Timing major conflict between mitochondrial and nuclear genes in species relationships of Polygonia butterflies (Nymphalidae: Nymphalini)

<p>Abstract</p> <p>Background</p> <p>Major conflict between mitochondrial and nuclear genes in estimating species relationships is an increasingly common finding in animals. Usually this is attributed to incomplete lineage sorting, but recently the possibility has been raised that hybridization is important in generating such phylogenetic patterns. Just how widespread ancient and/or recent hybridization is in animals and how it affects estimates of species relationships is still not well-known.</p> <p>Results</p> <p>We investigate the species relationships and their evolutionary history over time in the genus <it>Polygonia </it>using DNA sequences from two mitochondrial gene regions (COI and ND1, total 1931 bp) and four nuclear gene regions (EF-1α, wingless, GAPDH and RpS5, total 2948 bp). We found clear, strongly supported conflict between mitochondrial and nuclear DNA sequences in estimating species relationships in the genus <it>Polygonia</it>. Nodes at which there was no conflict tended to have diverged at the same time when analyzed separately, while nodes at which conflict was present diverged at different times. We find that two species create most of the conflict, and attribute the conflict found in <it>Polygonia satyrus </it>to ancient hybridization and conflict found in <it>Polygonia oreas </it>to recent or ongoing hybridization. In both examples, the nuclear gene regions tended to give the phylogenetic relationships of the species supported by morphology and biology.</p> <p>Conclusion</p> <p>Studies inferring species-level relationships using molecular data should never be based on a single locus. Here we show that the phylogenetic hypothesis generated using mitochondrial DNA gives a very different interpretation of the evolutionary history of <it>Polygonia </it>species compared to that generated from nuclear DNA. We show that possible cases of hybridization in <it>Polygonia </it>are not limited to sister species, but may be inferred further back in time. Furthermore, we provide more evidence that Haldane's effect might not be as strong a process in preventing hybridization in butterflies as has been previously thought.</p

Phylogenetic perspective on host plant use, colonization and speciation in butterflies

In this thesis we have studied speciation in three butterfly genera Polygonia (Nymphalidae, Nymphalini), Pararge (Nymphalidae, Satyrinae) and Celastrina (Lycaenidae: Polyommatinae). In the first paper a dated phylogeny, based on molecular data, of Polygonia was constructed. We found strong conflict between the nDNA and mtDNA datasets. Possibly this can be explained by ancestral and recent hybridizations between contemporary taxa. The results point to the importance in using different markers when we try to resolve evolution of taxa. In the second paper a sister group comparison was made in order to discover whether host plant range has had an effect on species diversity in Polygonia. Our result indicated higher diversification rates in clades which included species with larvae feeding on different, or additional, plants compared to the ”urticalean rosids” specialists. In the third paper our focus was on the colonization abilities in polyphagous butterflies. The haplotype structures of the mtDNA cytochromeoxidase I (COI) within the Nearctic species of Celastrina as well as within P. c-album and P. faunus were analysed in a network. We found little variation in Celastrina and P. c-album. This results imply that the genera have expanded recently and rapidly. There are indications of differentiation in COI in Celastrina and, possibly, host plant use is involved. However, in P. faunus we found structure among the haplotypes. We believe that several different haplotypes of this species have been preserved during glaciations in the Nearctic. In the fourth paper the evolution of the grassfeeding Pararge was analysed. The phylogeny was based on the mtDNA COI and the nDNA wingless (wgl) and times of divergences were calculated. We found a deep divergence between the European and Moroccan populations of P. aegeria which indicates the importance of the Mediterranean as a barrier for gene flow

Bayesian species delimitation reveals generalist and specialist parasitic wasps on Galerucella beetles (Chrysomelidae) : sorting by herbivore or plant host

Background: To understand the ecological and evolutionary consequences of species interactions in food webs necessitates that interactions are properly identified. Genetic analyses suggest that many supposedly generalist parasitoid species should rather be defined as multiple species with a more narrow diet, reducing the probability that such species may mediate indirect interactions such as apparent competition among hosts. Recent studies showed that the parasitoid Asecodes lucens mediate apparent competition between two hosts, Galerucella tenella and G. calmariensis, affecting both interaction strengths and evolutionary feedbacks. The same parasitoid was also recorded from other species in the genus Galerucella, suggesting that similar indirect effects may also occur for other species pairs. Methods: To explore the possibility of such interactions, we sequenced mitochondrial and nuclear genetic markers to resolve the phylogeny of both host and parasitoid and to test the number of parasitoid species involved. We thus collected 139 Galerucella larvae from 8 host plant species and sequenced 31 adult beetle and 108 parasitoid individuals. Results: The analysis of the Galerucella data, that also included sequences from previous studies, verified the five species previously documented as reciprocally monophyletic, but the Bayesian species delimitation for A. lucens suggested 3-4 cryptic taxa with a more specialised host use than previously suggested. The gene data analyzed under the multispecies coalescent model allowed us to reconstruct the species tree phylogeny for both host and parasitoid and we found a fully congruent coevolutionary pattern suggesting that parasitoid speciation followed upon host speciation. Conclusion: Using multilocus sequence data in a Bayesian species delimitation analysis we propose that hymenopteran parasitoids of the genus Asecodes that infest Galerucella larvae constitute at least three species with narrow diet breath. The evolution of parasitoid Asecodes and host Galerucella show a fully congruent coevolutionary pattern. This finding strengthens the hypothesis that the parasitoid in host search uses cues of the host rather than more general cues of both host and plant

