Auditory perception and the evolution of speech

Among topics related to the evolution of language, the evolution of speech is particularly fascinating. Early theorists believed that it was the ability to produce articulate speech that set the stage for the evolution of the «special» speech processing abilities that exist in modern-day humans. Prior to the evolution of speech production, speech processing abilities were presumed not to exist. The data reviewed here support a different view. Two lines of evidence, one from young human infants and the other from infrahuman species, neither of whom can produce articulate speech, show that in the absence of speech production capabilities, the perception of speech sounds is robust and sophisticated. Human infants and non-human animals evidence auditory perceptual categories that conform to those defined by the phonetic categories of language. These findings suggest the possibility that in evolutionary history the ability to perceive rudimentary speech categories preceded the ability to produce articulate speech. This in turn suggests that it may be audition that structured, at least initially, the formation of phonetic categories.     

Identifying G-protein coupled receptors using weighted Levenshtein distance and the nearest neighbor method

G-protein coupled receptors （GPCRs） are a class of seven-helix transmembrane proteins that have been used in bioinformatics as the targets to facilitate drug discovery for human diseases. Although thousands of GPCR sequences have been collected, the ligand specificity of many GPCRs is still unknown and only one crystal structure of the rhodopsin-like family has been solved. Therefore, identifying GPCR types only from sequence data has become an important research issue. In this study, a novel technique for identifying GPCR types based on the weighted Levenshtein distance between two receptor sequences and the nearest neighbor method （NNM） is introduced, which can deal with receptor sequences with different lengths directly. In our experiments for classifying four classes （acetylcholine, adrenoceptor, dopamine, and serotonin） of the rhodopsin-like family of GPCRs, the error rates from the leave-one-out procedure and the leave-half-out procedure were 0.62% and 1.24%, respectively. These results are prior to those of the covariant discriminant algorithm, the support vector machine method, and the NNM with Euclidean distance.     

Language evolution: syntax before phonology?

Phonology and syntax represent two layers of sound combination central to language''s expressive power. Comparative animal studies represent one approach to understand the origins of these combinatorial layers. Traditionally, phonology, where meaningless sounds form words, has been considered a simpler combination than syntax, and thus should be more common in animals. A linguistically informed review of animal call sequences demonstrates that phonology in animal vocal systems is rare, whereas syntax is more widespread. In the light of this and the absence of phonology in some languages, we hypothesize that syntax, present in all languages, evolved before phonology.     

Classification of vegetation sequences in Toohey Forest,Queensland

In this paper we consider one method of mapping larger units identified from the spatial pattern of sequences of vegetation types. The basic data were presence/absence data for 6450 stands arranged in 90 transects. A second set of data was derived by averaging the species occurrences in non-overlapping groups of 5 stands. A divisive numerical classification was used to determine the primary vegetation units. In all, 5 different sets of primary types were derived, using different species suites, different sample sizes and different numerical methods. We briefly discuss the types identified and their spatial patterns in the area.Each of these types was then used to define a string of type-codes for every transect so that each transect represents a sample from the landscape containing information on the frequency and spatial distribution of the primary vegetation types. The transects may be classified using a Levenshtein dissimilarity measure and agglomerative hierarchical classification, giving 5 analyses of transects, one for each of the primary types discussed above. We then examine these transect classifications to investigate the stability of the vegetation landspace patterns under changes in species used for the primary classification, in size of sample unit and in method of primary classifications. There is a considerable degree of stability in the results. However it seems with this vegetation that the tree species and non-tree species have considerable independence. We also indicate some problems with this approach and some possible extensions.     

A word in the hand: action, gesture and mental representation in humans and non-human primates

The movements we make with our hands both reflect our mental processes and help to shape them. Our actions and gestures can affect our mental representations of actions and objects. In this paper, we explore the relationship between action, gesture and thought in both humans and non-human primates and discuss its role in the evolution of language. Human gesture (specifically representational gesture) may provide a unique link between action and mental representation. It is kinaesthetically close to action and is, at the same time, symbolic. Non-human primates use gesture frequently to communicate, and do so flexibly. However, their gestures mainly resemble incomplete actions and lack the representational elements that characterize much of human gesture. Differences in the mirror neuron system provide a potential explanation for non-human primates' lack of representational gestures; the monkey mirror system does not respond to representational gestures, while the human system does. In humans, gesture grounds mental representation in action, but there is no evidence for this link in other primates. We argue that gesture played an important role in the transition to symbolic thought and language in human evolution, following a cognitive leap that allowed gesture to incorporate representational elements.     

Intra- and interspecific variation of the CCR5 gene in higher primates

We have evaluated the molecular evolution of the chemokine receptor CCR5 in primates. The chemokine receptor CCR5 serves as a major co-receptor for human immunodeficiency virus/simian immunodeficiency virus (HIV/SIV) infection. Knowledge of evolution of the CCR5 molecule and selection on the CCR5 gene may shed light on its functional role. The comparison of differences between intraspecific polymorphisms and interspecific fixed substitutions provides useful information regarding modes of selection during the course of evolution. There is marked polymorphism in the CCR5 gene sequence within different primate species, whereas sequence divergence between different species is small. By using contingency tests, we compared synonymous (SS) and nonsynonymous (NS) CCR5 mutations occurring within and between a broad range of primates. Our results demonstrate that CCR5 evolution did not follow expectations of strict neutrality at the level of the whole gene. The proportion of NS to SS at the intraspecific level was significantly higher than that observed at the interspecific level. These results suggest that most CCR5 NS polymorphisms are slightly deleterious. However, at domains more closely correlated with its known biological functions, there was no obvious evidence to support deviation from neutrality.     

