Conservation genetics of a rare Gerbil species: a comparison of the population genetic structures and demographic histories of the locally rare Pygmy Gerbil and the common Anderson's Gerbil

<p>Abstract</p> <p>Background</p> <p>One of the major challenges in evolutionary biology is identifying rare species and devising management plans to protect them while also sustaining their genetic diversity. However, in attempting a broad understanding of rarity, single-species studies provide limited insights because they do not reveal whether the factors that affect rare species differ from those that affect more common species. To illustrate this important concept and to arrive at a better understanding of the form of rarity characterizing the rare <it>Gerbillus henleyi</it>, we explored its population genetic structure alongside that of the locally common <it>Gerbillus andersoni allenbyi</it>. We trapped gerbils in several locations in Israel's western and inner Negev sand dunes. We then extracted DNA from ear samples, and amplified two mitochondrial sequences: the control region (CR) and the <it>cytochrome oxidase 2 </it>gene (CO2).</p> <p>Results</p> <p>Nucleotide diversity was low for all sequences, especially for the CR of <it>G. a. allenbyi</it>, which showed no diversity. We could not detect any significant population genetic structure in <it>G. henleyi</it>. In contrast, <it>G. a. allenbyi</it>'s CO2 sequence showed significant population genetic structure. Pairwise PhiPT comparisons showed low values for <it>G. henleyi </it>but high values for <it>G. a. allenbyi</it>. Analysis of the species' demographic history indicated that <it>G. henleyi</it>'s population size has not changed recently, and is under the influence of an ongoing bottleneck. The same analysis for <it>G. a. allenbyi </it>showed that this species has undergone a recent population expansion.</p> <p>Conclusions</p> <p>Comparing the two species, the populations of <it>G. a. allenbyi </it>are more isolated from each other, likely due to the high habitat specificity characterizing this species. The bottleneck pattern found in <it>G. henleyi </it>may be the result of competition with larger gerbil species. This result, together with the broad habitat use and high turnover rate characterizing <it>G. henleyi</it>, may explain the low level of differentiation among its populations. The evidence for a recent population expansion of <it>G. a. allenbyi </it>fits well with known geomorphological data about the formation of the Negev sand dunes and paleontological data about this species' expansion throughout the Levant. In conclusion, we suggest that adopting a comparative approach as presented here can markedly improve our understanding of the causes and effects of rarity, which in turn can allow us to better protect biodiversity patterns.</p

Copy number variation of the SELENBP1 gene in schizophrenia

<p>Abstract</p> <p>Background</p> <p>Schizophrenia is associated with rare copy-number (CN) mutations. Screening for such alleles genome-wide, though comprehensive, cannot study in-depth the causality of particular loci, therefore cannot provide the functional interpretation for the disease etiology. We hypothesized that CN mutations in the SELENBP1 locus could associate with the disorder and that these mutations could alter the gene product's activity in patients.</p> <p>Methods</p> <p>We analyzed SELENBP1 CN variation (CNV) in blood DNA from 49 schizophrenia patients and 49 controls (cohort A). Since CN of genes may vary among tissues, we investigated SELENBP1 CN in age- sex- and postmortem interval-matched cerebellar DNA samples from 14 patients and 14 controls (cohort B). Since CNV may either be <it>de-novo </it>or inherited we analyzed CNV of the SELENBP1 locus in blood DNA from 26 trios of schizophrenia probands and their healthy parents (cohort C). SELENBP1 mRNA levels were measured by real-time PCR.</p> <p>Results</p> <p>In cohort A reduced CN of the SELENBP1 locus was found in four patients but in none of the controls. In cohort B we found reduced CN of the SELENBP1 locus in two patients but in none of the controls. In cohort C three patients exhibited drastic CN reduction, not present in their parents, indicating <it>de-novo </it>mutation. A reduction in SELENBP1 mRNA levels in the postmortem cerebellar samples of schizophrenia patients was found.</p> <p>Conclusions</p> <p>We report a focused study of CN mutations in the selenium binding-protein1 (SELENBP1) locus previously linked with schizophrenia. We provide evidence for recurrence of decreased CN of the SELENBP1 locus in three unrelated patients' cohorts but not in controls, raising the possibility of functional involvement of these mutations in the etiology of the disease.</p

Temporal force governs the microbial assembly associated with Ulva fasciata (Chlorophyta) from an integrated multi-trophic aquaculture system

