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Elena Kochieva
Center “Bioengineering” RAS
Department of Genetic Engineering

Pisum genome variability detected by AFLP and RGA profiling


Author(s): Kochieva, EZ, Dyachenko, EA


Pea (P. sativum L.) is an important legume grown and consumed extensively worldwide. In the present study for the first time two different multiloci techniques - AFLP and RGA-profiling have been used for genetic diversity assessment and taxa boundaries delimitation in Pisum species. RGA-profiling technique was used to determine NBS-LRR plant pathogen resistance genes polymorphism. In contrast, AFLP technique allows to investigate mostly evolutionary neutral genome sequences. Both approaches can provide comprehensive genome diversity information. Genetic diversity of 110 Pisum accessions of different origin representing P. fulvum and P. sativum species, including abyssinicum, asiaticum, transcaucasicum and arvense accessions with unclear taxonomic status was analyzed using AFLP and RGA- profiling. By using preselected primer combinations 405 AFLP and 171 RGA polymorphic bands have been detected. As a result, for each pea genotype unique AFLP and RGA-specific patterns have been revealed. The dendrogram and PCA based on calculated GD values revealed two distinct groups corresponding to P. sativum and P. fulvum. Other taxa formed one mixed group with P. sativum accessions. Notably, on AFLP, PCA-plot all P. sativum formed continuum with two main poles, largely represented Asian or European accessions. On RGA-profiling PCA-plot, no geographical and taxonomical differentiations within P.sativum accessions were determined. No correlation between pea accession grouping and resistance status or ability to interact with arbuscular mycorrhiza was found. Obtained data suggested that genus Pisum is composed only of two clear species: P. sativum and P. fulvum. There is no differentiation between abyssinicum, asiaticum, arvense, transcaucasicum and sativum,that confirm their subspecies taxonomic status. Molecular characterization of Pisum genetic diversity levels may help to identify potential new sources useful in pea breeding. The work was supported by FRP "Biological Diversity".

Isa Pais
Instituto Gulbenkian de Ciência

A first genetic study of Microcebus tavaratra, a little known mouse lemur from the north of Madagascar


Author(s): Pais, IGA, Salmona, J, Kun-Rodrigues, C, Viana Meyler, S, Rabarivola, C, Mohamed-Thani, I, Chikhi, L


Madagascar is one of the most important Biodiversity Hotspots in the world. Still, many areas are poorly studied, as is the case of Daraina in the north of the island. In 2010, the highly fragmented forests of this region were surveyed, and the presence of several individuals belonging to the mouse lemur genus (Microcebus) was recorded. In the field, it proved difficult to identify the species encountered by using morphometric measurements, and mitochondrial DNA (mtDNA) was sequenced. Furthermore, seven nuclear loci (microsatellites) were genotyped. Altogether three mtDNA regions (COII, Cyt b and D-loop) were sequenced for 72 Microcebus individuals sampled in three forest fragments (Binara, Solaniampilana and Bekaraoka), in order to determine if all members belonged to the same species (M. tavaratra) as two individuals previously identified in this same region by other researchers. We also wanted to describe the patterns of genetic diversity of the sampled populations and determine if genetic clusters could be identified and potentially associated to specific features of the habitat, such large rivers or roads. The results suggest that all individuals belong to the M. tavaratra species and that high genetic variation at the nuclear level is maintained in all three populations. The same is observed at the mitochondrial level, with the exception of the population from Binara, which surprisingly did not present any genetic diversity across all mtDNA loci. Moreover, no clear clustering could be defined at the nuclear level, possibly due to the limited number of loci. Despite being currently the most geographically widespread study on Microcebus from Daraina, our results suggest that more research should be carried out across the whole region by increasing both the number of samples and loci. Studies like this one are important for the implementation of appropriate and effective conservation plans for threatened species.

