1 International Conference Molecular Ecology & Evolution Programme and Abstracts Vienna, Austria June 22-23, 2015
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International Conference
Molecular Ecology &
Evolution
Programme and Abstracts
Vienna, Austria
June 22-23, 2015
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Organizing Committee
Local Organizing Committee International Organizing Committee Prof. A. Touraev (President of Vienna
International Science Conference and
Events Association (VISCEA))
Thomas Stadler (Co-Chair)
Adam Eyre-Walker
Torsten Kristensen
Pär Ingvarsson
Severine Vuilleumier
Elizabeth Zimmer
Michael Gruenstaeudl
Barbara Mable
Yuanwen Teng
Robert Lanfear
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Dear Friends! DearColleagues!
Welcome to the International Conference “Molecular Ecology & Evolution”! Welcome to
Vienna!
Molecular Ecology & Evolution is a field of evolutionary biology, concerned with applying molecular
population genetics, molecular phylogenetics, and, more recently, “Omics” to traditional ecological
questions.
The main goal of the International Conference “Molecular Ecology & Evolution” is to review the state
of the art and progress in the knowledge of molecular evolution, species diagnosis, conservation and
assessment of biodiversity, species-area relationships, and behavioral ecology, to set research
priorities for the next era of research.
The program of Molecular Ecology & Evolution Conference consists of plenary lectures and session
talks, posters sessions, and tours of the beautiful city of Vienna.
Vienna is considered one of the most beautiful cities in the world, situated in the heart of Europe. Due
to its geographic and geopolitical location, Vienna has become a popular conference place in recent
years. Today, Vienna offers a range of sights from old historical palaces, classical concerts and
outstanding opera performances to typical Viennese coffee houses and restaurants – all brought
together in incomparable Viennese harmony. The International and Local Organizing Committees have
compiled a well-balanced agenda with state-of –the –art professional highlights and social events to
be remembered.
Prof. Thomas Stadler, Chair of the International Organizing Committee
Prof. Alisher Touraev, President of VISCEA, Chair of Local Organizing Committee
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Table of Contents
Scientific Programme …………………………………………………………… 7
Abstracts of Oral Presentations ……………………………………………. 10
Abstracts of Posters Presentations ………………………………………. 24
List of Poster Presentations …………………………………………………. 28
List of Participants ……………………………………………………………….. 29
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SCIENTIFIC PROGRAMME
June 22 (Monday) 08.00 – 17.00 Registration
09.00 – 09.20 Opening Welcome address by Alisher Touraev (Local Chair, VISCEA, Austria) Welcome address by Thomas Stadler (Co-Chair, Switzerland)
09.20 - 10.20 (+10) Keynote Lecture: Adam Eyre Walker (UK). Factors that Affect The Rate of Adaptive Molecular Evolution
10.30 - 11.00 Coffee break
11.00 - 12.30 Session I: Population & Landscape Genetics
Chairs Adam Eyre Walker (UK); Pär Ingvarsson (Sweden)
11.00 – 11.25 (+5) Thomas Staedler (Switzerland). Inference of Natural Selection from Genome-Wide Sequence Data in Wild Tomatoes
11.30 – 11.55 (+5) Pär Ingvarsson (Sweden). Genomic Signatures of Local Adaptation in European Aspen (Populus Tremula)
12.00 – 12.15 (+5) Marta Gallart (New Zealand). Insights on the Impact of Nitrogen Form on the Interplay Between Root System Architecture (RSA), ECM Fungi and Soil Microbiome
12.20 – 12.35 (+5) Tanya Singh (USA). The Dynamics of Super-Mutator Hitchhiking in Asexual Populations
12.40 - 14.00 Lunch + Poster Session
14.00 - 15.30 Session II: Genetic Variation & Diversity
Chairs Thomas Staedler (Switzerland); Severine Vuilleumier (Switzerland)
14.00 -14.30 (+5) Severine Vuilleumier (Switzerland). Association Between Cycles of Population Isolation and Connection and Species Diversification
14.35 – 14.50 (+5) Dace Grauda (Latvia). Detection of Genetic Diversity of Selected Model Species for Urban Ecology Studies
14.55 -15.10 (+5) James Buckley (UK). Disease Resistance Gene Variation Across Arabidopsis Lyrata Subspecies: Effects of Demographic History, Selection and Mating System
15.10 -15.25 (+5) Isaak Rashal (Latvia). Genetic Particularities of Some Localities of Cypripedium calceolus in Latvia
15.30 - 16.00 Coffee break
16.00 - 17.30 Session III: Phylogenetics & Phylogeography
Chairs: Robert Lanfear (Australia); Michael Gruenstaeudl (Germany)
16.00 -16.30 (+5) Elizabeth Zimmer (USA). Using Nuclear Gene Data for Plant Phylogenetics: Progress and Prospects
16.35 – 17.05 (+5) Michael Gruenstaeudl (Germany). Examples of Novel Methods in Model-Based Inference of Plant Phylogeny and Phylogeography
17.10 – 17.25 (+5) Daniela Borges (Italy). Evaluation of Paleoclimate Model for Atlantic Forest Refugia Using Molecular Tools
17.30 – 19.00 Welcome Reception + Poster Session
June 23 (Tuesday) 08.00 – 17.00 Registration
09.00 - 10.30 Session IV: Evolution of Adaptive Systems
Chair Bernhard Haubold (Germany)
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09.00 -09.30 (+5) Barbara Mable (UK). Mating Systems and Adaptive Genetic Variation
09.35 – 09.50 (+5) Nora Adam (Germany). Intraspecific Diversity in Plant Jasmonate Signalling Alters Plant Competitive Outcomes and Damage from Three Native Herbivores
09.55 -10.10 (+5) Yan Hou (Norway). From the North into the Himalayan-Hengduan Mountains: a Dated Phylogeny of the Arctic-Alpine Genus Cassiope (Ericaceae) Using RAD-seq
10.15 -10.30 (+5) Elvira De Matthaeis (Italy). The Evolutionary Ecology of Talitrid Amphipods (Crustacea)
10.35 – 11.00 Coffee break
11.00 - 12.30 Session V: Conservation Genetics & Genomics
Chairs Yuanwen Teng (China); Torsten N. Kristensen (Denmark)
11.00 -11.25 (+5) Yuanwen Teng (China). Recent Progresses in Molecular Phylogeny and Genetic Diverstiy of Pyrus L.
