Genomic Tools for Evolution and Conservation in the Chimpanzee: Pan troglodytes ellioti Is a Genetically Distinct Population

In spite of its evolutionary significance and conservation importance, the population structure of the common chimpanzee, Pan troglodytes, is still poorly understood. An issue of particular controversy is whether the proposed fourth subspecies of chimpanzee, Pan troglodytes ellioti, from parts of Nigeria and Cameroon, is genetically distinct. Although modern high-throughput SNP genotyping has had a major impact on our understanding of human population structure and demographic history, its application to ecological, demographic, or conservation questions in non-human species has been extremely limited. Here we apply these tools to chimpanzee population structure, using ∼700 autosomal SNPs derived from chimpanzee genomic data and a further ∼100 SNPs from targeted re-sequencing. We demonstrate conclusively the existence of P. t. ellioti as a genetically distinct subgroup. We show that there is clear differentiation between the verus, troglodytes, and ellioti populations at the SNP and haplotype level, on a scale that is greater than that separating continental human populations. Further, we show that only a small set of SNPs (10–20) is needed to successfully assign individuals to these populations. Tellingly, use of only mitochondrial DNA variation to classify individuals is erroneous in 4 of 54 cases, reinforcing the dangers of basing demographic inference on a single locus and implying that the demographic history of the species is more complicated than that suggested analyses based solely on mtDNA. In this study we demonstrate the feasibility of developing economical and robust tests of individual chimpanzee origin as well as in-depth studies of population structure. These findings have important implications for conservation strategies and our understanding of the evolution of chimpanzees. They also act as a proof-of-principle for the use of cheap high-throughput genomic methods for ecological questions

Experimental evolution of sperm competitiveness in a mammal

<p>Abstract</p> <p>Background</p> <p>When females mate with multiple partners, sperm from rival males compete to fertilise the ova. Studies of experimental evolution have proven the selective action of sperm competition on male reproductive traits. However, while reproductive traits may evolve in response to sperm competition, this does not necessarily provide evidence that sperm competitive ability responds to selection. Indeed, a study of <it>Drosophila </it>failed to observe divergence in sperm competitive ability of males in lines selected for enhanced sperm offence and defence.</p> <p>Results</p> <p>Adopting the naturally polygamous house mouse (<it>Mus domesticus</it>) as our vertebrate model, we performed an experimental evolution study and observed genetic divergence in sperm quality; males from the polygamous selection lines produced ejaculates with increased sperm numbers and greater sperm motility compared to males from the monogamous lines. Here, after 12 generations of experimental evolution, we conducted competitive matings between males from lineages evolving under sperm competition and males from lineages subject to relaxed selection. We reduced variation in paternity arising from embryo mortality by genotyping embryos <it>in utero </it>at 14 days gestation. Our microsatellite data revealed a significant paternity bias toward males that evolved under the selective regime of sperm competition.</p> <p>Conclusion</p> <p>We provide evidence that the sperm competitiveness phenotype can respond to selection, and show that improved sperm quality translates to greater competitive fertilisation success in house mice.</p

Complement C3 Deficiency Attenuates Chronic Hypoxia-Induced Pulmonary Hypertension in Mice

Background: Evidence suggests a role of both innate and adaptive immunity in the development of pulmonary arterial hypertension. The complement system is a key sentry of the innate immune system and bridges innate and adaptive immunity. To date there are no studies addressing a role for the complement system in pulmonary arterial hypertension. Methodology/Principal Findings: Immunofluorescent staining revealed significant C3d deposition in lung sections from IPAH patients and C57Bl6/J wild-type mice exposed to three weeks of chronic hypoxia to induce pulmonary hypertension. Right ventricular systolic pressure and right ventricular hypertrophy were increased in hypoxic vs. normoxic wild-type mice, which were attenuated in C3-/- hypoxic mice. Likewise, pulmonary vascular remodeling was attenuated in the C3-/- mice compared to wild-type mice as determined by the number of muscularized peripheral arterioles and morphometric analysis of vessel wall thickness. The loss of C3 attenuated the increase in interleukin-6 and intracellular adhesion molecule-1 expression in response to chronic hypoxia, but not endothelin-1 levels. In wild-type mice, but not C3-/- mice, chronic hypoxia led to platelet activation as assessed by bleeding time, and flow cytometry of platelets to determine cell surface P-selectin expression. In addition, tissue factor expression and fibrin deposition were increased in the lungs of WT mice in response to chronic hypoxia. These pro-thrombotic effects of hypoxia were abrogated in C3-/- mice. Conclusions: Herein, we provide compelling genetic evidence that the complement system plays a pathophysiologic role in the development of PAH in mice, promoting pulmonary vascular remodeling and a pro-thrombotic phenotype. In addition we demonstrate C3d deposition in IPAH patients suggesting that complement activation plays a role in the development of PAH in humans. © 2011 Bauer et al

Contrasting Diversity Patterns of Crenarchaeal, Bacterial and Fungal Soil Communities in an Alpine Landscape

