PERSPECTIVES (below 1 Å) in TEAM I, which is equipped with spherical and chromatic aberration correctors, was achieved with primary electrons of 80 keV, which are much less damaging to samples than the 300-keV electrons used in (13). The use of correctors that can tolerate objective lenses with larger gaps between the pole pieces also enhances the free space available for the specimen holders. With the new level of performance demonstrated in this work, Yuk et al. have studied in detail various (and unexpected) stages of the colloidal growth of Pt nanoparticles. Open questions remain, such as the role of the ligand molecules attached to the metallic species or how the first burst of electrons acts as the seed of the nucleation process. The properties of nanoparticles are highly dependent on their size, shape, and environment, and such studies should provide insights that may allow the design of homogeneous assemblies of nanoparticles of defined sizes, morphology, and connectivity. Their approach opens new domains of research in the physics and chemistry in the fluid phase in general. How this new generation of liquid cells will be useful for biochemical and biological problems, where the use of microchip-based liquid cells has not been fully exploited, in spite of the spectacular advances recently shown for imaging of whole biological cells in liquids (14) is to be further explored. References 1. R. Erni, M. D. Rossell, C. Kisielowski, U. Dahmen, Phys. Rev. Lett. 102, 096101 (2009). 2. D. A. Muller et al., Science 319, 1073 (2008). 3. L. F. Zagonel et al., Nano Lett. 11, 568 (2011). 4. J. M. Yuk et al., Science 336, 61 (2012). 5. See http://ncem.lbl.gov/team/TEAMpage/TEAMpage.html. 6. N. de Jonge, F. M. Ross, Nat. Nanotechnol. 6, 695 (2011). 7. E. Ruska, Kolloid Z 100, 212 (1942). 8. J. M. Grogan, L. Rotkina, H. H. Bau, Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 83, 061405 (2011). 9. A. Radisic et al., Nano Lett. 6, 238 (2006). 10. K. Suenaga et al., Science 290, 2280 (2000). 11. T. Okazaki et al., Angew. Chem. Int. Ed. 50, 4853 (2011). 12. J. M. Yuk et al., Nano Lett. 11, 3290 (2011). 13. H. Zheng et al., Science 324, 1309 (2009). 14. N. de Jonge, D. B. Peckys, G. J. Kremers, D. W. Piston, Proc. Natl. Acad. Sci. U.S.A. 106, 2159 (2009). 10.1126/science.1219835 ECOLOGY How Bacterial Lineages Emerge Bacterial speciation is driven by interplay between natural selection, genetic linkage, and lateral gene transfer. R. Thane Papke and J. Peter Gogarten M ost people today recognize bacterial names like Escherichia coli and Neisseria meningitidis. Yet, from an evolutionary viewpoint, the clarity of species labels for bacteria is blurred by rampant horizontal gene transfer between bacteria (1). The forces driving speciation in bacteria include niche adaptation, selective sweeps, genetic drift, recombination of genetic material, and geographic isolation. How do those forces maintain species homogeneity or bring about lineages, when gene swapping is apparently so rife? On page 48 of this issue, Shapiro et al. (2) address these questions by providing a highresolution snapshot of early lineage divergence in marine bacteria. They find clues to the dynamics of prokaryotic genomes, such as with whom the organisms frequently exchange genes, how lineages originate, and, ultimately, what is (or is not) in a name. Most theoretical and observational insights into what species are and how they came to be are derived from studies of sexually reproducing eukaryotes (3), in which reproduction and recombination are necessarily connected. Asexual lineages in both prokaryotes and eukaryotes have often been described in terms of selection and genomewide genetic linkage, which resets to zero the genetic diversity at every locus (4). However, even though Bacteria and Archaea reproduce Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269–3125, USA. E-mail: thane@ uconn.edu; [email protected] asexually, many prokaryotic populations evolve in ways that resemble randomly mating, sexually reproducing eukaryotes: Alleles in these bacterial populations are randomly assorted among individual cells (strains), and diversity at single loci can be purged independently of the other chromosomal loci. The only mechanism that can explain these observations is a high rate of horizon- tal gene flow compared to the rates of clonal expansion or reproduction. The main difference from eukaryotes is that