Confidence limits on the branching order of phylogenetic trees.

We describe a confidence test for branching order that can aid protein phylogeny reconstruction as well as the evaluation of the optimal tree. It is proposed that the process resulting in the observed amino acid residue differences, which is the basis for the identification of the order and relative times of divergence events, is appropriately described by a modification of the negative binomial distribution. The relative total numbers of mutations (accepted and nonaccepted), which result in a given number of amino acid differences, may be obtained as the expectation of this distribution. The associated variances enable significant differences in tree branching order to be established. If the total rates of mutation of the genes encoding the compared proteins are equal, the expected total mutations and their associated variances map identically to their relative times of divergence. In addition, significantly different rates of change (due to differences in total mutation rate and/or acceptance rate) may be identified without the requirement of outlying reference group. The method is equally applicable to phylogenies derived from DNA or RNA sequence information.     

Understanding global patterns of mammalian functional and phylogenetic diversity

Documenting and exploring the patterns of diversity of life on Earth has always been a central theme in biology. Species richness despite being the most commonly used measure of diversity in macroecological studies suffers from not considering the evolutionary and ecological differences among species. Phylogenetic diversity (PD) and functional diversity (FD) have been proposed as alternative measures to overcome this limitation. Although species richness, PD and FD are closely related, their relationships have never been investigated on a global scale. Comparing PD and FD with species richness corroborated the general assumptions of surrogacy of the different diversity measures. However, the analysis of the residual variance suggested that the mismatches between the diversity measures are influenced by environmental conditions. PD increased relative to species richness with increasing mean annual temperature, whereas FD decreased with decreasing seasonality relative to PD. We also show that the tropical areas are characterized by a FD deficit, a phenomenon, that suggests that in tropical areas more species can be packed into the ecological space. We discuss potential mechanisms that could have resulted in the gradient of spatial mismatch observed in the different biodiversity measures and draw parallels to local scale studies. We conclude that the use of multiple diversity measures on a global scale can help to elucidate the relative importance of historical and ecological processes shaping the present gradients in mammalian diversity.     

生态学的多样性指数:功能与系统发育

生物多样性是生态学的核心问题。传统的多样性指数仅包含物种数和相对多度的信息,这类基于分类学的多样性指数并不能很好地帮助理解群落构建和生态系统功能。不同物种对群落构建和生态系统功能所起到的作用类型和贡献也不完全相同,且物种在生态过程中的作用和贡献往往与性状密切相关,因此功能多样性已经成为反映物种群落构建、干扰以及环境因素对群落影响的重要指标。同时,由于亲缘关系相近的物种往往具有相似的性状,系统发育多样性也可以作为功能多样性的一个替代。功能多样性和系统发育多样性各自具有优缺点,但二者均比分类多样性更能揭示群落和生态系统的构建、维持与功能。     

Exploring the relationship between sequence similarity and accurate phylogenetic trees

We have characterized the relationship between accurate phylogenetic reconstruction and sequence similarity, testing whether high levels of sequence similarity can consistently produce accurate evolutionary trees. We generated protein families with known phylogenies using a modified version of the PAML/EVOLVER program that produces insertions and deletions as well as substitutions. Protein families were evolved over a range of 100-400 point accepted mutations; at these distances 63% of the families shared significant sequence similarity. Protein families were evolved using balanced and unbalanced trees, with ancient or recent radiations. In families sharing statistically significant similarity, about 60% of multiple sequence alignments were 95% identical to true alignments. To compare recovered topologies with true topologies, we used a score that reflects the fraction of clades that were correctly clustered. As expected, the accuracy of the phylogenies was greatest in the least divergent families. About 88% of phylogenies clustered over 80% of clades in families that shared significant sequence similarity, using Bayesian, parsimony, distance, and maximum likelihood methods. However, for protein families with short ancient branches (ancient radiation), only 30% of the most divergent (but statistically significant) families produced accurate phylogenies, and only about 70% of the second most highly conserved families, with median expectation values better than 10(-60), produced accurate trees. These values represent upper bounds on expected tree accuracy for sequences with a simple divergence history; proteins from 700 Giardia families, with a similar range of sequence similarities but considerably more gaps, produced much less accurate trees. For our simulated insertions and deletions, correct multiple sequence alignments did not perform much better than those produced by T-COFFEE, and including sequences with expressed sequence tag-like sequencing errors did not significantly decrease phylogenetic accuracy. In general, although less-divergent sequence families produce more accurate trees, the likelihood of estimating an accurate tree is most dependent on whether radiation in the family was ancient or recent. Accuracy can be improved by combining genes from the same organism when creating species trees or by selecting protein families with the best bootstrap values in comprehensive studies.     

