Complex evolution in Aphis gossypii group (Hemiptera: Aphididae), evidence of primary host shift and hybridization between sympatric species.

Aphids provide a good model system to understand the ecological speciation concept, since the majority of the species are host-specific, and they spend their entire lifecycle on certain groups of host plants. Aphid species that apparently have wide host plant ranges have often turned out to be complexes of host-specialized biotypes. Here we investigated the various host-associated populations of the two recently diverged species, Aphis gossypii and A. rhamnicola, having multiple primary hosts, to understand the complex evolution with host-associated speciation. Using mitochondrial DNA marker and nine microsatellite loci, we reconstructed the haplotype network, and analyzed the genetic structure and relationships. Approximate Bayesian computation was also used to infer the ancestral primary host and host-associated divergence, which resulted in Rhamnus being the most ancestral host for A. gossypii and A. rhamnicola. As a result, Aphis gossypii and A. rhamnicola do not randomly use their primary and secondary host plants; rather, certain biotypes use only some secondary and specific primary hosts. Some biotypes are possibly in a diverging state through specialization to specific primary hosts. Our results also indicate that a new heteroecious race can commonly be derived from the heteroecious ancestor, showing strong evidence of ecological specialization through a primary host shift in both A. gossypii and A. rhamnicola. Interestingly, A. gossypii and A. rhamnicola shared COI haplotypes with each other, thus there is a possibility of introgression by hybridization between them by cross-sharing same primary hosts. Our results contribute to a new perspective in the study of aphid evolution by identifying complex evolutionary trends in the gossypii sensu lato complex.

Low genetic diversity and potential inbreeding in an isolated population of alder buckthorn (Frangula alnus) following a founder effect.

Alder buckthorn (Frangula alnus) is one of Ireland's rarest tree species, and in Northern Ireland the species is now restricted to a single population in Peatlands Park, Co. Armagh numbering ca. 140 mature trees. Genotyping of 95% of the trees at nine nuclear microsatellite loci revealed that levels of genetic diversity within this population were generally lower than those reported from larger populations in Spain. Analysis of six chloroplast microsatellite loci revealed no variation. The level of F IS was significantly higher than that in the Spanish populations, as well as in other populations across Europe, potentially indicating inbreeding. Spatial autocorrelation analysis indicated some evidence of fine-scale genetic structuring, most likely due to limited seed dispersal, but the overall level of differentiation between subpopulations was low, indicating high levels of gene flow, probably due to cross-pollination by bees. Our results are consistent with a gradual population expansion from a limited number of individuals. We suggest that more immediate conservation efforts might be best focused on ensuring suitable habitat for the continued recovery of this isolated population.

Transatlantic invasion routes and adaptive potential in North American populations of the invasive glossy buckthorn, Frangula alnus.

BACKGROUND AND AIMS: Many invasive species severely threaten native biodiversity and ecosystem functioning. One of the most prominent questions in invasion genetics is how invasive populations can overcome genetic founder effects to establish stable populations after colonization of new habitats. High native genetic diversity and multiple introductions are expected to increase genetic diversity and adaptive potential in the invasive range. Our aim was to identify the European source populations of Frangula alnus (glossy buckthorn), an ornamental and highly invasive woody species that was deliberately introduced into North America at the end of the 18th century. A second aim of this study was to assess the adaptive potential as an explanation for the invasion success of this species. METHODS: Using a set of annotated single-nucleotide polymorphisms (SNPs) that were assigned a putative function based on sequence comparison with model species, a total of 38 native European and 21 invasive North American populations were subjected to distance-based structure and assignment analyses combined with population genomic tools. Genetic diversity at SNPs with ecologically relevant functions was considered as a proxy for adaptive potential. KEY RESULTS: Patterns of invasion coincided with early modern transatlantic trading routes. Multiple introductions through transatlantic trade from a limited number of European port regions to American urban areas led to the establishment of bridgehead populations with high allelic richness and expected heterozygosity, allowing continuous secondary migration to natural areas. CONCLUSIONS: Targeted eradication of the urban populations, where the highest genetic diversity and adaptive potential were observed, offers a promising strategy to arrest further invasion of native American prairies and forests.

Plant Invasions Associated with Change in Root-Zone Microbial Community Structure and Diversity.

