Browsing by Subject "AFLP"

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  • Van Steenberge, Maarten; Raeymaekers, Joost Andre Maria; Hablützel, Pascal Istvan; Vanhove, Maarten Pieterjan Maria; Koblmüller, Stephan; Snoeks, Jos (2018)
    BackgroundSpecies delineation is particularly challenging in taxa with substantial intra-specific variation. In systematic studies of fishes, meristics and linear measurements that describe shape are often used to delineate species. Yet, little is known about the taxonomic value of these two types of morphological characteristics. Here, we used Tropheus (Teleostei, Cichlidae) from the southern subbasin of Lake Tanganyika to test which of these types of characters best matched genetic lineages that could represent species in this group of stenotypic rock-dwelling cichlids. We further investigated intra-population variation in morphology. By linking this to a proxy of a population's age, we could assess the evolutionary stability of different kinds of morphological markers.ResultsMorphological data was collected from 570 specimens originating from 86 localities. An AFLP approach revealed the presence of five lineages in the southern subbasin: T. moorii, T. brichardi, T. sp. maculatus', T. sp. Mpimbwe' and T. sp. red', which we consider to represent distinct species. Although both types of morphological data supported this classification, a comparison of P-ST-values that describe inter-population morphological differentiation, revealed a better correspondence between the taxon delineation based on AFLP data and the patterns revealed by an analysis of meristics than between the AFLP-based taxon delineation and the patterns revealed by an analysis of shape. However, classifying southern populations of Tropheus was inherently difficult as they contained a large amount of clinal variation, both in genetic and in morphological data, and both within and among species. A scenario is put forward to explain the current-day distribution of the species and colour varieties and the observed clinal variation across the subbasin's shoreline. Additionally, we observed that variation in shape was larger in populations from shallow shores whereas populations from steep shores were more variable in meristics. This difference is explained in terms of the different timescales at which small and large scale lake level fluctuations affected populations of littoral cichlids at steep and shallow shores.ConclusionsOur results showed meristics to be more evolutionary stable, and of higher taxonomic value for species delimitation in Tropheus, than linear measurements that describe shape. These results should be taken into account when interpreting morphological differences between populations of highly stenotypic species, such as littoral cichlids from the Great East African Lakes.
  • Van Steenberge, Maarten; Raeymaekers, Joost A M; Hablützel, Pascal I; Vanhove, Maarten P M; Koblmüller, Stephan; Snoeks, Jos (BioMed Central, 2018)
    Abstract Background Species delineation is particularly challenging in taxa with substantial intra-specific variation. In systematic studies of fishes, meristics and linear measurements that describe shape are often used to delineate species. Yet, little is known about the taxonomic value of these two types of morphological characteristics. Here, we used Tropheus (Teleostei, Cichlidae) from the southern subbasin of Lake Tanganyika to test which of these types of characters best matched genetic lineages that could represent species in this group of stenotypic rock-dwelling cichlids. We further investigated intra-population variation in morphology. By linking this to a proxy of a population’s age, we could assess the evolutionary stability of different kinds of morphological markers. Results Morphological data was collected from 570 specimens originating from 86 localities. An AFLP approach revealed the presence of five lineages in the southern subbasin: T. moorii, T. brichardi, T. sp. ‘maculatus’, T. sp. ‘Mpimbwe’ and T. sp. ‘red’, which we consider to represent distinct species. Although both types of morphological data supported this classification, a comparison of PST-values that describe inter-population morphological differentiation, revealed a better correspondence between the taxon delineation based on AFLP data and the patterns revealed by an analysis of meristics than between the AFLP-based taxon delineation and the patterns revealed by an analysis of shape. However, classifying southern populations of Tropheus was inherently difficult as they contained a large amount of clinal variation, both in genetic and in morphological data, and both within and among species. A scenario is put forward to explain the current-day distribution of the species and colour varieties and the observed clinal variation across the subbasin’s shoreline. Additionally, we observed that variation in shape was larger in populations from shallow shores whereas populations from steep shores were more variable in meristics. This difference is explained in terms of the different timescales at which small and large scale lake level fluctuations affected populations of littoral cichlids at steep and shallow shores. Conclusions Our results showed meristics to be more evolutionary stable, and of higher taxonomic value for species delimitation in Tropheus, than linear measurements that describe shape. These results should be taken into account when interpreting morphological differences between populations of highly stenotypic species, such as littoral cichlids from the Great East African Lakes.