11.30 -12.00 (+5) Torsten Kristensen (Denmark). Small Populations and Conservation Genetics - Lessons from Drosophila And Livestock
12.05 – 12.25 (+5) Andrzej Kilian (Australia). DArTseq and KDDart Platforms for Population Genetics and Landscape Genomics 12.30 – 14.00 Lunch + Poster Session
14.00 - 15.50 Session VI: Molecular Evolution & Applied Molecular Ecology
Chair Elizabeth A. Zimmer (USA); Barbara Mable (UK)
14.00 – 14.25 (+5) Robert Lanfear (Australia). Understanding Rates of Molecular Evolution in Plants
14.30 – 14.55 (+5) Sagi Snir (Israel). A Universal PaceMaker as a Better Explanation of Genome Evolution
15.00 – 15.25 (+5) Bernhard Haubold (Germany). Fast Computation of Evolutionary Distances between Genomes
15.30 – 15.45 (+5) Ved Kumar (India). Resolving the Phylogenetic Status and Taxonomic Relationships of the Hangul (Cervus elaphus hanglu) in the Family Cervidae
15.50 - 16.30 Coffee break, Closing Ceremony, Conference Photo
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Factors that Affect the Rate of Adaptive Molecular Evolution
Adam Eyre Walker University of Sussex, UK
It has been shown that a substantial proportion of the amino acid differences between species have been fixed by positive adaptive evolution. But what determines which genes contribute to adaptation? In my talk I will cover recent work that we have done on the role of recombination, mutation and gene age in the adaptive process. I will show that the rate of adaptation depends both on the rate of mutation and the rate of recombination in Drosophila. We estimate that a lack of free recombination leads to a loss of almost 30% of all adaptive substitutions to Hill Robertson interference (HRi). We also demonstrate that this loss depends upon the mutation rate; genes with higher mutation rates suffer more loss due to HRi. However, despite the effect of limited recombination on adaptation we have also recently estimated that 25% of all amino acid substitutions are driven by positive selection in animal mitochondrial DNA, a genetic system in which there is little or no recombination. Finally, I will present some work in which we have shown that younger genes are undergoing more adaptation than older genes. Inference of Natural Selection from Genome-Wide Sequence Data in Wild Tomatoes Thomas Städler Plant Ecological Genetics, Institute of Integrative Biology, ETH Zurich, CH-8092 Zurich, Switzerland
Levels and patterns of nucleotide polymorphism across genomes are shaped by both negative and positive selection, genetic drift, and differences in recombination and mutation rates. With the recent availability of genome-wide polymorphism data in both model and non-model species, the fundamental question of how these evolutionary forces interact to determine patterns of sequence polymorphism has become amenable to empirical study. Empirical patterns in plants and animals, however, are not congruent across species, including the inferred preponderance of background selection (selection against deleterious mutations removing linked neutral diversity) versus selection for beneficial variants. We add to the empirical studies in plants by transcriptome sequencing of several wild tomato species (Solanum section Lycopersicon) sampled with species-wide coverage, yielding data for thousands of expressed genes. This clade spans a range of mating systems from obligate outcrossing to highly self-fertilizing, generating a range of effective recombination rates across species that should have implications for linked selection. I will discuss data on levels of synonymous and nonsynonymous polymorphism (that is, information on levels of purifying selection in coding regions), gene density, levels of physical recombination, and their interrelationships.
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Genomic Signatures of Local Adaptation in European Aspen (Populus Tremula) Pär Ingvarsson Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University, SE901 87 Umeå, Sweden
Local adaptation and adaptive clines are pervasive in natural plant populations, yet the effects of these types of adaptation on genomic diversity are not well understood. I will present data from a study where we have used whole-genome re-sequencing on accessions of European aspen sampled across a gradient spanning approximately 10 latitude degrees. The by far most important environmental variable across this gradient is variation in day length across the season. We detect a large number of loci that show strong association with the latitudinal gradient and these loci are enriched for genomic regions in the vicinity of genes from the photoperiodic pathway. When compared to a genome-wide sample of randomly drawn reference SNPs, candidate loci show elevated nucleotide polymorphism and differentiation between haplotypes carrying alternate alleles. These patterns of diversity are consistent with a history of soft selective sweeps acting on loci underlying adaptation to climate. Insights on the Impact of Nitrogen form on the Interplay between Root System Architecture (RSA), ECM Fungi and Soil Microbiome Marta Gallart School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
Insights on the impact of N form on the interplay between root system architecture (RSA), ECM fungi and soil microbiome. Marta Gallart,1,* Karen Adair,1 Jonathan Love,1 Matthew Turnbull,1 Jianming Xue2 and Peter W. Clinton2 1 Centre for Integrative Ecology, University of Canterbury, Private Bag 4800, Christchurch, NZ 2 ScionResearch, Christchurch, NZ. Microbial communities play a major role in terrestrial ecosystem functioning although the determinates of the community composition and its linkage with the morphology and function of plant roots are still uncertain. ECM fungi symbioses play a key role in carbon C cycle through the establishment of complex networks within plant roots for effective nutrient uptake in exchange for C sources that may influence the microbial community. We grew multiple Pinus radiata D. Don genotypes and supplied N in organic (L-Arginine) or inorganic (NH4NO3) form. Plant biomass was significantly influenced by genotype, N treatment and their interaction. A study of RSA between treatments showed similar correlation between root diameter and mycorrhizal colonization rate by root order with 20% higher colonisation in L-Arginine treatment. We carried out a metagenomic analysis to understand if differential plant resources allocation derived from the N form are derived by variation in C:N sensitivity of the ECM fungi and how changes in these relationships impact the broader soil community.
