Hybridization and introgression in Carex aquatilis and C. paleacea

The diversification and distribution of Abies species throughout the Mediterranean region has led to a complex of species which are difficult to classify. An open question is whether these mainly allopatric taxa have exchanged genetic information via secondary contact. We studied the variation and geographic distribution of paternally inherited chloroplast DNA markers in nine Mediterranean Abies taxa. Markers with high and low mutation rates were applied in order to differentiate among a scenario of secondary genetic contact and a scenario of complete isolation after speciation. The observed molecular variation was analysed using statistical parsimony, geostatistics, and measures of population genetic differentiation. Ancient paternal lineages, represented by markers with low mutation rates, were shared among species. The central and widespread A. alba retained all ancient lineages whereas other species exhibited fewer, down to a single lineage. In contrast, modern lineages, depicted by markers with high mutation rates, were largely separated among species. The western Mediterranean A. pinsapo and A. numidica were clearly separated from each other and from the remaining Abies species. This indicates the absence of secondary contact. The same scenario applies to the eastern Mediterranean Abies species. An exception is the parapatric complex of A. alba, A. cephalonica, and their supposed hybrid A. borisii regis, which exhibited evidence of secondary contact.     

Mapping of within-species segregation distortion in Drosophila persimilis and hybrid sterility between D. persimilis and D. pseudoobscura

In contrast to the prevailing dogma in the 1990s, recent studies have suggested that an evolutionary history of segregation distortion within species may contribute to sterility in species hybrids. However, this recent work identified segregation distortion exclusively in species hybrids that may never have had an evolutionary history of segregation distortion in either parent species. We expand on previous work using a strain of Drosophila persimilis exhibiting segregation distortion within species to generate QTL maps for segregation distortion and hybrid sterility in crosses between D. persimilis and D. pseudoobscura. The maps localize regions along the XR contributing to both phenotypes, and they indicate one region of overlap between the two maps. This overlap could provide preliminary evidence for an association between segregation distortion within species and hybrid sterility, but the localizations are currently too broad to have confidence in this conclusion. This work is a first step towards possibly supporting a genetic conflict model of speciation in this system.     

The interplay of hybridization and clonal reproduction in the evolution of willows – Experiments with hybrids of S. eriocephala[R] & S. exigua[X] and S. eriocephala & S. petiolaris[P].

Clonal reproduction may contribute to plant evolution either by affecting population biology or by allowing partially sterile individuals (e.g., hybrids) repeated opportunities to reproduce sexually. The interplay of hybridization and clonal reproduction was first proposed by Stebbins (1950), but previously has not been tested experimentally. Alternative models for the effects of hybridization include speciation, introgression, and swamping. Salix spp. were chosen to test comparatively these hypotheses because they are easily hybridized and cloned. Over 500 separate crosses and backcrosses were made and over 6000 separate plants were measured in field experiments and statistically compared for significance to both evolutionary theory and plant breeding for biomass production. The F₁ hybrids in this study always equalled, and in the case of the hybrid PR, outperformed their parents in vegetative parameters. It seems likely that even without reproducing sexually, these F₁ hybrids could exist as successful individuals (sensu Stebbins 1950). However, it also seems likely that they would sexually reproduce: three of four F₁ hybrids studied (RX, RP, and PR) equalled or surpassed their parents in sexual parameters when crossing with at least one other accession. Of the alternative models, experimental data suggest that introgression would be the most likely outcome of a hybridization event. The hybrid XR, however, was partially sterile and performed poorly when crossing with all other accessions in its group except S. exigua (pistillate parent). Thus, this hybrid may fit Stebbins' model of a partially sterile yet vegetatively vigorous plant that can exist as a successful individual and make some contribution to interspecific gene flow over time. This is the first experimental study to confirm the evolutionary importance of clonal reproduction coupled with hybridization. However, distinguishing any of these evolutionary pathways would be difficult in nature using morphological techniques, as interspecific hybrids tend to resemble their pistillate parents in terms of leaf shape.     

Assessment and Maintenance of Unigametic Germline Inheritance for C. elegans

1. Download high-res image (213KB)
2. Download full-size image

     

Karyotypic, palynological, and RAPD study on 12 taxa from two subsections of section Idaeobatus in Rubus L. and taxonomic treatment of R. ellipticus, R. pinfaensis, and R. ellipticus var. obcordatus