New views on primate origins

Most primates live in trees, and many of them have strikingly human-like hands and faces. Scientists who study primate evolution agree that these two facts must be connected in some way. The details, however, are a matter of debate. Early theories explained the human-like peculiarities of primates simply as arboreal adaptations. More recent accounts have traced the origins of these peculiarities to more specific ways of arboreal life, involving leaping locomotion, shrub-layer foraging, visually guided predation on insects, or fruit-eating.     

Intellectual activity during formation of quantitative concepts in the lower and higher monkeys

Results of study of formation of quantitative concepts in the lower and higher monkey are presented. Various authors used different methods of study of this issue. It has been established that not only the higher primates, such as chimpanzees and orangutans, but also the lower ones—macaques, capuchins, squirrel monkeys—have the “mathematical capabilities.” The detailed study of formation of quantitative concepts in primates of different levels of phylogenesis allows disclosing mechanisms of formation of this function in human.     

Dissimilarity for partially ranked data and its application to cover-abundance data

Cover-abundance estimates are commonly employed in phytosociological investigations to record the performance of species. Because the coded values are on an ordinal scale of measure, various authors have suggested that some transformation is necessary before such values can be used for classification and ordination. However, it is not clear that transformation is a sufficient treatment, and it would seem preferable to use ordinal data directly. In this paper we examine such direct use of partial rankings and show that several dissimilarity measures can be defined for this case without invoking any transformations. They include dissimilarity measures associated with various rank correlation measures and with distances between strings; all the measure are variant forms of Hausdorf's interset distance. Certain other kinds of data, such as those employing dominant and subdominant species and the dry-weight-rank estimation of biomass, are also on an ordinal scale and could be analysed using similar techniques.To illustrate the approach, a string dissimilarity measure is used to analyse a set of data from Slovakian grasslands which appear to reflect a simple gradient. The original data were recorded with 10 classes of performance and are analysed using hierarchical and nondeterministic, overlapping, classifications.     

Fossil Humankind and Other Anthropoid Primates of China

More than 70 sites have yielded human fossils in China. They are attributed to Homo sapiens erectus and Homo sapiens sapiens. The earliest one is possibly about 1.7 Ma. A series of common morphological features, including shovel-shaped incisors and flatness of the face, characterize them. There is a morphological mosaic between H. s. erectus and H. s. sapiens in China. The existence of common features and the morphological mosaic suggest continuity of human evolution in China. That there are a few features which are more commonly seen in the Neanderthal lineage, occurring in a few Chinese fossil skulls, probably suggests gene flow between China and the West. Based on them, in 1998 I proposed an hypothesis—continuity with hybridization—for human evolution in China. The hypothesis is supported by paleolithic archeology, and it supports the multiregional evolution hypothesis of modern human origins. The anatomically modern humans of East Asia originated most probably in China. Although some nonhuman anthropoid primates of China—Gigantopithecus, Sivapithecus, Ramapithecus and Lufengpithecus—have been suggested as the direct ancestors of human beings, the discovery of more specimens and further studies do not support these suggestions. Therefore, it is most probable that the transition between apes and humans did not occur in China.     

Modelling Primate Behavioral Ecology

Models play an important role in any mature science because they force us to make explicit our assumptions about how a phenomenon works and allow us to explore the way in which different variables influence a complex biological system. I review the principal kinds of models that could be used to study primate behavior and ecology: linear programming models, systems models, optimality models, stochastic dynamic programming models and agent-based simulation models. Although less use has been made of modelling in primatology than in some other areas of behavioral ecology, there is considerable scope for exploiting the predictive and explanatory power of models in the field.     

Special Issue ofHuman evolution on intelligence and evolutionary biology

This is a Special Issue on intelligence and evolutionary biology, based on selected lectures at a NATO Advanced Study Institute on this topic. The proceedings of the ASI have been published in a separate volume. The papers presented here have been reviewed and updated to reflect information available in 1988.     

Spectral tuning and evolution of primate short-wavelength-sensitive visual pigments

The peak sensitivities (λ(max)) of the short-wavelength-sensitive-1 (SWS1) pigments in mammals range from the ultraviolet (UV) (360-400 nm) to the violet (400-450 nm) regions of the spectrum. In most cases, a UV or violet peak is determined by the residue present at site 86, with Phe conferring UV sensitivity (UVS) and either Ser, Tyr or Val causing a shift to violet wavelengths. In primates, however, the tuning mechanism of violet-sensitive (VS) pigments would appear to differ. In this study, we examine the tuning mechanisms of prosimian SWS1 pigments. One species, the aye-aye, possesses a pigment with Phe86 but in vitro spectral analysis reveals a VS rather than a UVS pigment. Other residues (Cys, Ser and Val) at site 86 in prosimians also gave VS pigments. Substitution at site 86 is not, therefore, the primary mechanism for the tuning of VS pigments in primates, and phylogenetic analysis indicates that substitutions at site 86 have occurred at least five times in primate evolution. The sole potential tuning site that is conserved in all primate VS pigments is Pro93, which when substituted by Thr (as found in mammalian UVS pigments) in the aye-aye pigment shifted the peak absorbance into the UV region with a λ(max) value at 371 nm. We, therefore, conclude that the tuning of VS pigments in primates depends on Pro93, not Tyr86 as in other mammals. However, it remains uncertain whether the initial event that gave rise to the VS pigment in the ancestral primate was achieved by a Thr93Pro or a Phe86Tyr substitution.