The Rise of Modern Humans

Human beings are distinguished most strikingly by their unique “symbolic” way of processing information about the world. Although based on a long evolutionary history, the modern human cognitive style is not predicted by that history. It is not the product of a process of incremental refinement but is instead “emergent,” representing an entirely distinct level of complexity. Physically, Homo sapiens is very distinctive, its peculiarities clearly resulting from a significant developmental reorganization with numerous skeletal ramifications and quite plausibly others as well. It seems reasonable to suppose that the structural underpinnings of symbolic thought were acquired in this reorganization. Still, the fossil and archaeological records indicate that the first anatomically recognizable members of the species predated the first humans who behaved in a demonstrably symbolic manner. So while the biological potential for symbolic thinking most likely arose in the morphogenetic event that gave rise to H. sapiens as a distinctive anatomical entity, this new capacity was evidently exaptive, in the sense that it had to await its “discovery” and expression, clearly through a cultural stimulus that was plausibly the invention of language. One manifestation of symbolic reasoning is the adoption of technological change in response to environmental challenges, in contrast to earlier responses that typically used existing technologies in new ways. As climates changed at the end of the last Ice Age, this new technophile proclivity was expressed in a shift toward agriculture and sedentary lifestyles, precipitating a fundamentally new (and potentially self-destructive) relationship with Nature. Both of the two most radical and fateful evolutionary innovations in the history of life (symbolic thinking and sedentary lifestyles) were thus very recent occurrences, well within the short tenure of H. sapiens.     

The dual origin of modern humanity

Living Homo sapiens can define itself using both behavioral and anatomical uniquenesses. But is this possible when looking backward? Using a strict morphological definition, Homo sapiens can probably be traced back in the fossil record to about 150 kyr ago, which fits well with molecular estimates for the ancestor of all living human populations. However, activities reliably indicating established symbolic cognition can be recognized in the archaeological record only back to under 100 kyr ago. Since it is probable that the potential for symbolic cognition was born in the genetic/structural alterations that also gave rise to the distinctive morphological entity Homo sapiens, it appears that the expression of the human symbolic cognitive potential had to await, for many millennia, the >discovery< of that potential through a cultural rather than a biological stimulus. Most plausibly, this stimulus was the invention of language. Modern human symbolic cognition is not an extrapolation of pre-existing evolutionary trends, suggesting that Homo sapiens is not biologically >fine-tuned< for any specific behavior patterns.     

Rethinking the dispersal of Homo sapiens out of Africa

Current fossil, genetic, and archeological data indicate that Homo sapiens originated in Africa in the late Middle Pleistocene. By the end of the Late Pleistocene, our species was distributed across every continent except Antarctica, setting the foundations for the subsequent demographic and cultural changes of the Holocene. The intervening processes remain intensely debated and a key theme in hominin evolutionary studies. We review archeological, fossil, environmental, and genetic data to evaluate the current state of knowledge on the dispersal of Homo sapiens out of Africa. The emerging picture of the dispersal process suggests dynamic behavioral variability, complex interactions between populations, and an intricate genetic and cultural legacy. This evolutionary and historical complexity challenges simple narratives and suggests that hybrid models and the testing of explicit hypotheses are required to understand the expansion of Homo sapiens into Eurasia.     

Playing with language,creating complexity: Has play contributed to the evolution of complex language?

We argue that enhanced play may have contributed to the emergence of complex language systems in modern humans (Homo sapiens). To support this idea, we first discuss evidence for an expansion of playing behavior connected to the extended childhood of modern human children, and the potential of this period for the transmission of complex cultural traits, including language. We then link two of the most important functions of play—exploration and innovation—to the potential for cumulative cultural evolution in general and for the emergence of complex language in particular. If correct, the shorter childhood of Neanderthals—involving restrictions on time to experiment and innovate—may have restricted their language (and other symbolic) system/s. Consequently, fully investigating the role that play may have had in the transmission of language and the development of symbolic cultures in both modern humans and Neanderthals provides a new avenue of research for Paleolithic archaeology and related disciplines.     