Twelve taxa belonging to two subsections of section Idaeobatus in Rubus L. from southwestern China were characterized by karyotypic, palynological, and random amplified polymorphic DNA (RAPD) data as follows: (1) The 12 taxa were all diploid species (2n = 2x = 14), among which the chromosome counts for R. mesogaeus var. oxycomus, R. subtibetanus, R. ellipticus var. obcordatus, R. inopertus var. echinocalyx, and R. stans were reported for the first time; (2) All taxa except for R. ellipticus and R. pinfaensis could be distinguished from each other by karyotype, pollen morphology, and RAPD markers. Karyotypes were mainly characterized by the difference in numbers and positions of submetacentric chromosomes and chromosomes with satellited pair, the index of the karyotypic asymmetry, and the ratio of the longest to the shortest chromosome. Pollen morphology were mainly characterized by the discrepancy in specific pollen size, P/E ratio, colpi width, distance between the apices of two ectocolpi, and exine ornamentation characters. The cluster results based on RAPD markers were consistent with morphology classification except for R. pinfaensis; (3) Based on the general data of karyotypic, palynological, and RAPD, R. ellipticus var. obcordatus should be treated as a species R. obcordatus, R. ellipticus and R. pinfaensis should be combined as R. ellipticus, and it was more reasonable to place the combinants and R. obcordatus into subsection Stimulantes rather than into subsection Pungentes.     

Microsatellite mapping of genes that determine supernumerary spikelets in wheat (T. aestivum) and rye (S. cereale)

The wheat and rye spike normally bears one spikelet per rachis node, and the appearance of supernumerary spikelets is rare. The loci responsible for the ‘multirow spike’ or MRS trait in wheat, and the ‘monstrosum spike’ trait in rye were mapped by genotyping F₂ populations with microsatellite markers. Both MRS and the ‘monstrosum’ trait are under the control of a recessive allele at a single locus. The Mrs1 locus is located on chromosome 2DS, co-segregating with the microsatellite locus Xwmc453. The placement of flanking microsatellite loci into chromosome deletion bin 2DS-5 (FL 0.47–1.0) delimited the physical location of Mrs1 to the distal half of chromosome arm 2DS, within the gene rich region 2S0.8. The Mo1 locus maps about 10 cM from the centromere on chromosome arm 2RS. The similar effect on phenotype of mo1 and mrs1, together with their presence in regions of conserved synteny, suggest that they may well be members of an orthologous set of Triticeae genes governing spike branching. The practical importance of the MRS spike is that it produces more spikelets per spike, and thereby enhances the sink capacity of wheat, which is believed to limit the yield potential of the crop.     

Structural and Functional Analysis of E. coli Cyclopropane Fatty Acid Synthase

1. Download high-res image (198KB)
2. Download full-size image

     

Loss of intestinal nuclei and intestinal integrity in aging C. elegans

The roundworm C. elegans is widely used as an aging model, with hundreds of genes identified that modulate aging (Kaeberlein et al., 2002. Mech. Ageing Dev. 123 , 1115–1119). The development and bodyplan of the 959 cells comprising the adult have been well described and established for more than 25 years ( Sulston & Horvitz, 1977 . Dev. Biol. 56 , 110–156; Sulston et al., 1983. Dev. Biol. 100 , 64–119.). However, morphological changes with age in this optically transparent animal are less well understood, with only a handful of studies investigating the pathobiology of aging. Age‐related changes in muscle ( Herndon et al., 2002 . Nature 419 , 808–814), neurons ( Herndon et al., 2002 ), intestine and yolk granules ( Garigan et al., 2002 . Genetics 161 , 1101–1112; Herndon et al., 2002 ), nuclear architecture ( Haithcock et al., 2005 . Proc. Natl Acad. Sci. USA 102 , 16690–16695), tail nuclei ( Golden et al., 2007 . Aging Cell 6 , 179–188), and the germline ( Golden et al., 2007 ) have been observed via a variety of traditional relatively low‐throughput methods. We report here a number of novel approaches to study the pathobiology of aging C. elegans. We combined histological staining of serial‐sectioned tissues, transmission electron microscopy, and confocal microscopy with 3D volumetric reconstructions and characterized age‐related morphological changes in multiple wild‐type individuals at different ages. This enabled us to identify several novel pathologies with age in the C. elegans intestine, including the loss of critical nuclei, the degradation of intestinal microvilli, changes in the size, shape, and cytoplasmic contents of the intestine, and altered morphologies caused by ingested bacteria. The three‐dimensional models we have created of tissues and cellular components from multiple individuals of different ages represent a unique resource to demonstrate global heterogeneity of a multicellular organism.     