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The Dynamics of Super-Mutator Hitchhiking in Asexual Populations Tanya Singh1, Paul Sniegowski1, Philip Gerrish2 1Department of Biology, University of Pennsylvania, 433 S. University Avenue, Philadelphia, PA- 19104 2Department of Biology, Univeristy of New Mexico, Albuquerque, NM – 87131
Introduction: Most mutations are assumed to be deleterious and therefore, a high mutation rate genotype (hereafter referred to as a mutator) is not expected to be favored by selection. However, when the rate of beneficial mutations is sufficiently large, a mutator may hitchhike to high frequency by virtue of being associated with a beneficial mutation, especially in an asexual population where it is impossible to lose this association due to complete genetic linkage. Even though this phenomenon has been experimentally elucidated, the threshold beneficial mutation supply rate that favors the fixation of a mutator remains to be quantified, if such a threshold exists. We carry out computer simulations to test whether the proportion of available beneficial mutations can influence the fate of a mutator genotype of very strong effect (approximately 4500 fold higher than the wild type mutation rate, hereafter called the super-mutator). In order to simulate a negligible wait time before the first mutation, the mutator individuals in our simulations start with a large fitness advantage (~8%). Our simulation data suggest that, even with this initial competitive advantage, a super-mutator lineage fails to increase in frequency, due to a strong influx of deleterious mutations. Although the inequality mentioned above is satisfied in the parameter space that we use for our simulations, the super-mutator fails to fix unless: (1) the first beneficial mutation to arise is of sufficiently large effect or (2) the proportion of mutations that are beneficial is above a threshold (fb(fraction of all mutations that are beneficial) ~ 0.25 from our simulations). Association between Cycles of Population Isolation and Connection and Species Diversification
Séverine Vuilleumier
Insititut of Microbiology, Bugnon 48, University of Lausanne, 1011 Lausanne, Switzerland
Major climatic and geological events but also environmental and anthropogenic changes generate
cycles of population isolation and reconnection of long and short periods. Recent empirical and
theoretical studies suggest that fast evolutionary processes might be triggered by such events, as
commonly illustrated by the adaptive radiation of cichlid fishes (isolation and reconnection of lakes
and watersheds). It is tested whether cyclic population isolation and connection provide the raw
material (standing genetic variation) for species evolution and diversification. High excess of genetic
diversity (relative to what is expected at equilibrium) is provided to populations under cycles of
population isolation and connection. The value and the turnover of this excess of genetic diversity
depend on the duration of the population isolation periods. Accordingly, it is found that diversification
rates of animal clades are associated with specific periods of climatic cycles. The importance of these
results for macroevolution, evolutionary process and conservation will be discussed.
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Detection of Genetic Diversity of Selected Model Species for Urban Ecology Studies Dace Grauda, Isaak Rashal Institute of Biology, University of Latvia, Miera Str. 3, Salaspils, LV-2169, Latvia
The mute swan (Cygnus olor), white clover (Trifolium repens) and lime trees (Tilia sp.) were selected as model species for evolution of different aspects of adaptation to urban environment. The goal of this study was to investigate genetic diversity of populations of mentioned species in Riga in comparison with wild Latvian populations. For this purpose the universal IRAP (Inter-Retrotransposon Amplified Polymorphism) method was applied. For mute swans DNA was extracted from blood samples which were collected in Riga over year. The material of both plant species was collected in different regions of Riga and in several country side areas of Latvia. DNA was extracted from leaves dried in silicogel using standard NucleoSpin® Plant II protocol. DNA was amplified by PCR with specifically selected IRAP primers for each species. High number of polymorphic loci was revealed in all analysed species. Additionally, the BD FACSJazz® cell sorter was used for ploidy level detection. In presentation differences of genetic variation between urban and country side populations will be presented. ACKNOWLEDGMENTS the study was financially supported by the European Social Fund, the project No.2013/0060/1DP/1.1.1.2.0/13/APIA/VIAA/041
Disease Resistance Gene Variation across Arabidopsis Lyrata Subspecies: Effects of Demographic History, Selection and Mating System Buckley J1, Kilbride E1, Cevik V2, 3, Vicente JG2, Holub EB2 & Mable BK1 1University of Glasgow, UK 2University of Warwick UK 3The Sainsbury Laboratory, UK
Examining allelic variation of disease resistance genes in relatives of model plant taxa is important for understanding how demographic history and ecology interact with selection to shape patterns of adaptive variation. We finely sampled populations of Arabidopsis lyrata from the Great Lakes region of North America and broadly sampled six European countries to investigate allelic variation of two disease resistance (R-) genes and neutral genetic markers (Restriction Associated DNA sequences) in relation to mating system and phylogeographic structure. Fine-scale sampling of populations revealed strong effects of mating system and population structure on patterns of polymorphism for both neutral loci and R-genes, with no strong evidence for selection. Broad geographic sampling revealed evidence of balancing selection maintaining polymorphism in R-genes and sharing of alleles among diverged subspecies. Codon-based tests detected both positive and purifying selection for both R-genes, as commonly found for animal immune genes. Our results highlight that combining distinct sampling strategies can reveal the factors influencing polymorphism and divergence at potentially adaptive genes.