The Middle/Later Stone Age transition and cultural dynamics of late Pleistocene East Africa

The Middle to Later Stone Age (MSA/LSA) transition is a prominent feature of the African archeological record that began in some places ~30,000–60,000 years ago, historically associated with the origin and/or dispersal of “modern” humans. Unlike the analogous Middle to Upper Paleolithic transition in Eurasia and associated Neanderthal extinction, the African MSA/LSA record remains poorly documented, with its potential role in explaining changes in the behavioral diversity and geographic range of Homo sapiens largely unexplored. I review archeological and biogeographic data from East Africa, show regionally diverse pathways to the MSA/LSA transition, and emphasize the need for analytical approaches that document potential ancestor‐descendent relationships visible in the archeological record, needed to assess independent invention, population interaction, dispersal, and other potential mechanisms for behavioral change. Diversity within East Africa underscores the need for regional, rather than continental‐scale narratives of the later evolutionary history of H. sapiens.     

Primate-specific spliced <Emphasis Type="Italic">PMCHL</Emphasis> RNAs are non-protein coding in human and macaque tissues

Background  

Brain-expressed genes that were created in primate lineage represent obvious candidates to investigate molecular mechanisms that contributed to neural reorganization and emergence of new behavioural functions in Homo sapiens. PMCHL1 arose from retroposition of a pro-melanin-concentrating hormone (PMCH) antisense mRNA on the ancestral human chromosome 5p14 when platyrrhines and catarrhines diverged. Mutations before divergence of hylobatidae led to creation of new exons and finally PMCHL1 duplicated in an ancestor of hominids to generate PMCHL2 at the human chromosome 5q13. A complex pattern of spliced and unspliced PMCHL RNAs were found in human brain and testis.     

Molecular Phylogenetic Analysis of Candida krusei

Revealing the phylogenetic relationships of Candida krusei strains (sexual form Pichia kudriavzevii) is a prerequisite for understanding the evolution of its virulence-associated mechanisms and ecological lifestyles. Molecular phylogenetic analyses based on entire internal transcribed spacer region (ITS) and multilocus sequence typing (MLST) data were carried out with sequences available in public databases and Hungarian isolates from animals obtained for the study. The ITS haplotype network yielded a high frequency haplotype at the centre of the network (H1; n?=?204) indicating that various selective pressure might resulted in population expansion from H1. MLST analysis identified three new genotypes among animal-derived isolates, therefore overall 203 sequence types were investigated to determine the population structure of C. krusei. The most commonly encountered sequence types were ST 17 and ST 67. Phylogenetic analyses showed diverse genetic construction of C. krusei population. Evidence of potential recombination events were also observed that might play some role in high intraspecies genetic variability among strains, however, the limited data of C. krusei genotypes from different countries prevented us to identify accurate evolutionary routes of commensal and pathogenic strains or species-specific lineages. Further expansion of C. krusei MLST database may promote the better understanding of the mixed evolutionary history of this species.

     

Inbreeding shapes the evolution of marine invertebrates

Inbreeding is a potent evolutionary force shaping the distribution of genetic variation within and among populations of plants and animals. Yet, our understanding of the forces shaping the expression and evolution of nonrandom mating in general, and inbreeding in particular, remains remarkably incomplete. Most research on plant mating systems focuses on self-fertilization and its consequences for automatic selection, inbreeding depression, purging, and reproductive assurance, whereas studies of animal mating systems have often assumed that inbreeding is rare, and that natural selection favors traits that promote outbreeding. Given that many sessile and sedentary marine invertebrates and marine macroalgae share key life history features with seed plants (e.g., low mobility, modular construction, and the release of gametes into the environment), their mating systems may be similar. Here, we show that published estimates of inbreeding coefficients (F_IS) for sessile and sedentary marine organisms are similar and at least as high as noted in terrestrial seed plants. We also found that variation in F_IS within invertebrates is related to the potential to self-fertilize, disperse, and choose mates. The similarity of F_IS for these organismal groups suggests that inbreeding could play a larger role in the evolution of sessile and sedentary marine organisms than is currently recognized. Specifically, associations between traits of marine invertebrates and F_IS suggest that inbreeding could drive evolutionary transitions between hermaphroditism and separate sexes, direct development and multiphasic life cycles, and external and internal fertilization.     

