Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

/pdf/fast-tree-computing-large-minimum-evolution-trees-with-4grq0gwfpy.pdf

Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. However, the sheer volume and scope of data pose a significant challenge to the development of such tools.

Integrative Genomics Viewer

MUCKE aims to mine a large volume of images, to structure them conceptually and to use this conceptual structuring in order to improve large-scale image retrieval. The last decade witnessed important progress concerning low-level image representations. However, there are a number problems which need to be solved in order to unleash the full potential of image mining in applications. The central problem with low-level representations is the mismatch between them and the human interpretation of image content. This problem can be instantiated, for instance, by the incapability of existing descriptors to capture spatial relationships between the concepts represented or by their incapability to convey an explanation of why two images are similar in a content-based image retrieval framework. We start by assessing existing local descriptors for image classification and by proposing to use co-occurrence matrices to better capture spatial relationships in images. The main focus in MUCKE is on cleaning large scale Web image corpora and on proposing image representations which are closer to the human interpretation of images. Consequently, we introduce methods which tackle these two problems and compare results to state of the art methods. Note: some aspects of this deliverable are withheld at this time as they are pending review. Please contact the authors for a preview.

http://ieeexplore.ieee.org/iel2/4524/12820/00592460.pdf

Image Processing

Polyploids — organisms that have multiple sets of chromosomes — are common in certain plant and animal taxa, and can be surprisingly stable. The evidence that has emerged from genome analyses also indicates that many other eukaryotic genomes have a polyploid ancestry, suggesting that both humans and most other eukaryotes have either benefited from or endured polyploidy. Studies of polyploids soon after their formation have revealed genetic and epigenetic interactions between redundant genes. These interactions can be related to the phenotypes and evolutionary fates of polyploids. Here, I consider the advantages and challenges of polyploidy, and its evolutionary potential.

/pdf/the-advantages-and-disadvantages-of-being-polyploid-3szbdyr9u1.pdf

The advantages and disadvantages of being polyploid

Nuclear DNA content variation among Central European Koeleria taxa.

Genomic in situ hybridization (GISH) is a useful tool to analyse natural polyploids, hybrid plants, and their backcross progenies as to their origin, genomic composition, and intergenomic rearrangements. However, in angiosperms with very small genomes ( 60 h). According to our GISH data, Cardaminopsis carpatica (2n = 16) is most likely the diploid ancestor of the autotetraploid Arabidopsis arenosa (2n = 32). Furthermore, within the allotetraploid species Arabidopsis suecica (2n = 26), it was possible to elucidate the origin of chromosomes contributed by the parental species A. thaliana and A. arenosa for a specimen with 2n = 26 or a deviating chromosom...

Genomic in situ hybridization in plants with small genomes is feasible and elucidates the chromosomal parentage in interspecific Arabidopsis hybrids.

Chromosome painting (CP) refers to visualization of large chromosome regions, entire chromosome arms, or entire chromosomes via fluorescence in situ hybridization (FISH). For CP in plants, contigs of chromosome-specific bacterial artificial chromosomes (BAC) from the target species or from a closely related species (comparative chromosome painting, CCP) are typically applied as painting probes. Extended pachytene chromosomes provide the highest resolution of CP in plants. CP enables identification and tracing of particular chromosome regions and/or entire chromosomes throughout all meiotic stages as well as corresponding chromosome territories in premeiotic interphase nuclei. Meiotic pairing and structural chromosome rearrangements (typically inversions and translocations) can be identified by CP. Here, we describe step-by-step protocols of CP and CCP in plant species including chromosome preparation, BAC DNA labeling, and multicolor FISH.

Analysis of plant meiotic chromosomes by chromosome painting.

PREMISE OF THE STUDY: Despite being highly fertile and occupying a large geographic region, the North American heartleaf bittercress (Cardamine cordifolia; Brassicaceae) has a puzzling triploid- like chromosome number (2n = 3x = 24). As most triploids are sterile, we embarked on a detailed analysis of the C. cordifolia genome to elucidate its origin and structure. METHODS: Mitotic and meiotic chromosome complement of C. cordifolia was analyzed by comparative chromosome painting using chromosome-specific BAC contigs of Arabidopsis thaliana. Resulting chromosome patterns were documented by multicolor fluorescence microscopy and compared with known ancestral and extant Brassicaceae genomes. KEY RESULTS: We discovered that C. cordifolia is not a triploid hybrid but a diploidized tetraploid with the prevalence of regular, diploid-like meiotic pairing. The ancestral tetraploid chromosome number (2n = 32) was reduced to a triploid- like number (2n = 24) through four terminal chromosome translocations. CONCLUSIONS: The structure of the pseudotriploid C. cordifolia genome results from a stepwise diploidization process after whole-genome duplication. We showed that translocation-based descending dysploidy (from n = 16 to n = 12) was mediated by the formation of five new chromosomes. The genome of C. cordifolia represents the diploidization process in statu nascendi and provides valuable insights into mechanisms of postpolyploidy rediploidization in land plants. Our data further suggest that chromosome number alone does not need to be a reliable proxy of species' evolutionary past and that the same chromosome number may originate either by polyploidization (hybridization) or due to descending dysploidy.

How diploidization turned a tetraploid into a pseudotriploid

The unigeneric tribe Heliophileae includes ca. 90 Heliophila
species, all endemic to southern Africa. The tribe is
morphologically the most diverse Brassicaceae lineage in every
aspect of habit, foliage, flower and fruit morphology. Despite
this diversity, virtually nothing is known about its origin and
genome evolution. Here we present the first in-depth
information on chromosome numbers, rDNA in situ localization,
genome structure, and phylogenetic relationship within
Heliophileae. Chromosome numbers determined in 27 Heliophila
species range from 2n = 16 to 2n = ca. 88, but 2n = 20 and 22
prevail in 77% of the examined species. Chromosome-number
variation largely follows three major lineages (A, B, and C)
resolved in the ITS phylogeny. Clade A species mostly have a
chromosome number of 2n = 20, whereas 2n = 22 is the dominant
number in clade C (2n = 16 and 22 were counted in two diploid
species of clade B). The number and position of 5S and 45S rDNA
loci cannot be employed as phylogenetically informative
characters. Seven species with different chromosome number and
from the three ITS clades were analyzed by comparative
chromosome painting. In all species analyzed, 90% of painting
probes unveiled three homeologous chromosome regions in
Heliophila haploid chromosome complements. These results
suggest that all Heliophila species, and probably the entire
tribe Heliophileae, experienced a whole-genome triplication
(WGT) event. We hypothesize that the mesohexaploid ancestor
arose through hybridization between genomes resembling the
Ancestral Crucifer Karyotype with n = 8. The WGT has been
followed by species-specific chromosome rearrangements
(diploidization) resulting in descending dysploidy towards
extant quasi-diploid genomes. The WGT might have contributed to
diversification and species radiation in Heliophileae. To our
knowledge, this is the first study to document polyploidy as a
potential major mechanism for the radiation of a Cape plant
lineage.

Martin A. Lysak

Papers

Nuclear DNA content variation among Central European Koeleria taxa.

Genomic in situ hybridization in plants with small genomes is feasible and elucidates the chromosomal parentage in interspecific Arabidopsis hybrids.

Analysis of plant meiotic chromosomes by chromosome painting.

How diploidization turned a tetraploid into a pseudotriploid

Whole-genome triplication and species radiation in the southern African tribe Heliophileae (Brassicaceae)