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Genetic Particularities of Some Localities of Cypripedium Calceolus in Latvia Isaak Rashal1, Dace Grauda1, Dace Kļaviņa2 1Institute of Biology, University of Latvia, Miera Street 3, Salaspils, LV-2169, Latvia 2National Botanic Garden of Latvia, Miera Street 1, Salaspils, LV-2169, Latvia
In order to ensure an appropriate protection of plant the species, knowledge of its habitat diversity and genetic characteristics is crucial. Genetic composition of populations might define the relative differences in environmental plants response. This study aimed investigation of genetic variability of yellow lady ’ s slipper orchid (Cypripedium calceolus) from 11 localities of Latvia. For this purpose universal method of DNA fingerprinting – IRAP (Inter-Retrotransposon Amplified Polymorphism) was applied. Two IRAP primers yielded 67 loci, among them 55 were polymorphic. A rather high genetic diversity of plants within the same locations was found. Results allow speculating that all sites belong to a common general population with possible differentiation on the level of subpopulations. It has been found also that geographical distance between localities is not the major factor affecting the genetic distances among them. Using Nuclear Gene Data for Plant Phylogenetics: Progress and Prospects Elizabeth Zimmer Smithsonian NMNH Department of Botany, MRC 166, P.O. Box 37012, Washington DC 20013-7012, United States
Plant nuclear genes have proven effective in phylogenetic and molecular evolution studies. Initially the primary such marker was the nuclear ribosomal DNA repeat. Subsequently, individual single or low copy nuclear genes, one or several, have been employed. Most recently, hundreds of genes from transcriptome sequences can be harvested for producing phylogenies where taxon relationships have not been effectively resolved. Examples of each class of plant nuclear gene markers will be given in this talk.
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Examples of Novel Methods in Model-Based Inference of Plant Phylogeny and Phylogeography Michael Gruenstaeudl The Ohio State University, 318 W 12th Avenue, 300 Aronoff Laboratory, Columbus, OH 43210, USA
The majority of newly developed methods in plant phylogenetics and phylogeography are based on the evaluation of empirical data via biological models. For example, model-based inference of species trees, hybridization networks, ancestral distribution areas or species delimitation has become commonplace in contemporary studies of plant phylogenetics. Given the speed of methodological advances, it can be challenging to keep up-to-date with the latest developments, and many concepts developed in one area are adapted quickly to address entirely different biological questions. The present talk attempts to provide an update on a select group of methodological advances in plant phylogeny and phylogeography. Specifically, I will present aspects of novel model-based methods that can assist in the estimation of species trees, the detection of violations of the multispecies coalescent model, the identification of occurrences of interspecific hybridization, the reconstruction of ancestral character states and the partitioning of plastid genomes for phylogenomic inference. Results from recent investigations utilizing these methods on empirical and simulated data will complement this overview, followed by a brief outlook on possible future developments.
Evaluation of paleoclimate Model for Atlantic Forest Refugia using Molecular Tools Borges D. B.1, Mariano-Neto E.2, Gaiotto, F. A.1 1Centro de Biotecnologia e Genética, UESC 2Departamento de Botânica, UFBA
According to the hypothesis of forest refugia in the Atlantic Forest, during many glacial cycles, certain forest areas (called refugia) were reduced but remained forested during glaciations. It is believed that the highest genetic diversity is concentrated in refugia, when compared to recently colonized areas. Melanoxylon brauna, the biological model in this study, is a hardwood endangered tree species endemic to the Atlantic Forest. Our aims were to study the diversity and genetic structure of natural populations of M. brauna sampled inside and outside boundaries of Pleistocene refugia proposed by paleoclimatic simulations. We collected trees from 13 localities (seven inside and six outside refugia) totalizing 384 individuals and genotype with 17 microsatellites loci. Our results showed no statistical difference in alleles per locus (A), observed heterozygosity (Ho) and expected heterozygosity (He) values between refugia and non refugia areas, however refugia had more exclusive alleles (Aex). Structure analyses showed two clusters that do not reflect genetic differences between refugia and non refugia but the clustering was compatible with spatial location of populations. The Fst and UPGMA were congruent with the pattern showed on structure barplot. We do not find specific congruence between our data and Carnaval & Moritz model, but some recent works also showed a similar pattern than we detected. Our results will help in understanding the limits of forest refugia and assist in developing conservation strategies for this biome.