Human evolution and cognition

Human beings are distinguished from all other organisms by their symbolic way of processing information about the world. This unique cognitive style is qualitatively different from all the earlier hominid cognitive styles, and is not simply an improved version of them. The hominid fossil and archaeological records show clearly that biological and technological innovations have typically been highly sporadic, and totally out of phase, since the invention of stone tools some 2.5 million years ago. They also confirm that this pattern applied in the arrival of modern cognition: the anatomically recognizable species Homo sapiens was well established long before any population of it began to show indications of behaving symbolically. This places the origin of symbolic thought in the realms of exaptation, whereby new structures come into existence before being recruited to new uses, and of emergence, whereby entire new levels of complexity are achieved through new combinations of attributes unremarkable in themselves. Both these phenomena involve entirely routine evolutionary processes; special as we human beings may consider ourselves, there was nothing special about the way we came into existence. Modern human cognition is a very recent acquisition; and its emergence ushered in an entirely new pattern of technological (and other behavioral) innovation, in which constant change results from the ceaseless exploration of the potential inherent in our new capacity.     

Evolution of aromatic biosynthesis and fine-tuned phylogenetic positioning of Azomonas,Azotobacter and rRNA group I pseudomonads

The evolutionary history of biochemical pathways can be determined in microbial groupings for which phylogenetic trees have been established. This has been demonstrated best in Superfamily B, an assemblage of rRNA homology groups containing lineages that lead to genera such as Escherichia and other enteric microbes, Pseudomonas (Group I), Xanthomonas, Oceanospirillum, and Acinetobacter. The rRNA homology group that defines Group I pseudomonads also includes Azomonas and Azotobacter, but particular dendrogram points of evolutionary divergence for these genera within Superfamily B have not been established. Phylogenetic relationships at such intergeneric levels can be deduced by analysis of aromaticpathway enzyme arrangement and regulation in selected groupings where dynamic evolutionary changes have occurred. A case in point is illustrated by Axomonas insignis, Azotobacter paspali, and Azotobacter vinelandii — a grouping that appears to be homogeneous with respect to the evolutionary state of the aromatic pathway. The conclusion that this phylogenetic cluster diverges from an ancestor common to pseudomonad subgroup Ia (rather than to subgroup Ib) is based upon the absence of chorismate mutase-F and arogenate dehydratase, enzymes making up a twostep pathway of phenylalanine biosynthesis that is absent in subgroup Ia, but present in subgroup Ib. Of further interest, Azomonas insignis and Azotobacter sp. were found to comprise a distinctive and recently evolved sublineage, differing from subgroup Ia species in their loss of a regulatory isozyme of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (ADHP synthase-trp) that is subject to feedback inhibition by l-tryptophan. DAHP synthase-trp is an ancient character state of Superfamily B that has been retained during the evolutionary history of most members of this Superfamily.Abbreviation DAHP 3-Deoxy-d-arabino-heptulosonate 7-phosphate     

Is evolutionary biology becoming too politically correct? A reflection on the scala naturae,phylogenetically basal clades,anatomically plesiomorphic taxa,and ‘lower’ animals

