Depicting the Tree of Life: the Philosophical and Historical Roots of Evolutionary Tree Diagrams

It is a popularly held view that Darwin was the first author to draw a phylogenetic tree diagram. However, as is the case with most popular beliefs, this one also does not hold true. Firstly, Darwin never called his diagram of common descent a tree. Secondly, even before Darwin, tree diagrams were used by a variety of philosophical, religious, and secular scholars to depict phenomena such as “logical relationships,” “affiliations,” “genealogical descent,” “affinity,” and “historical relatedness” between the elements portrayed on the tree. Moreover, historically, tree diagrams themselves can be grouped into a larger class of diagrams that were drawn to depict natural and/or divine order in the world. In this paper, we trace the historical roots and cultural meanings of these tree diagrams. It will be demonstrated that tree diagrams as we know them are the outgrowth of ancient philosophical attempts to find the “true order” of the world, and to map the world “as it is” (ontologically), according to its true essence. This philosophical idea would begin a fascinating journey throughout Western European history. It lies at the foundation of the famous “scala naturae,” as well as religious and secular genealogical thinking, especially in regard to divine, familial (kinship), and linguistic pedigrees that were often depicted by tree images. These scala naturae would fuse with genealogical, pedigree thinking, and the trees that were the result of this blend would, from the nineteenth century onward, also include the element of time. The recognition of time would eventually lead to the recognition of evolution as a fact of nature, and subsequently, tree iconographies would come to represent exclusively the evolutionary descent of species.     

Fossil Horses, Orthogenesis, and Communicating Evolution in Museums

The 55-million-year fossil record of horses (Family Equidae) has been frequently cited as a prime example of long-term macroevolution. In the second half of the nineteenth century, natural history museum exhibits characteristically depicted fossil horses to be a single, straight-line (orthogenetic) progression from ancestor to descendent. By the beginning of the twentieth century, however, paleontologists realized that, rather than representing orthogenesis, the evolutionary pattern of fossil horses was more correctly characterized by a complexly branching phylogenetic tree. We conducted a systematic survey of 20 fossil horse exhibits from natural history museums in the United States. Our resulting data indicate that more than half (55%) of natural history museums today still depict horse evolution as orthogenetic, despite the fact that paleontologists have known for a century that the actual evolutionary pattern of the Family Equidae is branching. Depicting outmoded evolutionary patterns and concepts via museum exhibits, such as fossils horses exemplifying orthogenesis, not only communicates outmoded knowledge but also likely contributes to general misconceptions about evolution for natural history museum visitors.     

中生代银杏类植物系统发育、分类和演化趋向

长期以来银杏类植物化石分类都依据营养叶形态为基础。由于叶形态的多型性和异源性,导致分类和系统发育解释的紊乱。根据对保存完好的繁殖器官(胚珠器官)系统发育分析结果所作的银杏目分类表明中生代除了银杏和银杏科以外,至少还存在着3．5个已灭绝的科级单元。此方案把已知其繁殖器官的成员和仅仅根据营养器官建立起来的分类位置不明的属严格地区分开来,并注明各科的限定性特征和已知成员的地质地理分布。银杏目植物自古生代起源,至早中生代以后朝着不同的方向辐射,呈现出丰富的多样性并经历了错综复杂的演化过程,其总的演化趋向是退缩：叶片扁化、蹊化和融合;胚珠器官简化,胚珠增大、数目减少,珠柄趋于消失。     

The Bayesian Paradigm and Tree Diagrams with Applications in Genetics

Probability tree diagrams are developed for the calculation and interpretation of conditional probabilities. Their use in Bayesian calculations and, most importantly, for the correct interpretation of results is described. Key practical applications to linkage analysis and evaluation of evidentiary DNA material given.     