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Mating Systems and Adaptive Genetic Variation Barbara Mable Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow
There has been a long-standing view that reduction in genetic variation associated with inbreeding will reduce the adaptive potential of natural populations and so conservation efforts are often focused on increasing opportunities for mating with unrelated individuals. Nevertheless, shifts from outcrossing to inbreeding are among the most frequent evolutionary transitions in plants and there are many examples of highly successful species that are capable of expanding into multiple environments, despite high levels of self-fertilisation and low levels of within-population genetic variation. We have been using Arabidopsis lyrata as a model to investigate the consequences of recent shifts in mating system on: 1) genome-wide genetic variation assessed through Restriction Associated DNA sequencing; 2) survival, reproduction and metabolic profiles in a novel environmental setting; 3) response to biotrophic pathogens; and 4) variation at genes that could be important for adaptation (e.g. R genes). Although we find the expected reduction in genome-wide genetic diversity and heterozygosity in inbred compared to outcrossed populations, we have found few differences in adaptive responses to novel environments. However, variation at R genes is reduced similarly to neutral markers, which could suggest a cost to adaptive genetic diversity. Intraspecific Diversity in Plant Jasmonate Signaling Alters Plant Competitive Outcomes and Damage from Three Native Herbivores
Nora Adam, Pia Backmann1, Mario Kallenbach, Stefan Meldau3, Nicole M. van Dam2, Ian T. Baldwin, and Meredith C. Schuman
Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany 1Helmholtz Centre for Environmental Research (UFZ), Permoserstraße 15, 04318 Leipzig, Germany 2German Centre for Integrative Biodiversity Research (iDiv), Deutscher Platz 5e, 04103 Leipzig, Germany 3KWS SAAT AG, Grimsehlstraße 31, 37574 Einbeck, Germany
Nicotiana attenuata plants in natural populations differ in their jasmonate (JA) defense hormone biosynthesis, signaling, and associated defense metabolites. Variation among individuals in stress signaling systems might increase populations’ productivity and resistance under biotic stress, such as attack by multiple herbivore species. In this study, we showed that populations of N. attenuata comprising two genotypes differing only in their expression of the JA biosynthetic gene lipoxygenase 3 (LOX3) have higher productivity than monocultures of either genotype when populations are challenged with three native herbivores. This results from a combination of differences in plant competitive ability, which are inversely correlated to JA production; and plant-mediated negative interspecific interactions among the herbivores. We analyzed this complex interaction in a mesocosm experiment and addressed plant growth and fitness consequences at individual and population levels. Populations in a shared environment were challenged sequentially with the generalist leafhopper Empoasca sp., the specialist mirid Tupiocoris notatus, and specialist caterpillar Manduca sexta. T. notatus avoids plants infested with Empoasca sp., which in turn feeds preferentially on individual plants with reduced JA accumulation. However in populations having equal numbers of wild-type plants and asLOX3 plants rendered JA-deficient by RNAi, Empoasca sp. feeding is distributed among both JA-producing and JA-deficient genotypes, and this, rather than plant JA production, determines damage patterns from T. notatus. Finally, feeding damage and growth of voracious M. sexta larvae also differs in mixed versus monocultures. Thus in the end, WT plants growing in polycultures produced more flowers and seed than WT plants growing in monocultures, whereas the flower and seed production of asLOX3 plants in polycultures did not differ in comparison to those growing in monocultures.
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From the North into the Himalayan-Hengduan Mountains: a Dated Phylogeny of the Arctic-Alpine Genus Cassiope (Ericaceae) Using RAD-seq Yan Hou1, Michael D. Nowak1,2, Charlotte Sletten Bjora1, Christian Brochmann1, Magnus Popp1 1Natural History Museum, University of Oslo, NO-0318 Oslo, Norway 2Science for Life Laboratory, Stockholm University, Tomtebodavägen 23, S-17165 Solna, Sweden
Many arctic-alpine plants display a highly disjunct distribution between the Arctic/Boreal regions and southern Asian mountains. Two main hypotheses have been proposed to explain the origin of this biogeographic pattern: 1) south-to-north migration in the late Pliocene/early Pleistocene, and 2) north-to-south migration during the Miocene. The genus Cassiope is disjunctly distributed between the Arctic/Boreal regions and the Himalayan-Hengduan Mountains (HHM) and was selected to test these hypotheses. Thousands of RAD-seq loci were produced to reconstruct the phylogeny of Cassiope, and secondary calibration approach was used to infer divergence times in the genus. The crown group age of Cassiope was estimated to the Miocene. All HHM species formed a clade together with one eastern Siberian species. This clade was sister to all other Arctic/Boreal species. This topology implies a northern origin of Cassiope, which was confirmed by our biogeographic analysis. Our results thus suggest that the ancient north-to-south migration hypothesis is most consistent with the origin of Cassiope. The Evolutionary Ecology of Talitrid Amphipods (Crustacea) Domenico Davolos1, 2, Elvira De Matthaeis2 1INAIL, Research Area, Department of Technological Innovations and Safety of Plants, Products and Anthropic Settlements (DIT), Rome, Italy 2Department of Biology and Biotechnology, Sapienza University of Rome, Viale dell’Università, 32, Rome, Italy
The members of the Talitridae family (Amphipoda) are detritivores with important roles for the ecology of marine (supralittoral), freshwater (riparian), and terrestrial (forest) ecosystems. We investigate the mitochondrial COI and COII genes, as well as the nuclear histone H3 genes of species belonging to this intriguing family. Our analysis indicates that there was a rearrangement of a mitochondrial tRNA(Leu) gene in the lineage leading to talitrid amphipods, which gave rise to the presence of a short non-coding motif between the COI and COII genes. We use the mitochondrial and nuclear coding sequences to carry out a phylogenetic analysis of morphologically recognised species covering the genera Africorchestia, Britorchestia, Cryptorchestia, Deshayesorchestia, Macarorchestia, Orchestia, Palmorchestia, Platorchestia, Sardorchestia, and Talitrus of the Mediterranean-East Atlantic area, including the Canary Islands. Overall, our observations contribute to drive future high throughput sequencing studies for exploring the detritivore–gut microbe interactions in marine, riparian and forest talitrid amphipods.