The notion of scala naturae dates back to thinkers such as Aristotle, who placed plants below animals and ranked the latter along a graded scale of complexity from ‘lower’ to ‘higher’ animals, such as humans. In the last decades, evolutionary biologists have tended to move from one extreme (i.e. the idea of scala naturae or the existence of a general evolutionary trend in complexity from ‘lower’ to “higher” taxa, with Homo sapiens as the end stage) to the other, opposite, extreme (i.e. to avoid using terms such as ‘phylogenetically basal’ and ‘anatomically plesiomorphic’ taxa, which are seen as the undesired vestige of old teleological theories). The latter view tries to avoid any possible connotations with the original anthropocentric idea of a scala naturae crowned by man and, in that sense, it can be regarded as a more politically correct view. In the past years and months there has been renewed interest in these topics, which have been discussed in various papers and monographs that tend to subscribe, in general, to the points defended in the more politically correct view. Importantly, most evolutionary and phylogenetic studies of tetrapods and other vertebrates, and therefore most discussions on the scala naturae and related issues have been based on hard tissue and, more recently, on molecular data. Here we provide the first discussion of these topics based on a comparative myological study of all the major vertebrate clades and of myological cladistic and Bayesian phylogenetic analyses of bony fish and tetrapods, including Primates. We specifically (i) contradict the notions of a scala naturae or evolutionary progressive trends leading to more complexity in ‘higher’ animals and culminating in Homo sapiens, and (ii) stress that the refutation of these old notions does not necessarily mean that one should not keep using the terms ‘phylogenetically basal’ and particularly ‘anatomically plesiomorphic’ to refer to groups such as the urodeles within the Tetrapoda, or the strepsirrhines and lemurs within the Primates, for instance. This review will contribute to improving our understanding of these broad evolutionary issues and of the evolution of the vertebrate Bauplans, and hopefully will stimulate future phylogenetic, evolutionary and developmental studies of these clades.     

The Origin of Homo sapiens in the Light of Different Research Methods

The origins of Homo sapiens is a central issue of modern paleoanthropology. The available fossil material serves as a basis for postulating different hypotheses and models, but as is widely appreciated, anthropologists have yet to reach a consensus about human origins. It seems possible that the main reasons behind such an irreducible divergence of opinions are different methodological approaches rather than the analyses of fossil material. Some scientists would say that it is the fragmentary nature of fossil material which accounts for the debates about the origins of H. sapiens. Had the debate been only a matter of the empirical considerations many disagreements concerning H. sapiens would have probably disappeared long ago. But since the controversies are imbued in methodological reality the closure of the debate is not to be expected soon. There are three research methods: morphological, archaeological and genetic. Each approach has a specific definition of H. sapiens at its disposal, which largely accounts for the different scenarios for the origin of our species. Any debate concerning this problem must therefore begin with a discussion about the research methods. The controversy about our origins thus appears to be of secondary importance. The present paper aims at presenting the methodological controversy in relation to the origins of H. sapiens. The discussion about the genealogy of H. sapiens certainly is in urgent need of a new, more integrated way of approaching the past.     

Human taxonomic diversity in the pleistocene: Does Homo erectus represent multiple hominid species?

Recently, nomina such as “Homo heidelbergensis” and “H. ergaster” have been resurrected to refer to fossil hominids that are perceived to be specifically distinct from Homo sapiens and Homo erectus. This results in a later human fossil record that is nearly as speciose as that documenting the earlier history of the family Hominidae. However, it is agreed that there remains only one extant hominid species: H. sapiens. Has human taxonomic diversity been significantly pruned over the last few hundred millennia, or have the number of taxa been seriously overestimated? To answer this question, the following null hypothesis is tested: polytypism was established relatively early and the species H. erectus can accommodate all spatio-temporal variation from ca. 1.7 to 0.5 Ma. A disproof of this hypothesis would suggest that modern human polytypism is a very recent phenomenon and that speciation throughout the course of human evolution was the norm and not the exception. Cranial variation in a taxonomically mixed sample of fossil hominids, and in a modern human sample, is analyzed with regard to the variation present in the fossils attributed to H. erectus. The data are examined using both univariate (coefficient of variation) and multivariate (determinant) analyses. Employing randomization methodology to offset the small size and non-normal distribution of the fossil samples, the CV and determinant results reveal a pattern and degree of variation in H. erectus that most closely approximates that of the single species H. sapiens. It is therefore concluded that the null hypothesis cannot be rejected. © 1993 Wiley-Liss, Inc.     

