Automated simultaneous analysis phylogenetics (ASAP): an enabling tool for phlyogenomics.

BACKGROUND: The availability of sequences from whole genomes to reconstruct the tree of life has the potential to enable the development of phylogenomic hypotheses in ways that have not been before possible. A significant bottleneck in the analysis of genomic-scale views of the tree of life is the time required for manual curation of genomic data into multi-gene phylogenetic matrices. RESULTS: To keep pace with the exponentially growing volume of molecular data in the genomic era, we have developed an automated technique, ASAP (Automated Simultaneous Analysis Phylogenetics), to assemble these multigene/multi species matrices and to evaluate the significance of individual genes within the context of a given phylogenetic hypothesis. CONCLUSION: Applications of ASAP may enable scientists to re-evaluate species relationships and to develop new phylogenomic hypotheses based on genome-scale data.

ESTimating plant phylogeny: lessons from partitioning.

BACKGROUND: While Expressed Sequence Tags (ESTs) have proven a viable and efficient way to sample genomes, particularly those for which whole-genome sequencing is impractical, phylogenetic analysis using ESTs remains difficult. Sequencing errors and orthology determination are the major problems when using ESTs as a source of characters for systematics. Here we develop methods to incorporate EST sequence information in a simultaneous analysis framework to address controversial phylogenetic questions regarding the relationships among the major groups of seed plants. We use an automated, phylogenetically derived approach to orthology determination called OrthologID generate a phylogeny based on 43 process partitions, many of which are derived from ESTs, and examine several measures of support to assess the utility of EST data for phylogenies. RESULTS: A maximum parsimony (MP) analysis resulted in a single tree with relatively high support at all nodes in the tree despite rampant conflict among trees generated from the separate analysis of individual partitions. In a comparison of broader-scale groupings based on cellular compartment (ie: chloroplast, mitochondrial or nuclear) or function, only the nuclear partition tree (based largely on EST data) was found to be topologically identical to the tree based on the simultaneous analysis of all data. Despite topological conflict among the broader-scale groupings examined, only the tree based on morphological data showed statistically significant differences. CONCLUSION: Based on the amount of character support contributed by EST data which make up a majority of the nuclear data set, and the lack of conflict of the nuclear data set with the simultaneous analysis tree, we conclude that the inclusion of EST data does provide a viable and efficient approach to address phylogenetic questions within a parsimony framework on a genomic scale, if problems of orthology determination and potential sequencing errors can be overcome. In addition, approaches that examine conflict and support in a simultaneous analysis framework allow for a more precise understanding of the evolutionary history of individual process partitions and may be a novel way to understand functional aspects of different kinds of cellular classes of gene products.

Support versus corroboration.

Numerous metrics have been developed that attempt to assess the reliability of phylogenetic trees. Several of these commonly used measures of tree and tree branch support are described and discussed in the context of their relationship to Popperian corroboration. Claims that measures of support indicate the accuracy of phylogenetic trees or provide information for tree choice are rebutted. Measures of support are viewed as being of heuristic value within a given phylogenetic framework for describing the precision of the data based on perturbations to the data. However, no direct link is observed between the calculation of measures of support and corroboration. Direct measures of support, but not re-sampling or randomization methods, may play a more specific role in phylogenetic inference by providing the tools to search for falsifiers that could be the subject of future rounds of hypothesis testing.

Utility of North Atlantic Right Whale Museum Specimens for Assessing Changes in Genetic Diversity.

We examined six historical specimens of the endangered North Atlantic right whale (Eubalaena glacialis) using DNA isolated from documented baleen plates from the late nineteenth and early twentieth centuries. Sequences from the mitochondrial DNA (mtDNA) control region from these samples were compared with those from a near-exhaustive survey (269 of approximately 320 individuals) of the remaining right whales in the western North Atlantic Ocean. Our results suggest that there has been only relatively modest change in maternal lineage diversity over the past century in the North Atlantic right whale population. Any significant reduction in genetic variation in the species most likely occurred prior to the late nineteenth century. One historical specimen was from the last documented female capable of propagating one of the maternal lineages in the population today; no females in the existing population have been found to carry this mtDNA haplotype. Analysis of the only specimens from the eastern North Atlantic right whale population ever to be examined revealed that eastern and western North Atlantic right whales may not have been genetically differentiated populations. Loss of gene diversity experienced by North Atlantic right whales over the last century has been modest, and the six decades of protection have been successful in maintaining much of the maternal lineage diversity that was present in the late nineteenth century.