Two new Cladophialophora species,C. tumbae sp. nov. and C. tumulicola sp. nov., and chaetothyrialean fungi from biodeteriorated samples in the Takamatsuzuka and Kitora Tumuli

During dismantling and relocation of the Takamatsuzuka Tumulus stone chamber, many Cladophialophora and chaetothyrialean black fungi, such as Exophiala and Phialophora, were isolated from samples taken from the joints between the stone walls. However, inside the stone chamber of the Kitora Tumulus, after intermittent UV irradiation in 2009, these black fungi were also isolated from samples taken from the stone walls. Molecular phylogenetic analyses based on only nrLSU and the concatenated (nrLSU D1/D2 + ITS) sequences revealed that the 35 Takamatsuzuka and Kitora Tumuli isolates of Cladophialophora and the chaetothyrialean black fungi were divergent. Two new species of Cladophialophora are described herein: C. tumulicola from the viscous gels and various substrates on the stone walls of the Takamatsuzuka and Kitora Tumuli and C. tumbae from black substances on the plastic cover over the “thief hole,” soil and plaster pieces between the stone walls, and the exterior of the Takamatsuzuka Tumulus chamber. Also, molecular phylogenetic placements for the remaining eight Takamatsuzuka and Kitora Tumuli isolates of chaetothyrialean black fungi have been determined or suggested.     

A mitochondrial species identification assay for Australian blacktip sharks (Carcharhinus tilstoni, C. limbatus and C. amblyrhynchoides) using real-time PCR and high-resolution melt analysis

Tropical Australian shark fisheries target two morphologically indistinguishable blacktip sharks, the Australian blacktip (Carcharhinus tilstoni) and the common blacktip (C. limbatus). Their relative contributions to northern and eastern Australian coastal fisheries are unclear because of species identification difficulties. The two species differ in their number of precaudal vertebrae, which is difficult and time consuming to obtain in the field. But, the two species can be distinguished genetically with diagnostic mutations in their mitochondrial DNA ND4 gene. A third closely related sister species, the graceful shark C. amblyrhynchoides, can also be distinguished by species‐specific mutations in this gene. DNA sequencing is an effective diagnostic tool, but is relatively expensive and time consuming. In contrast, real‐time high‐resolution melt (HRM) PCR assays are rapid and relatively inexpensive. These assays amplify regions of DNA with species‐specific genetic mutations that result in PCR products with unique melt profiles. A real‐time HRM PCR species‐diagnostic assay (RT‐HRM‐PCR) has been developed based on the mtDNA ND4 gene for rapid typing of C. tilstoni, C. limbatus and C. amblyrhynchoides. The assay was developed using ND4 sequences from 66 C. tilstoni, 33. C. limbatus and five C. amblyrhynchoides collected from Indonesia and Australian states and territories; Western Australia, the Northern Territory, Queensland and New South Wales. The assay was shown to be 100% accurate on 160 unknown blacktip shark tissue samples by full mtDNA ND4 sequencing.     

Cross-species amplification of 44 microsatellite loci developed for Chaetodon trifascialis, C. lunulatus and C. vagabundus in 22 related butterflyfish species

Forty‐four microsatellite primers developed for three species of butterflyfish were cross‐tested against 22 related confamilial species. Amplification success and cross‐species transferability of these markers were moderately high. Between 24 and 37 loci were amplified successfully in each species, with a mean success rate per species of 71.7% (± 1.8 SE). Rates of amplification success were comparable among primers designed for the three source species, ranging from a mean success rate per species of 16.9 loci (± 0.8 SE) for Chaetodon trifascialis source loci to 13.7 loci (± 1.5 SE) for C. vagabundus source loci. Polymorphism rates were high (76.1%± 3.1 SE of all successfully amplified loci), and 10 loci were polymorphic in all successfully amplified species (Tri14, B11, C5, D3, D113, D6, D117, D120, D111, D118). The number of alleles per polymorphic locus ranged from 2 to 8, and the average number of alleles across all polymorphic loci and all species was 3.6 (± 0.07 SE). Polymorphism rates were higher overall in primers designed for C. vagabundus (89.9%± 3.9 SE). Overall cross‐testing success was lowest for Heniochus chrysostomus, the most phylogenetically divergent species. The significant cross‐testing reported here provides a valuable resource that will enable population genetics studies to be undertaken on a range of butterflyfishes without the need for expensive and time‐consuming de novo microsatellite development.     

Coupling of Rigor Mortis and Intestinal Necrosis during C. elegans Organismal Death

Download video (5MB)Help with mp4 files     

Multiscale Structuring of the E. coli Chromosome by Nucleoid-Associated and Condensin Proteins

1. Download high-res image (190KB)
2. Download full-size image

     

Discovery and characterization of a large number of diagnostic markers to discriminate Oncorhynchus mykiss and O. clarkii