prokaryotic reproduction is independent of DNA acquisition and recombination. Instead, DNA is obtained from fragmented chromosomes obtained via parasexual means (that is, without reproduction). These mechanisms of DNA exchange are not restricted to gene exchange within species, and therefore traits can and J J do come from highly divergent organisms. For example, imagine that acacia trees A B could exchange DNA with lions and that the resulting new tree developed “limbs” B that allowed them to attack A K grazing giraffes. This is in a sense what prokaryotes do K all the time. Very different B pathways for bacterial speciation have been described A (5, 6); often the data reveal B frequent gene flow within A C multiple exchange groups. Horizontal gene flow is A structured exchange community. Members of two distinct niches are thus both a homogenizing shown as green and orange squares; gray squares are relatives occupy- and a diversifying force. It ing different niches. Genes that adapt their hosts to these niches are typically involves groups mostly exchanged or recombined between members of the same niche of organisms that preferen(green and orange arrows), but they might also be shared with recent niche invaders (blue square), accelerating their adaptation to a new hab- tially exchange genetic mateitat. Other genes are freely exchanged between members of different rial. Mathematical models niches (gray arrows). Shapiro et al. show that semi-stable adaptations of gene flow independent to specific niches can emerge in the presence of high rates of gene flow of selection and based on within and between lineages. sequence similarity alone www.sciencemag.org SCIENCE VOL 336 6 APRIL 2012 Published by AAAS 45 PERSPECTIVES show that even when rates of relative homologous recombination to mutation are low [in the range of 0.25 to 4 (7)], populations remain recognizably coherent, indicating that selection is not required to give the appearance of delineated species. However, such models do not capture the complexity of gene flow in natural populations. Genetic analysis of closely related strains has shown that genes rarely have the same phylogenetic history (8). Shapiro et al. now examine the genomes of 20 closely related, yet ecologically differentiated strains of Vibrio cyclitrophicus adapted to living on various-sized particles in the Atlantic Ocean. They find that 99% of the core gene families (which are common to all strains) have different evolutionary histories. Thus, gene acquisition from other lineages, selection on those adaptive alleles, and frequent intraspecies recombination unlinking loci within V. cyclitrophicus have created a thousand-organism chimera. A further indication of vast and frequent gene flow in these asexual organisms comes from pairwise comparisons of genomes. The authors report that in the time it took to accumulate a handful of nucleotide polymorphisms in the core genes, individuals gained reams of new DNA encoding proteins and enzymes that other cells in the population did not have. These astounding observations reiterate that prokaryotic genomes can be extreme mosaics caused by high rates of gene flow and strong selection. When 99% of genes from a population of very closely related strains do not have the same common ancestor, the only reasonable conclusion is that prokaryotic speciation does not have much to do with divergence from common ancestors—a startling anti-Darwinian outcome. Surprisingly, in terms of evolutionary outcomes, prokaryotes tend to resemble Darwin’s finches. Finches from different species coexisting on the same island become more similar to one another in their overall genome through frequent introgression (incorporation of genetic material via repeated backcrossing of an interspecific hybrid), but the characters defining their ecological niche appear to be maintained through selection. Genetic exchange groups appear to be the basis of many lineages observed in prokaryotes and are initiated or extinguished by sharing a common spatiotemporal existence with other exchange groups (9, 10). Exchange groups can degenerate through movement to a new habitat or geographic location, or by any mechanism that generates “sexual” isolation, including illegitimately recombined loci (11) and the molecular machinery that shuttles DNA between cells. Perhaps a common 46 mechanism for biasing gene exchange and generating “sexual” isolation is