Ulva spp., one of the most important providers of marine ecosystem services, has gained substantial attention lately in both ecological and applicational aspects. It is known that macroalgae and their associated microbial community form an inseparable unit whose intimate relationship can affect the wellbeing of both. Different cultivation systems, such as integrated multi-trophic aquaculture (IMTA), are assumed to impact Ulva bacterial community significantly in terms of compositional guilds. However, in such a highly dynamic environment, it is crucial to determine how the community dynamics change over time. In the current study, we characterized the microbiota associated with Ulva fasciata grown as a biofilter in an IMTA system in the Gulf of Aqaba (Eilat, Israel) over a developmental period of 5 weeks. The Ulva-associated microbial community was identified using the 16S rRNA gene amplicon sequencing technique, and ecological indices were further analyzed. The Ulva-associated microbiome revealed a swift change in composition along the temporal succession, with clusters of distinct communities for each timepoint. Proteobacteria, Bacteroidetes, Planctomycetes, and Deinococcus-Thermus, the most abundant phyla that accounted for up to 95% of all the amplicon sequence variants (ASVs) found, appeared in all weeks. Further analyses highlighted microbial biomarkers representing each timepoint and their characteristics. Finally, the presence of highly abundant species in Ulva microbiota yet underestimated in previous research (such as phyla Deinococcus-Thermus, families Saprospiraceae, Thiohalorhabdaceae, and Pirellulaceae) suggests that more attention should be paid to the temporal succession of the assembly of microbes inhabiting macroalgae in aquaculture, in general, and IMTA, in particular. Characterizing bacterial communities associated with Ulva fasciata from an IMTA system provided a better understanding of their associated microbial dynamics and revealed this macroalgae's adaptation to such a habitat

Differences in mtDNA haplogroup distribution among 3 Jewish populations alter susceptibility to T2DM complications

BACKGROUND: Recent genome-wide association studies searching for candidate susceptibility loci for common complex diseases such as type 2 diabetes mellitus (T2DM) and its common complications have uncovered novel disease-associated genes. Nevertheless these large-scale population screens often overlook the tremendous variation in the mitochondrial genome (mtDNA) and its involvement in complex disorders. RESULTS: We have analyzed the mitochondrial DNA (mtDNA) genetic variability in Ashkenazi (Ash), Sephardic (Seph) and North African (NAF) Jewish populations (total n = 1179). Our analysis showed significant differences (p < 0.001) in the distribution of mtDNA genetic backgrounds (haplogroups) among the studied populations. To test whether these differences alter the pattern of disease susceptibility, we have screened our three Jewish populations for an association of mtDNA genetic haplogroups with T2DM complications. Our results identified population-specific susceptibility factors of which the best example is the Ashkenazi Jewish specific haplogroup N1b1, having an apparent protective effect against T2DM complications in Ash (p = 0.006), being absent in the NAF population and under-represented in the Seph population. We have generated and analyzed whole mtDNA sequences from the disease associated haplogroups revealing mutations in highly conserved positions that are good candidates to explain the phenotypic effect of these genetic backgrounds. CONCLUSION: Our findings support the possibility that recent bottleneck events leading to over-representation of minor mtDNA alleles in specific genetic isolates, could result in population-specific susceptibility loci to complex disorders

Gene Expression Patterns of Oxidative Phosphorylation Complex I Subunits Are Organized in Clusters

After the radiation of eukaryotes, the NUO operon, controlling the transcription of the NADH dehydrogenase complex of the oxidative phosphorylation system (OXPHOS complex I), was broken down and genes encoding this protein complex were dispersed across the nuclear genome. Seven genes, however, were retained in the genome of the mitochondrion, the ancient symbiote of eukaryotes. This division, in combination with the three-fold increase in subunit number from bacteria (N = ∼14) to man (N = 45), renders the transcription regulation of OXPHOS complex I a challenge. Recently bioinformatics analysis of the promoter regions of all OXPHOS genes in mammals supported patterns of co-regulation, suggesting that natural selection favored a mechanism facilitating the transcriptional regulatory control of genes encoding subunits of these large protein complexes. Here, using real time PCR of mitochondrial (mtDNA)- and nuclear DNA (nDNA)-encoded transcripts in a panel of 13 different human tissues, we show that the expression pattern of OXPHOS complex I genes is regulated in several clusters. Firstly, all mtDNA-encoded complex I subunits (N = 7) share a similar expression pattern, distinct from all tested nDNA-encoded subunits (N = 10). Secondly, two sub-clusters of nDNA-encoded transcripts with significantly different expression patterns were observed. Thirdly, the expression patterns of two nDNA-encoded genes, NDUFA4 and NDUFA5, notably diverged from the rest of the nDNA-encoded subunits, suggesting a certain degree of tissue specificity. Finally, the expression pattern of the mtDNA-encoded ND4L gene diverged from the rest of the tested mtDNA-encoded transcripts that are regulated by the same promoter, consistent with post-transcriptional regulation. These findings suggest, for the first time, that the regulation of complex I subunits expression in humans is complex rather than reflecting global co-regulation

Stable isotope analysis provides new information on winter habitat use of declining avian migrants that is relevant to their conservation

