Philippe Helsen

Low levels of genetic differentiation between Opuntia echios varieties on Santa Cruz (Galapagos)

Three processes play an important role in plant speciation: isolation, hybridization and polyploidization. Galapagos endemic Opuntia display putatively all of these processes. On this archipelago most islands are inhabited by a single Opuntia taxon. Santa Cruz, however, houses two morphologically distinct O. echios varieties (echios and gigantea). Morphological intermediates are found where these two geographically isolated varieties meet. Here we used ten microsatellite loci to reveal the population genetic structure of this system. In contrast to earlier studies, we found high genetic variability within localities. Genetic structuring was weak and no evidence for the existence of hybrids was found. The reasons for this weak genetic structure may include: the species’ hexaploid nature, high levels of gene flow, recent colonization, and the lack of geographic barriers. This first detailed genetic study on these threatened species will be important for further conservation planning.

Oxytocin and Vasopressin Receptor Gene Variation as a Proximate Base for Inter- and Intraspecific Behavioral Differences in Bonobos and Chimpanzees

Recent literature has revealed the importance of variation in neuropeptide receptor gene sequences in the regulation of behavioral phenotypic variation. Here we focus on polymorphisms in the oxytocin receptor gene (OXTR) and vasopressin receptor gene 1a (Avpr1a) in chimpanzees and bonobos. In humans, a single nucleotide polymorphism (SNP) in the third intron of OXTR (rs53576 SNP (A/G)) is linked with social behavior, with the risk allele (A) carriers showing reduced levels of empathy and prosociality. Bonobos and chimpanzees differ in these same traits, therefore we hypothesized that these differences might be reflected in variation at the rs53576 position. We sequenced a 320 bp region surrounding rs53576 but found no indications of this SNP in the genus Pan. However, we identified previously unreported SNP variation in the chimpanzee OXTR sequence that differs from both humans and bonobos. Humans and bonobos have previously been shown to have a more similar 5′ promoter region of Avpr1a when compared to chimpanzees, who are polymorphic for the deletion of ∼360 bp in this region (+/− DupB) which includes a microsatellite (RS3). RS3 has been linked with variation in levels of social bonding, potentially explaining part of the interspecies behavioral differences found in bonobos, chimpanzees and humans. To date, results for bonobos have been based on small sample sizes. Our results confirmed that there is no DupB deletion in bonobos with a sample size comprising approximately 90% of the captive founder population, whereas in chimpanzees the deletion of DupB had the highest frequency. Because of the higher frequency of DupB alleles in our bonobo population, we suggest that the presence of this microsatellite may partly reflect documented differences in levels of sociability found in bonobos and chimpanzees.

Prospects and challenges for the conservation of farm animal genomic resources, 2015-2025

Livestock conservation practice is changing rapidly in light of policy developments, climate change and diversifying market demands. The last decade has seen a step change in technology and analytical approaches available to define, manage and conserve Farm Animal Genomic Resources (FAnGR). However, these rapid changes pose challenges for FAnGR conservation in terms of technological continuity, analytical capacity and integrative methodologies needed to fully exploit new, multidimensional data. The final conference of the ESF Genomic Resources program aimed to address these interdisciplinary problems in an attempt to contribute to the agenda for research and policy development directions during the coming decade. By 2020, according to the Convention on Biodiversitys Aichi Target 13, signatories should ensure that “…the genetic diversity of …farmed and domesticated animals and of wild relatives …is maintained, and strategies have been developed and implemented for minimizing genetic erosion and safeguarding their genetic diversity.” However, the real extent of genetic erosion is very difficult to measure using current data. Therefore, this challenging target demands better coverage, understanding and utilization of genomic and environmental data, the development of optimized ways to integrate these data with social and other sciences and policy analysis to enable more flexible, evidence-based models to underpin FAnGR conservation. At the conference, we attempted to identify the most important problems for effective livestock genomic resource conservation during the next decade. Twenty priority questions were identified that could be broadly categorized into challenges related to methodology, analytical approaches, data management and conservation. It should be acknowledged here that while the focus of our meeting was predominantly around genetics, genomics and animal science, many of the practical challenges facing conservation of genomic resources are societal in origin and are predicated on the value (e.g., socio-economic and cultural) of these resources to farmers, rural communities and society as a whole. The overall conclusion is that despite the fact that the livestock sector has been relatively well-organized in the application of genetic methodologies to date, there is still a large gap between the current state-of-the-art in the use of tools to characterize genomic resources and its application to many non-commercial and local breeds, hampering the consistent utilization of genetic and genomic data as indicators of genetic erosion and diversity. The livestock genomic sector therefore needs to make a concerted effort in the coming decade to enable to the democratization of the powerful tools that are now at its disposal, and to ensure that they are applied in the context of breed conservation as well as development.