RESUMEN: Examinamos seis especímenes históricos de la ballena franca septentrional Eubalaena glacialis del Atlántico Norte, usando ADN aislado de placas de las barbas documentadas de finales de siglo diecinueve y principios del siglo veinte. Las secuencias del ADN mitocondrial (mtADN) de la región control de estas muestras comparadas con aquéllas de una muestra casi exhaustiva (269 de aproximadamente 320 individuos) de las ballenas francas remanentes en el océano Atlántico Norte Occidental. Nuestros resultados sugieren que solo ha habido ligeros cambios en la diversidad del linaje materno a lo largo del siglo pasado. Probablemente, cualquier reducción en la variación genética en las especies ocurrió antes del final del siglo diecinueve. Uno de los especímenes históricos fue de la última hembra documentada capaz de propagar uno de los linajes maternos en la población actual. Ninguna de las hembras en las poblaciones existentes ha sido identificada como portadora de este haplotipo de mtADN. El análisis de los especímenes de la población de ballenas del Atlántico Norte Oriental examinados revelan que las ballenas francas del este y del oeste del Atlántico Norte podrían no haber sido poblaciones genéticamente diferentes. La pérdida de diversidad genética experimentada en las poblaciones de ballena franca del Atlántico Norte a lo largo del siglo pasado ha sido modesta y las seis décadas de protección han sido exitosas en el mantenimiento de la mayoría de la diversidad del linaje materno que estaba presente a finales del siglo diecinueve.

Gene flow on ice: the role of sea ice and whaling in shaping Holarctic genetic diversity and population differentiation in bowhead whales (Balaena mysticetus).

Sea ice is believed to be a major factor shaping gene flow for polar marine organisms, but it remains unclear to what extent it represents a true barrier to dispersal for arctic cetaceans. Bowhead whales are highly adapted to polar sea ice and were targeted by commercial whalers throughout Arctic and subarctic seas for at least four centuries, resulting in severe reductions in most areas. Both changing ice conditions and reductions due to whaling may have affected geographic distribution and genetic diversity throughout their range, but little is known about range-wide genetic structure or whether it differed in the past. This study represents the first examination of genetic diversity and differentiation across all five putative stocks, including Baffin Bay-Davis Strait, Hudson Bay-Foxe Basin, Bering-Beaufort-Chukchi, Okhotsk, and Spitsbergen. We also utilized ancient specimens from Prince Regent Inlet (PRI) in the Canadian Arctic and compared them with modern stocks. Results from analysis of molecular variance and demographic simulations are consistent with recent and high gene flow between Atlantic and Pacific stocks in the recent past. Significant genetic differences between ancient and modern populations suggest PRI harbored unique maternal lineages in the past that have been recently lost, possibly due to loss of habitat during the Little Ice Age and/or whaling. Unexpectedly, samples from this location show a closer genetic relationship with modern Pacific stocks than Atlantic, supporting high gene flow between the central Canadian Arctic and Beaufort Sea over the past millennium despite extremely heavy ice cover over much of this period.

OrthologID: automation of genome-scale ortholog identification within a parsimony framework.

MOTIVATION: The determination of gene orthology is a prerequisite for mining and utilizing the rapidly increasing amount of sequence data for genome-scale phylogenetics and comparative genomic studies. Until now, most researchers use pairwise distance comparisons algorithms, such as BLAST, COG, RBH, RSD and INPARANOID, to determine gene orthology. In contrast, orthology determination within a character-based phylogenetic framework has not been utilized on a genomic scale owing to the lack of efficiency and automation. RESULTS: We have developed OrthologID, a Web application that automates the labor-intensive procedures of gene orthology determination within a character-based phylogenetic framework, thus making character-based orthology determination on a genomic scale possible. In addition to generating gene family trees and determining orthologous gene sets for complete genomes, OrthologID can also identify diagnostic characters that define each orthologous gene set, as well as diagnostic characters that are responsible for classifying query sequences from other genomes into specific orthology groups. The OrthologID database currently includes several complete plant genomes, including Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, as well as a unicellular outgroup, Chlamydomonas reinhardtii. To improve the general utility of OrthologID beyond plant species, we plan to expand our sequence database to include the fully sequenced genomes of prokaryotes and other non-plant eukaryotes. AVAILABILITY: http://nypg.bio.nyu.edu/orthologid/

The unholy trinity: taxonomy, species delimitation and DNA barcoding.

Recent excitement over the development of an initiative to generate DNA sequences for all named species on the planet has in our opinion generated two major areas of contention as to how this 'DNA barcoding' initiative should proceed. It is critical that these two issues are clarified and resolved, before the use of DNA as a tool for taxonomy and species delimitation can be universalized. The first issue concerns how DNA data are to be used in the context of this initiative; this is the DNA barcode reader problem (or barcoder problem). Currently, many of the published studies under this initiative have used tree building methods and more precisely distance approaches to the construction of the trees that are used to place certain DNA sequences into a taxonomic context. The second problem involves the reaction of the taxonomic community to the directives of the 'DNA barcoding' initiative. This issue is extremely important in that the classical taxonomic approach and the DNA approach will need to be reconciled in order for the 'DNA barcoding' initiative to proceed with any kind of community acceptance. In fact, we feel that DNA barcoding is a misnomer. Our preference is for the title of the London meetings--Barcoding Life. In this paper we discuss these two concerns generated around the DNA barcoding initiative and attempt to present a phylogenetic systematic framework for an improved barcoder as well as a taxonomic framework for interweaving classical taxonomy with the goals of 'DNA barcoding'.