Decoding the genomic tree of life

Abstract

Genomes hold within them the record of the evolution of life on Earth. But genome fusions and horizontal gene transfer (HGT) seem to have obscured sufficiently the gene sequence record such that it is difficult to reconstruct the phylogenetic tree of life. HGT among prokaryotes is not random, however. Some genes (informational genes) are more difficult to transfer than others (operational genes). Furthermore, environmental, metabolic, and genetic differences among organisms restrict HGT, so that prokaryotes preferentially share genes with other prokaryotes having properties in common, including genome size, genome G؉C composition, carbon utilization, oxygen utilization͞sensitivity, and temperature optima, further complicating attempts to reconstruct the tree of life. A new method of phylogenetic reconstruction based on gene presence and absence, called conditioned reconstruction, has improved our prospects for reconstructing prokaryotic evolution. It is also able to detect past genome fusions, such as the fusion that appears to have created the first eukaryote. This genome fusion between a deep branching eubacterium, possibly an ancestor of the cyanobacterium and a proteobacterium, with an archaeal eocyte (crenarchaea), appears to be the result of an early symbiosis. Given new tools and new genes from relevant organisms, it should soon be possible to test current and future fusion theories for the origin of eukaryotes and to discover the general outlines of the prokaryotic tree of life.

Hybrid vigor between native and introduced salamanders raises new challenges for conservation

“…In evolutionary biology, hybrid fitness and its genetic basis are important for understanding the evolution of reproductive isolation and the consequences of horizontal gene flow on the diversity and complexity of life (4)(5)(6)(7). In conservation biology, hybrid fitness is a key to the mechanistic basis of inbreeding and outbreeding depression, the potential loss of biodiversity due to genetic swamping, and the evolution of invasiveness (8)(9)(10)(11).…”

What Genetics Offers Geobiology

“…Moreover, as the complexity or diffi culty of a metabolic process increases, we might expect the repertoire of solutions to become even more limited. This conclusion appears to be robust, albeit facilitated through horizontal gene transfer, given the conservation of metabolic genes in the genomes of phylogenetically distant organisms (Doolittle 1999;Friedrich 2002;Nixon et al 2002;Malasarn et al 2004;Simonson et al 2005). Interestingly, microbiologists of the Delft school anticipated these fi ndings nearly a century ago, noting the "manifest unity" in the biochemistry that forms the basis for the ecological relationships of microorganisms in nature (Kluyver 1924).…”

Systematics and the origin of species: An introduction

“…One example of the way our view has changed is provided in the article by Ochman et al (45) that is mentioned above. Another example lies in the paper by James Lake and colleagues (47), who use genomic data to reconstruct the process by which eukaryotes arose from prokaryotes. Unlike typical phylogenetic events, such as the splitting of lineages, eukaryotes appear to have arisen by the fusion of genomes.…”