  • Klingenberg, Daniela (Helsingfors universitet, 2011)
    The bacterial genus Stenotrophomonas comprises 12 species. They are widely found throughout the environment and particularly S. maltophilia, S. rhizophila and S. pavanii are closely associated with plants. Strains of the most common Stenotrophomonas species, S. maltophilia, promote plant growth and health, degrade natural and man-made pollutants and produce biomolecules of biotechnological and economical value. Many S. maltophilia –strains are also multidrug resistant and can act as opportunistic human pathogens. During an INCO-project (1998-2002) rhizobia were collected from root nodules of the tropical leguminous tree Calliandra calothyrsus Meisn. from several countries in Central America, Africa and New Caledonia. The strains were identified by the N2-group (Helsinki university) and some strains turned out to be members of the genus Stenotrophomonas. Several Stenotrophomonas strains induced white tumor- or nodule-like structures on Calliandra?s roots in plant experiments. The strains could, besides from root nodules, also be isolated from surface sterilized roots and stems. The purpose of my work was to investigate if the Stenotrophomonas strains i) belong to a new Stenotrophomonas species, ii) have the same origin, iii) if there are other differences than colony morphology between phase variations of the same strain, iv) have plant growth-promoting (PGP) activity or other advantageous effects on plants, and v) like rhizobia have ability to induce root nodule formation. The genetic diversity and clustering of the Stenotrophomonas strains were analyzed with AFLP fingerprinting to get indications about their geographical origin. Differences in enzymatic properties and ability to use different carbon and energy sources were tested between the two phases of each strain with commercial API tests for bacterial identification. The ability to infect root hairs and induce root nodule formation was investigated both using plant tests with the host plant Calliandra and PCR amplification of nodA and nodC genes for nodulation. The PGP activity of the strains was tested in vitro mainly with plate methods. The impact on growth, nitrogen content and nodulation in vivo was investigated through greenhouse experiments with the legumes Phaseolus vulgaris and Galega orientalis. Both the genetic and phenotypic diversity among the Stenotrophomonas strains was small, which proposes that they have the same origin. The strains brought about changes on the root hairs of Calliandra and they also increased the amount of root hairs. However, no root nodules were detected. The strains produced IAA, protease and lipase in vitro. They also showed plant a growth-promoting effect on G. orientalis, both alone and together with R. galegae HAMBI 540, and also activated nodulation among efficient rhizobia on P. vulgaris in greenhouse. It requires further research to get a better picture about the mechanisms behind the positive effects. The results in this thesis, however, confirm earlier studies concerning Stenotrophomonas positive impact on plants.
  • L’opez, Sara C; Theelen, Bart; Manserra, Serena; Issak, Tedros Y; Rytioja, Johanna; Mäkelä, Miia R; de Vries, Ronald P (BioMed Central, 2017)
    Abstract Dichomitus squalens is a white-rot fungus that colonizes and grows mainly on softwood and is commonly found in the northern parts of Europe, North America, and Asia. We analyzed the genetic and physiological diversity of eight D. squalens monokaryons derived from a single dikaryon. In addition, an unrelated dikaryon and a newly established dikaryon from two of the studied monokaryons were included. Both growth and lignocellulose acting enzyme profiles were highly variable between the studied monokaryotic and dikaryotic strains, demonstrating a high level of diversity within the species.
  • Qaderi, Ardashir; Omidi, Mansour; Pour-Aboughadareh, Alireza; Poczai, Péter; Shaghaghi, Javad; MehrAfarin, Ali; Nohooji, Majid Ghorbani; Etminan, Alireza (2019)
    In the present investigation, 72 accessions of the Iranian poppy (Papaver bracteatum Lindl.) were analyzed for genetic diversity and population structure using start codon targeted polymorphism (SCoT) and inter simple sequence repeat (ISSR) markers along with four important phytochemical traits to provide baseline knowledge for the Iranian poppy’s breeding and conservation plans. Twelve ISSR and thirteen SCoT primers generated a total of 98 and 186 fragments with a mean of 8.17 and 14.31 fragments per primer, respectively. Polymorphic information content for ISSR and SCoT primers ranged from 0.39 to 0.45 and 0.28 to 0.34, with the resolving power ranging from 21.61 to 3.97 and 13.08 to 28.02, respectively. Neighbour-joining (NJ) based clustering grouped 72 accessions into three main groups based on two markers studied (ISSR and SCoT) and the combined data (ISSR + SCoT), which associated with their eco-geographical regions. Population structure based analysis divided 72 accessions into 3 subpopulations using ISSR markers, when SCoT was used eight subpopulations were observed. However, when the combined data was used only three subpopulations were found, which corresponded to the grouping observed with the NJ method and these results were supported by principal coordinate analyses (PCoA). Phytochemical analysis revealed that plant capsule has higher total amounts of the alkaloids; thebaine, morphine and oripavine than stem tissues. Interestingly, for the geographical parameters, latitude showed a significant and positive correlation with thebaine extracted from both stem and capsules and the regression results confirmed these associations. Taken together, our results indicated that three populations Ploor, Eil-Teymoor and Anjomane due to their high contents of alkaloids like thebaine as well as the Taham population due to its high content of morphine and oripavine have a strong enough potency to be used in the pharmacy industry.