Tree Reconciliation: Reconstruction of Species Phylogeny by Phylogenetic Gene Trees

It is well known that phylogenetic trees derived from different protein families are often incongruent. This is explained by mapping errors and by the essential processes of gene duplication, loss, and horizontal transfer. Therefore, the problem is to derive a consensus tree best fitting the given set of gene trees. This work presents a new method of deriving this tree. The method is different from the existing ones, since it considers not only the topology of the initial gene trees, but also the reliability of their branches. Thereby one can explicitly take into account the possible errors in the gene trees caused by the absence of reliable models of sequence evolution, by uneven evolution of different gene families and taxonomic groups, etc.     

Phylogeny and Evolutionary Patterns in the Dwarf Crayfish Subfamily (Decapoda: Cambarellinae)

The Dwarf crayfish or Cambarellinae, is a morphologically singular subfamily of decapod crustaceans that contains only one genus, Cambarellus. Its intriguing distribution, along the river basins of the Gulf Coast of United States (Gulf Group) and into Central México (Mexican Group), has until now lacked of satisfactory explanation. This study provides a comprehensive sampling of most of the extant species of Cambarellus and sheds light on its evolutionary history, systematics and biogeography. We tested the impact of Gulf Group versus Mexican Group geography on rates of cladogenesis using a maximum likelihood framework, testing different models of birth/extinction of lineages. We propose a comprehensive phylogenetic hypothesis for the subfamily based on mitochondrial and nuclear loci (3,833 bp) using Bayesian and Maximum Likelihood methods. The phylogenetic structure found two phylogenetic groups associated to the two main geographic components (Gulf Group and Mexican Group) and is partially consistent with the historical structure of river basins. The previous hypothesis, which divided the genus into three subgenera based on genitalia morphology was only partially supported (P = 0.047), resulting in a paraphyletic subgenus Pandicambarus. We found at least two cases in which phylogenetic structure failed to recover monophyly of recognized species while detecting several cases of cryptic diversity, corresponding to lineages not assigned to any described species. Cladogenetic patterns in the entire subfamily are better explained by an allopatric model of speciation. Diversification analyses showed similar cladogenesis patterns between both groups and did not significantly differ from the constant rate models. While cladogenesis in the Gulf Group is coincident in time with changes in the sea levels, in the Mexican Group, cladogenesis is congruent with the formation of the Trans-Mexican Volcanic Belt. Our results show how similar allopatric divergence in freshwater organisms can be promoted through diverse vicariant factors.     

Phylogeny and Evolutionary History of the Ground Squirrels (Rodentia: Marmotinae)

Although ground squirrels (Spermophilus) and prairie dogs (Cynomys) are among the most intensively studied groups of mammals with respect to their ecology and behavior, a well-resolved phylogeny has not been available to provide a framework for comparative and historical analyses. We used complete mitochondrial cytochrome b sequences to construct a phylogeny that includes all 43 currently recognized species in the two genera, as well as representatives of two closely related genera (Marmota and Ammospermophilus). In addition, divergence times for ground squirrel lineages were estimated using Bayesian techniques that do not assume a molecular clock. All methods of phylogenetic analysis recovered the same major clades, and showed the genus Spermophilus to be paraphyletic with respect to both Marmota and Cynomys. Not only is the phylogeny at odds with previous hypotheses of ground squirrel relationships, but it suggests that convergence in morphology has been a common theme in ground squirrel evolution. A well-supported basal clade, including Ammospermophilus and two species in the subgenus Otospermophilus, diverged from all other ground squirrels an estimated 17.5 million years ago. Between 10 and 14 million years ago, a relatively rapid diversification gave rise to lineages leading to marmots and to several distinct groups of ground squirrels. The Eurasian ground squirrels diverged from their North American relatives during this period, far earlier than previously hypothesized. This period of diversification corresponded to warming climate and spread of grasslands in western North America and Eurasia. Close geographic proximity of related forms suggests that most species evolved in or near their current ranges.     

The Evolutionary History of Protein Domains Viewed by Species Phylogeny

Background

Protein structural domains are evolutionary units whose relationships can be detected over long evolutionary distances. The evolutionary history of protein domains, including the origin of protein domains, the identification of domain loss, transfer, duplication and combination with other domains to form new proteins, and the formation of the entire protein domain repertoire, are of great interest.