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Recent Progresses in Molecular Phylogeny and Genetic Diverstiy of Pyrus L Yuanwen Teng Department of Horticulture, Zhejiang University, PR China
The genus Pyrus, with the common name pear, belongs to subtribe Malinae of the family Rosaceae. Based on their geographic distribution, Pyrus species are divided into two native groups: occidental pears and oriental pears. The identification and description of Pyrus species have relied on traditional morphological characters, mainly from fruits and leaves. Wide distributions and extensive hybridization make it difficult to identify and distinguish Pyrus species by morphological characters; thus, the number of species recognized in Pyrus has varied among taxonomists. During the last 50 years, scientists have not stopped their efforts to understand evolutionary relationships among Pyrus species. Chemical and botanical characters, pollen structure and isozyme markers have been used for characterizations and identification of species, but these data were not informative for phylogeny reconstruction. DNA markers such as RFLP, RAPD, SSR and AFLP were also applied for revealing genetic relationships and diversity of Pyrus species, but these markers are too variable to study interspecific relationships among Pyrus species. During the last two decades, noncoding DNA regions of chloroplast and nuclear genes have been successfully applied to phylogenetic studies of plants at lower taxonomic levels. We used internal transcribed spacer (ITS) data, but resulted in a complex and poorly resolved phylogeny due to low sequence divergence and non-concerted evolution of nrDNA arrays. Thereafter, two noncoding regions of cpDNA (trnL-F and accD-psaI) and one LCNG (LFY2int2) were used to reconstruct the phylogeny of Pyrus, A phylogenetic network of LFY2int2 suggested that reticulation caused by hybridization is one of the major evolutionary processes for Pyrus species. Polytomies of the gene trees and star-like structure of cpDNA networks suggested rapid radiation is another major evolutionary process, especially for the occidental species. Noncoding regions of cpDNA were also successfully used to reveal the genetic diversity and population structure of wild Pyrus species. The latest research using fluorescent sequence-specific amplification polymorphism (SSAP) markers based on retrotransposons revealed primitive genepools of Asian pears and their complex hybrid origins which will be of great help for understanding the origin and evolution of Pyrus.
Small Populations and Conservation Genetics - Lessons from Drosophila and Livestock Torsten Nygaard Kristensen Aalborg University, Biology and Environmental Science, Fredrik Bajers Vej 7H, 9220 Aalborg East, Denmark The management of livestock breeds and threatened natural population share common challenges, including small effective population sizes, high risk of inbreeding, and the potential benefits and costs associated with mixing disparate gene pools. Here I consider what has been learnt about these issues, ways in which the knowledge gained from one area might be applied to the other, and the potential of genomics to provide new insights. Focus will be on examples from our work on Drosophila and domestic animals that provide information of general relevance for conservation of small populations.
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DArTseq and KDDart Platforms for Population Genetics and Landscape Genomics Andrzej Kilian Diversity Arrays Technology Pty Ltd, University of Canberra, Australia
Diversity Arrays Technology (DArT) PL has been established in 2001 to deliver world’s first affordable genome profiling. Our initial work focused on plants and agriculture, but in the last few years we expanded our services to a wide range of non-model organisms. For genome profiling we use DArTseq platform, the most cost effective and robust Genotyping by Sequencing (GBS) method. DArTseq represents a combination of complexity reduction methods targeting low copy, gene-rich fraction of a genome with sequencing of genomic representations on the most cost effective platforms. The technology is supported by a very mature data storage platform combined with LIMS (DArTdb) integrated with various analytical pipelines. I will present technical details about DArTseq and some examples of population genetics and landscape genomics applications. I will also present KDDart, a new IT infrastructure designed to integrate high volumes of data from several sources. The core module collects phenotypic data from either breeding or natural populations. The environmental data can be either from sensors enabled to communicate with KDDart remotely or GIS/remote sensing data. Molecular data module is capable of storing marker data from any platform and any density. KDDart is capable of storing inventory and pedigree/relatedness information and enables synchronisation of data captured on mobile devices with central database.
Understanding Rates of Molecular Evolution in Plants Robert Lanfear ARC Future Fellow and Senior Lecturer, School of Biological Sciences, Macquarie University, Sydney
Rates of molecular evolution vary dramatically between species, but the reasons for this variation remain poorly understood. In this talk, I'll discuss two complementary approaches to understanding this variation. The first uses the comparative method to understand how life history is linked to long-term substitution rates in plants. Using this method, we have discovered intriguing links between rates of molecular evolution, height, genome size, and other characteristics. The second method uses a new approach to measure rates of mutation in individual plants. Combining these two approaches, which measure molecular evolution at very different spatial and temporal scales, can offer important insights into the causes and consequences of molecular evolution in plants.
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A Universal PaceMaker as a Better Explanation of Genome Evolution Sagi Snir Department of Evolutionary and Environmental Biology, University of Haifa, Israel
One of the central and most fundamental, yet debated, concept of evolution is the Molecular Clock (MC) hypothesis, according to which each gene evolves at a characteristic, near constant rate. Numerous studies support the Molecular Clock hypothesis in principle but also show that the clock is indeed very dispersed. Genome-wide comparative analysis of thousands of genes across long evolutionary spans, reveals surprising and unexpected correlation of evolutionary rates of the different genes within each evolving genome. This correlation could be explained by a new model that we devised, denoted Universal PaceMaker (UPM) of genome evolution. The UPM model posits that the rate of evolution changes synchronously across genome-wide sets of genes in all evolving lineages. Alternatively, however, this correlation between the evolutionary rates of genes could be a simple consequence of MC. We sought to differentiate between the MC and UPM models by fitting these genes' histories in bacterial and archaeal species to supertrees that reflect the dominant trend of vertical descent in evolution and that were constrained according to the two models. The goodness of fit for the UPM model was better than the fit for the MC model, with overwhelming statistical significance, revealing a universal, genome-wide pacemaker of evolution that could have been in operation throughout the history of life. In the talk, I will discuss these and further efforts including very recent results in this direction. Based on joint works with Eugene Koonin and Yuri Wolf from the NIH Fast Computation of Evolutionary Distances between Genomes Bernhard Haubold Groupleader Bioinformatics, Honorarprofessor Universität zu Lübeck, Max-Planck-Institute for Evolutionary Biology, Department of Evolutionary Genetics, Room 254, August-Thienemann-Strasse 2, 24306 Ploen, Germany
Evolutionary distances are usually computed from alignments. These are difficult to construct for long sequences. Therefore, a number of highly efficient alignment-free methods for distance computation have been developed. However, most of them do not return the rate of substitution, the most widely used measure of evolutionary time. We have recently developed a fast metric, the anchor distance, that closely approximates the rate of substitution. It is implemented in our program andi, for ANchor DIstance, available from https://www.github.com/evolbioinf/andi andi takes as input sets of unaligned genomes and works best if these are diverged by less than 0.5 substitutions per site. For example, it computes all pairwise distances between 2010 E. coligenomes in just under 10 h on a machine with 32 CPUs and 20 GB of free RAM. In this talk I explain the anchor distance and demonstrate its usefulness though application to simulated and empirical genome data from plants and bacteria.
