Cécile Berthouly-Salazar

Long-distance dispersal maximizes evolutionary potential during rapid geographic range expansion

Conventional wisdom predicts that sequential founder events will cause genetic diversity to erode in species with expanding geographic ranges, limiting evolutionary potential at the range margin. Here, we show that invasive European starlings (Sturnus vulgaris) in South Africa preserve genetic diversity during range expansion, possibly as a result of frequent long‐distance dispersal events. We further show that unfavourable environmental conditions trigger enhanced dispersal, as indicated by signatures of selection detected across the expanding range. This brings genetic variation to the expansion front, counterbalancing the cumulative effects of sequential founding events and optimizing standing genetic diversity and thus evolutionary potential at range margins during spread. Therefore, dispersal strategies should be highlighted as key determinants of the ecological and evolutionary performances of species in novel environments and in response to global environmental change.

Vietnamese chickens: a gate towards Asian genetic diversity

BackgroundChickens represent an important animal genetic resource and the conservation of local breeds is an issue for the preservation of this resource. The genetic diversity of a breed is mainly evaluated through its nuclear diversity. However, nuclear genetic diversity does not provide the same information as mitochondrial genetic diversity. For the species Gallus gallus, at least 8 maternal lineages have been identified. While breeds distributed westward from the Indian subcontinent usually share haplotypes from 1 to 2 haplogroups, Southeast Asian breeds exhibit all the haplogroups. The Vietnamese Ha Giang (HG) chicken has been shown to exhibit a very high nuclear diversity but also important rates of admixture with wild relatives. Its geographical position, within one of the chicken domestication centres ranging from Thailand to the Chinese Yunnan province, increases the probability of observing a very high genetic diversity for maternal lineages, and in a way, improving our understanding of the chicken domestication process.ResultsA total of 106 sequences from Vietnamese HG chickens were first compared to the sequences of published Chinese breeds. The 25 haplotypes observed in the Vietnamese HG population belonged to six previously published haplogroups which are: A, B, C, D, F and G. On average, breeds from the Chinese Yunnan province carried haplotypes from 4.3 haplogroups. For the HG population, haplogroup diversity is found at both the province and the village level (0.69).The AMOVA results show that genetic diversity occurred within the breeds rather than between breeds or provinces. Regarding the global structure of the mtDNA diversity per population, a characteristic of the HG population was the occurrence of similar pattern distribution as compared to G. gallus spadiceus. However, there was no geographical evidence of gene flow between wild and domestic populations as observed when microsatellites were used.ConclusionsIn contrast to other chicken populations, the HG chicken population showed very high genetic diversity at both the nuclear and mitochondrial levels. Due to its past and recent history, this population accumulates a specific and rich gene pool highlighting its interest and the need for conservation.

Spatial sorting drives morphological variation in the invasive bird, Acridotheris tristis.

The speed of range expansion in many invasive species is often accelerating because individuals with stronger dispersal abilities are more likely to be found at the range front. This ‘spatial sorting’ of strong dispersers will drive the acceleration of range expansion. In this study, we test whether the process of spatial sorting is at work in an invasive bird population (Common myna, Acridotheris tristis) in South Africa. Specifically, we sampled individuals across its invasive range and compared morphometric measurements relevant and non-relevant to the dispersal ability. Besides testing for signals of spatial sorting, we further examined the effect of environmental factors on morphological variations. Our results showed that dispersal-relevant traits are significantly correlated with distance from the range core, with strong sexual dimorphism, indicative of sex-biased dispersal. Morphological variations were significant in wing and head traits of females, suggesting females as the primary dispersing sex. In contrast, traits not related to dispersal such as those associated with foraging showed no signs of spatial sorting but were significantly affected by environmental variables such as the vegetation and the intensity of urbanisation. When taken together, our results support the role of spatial sorting in facilitating the expansion of Common myna in South Africa despite its low propensity to disperse in the native range.

