Alexandre Courtiol

MHC genotyping of non-model organisms using next-generation sequencing: a new methodology to deal with artefacts and allelic dropout.

BackgroundThe Major Histocompatibility Complex (MHC) is the most important genetic marker to study patterns of adaptive genetic variation determining pathogen resistance and associated life history decisions. It is used in many different research fields ranging from human medical, molecular evolutionary to functional biodiversity studies. Correct assessment of the individual allelic diversity pattern and the underlying structural sequence variation is the basic requirement to address the functional importance of MHC variability. Next-generation sequencing (NGS) technologies are likely to replace traditional genotyping methods to a great extent in the near future but first empirical studies strongly indicate the need for a rigorous quality control pipeline. Strict approaches for data validation and allele calling to distinguish true alleles from artefacts are required.ResultsWe developed the analytical methodology and validated a data processing procedure which can be applied to any organism. It allows the separation of true alleles from artefacts and the evaluation of genotyping reliability, which in addition to artefacts considers for the first time the possibility of allelic dropout due to unbalanced amplification efficiencies across alleles. Finally, we developed a method to assess the confidence level per genotype a-posteriori, which helps to decide which alleles and individuals should be included in any further downstream analyses. The latter method could also be used for optimizing experiment designs in the future.ConclusionsCombining our workflow with the study of amplification efficiency offers the chance for researchers to evaluate enormous amounts of NGS-generated data in great detail, improving confidence over the downstream analyses and subsequent applications.

Natural and sexual selection in a monogamous historical human population

Whether and how human populations exposed to the agricultural revolution are still affected by Darwinian selection remains controversial among social scientists, biologists, and the general public. Although methods of studying selection in natural populations are well established, our understanding of selection in humans has been limited by the availability of suitable datasets. Here, we present a study comparing the maximum strengths of natural and sexual selection in humans that includes the effects of sex and wealth on different episodes of selection. Our dataset was compiled from church records of preindustrial Finnish populations characterized by socially imposed monogamy, and it contains a complete distribution of survival, mating, and reproductive success for 5,923 individuals born 1760–1849. Individual differences in early survival and fertility (natural selection) were responsible for most variation in fitness, even among wealthier individuals. Variance in mating success explained most of the higher variance in reproductive success in males compared with females, but mating success also influenced reproductive success in females, allowing for sexual selection to operate in both sexes. The detected opportunity for selection is in line with measurements for other species but higher than most previous reports for human samples. This disparity results from biological, demographic, economic, and social differences across populations as well as from failures by most previous studies to account for variation in fitness introduced by nonreproductive individuals. Our results emphasize that the demographic, cultural, and technological changes of the last 10,000 y did not preclude the potential for natural and sexual selection in our species.

MATE CHOICE AND HUMAN STATURE: HOMOGAMY AS A UNIFIED FRAMEWORK FOR UNDERSTANDING MATING PREFERENCES

Assortative mating for human height has long attracted interest in evolutionary biology, and the phenomenon has been demonstrated in numerous human populations. It is often argued that mating preferences generate this pattern, but other processes can also induce trait correlations between mates. Here, we present a methodology tailored to quantify continuous preferences based on choice experiments between pairs of stimuli. In particular, it is possible to explore determinants of interindividual variations in preferences, such as the height of the chooser. We collected data from a sample of 200 individuals from France. Measurements obtained show that the perception of attractiveness depends on both the height of the stimuli and the stature of the individual who judged them. Therefore, this study demonstrates that homogamy is present at the level of preferences for both sexes. We also show that measurements of the function describing this homogamy are concordant with several distinct mating rules proposed in the literature. In addition, the quantitative approach introduced here fulfills metrics that can be used to compare groups of individuals. In particular, our results reveal an important disagreement between sexes regarding height preferences in the context of mutual mate choice. Finally, both women and men prefer individuals who are significantly taller than average. All major findings are confirmed by a reanalysis of previously published data.