  • Seppä, Perttu; Bonelli, Mariaelena; Dupont, Simon; Hakala, Sanja Maria; Bagnères, Anne-Geneviève; Lorenzi, M. Cristina (2020)
    Simple Summary The co-evolution of hosts and parasites depends on their ability to adapt to each other's defense and counter-defense mechanisms. The strength of selection on those mechanisms may vary among populations, resulting in a geographical mosaic of co-evolution. The boreo-montane paper wasp Polistes biglumis and its parasite Polistes atrimandibularis exemplify this type of co-evolutionary system. Here, we used genetic markers to examine the genetic population structures of these wasps in the western Alps. We found that both host and parasite populations displayed similar levels of genetic variation. In the host species, populations located near to each other were genetically similar; in both the host and the parasite species populations farther apart were significantly different. Thus, apparent dispersal barriers (i.e., high mountains) did not seem to restrict gene flow across populations as expected. Furthermore, there were no major differences in gene flow between the two species, perhaps because P. atrimandibularis parasitizes both alpine and lowland host species and annually migrates between alpine and lowland populations. The presence of strong gene flow in a system where local populations experience variable levels of selection pressure challenges the classical hypothesis that restricted gene flow is required for local adaptations to evolve. The co-evolutionary pathways followed by hosts and parasites strongly depend on the adaptive potential of antagonists and its underlying genetic architecture. Geographically structured populations of interacting species often experience local differences in the strength of reciprocal selection pressures, which can result in a geographic mosaic of co-evolution. One example of such a system is the boreo-montane social wasp Polistes biglumis and its social parasite Polistes atrimandibularis, which have evolved local defense and counter-defense mechanisms to match their antagonist. In this work, we study spatial genetic structure of P. biglumis and P. atrimandibularis populations at local and regional scales in the Alps, by using nuclear markers (DNA microsatellites, AFLP) and mitochondrial sequences. Both the host and the parasite populations harbored similar amounts of genetic variation. Host populations were not genetically structured at the local scale, but geographic regions were significantly differentiated from each other in both the host and the parasite in all markers. The net dispersal inferred from genetic differentiation was similar in the host and the parasite, which may be due to the annual migration pattern of the parasites between alpine and lowland populations. Thus, the apparent dispersal barriers (i.e., high mountains) do not restrict gene flow as expected and there are no important gene flow differences between the species, which contradict the hypothesis that restricted gene flow is required for local adaptations to evolve.
  • Lonardi, Stefano; Muñoz-Amatriaín, María; Liang, Qihua; Shu, Shengqiang; Wanamaker, Steve I.; Lo, Sassoum; Tanskanen, Jaakko; Schulman, Alan H.; Zhu, Tingting; Luo, Ming-Cheng; Alhakami, Hind; Ounit, Rachid; Hasan, Abid Md.; Verdier, Jerome; Roberts, Philip A.; Santos, Jansen R.P.; Ndeve, Arsenio; Doležel, Jaroslav; Vrána, Jan; Hokin, Samuel A.; Farmer, Andrew D.; Cannon, Steven B.; Close, Timothy J. (2019)
    Cowpea (Vigna unguiculata [L.] Walp.) is a major crop for worldwide food and nutritional security, especially in sub-Saharan Africa, that is resilient to hot and drought-prone environments. An assembly of the single-haplotype inbred genome of cowpea IT97K-499-35 was developed by exploiting the synergies between single-molecule real-time sequencing, optical and genetic mapping, and an assembly reconciliation algorithm. A total of 519 Mb is included in the assembled sequences. Nearly half of the assembled sequence is composed of repetitive elements, which are enriched within recombination-poor pericentromeric regions. A comparative analysis of these elements suggests that genome size differences between Vigna species are mainly attributable to changes in the amount of Gypsy retrotransposons. Conversely, genes are more abundant in more distal, high-recombination regions of the chromosomes; there appears to be more duplication of genes within the NBS-LRR and the SAUR-like auxin superfamilies compared with other warm-season legumes that have been sequenced. A surprising outcome is the identification of an inversion of 4.2 Mb among landraces and cultivars, which includes a gene that has been associated in other plants with interactions with the parasitic weed Striga gesnerioides. The genome sequence facilitated the identification of a putative syntelog for multiple organ gigantism in legumes. A revised numbering system has been adopted for cowpea chromosomes based on synteny with common bean (Phaseolus vulgaris). An estimate of nuclear genome size of 640.6 Mbp based on cytometry is presented.