Biology subjects

Crochet, P.-A.

Publications and source records attributed to Crochet, P.-A..

10 recordsLinked to original sources

bioRxiv2026

The role of miscarriage and sororal birth order in male same-sex orientation: Theoretical predictions and empirical data

This study explores the proximal and biological mechanisms underlying male same-sex orientation, with a focus on the Fraternal Birth Order Effect (FBOE), a robust phenomenon whereby same-sex oriented men tend to have more older brothers than the population average, and its relationship with the Sororal Birth Order Effect (SBOE), whereby older sisters also appear to influence sexual orientation, albeit less consistently. The Maternal Immune Hypothesis (MIH), which posits that maternal immune responses to male-specific antigens accumulate across successive male pregnancies, provides a compelling proximal explanation for the FBOE, but it fails to fully account for the SBOE and other birth order patterns, such as the elevated prevalence of same-sex orientation among only-children compared to firstborns in larger sibships. Through explicit modelling of the MIH, our simulations reveal that the correlation between the number of older brothers and sisters generates a spurious SBOE, which disappears when controlling for older brothers. However, this control becomes insufficient when miscarriages are included in the simulations. Additionally, the increased prevalence of same-sex orientation among only-children, relative to firstborns with siblings, only emerges when miscarriages are incorporated into the model. Empirical analyses across eight diverse populations (Indonesia, France, French Polynesia, Greece, Canada, Czech Republic, Samoa, Iran) confirm the presence of an overall significant FBOE and, critically, an overall significant SBOE even after controlling for the number of older brothers. The higher frequency of same-sex orientation men among only-children, compared to firstborns in larger sibships, supports a possible role of miscarriage for this SBOE. However, the estimated miscarriage rates (37% - 58%) explaining the observed SBOE slightly exceeds reported rates (30% - 45%) which conservatively include early pregnancy losses. This possibly suggests that additional mechanisms contribute to a spurious SBOE or that a genuine SBOE coexists with the FBOE. Limitations of this study are discussed, as well as whether the MIH framework can be extended to accommodate these findings, or if alternative explanations are needed to resolve these discrepancies.

evolutionary biology↗

bioRxiv2024

Genomic, phenotypic and environmental correlates of speciation in the midwife toads (Alytes)

Speciation, i.e., the formation of new species, implies that diverging populations evolve genetic and phenotypic factors that promote reproductive isolation (RI), but the adaptive vs. neutral origin of these factors and their relative contributions across the speciation continuum remain elusive. Here we test which of genomic, bioacoustic, morphological and environmental differentiation best predicts RI across the midwife toads (genus Alytes), a diversification of Mediterranean amphibians. Hybrid zone analyses in the A. obstetricans complex support that without strong geographic barriers to dispersal, the extent of introgression (which should reflect the strength of RI) covaries with genomic divergence irrespective of other factors. Phenotypic divergence become important later along the continuum, namely between non-admixing species attributed to distinct subgenera. Our results suggest that by putatively causing intrinsic incompatibilities in hybrids, the genetic mutations accumulating randomly between allopatric populations act as the initial trigger of RI, while substantial ecological and behavioral differentiation is a long-term consequence of species divergence that ultimately promotes sympatry. Whereas speciation is usually claimed to be primarily adaptive, our study corroborates recent findings that new species may also be a neutral outcome of gradual phylogeographic divergence, which has practical implications for species delimitation.

evolutionary biology↗

bioRxiv2023

Exploring the impact of read clustering thresholds on RADseq-based systematics: an empirical example from European amphibians.

Restriction site-Associated DNA sequencing (RADseq) has great potential for genome-wide systematics studies of non-model organisms. However, accurately assembling RADseq reads into orthologous loci remains a major challenge in the absence of a reference genome. Traditional assembly pipelines cluster putative orthologous sequences based on a user-defined clustering threshold. Because improper clustering of orthologs is expected to affect results in downstream analyses, it is crucial to design pipelines for empirically optimizing the clustering threshold. While this issue has been largely discussed from a population genomics perspective, it remains understudied in the context of phylogenomics and coalescent species delimitation. To address this issue, we generated RADseq assemblies of representatives of the amphibian genera Discoglossus, Rana, Lissotriton and Triturus using a wide range of clustering thresholds. Particularly, we studied the effects of the intra-sample Clustering Threshold (iCT) and between-sample Clustering Threshold (bCT) separately, as both are expected to differ in multi-species data sets. The obtained assemblies were used for downstream inference of concatenation-based phylogenies, and multi-species coalescent species trees and species delimitation. The results were evaluated in the light of a reference genome-wide phylogeny calculated from newly generated Hybrid-Enrichment markers, as well as extensive background knowledge on the species systematics. Overall, our analyses show that the inferred topologies and their resolution are resilient to changes of the iCT and bCT, regardless of the analytical method employed. Except for some extreme clustering thresholds, all assemblies yielded identical, well-supported inter-species relationships that were mostly congruent with those inferred from the reference Hybrid-Enrichment data set. Similarly, coalescent species delimitation was consistent among similarity threshold values. However, we identified a strong effect of the bCT on the branch lengths of concatenation and species trees, with higher bCTs yielding trees with shorter branches, which might be a pitfall for downstream inferences of evolutionary rates. Our results suggest that the choice of assembly parameters for RADseq data in the context of shallow phylogenomics might be less challenging than previously thought. Finally, we propose a pipeline for empirical optimization of the iCT and bCT, implemented in optiRADCT, a series of scripts readily usable for future RADseq studies.