Molecular dataset for phylogenetic analysis of the butterfly subfamily Satyrinae (Nymphalidae)

<p>Molecular dataset for species in the butterfly subfamily Satyrinae. There are three gene blocks: Cytochrome oxidase I (COI), elongation factor 1 (EF1a) and wingless.</p> <p>This dataset was used in the study:</p> <p> </p> <p>Peña, C., N. Wahlberg, E. Weingartner, U. Kodandaramaiah, S. Nylin, A.V.L. Freitas & A.V.Z. Brower. 2006. Higher level phylogeny of Satyrinae butterflies (Lepidoptera: Nymphalidae) based on DNA sequence data. Molecular Phylogenetics and Evolution 40(1): 29-49. doi:10.1016/j.ympev.2006.02.007</p

Number of mitochondrial haplotypes and haplotype diversity values of each population.

<p>Idaho, Quebec and Georgia were excluded from the analysis since they were represented by less than five individuals.</p

Population structure inferred in STRUCTURE based on microsatellite data.

<p>Each genetic cluster is represented by a colour. Every individual is represented by a single vertical line with coloured segments depicting the estimated proportion of ancestry from a given cluster. a) Results from the analysis where individuals were grouped into populations <i>a priori</i>; K = 5. b) Results from the analysis where individuals were grouped into subspecies <i>a priori</i>; K = 6.</p

Pairwise Ф_ST values between populations calculated from mitochondrial haplotype frequencies in Arlequin.

<p>Values significantly different in the exact tests of differentiation are in bold. Population abbreviations are as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041058#pone-0041058-t001" target="_blank">Table 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041058#pone-0041058-g002" target="_blank">Figure 2</a>.</p

Investigating Concordance among Genetic Data, Subspecies Circumscriptions and Hostplant Use in the Nymphalid Butterfly <em>Polygonia faunus</em>

<div><p>Subspecies are commonly used taxonomic units to formally describe intraspecific geographic variation in morphological traits. However, the concept of subspecies is not clearly defined, and there is little agreement about what they represent in terms of evolutionary units, and whether they can be used as reliably useful units in conservation, evolutionary theory and taxonomy. We here investigate whether the morphologically well-characterized subspecies in the North American butterfly <em>Polygonia faunus</em> are supported by genetic data from mitochondrial sequences and eight microsatellite loci. We also investigate the phylogeographic structure of <em>P. faunus</em> and test whether similarities in host-plant use among populations are related to genetic similarity. Neither the nuclear nor the mitochondrial data corroborated subspecies groupings. We found three well defined genetic clusters corresponding to California, Arizona and (New Mexico+Colorado). There was little structuring among the remaining populations, probably due to gene flow across populations. We found no support for the hypothesis that similarities in host use are related to genetic proximity. The results indicate that the species underwent a recent rapid expansion, probably from two glacial refugia in western North America. The mitochondrial haplotype network indicates at least two independent expansion phases into eastern North America. Our results clearly demonstrate that subspecies in <em>P. faunus</em> do not conform to the structuring of genetic variation. More studies on insects and other invertebrates are needed to better understand the scope of this phenomenon. The results of this study will be crucial in designing further experiments to understand the evolution of hostplant utilization in this species.</p> </div

Pairwise Ф_ST values between subspecies calculated from mitochondrial haplotype frequencies in Arlequin.

<p>Values significantly different in the exact tests of differentiation are in bold.</p

Pairwise F_ST values between populations calculated from the microsatellite data.

<p>Numbers to the left of the diagonal are calculated in Arlequin without correcting for the presence of null alleles. Values in bold are significantly greater than zero. Numbers to the right of the diagonal are F_ST values calculated in FreeNA after ENA correction for null alleles. Population abbreviations are as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041058#pone-0041058-t001" target="_blank">Table 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041058#pone-0041058-g002" target="_blank">Figure 2</a>.</p