A meta-analysis of observational epidemiological studies of Newcastle disease in African agro-systems, 1980-2009

Newcastle disease (ND) is one of the most important and widespread avian pests. In Africa, backyard poultry production systems are an important source of protein and cash for poor rural livelihoods. ND mortality in these production systems is important and seriously disrupts benefits derived from it. This study undertook an African continental approach of ND epidemiology in backyard poultry. After a systematic literature review of studies published from 1980 to 2009, a meta-analysis of spatio-temporal patterns of serological prevalence and outbreak occurrence was performed. Average ND serological prevalence was estimated at 0·67 [95% confidence interval (CI) 0·58-0·75] in regions characterized by humid ecosystems, high human and poultry densities and low altitudes; 0·36 (95% CI 0·30-0·41) in dry ecosystems at intermediate altitude where human and poultry densities are low and 0·27 (95% CI 0·19-0·38) in mountain ecosystems where human and poultry densities are intermediate. In terms of seasonality, ND outbreaks occur mostly during the dry seasons in Africa, when environmental conditions are likely to be harshest for backyard poultry. In addition, a phylogeographical analysis revealed the regionalization of ND virus strains, their potential to evolve towards a higher pathogenicity from the local viral pool and suggests a risk for vaccine strains to provide new wild strains. These results present for the first time a continent-wide approach to ND epidemiology in Africa. More emphasis is needed for ND management and control in rural African poultry production systems.

Genome scan reveals selection acting on genes linked to stress response in wild pearl millet

Uncovering genomic regions involved in adaption is a major goal in evolutionary biology. High‐throughput sequencing now makes it possible to tackle this challenge in nonmodel species. Yet, despite the increasing number of methods targeted to specifically detect genomic footprints of selection, the complex demography of natural populations often causes high rates of false positive in gene discoveries. The aim of this study was to identify climate adaptations in wild pearl millet populations, Cenchrus americanus ssp. monodii. We focused on two climate gradients, one in Mali and one in Niger. We used a two‐step strategy to limit false‐positive outliers. First, we considered gradients as biological replicates and performed RNA sequencing of four populations at the extremities. We combined four methods—three based on differentiation among populations and one based on diversity patterns within populations—to identify outlier SNPs from a set of 87 218 high‐quality SNPs. Among 11 155 contigs of pearl millet reference transcriptome, 540 exhibited selection signals as evidenced by at least one of the four methods. In a second step, we genotyped 762 samples in 11 additional populations distributed along the gradients using SNPs from the detected contigs and random SNPs as control. We further assessed selection on this large data set using a differentiation‐based method and a method based on correlations with environmental variables based. Four contigs displayed consistent signatures between the four extreme and 11 additional populations, two of which were linked to abiotic and biotic stress responses.

Genotyping-by-Sequencing SNP Identification for Crops without a Reference Genome: Using Transcriptome Based Mapping as an Alternative Strategy

Next-generation sequencing opens the way for genomic studies of diversity even for non-model crops and animals. Genome reduction techniques are becoming progressively more popular as they allow a fraction of the genome to be sequenced for multiple individuals and/or populations. These techniques are an efficient way to explore genome diversity in non-model crops and animals for which no reference genome is available. Genome reduction techniques emerged with the development of specific pipelines such as UNEAK (Universal Network Enabled Analysis Kit) and Stacks. However, even for non-model crops and animals, transcriptomes are easier to obtain, thereby making it possible to directly map reads. We investigate the direct use of transcriptome as an alternative strategy. Our specific objective was to compare SNPs obtained from the UNEAK pipeline as well as SNPs obtained by directly mapping genotyping-by-sequencing reads on a transcriptome. We assessed the feasibility of both SNP datasets, UNEAK and transcriptome mapping, to investigate the diversity of 91 samples of wild pearl millet sampled across its distribution area. Both approaches produced several tens of thousands of single nucleotide variants, but differed in the way the variants were identified, leading to differences in the frequency spectrum associated with marked differences in the assessment of diversity. Difference in the frequency spectrum significantly biased a large set of diversity analyses as well as detection of selection approaches. However, whatever the approach, we found very similar inference of genetic structure, with three major genetic groups from West, Central, and East Africa. For non-model crops, using transcriptome data as a reference is thus a particularly promising way to obtain a more thorough analysis of datasets generated using genome reduction techniques.