evolutionary biology↗

bioRxiv2023

Color polymorphism and conspicuousness do not increase speciation rates in Lacertids

Conspicuous body colours and colour polymorphism have been hypothesized to increase rates of speciation. Conspicuous colours are evolutionary labile, and often involved in intraspecific sexual signalling and thus may provide a raw material from which reproductive isolation can easily evolve, while polymorphism could favour rapid evolution of new lineages through morphic speciation. Here, we investigated the influence of the presence/absence of conspicuous colourations, and of colour polymorphism on the speciation of Lacertids. We used several state-dependent diversification models, and showed that, regardless of the methods, conspicuous colourations and colour polymorphism were not related to species speciation. While the lack of correlation between conspicuous colourations and speciation rates is in line with most of the literature testing this hypothesis, the results for colour polymorphism contradict previous studies, and question the generality of the morphic speciation hypothesis.

evolutionary biology↗

bioRxiv2023

Inconsistent estimates of hybridization frequency in newts revealed by SNPs and microsatellites

Hybridization between the European smooth and palmate newts has recurrently been mentioned in the literature. The only two studies that attempted to quantify the frequency of hybridization and gene admixture between these two species came to strikingly opposite conclusions. According to Arntzen et al (1998, 42 allozymes), hybrids are rare in nature and introgression negligible, while according to Johanet et al (2011, 6 microsatellites), introgressive hybridization is significant and widespread across the shared distribution range. To clarify this question, we implemented high-throughput SNP genotyping with diagnostic biallelic SNPs on 965 specimens sampled across Europe. Our results are in line with Arntzen et al, since only two F1 hybrids were identified in two distinct French localities, and no further hybrid generations or backcrosses. Moreover, reanalysis of 78 of the samples previously studied by Johanet et al. (2011) using our SNPs panel could not reproduce their results, suggesting that microsatellite-based inference overestimated the hybridization frequency between these two species. Since we did not detect methodological issues with the analyses of Johanet et al., our results suggest that SNP approaches outperform microsatellite-based assessments of hybridization frequency, and that conclusions previously published on this topic with a small number of microsatellite loci should be taken with caution, and ideally be repeated with an increased genomic coverage.

genetics↗

bioRxiv2022

Phylogeographic breaks and how to find them: Separating vicariance from isolation by distance in a lizard with restricted dispersal

AimDiscontinuity in the distribution of genetic diversity (often based on mtDNA) is usually interpreted as evidence for phylogeographic breaks, underlying vicariant units. However, a misleading signal of phylogeographic break can arise in the absence of barrier to gene flow, under mechanisms of isolation by distance (IBD). How and under which conditions phylogeographic breaks can be reliably differentiated from populations evolving under IBD remain unclear. Here, we use multi-locus sequence data from a widely distributed lizard species to address these questions in an empirical setting. LocationMorocco TaxonSpiny-footed lizard (Acanthodactylus erythrurus), Squamata: Lacertidae MethodsUsing 325 samples from 40 localities, we identified genetic discontinuities within A. erythrurus based on a mitochondrial fragment and nine nuclear markers independently. Using the nuclear markers, we then applied linear regression models to investigate whether genetic divergence could be explained by geographical distances alone, or barriers to gene flow (real phylogeographic breaks). ResultA. erythrurus is characterized by an important mitochondrial diversity, with 11 strongly supported phylogeographic lineages with a crown age of 6 Mya. Nuclear markers, however, yielded weak phylogenetic support for these lineages. Using clustering methods based on genotypes at nine nuclear loci, we identified phylogeographic clusters that were partly discordant with the mtDNA lineages. Tests of IBD delimited at least four groups of populations separated by barriers to gene flow, but unambiguous separation of vicariance from IBD remained challenging in several cases. Main conclusionsThe genetic diversity of A. erythrurus originates from a mix of IBD and vicariance, which were difficult to distinguish, and resulted in similar levels of mitochondrial differentiation. These results highlight that phylogeographic breaks inferred from mitochondrial data should be further investigated using multi-locus data and explicit testing to rule out alternative processes generating discontinuities in mitochondrial diversity, including IBD. We identified four groups of populations within A. erythrurus, separated by barriers to gene flow, but even using nine independent nuclear makers the power of our approach was limited, and further investigation using genome-wide data will be required to resolve the phylogeographic history of this species.

evolutionary biology↗

bioRxiv2022

Combining RADseq and contact zone analysis to decipher cryptic diversification in reptiles: insights from Acanthodactylus erythrurus (Reptilia: Lacertidae)

