Genome trees and the tree of life

Genome comparisons indicate that horizontal gene transfer and differential gene loss are major evolutionary phenomena that, at least in prokaryotes, involve a large fraction, if not the majority, of genes. The extent of these events casts doubt on the feasibility of constructing a 'Tree of Life', because the trees for different genes often tell different stories. However, alternative approaches to tree construction that attempt to determine tree topology on the basis of comparisons of complete gene sets seem to reveal a phylogenetic signal that supports the three-domain evolutionary scenario and suggests the possibility of delineation of previously undetected major clades of prokaryotes. If the validity of these whole-genome approaches to tree building is confirmed by analyses of numerous new genomes, which are currently being sequenced at an increasing rate, it would seem that the concept of a universal 'species' tree is still appropriate. However, this tree should be reinterpreted as a prevailing trend in the evolution of genome-scale gene sets rather than as a complete picture of evolution.     

Cutting of lichen trees: a survival strategy used before the 20th century in northern Sweden

Sami reindeer herders in northern Fennoscandia have historically cut trees with high quantities of arboreal lichens to feed their animals during harsh winters. In this study we analysed temporal and spatial patterns of lichen-tree cuttings of Scots pine in a remote forest landscape in northern Sweden. We wanted to test the hypothesis that repeated cutting of such trees may have had long-lasting effects on the forest ecosystem that are still discernable today. Our analyses included an inventory of remaining lichen-tree stumps, and a field survey of forest variables to relate structural variation within the forest to these cuttings. We used dendrochronological methods to date stumps and reconstruct forest structure. Our results show that more than 7,000 trees were cut for this purpose over a period of almost 300 years within an area covering 6 km². Lichen-tree cutting was most intense during the late 18th century when ca. 600–1,000 trees were cut during each decade. We did not detect any significant relationship between past lichen-tree cutting and present small-scale forest heterogeneity, and suggest that this might be due to the small size of the cut trees and the long time elapsed since most of the cuttings. We conclude that vestiges such as stumps from lichen-tree cutting are highly valuable for our understanding of past land use. Furthermore, since they are located in an unlogged and very old forest, this highlights the need to acknowledge the interconnectedness between ecological and cultural values of such forests and the need to identify and protect them.     

Species trees for the tree swallows (Genus Tachycineta): An alternative phylogenetic hypothesis to the mitochondrial gene tree

The New World swallow genus Tachycineta comprises nine species that collectively have a wide geographic distribution and remarkable variation both within- and among-species in ecologically important traits. Existing phylogenetic hypotheses for Tachycineta are based on mitochondrial DNA sequences, thus they provide estimates of a single gene tree. In this study we sequenced multiple individuals from each species at 16 nuclear intron loci. We used gene concatenated approaches (Bayesian and maximum likelihood) as well as coalescent-based species tree inference to reconstruct phylogenetic relationships of the genus. We examined the concordance and conflict between the nuclear and mitochondrial trees and between concatenated and coalescent-based inferences. Our results provide an alternative phylogenetic hypothesis to the existing mitochondrial DNA estimate of phylogeny. This new hypothesis provides a more accurate framework in which to explore trait evolution and examine the evolution of the mitochondrial genome in this group.     