The importance of plant-microbe associations for the invasion of plant species have not been often tested under field conditions. The research sought to determine patterns of change in microbial communities associated with the establishment of invasive plants with different taxonomic and phenetic traits. Three independent locations in Virginia, USA were selected. One site was invaded by a grass (Microstegium vimineum), another by a shrub (Rhamnus davurica), and the third by a tree (Ailanthus altissima). The native vegetation from these sites was used as reference. 16S rRNA and ITS regions were sequenced to study root-zone bacterial and fungal communities, respectively, in invaded and non-invaded samples and analyzed using Quantitative Insights Into Microbial Ecology (QIIME). Though root-zone microbial community structure initially differed across locations, plant invasion shifted communities in similar ways. Indicator species analysis revealed that Operational Taxonomic Units (OTUs) closely related to Proteobacteria, Acidobacteria, Actinobacteria, and Ascomycota increased in abundance due to plant invasions. The Hyphomonadaceae family in the Rhodobacterales order and ammonia-oxidizing Nitrospirae phylum showed greater relative abundance in the invaded root-zone soils. Hyphomicrobiaceae, another bacterial family within the phyla Proteobacteria increased as a result of plant invasion, but the effect associated most strongly with root-zones of M. vimineum and R. davurica. Functional analysis using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) showed bacteria responsible for nitrogen cycling in soil increased in relative abundance in association with plant invasion. In agreement with phylogenetic and functional analyses, greater turnover of ammonium and nitrate was associated with plant invasion. Overall, bacterial and fungal communities changed congruently across plant invaders, and support the hypothesis that nitrogen cycling bacteria and functions are important factors in plant invasions. Whether the changes in microbial communities are driven by direct plant microbial interactions or a result of plant-driven changes in soil properties remains to be determined.

The population genomic signature of environmental selection in the widespread insect-pollinated tree species Frangula alnus at different geographical scales.

The evaluation of the molecular signatures of selection in species lacking an available closely related reference genome remains challenging, yet it may provide valuable fundamental insights into the capacity of populations to respond to environmental cues. We screened 25 native populations of the tree species Frangula alnus subsp. alnus (Rhamnaceae), covering three different geographical scales, for 183 annotated single-nucleotide polymorphisms (SNPs). Standard population genomic outlier screens were combined with individual-based and multivariate landscape genomic approaches to examine the strength of selection relative to neutral processes in shaping genomic variation, and to identify the main environmental agents driving selection. Our results demonstrate a more distinct signature of selection with increasing geographical distance, as indicated by the proportion of SNPs (i) showing exceptional patterns of genetic diversity and differentiation (outliers) and (ii) associated with climate. Both temperature and precipitation have an important role as selective agents in shaping adaptive genomic differentiation in F. alnus subsp. alnus, although their relative importance differed among spatial scales. At the 'intermediate' and 'regional' scales, where limited genetic clustering and high population diversity were observed, some indications of natural selection may suggest a major role for gene flow in safeguarding adaptability. High genetic diversity at loci under selection in particular, indicated considerable adaptive potential, which may nevertheless be compromised by the combined effects of climate change and habitat fragmentation.

Rangewide phylogeography of a bird-dispersed Eurasian shrub: contrasting Mediterranean and temperate glacial refugia.

We studied the phylogeography of alder buckthorn (Frangula alnus), a bird-dispersed shrub or small tree distributed over most of Europe and West Asia and present in three of the four main refugia of West Palaearctic temperate woody plants: the Iberian Peninsula, the Balkans and Anatolia. A total of 78 populations from 21 countries were analysed for chloroplast DNA variation using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), and 21 different haplotypes were distinguished. We found a very strong overall population differentiation (GST = 0.81) and phylogeographical structure, and a sharp contrast between the haplotype-rich refugia and the almost completely uniform area of postglacial colonization. The haplotype network comprises three lineages made up of haplotypes from the Iberian Peninsula, Anatolia with the Caucasus, and temperate Europe. The Iberian and the Anatolian branches represent parts of a major lineage that spans over the whole northern Mediterranean Basin and some neighbouring areas and probably dates back to the Tertiary. Many haplotypes of this lineage are distributed locally and most populations are fixed for a single haplotype; these populations have apparently been very stable since their establishment, experiencing negligible gene flow and few mutations. The temperate European lineage consists of one very widespread and abundant plus six locally distributed haplotypes. Four of them are located in Southeast Europe, the putative refugium of all extant temperate European populations. Contrary to populations from Iberia and Anatolia, F. alnus populations from the southeastern European refugium have most genetic variation within populations. Bird-mediated seed dispersal has apparently allowed not only a very rapid postglacial expansion of F. alnus but also subsequent regular seed exchanges between populations of the largely continuous species range in temperate Europe. In contrast, the disjunct F. alnus populations persisting in Mediterranean mountain ranges seem to have experienced little gene flow and have therefore accumulated a high degree of differentiation, even at short distances. Populations from the southern parts of the glacial refugia have contributed little to the postglacial recolonization of Europe, but their long-term historical continuity has allowed them to maintain a unique store of genetic variation.