Phylogenetics and sequence analysis--some problems for the unwary.

DNA sequence comparisons can provide deep insight into phylogenetic relationships, but can also present problems for the unwary. Alignment comparisons are not always as straightforward as they might seem, and comparative models applied to deduce relationships need to be carefully chosen with full regard to the assumptions on which they are based. Most importantly perhaps, genes are not organisms, so some sequence analyses can be poorly informative about relationships - especially if evolution of those organisms has involved significant epigenetic factors, for example, in controlling gene expression. This review highlights some of the most prevalent problems in sequence-based phylogenetic studies of parasite systems

Trypanosomes are monophyletic: evidence from genes for glyceraldehyde phosphate dehydrogenase and small subunit ribosomal RNA.

The genomes of Trypanosoma brucei, Trypanosoma cruzi and Leishmania major have been sequenced, but the phylogenetic relationships of these three protozoa remain uncertain. We have constructed trypanosomatid phylogenies based on genes for glycosomal glyceraldehyde phosphate dehydrogenase (gGAPDH) and small subunit ribosomal RNA (SSU rRNA). Trees based on gGAPDH nucleotide and amino acid sequences (51 taxa) robustly support monophyly of genus Trypanosoma, which is revealed to be a relatively late-evolving lineage of the family Trypanosomatidae. Other trypanosomatids, including genus Leishmania, branch paraphyletically at the base of the trypanosome clade. On the other hand, analysis of the SSU rRNA gene data produced equivocal results, as trees either robustly support or reject monophyly depending on the range of taxa included in the alignment. We conclude that the SSU rRNA gene is not a reliable marker for inferring deep level trypanosome phylogeny. The gGAPDH results support the hypothesis that trypanosomes evolved from an ancestral insect parasite, which adapted to a vertebrate/insect transmission cycle. This implies that the switch from terrestrial insect to aquatic leech vectors for fish and some amphibian trypanosomes was secondary. We conclude that the three sequenced pathogens, T. brucei, T. cruzi and L. major, are only distantly related and have distinct evolutionary histories

REFGEN and TREENAMER: Automated Sequence Data Handling for Phylogenetic Analysis in the Genomic Era

The phylogenetic analysis of nucleotide sequences and increasingly that of amino acid sequences is used to address a number of biological questions. Access to extensive datasets, including numerous genome projects, means that standard phylogenetic analyses can include many hundreds of sequences. Unfortunately, most phylogenetic analysis programs do not tolerate the sequence naming conventions of genome databases. Managing large numbers of sequences and standardizing sequence labels for use in phylogenetic analysis programs can be a time consuming and laborious task. Here we report the availability of an online resource for the management of gene sequences recovered from public access genome databases such as GenBank. These web utilities include the facility for renaming every sequence in a FASTA alignment file, with each sequence label derived from a user-defined combination of the species name and/or database accession number. This facility enables the user to keep track of the branching order of the sequences/taxa during multiple tree calculations and re-optimisations. Post phylogenetic analysis, these webpages can then be used to rename every label in the subsequent tree files (with a user-defined combination of species name and/or database accession number). Together these programs drastically reduce the time required for managing sequence alignments and labelling phylogenetic figures. Additional features of our platform include the automatic removal of identical accession numbers (recorded in the report file) and generation of species and accession number lists for use in supplementary materials or figure legends

A tale of two hatcheries: Assessing bias in the hatchery process for Atlantic salmon (Salmo salar L.)

