Detecting distant homologs using phylogenetic tree-based HMMs

It is often desired to identify further homologs of a family of biological sequences from the ever-growing sequence databases. Profile hidden Markov models excel at capturing the common statistical features of a group of biological sequences. With these common features, we can search the biological database and find new homologous sequences. Most general profile hidden Markov model methods, however, treat the evolutionary relationships between the sequences in a homologous group in an ad-hoc manner. We hereby introduce a method to incorporate phylogenetic information directly into hidden Markov models, and demonstrate that the resulting model performs better than most of the current multiple sequence-based methods for finding distant homologs.     

Using Homolog Groups to Create a Whole-Genomic Tree of Free-Living Organisms: An Update

Genomic trees have been constructed based on the presence and absence of families of protein-encoding genes observed in 27 complete genomes, including genomes of 15 free-living organisms. This method does not rely on the identification of suspected orthologs in each genome, nor the specific alignment used to compare gene sequences because the protein-encoding gene families are formed by grouping any protein with a pairwise similarity score greater than a preset value. Because of this all inclusive grouping, this method is resilient to some effects of lateral gene transfer because transfers of genes are masked when the recipient genome already has a homolog (not necessarily an ortholog) of the incoming gene. Of 71 genes suspected to have been laterally transferred to the genome of Aeropyrum pernix, only approximately 7 to 15 represent genes where a lateral gene transfer appears to have generated homoplasy in our character dataset. The genomic tree of the 15 free-living taxa includes six different bacterial orders, six different archaeal orders, and two different eukaryotic kingdoms. The results are remarkably similar to results obtained by analysis of rRNA. Inclusion of the other 12 genomes resulted in a tree only broadly similar to that suggested by rRNA with at least some of the differences due to artifacts caused by the small genome size of many of these species. Very small genomes, such as those of the two Mycoplasma genomes included, fall to the base of the Bacterial domain, a result expected due to the substantial gene loss inherent to these lineages. Finally, artificial ``partial genomes' were generated by randomly selecting ORFs from the complete genomes in order to test our ability to recover the tree generated by the whole genome sequences when only partial data are available. The results indicated that partial genomic data, when sampled randomly, could robustly recover the tree generated by the whole genome sequences. Received: 30 May 2001 / Accepted: 10 October 2001     

Tree species diversity in small, tropical riparian forest fragments in Belize, Central America

Tree species diversity was measured in a network of very small galleryforests within the Mountain Pine Ridge savanna in Belize. Research focussed onforest patches smaller than 1 ha in size (micro-forests) and linearstrips of trees along creeks lacking interior core zones with low understoreylight levels (tree thickets). Twenty-five micro-forests and 51 tree thicketsites were sampled throughout the savanna. A total of 144 morphospecies 5cm dbh (106 in micro-forests and 117 in tree thickets) werefound, which represents 1/5 of the approximately 700 native tree species in Belize.Most (85.3%) of the species encountered are typically found in tropical rainforests and few are restricted to savanna or riparian environments. Speciesaccumulated at a much faster rate in micro-forests than in tree thickets. Onlyone species, the palm Acoelorraphe wrightii, was extremelyabundant, accounting for almost 30% of all stems. Many of the species werepresent in very low densities: 19% of all species found in micro-forests and 42%of those found in tree thickets had on average one or fewer stems per hectare. Alarge proportion of species were also found infrequently across the landscape,being present in only 36% of micro-forests and at 52% of tree thicket sites. Theresults indicate that networks of very small forest patches can contain highnumbers of species and could therefore contribute to the maintenance of regionalbiodiversity.     

Direct Calculation of a Tree Length Using a Distance Matrix

Comparative studies of tree-building methods have shown minimum evolution to be in general an accurate criterion for selecting a true tree. To improve the use of this criterion, this paper proposes a method for rapidly and directly calculating a length of a dichotomous tree without having to resort to branch length calculations. This direct calculation (DC) method applies to the complete final topology, giving equal importance to each branch after a dichotomy. According to this method, the tree length S _DC is S _DC =∑ _i ∑ _j (D _ij /2 ^Bij ) = (∑ _i<j ∑D _ij 2 ^Bmax−Bij )/2 ^{Bmax −1} where D _ij is the observed distance between taxa i and j, B _ij is the number of branches connecting i and j, Bmax is the greatest B _ij in the tree, and the powers of two are due to the dichotomy of the tree. This tree length expression may be used as a rapid method for selecting the shortest tree from a set of hypothetical or subobtimal trees. Received: 2 March 2000 / Accepted: 24 March 2000     

The Path from the RNA World

We describe a sequential (step by step) Darwinian model for the evolution of life from the late stages of the RNA world through to the emergence of eukaryotes and prokaryotes. The starting point is our model, derived from current RNA activity, of the RNA world just prior to the advent of genetically-encoded protein synthesis. By focusing on the function of the protoribosome we develop a plausible model for the evolution of a protein-synthesizing ribosome from a high-fidelity RNA polymerase that incorporated triplets of oligonucleotides. With the standard assumption that during the evolution of enzymatic activity, catalysis is transferred from RNA → RNP → protein, the first proteins in the ``breakthrough organism' (the first to have encoded protein synthesis) would be nonspecific chaperone-like proteins rather than catalytic. Moreover, because some RNA molecules that pre-date protein synthesis under this model now occur as introns in some of the very earliest proteins, the model predicts these particular introns are older than the exons surrounding them, the ``introns-first' theory. Many features of the model for the genome organization in the final RNA world ribo-organism are more prevalent in the eukaryotic genome and we suggest that the prokaryotic genome organization (a single, circular genome with one center of replication) was derived from a ``eukaryotic-like' genome organization (a fragmented linear genome with multiple centers of replication). The steps from the proposed ribo-organism RNA genome → eukaryotic-like DNA genome → prokaryotic-like DNA genome are all relatively straightforward, whereas the transition prokaryotic-like genome → eukaryotic-like genome appears impossible under a Darwinian mechanism of evolution, given the assumption of the transition RNA → RNP → protein. A likely molecular mechanism, ``plasmid transfer,' is available for the origin of prokaryotic-type genomes from an eukaryotic-like architecture. Under this model prokaryotes are considered specialized and derived with reduced dependence on ssRNA biochemistry. A functional explanation is that prokaryote ancestors underwent selection for thermophily (high temperature) and/or for rapid reproduction (r selection) at least once in their history. Received: 14 January 1997 / Accepted: 19 May 1997     