Bonobo personality traits are heritable and associated with vasopressin receptor gene 1a variation

Despite being closely related, bonobos and chimpanzees show remarkable behavioral differences, the proximate origins of which remain unknown. This study examined the link between behavioral variation and variation in the vasopressin 1a receptor gene (Avpr1a) in bonobos. Chimpanzees are polymorphic for a ~360 bp deletion (DupB), which includes a microsatellite (RS3) in the 5′ promoter region of Avpr1a. In chimpanzees, the DupB deletion has been linked to lower sociability, lower social sensitivity, and higher anxiety. Chimpanzees and bonobos differ on these traits, leading some to believe that the absence of the DupB deletion in bonobos may be partly responsible for these differences, and to the prediction that similar associations between Avpr1a genotypes and personality traits should be present in bonobos. We identified bonobo personality dimensions using behavioral measures (SociabilityB, BoldnessB, OpennessB, ActivityB) and trait ratings (AssertivenessR, ConscientiousnessR, OpennessR, AgreeablenessR, AttentivenessR, ExtraversionR). In the present study we found that all 10 dimensions have nonzero heritabilities, indicating there is a genetic basis to personality, and that bonobos homozygous for shorter RS3 alleles were lower in AttentivenessR and higher in OpennessB. These results suggest that variations in Avpr1a genotypes explain both within and between species differences in personality traits of bonobos and chimpanzees.

Dealing with food and eggs in mouthbrooding cichlids: structural and functional trade-offs in fitness related traits

Background As in any vertebrate, heads of fishes are densely packed with functions. These functions often impose conflicting mechanical demands resulting in trade-offs in the species-specific phenotype. When phenotypical traits are linked to gender-specific parental behavior, we expect sexual differences in these trade-offs. This study aims to use mouthbrooding cichlids as an example to test hypotheses on evolutionary trade-offs between intricately linked traits that affect different aspects of fitness. We focused on the oral apparatus, which is not only equipped with features used to feed and breathe, but is also used for the incubation of eggs. We used this approach to study mouthbrooding as part of an integrated functional system with diverging performance requirements and to explore gender-specific selective environments within a species. Methodology/Principal Findings Because cichlids are morphologically very diverse, we hypothesize that the implications of the added constraint of mouthbrooding will primarily depend on the dominant mode of feeding of the studied species. To test this, we compared the trade-off for two maternal mouthbrooding cichlid species: a “suction feeder” (Haplochromis piceatus) and a “biter” (H. fischeri). The comparison of morphology and performance of both species revealed clear interspecific and intersex differences. Our observation that females have larger heads was interpreted as a possible consequence of the fact that in both the studied species mouthbrooding is done by females only. As hypothesized, the observed sexual dimorphism in head shape is inferred as being suboptimal for some aspects of the feeding performance in each of the studied species. Our comparison also demonstrated that the suction feeding species had smaller egg clutches and more elongated eggs. Conclusions/Significance Our findings support the hypothesis that there is a trade-off between mouthbrooding and feeding performance in the two studied haplochromine cichlids, stressing the importance of including species-specific information at the gender level when addressing interspecific functional/morphological differences.

The normal distribution as appropriate model of developmental instability in Opuntia cacti flowers

Developmental instability (DI) as measured by fluctuating asymmetry (FA) has been proposed to reflect fitness and stress. Furthermore, the associated developmental buffering may reduce morphological variation, conceal the expression of genetic variation and as such play an important role in evolutionary biology. However, observed associations between FA and various forms of stress and quality appear very heterogeneous. Presently it is difficult to interpret the biological relevance of this heterogeneity because little is known about the link between FA and the underlying process of DI, casting doubt whether DI can be viewed as an individual property and how closely FA reflects the underlying process of DI. Therefore, studies that explicitly test the validity of assumptions of the proposed theoretical models and estimate between‐individual variations in DI are needed. We present data on Opuntia cacti floral traits confirming that the normal distribution can be viewed as an appropriate approximation of the distribution of DI and that the concept of hypothetical repeatability can provide useful insights into the interpretation of patterns in FA as a measure of DI. Furthermore, we detected significant between‐individual variation in DI. Measuring petals from several flowers within individual plants allowed making inference of individual DI.