Homo erectus: Ancestor or evolutionary side branch?

Controversies in paleoanthropology wax and wane, but substantial interest is currently focused on Homo erectus. This species has traditionally been regarded as a member in good standing of the human family, where it is placed as an evolutionary intermediate between earlier Homo habilis and later Homo sapiens. Recently, however, some workers have questioned whether the species exists at all. If its populations have been transformed slowly toward the modern condition, and if continuity with living people can be demonstrated in many geographic regions, then any separation of Homo erectus from Homo sapiens must be largely arbitrary. In that case, only one species should be recognized and this slowly changing lineage would have to be called Homo sapiens. Other paleontologists adopt a different view, arguing that Homo erectus is not only anatomically distinctive but also restricted in its geographic distribution. They claim that the fossils from Java and China are so specialized in appearance that they cannot lie in the mainstream of human evolution. Homo erectus, strictly defined as limited to the Far East, probably went extinct without issue. If so, more modern populations must have evolved from another source, perhaps one outside of Asia altogether.     

Sporoderm ultrastructure ofLophosoria andCyatheacidites (Filicopsida): Systematic and evolutionary implications

The distinctive spores produced byLophosoria, an extant monotypic fern, are examined ultrastructurally and correlated with the sporoderm of fossilCyatheacidites. The morphological and ultrastructural similarity of the two taxa provide additional information that can be used to trace the evolutionary history of this spore type.     

Understanding the Effect of Secondary Structures and Aggregation on Human Protein Folding Class Evolution

Using several model organisms it has been shown earlier that protein designability is related to contact density or fraction of buried residues and influence protein evolutionary rates dramatically. Here, using Homo sapiens as a model organism, we have analyzed two main folding classes (all-α and all-β) to examine the factors affecting their evolutionary rates. Since, secondary structures are the most fundamental components of the protein folding classes, we explored the effect of protein secondary structure composition on evolution. Our results show that sheet and helix fractions exhibit positive and negative correlations, respectively, with the rate of protein evolution. On dividing the secondary structure components according to solvent accessibility, linear regression model identified two factors namely buried sheet fraction and relative aggregation propensity. Both these factors together can explain about 13.4% variability in the rate of human protein evolution, while buried sheet residues can alone account to 9.9% variability.     

LB1’s virtual endocast, microcephaly, and hominin brain evolution

Earlier observations of the virtual endocast of LB1, the type specimen for Homo floresiensis, are reviewed, extended, and interpreted. Seven derived features of LB1's cerebral cortex are detailed: a caudally-positioned occipital lobe, lack of a rostrally-located lunate sulcus, a caudally-expanded temporal lobe, advanced morphology of the lateral prefrontal cortex, shape of the rostral prefrontal cortex, enlarged gyri in the frontopolar region, and an expanded orbitofrontal cortex. These features indicate that LB1's brain was globally reorganized despite its ape-sized cranial capacity (417 cm³). Neurological reorganization may thus form the basis for the cognitive abilities attributed to H. floresiensis. Because of its tiny cranial capacity, some workers think that LB1 represents a Homo sapiens individual that was afflicted with microcephaly, or some other pathology, rather than a new species of hominin. We respond to concerns about our earlier study of microcephalics compared with normal individuals, and reaffirm that LB1 did not suffer from this pathology. The intense controversy about LB1 reflects an older continuing dispute about the relative evolutionary importance of brain size versus neurological reorganization. LB1 may help resolve this debate and illuminate constraints that governed hominin brain evolution.     