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Resolving the Phylogenetic Status and Taxonomic Relationships of the Hangul (Cervus elaphus hanglu) in the Family Cervidae Ved P. Kumar, Ankita Rajpoot, Dhyanendra Kumar and Surendra P. Goyal Wildlife Institute of India, Chandrabni, Dehardun, India
The Hangul (Cervus elaphus hanglu) is a ‘Least Concern’ deer species, and it is the only survivor of the Red Deer group in the Indian subcontinent. The phylogenetic status of the Hangul relative to the other members of the family Cervidae is not known because sequence data are not available in public databases. Therefore, this study was carried out to determine the phylogenetic status and delineate the genetic boundaries of the Hangul with respect to the other Red Deer subspecies on the basis of cytochrome b gene sequence data (ca 421 bp). There are three major monophyletic groups of the Red Deer in the phylogenetic tree, which are referred to as the western (Hap-01 to Hap-10), eastern (Hap-11 to Hap-20) and tarim (Hap-21 to Hap-25) groups. The overall haplotype diversity and per-site nucleotide diversity were 0.9771 (±0.0523) and 0.0388 (±0.00261), respectively. In the phylogenetic tree, the Hangul clustered with the tarim group (Yarkand and Bactrian deer) with a strong bootstrap support (92%) and was found to be genetically closer to the Bactrian Deer than to the Yarkand Deer. Our molecular analysis supported the idea that the Hangul diverged from the Bactrian Red Deer and migrated to India from Tajikistan approximately 1.2 MYA. Keywords: Hangul, phylogenetic tree, mtDNA, cytochrome b gene, immigration.
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N 1 Measuring Introgression Between Plants with Contrasting Mating Systems Crispin Y. Jordan and Richard A. Ennos University of Edinburgh
Studies of introgression between species with different mating systems can provide insight into speciation. Highly self-fertilizing species frequently evolve from outcrossing ancestors, and their respective traits will determine patterns of introgression: differences in reproductive traits will govern the mating process, and their genomic qualities (e.g., segregation distortion) may affect post-pollination processes that influence introgression. We used ddRAD sequencing to describe introgression between the selfing and outcrossing plant species, Geum urbanum and G. rivale, respectively, which form hybrid swarms throughout the UK. We sampled individuals from “pure” populations of each species, as well as 39 populations where introgression seemed likely to occur. Preliminary STACKS analyses confirm basic expectations for patterns of genetic variation: pure populations of G. rivale have more than twice the number of snps as G. urbanum (e.g., 12676 vs 4890 for ~5000 loci, each), and lower population structure (G. rivale mean Fst = 0.03; G. urbanum mean Fst = 0.15). However, preliminary fastStructure analyses suggest a lack of introgression between these two species, supporting previous conclusions that strong selection on hybrids reduces gene flow. We will present more complete analyses that utilize a new draft genome assembly for G. urbanum.
N 2 Separation of the Taxol-Producing Capacity in The Genus Colletotrichum from the Molecular Evolution Events Jinhee Choi1,2, Seong Jin Choi3 and Kwang-Hyun Baek1,2 1Institute of Biotechnology 2School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, South Korea 3Department of Biotechnology, Catholic University of Daegu, Gyeongsan, Gyeongbuk 712-702, South Korea A potent anticancer agent taxol (paclitaxel) has been used to treat various cancers. Taxol was first isolated from Taxus species in 1971 however, after isolating a fungal species Taxus andreanana producing taxol in 1993, many endophytes have been identified as taxol-producing fungi. In our research finding taxol-producing fungi from various sources, including endophytes, plant pathogens and food-derived fungi, we intensively studied taxol-product from a genus Colletotrichum which are fungi causing serious plant diseases. Many of Colletotrichum spp. were equipped with the gene of taxadiene synthase (TS), which cyclizes geranylgeranyl diphosphate to produce taxadiene, the unique skeletal core structure of paclitaxel and the first committed step for initialization of the synthesis of taxol. The detection was done by a simple PCR with several pairs of PCR primers. The production of taxol in the TS-equipped fungi was confirmed positive using LC/MS. Some of Colletotrichum spp. have evolved to contain the gene of taxadiene synthase and produce taxol, however the distribution of the TS gene is not limited to closely related species in the Colletotrichum genus. Our data clearly suggest that TS gene integration and taxol-producing in Colletotrichum follows species-specific pattern with random integration of the gene into the genomes of Colletotrichum species.