Methodology/Principal Findings

A methodology is presented for providing a parsimonious domain history based on gain, loss, vertical and horizontal transfer derived from the complete genomic domain assignments of 1015 organisms across the tree of life. When mapped to species trees the evolutionary history of domains and domain combinations is revealed, and the general evolutionary trend of domain and combination is analyzed.

Conclusions/Significance

We show that this approach provides a powerful tool to study how new proteins and functions emerged and to study such processes as horizontal gene transfer among more distant species.     

Shaking the Tree: Multi-locus Sequence Typing Usurps Current Onchocercid (Filarial Nematode) Phylogeny

During the past twenty years, a number of molecular analyses have been performed to determine the evolutionary relationships of Onchocercidae, a family of filarial nematodes encompassing several species of medical or veterinary importance. However, opportunities for broad taxonomic sampling have been scarce, and analyses were based mainly on 12S rDNA and coxI gene sequences. While being suitable for species differentiation, these mitochondrial genes cannot be used to infer phylogenetic hypotheses at higher taxonomic levels. In the present study, 48 species, representing seven of eight subfamilies within the Onchocercidae, were sampled and sequences of seven gene loci (nuclear and mitochondrial) analysed, resulting in the hitherto largest molecular phylogenetic investigation into this family. Although our data support the current hypothesis that the Oswaldofilariinae, Waltonellinae and Icosiellinae subfamilies separated early from the remaining onchocercids, Setariinae was recovered as a well separated clade. Dirofilaria, Loxodontofilaria and Onchocerca constituted a strongly supported clade despite belonging to different subfamilies (Onchocercinae and Dirofilariinae). Finally, the separation between Splendidofilariinae, Dirofilariinae and Onchocercinae will have to be reconsidered.     

Search for Clues to the Evolutionary Meaning of Ciliate Phylogeny*†

SYNOPSIS. Progress in ciliatology and in allied fields may demystify ciliate phylogenetics. Concentration on hymenostomes (mainly Tetrahymena and Paramecium) may have obscured directional features of ciliate physiology in phylogenetic problems. Therefore, means are suggested for “domesticating” the presumptively primitive, predominantly marine, sand-dwelling gymnostomes having nondividing diploid macronuclei. The prize quarry is the marine psammophile Stephanopogon whose homokaryotic condition may mark it as a living fossil. Eventual axenic cultivation of these “primitive” ciliates may be aided by use as food of easily grown photosynthetic prokaryotes, some isolated from the marine sulfuretum or adjacent aerobic muds and sands where “karyorelictid” ciliates flourish. We assume that: (a) the macronucleus evolved as a coordinator of chemical and physical signals, for efficient detection of food and toxins; (b) oral structures evolved meanwhile as sensors as well as mechanical food-gatherers. This conjunction enabled complexity of adaptive behavior and evolutionary success. Ciliate origins cannot be considered apart from origin(s) of phagotrophy and its underlying versatile heterotrophy. Because of the well developed heterotrophy in some photosynthetic prokaryotes (including several proposed as food organisms), they are viewed as alternatives to blue-green algae as forebears of eukaryotes. Nor can ciliate origins be considered apart from origin(s) of eukaryotes. A check of these assumptions—that Stephanopogon and gymnostomes with nondividing macronuclei are primitive—may be forthcoming from sequencing amino acids in certain key enzymes, given an adequate sampling of ciliates, flagellates (especially dinoflagellates and cryptomonads), lower fungi, and photosynthetic prokaryotes other than blue-green algae.     