Mehrnoush Panahi
Institute of Botany, Faculty of Biology, University of Warsaw
Systematics and Plant Geography

A phylogeny of subtribe Ferulinae (tribe Scandiceae, Apiaceae) inferred from nuclear rDNA ITS and cpDNA (rps16, rpoC1 introns and rpoB-trnC spacer) sequence variation


Author(s): Panahi, M, Spalik, K, Banasiak, Ł


Phylogenetic relationships within Apiaceae tribe Scandiceae subtribe Ferulinae were investigated using sequence data from the chloroplast DNA and nuclear ribosomal DNA internal transcribed spacer (ITS) regions. One hundred and seventy-six accessions were examined, representing the genera of the subtribe (Ferula, Dorema, Leutea) and outgroup taxa. The cpDNA markers included three non-coding loci: rpoB-trnC intergenic spacer, rps16 intron and rpoC1 intron. These loci were analyzed separately and combined to assess their relative utility for resolving relationships. Partition homogeneity tests yielded trees that demonstrated the incongruency between cpDNA and nrDNA regions. Among the loci examined, rps16 intron showed less variability relative to its size than the other used cpDNA markers. Phylogenies derived from maximum parsimony and Bayesian analyses of combined cp and nr DNA sequences for 156 accessions (representing 114 species of Ferula, 6 species of Dorema, 9 species of Leutea and 10 outgroup taxa) were resolved to some extent. Based on these analyses, Dorema is nested within Ferula and should be therefore subsumed within the latter. In contrast, Leutea appears to be in a sister position to Ferula and should be retained as a separate genus. Subtribe Ferulinae is diversified in central Asia, floristically encompassing the central and eastern part of the Irano-Turanian Floristic Region where the representatives of nearly all major groups occur, with the notable exception of two groups that are mostly distributed in the Mediterranean region and in China. However, since the species boundaries in Ferula are not clear, one may also suspect that the high number of species, particularly of the central Asiatic endemics, may have resulted from taxonomic splitting rather than rapid radiation of the genus in this region.

Isabel Liberal
Real Jardín Botánico (CSIC)
Departament of Biodiversity and Conservation

Accommodating hybrid/introgressed lineages in the multispecies coalescent: the complex evolutionary history of Antirrhinum unraveled


Author(s): Liberal, IM, Blanco-Pastor, J, Pfeil, BE, Vargas, P


Antirrhinum L. (snapdragons; c. 25 spp.) is an Old World plant genus primarily distributed in the western Mediterranean basin. Antirrhinum exhibits many interesting ecological and morphological features. Active research has been undertaken on pollination biology and biogeography and some species (mainly Antirrhinum majus L.) have been traditionally much appreciated due to its ornamental value as well as to its importance as a model system for molecular floral development. In spite of this research attention, and regardless the extensive efforts made, the phylogenetic relationships within the genus are far from being well resolved. Previous phylogenetic analyses failed to infer species relationships within the genus. The difficulty in defining species boundaries and the low phylogenetic resolution suggested an early rapid diversification of the genus. Under this scenario, processes obscuring phylogenetic reconstruction such as hybridization/introgression and/or incomplete lineage sorting are likely to have occurred. Moreover, hybridization processes in field and under controlled conditions were previously reported in several Antirrhinum species. In order to obtain accurate phylogenetic relationships within Antirrhinum we obtained allelic data from two low-copy nuclear genes and three plastid loci. We carried out coalescent-based simulations to distinguish hybridization from coalescent stochasticity. Additionally, we incorporated hybrids/introgressed species in the multispecies coalescent model by using a multilabelling approach in which a lineage of hybrid origin is represented with two sources of parental contribution. This methodology allowed the accurate reconstruction of complex evolutionary patterns that have occurred in this group of species extensively used for evolutionary research.

Praveen Karanth
Indian Institute of Science
Centre for Ecological Sciences

An island called India: Phylogenetic patterns across multiple taxonomic groups reveal endemic radiations


Author(s): Karanth, P


The Indian subcontinent is an interesting biogeographical entity as it is isolated from the rest of the Asian landmass by very high mountain ranges like the Himalayas in the north and is surrounded by ocean in the south. Furthermore much of this landmass was part of a Gondwanan fragment that merged with Asia around 35-55 mya. Thus Indian subcontinent has witnessed prolonged periods of isolation and continues to be largely cut off from much of Asia. In this regard the subcontinent is very similar to an island separated from the mainland (Asia). One interesting feature of an isolated island is the presence of endemic radiations, i.e., unique clades of taxa whose members are endemic to the island. Recent phylogenetic studies have revealed that India also harbors numerous endemic radiations and these endemic assemblages were generated through in-situ diversification. Thus to this day India is very similar to an isolated island. It is interesting to contrast the Indian scenario with Madagascar an island with which India shares a geological past. Furthermore these finding have important implications for ecological and evolutionary studies on Indian biota.

