Ecological Niche Models and Coalescent Analysis of Gene Flow Support Recent Allopatric Isolation of Parasitoid Wasp Populations in the Mediterranean

Background: The integration of multiple complementary approaches is a powerful way to understand the processes of diversification and speciation. The parasitoid wasp Aphidius transcaspicus Telenga (Hymenoptera: Braconidae) is a parasitoid of Hyalopterus aphids across a wide geographic range. This species shows a remarkable degree of genetic structure among western, central, and eastern Mediterranean population clusters. In this paper we attempt to better characterize this genetic structure. Methodology/Principal Findings: We use a Bayesian coalescent analysis of gene flow under the Isolation with Migration model using mitochondrial and microsatellite markers together with climate-based ecological niche models to better understand the genetic structure of A. transcaspicus in the Mediterranean. The coalescent analysis revealed low levels of migration among western and eastern Mediterranean populations (Nm,1) that were not statistically distinguishable from zero. Niche models showed that localities within population clusters each occupy areas of continuously high environmental suitability, but are separated from each other by large regions of completely unsuitable habitat that could limit dispersal. Overall, environmental characteristics were similar among the population clusters, though significant differences did emerge. Conclusions/Significance: These results support contemporary allopatric isolation of Mediterranean populations of A

Relocation risky for bumblebee colonies

Climate change impacts on bumblebees converge across continentsFil: Lozier, Jeffrey. University of Alabama; Estados UnidosFil: Cameron, Sydney. University of Illinois; Estados UnidosFil: Duennes, Michelle. University of Illinois; Estados UnidosFil: Strange, James. State University of Utah; Estados UnidosFil: Williams, Paul. Natural History Museum; Reino UnidoFil: Goulson, David. University of Sussex; Reino UnidoFil: Brown, Mark. University of London; Reino UnidoFil: Morales, Carolina Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto de Investigaciones en Biodiversidad y Medioambiente. Universidad Nacional del Comahue. Centro Regional Universidad Bariloche. Instituto de Investigaciones en Biodiversidad y Medioambiente; ArgentinaFil: Jepsen, Sarina. Xerces Society; Estados Unido

Environment and Co-occurring Native Mussel Species, but Not Host Genetics, Impact the Microbiome of a Freshwater Invasive Species (Corbicula fluminea)

The Asian clam Corbicula fluminea (Family: Cyneridae) has aggressively invaded freshwater habitats worldwide, resulting in dramatic ecological changes and declines of native bivalves such as freshwater mussels (Family: Unionidae), one of the most imperiled faunal groups. Despite increases in our knowledge of invasive C. fluminea biology, little is known of how intrinsic and extrinsic factors, including co-occurring native species, influence its microbiome. We investigated the gut bacterial microbiome across genetically differentiated populations of C. fluminea in the Tennessee and Mobile River Basins in the Southeastern United States and compared them to those of six co-occurring species of native freshwater mussels. The gut microbiome of C. fluminea was diverse, differed with environmental conditions and varied spatially among rivers, but was unrelated to host genetic variation. Microbial source tracking suggested that the gut microbiome of C. fluminea may be influenced by the presence of co-occurring native mussels. Inferred functions from 16S rRNA gene data using PICRUST2 predicted a high prevalence and diversity of degradation functions in the C. fluminea microbiome, especially the degradation of carbohydrates and aromatic compounds. Such modularity and functional diversity of the microbiome of C. fluminea may be an asset, allowing to acclimate to an extensive range of nutritional sources in invaded habitats, which could play a vital role in its invasive success

The genomes of two key bumblebee species with primitive eusocial organization

Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits. Conclusions: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation

Journal of Microelectronic Research 2010

https://scholarworks.rit.edu/meec_archive/1018/thumbnail.jp

Data from: Revisiting comparisons of genetic diversity in stable and declining species: assessing genome-wide polymorphism in North American bumble bees using RAD sequencing