quorum sensing. Many prokaryotes, including pathogens, soil, and marine dwellers, use quorum sensing to regulate gene exchange (12): They only exchange DNA when their numbers dominate in any particular place and time—for example, in a biofilm (13). Quorum sensing is also used by Vibrio populations in biofilms to regulate gene exchange (14). But gene flow regulation does not prohibit divergent DNA from entering or recombining, and exchange groups may be as numerous as potential niches and geographic locations allow. As Shapiro et al. show, the habitat-specialized Vibrio strains of their study have a gene and niche bias for genetic exchange. Loci that are less important for niche adaptation participate in different and more diverse exchange groups (see the figure). It would seem that the genetic exchange group that has dominated a bacterial population most recently will determine how we observers interpret their evolutionary history of divergence—hopefully while realizing the possibility that newly acquired exchange partners purge evidence of past ones (9, 10). Instead of prokaryotic species having common ancestors, it seems that they are each more like emergent ports-of-call, defined by which genetic vessels are currently moored in their chromosomal harbors. References 1. W. P. Hanage, C. Fraser, B. G. Spratt, BMC Biol. 3, 6 (2005). 2. B. J. Shapiro et al., Science 336, 48 (2012). 3. J. A. Coyne, H. A. Orr, Speciation (Sinauer, Sunderland, MA, 2004). 4. J. F. Crow, M. Kimura, Am. Nat. 99, 439 (1965). 5. D. Gevers et al., Nat. Rev. Microbiol. 3, 733 (2005). 6. W. F. Doolittle, O. Zhaxybayeva, Genome Res. 19, 744 (2009). 7. C. Fraser et al., Science 315, 476 (2007). 8. R. T. Papke et al., Proc. Natl. Acad. Sci. U.S.A. 104, 14092 (2007). 9. O. Zhaxybayeva et al., Genome Biol. Evol. 1, 325 (2009). 10. O. Zhaxybayeva et al., Proc. Natl. Acad. Sci. U.S.A. 106, 5865 (2009). 11. A. C. Retchless, J. G. Lawrence, Science 317, 1093 (2007). 12. L. S. Havarstein, D. A. Morrison, in Cell-Cell Signaling in Bacteria, G. M. Dunny, S. C. Winans, Eds. (American Society for Microbiology, Washington, DC, 1999). 13. Y. H. Li et al., J. Bacteriol. 184, 2699 (2002). 14. K. L. Meibom et al., Science 310, 1824 (2005). 10.1126/science.1219241 PALEONTOLOGY Reading Pliocene Bones Jackson Njau Standardized criteria will help to reliably distinguish marks made by hominid tools from feeding traces of other animals. T he human ability to make complex tools is unparalleled in the animal kingdom and is a key character of Homo sapiens. Flaked stone tools and cutmarked bones are the first traces of this behavior. Yet the interpretation of bone modifications is complicated by similar traces left, for example, by carnivorous animals (see the figure). Given the scarcity of butchered bones from the Pliocene (5.3 to 2.6 million years ago) and Early Pleistocene (2.6 to 0.76 million years ago), even a single misidentification can have profound effects on the interpretation of early hominid behavior. How can such misidentification be avoided? The current consensus is that the world’s oldest tools and associated butchered bones come from Gona, Ethiopia, dated to 2.6 million years ago (1, 2). This early technology, termed Oldowan, has also been found elseDepartment of Geological Sciences, Indiana University, Bloomington, IN 47405, USA. E-mail: [email protected] where in Africa but did not extend beyond this continent until about 2 million years ago. Although there is one report of butchered bones 3.4 million years old from Dikika, Ethiopia (3), this evidence has been disputed (4), in part because tools older than 2.6 million years have yet to be found anywhere, despite intensive searching in older African sediments during the past 40 years. By the mid-19th century, scientists had begun to recognize cut marks, associated with worked flints, on the bones of extinct Pleistocene animals ( 5). These physical traces were correctly attributed to past human butchery, but the importance of bone modification was not recognized until a century later, after a surge of hominid discoveries in eastern Africa. Major excavations at sites such as Olduvai Gorge, where associated stone artifacts and fossils were recovered, led archaeologists to speculate that by 2 million years ago, hominids were hunting and butchering at home bases (6). Others 6 APRIL 2012 VOL 336 SCIENCE www.sciencemag.org Published by AAAS
© Copyright 2025 Paperzz