Investigating Morphospace Occupation in Multi-Scale Ecological and Evolutionary Data Using Regression Tree: Case Studies and Perspectives

A key challenge in ecology and evolutionary biology is to explain the origin, structure and temporal patterns of phenotypic diversity. With regard to the potentially complex determinism of phenotypic differences, the issue should be comprehended in a general view, across multiple scales and an increasing number of phenomic studies investigate shape variation through large taxonomic, biogeographic or temporal scales. In this context, there is an ever-increasing need to develop new tools for a coherent understanding of morphospace occupation by disentangling and quantifying the main determinants of phenotypic changes. The present study briefly introduce the possibility to use multivariate regression tree technique to cope with morphological data, as embedded in a geometric morphometric framework. It emphasizes that hierarchical partitioning methods produce a hierarchy between causal variables that may help analyzing complexity in multi-scale ecological and evolutionary data. I therefore suggest that morphological studies would benefit from the combined use of the classical statistical models with rapidly emerging and diversifying methods of machine-learning. Doing so allows one to primary explore in an extensive exploratory manner the hierarchy of nested organisational levels underlying morphological variation, and then conduct hypothesis-driven analysis by focusing on a relevant scale or by investigating the appropriate model that reflects hypothesized nested influence of explanatory variables. The outlined approach may help investigating morphospace occupation in an explicitly hierarchical quantitative context.     

The Bryophyta (Mosses): Systematic and Evolutionary Inferences from an rps4 Gene (cpDNA) Phylogeny

Phylogenetic analyses of nucleotide and amino acid sequencesof the chloroplast protein coding generps4 were performed for225 species of mosses, representing 84% of families recognizedby Vitt (1984. In: Schuster RM, ed. New manual of bryology,vol 2. Nichinan: Hattori Botanical Laboratory), under the criterionof maximum parsimony with Takakia and Sphagnum as outgroups.Most parsimonious topologies converge to a scenario whereinthe Andreaeidae are monophyletic and sister to the Bryidae (peristomatemosses), the Nematodonteae and the Buxbaumiaceae form a monophyleticlineage, the Diphysciaceae are sister to the Arthrodonteae and,within the latter, the Funarineae-Encalyptineae-Timmiaceae-Haplolepideaecompose a monophyletic clade sister to remaining diplolepideousmosses. This hypothesis suggests that early in the evolutionof the Arthrodonteae, two major lineages diverged, with oppositeand alternate peristomes, respectively. Bootstrap support forthe deep dichotomies is poor or lacking but increases when proteintranslations ofrps 4 sequences are included in the analysis.Several novel systematic hypotheses are raised, including (a)a diplolepideous rather than haplolepideous origin of the Pleurophascaceae;(b) an affinity of the Catascopiaceae with the Funariineae ratherthan the Bryineae; and (c) a close relationship of the Calomniaceaeand Mitteniaceae to the Rhizgoniaceae. The advantages and disadvantagesof a single gene phylogeny are discussed with respect to theidentification of polyphyletic familial or suprafamilial taxa.Copyright 2001 Annals of Botany Company Bryophyta, mosses, phylogeny, rps4, evolution, peristome, parsimony, sequences     

Molecular Phylogeny of Echiuran Worms (Phylum: Annelida) Reveals Evolutionary Pattern of Feeding Mode and Sexual Dimorphism

The Echiura, or spoon worms, are a group of marine worms, most of which live in burrows in soft sediments. This annelid-like animal group was once considered as a separate phylum because of the absence of segmentation, although recent molecular analyses have placed it within the annelids. In this study, we elucidate the interfamily relationships of echiuran worms and their evolutionary pattern of feeding mode and sexual dimorphism, by performing molecular phylogenetic analyses using four genes (18S, 28S, H3, and COI) of representatives of all extant echiuran families. Our results suggest that Echiura is monophyletic and comprises two unexpected groups: [Echiuridae+Urechidae+Thalassematidae] and [Bonelliidae+Ikedidae]. This grouping agrees with the presence/absence of marked sexual dimorphism involving dwarf males and the paired/non-paired configuration of the gonoducts (genital sacs). Furthermore, the data supports the sister group relationship of Echiuridae and Urechidae. These two families share the character of having anal chaetae rings around the posterior trunk as a synapomorphy. The analyses also suggest that deposit feeding is a basal feeding mode in echiurans and that filter feeding originated once in the common ancestor of Urechidae. Overall, our results contradict the currently accepted order-level classification, especially in that Echiuroinea is polyphyletic, and provide novel insights into the evolution of echiuran worms.     

