Using a RAD-seq-generated large SNP data set, we estimated the capacity of the leaf beetle Gonioctena quinquepunctata to disperse inside the Vosges mountains (eastern France), where the species is common. For this purpose, we simulated SNP data under a spatially explicit model of population evolution (essentially a grid overlapping a map, in which each cell is considered a different population) and compared the simulated and real data with an approximate Bayesian computation (ABC) approach. For this purpose, we assessed a new SNP statistic, the DSVSF (distribution of spatial variation in SNP frequencies) that summarizes genetic variation in a spatially explicit context, and compared its usefulness to standard statistics often used in population genetic analyses. The results suggested that this insect disperses well within the Vosges mountains, much more than was initially expected given the current and probably past fragmentation of its habitat and given the results of previous studies on genetic variation in other mountain leaf beetles.
LUKICHEVA S., MARDULYN P. 2021. Whole genome sequencing reveals asymetric introgression between two sister species of cold-resistant leaf beetles. Molecular Ecology, 30: 4077-4089. [open access]
We have further explored introgression in the nuclear genome between two sister species of leaf beetles in the Alps (Gonioctena quinquepunctata and G. intermedia), this time by sequencing the whole genome of multiple individuals from both species. Our analyses, based on a machine learning approach, reveals that about 2% of the nuclear genome was transferred from Gonioctena quinquepunctata to G. intermedia, in the same direction than what was found previously for the mitochondrial genome. We suggest that this asymetric introgression can be explained by two non exclusive hypotheses: (1) G. intermedia is currently expanding its range and invading the range of G. quinquepunctata and (2) natural selection favors at least some of the introgressed alleles, which may have facilitated the adaptation of G. intermedia to the Alpine environment.
LUKICHEVA S., FLOT J.-F., MARDULYN P. 2021. Genome assembly of the cold-tolerant leaf beetle Gonioctena quinquepunctata, an important resource for studying its evolution and reproductive barriers between species. Genome Biology and Evolution, 13: evab134. [open access]
We generated a de novo genome assembly and genome annotation for a new Coleoptera species, the cold-resistant leaf beetle Gonioctena quinquepunctata. The assembly produced was characterized by a size of 1.7 Gb and the genome was predicted to encode more than 40,000 proteins. These numbers are unusually high for insects, even for Chrysomelids, that seem to harbor particularly large genomes, and are at least partially explained by the presence of a large fraction of highly repetitive DNA.
KASTALLY C., TRASOLETTI M, MARDULYN P. 2019. Limited gene exchange between two sister species of leaf beetles within a hybrid zone in the Alps. Journal of Evolutionary Biology, 32: 1406-1417. [PDF: see Publication request page]
Following a prior study (Quinzin & Mardulyn 2014) that revealed extensive mitochondrial genome introgression between two sister species of leaf beetles (Gonioctena quinquepunctata and G. intermedia) in the Alps, suggesting recent hybridisation, we sampled individuals inside and outside this hybrid zone and analysed their genomic variation using RAD-seq markers. Contrary to what was found for mitochondrial markers, little, if any, genetic exchange was highlighted in the nuclear genome, suggesting strong intrinsic barriers to reproduction between the two species.
KASTALLY C., MARDULYN P. 2017. Widespread co-occurrence of two distantly-related mitochondrial genomes in individuals of the leaf beetle Gonioctena intermedia. Biology Letters, 13: 20170570. [PDF: see Publication request page]
We detected mitochondrial genome heteroplasmy (two genomes separated by > 1% sequence divergence) in two individuals of the leaf beetle Gonioctena intermedia, using massive parallel sequencing , and further established that this pattern of heteroplasmy is widespread for this species in the Ardennes region.
QUINZIN M. C., NORMAND S., DELLICOUR S., SVENNING J.-C., MARDULYN P. 2017. Glacial survival of trophically linked boreal species in northern Europe. Proceedings of the Royal Society B, 284: 20162799. [PDF: see Publication request page]
A comparison of the current pattern of genetic variation across the range of Gonioctena intermedia to patterns simulated under different coalescence models (representing alternative historical hypotheses) implemented in a spatially explicit context, led us to suggest that this leaf beetle (and therefore its host tree) has survived in northern Europe during the last glaciation.
