On the benefits and difficulties of obtaining 'complete' phylogenetic trees, with examples from plants
I will mainly use our ongoing studies of the woody angiosperm clade Viburnum to provide examples of the role that phylogenetic trees can play in integrating information across disciplines. One example connects phylogenies with patterns of geographic movement in response to global change. A second example connects a global spatial pattern in leaf form to details of anatomy, physiology, and geometric models. A third one features the generation and experimental testing of a hypothesis on plant-animal interactions. An overriding theme is the increasing value and the great difficulty of obtaining 'complete' phylogenies, as opposed to very large, but sparsely sampled, trees. I will argue that sparsely sampled trees will seldom provide the level of detail necessary to provide highly satisfying answers to real biological problems.
Hot spots in the coevolution of life and Earth
S Blair Hedges（ペンシルバニア州立大学）
Knowing the history of life on Earth will reveal much about evolutionary mechanisms and the coevolution of life and the planet, but we're not there yet. This is still the age of discovery for evolutionary biology, and breakthroughs often come after learning two basic things about a group of organisms: their relationships and their timescale of evolution, which together define a timetree. Historically, fossils have been the only source for timescales of evolution, but molecular clocks are now filling many gaps in the timetree of life. Earth-life coevolution has been continuous, but there were episodes in Earth history when this interaction had unusually large and global effects. In one case, molecular timetrees revealed that two-thirds of all prokaryotes form a natural group, terrabacteria, inferred to have had a common ancestor that lived on land about three billion years ago. Oxygen production and complex multicellularity (deriving from the energy in oxygen) may be tied to this terrestrial ancestry and invasion of a new, global niche. In a second case, a Neoproterozoic hot spot also appears to have involved terrestriality—this time of eukaryotes (plants and fungi), followed by another oxygen surge. It is unlikely a coincidence that the subsequent explosion in animal diversity is tied to this second major hot spot. Macroscopic animals with hard parts require sufficient oxygen, provided by the surge. The Cambrian explosion is now better understood in the context of rising oxygen levels. There were other hotspots in the coevolution of life and Earth, with some involving, similarly, changes in levels of atmospheric gases, and others involving different types of interactions such as temperature change, extraterrestrial impact, and human impact. All of these are of interest in understanding the evolution of life in the universe, and how a planet and its biota coevolve.
New methods and tools for the next generation phylogenetics
Molecular data have become an important means to add a temporal dimension to the Tree of Life and to survey the diversity of life in different habitats via metagenomics. Molecular dating methods are now being applied to datasets that have been quickly expanding in the numbers of species and the taxonomic diversity. This research has been hampered by an exponential increase in the computational time needed by the application of current methods to an increasing number of sequences. Similarly, the metagenomics studies are being applied to an increasingly large number of sequences and species. I will present new methods for Molecular Dating and Metagenomics analysis that appear to be very accurate and quite fast in respective analyses when applied to large problems. They will serve as enabling technologies for conducting molecular evolutionary analysis of very large contemporary datasets. This work is in collaboration with Drs. Koichiro Tamura (Japan) and Alan Filipski (USA).
Perspectives on evolutionary biology based on phylogeny
Advancement of molecular phylogenetics revealed most of major phylogenetic relationships in last twenty years and the inferred phylogeny brought us new and interesting questions. One of current subjects is a discrepancy between a traditional classification based on morphology and an inferred phylogeny based on DNA data. A morphological character can be described as developmental regulatory gene networks and the increase of the information by the reduction made us compromise the discrepancy and gave new evolutionary insights. I will introduce such examples on gymnosperms and ferns. Solid phylogenetic inference and genome technology enabled us to deduce genome-wide evolution of gene networks managing a body plan in both metazoans and land plants. I will discuss on the unexpected divergence of land plant developmental gene networks. As well as species trees, reliable gene trees are indispensable to discuss evolutionary processes at a genetic level. We found a receptor-like kinase (RLK) functioning to release sperm cells from pollen tube at fertilization. A gene tree showed that the male RLK is sister to a female specific RLK necessary for fertilization. These indicate that male and female interactions using pollen tube evolved via gene duplication. In this way, phylogenetic analyses blow evolutionary insights in other fields of biology. On the other hand, the opposite way is also effective. When we made a loss-of-function mutant of CURLY LEAF gene encoding a component of chromatin modification complex in a bryophyte, unexpectedly mutant morphology was similar to protracheophytes. This new evolutionary connection between bryophytes and protoracheophytes appear to compromise the long debate whether the common ancestor of land plants was similar to bryophytes or protracheophytes, which will be discussed in details. Lastly, I will introduce our challenge to identify genes involved in a host race change of the moth Acrocercops transecta, which is directly related to speciation at the branching point of a phylogenetic tree.
Characteristics of mitogenomic data for vertebrate phylogenetics
DNA or protein sequence data utilized for molecular phylogenetics are expanding in size and taxon numbers. Genes from the complete mitochondrial genome have been used for diverse vertebrate groups, while recent technical advancement in the high-throughput sequencing facilitates to explore genes encoded by nuclear genomes for phylogenetic inference.
Mitochondrial and nuclear genes have some distinct features relevant to phylogenetic performance with respect to, e.g., rates of sequence evolution, base composition bias, frequency of gene duplication/deletion and susceptibility to meiosis-associated DNA recombination. Some recent studies cast doubt on the dating performance of mitochondrial genes mainly due to their high evolutionary rates. The orthology/paralogy issue remains to be a critical problem for nuclear genes.
Mitochondrial and nuclear genes provide mostly concordant phylogenetic relationships between lizard families. However, they give rise to different placement of snakes on the lizard tree. Snake mitochondrial genomes have extremely high evolutionary rates and may be affected by a sort of convergent sequence evolution. Nuclear genes suggest that snakes cluster with iguanian and/or anguimorphan lizards, which should be further investigated with more data from, e.g., transcriptomic analyses.
In the present talk, we present results on the comparison of phylogenetic performance between mitochondrial genes and provide some comments toward more efficient and accurate phylogenetics.