Magdalena Herdegen
Jagiellonian University
Institute of Environmental Sciences

Analysis of population structure of guppies in north-eastern Venezuela, the area of putative incipient speciation


Author(s): Herdegen, M, Alexander, H, Babik, W, Radwan, J, Mavárez, J, Breden, F


Geographic barriers to gene flow are one of the main causes of genetic isolation. Reproductive isolation often follows, which in turn may lead to speciation. The guppy from the Cumaná region of Eastern Venezuela has been previously described as a case of incipient speciation, significantly differentiated from the common guppy, Poecilia reticulata, which occurs on the other side of Cordillera de la Costa in streams belonging to the Orinoco drainage. Here, we present a comprehensive analysis of differentiation between guppy populations in these two regions of Eastern Venezuela based on mtDNA and a set of 15 microsatellites. We also analyse four phenotypic traits which have been found in earlier work to differ between the Cumaná and common guppy. Guppies inhabiting the two regions divided by Cordillera de la Costa indeed show significant genetic differentiation, but most genetic variation was distributed among populations within regions. Most guppies in the Cumaná region had mtDNA from a distinct lineage, but we also found evidence for a widespread introgression of mtDNA from the Orinoco drainage into the Cumaná region. Populations from the two regions differed significantly in the number of black crescents, but not in other phenotypic traits analysed. Overall, our findings are consistent with only partial genetic isolation between the two geographic regions. Gene flow from the Orinoco drainage may have caused the loss of typical Cumaná morphology in many populations.

Joana Marques
Lund University
Department of Biology

Are the divergent migration destinations of Bogong moths Agrotis infusa (Noctuidae: Lepidoptera) related to genetic differentiation?


Author(s): Marques, JF, Heinze, S, Fatarova, M, Svensson, GP, Anderbrant, O, Green, K, Warrant, E


Long-distance seasonal migration mechanisms are still unclear, albeit their importance to species persistence and ecosystem functioning. Many populations have well defined migratory destinations and this might have important consequences on their genetic structuring: whereas different breeding grounds and divergent migratory pathways and destinations may result in a lower degree of genetic mixing hence promoting genetic differentiation, the use of common breeding and overwintering/summering grounds may result in a lack of genetic differentiation. Every spring, adult Australian Bogong moths (Agrotis infusa) migrate from western New South Wales and south-eastern Queensland to the Snowy Mountains (the highest peaks of the Great Dividing Range) to estivate in cool rock crevices and caves; they then return to their breeding grounds during the autumn to mate. During estivation, the moths are gregarious and remain in diapause serving as food for many insectivorous animals given their high body fat content (around 65%). Owing to their different summering sites, some may fly up to 1000 km in a single direction. Although some attempts to use genetic markers to identify specific natal sites of adult Bogong moths have been made, it is still unknown whether the different migratory pathways and destinations have a genetic basis. In summer 2012-2013, Bogong moths were collected live by hand at four estivation sites in New South Wales (Mount Gingera, South Ramshead, Mount Morgan, and Mount Tingaringy) and examined for sequence and haplotype diversity and genetic distance at mitochondrial and nuclear genes. The data will elucidate if differences in the migration routes and summering sites of these moths depend on—or have resulted in—genetic divergence, which will be essential for Bogong moth conservation. The Bogong moth is an iconic Australian species and the protection of their summering sites may be crucial to maintain species variability.