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N 3 Revaluation of taxonomy of the genus Soldanella section Soldanella in Carpathians and adjacent regions Eliska Stubnova, Iva Hodalova, Judita Kochjarova, Jaromir Kucera, Andrea Plecenikova, Milan Valachovic and Marek Slovak Institute of Botany, Slovak Academy of Sciences, Dubravska cesta 9, 845 23 Bratislava, Slovakia Genus Soldanella (Primulaceae) is one of the most striking genera of the mountain plants endemic to Europe. Evolutionary relationships of Soldanella taxa are not conveniently resolved and their current taxonomic concepts are highly contradictive. The aim of our study is to investigate and revaluate evolutionary relationships and taxonomy of members from the genus Soldanella section Soldanella with special focus on Carpathian bioecological region. Asked questions will be solved using combination of detail morphological (multivariate morphometrics), karyological (flow cytometry), genetic analyses (RAD-seq) as well as autecological features at the population level. Preliminary results of karyological analyses revealed that analysed taxa (S. angusta, S. carpatica, S. hungarica, S major, S. montana, S pseudomontana and S. oreodoxa) are uniformly diploids (2n=2x=40) with absolute DNA content varying from 2C = 3.3 to 3.5 pg. Morphological evolutions indicates existence of three main morphotype groups what is only partly congruent with current taxonomic concepts. Molecular analyses are under progress.
N 4 Population Genetic Structure of Endemic Verbascum Alyssifolium in Erzincan Region of Turkey Muhip Hilooğlu1, Emel Sözen1, Ali Kandemir2 1Department of Biology, Faculty of Science, Anadolu University, 26470, Eskisehir, Turkey 2Department of Biology, Faculty of Science and Art, Erzincan University, 2400, Erzincan, Turkey Verbascum alyssifolium is endemic species having considerable narrow distribution in Erzincan (Turkey) Region. Genetic diversity in three natural populations of V. alyssifolium was investigated by ISSR markers. Twenty primers amplified a total of 390 bright and discernible bands of 200–3000 bp, of which 389 bands (P = 99.74%) were polymorphic in 3 populations. The genetic diversity was high at the populations level; the effective number of alleles (Ne) was 1.4107, and the difference value between observed number of alleles (Na) was 1.9974 and the Nei’s genetic diversity (H) was 0.2651, and the Shannon’s information index (I) was 0.4206 and a high level of gene flow (Nm = 4.407) were observed. Analysis of molecular variance showed that 12% of the total genetic diversity resided among populations, while 88% within the populations, in line with low the gene differentiation coefficient (GST = 0.0947). The low genetic differentiation among populations implies that the conservation efforts should aim to preserve all the extant populations of this endangered species. Keywords: Genetic diversity, ISSR, Endemic, Verbascum alyssifolium
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List of Poster Presentations
Poster number. Author and title
Page in
abstract
book
Poster № 1. Crispin Y. Jordan. Measuring Introgression Between Plants with Contrasting Mating Systems
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Poster № 2. Jinhee Choi. Separation of the Taxol-Producing Capacity in The Genus Colletotrichum from the Molecular Evolution Events
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Poster № 3. Marek Slovak. Revaluation of taxonomy of the genus Soldanella section Soldanella in Carpathians and adjacent regions
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Poster № 4. Muhip Hilooğlu. Population Genetic Structure of Endemic Verbascum Alyssifolium in Erzincan Region of Turkey
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List of Participants
Adam Nora Molecular Ecology, Max Planck Institute
For Chemical Ecology, Jena, Germany [email protected]
Alshaye Najla College Of Science, Biology Department,
Riyadh, Saudi Arabia [email protected]
Buckley James Institute Of Integrative Biology, Zürich,
Switzerland [email protected]
Choi Jinhee Institute Of Biotechnology
Gyeongsan, Gyeongbuk, Korea South [email protected]
CUI Zhenling China Agricultural University, CHINA
De Matthaeis Elvira Dep. Biology Biotechnology C. Darwin ,
Zoology Section, Rome [email protected]
Eyre-Walker Adam University Of Sussex, Uk
Gallart Marta Center For Integrative Ecology, School Of Biology, University Of Canterbury,
New Zealand [email protected]
Grauda Dace Institute Of Biology University Of Latvia,
Salaspils, Latvia [email protected]
Gruenstaeudl Michael The Ohio State University, Columbus,
Haubold Bernhard Max-Planck-Institute For Evolutionary
Biology, Plön, Germany [email protected]
Hilooðlu Muhip Anadolu University, TURKEY [email protected]
Hou Yan University of Oslo, NORWAY
Ingvarsson Pär Umea University, Umea, Sweden
[email protected] [email protected]
Jordan Crispin Institute Of Evolutionary Biology,
University Of Edinburgh, Edinburgh, United Kingdom
Kilian Andrzej Diversity Arrays Technology Pty,
Australia [email protected]
Kristensen Torsten Nygaard Department Of Chemistry And
Bioscience, Aalborg University, Aalborg, Denmark
Lanfear Robert Department Of Biological Sciences, Macquarie University, North Ryde,
Australia [email protected]
Mable Barbara Institute Of Biodiversity, Animal Health
& Comparative Medic, Glasgow, UK [email protected]
Ophir Ron Aro, Bet-Dagan, Israel
Rashal Isaak Institute Of Biology University Of Latvia,
Salaspils, Latvia [email protected]
Singh Tanya University Of Pennsylvania, Usa
Slovak Marek Institute Of Botany, Slovak Academy Of
Sciences, Bratislava, Slovakia [email protected]
Snir Sagi University Of Haifa, Israel
Ssebbagala Ibrahim Fresh Mind College, Uganda
Städler Thomas Institute Of Integrated Biology (Ibz), Eth
Zurich, Zurich, Switzerland [email protected]
Stasolla Claudio Plant Science, University Of Manitoba,
Winnipeg, Canada [email protected]
Teng Yuanwen College Of Agriculture And
Biogechnology, China [email protected]
Tumwesigire Clever Great Minds College, Uganda
Vuilleumier Severine University Of Lausanne, Switzerland
Zimmer Elisabeth Department Of Botany, National Museum Of Natural History, Usa
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