CLADISTIC TESTS OF HYPOTHESES CONCERNING EVOLUTION OF XEROPHYTES AND MESOPHYTES WITHIN TILLANDSIA SUBG. PHYTARRHIZA (BROMELIACEAE)

Tillandsia L. Subg. Phytarrhiza (Visiani) Baker (Bromeliaceae) is a distinctive group of about 35 epiphytic species. These exhibit a range of habits from xeric to mesic. The evolutionary relationships of the contrasting adaptations need to be established here as well as in the subfamily as a whole. Relations between the subgenus and other tillandsioids are problematical and phylogenetic reconstruction of its member-species would be facilitated by identification of Phytarrhiza's relative (sister taxon) sharing the same most recent common ancestor with Phytarrhiza. This paper examines the two most likely sister taxa, Subg. Pseudo-Catopsis Baker and Subg. Diaphoranthema (Beer) Baker. Diaphoranthema is rejected as sister taxon. The accepted evolutionary tree, rooted by Pseudo-Catopsis, indicates that most habital evolutionary changes in Phytarrhiza have been between mesic and semi-mesic forms and from mesic to xeric forms. Methods developed for testing specific evolutionary hypotheses are broadly applicable.     

Molecular evolution of the antiretroviral <Emphasis Type="Italic">TRIM5</Emphasis> gene

In 2004, the first report of TRIM5α as a cellular antiretroviral factor triggered intense interest among virologists, particularly because some primate orthologs of TRIM5α have activity against HIV. Since that time, a complex and eventful evolutionary history of the TRIM5 locus has emerged. A review of the TRIM5 literature constitutes a veritable compendium of evolutionary phenomena, including elevated rates of nonsynonymous substitution, divergence in subdomains due to short insertions and deletions, expansions and contractions in gene copy number, pseudogenization, balanced polymorphism, trans-species polymorphism, convergent evolution, and the acquisition of new domains by exon capture. Unlike most genes, whose history is dominated by long periods of purifying selection interspersed with rare instances of genetic innovation, analysis of restriction factor loci is likely to be complicated by the unpredictable and more-or-less constant influence of positive selection. In this regard, the molecular evolution and population genetics of restriction factor loci most closely resemble patterns that have been documented for immunity genes, such as class I and II MHC genes, whose products interact directly with microbial targets. While the antiretroviral activity encoded by TRIM5 provides plausible mechanistic hypotheses for these unusual evolutionary observations, evolutionary analyses have reciprocated by providing significant insights into the structure and function of the TRIM5α protein. Many of the lessons learned from TRIM5 should be applicable to the study of other restriction factor loci, and molecular evolutionary analysis could facilitate the discovery of new antiviral factors, particularly among the many TRIM genes whose functions remain as yet unidentified.     

A new phylogenetic method for identifying exceptional phenotypic diversification

Currently available phylogenetic methods for studying the rate of evolution in a continuously valued character assume that the rate is constant throughout the tree or that it changes along specific branches according to an a priori hypothesis of rate variation provided by the user. Herein, we describe a new method for studying evolutionary rate variation in continuously valued characters given an estimate of the phylogenetic history of the species in our study. According to this method, we propose no specific prior hypothesis for how the variation in evolutionary rate is structured throughout the history of the species in our study. Instead, we use a Bayesian Markov Chain Monte Carlo approach to estimate evolutionary rates and the shift point between rates on the tree. We do this by simultaneously sampling rates and shift points in proportion to their posterior probability, and then collapsing the posterior sample into an estimate of the parameters of interest. We use simulation to show that the method is quite successful at identifying the phylogenetic position of a shift in the rate of evolution, and that estimated rates are asymptotically unbiased. We also provide an empirical example of the method using data for Anolis lizards. [This article was published online on September 20, 2011. An error in a co‐author's name was subsequently identified. This notice is included in the online and print versions to indicate that both have been corrected September 21, 2011.]