Counting Australia’s protected rivers

Summary Australia is committed to protecting its important and representative ecosystems. Foremost among protection measures is the network of terrestrial and marine protected areas that comprise the National Reserve System (NRS). However, these reserves were often established with little regard for the conservation needs of riverine ecosystems. There has been no conservation status assessment to determine whether riverine ecosystems are adequately protected within terrestrial reserves. This study begins this task by determining the extent of riverine protection through the NRS. Three classes of protection are defined based on the proportion of the catchment of each stream segment (the link between tributary confluences) that is contained within a protected area, and the presence of major in‐stream barriers. The analysis reveals cause for concern. While nearly 225 000 km (7.6%) of the 2.9 million kilometres of streams assessed fall within a protected area of IUCN class I to IV where the principal objective is nature conservation, just 12 334 km of stream, less than half of one per cent of the total stream length, receives Class A protection, the strongest level of protection against threat. Class A is achieved where an entire drainage basin is contained within a protected area. Most of the protected stream length of the larger, named streams is potentially threatened by land‐use activities occurring in unprotected headwaters or is fragmented by major dams and thus receives the lowest class of protection. Owing to a variety of pervasive threats, a more comprehensive conservation status assessment of these ecosystems would undoubtedly yield an even more pessimistic result. Such an assessment is recommended.     

Evaluating the sufficiency of protected lands for maintaining wildlife population connectivity in the U.S. northern Rocky Mountains

Aim The goal of this study was to evaluate the sufficiency of the network of protected lands in the U.S. northern Rocky Mountains in providing protection for habitat connectivity for 105 hypothetical organisms. A large proportion of the landscape falls into one of several categories of protected lands. However, protected lands in the region are primarily higher elevation forest and mountain habitats. Little is known about how the network of protected lands may maintain connectivity for a broad spectrum of species expressing different habitat requirements and dispersal abilities. Location The study was conducted across the states of Montana and northern Idaho, USA, comprising an area of 30.2 million hectares. Methods We used resistant kernel modelling to map the extent of the study area predicted to be connected by dispersal for each of 35 species groups with different ecological associations. We evaluated the effect of vagility on protected area sufficiency by varying dispersal ability across three levels for each species group. We evaluated the degree of vulnerability of each of the 105 hypothetical species (35 species groups × 3 dispersal abilities) in terms of the extent of the total study area predicted to be connected by dispersal. We defined nine categories of risk as the combination of species vulnerability because of the extent of connected habitat and the degree to which that habitat was protected. Results We found high variation in the vulnerability of species because of the extent of connected habitat, and the extent to which connected habitat overlapped protected lands. Species associated with high elevations and species associated with lower elevations were predicted to have limited extent of connected habitat. Species associated with high elevations were predicted to have the vast majority of their connected habitat protected by federal Forest Service and National Park Service lands. In contrast, species associated with lower elevations were poorly protected by the existing network of protected lands. Main conclusions Low elevation and non‐forest habitats are at highest risk of human‐induced habitat loss and fragmentation in the study area. Conservation efforts in the region may be most effective if they focus on expanding the network of lower elevation protected lands in such a way that maximizes connectivity across the landscape.     

Biomechanics and functional preconditions for terrestrial lifestyle in basal tetrapods,with special consideration of Tiktaalik roseae

The fossil Tiktaalik roseae from the Late Devonian induces clear definition of the biomechanical and functional preconditions for a terrestrial lifestyle including quadrupedal standing and locomotion on limbs. Therefore, we determined the internal stresses in this model organism under the influence of gravity using the finite element method. Stress patterns during symmetrical two-forelimb support result from bending of trunk and neck. During asymmetrical one-forelimb support, as occurs during terrestrial locomotion, torsional stresses are higher than those caused by bending. The observed patterns of compressive stresses correspond well with the arrangement of compression-resistant materials: vertebral column, shoulder girdle and ribs. The tensile stresses are in accordance with the arrangement of longitudinal and oblique muscles forming the body wall. Torsional stresses concentrate along the periphery of the trunk, leaving its cavity free from mechanical stresses. Theoretical mechanics indicate that the flat skull and the mobility of the neck were advantageous for lateral snapping, similar to crocodiles. The same movement on land requires sprawling and flexed forelimbs. Our results can be interpreted as explanations for the tetrapod bauplan as well as confirmation and refinement of existing hypotheses about the lifestyle at the border between water and land of this early predecessor of terrestrial tetrapods.     