Genetic variation is of key importance for a species’ evolutionary potential, and its estimation is a major component of conservation studies. New DNA sequencing technologies have enabled the analysis of large portions of the genome in nonmodel species, promising highly accurate estimates of such population genetic parameters. Restriction site-associated DNA sequencing (RADseq) is used to analyse thousands of variants in the bumble bee species Bombus impatiens, which is common, and Bombus pensylvanicus, which is in decline. Previous microsatellite-based analyses have shown that gene diversity is lower in the declining B. pensylvanicus than in B. impatiens. RADseq nucleotide diversities appear much more similar in the two species. Both species exhibit allele frequencies consistent with historical population expansions. Differences in diversity observed at microsatellites thus do not appear to have arisen from long-term differences in population size and are either recent in origin or may result from mutational processes. Additional research is needed to explain these discrepancies and to investigate the best ways to integrate next-generation sequencing data and more traditional molecular markers in studies of genetic diversity

Lozier_Bimp-Bpen-RADtags_MolEcol_Dryad_120813

######## Description of files for Lozier et al. "Revisiting comparisons of genetic diversity in stable and declining species: Assessing genome-wide polymorphism in North American bumble bees using RAD sequencing" for Mol. Ecol. ######## Files contained in "Lozier_Bimp-Bpen-RADtags_MolEcol_Dryad_120813.zip" ######## imp_bamfiles: bam formatted alignment files for each individual used in the paper for B. impatiens, indexed by samtools; note file names correspond with county and state listed in the main paper, and headers contain the actual specimen ID number. imp_radreferencegenome: fasta file (and fai index) for the B. impatiens "RAD reference" genome used for aligning RAD tag reads. pen_bamfiles: bam formatted alignment files for each individual used in the paper for B. pensylvanicus, indexed by samtools; note file names correspond with county and state listed in the main paper, and headers contain the actual specimen ID number. pen_radreferencegenome: fasta file (and fai index) for the B. impatiens "RAD reference" genome used for aligning RAD tag reads. ######## The variant call formatted files (VCF 4.1) that are used for "Filter Set 1" in the paper. The files named: Bombus_imp_stringentRAD_DP_HWEfiltered.vcf Bombus_pen_stringentRAD_DP_HWEfiltered.vcf contain sample names as referred to in @PG in the headers of the .bam files (specimen IDs) that were used in actual analyses in the paper. The files named: Lozier_Bombus_imp_Finalvcf.vcf Lozier_Bombus_pen_Finalvcf.vcf contain sample names renamed to State/County format for easier interpretation, but should otherwise be identical. These can readily be further filtered by other criteria using software such as vcftools, or are small enough to be manipulated by excel if so desired.######## Also included is an excel file "ANGSD_ThetaPi_Bpen_Bimp_LozierBombusRADtags_DRYAD.xls" This file contains per-site estimates of Theta_pi (or nucleotide diversity) from ANGSD, sorted by Chromosome (RADref) and position. ######## please contact [email protected] with any problems

Ecological niche models and coalescent analysis of gene flow support recent allopatric isolation of parasitoid wasp populations in the Mediterranean.

BackgroundThe integration of multiple complementary approaches is a powerful way to understand the processes of diversification and speciation. The parasitoid wasp Aphidius transcaspicus Telenga (Hymenoptera: Braconidae) is a parasitoid of Hyalopterus aphids across a wide geographic range. This species shows a remarkable degree of genetic structure among western, central, and eastern Mediterranean population clusters. In this paper we attempt to better characterize this genetic structure.Methodology/principal findingsWe use a Bayesian coalescent analysis of gene flow under the Isolation with Migration model using mitochondrial and microsatellite markers together with climate-based ecological niche models to better understand the genetic structure of A. transcaspicus in the Mediterranean. The coalescent analysis revealed low levels of migration among western and eastern Mediterranean populations (Nm<1) that were not statistically distinguishable from zero. Niche models showed that localities within population clusters each occupy areas of continuously high environmental suitability, but are separated from each other by large regions of completely unsuitable habitat that could limit dispersal. Overall, environmental characteristics were similar among the population clusters, though significant differences did emerge.Conclusions/significanceThese results support contemporary allopatric isolation of Mediterranean populations of A. transcaspicus, which together with previous analyses indicating partial behaviorally mediated reproductive isolation, suggest that the early stages of cryptic speciation may be in progress