International audienceBackground: The advent of molecular techniques in microbial ecology has aroused interest in gaining an understanding about the spatial distribution of regional pools of soil microbes and the main drivers responsible of these spatial patterns. Here, we assessed the distribution of crenarcheal, bacterial and fungal communities in an alpine landscape displaying high turnover in plant species over short distances. Our aim is to determine the relative contribution of plant species composition, environmental conditions, and geographic isolation on microbial community distribution. Methodology/Principal Findings: Eleven types of habitats that best represent the landscape heterogeneity were investigated. Crenarchaeal, bacterial and fungal communities were described by means of Single Strand Conformation Polymorphism. Relationships between microbial beta diversity patterns were examined by using Bray-Curtis dissimilarities and Principal Coordinate Analyses. Distance-based redundancy analyses and variation partitioning were used to estimate the relative contributions of different drivers on microbial beta diversity. Microbial communities tended to be habitat- specific and did not display significant spatial autocorrelation. Microbial beta diversity correlated with soil pH. Fungal beta- diversity was mainly related to soil organic matter. Though the effect of plant species composition was significant for all microbial groups, it was much stronger for Fungi. In contrast, geographic distances did not have any effect on microbial beta diversity. Conclusions/Significance: Microbial communities exhibit non-random spatial patterns of diversity in alpine landscapes. Crenarcheal, bacterial and fungal community turnover is high and associated with plant species composition through different set of soil variables, but is not caused by geographical isolation

Gut mucosal DAMPs in IBD: From mechanisms to therapeutic implications

Endogenous damage-associated molecular patterns (DAMPs) are released during tissue damage and have increasingly recognized roles in the etiology of many human diseases. The inflammatory bowel diseases (IBD), ulcerative colitis (UC) and Crohn’s disease (CD), are immune-mediated conditions where high levels of DAMPs are observed. DAMPs such as calprotectin (S100A8/9) have an established clinical role as a biomarker in IBD. In this review, we use IBD as an archetypal common chronic inflammatory disease to focus on the conceptual and evidential importance of DAMPs in pathogenesis and why DAMPs represent an entirely new class of targets for clinical translation. </p

The long-term consequences of retrieval demands during working memory

Although it is well known that distraction impairs immediate retrieval of items maintained in working memory (WM; e.g., during complex span tasks), some evidence suggests that these items are more likely to be recalled from episodic memory (EM) compared with items that were studied without any distraction (e.g., during simple span tasks). One account for this delayed advantage of complex span over simple span, or the McCabe effect (McCabe, Journal of Memory and Language, 58[2], 480–494, 2008), is that complex span affords covert retrieval opportunities that facilitate later retrieval from EM by cumulatively reactivating each successively presented item after distraction. This explanation focuses on the processing that occurs during presentation and maintenance of the items, but no work to date has explored whether the differential demands of immediate retrieval between simple and complex span may explain the effect. Accordingly, these experiments examined the impact of immediate retrieval demands on the McCabe effect by comparing typical immediate serial-recall instructions (i.e., recalling the words in their exact order of presentation) to immediate free-recall (Experiments 1–2) and no-recall (Experiments 2 and 3) instructions. The results suggested that the nature of retrieval may constrain the McCabe effect in some situations (Experiments 1–2), but its demands do not drive the McCabe effect given that it was observed in both serial-recall and no-recall conditions (Experiment 3). Instead, activities such as covert retrieval during the processing phase may underlie the McCabe effect, thus further evidencing the importance of processing in WM for the long-term retention of information

RECAPP-XPR: A smartphone application for presenting and recalling experimentally controlled stimuli over longer timescales

We report two experiments that used smartphone applications for presenting and recalling verbal stimuli over extended timescales. In Experiment 1, we used an iPhone application that we had developed, called RECAPP-XPR, to present 76 participants with a single list of eight words presented at a rate of one word every hour, followed by a test of free recall an hour later. The experiment was exceptionally easy to schedule, taking only between 5 and 10 min to set up using a web-based interface. RECAPP-XPR randomly samples the stimuli, presents the stimuli, and collects the free recall data. The stimuli disappear shortly after they have been presented, and RECAPP-XPR collects data on when each stimulus was viewed. In Experiment 2, the study was replicated using the widely used image-sharing application Snapchat. A total of 197 participants were tested by 38 student experimenters, who manually presented the stimuli as “snaps” of experimentally controlled stimuli using the same experimental rates that had been used in Experiment 1. Like all snaps, these stimuli disappeared from view after a very short interval. In both experiments, we observed significant recall advantages for the first and last list items (primacy and recency effects, respectively), and there were clear tendencies to make more transitions at output between near-neighboring items, with a forward-ordered bias, consistent with temporal contiguity effects. The respective advantages and disadvantages of RECAPP-XPR and Snapchat as experimental software packages are discussed, as is the relationship between single-study-list smartphone experiments and long-term recency studies of real-world events