BRANDERS V., MARDULYN P. 2016. Improving intraspecific allele networks inferred by maximum parsimony. Methods in Ecology and Evolution, 7: 90-95. [software download][PDF]
We introduced a program capable of building anallele (or haplotype) network by first deriving all possible phylograms corresponding to a set of most parsimonious trees, and then combining them into a network graph. We showed that this approach often results in a more complete network (additional most parsimonious paths) than those provided by other methods.
MAYER F., PIEL F. B., CASSEL-LUNDHAGEN A., KIRICHENKO N., GRUMIAU L., ØKLAND B., BERTHEAU C., GREGOIRE J.-C., MARDULYN P. 2015. Comparative multi-locus phylogeography of two Palaearctic spruce bark beetles: influence of contrasting ecological strategies on genetic variation. Molecular Ecology, 24:1292-1310. [PDF]
We highlighted widely divergent patterns of genetic variation for two Palearctic spruce bark beetles and argued that the difference is largely compatible with their contrasting dispersal strategies and modes of reproduction.
QUINZIN M. C., MAYER F., ELVINGER N., MARDULYN P. 2015. Theoretical expectations of the Isolation-Migration model of population evolution for inferring demographic parameters. Methods in Ecology and Evolution, 6: 610-620. [PDF]
We assessed the performance of the Isolation-Migration (IM) model to infer demographic parameters when the model used to simulate DNA sequence data meets the assumptions of the IM model completely. We thus identified conditions under which the method works best, and highlighted its theoretical limitations.
DELLICOUR S., MICHEZ D., RASPLUS J.-Y., MARDULYN P. 2015. Impact of past climatic changes and resource availability on the population demography of three food-specialist bees. Molecular Ecology, 24: 1074-1090. [PDF]
We investigated the impact of (1) past climate modifications, and (2) host plant abundance, on intraspecific genetic variation in three codistributed and related specialized solitary bees of the genus Melitta with similar life history traits and dispersal capacities. Distribution of genetic variation at five loci, and estimation of past and current geographic ranges for the three species, indicated that both factors probably played a role in shaping phylogeographic patterns.
DELLICOUR S., KASTALLY C., HARDY O. J., MARDULYN P. 2014. Comparing phylogeographic hypotheses by simulating DNA sequences under a spatially explicit model of coalescence. Molecular Biology and Evolution, 31:3359-3372. [PDF][software download]
We described a simple method to generate DNA sequences under a model of population evolution set in a spatially explicit context, and used it to evaluate the potential of several summary statistics characterizing genetic variation to differentiate three typical phylogeographic scenarios. We also investigated the benefits of using a spatially explicit model by comparing its performance to alternative models that are less spatially explicit (i.e. offering a lower geographic resolution).
DELLICOUR S., FEARNLEY S., LOMBAL A., HEIDL S., DAHLHOFF E., RANK N. E., MARDULYN P. 2014. Inferring the past and present connectivity across the range of a North American leaf beetle: combining ecological-niche modeling and a geographically explicit model of coalescence. Evolution, 68:2371-2385. [PDF]
We derived ecological niche-modeling estimates of past and current species ranges for the leaf beetle Chrysomela aeneicollis (Western North America), and confronted these estimates with DNA sequence variation data. Simulations of similar genetic data under various spatially explicit models of population evolution (representing alternative historical hypotheses) suggested a long period of range fragmentation for this species, contradicting the hypothesis of a current and past high population connectivity that was supported by ecological niche-modeling results.