Impact of enrichment conditions on cross-species capture of fresh and degraded DNA

By combining high‐throughput sequencing with target enrichment (‘hybridization capture’), researchers are able to obtain molecular data from genomic regions of interest for projects that are otherwise constrained by sample quality (e.g. degraded and contamination‐rich samples) or a lack of a priori sequence information (e.g. studies on nonmodel species). Despite the use of hybridization capture in various fields of research for many years, the impact of enrichment conditions on capture success is not yet thoroughly understood. We evaluated the impact of a key parameter – hybridization temperature – on the capture success of mitochondrial genomes across the carnivoran family Felidae. Capture was carried out for a range of sample types (fresh, archival, ancient) with varying levels of sequence divergence between bait and target (i.e. across a range of species) using pools of individually indexed libraries on Agilent SureSelect™ arrays. Our results suggest that hybridization capture protocols require specific optimization for the sample type that is being investigated. Hybridization temperature affected the proportion of on‐target sequences following capture: for degraded samples, we obtained the best results with a hybridization temperature of 65 °C, while a touchdown approach (65 °C down to 50 °C) yielded the best results for fresh samples. Evaluation of capture performance at a regional scale (sliding window approach) revealed no significant improvement in the recovery of DNA fragments with high sequence divergence from the bait at any of the tested hybridization temperatures, suggesting that hybridization temperature may not be the critical parameter for the enrichment of divergent fragments.

Variation in koala microbiomes within and between individuals: effect of body region and captivity status.

Metagenomic analysis of 16S ribosomal RNA has been used to profile microbial communities at high resolution, and to examine their association with host diet or diseases. We examined the oral and gut microbiome composition of two captive koalas to determine whether bacterial communities are unusual in this species, given that their diet consists almost exclusively of Eucalyptus leaves. Despite a highly specialized diet, koala oral and gut microbiomes were similar in composition to the microbiomes from the same body regions of other mammals. Rectal swabs contained all of the diversity present in faecal samples, along with additional taxa, suggesting that faecal bacterial communities may merely subsample the gut bacterial diversity. Furthermore, the faecal microbiomes of the captive koalas were similar to those reported for wild koalas, suggesting that captivity may not compromise koala microbial health. Since koalas frequently suffer from ocular diseases caused by Chlamydia infection, we also examined the eye microbiome composition of two captive koalas, establishing the healthy baseline for this body part. The eye microbial community was very diverse, similar to other mammalian ocular microbiomes but with an unusually high representation of bacteria from the family Phyllobacteriaceae.

The Demographic Transition Influences Variance in Fitness and Selection on Height and BMI in Rural Gambia

Summary Recent human history is marked by demographic transitions characterized by declines in mortality and fertility [1]. By influencing the variance in those fitness components, demographic transitions can affect selection on other traits [2]. Parallel to changes in selection triggered by demography per se, relationships between fitness and anthropometric traits are also expected to change due to modification of the environment. Here we explore for the first time these two main evolutionary consequences of demographic transitions using a unique data set containing survival, fertility, and anthropometric data for thousands of women in rural Gambia from 1956–2010 [3]. We show how the demographic transition influenced directional selection on height and body mass index (BMI). We observed a change in selection for both traits mediated by variation in fertility: selection initially favored short females with high BMI values but shifted across the demographic transition to favor tall females with low BMI values. We demonstrate that these differences resulted both from changes in fitness variance that shape the strength of selection and from shifts in selective pressures triggered by environmental changes. These results suggest that demographic and environmental trends encountered by current human populations worldwide are likely to modify, but not stop, natural selection in humans.

camtrapR: an R package for efficient camera trap data management

Summary Camera trapping is a widely applied method to study mammalian biodiversity and is still gaining popularity. It can quickly generate large amounts of data which need to be managed in an efficient and transparent way that links data acquisition with analytical tools. We describe the free and open-source R package camtrapR, a new toolbox for flexible and efficient management of data generated in camera trap-based wildlife studies. The package implements a complete workflow for processing camera trapping data. It assists in image organization, species and individual identification, data extraction from images, tabulation and visualization of results and export of data for subsequent analyses. There is no limitation to the number of images stored in this data management system; the system is portable and compatible across operating systems. The functions provide extensive automation to minimize data entry mistakes and, apart from species and individual identification, require minimal manual user input. Species and individual identification are performed outside the R environment, either via tags assigned in dedicated image management software or by moving images into species directories. Input for occupancy and (spatial) capture–recapture analyses for density and abundance estimation, for example in the R packages unmarked or secr, is computed in a flexible and reproducible manner. In addition, survey summary reports can be generated, spatial distributions of records can be plotted and exported to gis software, and single- and two-species activity patterns can be visualized. camtrapR allows for streamlined and flexible camera trap data management and should be most useful to researchers and practitioners who regularly handle large amounts of camera trapping data.

