Selective breeding for high endurance running increases hindlimb symmetry

Comparative studies provide correlational evidence of morphological adaptations for high locomotor performance, such as the classical indicators of cursoriality in mammals, long limbs and high metatarsal/femur ratios. More recently, enlarged femoral condyles have been suggested as an adaptation for high endurance running in the genus Homo. Asymmetry of locomotor appendages should adversely affect locomotor abilities, but this has not been studied in a rigorous evolutionary context. We used experimental evolution to test for morphological adaptations associated with high voluntary wheel running in selectively bred lines of mice. Surprisingly, the classical indicators of cursoriality had not evolved in concert with high activity levels. Instead, high runners had larger femoral condyles and reduced directional asymmetry of hindlimb bones. We hypothesize that greater limb symmetry and larger femoral heads are general adaptations associated with sustained, high-speed locomotion.     

From apes to humans: locomotion as a key feature for phylogeny

If bipedalism has often been considered to be of a crucial interest for understanding hominid evolution, the acceptance of locomotor features to build phylogenies is still far from being a reality in the field. Especially for hominid evolution, it still seems to be difficult to accept that traits, other than craniodental ones, can be useful for defining the major dichotomies. The recent discovery of Australopithecus anamensis suggests a challenging view of the major dichotomy between apes and humans. Whilst it is widely accepted that Ardipithecus ramidus is ancestral to Australopithecus anamensis, which in its turn is ancestral to Australopithecus afarensis and then to later hominids, the postcranial adaptations, which should be taken into account, suggest another branching pattern. Based on the fact that by 4.0 million years two different locomotor patterns can be identified in hominids, two lineages would appear to be present: the "Australopithecine" lineage (with Australopithecus afarensis or Ardipithecus ramidus if the latter is really a hominid sensu stricto) and the "Hominine" lineage (with Australopithecus anamensis = Praeanthropus africanus).     

The origin of plastids

It is generally accepted that plastids first arose by acquisition of photosynthetic prokaryotic endosymbionts by non-photosynthetic eukaryotic hosts. It is also accepted that photosynthetic eukaryotes were acquired on several occasions as endosymbionts by non-photosynthetic eukaryote hosts to form secondary plastids. In some lineages, secondary plastids were lost and new symbionts were acquired, to form tertiary plastids. Most recent work has been interpreted to indicate that primary plastids arose only once, referred to as a 'monophyletic' origin. We critically assess the evidence for this. We argue that the combination of Ockham's razor and poor taxon sampling will bias studies in favour of monophyly. We discuss possible concerns in phylogenetic reconstruction from sequence data. We argue that improved understanding of lineage-specific substitution processes is needed to assess the reliability of sequence-based trees. Improved understanding of the timing of the radiation of present-day cyanobacteria is also needed. We suggest that acquisition of plastids is better described as the result of a process rather than something occurring at a discrete time, and describe the 'shopping bag' model of plastid origin. We argue that dinoflagellates and other lineages provide evidence in support of this.     

The entD gene of the Escherichia coli K12 enterobactin gene cluster

The Escherichia coli entD gene encodes a product necessary for the synthesis of the iron-chelating and transport molecule enterobactin (Ent); cells harbouring entD mutations fail to grow in iron-deficient environments. For unknown reasons, it has not been possible to identify the entD product. The nucleotide sequence of the entD region has now been determined. An open reading frame extending in the same direction as the adjacent fepA gene and capable of encoding an approximately 24 kDa polypeptide was found; it contained a high percentage of rare codons and two possible translational start sites. Complementation data suggested that EntD proteins truncated at the carboxy terminus retain some activity. Two REP sequences were present upstream of entD and an IS186 sequence was observed downstream. RNA dot-blot hybridizations demonstrated that entD is transcribed from the strand predicted by the sequencing results. An entD-lacZ recombinant plasmid was constructed and shown to express low amounts of a fusion protein of the anticipated size (approximately 125 kDa). The evidence suggests a number of possible explanations for difficulties in detecting the entD product. Sequence data indicate that if entD has its own promoter, it is weak; the REP sequences suggest that entD mRNA may be destabilized; and translation may be slow because of the frequency of rare codons and a possible unusual start codon (UUG). The data are also consistent with previous evidence that the entD product is unstable.     