Hybridization of cutthroat trout and steelhead/rainbow trout is ubiquitous where they are sympatric, either naturally or owing to introductions. The ability to detect hybridization and introgression between the two species would be greatly improved by the development of more diagnostic markers validated across the two species' many phylogenetic lineages. Here, we describe 81 novel genetic markers and associated assays for discriminating the genomes of these sister species. These diagnostic nucleotide polymorphisms were discovered by sequencing of rainbow trout expressed sequence tags (ESTs) in a diverse panel of both cutthroat trout and steelhead/rainbow trout. The resulting markers were validated in a large number of lineages of both species, including all extant subspecies of cutthroat trout and most of the lineages of rainbow trout that are found in natural sympatry with cutthroat trout or used in stocking practices. Most of these markers (79%) distinguish genomic regions for all lineages of the two species, but a small number do not reliably diagnose coastal, westslope and/or other subspecies of cutthroat trout. Surveys of natural populations and hatchery strains of trout and steelhead found rare occurrences of the alternative allele, which may be due to either previous introgression or shared polymorphism. The availability of a large number of genetic markers for distinguishing genomic regions originating in these sister species will allow the detection of both recent and more distant hybridization events, facilitate the study of the evolutionary dynamics of hybridization and provide a powerful set of tools for the conservation and management of both species.     

Xanthophyceaen assemblages during winter–spring flood: autecology and ecophysiology of Tribonema fonticolum and T. monochloron

The autecology and ecophysiology of two selected periphytic species of Xanthophyceae (Tribonema fonticolum and T. monochloron) were studied from seasonal pools of the inundation area, in the upper part of the Lužnice River (Třeboňsko Biosphere Reserve, Czech Republic) during winter–spring flood. Our studies have shown that these species differ in their ecological requirements (their temperature and light optima; inorganic carbon sources for photosynthesis; and also their ability to survive freezing and desiccation injuries). In our experiments, the optimal growth temperatures for both strains were higher than the temperatures of the water they were collected and isolated from. Tribonema monochloron has the rate of photosynthesis several times higher than T. fonticolum. In addition, the optimal growth temperatures were about 3–4°C lower for Tribonema monochloron than for T. fonticolum. From our results, we concluded that both strains of Tribonema prefer low intensities of irradiance. Both Tribonema strains were determined as CO₂ users, but we revealed the ability of T. fonticolum to use HCO₃⁻ in small amounts. In both Tribonema strains, 100% of the cells survived freezing down to −4°C. The cells’ viability after freezing at −40, −100 and −196°C was much higher for T. monochloron (about 40%) than for T. fonticolum (about 4%). With respect to desiccation damages, at temperatures of +4 and +20°C, T. monochloron (the species better adapted to low temperatures) did not survive. In contrast, about 80% cells of T. fonticolum survived desiccation at both temperatures. Handling editor: J. Padisak.     

Speciation history of three closely related pines Pinus mugo (T.), P. uliginosa (N.) and P. sylvestris (L.)

Nucleotide polymorphisms at genomic regions including 17 nuclear loci, two chloroplast and one mitochondrial DNA fragments were used to study the speciation history of three pine species: dwarf mountain pine (Pinus mugo), peat‐bog pine (P. uliginosa) and Scots pine (P. sylvestris). We set out to investigate three specific speciation scenarios: (I) P. uliginosa is a homoploid hybrid between the other two, (II) the species have evolved without gene flow after divergence and (III) there has been substantial gene flow between the species since their divergence. Overall, the genetic data suggest that P. mugo and P. uliginosa share the same gene pool (average net divergence of 0.0001) and that the phenotypic differences (e.g. growth form) are most likely due to very limited areas of the genome. P. mugo and P. uliginosa are more diverged from P. sylvestris than from each other (average net divergence of 0.0027 and 0.0026, respectively). The nucleotide patterns can best be explained by the divergence with migration speciation scenario, although the hybrid speciation scenario with small genomic contribution from P. sylvestris cannot be completely ruled out. We suggest that the large amount of shared polymorphisms between the pine taxa and the lack of monophyly at all loci studied between P. sylvestris and P. mugo–P. uliginosa can largely be explained by relatively recent speciation history and large effective population sizes but also by interspecific gene flow. These closely related pine taxa form an excellent system for searching for loci involved in adaptive variation as they are differentiated in phenotype and ecology but have very similar genetic background.     

Cell Boundary Confinement Sets the Size and Position of the E. coli Chromosome

1. Download : Download high-res image (209KB)
2. Download : Download full-size image

     

Molecular identification and properties of a light-insensitive rice catalase-B expressed in E. coli

Catalase plays a central role in plant stress responses but is highly susceptible to photoinhibition. A rice catalase-B protein avoiding photoinhibition was developed by mutagenesis of specific amino acids: Leu-189 to Trp-189 and His-225 to Thr-225 and then recombinantly expressed in E. coli. In addition, the site specific mutation also induced 2–2.5-fold increase in enzyme velocity with high affinity for its substrate and showed nearly a 3-fold lower K _m than the wild protein. These characteristic of mutated rice catalase-B is highly promising in transgenic research to increase plant productivity under stress conditions.     

A Sex Chromosome piRNA Promotes Robust Dosage Compensation and Sex Determination in C. elegans

1. Download high-res image (129KB)
2. Download full-size image