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".
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.
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.
A range-wide synthesis and timeline for phylogeographic events in the red fox (Vulpes vulpes)
Author(s): Kutschera, VE, Hailer, F
Many boreo-temperate mammals have a Pleistocene fossil record throughout Eurasia and North America, but only few have a contemporary distribution that spans this large area. Examples of Holarctic-distributed carnivores are the brown bear, grey wolf and red fox, all three ecological generalists with large dispersal capacity and a high adaptive flexibility. While the two former have been examined extensively across their ranges, no phylogeographic study of the red fox has been conducted across its entire Holarctic range. Moreover, no study included samples from central Asia, leaving a large sampling gap in the middle of the Eurasian landmass. We obtained the first mitochondrial DNA sequence data of red foxes from Siberia, and new sequences from several European populations. In a range-wide synthesis of more than 500 previously published and publicly available red fox mitochondrial control region sequences and 52 newly obtained sequences, we describe the pattern and timing of major phylogeographic events in red foxes, using a Bayesian coalescence approach with multiple fossil tip and root calibration points. All newly sequenced individuals belonged to the previously described Holarctic lineage. Our analyses confirmed the presence of three Nearctic- and two Japan-restricted lineages that were formed since the Mid/Late Pleistocene. The phylogeographic history of red foxes is highly similar to that previously described for grey wolves and brown bears, indicating that climatic fluctuations and habitat changes since the Pleistocene had similar effects on these highly mobile generalist species. All three species originally diversified in Eurasia and later colonized North America and Japan several times independently. North American lineages persisted through the last glacial maximum south of the ice sheets, meeting more recent colonizers from Beringia during postglacial expansion into the northern Nearctic.
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.
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.
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.
Department of Biological Science
Anchored Phylogenomics: Accelerating the Resolution of Life
Author(s): Lemmon, EM
The field of phylogenomics is undergoing a revolution, enabled by new methods of data collection that leverage both genomic resources and recent advances in DNA sequencing. We developed a cost-efficient and rapid approach to obtaining data from 100s to 1000s of loci and individuals for deep and shallow phylogenetic studies. Specifically, we designed probes for target hybrid enrichment of 100s of loci in conserved anchor regions of genomes (flanked by less conserved regions). We enriched genomic DNA libraries for these anchor regions, and sequenced these targets using high-throughput sequencing. The resulting data sets contain 100s of loci with low levels of missing data and high levels of phylogenetic information across taxonomic scales and produce phylogenies with high levels of resolution. This approach is expediting resolution of deep-scale portions of the Tree of Life and greatly accelerating resolution of the large number of shallow clades that remain unresolved. The combination of low cost (∼1% of the cost of traditional Sanger sequencing and ∼3.5% of the cost of high-throughput amplicon sequencing for projects on the scale of 500 loci × 100 individuals) and rapid data collection (∼2 weeks of laboratory time) make this approach tractable even for researchers working on systems with limited genomic resources. Here, I present new work from vertebrates and unpublished data from various non-vertebrate (e.g., Coleoptera, Hymenoptera, etc.) and plant (e.g., Angiosperm) clades; I also discuss future directions and new applications.
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.
Assessing the confounding effect of population structure on Bayesian skyline plot inferences of demographic history
Author(s): Heller, R, Chikhi, L, Siegismund, HR
It is well known that population structure can confound coalescent-based inferences of past population size changes when it is not properly accounted for. Although the vast majority of species are genetically structured to some extent, few studies have quantified how different types and levels of structure might confound demographic inference. Among the most widely applied demographic inference methods is the Bayesian skyline plot (BSP and the derived EBSP), which assume a panmictic model without structure. We simulated DNA sequence data under a variety of scenarios involving structured populations with variable levels of gene flow and analysed them using EBSPs as implemented in the software package BEAST. Results revealed that BSPs can show false signals of population decline under several biologically plausible combinations of population structure and sampling strategy, suggesting that the interpretation of several previous studies may need to be re-evaluated. We found that sampling strategies present a trade-off between minimizing the risk of false positives and maximizing the power to detect recent demographic events. Therefore, a balanced sampling strategy whereby samples are distributed over several populations provides the best scheme for inferring demographic change over the time scale that is typically of interest. Case studies demonstrate that although the structure effect should always be accounted for, some systems will be more susceptible than others. Our study provides a much-needed quantification of the structure effect in BSP analyses and some practical guidelines to keep in mind before attempting such analyses.