Ancient Duplications Have Led to Functional Divergence of Vitellogenin-Like Genes Potentially Involved in Inflammation and Oxidative Stress in Honey Bees

Protection against inflammation and oxidative stress is key in slowing down aging processes. The honey bee (Apis mellifera) shows flexible aging patterns linked to the social role of individual bees. One molecular factor associated with honey bee aging regulation is vitellogenin, a lipoglycophosphoprotein with anti-inflammatory and antioxidant properties. Recently, we identified three genes in Hymenopteran genomes arisen from ancient insect vitellogenin duplications, named vg-like-A, -B, and -C. The function of these vitellogenin homologs is unclear. We hypothesize that some of them might share gene-and protein-level similarities and a longevity-supporting role with vitellogenin. Here, we show how the structure and modifications of the vg-like genes and proteins have diverged from vitellogenin. Furthermore, all three vg-like genes show signs of positive selection, but the spatial location of the selected protein sites differ from those found in vitellogenin. We show that all these genes are expressed in both long-lived winter worker bees and in summer nurse bees with intermediate life expectancy, yet only vg-like-A shows elevated expression in winter bees as found in vitellogenin. Finally, we show that vg-like-A responds more strongly than vitellogenin to inflammatory and oxidative conditions in summer nurse bees, and that also vg-like-B responds to oxidative stress. We associate vg-like-A and, to lesser extent, vg-like-B to the antiaging roles of vitellogenin, but that vg-like-C probably is involved in some other function. Our analysis indicates that an ancient duplication event facilitated the adaptive and functional divergence of vitellogenin and its paralogs in the honey bee.Peer reviewe

Conservation Genomics of the Declining North American Bumblebee Bombus terricola Reveals Inbreeding and Selection on Immune Genes

The yellow-banded bumblebee Bombus terricola was common in North America but has recently declined and is now on the IUCN Red List of threatened species. The causes of B. terricola’s decline are not well understood. Our objectives were to create a partial genome and then use this to estimate population data of conservation interest, and to determine whether genes showing signs of recent selection suggest a specific cause of decline. First, we generated a draft partial genome (contig set) for B. terricola, sequenced using Pacific Biosciences RS II at an average depth of 35×. Second, we sequenced the individual genomes of 22 bumblebee gynes from Ontario and Quebec using Illumina HiSeq 2500, each at an average depth of 20×, which were used to improve the PacBio genome calls and for population genetic analyses. The latter revealed that several samples had long runs of homozygosity, and individuals had high inbreeding coefficient F, consistent with low effective population size. Our data suggest that B. terricola’s effective population size has decreased orders of magnitude from pre-Holocene levels. We carried out tests of selection to identify genes that may have played a role in ameliorating environmental stressors underlying B. terricola’s decline. Several immune-related genes have signatures of recent positive selection, which is consistent with the pathogen-spillover hypothesis for B. terricola’s decline. The new B. terricola contig set can help solve the mystery of bumblebee decline by enabling functional genomics research to directly assess the health of pollinators and identify the stressors causing declines

Genetic variation and population structure in wild isolates of Caenorhabditis elegans collected from California

Though much widespread in distribution, the nematode worm Caenorhabditis elegans exhibits low levels of genetic variation at the DNA sequence level, a paradox which may be partly explained by its typical self-fertilization mode of reproduction. However recent work on the genetic structure of natural populations of C. elegans from France, Scotland and Portugal suggests a substantial level of outcrossing together with finding of a very strong local population structure. To find out whether this same occurrence extrapolates to other wild isolates of worm populations, the present study was carried on worm populations from California. Here, genetic variation is studied by detecting single nucleotide polymorphisms in a random genome-wide manner using Amplified Fragment Length Polymorphism analysis (AFLP). The worms used in this study are natural isolates of C. elegans collected from parks and gardens around the Los Angeles area in southern California. Some populations sampled were a few meters apart, enabling the assessment of variation and population structure on a very local scale. As previous studies, a low overall genetic diversity was found with these worm populations. The finding of a strong population structure and high linkage disequilibrium both within and between chromosomes was also concurrent with the findings from other wild isolates. All these findings elucidate the extra-ordinary evolutionary dynamics of these sets of worm from the wild.M.S.Includes bibliographical references (p. 38-41)

Population Genetics and Speciation in Outcrossing Species in the Nematode Genus Caenorhabditis

In Caenorhabditis nematodes, the androdioecious, self-fertilizing reproductive strategy has evolved relatively recently from gonochoristic, outcrossing ancestors. Transitions in mating system impact how genes are vertically transmitted between generations and horizontally between populations through gene flow. To date, species-wide studies have targeted selfing species, and we have limited understanding about how population genetic processes have shaped the genome structure and evolutionary history of outcrossing species of Caenorhabditis. To fill this gap, I investigate patterns of genetic variation and population genetic processes focusing on two outcrossing species in the genus, C. brenneri and C. remanei, using a survey of nucleotide polymorphisms in a multipopulation, multilocus context. I discover extensive genetic diversity in Caenorhabditis brenneri, termed hyperdiversity, giving this species the highest known levels of nucleotide polymorphism for any multicellular eukaryote. Genetic crosses between populations, extensive intra-locus recombination, and evidence of weak selection on codon usage all suggest that this is due to a large effective population size in the species and not an artifact of cryptic species divergence. I demonstrate that C. remanei also is characterised by high genetic variation globally, albeit not as extreme as in C. brenneri, and within each local population. Despite geographic barriers, considerable gene flow occurs between inter-continental locations. While exploring genetic diversity in C. remanei, I discovered C. sp. 23, a new, gonochoristic species reproductively isolated and highly divergent from it. Subsequently, taking advantage of this newly discovered species pair, I explore the patterns of postzygotic reproductive isolation between C. remanei and C. sp. 23. I find evidence of partial F1 hybrid inviability, strong F1 hybrid male sterility (Haldane’s rule) and strong F2 hybrid breakdown between the two. The findings from this thesis, especially the notion of hyperdiversity, can be taken advantage of to answer key questions on testing limits of natural selection, of evolution of genome complexity as well as identifying and characterising functional, non-coding regulatory elements. Discovery of a new species pair in Caenorhabditis helps establish an emerging age of speciation genetics in the worm.Ph

Gonad morphogenesis defects drive hybrid male sterility in asymmetric hybrid breakdown ofCaenorhabditisnematodes

Tram tracks running past the Rembrandtplein (Rembrandt Square), center; Topographical shots taken both inside and outside the 17th century inner canal ring (the Grachtengordel). In the 19th and 20th centuries, the city expanded, and many new neighborhoods and suburbs were planned and built. The Jordaan area is a former working class neighborhood. The Damrak is an avenue and partially filled in canal at the center of Amsterdam, running between Amsterdam Centraal in the north and Dam Square in the south. It is the main street where people arriving at the station enter the center of Amsterdam. Also it is one of the two GVB tram routes from the station into the center (16 tram total current tram routes). Source: Wikipedia; http://en.wikipedia.org/wiki/Main_Page (accessed 7/15/2014