Scheffer, M., & van Nes, E. H. (2006). Self-organized similarity, the evolutionary emergence of groups of similar species. Proc. Natl. Acad. Sci. U.S.A., 103(16), 6230–6235.
Abstract: Ecologists have long been puzzled by the fact that there are so many similar species in nature. Here we show that self-organized clusters of look-a-likes may emerge spontaneously from coevolution of competitors. The explanation is that there are two alternative ways to survive together: being sufficiently different or being sufficiently similar. Using a model based on classical competition theory, we demonstrate a tendency for evolutionary emergence of regularly spaced lumps of similar species along a niche axis. Indeed, such lumpy patterns are commonly observed in size distributions of organisms ranging from algae, zooplankton, and beetles to birds and mammals, and could not be well explained by earlier theory. Our results suggest that these patterns may represent self-constructed niches emerging from competitive interactions. A corollary of our findings is that, whereas in species-poor communities sympatric speciation and invasion of open niches is possible, species-saturated communities may be characterized by convergent evolution and invasion by look-a-likes.
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Jansen, T., Forster, P., Levine, M. A., Oelke, H., Hurles, M., Renfrew, C., et al. (2002). Mitochondrial DNA and the origins of the domestic horse. Proc. Natl. Acad. Sci. U.S.A., 99(16), 10905–10910.
Abstract: The place and date of the domestication of the horse has long been a matter for debate among archaeologists. To determine whether horses were domesticated from one or several ancestral horse populations, we sequenced the mitochondrial D-loop for 318 horses from 25 oriental and European breeds, including American mustangs. Adding these sequences to previously published data, the total comes to 652, the largest currently available database. From these sequences, a phylogenetic network was constructed that showed that most of the 93 different mitochondrial (mt)DNA types grouped into 17 distinct phylogenetic clusters. Several of the clusters correspond to breeds and/or geographic areas, notably cluster A2, which is specific to Przewalski's horses, cluster C1, which is distinctive for northern European ponies, and cluster D1, which is well represented in Iberian and northwest African breeds. A consideration of the horse mtDNA mutation rate together with the archaeological timeframe for domestication requires at least 77 successfully breeding mares recruited from the wild. The extensive genetic diversity of these 77 ancestral mares leads us to conclude that several distinct horse populations were involved in the domestication of the horse.
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Hoy, R. (2005). Animal awareness: The (un)binding of multisensory cues in decision making by animals. Proc. Natl. Acad. Sci. U.S.A., 102(7), 2267–2268.
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Uzawa, T., Akiyama, S., Kimura, T., Takahashi, S., Ishimori, K., Morishima, I., et al. (2004). Collapse and search dynamics of apomyoglobin folding revealed by submillisecond observations of alpha-helical content and compactness. Proc. Natl. Acad. Sci. U.S.A., 101(5), 1171–1176.
Abstract: The characterization of protein folding dynamics in terms of secondary and tertiary structures is important in elucidating the features of intraprotein interactions that lead to specific folded structures. Apomyoglobin (apoMb), possessing seven helices termed A-E, G, and H in the native state, has a folding intermediate composed of the A, G, and H helices, whose formation in the submillisecond time domain has not been clearly characterized. In this study, we used a rapid-mixing device combined with circular dichroism and small-angle x-ray scattering to observe the submillisecond folding dynamics of apoMb in terms of helical content (f(H)) and radius of gyration (R(g)), respectively. The folding of apoMb from the acid-unfolded state at pH 2.2 was initiated by a pH jump to 6.0. A significant collapse, corresponding to approximately 50% of the overall change in R(g) from the unfolded to native conformation, was observed within 300 micros after the pH jump. The collapsed intermediate has a f(H) of 33% and a globular shape that involves >80% of all its atoms. Subsequently, a stepwise helix formation was detected, which was interpreted to be associated with a conformational search for the correct tertiary contacts. The characterized folding dynamics of apoMb indicates the importance of the initial collapse event, which is suggested to facilitate the subsequent conformational search and the helix formation leading to the native structure.
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Ballew, R. M., Sabelko, J., & Gruebele, M. (1996). Direct observation of fast protein folding: the initial collapse of apomyoglobin. Proc. Natl. Acad. Sci. U.S.A., 93(12), 5759–5764.
Abstract: The rapid refolding dynamics of apomyoglobin are followed by a new temperature-jump fluorescence technique on a 15-ns to 0.5-ms time scale in vitro. The apparatus measures the protein-folding history in a single sweep in standard aqueous buffers. The earliest steps during folding to a compact state are observed and are complete in under 20 micros. Experiments on mutants and consideration of steady-state CD and fluorescence spectra indicate that the observed microsecond phase monitors assembly of an A x (H x G) helix subunit. Measurements at different viscosities indicate diffusive behavior even at low viscosities, in agreement with motions of a solvent-exposed protein during the initial collapse.