Rooting the tree of life: the phylogenetic jury is still out

This article aims to shed light on difficulties in rooting the tree of life (ToL) and to explore the (sociological) reasons underlying the limited interest in accurately addressing this fundamental issue. First, we briefly review the difficulties plaguing phylogenetic inference and the ways to improve the modelling of the substitution process, which is highly heterogeneous, both across sites and over time. We further observe that enriched taxon samplings, better gene samplings and clever data removal strategies have led to numerous revisions of the ToL, and that these improved shallow phylogenies nearly always relocate simple organisms higher in the ToL provided that long-branch attraction artefacts are kept at bay. Then, we note that, despite the flood of genomic data available since 2000, there has been a surprisingly low interest in inferring the root of the ToL. Furthermore, the rare studies dealing with this question were almost always based on methods dating from the 1990s that have been shown to be inaccurate for much more shallow issues! This leads us to argue that the current consensus about a bacterial root for the ToL can be traced back to the prejudice of Aristotle''s Great Chain of Beings, in which simple organisms are ancestors of more complex life forms. Finally, we demonstrate that even the best models cannot yet handle the complexity of the evolutionary process encountered both at shallow depth, when the outgroup is too distant, and at the level of the inter-domain relationships. Altogether, we conclude that the commonly accepted bacterial root is still unproven and that the root of the ToL should be revisited using phylogenomic supermatrices to ensure that new evidence for eukaryogenesis, such as the recently described Lokiarcheota, is interpreted in a sound phylogenetic framework.     

20th century at a glance: the streptomycin story

The discovery of streptomycin is attributed to a microbiologist, Selman Waksman, Nobel Prize 1952, a paternity that was disputed by his collaborator Albert Schatz, who was the first author of the princeps article. Two pioneering clinical studies involved streptomycin, both of which have been widely used as reference works. The first one was English, under the name of Austin Bradford Hill. It inaugurated a randomization in medicine. The second trial was American, and carried out by the Veteran Administration. It made use for the first time of the "control group". The present article analyses the genesis of clinical trials and illustrates the recurrent difficulties encountered in their implementation.     

Effect of seasonal hypoxia on the benthic foraminiferal community of the Louisiana inner continental shelf: The 20th century record

A species census in sediment core samples reveals significant changes in the composition of the Louisiana-shelf benthic foraminiferal community in the past century; these changes can be explained by an increase in the severity of seasonal hypoxia in bottom waters. Agglutinated and porcelaneous orders living in water depths less than 60 m suffered a noticeable decline during this time. In particular, the genus Quinqueloculina was severely affected by the progression of hypoxia, and nearly disappeared from parts of the study area. In contrast, several hyaline taxa, especially Nonionella basiloba, Buliminella morgani, and Epistominella vitrea, tolerated the progressive oxygen depletion well. Results of cluster and principal components analyses of the foraminiferal assemblage data match the observed species distribution trends and indicate that seasonal hypoxia on the Louisiana shelf, related to eutrophication and water stratification, worsened in the past century, even near the outer edge of the present-day zone of spring and summer oxygen depletion. The temporal trends in the foraminiferal record correspond to that of fertilizer use in the U.S. and nitrogen loading in the Mississippi River, suggesting that the anthropogenic factor has been particularly strong in the development of coastal hypoxia since the early 1940s.     

A small skull from Flores dated to the 20th century

A human skull with mandible from the Ngada District on the island of Flores, Indonesia, is described in order to contribute to the knowledge of variation in cranial architecture, which is important in interpretations of evolutionary cerebralisation. The skull was excavated in 1924 and sent to the National Museum in Copenhagen. The “Copenhagen Flores” (CF) male skull is radiocarbon-dated and of modern age. The cranium is small, but larger than e.g. Liang Bua skull (LB1) in every measurement. The (CT-scan based) cranial capacity of 1258 ml is normal for modern humans, but somewhat lower than values from the middle or upper Palaeolithics. The metric cranial data analysed in FORDISC, characterize the skull as a male Vietnamese rather than a Chinese or White individual. Tooth morphology shows the sundadont pattern and tooth size corresponds to that of teeth from Bali, Java and Malayan Orang Asli. Remarkable are the marked asymmetries in the dentition with rotation of an upper premolar and congenital absence of a third molar. In these respects the CF skull is similar to dentitions belonging to the pygmoid villagers of Rampasasa, a village not far from the Liang Bua cave, and to LB1.     

