Dendroscope: An interactive viewer for large phylogenetic trees

Background  

Research in evolution requires software for visualizing and editing phylogenetic trees, for increasingly very large datasets, such as arise in expression analysis or metagenomics, for example. It would be desirable to have a program that provides these services in an effcient and user-friendly way, and that can be easily installed and run on all major operating systems. Although a large number of tree visualization tools are freely available, some as a part of more comprehensive analysis packages, all have drawbacks in one or more domains. They either lack some of the standard tree visualization techniques or basic graphics and editing features, or they are restricted to small trees containing only tens of thousands of taxa. Moreover, many programs are diffcult to install or are not available for all common operating systems.     

SplitsTree: analyzing and visualizing evolutionary data

MOTIVATION: Real evolutionary data often contain a number of different and sometimes conflicting phylogenetic signals, and thus do not always clearly support a unique tree. To address this problem, Bandelt and Dress (Adv. Math., 92, 47-05, 1992) developed the method of split decomposition. For ideal data, this method gives rise to a tree, whereas less ideal data are represented by a tree-like network that may indicate evidence for different and conflicting phylogenies. RESULTS: SplitsTree is an interactive program, for analyzing and visualizing evolutionary data, that implements this approach. It also supports a number of distances transformations, the computation of parsimony splits, spectral analysis and bootstrapping.      

The first branch of the lateral plantar nerve and heel pain

The course and ramification pattern of the lateral plantar nerve was studied in serial sections from 4 fetal feet and in dissections from 34 adult feet with special reference to the so called first branch. This branch was found in all of the observed fetal and adult specimen. From its originating point the nerve runs immediately distally to the medial process of the calcaneal tuberosity in a lateral direction to the proximal part of the abductor digiti minimi muscle. During its course the FB gives two branches. One of them penetrates sometimes the insertion of the quadratus plantae muscle, whereas in adult feet it always sends fibres to the periosteum around the medial process of the calcaneal tuberosity and the long plantar ligament. The other innervates the flexor digitorum brevis muscle. The site of a possible entrapment is located between the abductor hallucis muscle and the medial head of the quadratus plantae muscle. There is strong indirect evidence that the nerve is of a mixed type consisting of sensory fibres for the calcaneal periosteum and the medial head of the quadratus plantae muscle. There is strong indirect evidence that the nerve is of a mixed type consisting of sensory fibres for the calcaneal periosteum and the long plantar ligament as well as motor fibres for the quadratus plantae, flexor digitorum brevis and abductor digiti minimi muscles, which may explain the characteristic pain complaints of the heel pain syndrome. The occurrence of a stiff fascia perforated by the nerve branch or a bursa around the insertion of the plantar aponeurosis as has been described by several authors and which was put forward as a possible aetiological factor could not be confirmed in our material.     

All sheeps and sizes: a genetic investigation of mature body size across sheep breeds reveals a polygenic nature

Mature body size is genetically correlated with growth rate, an important economic trait in the sheep industry. Mature body size has been studied extensively in humans as well as cattle and other domestic animal populations but not in sheep. Six‐hundred and sixteen ewes, across 22 breeds, were measured for 28 linear measurements representing various skeletal parts. PCA from these measures generated principal components 1 and 2 which represented 66 and 7% of the phenotypic variation respectively. Two‐hundred and twenty sheep were genotyped on the Illumina Ovine HD beadchip for a GWAS investigating mature body size and linear body measurements. Forty‐six (Bonferroni P < 0.05) SNP associations across 14 chromosomes were identified utilizing principal component 1, representing overall body size, revealing mature body size to have fewer loci of large effect than other domestic species such as dogs and horses. Genome‐wide associations for individual linear measures identified major quantitative trait loci for withers height and ear length. Withers height was associated (Bonferroni P < 0.05) with 12 SNPs across six chromosomes whereas ear length was associated with a single locus on chromosome 3, containing MSRB3. This analysis identified several loci known to be associated with mature body size in other species such as NCAPG, LCORL, and HMGA2. Mature body size is more polygenic in sheep than other domesticated species, making the development of genomic selection for the trait the most efficient option for maintaining or reducing mature body size in sheep.     

A pericentric inversion of chromosome six in a patient with Peutz-Jeghers’ syndrome and the use of FISH to localise the breakpoints on a genetic map

Karyotypic analysis in a patient with Peutz-Jeghers’ syndrome demonstrated a pericentric inversion on chromosome 6. Further investigation was undertaken using fluorescence in situ hybridisation (FISH) with yeast artificial chromosome clones selected to contain genetic markers from chromosome 6, and a probe for the centromeric alphoid repeat array. This analysis located one inversion breakpoint within the alphoid array, in a 1-cM interval between D6S257 and D6S402, and the other in a 4-cM interval between D6S403 and D6S311. The oestrogen receptor gene locus (ESR) is excluded from the latter interval. Received: 23 January 1996 / Revised: 26 February 1996