Reticulate Evolutionary History of a Complex Group of Grasses: Phylogeny of Elymus StStHH Allotetraploids Based on Three Nuclear Genes

Background

Elymus (Poaceae) is a large genus of polyploid species in the wheat tribe Triticeae. It is polyphyletic, exhibiting many distinct allopolyploid genome combinations, and its history might be further complicated by introgression and lineage sorting. We focus on a subset of Elymus species with a tetraploid genome complement derived from Pseudoroegneria (genome St) and Hordeum (H). We confirm the species'' allopolyploidy, identify possible genome donors, and pinpoint instances of apparent introgression or incomplete lineage sorting.

Methodology/Principal Findings

We sequenced portions of three unlinked nuclear genes—phosphoenolpyruvate carboxylase, β-amylase, and granule-bound starch synthase I—from 27 individuals, representing 14 Eurasian and North American StStHHElymus species. Elymus sequences were combined with existing data from monogenomic representatives of the tribe, and gene trees were estimated separately for each data set using maximum likelihood. Trees were examined for evidence of allopolyploidy and additional reticulate patterns. All trees confirm the StStHH genome configuration of the Elymus species. They suggest that the StStHH group originated in North America, and do not support separate North American and European origins. Our results point to North American Pseudoroegneria and Hordeum species as potential genome donors to Elymus. Diploid P. spicata is a prospective St-genome donor, though conflict among trees involving P. spicata and the Eurasian P. strigosa suggests either introgression of GBSSI sequences from P. strigosa into North American Elymus and Pseudoroegneria, or incomplete lineage sorting of ancestral GBSSI polymorphism. Diploid H. californicum and/or allotetraploid H. jubatum are possible H-genome donors; direct involvement of an allotetraploid Hordeum species would simultaneously introduce two distinct H genomes to Elymus, consistent with some of the relationships among H-genome sequences in Hordeum and Elymus.

Conclusions/Significance

Comparisons among molecular phylogenetic trees confirm allopolyploidy, identify potential genome donors, and highlight cases of apparent introgression or incomplete lineage sorting. The complicated history of this group emphasizes an inherent problem with interpreting conflicts among bifurcating trees—identifying introgression and determining its direction depend on which tree is chosen as a starting point of comparison. In spite of difficulties with interpretation, differences among gene trees allow us to identify reticulate species and develop hypotheses about underlying evolutionary processes.     

Explanation in Two Dimensions: Diagrams and Biological Explanation

Molecular biologists and biochemists often use diagrams to present hypotheses. Analysis of diagrams shows that their content can be expressed with linguistic representations. Why do biologists use visual representations instead? One reason is simple comprehensibility: some diagrams present information which is readily understood from the diagram format, but which would not be comprehensible if the same information was expressed linguistically. But often diagrams are used even when concise, comprehensible linguistic alternatives are available. I explain this phenomenon by showing why diagrammatic representation is especially well suited for a particular kind of explanation common in molecular biology and biochemistry: namely, functional analysis, in which a capacity of the system is explained in terms of capacities of its component parts.     

Evolutionary Origin of Nonuniversal Cug(ser) Codon in Some Candida Species as Inferred from a Molecular Phylogeny

CUG, a universal leucine codon, has been reported to be read as serine in various yeast species belonging to the genus Candida. To gain a deeper insight into the origin of this deviation from the universal genetic code, we carried out a phylogenetic analysis based on the small-subunit ribosomal RNA genes from some Candida and other related Hemiascomycetes. Furthermore, we determined the phylogenetic relationships between the tRNA(Ser)CAG, responsible for the translation of CUG, from some Candida species and the other serine and leucine isoacceptor tRNAs in C. cylindracea. We demonstrate that the group of Candida showing the genetic code deviation is monophiletic and that this deviation could have been originated more than 150 million years ago. We also describe how phylogenetic analysis can be used for genetic code predictions.