Conserving the functional and phylogenetic trees of life of European tetrapods

Protected areas (PAs) are pivotal tools for biodiversity conservation on the Earth. Europe has had an extensive protection system since Natura 2000 areas were created in parallel with traditional parks and reserves. However, the extent to which this system covers not only taxonomic diversity but also other biodiversity facets, such as evolutionary history and functional diversity, has never been evaluated. Using high-resolution distribution data of all European tetrapods together with dated molecular phylogenies and detailed trait information, we first tested whether the existing European protection system effectively covers all species and in particular, those with the highest evolutionary or functional distinctiveness. We then tested the ability of PAs to protect the entire tetrapod phylogenetic and functional trees of life by mapping species'' target achievements along the internal branches of these two trees. We found that the current system is adequately representative in terms of the evolutionary history of amphibians while it fails for the rest. However, the most functionally distinct species were better represented than they would be under random conservation efforts. These results imply better protection of the tetrapod functional tree of life, which could help to ensure long-term functioning of the ecosystem, potentially at the expense of conserving evolutionary history.     

Seed Physiology: Its History from antiquity to the beginning of the 20th century

Seed physiology, especially seed germination, has intrigued the human mind since antiquity, partly out of curiosity, partly because of practical reasons. Theophrastus could be called the father of seed physiology since he already described many of the facts and problems which up to this day are being investigated by seed physiologists. Most of the other ancient authors writing about natural history or agriculture (Columella, Varro, Pliny the elder, Virgil) added little to Theophrastus’ all encompassing knowledge of seed physiology. The 1700 years from the first century A.D. to the end of the 18th century were a “black out” (Johansen, 1951) of seed physiology. At the beginning of the 19th century people like Schleiden, Amici, Brown and Hofmeister first understood structure and function of ovule, embryo sac and pollen tube whereas fertilization and double fertilization were only detected at the end of the 19th century by Strasburger, Nawaschin and Guignard. The physiology and biochemistry of seed maturation were first investigated by Sachs and Pfeffer, two great masters of modern plant physiology. In modern times our detailed knowledge of the effect of external factors on seed germination is due to the many authors working at the end of the 19th and the beginning of the 20th centuries. Our knowledge of the impact of temperature on germination derives mainly from the investigations of Sachs, De Vries and Haberlandt, and of light from those of Caspary, Cieslar, Heinricher and Kinzel. The action spectrum of light was first investigated by Cieslar, and Flint and McAllister whereas the most important discovery of the effect of light on germination (and on many other physiological phenomena), the R-FR photoreversible system, was made by Borthwick et al. leading later to the discovery of the phytochrome. The first germination inhibiting and stimulating substances were found by Siegmund and Lehman. The long history of seed physiology should make today’s seed physiologists conscious of the fact that they stand on the “shoulders of giants.”     

The quality of the fossil record and the accuracy of phylogenetic inferences about sampling and diversity

Because phylogenies can be estimated without stratigraphic data and because estimated phylogenies also infer gaps in sampling, some workers have used phylogeny estimates as templates for evaluating sampling from the fossil record and for "correcting" historical diversity patterns. However, it is not known how sampling intensity (the probability of sampling taxa per unit time) and completeness (the proportion of taxa sampled) affect the accuracy of phylogenetic inferences, nor how phylogenetically inferred estimates of sampling and diversity respond to inaccurate estimates of phylogeny. Both issues are addressed with a series of simulations using simple models of character evolution, varying speciation patterns, and various rates of speciation, extinction, character change, and preservation. Parsimony estimates of simulated phylogenies become less accurate as sampling decreases, and inaccurate trees chronically underestimate sampling. Biotic factors such as rates of morphologic change and extinction both affect the accuracy of phylogenetic estimates and thus affect estimated gaps in sampling, indicating that differences in implied sampling need not reflect actual differences in sampling. Errors in inferred diversity are concentrated early in the history of a clade. This, coupled with failure to account for true extinction times (i.e., the Signor-Lipps effect), inflates relative diversity levels early in clade histories. Because factors other than differences in sampling predict differences in the numbers of gaps implied by phylogeny estimates, inferred phylogenies can be misleading templates for evaluating sampling or historical diversity patterns.     