Ângela Ribeiro
University of Porto
CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental

Coagulation cascade: an evolutionary perspective across vertebrates


Author(s): Ribeiro, ÂM, Zepeda, L, Gilbert, T, Da Fonseca, RR


Blood coagulation is a defense mechanism that enhances organism survival by preventing uncontrolled blood loss in vertebrates. This defense mechanism has to be tightly controlled so the clot forms when and where it is required. Birds exhibit prolonged coagulation time relative to values obtained for mammals. The prolonged coagulation time phenotype observed in birds is shared with reptiles, and within Aves an inter-specific variation has also been described. Despite biochemically and physiologically extensively studied, our understanding about the evolution of the coagulation network in vertebrates is still lagging. Given the increasing availability of genomic-level data we set to uncover the evolutionary story of this fine-tuned network, with a particular emphasis in Aves. The human transcripts for eighteen genes known to encode proteins associated with coagulation response were blasted against the protein coding genes of extant vertebrates available from genomic databases. We included mammals, birds, reptiles, amphibians and fishes. The orthologous proteins were aligned, coverage and protein identity estimated. We found that the clotting cascade in birds involves fewer genes than the mammalian one. The main difference uncovered pertains the membrane receptors from platelet (mammals)/thrombocytes (non-mammals). We propose that the mammalian innovations, i.e. factors only present in mammals, stem for the platelet ability to form resistant clots. And we put forward, that this might be an efficient mechanism for fast and effective control of bleeding from the placental site to prevent fatal hemorrhage during delivery.

Eduardo Marabuto
Faculty of Sciences, University of Lisbon
Department of Animal Biology

Comparative phylogeography and genetic population structure of two butterfly species from the Iberian Peninsula


Author(s): Marabuto, E, Martins, R, Silva, DN, Seabra, SS, Paulo, OS


The Iberian Peninsula is recognized as one of the most important refugia for temperate species during the cyclic climatic changes of the Plio-Pleistocene glacial periods. Mountainous regions within these refugia areas are also believed to retain high levels of endemism and genetic diversity due to the easily tracked suitable habitats by upward-downward movements. Here we examine population genetic structure, phylogeographic and demographic patterns of Lycaena bleusei, a butterfly species endemic to the Central Iberian Mountain System and contrast this to the patterns found for a congeneric widespread species, also occurring in the Iberian Peninsula, Lycaena tityrus. We use two molecular markers to understand if there is congruency in their evolutionary histories or, conversely, if different evolutionary drivers may have shaped these species differently. We find that the two species, which exhibit similar dispersal abilities and ecological requirements, show different demographic and genetic patterns. We hypothesize that these differences are due to the evolutionary forces acting on species that contracted to southern refugia during the Pleistocene and that, ultimately, drove to population differentiation and speciation. We also find evidence for hybridization events between these two species, with L. bleusei males coming in contact with L. tityrus females on a secondary contact zone described here for the first time.

Eva Jimenez-Guri
Centre de Regulacio Genomica
Biologia de Sistemes

Comparative transcriptomics of early Dipteran development


Author(s): Jimenez-Guri, E, Huerta-Cepas, J, Cozzuto, L, Wotton, KR, Roma, G, Gabaldon, T, Jaeger, J


We are carrying out a comparative analysis of transcriptomic sequence data in early embryos of three emerging experimental dipteran model systems. Clogmia albipunctata belongs to a lineage of flies believed to have diverged early in the evolution of the dipterans, while the lineage leading to Megaselia abdita branched intermediately, at the base of the cyclorraphans, and the lineage leading to Episyrphus balteatus diverged later in the cyclorraphans.

We have acquired and assembled transcriptomic sequences at early embryonic stages in Clogmia albipunctata and Megaselia abdita. We compare these sequences to those from Episyrphus balteatus as well as transcriptomic and genomic sequences from drosophilids and/or mosquitoes. These datasets form the basis of a new phylogenomic assessment of dipteran relationships. It places psychodid moth midges (such as Clogmia) as a sister group to the brachycerans, rather than within the culicomorph lineage, in contrast to another recent study (Wiegman et al., 2011). Furthermore, we have analysed patterns of gene duplication in our datasets. Finally, we have verified information present in our transcriptomes by manual curation, in situ hybridization, and verification of alternative splicing events among a subset of genes present in the data.


Chairman: Octávio S. Paulo
Tel: 00 351 217500614 direct
Tel: 00 351 217500000 ext22359
Fax: 00 351 217500028


XIV Congress of the European Society for Evolutionary Biology

Organization Team
Department of Animal Biology (DBA)
Faculty of Sciences of the University of Lisbon
P-1749-016 Lisbon


Computational Biology & Population Genomics Group