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Chloroplasts arose from cyanobacteria, mitochondria arose from proteobacteria. Both organelles have conserved their prokaryotic biochemistry, but their genomes are reduced, and most organelle proteins are encoded in the nucleus. Endosymbiotic theory posits that bacterial genes in eukaryotic genomes entered the eukaryotic lineage via organelle ancestors. It predicts episodic influx of prokaryotic genes into the eukaryotic lineage, with acquisition corresponding to endosymbiotic events. Eukaryotic genome sequences, however, increasingly implicate lateral gene transfer, both from prokaryotes to eukaryotes and among eukaryotes, as a source of gene content variation in eukaryotic genomes, which predicts continuous, lineage-specific acquisition of prokaryotic genes in divergent eukaryotic groups. Here we discriminate between these two alternatives by clustering and phylogenetic analysis of eukaryotic gene families having prokaryotic homologues. Our results indicate (1) that gene transfer from bacteria to eukaryotes is episodic, as revealed by gene distributions, and coincides with major evolutionary transitions at the origin of chloroplasts and mitochondria; (2) that gene inheritance in eukaryotes is vertical, as revealed by extensive topological comparison, sparse gene distributions stemming from differential loss; and (3) that continuous, lineage-specific lateral gene transfer, although it sometimes occurs, does not contribute to long-term gene content evolution in eukaryotic genomes., In prokaryotes, inheritance involves recombination superimposed upon clonal growth (1) and the mechanisms of recombination are the mechanisms of lateral gene transfer (LGT): transformation, conjugation, transduction, and gene transfer agents [...]

The mechanisms that underlie the origin of major prokaryotic groups are poorly understood. In principle, the origin of both species and higher taxa among prokaryotes should entail similar mechanisms--ecological interactions with the environment paired with natural genetic variation involving lineage-specific gene innovations and lineage-specific gene acquisitions (1-4). To investigate the origin of higher taxa in archaea, we have determined gene distributions and gene phylogenies for the 267,568 protein-coding genes of 134 sequenced archaeal genomes in the context of their homologues from 1,847 reference bacterial genomes. Archaeal-specific gene families define 13 traditionally recognized archaeal higher taxa in our sample. Here we report that the origins of these 13 groups unexpectedly correspond to 2,264 group-specific gene acquisitions from bacteria. Interdomain gene transfer is highly asymmetric, transfers from bacteria to archaea are more than fivefold more frequent than vice versa. Gene transfers identified at major evolutionary transitions among prokaryotes specifically implicate gene acquisitions for metabolic functions from bacteria as key innovations in the origin of higher archaeal taxa., Genome evolution in prokaryotes entails both tree-like components generated by vertical descent and network-like components generated by lateral gene transfer (LGT) (5,6). Both processes operate in the formation of prokaryotic [...]

Context: Many threatened species persist in modified landscapes. Species in these landscapes often inhabit vegetation strips adjacent to linear structures such as roads, railways and artificial waterways. These vegetation strips may act as refugia or provide resources, but the associated structures (e.g. roads) may also act as barriers to movement. The southern brown bandicoot (eastern subspecies) is listed as Endangered in Australia and is known to inhabit modified landscapes. Aim: We aim to determine the extent of occupancy of southern brown bandicoots and the relative importance of different habitat types. Our data are intended to provide a baseline for future monitoring of changes to bandicoot populations, and to further our understanding of the relative importance of different habitat types for management and conservation. Methods: We conducted a remote-camera survey of southern brown bandicoots, at 98 locations across a 60 000 ha region south-east of Melbourne. Bandicoots in this area inhabit patches of remnant habitat in reserves and remnant, modified or non-native vegetation strips along roadsides and artificial waterways created in the 19th century to drain swampland. These habitat fragments sit within a matrix of agricultural, residential and commercial land. Key results: Our results suggest that bandicoot occupancy is higher along artificial waterways (0.76) than along roadsides (0.35) or within reserves (0.39). Implications: Habitat along waterways is often different from remnants, with a mix of weedy and native vegetation. The implication of this is a potential conflict between habitat and vegetation management for bandicoots, weed control and maintenance of drains and associated levees. Like many threatened species, the Endangered southern brown bandicoot persists in modified landscapes. In our study area, located to the south-east of Melbourne, we found that bandicoot occupancy is higher along artificial waterways (drains) than along roadsides or within reserves. There is a potential conflict between habitat and vegetation management for bandicoots, weed control and maintenance of drains and associated levees. Photograph by remote camera. [ABSTRACT FROM AUTHOR]