Seeing the forest for the trees: partitioning ecological and phylogenetic components of Bergmann's rule in European Carnivora

Comparative methods have commonly been applied in macroecological research. However, few methods exist to map and analyze phylogenetic variation in geographical space. Here we develop a general analytical framework to partition the phylogenetic and ecological structures of macroecological patterns in geographic space. As an example, we apply the framework to evaluate interspecific patterns of body size geographic variation (Bergmann's rule) in European Carnivora. We model the components of variance attributable to ecological and phylogenetic effects, and to the shared influence of both factors. Spatial patterns in the ecological component are stronger than those in the original body size data. More importantly, the magnitude of intraspecific body size patterns (as measured by the correlation coefficient between body size and latitude) is significantly correlated with the ecological component across species, providing a unified interpretation for Bergmann's rule at multiple levels of biological hierarchy. This approach provides a better understanding of patterns in macroecological traits and allows improved understanding of their underlying ecological and evolutionary mechanisms.     

Construction and comparative analysis of two-component system and metabolic network profile based phylogenetic trees

In this study, two-component system (TCS) gene profile and metabolic network gene profile based phylogenetic trees were constructed and compared to each other to evaluate the evolutionary relationship between the bacterial sensing system and metabolism. The gene profiles of the these systems suggested that bacteria employed different evolutionary strategies to optimize the two-component system and metabolic network. In addition, comparative analysis revealed that the TCS based tree showed better family grouping than the metabolic network based tree, which indicated that the TCS and metabolic network have been modified via self-evolution and recruitment methods, respectively.     

Reconstruction of the cophylogenetic history of related phylogenetic trees with divergence timing information

In this paper, we present a method and a corresponding tool called Tarzan for cophylogeny analysis of phylogenetic trees where the nodes are labelled with divergence timing information. The tool can be used for example to infer the common history of hosts and their parasites, of insect–plant relations or symbiotic relationships. Our method does the reconciliation analysis using an event-based concept where each event is assigned a cost and cost minimal solutions are sought. The events that are used by Tarzan are cospeciations, sortings, duplications, and (host) switches. Different from existing tools Tarzan can handle more complex timing information of the phylogenetic trees for the analysis. This is important because several recent studies of cophylogenetic relationships have shown that timing information can be very important for the correct interpretation of results from cophylogenetic analysis. We present two examples (one host–parasite system and one insect–plant system) that show how divergence timing information can be integrated into reconciliation analysis and how this influences the results.     

Effect of co-evolving amino acid residues on topology of phylogenetic trees

The presence in proteins of amino acid residues that change in concert during evolution is associated with keeping constant the protein spatial structure and functions. As in the case with morphological features, correlated substitutions may become the cause of homoplasies--the independent evolution of identical non-homological adaptations. Our data obtained on model phylogenetic trees and corresponding sets of sequences have shown that the presence of correlated substitutions distorts the results of phylogenetic reconstructions. A method for accounting for co-evolving amino acid residues in phylogenetic analysis is proposed. According to this method, only a single site from the group of correlated amino acid positions should remain, whereas other positions should not be used in further phylogenetic analysis. Simulations performed have shown that replacement on the average of 8% of variable positions in a pair of model sequences by coordinately evolving amino acid residues is able to change the tree topology. The removal of such amino acid residues from sequences before phylogenetic analysis restores the correct topology.     

Socio-economic and ecological prospects for multiple use of protected areas in Africa

Largely triggered by the Bali debate, conservation literature over the last decade has seen increasing realization of man's responsibility in ensuring survival of the world's protected areas. In African terms, there has been an overwhelming number of pilot projects which have the people label. Whereas this trend has been ecouraging, the overall conservation picture has not been very bright as the wildlife resources have continued to dwindle under surmounting human pressure. The problem does not seem to be awareness of the necessity for protected areas any more but rather whether it is feasible under the present prevailing circumstances.     