Stock enhancement of Atlantic salmon (Salmo salarL.), a fish of considerable economic and social importance, is commonplace. Supportive-breeding is a well-recognised method of enhancement which, when compared with traditional hatchery practices, is thought to reduce the severity of selection pressures on broodstock fish. Critically, in supportive-breeding programmes, the eggs and sperm used in the breeding process are taken from wild adult fish originating from the same catchment that resulting juvenile fish are subsequently stocked into, thereby avoiding problems associated with a lack of local adaptation in the stocked fish. Previous studies have indicated that sex bias during the hatchery process may result in reduced genetic diversity of the offspring. Utilising 16 microsatellite loci and two expressed sequence tag (EST) loci, we examined progeny from two hatcheries located on the rivers Exe and Tamar in southwest England, assessing the genetic diversity and parental contribution at each. Two strains were assessed within each hatchery. Genetic diversity was found to be reduced in offspring compared with that of the parent fish. This is likely the result of utilising a small number of broodstock in combination with parental bias. In the four hatchery strains studied (Bar, LEx, Lyd and TXL), parental contribution ranged between 2.1 and 29.2%, 12.2–51.0%, 2.0–70.0% and 4.0–40.0%, respectively. If this practice is to be continued, efforts should be made to improve adherence to national rearing guidelines by increasing the number of broodstock fish utilised and ensuring a more balanced contribution of all adults during the crossing process. Ultimately, we suggest a need to review the suitability of current national Atlantic salmon hatchery guidelines, particularly with regard to their use and relevance in small European rearing systems

Breeding system and spatial isolation from congeners strongly constrain seed set in an insect-pollinated apomictic tree: Sorbus subcuneata (Rosaceae)

The article associated with this dataset is in ORE at: http://hdl.handle.net/10871/26965The datasets are the results of 1) pollen grain accumulation on stigmas. 2) Flowering phenology of individual trees as % of opened buds, with 50 percentile values of the cumulative flowering curve. 3) Location data for all trees of both species of flowering size (see article text) plus connectivity measures of maternal seed trees to all S. admonitor trees. X and y coordinates are GB OS National Grid. This data is related to the Scientific Reports paper of the same title.Whitley Wildlife Conservation Trust, Paignton Zoo Environmental ParkNER

Genetic stock identification of Atlantic salmon (Salmo salar) populations in the southern part of the European range

notes: PMCID: PMC2882343© 2010 Griffiths et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Anadromous migratory fish species such as Atlantic salmon (Salmo salar) have significant economic, cultural and ecological importance, but present a complex case for management and conservation due to the range of their migration. Atlantic salmon exist in rivers across the North Atlantic, returning to their river of birth with a high degree of accuracy; however, despite continuing efforts and improvements in in-river conservation, they are in steep decline across their range. Salmon from rivers across Europe migrate along similar routes, where they have, historically, been subject to commercial netting. This mixed stock exploitation has the potential to devastate weak and declining populations where they are exploited indiscriminately. Despite various tagging and marking studies, the effect of marine exploitation and the marine element of the salmon lifecycle in general, remain the "black-box" of salmon management. In a number of Pacific salmonid species and in several regions within the range of the Atlantic salmon, genetic stock identification and mixed stock analysis have been used successfully to quantify exploitation rates and identify the natal origins of fish outside their home waters - to date this has not been attempted for Atlantic salmon in the south of their European range.European Union INTERREG IIIB programme (Atlantic Salmon Arc Project [ASAP], Project No. 040)

Detection of a coherent magnetic field in the Magellanic Bridge through Faraday rotation

We present an investigation into the magnetism of the Magellanic Bridge, carried out through the observation of Faraday rotation towards 167 polarized extragalactic radio sources spanning the continuous frequency range of 1.3–3.1 GHz with the Australia Telescope Compact Array. Comparing measured Faraday depth values of sources ‘on’ and ‘off’ the Bridge, we find that the two populations are implicitly different. Assuming that this difference in populations is due to a coherent field in the Magellanic Bridge, the observed Faraday depths indicate a median line-of-sight coherent magnetic-field strength of B∥ ≃ 0.3 μG directed uniformly away from us. Motivated by the varying magnitude of Faraday depths of sources on the Bridge, we speculate that the coherent field observed in the Bridge is a consequence of the coherent magnetic fields from the Large and Small Magellanic Clouds being pulled into the tidal feature. This is the first observation of a coherent magnetic field spanning the entirety of the Magellanic Bridge and we argue that this is a direct probe of a ‘pan-Magellanic’ fieldThe Australia Telescope is funded by the Commonwealth of Australia for operation as a National Facility managed by CSIRO. BMG and CRP acknowledge the support of the Australian Research Council through grant FL100100114. The Dunlap Institute is funded through an endowment established by the David Dunlap family and the University of Toronto. NMM-G acknowledges the support of the Australian Research Council through Future Fellowship FT15010002