Shoot regeneration from leaves of Prunus serotina Ehrh. (black cherry) and P. avium L. (wild cherry)

Leaves excised from shoot cultures of Prunus avium cvs. F12/1 and Charger and genotype 1908, and from five genotypes of P. serotina and two hybrids of P. avium×P. sargentii developed shoots on Woody Plant medium (WPM) supplemented with either benzyladenine (BA) or thidiazuron (TDZ). Regeneration in both P. avium 1908 and a genotype of P. serotina was improved using TDZ rather than BA in the medium. Regeneration occurred more frequently in P. serotina if leaves were cultured on medium with WPM rather than modified Driver and Kuniyuki walnut medium. The proportions of leaves that regenerated varied between genotypes of the same species. Regenerated shoots of both P. avium and P. serotina developed into shoot cultures following transfer to the media used to produce the shoot cultures used as explant sources. Received: 10 July 1996 / Revision received: 11 November 1996 / Accepted: 6 January 1997     

Formation of the Dermal Chromatophore Unit (DCU) in the Tree Frog Hyla Arborea

In the tadpole of the tree frog Hyla arborea, the color of the dorsal skin was dark brown. Dermal melanophores, xanthophores, and iridophores were scattered randomly under the subepidermal collagen layer (SCL). After metamorphosis, the dorsal color of the animal changed to green and the animal acquired the ability of dramatic color change, demonstrating that the dermal chromatophore unit (DCU) was formed at metamorphosis. Fibroblasts invaded the SCL and divided it into two parts: the stratum spongiosum (SS) and the stratum compactum (SC). The activity of collagenase increased at metamorphosis. The fibroblasts appeared to dissolve the collagen matrix as they invaded the SCL. Then, three types of chromatophores migrated through the SCL and the DCU was formed in the SS. The mechanism how the three types of chromatophores were organized into a DCU is uncertain, but different migration rates of the three chromatophore types may be a factor that determines the position of the chromatophores in the DCU. Almost an equal number of each chromatophore type is necessary to form the DCUs. However, the number of dermal melanophores in the tadpoles was less than the number of xanthophores and iridophores. It was suggested that epidermal melanophores migrated to the dermis at metamorphosis and developed into dermal melanophores. This change may account for smaller number of dermal melanophores available to form the DCU_s.     

Biophysical stratification of the Amazon basin

In field measurement programmes, stratified sampling can optimize sampling efficiency, but stratification is often undertaken subjectively, and is frequently based on a priori classification schemes such as those used for vegetation maps. In order to avoid the problems associated with a priori subjective schemes, we explore here an objective procedure, Regression Tree Analysis (RTA). RTA has previously been used in local-scale studies, but here we apply it to a very large study domain, namely the entire humid tropical zone of South America. The aim of the study was to develop an optimal sampling design in preparation for the Large Scale Biosphere-Atmosphere Experiment in Amazonia (LBA). Co-registered spatially continuous fields of rainfall, temperature, photosynthetically active radiation (PAR), the normalized difference index (NDVI), an index of surface moisture, and other independent variables were used to predict three dependent variables, annual net radiation (Rn), latent heat (LE) and net primary production (NPP). Rather than simply dividing the study area based on differing levels of the three dependent variables, empirical models were developed using RTA to indicate how the relationships between these and possible forcing variables vary across the study area. For each variable long-term seasonal indices such as annual average, monthly minimum and amplitude were used to exclude effects of temporal phase differences between the hemispheres. The resulting hierarchical models revealed variations in the interdependence of the forcing variables throughout the study area and therefore provided a basis for a stratified sampling and identifying the most important variables to be collected in LBA for the Amazon basin as a whole as well as optimizing the sampling scheme for scaling up findings from the field scale to larger areas.     

Effects of nest-box density on the behavior of Tree Swallows during nest building

ABSTRACT.   In territorial species, increased density is often linked to an increase in aggressive interactions, which may result in trade-offs between competitive behavior and nest construction. We examined the impact of nesting in areas of high-density versus low-density nest boxes on conspecific interactions and nest-building effort in a population of Tree Swallows ( Tachycineta bicolor ). We also examined whether expected differences in behavior related to variation in nest quality and reproductive success in high-density and low-density areas. No differences in either nest-building behavior or reproductive success were observed between areas of high-density and low-density boxes, but there was a tendency of more frequent behavioral interactions at high density. Similarly, there was a significant difference between pairs defending single nest boxes and those defending multiple nest boxes in the number of interactions with conspecifics. These results suggest that although there may be more competition with conspecifics for Tree Swallows nesting at high density, this does not appear to affect either nest quality or reproductive success.