species.

Location

Global.

Time period

Present.

Major taxa studied

Terrestrial amphibians, reptiles, birds and mammals.

Methods

We collected population density estimates for a range of terrestrial vertebrates, including 364 estimates for amphibians, 850 for reptiles, 5,667 for birds and 7,651 for mammals. We contrasted the importance of life history traits and environmental predictors using mixed models and tested different hypotheses to explain the variation in population density for the four groups. We assessed the predictive accuracy of models through cross‐validation and mapped the partial response of vertebrate population density to environmental variables globally.

Results

Amphibians were more abundant in wet areas with high productivity levels, whereas reptiles showed relatively higher densities in arid areas with low productivity and stable temperatures. The density of birds and mammals was typically high in temperate wet areas with intermediate levels of productivity. The models showed good predictive abilities, with pseudo‐R² ranging between 0.68 (birds) and 0.83 (reptiles).

Main conclusions

Traits determine most of the variation in population density across species, whereas environmental conditions explain the intraspecific variation across populations. Species traits, resource availability and climatic stability have a different influence on the population density of the four groups. These models can be used to predict the average species population density over large areas and be used to explore macroecological patterns and inform conservation analyses.     

The erratic mitochondrial clock: variations of mutation rate, not population size, affect mtDNA diversity across birds and mammals

Background  

During the last ten years, major advances have been made in characterizing and understanding the evolution of mitochondrial DNA, the most popular marker of molecular biodiversity. Several important results were recently reported using mammals as model organisms, including (i) the absence of relationship between mitochondrial DNA diversity and life-history or ecological variables, (ii) the absence of prominent adaptive selection, contrary to what was found in invertebrates, and (iii) the unexpectedly large variation in neutral substitution rate among lineages, revealing a possible link with species maximal longevity. We propose to challenge these results thanks to the bird/mammal comparison. Direct estimates of population size are available in birds, and this group presents striking life-history trait differences with mammals (higher mass-specific metabolic rate and longevity). These properties make birds the ideal model to directly test for population size effects, and to discriminate between competing hypotheses about the causes of substitution rate variation.     

Comparative phylogeography of two co‐distributed but ecologically distinct rainbowfishes of far‐northern Australia

Aim

To test the influence of historical and contemporary environment in shaping the genetic diversity of freshwater fauna we contrast genetic structure in two co‐distributed, but ecologically distinct, rainbowfish; a habitat generalist (Melanotaenia splendida) and a habitat specialist (M. trifasciata).

Location

Fishes were sampled from far northern Australia (Queensland and Northern Territory).

Methods

We used sequence data from one mitochondrial gene and one nuclear gene to investigate patterns of genetic diversity in M. splendida and M. trifasciata to determine how differences in habitat preference and historical changes in drainage boundaries affected patterns of connectivity.

Results

Melanotaenia splendida showed high levels of genetic diversity and little population structure across its range. In contrast, M. trifasciata showed high levels of population structure. Whereas phylogeographic patterns differed, both species showed a strong relationship between geographical distance and genetic differentiation between populations. Melanotaenia splendida showed a shallower relationship with geographical distance, and genetic differentiation was best explained by stream length and a lower scaled ocean distance (11.98 times coast length). For M. trifasciata, genetic differentiation was best explained by overwater distance between catchments and ocean distance scaled at 1.16 × 10⁶ times coast length.

Main conclusions

Connectivity of freshwater populations inhabiting regions periodically interconnected during glacial periods appears to have been affected by ecological differences between species. Species‐specific differences are epitomized here by the contrast between co‐distributed congeners with different habitat requirements: for the habitat generalist, M. splendida, there was evidence for greater historical genetic connectivity with oceans as a weaker barrier to gene exchange in contrast with the habitat specialist, M. trifasciata.     

Similar rates of protein adaptation in <Emphasis Type="Italic">Drosophila miranda</Emphasis> and <Emphasis Type="Italic">D. melanogaster</Emphasis>, two species with different current effective population sizes

Background  

Adaptive protein evolution is common in several Drosophila species investigated. Some studies point to very weak selection operating on amino-acid mutations, with average selection intensities on the order of N _e s ~ 5 in D. melanogaster and D. simulans. Species with lower effective population sizes should undergo less adaptation since they generate fewer mutations and selection is ineffective on a greater proportion of beneficial mutations.     

Influence of hydrological conditions on the <Emphasis Type="Italic">Escherichia coli</Emphasis> population structure in the water of a creek on a rural watershed

Background  

Escherichia coli is a commensal bacterium of the gastro-intestinal tract of human and vertebrate animals, although the aquatic environment could be a secondary habitat. The aim of this study was to investigate the effect of hydrological conditions on the structure of the E. coli population in the water of a creek on a small rural watershed in France composed of pasture and with human occupation.