Influence of functional unit on the life cycle assessment of traction batteries

Goal, Scope and Background This paper describes the influence of the choice of the functional unit on the results of an environmental assessment of different battery technologies for electric and hybrid vehicles. Battery, hybrid and fuel cell electric vehicles are considered as being environmentally friendly. However, the batteries they use are sometimes said to be environmentally unfriendly. At the current state of technology different battery types can be envisaged: lead-acid, nickel-cadmium, nickel-metal hydride, lithium-ion and sodium-nickel chloride. The environmental impacts described in this paper are based on a life cycle assessment (LCA) approach. One of the first critical stages of LCA is the definition of an appropriate and specific functional unit for electric and hybrid vehicle application. Most of the known LCA studies concerning batteries were performed while choosing different functional units, although this choice can influence the final results. An adequate functional unit, allowing to compare battery technologies in their real life vehicle application should be chosen. The results of the LCA are important as they will be used as a decision support for the end-of-life vehicles directive 2000/53/EC (Official Journal of the European Communities L269/24 2000). As a consequence, a thorough analysis is required to define an appropriate functional unit for the assessment of batteries for electric vehicles. This paper discusses this issue and will mainly focus on traction batteries for electric vehicles. Main Features An overview of the different parameters to be considered in the definition of a functional unit to compare battery technologies for battery electric vehicle application is described and discussed. An LCA study is performed for the most relevant potential functional units. SimaPro 6 is used as a software tool and Eco-indicator 99 as an impact assessment method. The influence of the different selected functional units on the results (Eco-indicator Points) is discussed. The environmental impact of the different electric vehicle battery technologies is described. A sensitivity analysis illustrates the robustness of the obtained results. Results and Discussion Five main parameters are considered in each investigated functional unit: an equal depth of discharge is assumed, a relative number of batteries required during the life of the vehicle is calculated, the energy losses in the battery and the additional vehicle consumption due to the battery mass is included and the same lifetime distance target is taken into account. On the basis of the energy content, battery mass, number of cycles and vehicle autonomy three suitable functional units are defined: ‘battery packs with an identical mass’, ‘battery packs with an identical energy content’ and ‘battery packs with an identical one-charge range’. The results show that the differences in the results between these three functional units are small and imply less variation on the results than the other uncertainties inherent to LCA studies. On the other hand, the results obtained using other, less adequate, functional units can be quite different. Conclusions When performing an LCA study, it’s important to choose an appropriate functional unit. Most of the time, this choice is unambiguous. However, sometimes this choice is more complicated when different correlated parameters have to be considered, as it is the case for traction batteries. When using a realistic functional unit, the result is not influenced significantly by the choice of one out of the three suitable functional units. Additionally, the life cycle assessment allowed concluding that three electric vehicle battery technologies have a comparable environmental impact: lead-acid, nickel-cadmium and nickel-metal hydride. Lithium-ion and sodium-nickel chloride have lower environmental impacts than the three previously cited technologies when used in a typical battery electric vehicle application. Recommendations and Perspectives The article describes the need to consider all relevant parameters for the choice of a functional unit for an electric vehicle battery, as this choice can influence the conclusions. A more standardised method to define the functional unit could avoid these differences and could make it possible to compare the results of different traction battery LCA studies more easily.     

The morphology of the European miocene hominid frontal bone: functional,developmental and phylogenetic considerations

This paper re-interprets the morphology of fossil and extant hominid frontal bones in light of development, functional and phylogenetic considerations. It is argued that the suggested inclusion of Hispanopithecus and Ankarapithecus as members of the Ponginae (which has partly been based on frontal bone morphology) remains problematic as their similarity with other members of the Ponginae is likely the result of distinct developmental processes resulting in Hispanopithecus and Ankarapithecus sharing an anatomical analogy with this subfamily. Whether this can be used to argue against their inclusion within the Ponginae remains debatable, as we still do not appreciate degrees of developmental variability within and between taxa, nor their phylogenetic significance in closely related taxa. The frontal bone morphology as observed in Hispanopithecus and Ankarapithecus, however, suggests that they share a sister-group relationship. In terms of the Homininae, Graecopithecus is supported as a likely member of this subfamily, while Dryopithecus is considered as a primitive member of the Hominidae.     

Finding the tree of life: matching phylogenetic trees to the fossil record through the 20th century

Phylogenies, or evolutionary trees, are fundamental to biology. Systematists have laboured since the time of Darwin to discover the tree of life. Recent developments in systematics, such as cladistics and molecular sequencing, have led practitioners to believe that their phylogenies are more testable now than equivalent efforts from the 1960s or earlier. Whole trees, and nodes within trees, may be assessed for their robustness. However, these quantitative approaches cannot be used to demonstrate that one tree is more likely to be correct than another. Congruence assessments may help. Comparison of a sample of 1000 published trees with an essentially independent standard (dates of origin of groups in geological time) shows that the order of branching has improved slightly, but the disparity between estimated times of origination from phylogeny and stratigraphy has, if anything, become worse. Controlled comparisons of phylogenies of four major groups (Agnatha, Sarcopterygii, Sauria and Mammalia) do not show uniform improvement, or decline, of fit to stratigraphy through the twentieth century. Nor do morphological or molecular trees differ uniformly in their performance.