Climatic variation and age‐specific survival in Asian elephants from Myanmar

Concern about climate change has intensified interest in understanding how climatic variability affects animal life histories. Despite such effects being potentially most dramatic in large, long-lived, and slowly reproducing terrestrial mammals, little is known of the effects of climatic variation on survival in those species. Asian elephants (Elephas maximus) are endangered across their distribution, and inhabit regions characterized by high seasonality of temperature and rainfall. We investigated the effects of monthly climatic variation on survival and causes of death in Asian elephants using a unique demographic data set of 1024 semi-captive, longitudinally monitored elephants from four sites in Myanmar between 1965 and 2000. Temperature had a significant effect on survival in both sexes and across all ages. For elephants between 1 month and 17 years of age, maximal survival was reached at -24 degrees C, and any departures from this temperature increased mortality, whereas neonates and mature elephants had maximal survival at even lower temperatures. Although males experienced higher mortality overall, sex differences in these optimal temperatures were small. Because the elephants spent more time during a year in temperatures above 24 degrees C than in temperatures below it, most deaths occurred at hot (temperatures>24 degrees C) rather than cold periods. Decreased survival at higher temperatures resulted partially from increased deaths from infectious disease and heat stroke, whereas the lower survival in the coldest months was associated with an increase in noninfectious diseases and poor health in general. Survival was also related to rainfall, with the highest survival rates during the wettest months for all ages and sexes. Our results show that even the normal-range monsoon variation in climate can exert a large impact on elephant survival in Myanmar, leading to extensive absolute differences in mortality; switching from favorable to unfavorable climatic conditions within average years doubled the odds for mortality. The persistence of a long-term trend toward higher global temperatures, combined with the possibility of higher variation in temperature between seasons, may pose a challenge to the survival of species such as Asian elephants.

Planning tiger recovery: Understanding intraspecific variation for effective conservation

Radical revision of tiger taxonomy for a pragmatic and scientifically sound approach to tiger conservation management. Although significantly more money is spent on the conservation of tigers than on any other threatened species, today only 3200 to 3600 tigers roam the forests of Asia, occupying only 7% of their historical range. Despite the global significance of and interest in tiger conservation, global approaches to plan tiger recovery are partly impeded by the lack of a consensus on the number of tiger subspecies or management units, because a comprehensive analysis of tiger variation is lacking. We analyzed variation among all nine putative tiger subspecies, using extensive data sets of several traits [morphological (craniodental and pelage), ecological, molecular]. Our analyses revealed little variation and large overlaps in each trait among putative subspecies, and molecular data showed extremely low diversity because of a severe Late Pleistocene population decline. Our results support recognition of only two subspecies: the Sunda tiger, Panthera tigris sondaica, and the continental tiger, Panthera tigris tigris, which consists of two (northern and southern) management units. Conservation management programs, such as captive breeding, reintroduction initiatives, or trans-boundary projects, rely on a durable, consistent characterization of subspecies as taxonomic units, defined by robust multiple lines of scientific evidence rather than single traits or ad hoc descriptions of one or few specimens. Our multiple-trait data set supports a fundamental rethinking of the conventional tiger taxonomy paradigm, which will have profound implications for the management of in situ and ex situ tiger populations and boost conservation efforts by facilitating a pragmatic approach to tiger conservation management worldwide.

How choosy should I be? The relative searching time predicts evolution of choosiness under direct sexual selection

Most theoretical research in sexual selection has focused on indirect selection. However, empirical studies have not strongly supported indirect selection. A well-established finding is that direct benefits and costs exert a strong influence on the evolution of mate choice. We present an analytical model in which unilateral mate choice evolves solely by direct sexual selection on choosiness. We show this is sufficient to generate the evolution of all possible levels of choosiness, because of the fundamental trade-off between mating rate and mating benefits. We further identify the relative searching time (RST, i.e. the proportion of lifetime devoted to searching for mates) as a predictor of the effect of any variable affecting the mating rate on the evolution of choosiness. We show that the RST: (i) allows one to make predictions about the evolution of choosiness across a wide variety of mating systems; (ii) encompasses all alternative variables proposed thus far to explain the evolution of choosiness by direct sexual selection; and (iii) can be empirically used to infer qualitative differences in choosiness.