The development of biochemistry in the 20th century

Summary This lecture consists of a short appraisal of some of the main features that have characterized the growth of biochemistry during the course of the 20th century. It dwells on the early impacts of vitalism, the emergence and elucidation of the vitamins, the discovery of coenzymes, the concept of active centres of enzymes, the development of experimental techniques (including the use of isotopes), the genetic code, and on the development of molecular biology and closely allied fields of investigation. It concludes with a consideration of the influence of the study of membranes and of neurochemistry on current biochemical thought.Résumé Dans cet exposé, nous examinons brièvement certains des principaux aspects qui ont caractérisé la croissance de la biochimie au cours du 20^e siècle. Nous insistons sur les premiers impacts du vitalisme, l'émer-gence et la mise en lumière des vitamines, la découverte des coenzymes, le concept des centres actifs dans les enzymes, le développement des techniques expérimentales (y compris l'emploi des isotopes), le code genetique et le développement de la biologie moléculaire et des domaines étroitement apparentés de la recherche. En conclusion, nous considérons l'influence de l'étude des membranes et de la neurochimie sur la pensée biochimique actuelle.The substance of this paper was presented in the Rossiter Research Conference Structure and Function of Biological Membranes held October 1–4, 1983, at the Geneva Park Conference Centre, Lake Couchiching, Ont.Professor Emeritus (Neurochemistry) at University of British Columbia.     

Admixture studies in Latin America: from the 20th to the 21st century

The present study is a review of admixture studies in Latin America, an interesting subject because of the unique history of the area, in which populations from 3 different origins had contact and intercrossed. The most often used methods of analysis of admixture in Latin America and some problems related to them, such as the determination of the parental populations and selection of genetic markers, are briefly reviewed. Several sources of data for admixture studies (surnames, quantitative traits, proteins, and molecular information) are summarized. The results obtained using protein systems and blood groups, the most often used markers in Latin America, are considered. They are classified according to their application in 3 groups of populations: urban centers, native Americans, and African-descended subjects. The data show that almost every population is dihybrid or trihybrid, and when African influence is not detected, it is probably due more to the method than to an absence of that contribution. A special section is dedicated to the direction of gene flow, and results about directional mating based on mtDNA, Y-chromosome, and nuclear DNA or proteins are also given. From these studies it is possible to conclude that Amerindian admixture came mainly from female lineages, but it is difficult to establish what happened with the African contribution. A last subject considered is the relation between interethnic crosses and diseases; it is easy to analyze that relation when the pathological condition is related to a unique allele, but when complex diseases are considered, the results are not as clear because of the influence of nongenetic factors. Finally, the perspectives for admixture studies in the 21st century are considered, and some attempts to predict their future in Latin America are made.     

Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees

Phylogenetic analyses using genome-scale data sets must confront incongruence among gene trees, which in plants is exacerbated by frequent gene duplications and losses. Gene tree parsimony (GTP) is a phylogenetic optimization criterion in which a species tree that minimizes the number of gene duplications induced among a set of gene trees is selected. The run time performance of previous implementations has limited its use on large-scale data sets. We used new software that incorporates recent algorithmic advances to examine the performance of GTP on a plant data set consisting of 18,896 gene trees containing 510,922 protein sequences from 136 plant taxa (giving a combined alignment length of >2.9 million characters). The relationships inferred from the GTP analysis were largely consistent with previous large-scale studies of backbone plant phylogeny and resolved some controversial nodes. The placement of taxa that were present in few gene trees generally varied the most among GTP bootstrap replicates. Excluding these taxa either before or after the GTP analysis revealed high levels of phylogenetic support across plants. The analyses supported magnoliids sister to a eudicot + monocot clade and did not support the eurosid I and II clades. This study presents a nuclear genomic perspective on the broad-scale phylogenic relationships among plants, and it demonstrates that nuclear genes with a history of duplication and loss can be phylogenetically informative for resolving the plant tree of life.