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Plotnik, J. M., de Waal, F. B. M., & Reiss, D. (2006). Self-recognition in an Asian elephant. Proc. Natl. Acad. Sci. U.S.A., 103(45), 17053–17057.
Abstract: Considered an indicator of self-awareness, mirror self-recognition (MSR) has long seemed limited to humans and apes. In both phylogeny and human ontogeny, MSR is thought to correlate with higher forms of empathy and altruistic behavior. Apart from humans and apes, dolphins and elephants are also known for such capacities. After the recent discovery of MSR in dolphins (Tursiops truncatus), elephants thus were the next logical candidate species. We exposed three Asian elephants (Elephas maximus) to a large mirror to investigate their responses. Animals that possess MSR typically progress through four stages of behavior when facing a mirror: (i) social responses, (ii) physical inspection (e.g., looking behind the mirror), (iii) repetitive mirror-testing behavior, and (iv) realization of seeing themselves. Visible marks and invisible sham-marks were applied to the elephants' heads to test whether they would pass the litmus “mark test” for MSR in which an individual spontaneously uses a mirror to touch an otherwise imperceptible mark on its own body. Here, we report a successful MSR elephant study and report striking parallels in the progression of responses to mirrors among apes, dolphins, and elephants. These parallels suggest convergent cognitive evolution most likely related to complex sociality and cooperation.
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Dusek, J. A., & Eichenbaum, H. (1997). The hippocampus and memory for orderly stimulus relations. Proc. Natl. Acad. Sci. U.S.A., 94(13), 7109–7114.
Abstract: Human declarative memory involves a systematic organization of information that supports generalizations and inferences from acquired knowledge. This kind of memory depends on the hippocampal region in humans, but the extent to which animals also have declarative memory, and whether inferential expression of memory depends on the hippocampus in animals, remains a major challenge in cognitive neuroscience. To examine these issues, we used a test of transitive inference pioneered by Piaget to assess capacities for systematic organization of knowledge and logical inference in children. In our adaptation of the test, rats were trained on a set of four overlapping odor discrimination problems that could be encoded either separately or as a single representation of orderly relations among the odor stimuli. Normal rats learned the problems and demonstrated the relational memory organization through appropriate transitive inferences about items not presented together during training. By contrast, after disconnection of the hippocampus from either its cortical or subcortical pathway, rats succeeded in acquiring the separate discrimination problems but did not demonstrate transitive inference, indicating that they had failed to develop or could not inferentially express the orderly organization of the stimulus elements. These findings strongly support the view that the hippocampus mediates a general declarative memory capacity in animals, as it does in humans.
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Amé, J. - M., Halloy, J., Rivault, C., Detrain, C., & Deneubourg, J. L. (2006). Collegial decision making based on social amplification leads to optimal group formation. Proc. Natl. Acad. Sci. U.S.A., 103(15), 5835–5840.
Abstract: Group-living animals are often faced with choosing between one or more alternative resource sites. A central question in such collective decision making includes determining which individuals induce the decision and when. This experimental and theoretical study of shelter selection by cockroach groups demonstrates that choices can emerge through nonlinear interaction dynamics between equal individuals without perfect knowledge or leadership. We identify a simple mechanism whereby a decision is taken on the move with limited information and signaling and without comparison of available opportunities. This mechanism leads to optimal mean benefit for group individuals. Our model points to a generic self-organized collective decision-making process independent of animal species.
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Seyfarth, R. M., & Cheney, D. L. (2002). What are big brains for? Proc. Natl. Acad. Sci. U.S.A., 99(7), 4141–4142.
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Reader, S. M., & Laland, K. N. (2002). Social intelligence, innovation, and enhanced brain size in primates. Proc. Natl. Acad. Sci. U.S.A., 99(7), 4436–4441.
Abstract: Despite considerable current interest in the evolution of intelligence, the intuitively appealing notion that brain volume and “intelligence” are linked remains untested. Here, we use ecologically relevant measures of cognitive ability, the reported incidence of behavioral innovation, social learning, and tool use, to show that brain size and cognitive capacity are indeed correlated. A comparative analysis of 533 instances of innovation, 445 observations of social learning, and 607 episodes of tool use established that social learning, innovation, and tool use frequencies are positively correlated with species' relative and absolute “executive” brain volumes, after controlling for phylogeny and research effort. Moreover, innovation and social learning frequencies covary across species, in conflict with the view that there is an evolutionary tradeoff between reliance on individual experience and social cues. These findings provide an empirical link between behavioral innovation, social learning capacities, and brain size in mammals. The ability to learn from others, invent new behaviors, and use tools may have played pivotal roles in primate brain evolution.
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