Winter habitat use and the magnitude of migratory connectivity are important parameters when assessing drivers of the marked declines in avian migrants. Such information is unavailable for most species. We use a stable isotope approach to assess these factors for three declining African-Eurasian migrants whose winter ecology is poorly known: wood warbler Phylloscopus sibilatrix, house martin Delichon urbicum and common swift Apus apus. Spatially segregated breeding wood warbler populations (sampled across a 800 km transect), house martins and common swifts (sampled across a 3,500 km transect) exhibited statistically identical intra-specific carbon and nitrogen isotope ratios in winter grown feathers. Such patterns are compatible with a high degree of migratory connectivity, but could arise if species use isotopically similar resources at different locations. Wood warbler carbon isotope ratios are more depleted than typical for African-Eurasian migrants and are compatible with use of moist lowland forest. The very limited variance in these ratios indicates specialisation on isotopically restricted resources, which may drive the similarity in wood warbler populations' stable isotope ratios and increase susceptibility to environmental change within its wintering grounds. House martins were previously considered to primarily use moist montane forest during the winter, but this seems unlikely given the enriched nature of their carbon isotope ratios. House martins use a narrower isotopic range of resources than the common swift, indicative of increased specialisation or a relatively limited wintering range; both factors could increase house martins' vulnerability to environmental change. The marked variance in isotope ratios within each common swift population contributes to the lack of population specific signatures and indicates that the species is less vulnerable to environmental change in sub-Saharan Africa than our other focal species. Our findings demonstrate how stable isotope research can contribute to understanding avian migrants' winter ecology and conservation status

Parental diabetes status reveals association of mitochondrial DNA haplogroup J1 with type 2 diabetes

<p>Abstract</p> <p>Background</p> <p>Although mitochondrial dysfunction is consistently manifested in patients with Type 2 Diabetes mellitus (T2DM), the association of mitochondrial DNA (mtDNA) sequence variants with T2DM varies among populations. These differences might stem from differing environmental influences among populations. However, other potentially important considerations emanate from the very nature of mitochondrial genetics, namely the notable high degree of partitioning in the distribution of human mtDNA variants among populations, as well as the interaction of mtDNA and nuclear DNA-encoded factors working in concert to govern mitochondrial function. We hypothesized that association of mtDNA genetic variants with T2DM could be revealed while controlling for the effect of additional inherited factors, reflected in family history information.</p> <p>Methods</p> <p>To test this hypothesis we set out to investigate whether mtDNA genetic variants will be differentially associated with T2DM depending on the diabetes status of the parents. To this end, association of mtDNA genetic backgrounds (haplogroups) with T2DM was assessed in 1055 Jewish patients with and without T2DM parents ('DP' and 'HP', respectively).</p> <p>Results</p> <p>Haplogroup J1 was found to be 2.4 fold under-represented in the 'HP' patients (p = 0.0035). These results are consistent with a previous observation made in Finnish T2DM patients. Moreover, assessing the haplogroup distribution in 'DP' versus 'HP' patients having diabetic siblings revealed that haplogroup J1 was virtually absent in the 'HP' group.</p> <p>Conclusion</p> <p>These results imply the involvement of inherited factors, which modulate the susceptibility of haplogroup J1 to T2DM.</p

Jack of All Trades, Master of All: A Positive Association between Habitat Niche Breadth and Foraging Performance in Pit-Building Antlion Larvae

Species utilizing a wide range of resources are intuitively expected to be less efficient in exploiting each resource type compared to species which have developed an optimal phenotype for utilizing only one or a few resources. We report here the results of an empirical study whose aim was to test for a negative association between habitat niche breadth and foraging performance. As a model system to address this question, we used two highly abundant species of pit-building antlions varying in their habitat niche breadth: the habitat generalist Myrmeleon hyalinus, which inhabits a variety of soil types but occurs mainly in sandy soils, and the habitat specialist Cueta lineosa, which is restricted to light soils such as loess. Both species were able to discriminate between the two soils, with each showing a distinct and higher preference to the soil type providing higher prey capture success and characterizing its primary habitat-of-origin. As expected, only small differences in the foraging performances of the habitat generalist were evident between the two soils, while the performance of the habitat specialist was markedly reduced in the alternative sandy soil. Remarkably, in both soil types, the habitat generalist constructed pits and responded to prey faster than the habitat specialist, at least under the temperature range of this study. Furthermore, prey capture success of the habitat generalist was higher than that of the habitat specialist irrespective of the soil type or prey ant species encountered, implying a positive association between habitat niche-breadth and foraging performance. Alternatively, C. lineosa specialization to light soils does not necessarily confer upon its superiority in utilizing such habitats. We thus suggest that habitat specialization in C. lineosa is either an evolutionary dead-end, or, more likely, that this species' superiority in light soils can only be evident when considering additional niche axes