Limited MHC class I intron 2 repertoire variation in bonobos

Common chimpanzees (Pan troglodytes) experienced a selective sweep, probably caused by a SIV-like virus, which targeted their MHC class I repertoire. Based on MHC class I intron 2 data analyses, this selective sweep took place about 2–3 million years ago. As a consequence, common chimpanzees have a skewed MHC class I repertoire that is enriched for allotypes that are able to recognise conserved regions of the SIV proteome. The bonobo (Pan paniscus) shared an ancestor with common chimpanzees approximately 1.5 to 2 million years ago. To investigate whether the signature of this selective sweep is also detectable in bonobos, the MHC class I gene repertoire of two bonobo panels comprising in total 29 animals was investigated by Sanger sequencing. We identified 14 Papa-A, 20 Papa-B and 11 Papa-C alleles, of which eight, five and eight alleles, respectively, have not been reported previously. Within this pool of MHC class I variation, we recovered only 2 Papa-A, 3 Papa-B and 6 Papa-C intron 2 sequences. As compared to humans, bonobos appear to have an even more diminished MHC class I intron 2 lineage repertoire than common chimpanzees. This supports the notion that the selective sweep may have predated the speciation of common chimpanzees and bonobos. The further reduction of the MHC class I intron 2 lineage repertoire observed in bonobos as compared to the common chimpanzee may be explained by a founding effect or other subsequent selective processes.

Associations between Floral Asymmetry and Individual Genetic Variability Differ among Three Prickly Pear (Opuntia echios) Populations

While stress is expected to increase developmental instability (DI), not all studies confirm this. This heterogeneity could in part be due to the use of subtle differences between the left and right side of bilateral symmetrical organisms to quantify DI, leading to large sampling error obscuring associations with DI. Traits that develop simultaneously more than twice (such as flower petals or bird feathers) reflect individual DI more reliably, such that stronger associations are expected to emerge. Furthermore, some studies have shown differences in strengths of associations among populations. We studied the association between individual genetic diversity and DI in flower petals within three Opuntia echios populations inhabiting Galapagos. Quantifying individual DI through variation in length and width of a high number of petals within individual cacti, lead to a strong association between DI and genetic diversity in one population. We conclude that associations between individual DI and genetic diversity can be more easily revealed by measuring traits that develop repeatedly.

The Influence of Historical Geneflow, Bathymetry and Distribution Patterns on the Population Genetics of Morphologically Diverse Galápagos’ Opuntia echios

Throughout history, remote archipelagos have repeatedly been designated natural laboratories to study evolutionary processes. The extensive, geographically structured, morphological variation within Galápagos’ Opuntia cacti has been presumed to be another example of how such processes shape diversity. However, recent genetic studies on speciation and potential effects of plasticity within this system failed to confirm earlier classification and hypothesized radiation on both global and single island levels. Detailed population genetic information, however, is crucial in conserving these semi-arid ecosystem keystone species. In this article, we re-evaluate the genetics of Opuntia echios inhabiting one of the most taxon rich places on the archipelago: Santa Cruz and its surrounding satellite islands, using microsatellite data. Our analysis revealed high genetic variability within all sampled locations, providing little support for the hypothesis of clonal reproduction. Inter-island gene flow patterns appear to be largely influenced by bathymetry and sea levels during last ice ages. Although O. echios from Seymour Norte are morphologically recognized as being a separate taxon, Daphné Major’s cacti are the most differentiated. In addition, we found a potential barrier for gene flow along the ring-like distribution of Opuntias at the western side of Santa Cruz, suggesting potential links with geology.

Mixed breeding system in the hermaphroditic land slug Arion intermedius (Stylommatophora, Arionidae)

Theory suggests that hermaphroditic plants and animals should be either entirely outcrossing or entirely selfing. As such, very few hermaphroditic plants and basommatophoran snails have a mixed breeding system. However, reliable estimates of selfing rates are lacking for most hermaphroditic animals. This partly prevents to delineate the relative contributions of the selective factors that determine selfing and outcrossing rates in hermaphroditic animal taxa. Here, we studied the population genetic structure of, and breeding system in, 11 populations of the hermaphroditic land slug Arion intermedius using five polymorphic microsatellite loci. Moreover, genotype frequencies deviated significantly from Hardy-Weinberg equilibrium expectations for most of the loci in all populations suggesting some level of selfing. Estimates of the selfing level s, suggest moderate levels of outcrossing (mean s based on FIS = 0.84; mean s based on the two-locus heterozygosity disequilibrium = 0.20, or with a ML approach = 0.22). Our study therefore suggests that A. intermedius has a mixed breeding system. A re-analysis of allozyme data from another arionid slug ( subgenus Carinarion) indicates that mixed breeding may be more common in arionid slugs than hitherto was assumed. These results seem therefore at variance with current theoretical and empirical predictions and opens perspectives for the study on the evolutionary factors driving mixed breeding systems in animals.