Linnaean and Wallacean shortfalls (Uncertainties on species taxonomy and distribution, respectively) are major factors hampering efficient conservation planning in the current context of biodiversity erosion. These shortfalls concern even widespread and abundant species in relatively well-studied regions such as the Mediterranean biodiversity hotspot which still hosts a large fraction of unrecognised biodiversity, notably in small vertebrates. Species delimitations have long been based on phylogenetic analyses of a small number of standard markers, but accurate lineage identification in this context can be obscured by incomplete lineage sorting, introgression or isolation by distance. Recently, integrative approaches coupling various sets of characters or analyses of contact zones aiming at estimating reproductive isolation (RI) have been advocated instead. Analyses of introgression patterns in contact zone with genomic data represent a powerful way to confirm the existence of independent lineages and estimate the strength of their RI at the same time. The Spiny-footed Lizard Acanthodactylus erythrurus (Schinz, 1833) is widespread in the Iberian Peninsula and the Maghreb and exhibits a large amount of genetic diversity, although the precise number and distribution of its genetic lineages remain poorly understood. We applied a RADseq approach to obtain a genome wide SNPs dataset on a contact zone in central Morocco between the previously described Rif and Middle-Atlas lineages. We show that these two lineages exhibit strong RI across this contact zone, as shown by the limited amount and restricted spatial extant of gene flow. We interpret these results as evidence for species-level divergence of these two lineages. Our study confirms the usefulness of RADseq approaches applied on contact zones for cryptic diversity studies and therefore to resolve Linnaean and Wallacean shortfalls.

genomics↗

bioRxiv2022

Increased birth rank of homosexual males: disentangling the older brother effect and sexual antagonism hypothesis

Male homosexual orientation remains a Darwinian paradox, as there is no consensus on its evolutionary (ultimate) determinants. One intriguing feature of homosexual men is their higher male birth rank compared to heterosexual men. This can be explained by two non-exclusive mechanisms: an antagonistic effect (AE), implying that more fertile women have a higher chance of having a homosexual son and to produce children with a higher mean birth rank, or a fraternal birth effect (FBOE), where each additional older brother increases the chances for a male embryo to develop a homosexual orientation due to an immunoreactivity process. However, there is no consensus on whether both FBOE and AE are present in human populations, or if only one of these mechanisms is at play with its effect mimicking the signature of the other mechanism. An additional sororal birth order effect (SBOE) has also recently been proposed. To clarify this situation, we developed theoretical and statistical tools to study FBOE and AE independently or in combination, taking into account all known sampling biases. These tools were applied on new individual data, and on various available published data (two individual datasets, and all relevant aggregated data). Support for FBOE was apparent in aggregated data, with the FBOE increasing linearly with fertility. The FBOE was also supported in two individual datasets. An SBOE is generated when sampling in presence of FBOE, suggesting that controlling for FBOE is required to avoid artefactual SBOE. AE was not supported in individual datasets, including the analysis of the extended maternal family. The evolutionary implications of these findings are discussed.

evolutionary biology↗

bioRxiv2022

Bimodal breeding phenology in the parsley frog Pelodytes punctatus as a bet-hedging strategy in an unpredictable environment despite strong priority effects

AO_SCPLOWBSTRACTC_SCPLOWWhen environmental conditions are unpredictable, expressing alternative phenotypes spreads the risk of failure, a mixed strategy called bet-hedging. In the southern part of its range, the Parsley Frog Pelodytes punctatus breeds both in autumn and in spring. Our aim was to study the breeding phenology and reproductive success associated with the use of those two seasonal niches to understand how this breeding strategy can be maintained. Field surveys revealed that breeding phenology was typically bimodal with a higher breeding effort in autumn. More importantly, in spring, the survival rate of offspring was severely reduced by the presence of autumn tadpoles, indicating a clear priority effect. However, the autumn cohort often failed to survive over winter, in which case spring cohorts were often successful. Based on those results, we constructed a model in which females can allocate a variable portion of eggs to each season and added a priority effect. We conclude that the existence of the two breeding seasons may indeed constitute a bet-hedging strategy.

evolutionary biology↗

bioRxiv2019

Looking for mimicry in a snake assemblage using deep learning

Batesian mimicry, with its highly colorful species and astonishing mimic-model resemblance, is a canonical example of evolution by natural selection. However, Batesian mimicry could also occur in inconspicuous species and rely on subtle resemblance. Although potentially widespread, such instances have been rarely investigated, such that the real frequency of Batesian mimicry has remained largely unknown. To fill this gap, we developed a new approach using deep learning to quantify the resemblance between putative mimics and models from photographs. We applied this method to quantify the frequency of Batesian mimicry in Western Palearctic snakes. Potential mimics were revealed by an excess of resemblance with sympatric venomous snakes compared to random expectations. We found that 8% of the non-venomous species were potential mimics, among which all were imperfect mimics. This study is the first to quantify the frequency of Batesian mimicry in a whole community of vertebrates, and shows that even concealed species can be reliably identified as potential models. Our approach should prove useful to detect mimicry in other communities, and more generally it highlights the benefits of deep learning for quantitative studies of phenotypic resemblance.

evolutionary biology↗