Uncontrolled admixture and loss of genetic diversity in a local Vietnamese pig breed

The expansion of intensive livestock production systems in developing countries has increased the introduction of highly productive exotic breeds facilitating indiscriminate crossbreeding with local breeds. In this study, we set out to investigate the genetic status of the Vietnamese Black H’mong pig breed by evaluating (1) genetic diversity and (2) introgression from exotic breeds. Two exotic breeds, namely Landrace and Yorkshire used for crossbreeding, and the H’mong pig population from Ha Giang (HG) province were investigated using microsatellite markers. Within the province, three phenotypes were observed: a White, a Spotted and a Black phenotype. Genetic differentiation between phenotypes was low (0.5–6.1%). The White phenotypes showed intermediate admixture values between exotic breeds and the Black HG population (0.53), indicating a crossbreed status. Management practices were used to predict the rate of private diversity loss due to exotic gene introgressions. After 60 generations, 100% of Black private alleles will be lost. This loss is accelerated if the admixture rate is increased but can be slowed down if the mortality rate (e.g., recruitment rate) is decreased. Our study showed that a large number of markers are needed for accurately identifying hybrid classes for closely related populations. While our estimate of admixture still seems underestimated, genetic erosion can occur very fast even through indiscriminate crossbreeding.

No excess of cis-regulatory variation associated with intraspecific selection in wild pearl millet (Cenchrus americanus)

Several studies suggest that cis-regulatory mutations are the favorite target of evolutionary changes, one reason being that cis-regulatory mutations might have fewer deleterious pleiotropic effects than protein-coding mutations. A review of the process also suggests that this bias towards adaptive cis-regulatory variation might be less pronounced at the intraspecific level compared with the interspecific level. In this study, we assessed the contribution of cis-regulatory variation to adaptation at the intraspecific level using populations of wild pearl millet (Cenchrus americanus ssp. monodii) sampled along an environmental gradient in Niger. From RNA sequencing of hybrids to assess allele-specific expression, we identified genes with cis-regulatory divergence between two parental accessions collected in contrasted environmental conditions. This revealed that ∼15% of transcribed genes showed cis-regulatory variation. Intersecting the gene set exhibiting cis-regulatory variation with the gene set identified as targets of selection revealed no excess of cis-acting mutations among the selected genes. We additionally found no excess of cis-regulatory variation among genes associated with adaptive traits. As our approach relied on methods identifying mainly genes submitted to strong selection pressure or with high phenotypic effect, the contribution of cis-regulatory changes to soft selection or polygenic adaptive traits remains to be tested. However our results favor the hypothesis that enrichment of adaptive cis-regulatory divergence builds up over time. For short evolutionary time-scales, cis-acting mutations are not predominantly involved in adaptive evolution associated with strong selective signal.

The molecular ecology of biological invasions: what do we know about non-additive genotypic effects and invasion success?

Recent research suggests that non-additive genotypic effects may play an important role in the establishment success of invasive species. However, most empirical data for these inferences come from greenhouse experiments. Only recently has researchers tested non-additive genotypic effects and establishment success of invasive alien species under field conditions. Here we give a brief overview of this research and also carefully consider data from the first publication, to our knowledge, to report on non-additive genotypic effects on invasion success under field conditions. We identify some shortcomings in this important study and make suggestions for future research aimed at better understanding the contributions of non-additive genotypic effects to establishment success and invasion.

Development and characterization of 13 new, and cross amplification of 3, polymorphic nuclear microsatellite loci in the common myna (Acridotheres tristis)

We used a next generation sequencing (NGS) approach to screen for genome-wide nuclear microsatellite loci in the common (Indian) myna, Acridotheres tristis. In addition, markers previously developed for other Sturnidae species were tested for cross-amplification in A. tristis. In total, we identified 20 loci from NGS data and tested 26 loci for cross-amplification. Out of all loci (NGS developed and cross-amplified), 16 unlinked loci showed polymorphism, ranging from 2 to 9 alleles per locus. Test individuals were obtained from the invasive ranges of common myna in South Africa. Overall, expected and observed heterozygosities ranged from 0.089 to 0.802 and from 0.094 to 0.906, respectively. These markers will be used to shed light on invasion genetics and landscape-scale dynamics of invasive A. tristis in South Africa.