QUINZIN M. C., MARDULYN P. 2014. Multi-locus DNA sequence variation in a complex of four leaf beetle species with parapatric distributions: Mitochondrial and nuclear introgressions reveal recent hybridization. Molecular Phylogenetics and Evolution, 78:14-24. [PDF]
By analyzing range-wide DNA sequence variation data (5 loci), we delimited the geographic distribution of the four Gonioctena leaf beetles from subgenus Goniomena and identified multiple instances of mitochondrial and nuclear introgression (transfer of genetic material) between G. intermedia and G. quinquepunctata across their range. Observed genetic variation showed unidirectional introgression, from G. quinquepunctata to G. intermedia, suggesting frequent and recent hybridizations between the two species, and that G. intermedia has recently expanded its range into that of G. quinquepunctata.
DELLICOUR S., MARDULYN P. 2014. SPADS 1.0: a toolbox to perform spatial analyses on DNA sequence datasets. Molecular Ecology Resources, 14:647-651. [PDF][software download]
We introduced a user-friendly program for characterizing genetic diversity and population structure from DNA sequence variation data. The program calculates standard summary statistics on populations and groups of populations, implements multilocus clustering algorithms to highlight population structure, generates input files for several other programs, and generates Matlab and R functions to display genetic differentiation and diversity across a geographic map.
DELLICOUR S., MARDULYN P., HARDY O. J., HARDY C., ROBERTS S.P.M., VEREECKEN N. J. 2014. Inferring the mode of colonisation of the rapid range expansion of a solitary bee from multi-locus DNA sequence variation. Journal of Evolutionary Biology, 27:116-132. [PDF]
Based on field records collected over the past two decades, we reported the recent and rapid geographic range expansion of the solitary bee Colletes hederae across Western Europe. We then analyzed its range-wide DNA sequence variation and compared it to data simulated under a spatially explicit coalescence model to characterize its mode of colonization.
MARDULYN P., GOFFREDO M., CONTE A., HENDRICKX G., MEISWINKEL R., BALENGHIEN T., SGHAIER S., LOHR Y., GILBERT M. 2013. Climate change and the spread of vector-borne diseases: using approximate Bayesian computation to compare invasion scenarios for the bluetongue virus vector Culicoides imicola in Italy. Molecular Ecology, 22:2456-2466. [PDF]
The bluetongue virus vector Culicoides imicola was believed to have recently expanded its range from northern Africa to southern Europe, enabling the emergence of bluetongue in the region. We tested the scenario of a recent colonization of Italy by C. imicola by analyzing microsatellite variation across north Africa and Mediterranean Europe, and comparing it to alternative scenarios, in an approximate Bayesian computation framework. The hypothesis of an ancient presence of C. imicola in Italy was strongly favored by the data, suggesting that other causes than a northward range expansion of C. imicola have triggered the emergence of bluetongue in southern Europe.
VEREECKEN N. J., WILSON C. A., HÖTLING S., SCHULZ S., BANKETOV S. A., MARDULYN P. 2012. Pre-adaptations and the evolution of pollination by sexual deception: Cope’s rule of specialization revisited. Proceedings of the Royal Society B, 279 :4786-4794. [PDF]
Based on phylogenetic reconstructions of ancestral pollination strategies, we provide evidence for independent and bidirectional evolutionary transitions between generalized (shelter mimicry) and specialized (sexual deception) pollination strategies in three groups of flowering plants (Ophrys, Serapias, Oncocyclus), and suggest that pseudocopulation has evolved from pre-adaptations (floral colours, shapes and odour bouquets) that selectively attract male pollinators through shelter mimicry.
MARDULYN P. 2012. Trees and/or networks to display intraspecific DNA sequence variation? Molecular Ecology, 21:3385-3390. [PDF]
While both phylogenetic trees and networks are used to display DNA sequence variation at the intraspecific level, I argued that the process of inferring the most parsimonious genealogical relationships among a set of DNA sequences should be dissociated from the problem of displaying this information in a graph. I showed that current phylogenetic inference and network-building algorithms are both unable to guarantee the finding of all most parsimonious (MP) connections, although it should be possible to improve the phylogenetic approach. This work led to the development of a new program by Branders and Mardulyn (2016; see above).