探究早期现代人的南方扩散路线

本文从扩散时间、扩散路径、主要争论以及考古学证据等方面,对早期现代人南方扩散路线的研究现状进行梳理,对相关问题进行了探究。越来越多的证据显示,使用旧石器中期石器技术的早期现代人在晚更新世早期（MIS 5阶段）已经开始沿南方路线扩散,但学术界对于此次扩散的范围和影响程度仍存在争议。在距今约5万年以后,南方扩散路线上的早期现代人出现诸如使用赭石颜料、制作串珠和骨质工具、创作岩画艺术等行为,同时也独立发展出一些区域性适应行为。石器研究显示,南亚地区在5-3万年前逐渐出现了细石器技术及相关产品（细石叶、修背工具等）,而东南亚和大洋洲地区表现出以生产细小石片为主的权宜性石器技术体系,一些细小石片曾被用来加工有机质工具或作为复合型工具使用。中国南方地区紧邻东南亚和印度半岛,无论是从地理位置还是从生态环境来看,都可以纳入南方扩散路线的研究范围。建议从旧石器中期石制品组合和旧石器晚期细小石制品组合两方面入手,开展跨区域比较研究,为探索中国南方地区早期现代人的出现和演化提供重要考古学证据。     

Continuity and change in the eastern Aleutian archaeological sequence

The eastern Aleutian prehistoric archaeological sequence is key for understanding population movements, cultural exchanges, and adaptations to environmental changes over a wide area of the north Pacific and Bering Sea during the Holocene. An important question is, Can the settlement history of the eastern Aleutians be understood as a single continuous tradition lasting some 9,000 years, or were there major population and cultural influxes along with periods of widespread population abandonment? We review the available archaeological evidence with reference to recent mtDNA and nucleic DNA studies of prehistoric and contemporary Arctic and Subarctic populations and conclude that the evidence points to an overall cultural continuity with notable incursions and excursions of people and cultural elements into and out of the eastern Aleutians.     

A partial skeleton of the fossil great ape Hispanopithecus laietanus from Can Feu and the mosaic evolution of crown-hominoid positional behaviors

The extinct dryopithecine Hispanopithecus (Primates: Hominidae), from the Late Miocene of Europe, is the oldest fossil great ape displaying an orthograde body plan coupled with unambiguous suspensory adaptations. On the basis of hand morphology, Hispanopithecus laietanus has been considered to primitively retain adaptations to above-branch quadrupedalism-thus displaying a locomotor repertoire unknown among extant or fossil hominoids, which has been considered unlikely by some researchers. Here we describe a partial skeleton of H. laietanus from the Vallesian (MN9) locality of Can Feu 1 (Vallès-Penedès Basin, NE Iberian Peninsula), with an estimated age of 10.0-9.7 Ma. It includes dentognathic and postcranial remains of a single, female adult individual, with an estimated body mass of 22-25 kg. The postcranial remains of the rib cage, shoulder girdle and forelimb show a mixture of monkey-like and modern-hominoid-like features. In turn, the proximal morphology of the ulna-most completely preserved in the Can Feu skeleton than among previously-available remains-indicates the possession of an elbow complex suitable for preserving stability along the full range of flexion/extension and enabling a broad range of pronation/supination. Such features, suitable for suspensory behaviors, are however combined with an olecranon morphology that is functionally related to quadrupedalism. Overall, when all the available postcranial evidence for H. laietanus is considered, it emerges that this taxon displayed a locomotor repertoire currently unknown among other apes (extant or extinct alike), uniquely combining suspensory-related features with primitively-retained adaptations to above-branch palmigrady. Despite phylogenetic uncertainties, Hispanopithecus is invariably considered an extinct member of the great-ape-and-human clade. Therefore, the combination of quadrupedal and suspensory adaptations in this Miocene crown hominoid clearly evidences the mosaic nature of locomotor evolution in the Hominoidea, as well as the impossibility to reconstruct the ancestral locomotor repertoires for crown hominoid subclades on the basis of extant taxa alone.     

Frequency and timing of scaphoid-centrale fusion in hominoids

Fusion between the os centrale and the scaphoid has played a central role in many functional and phylogenetic interpretations of hominoid evolution. In particular, scaphoid-centrale fusion shared among African apes and humans has been interpreted as an adaptation in knuckle-walkers, an exaptation in hominins, and has been offered as evidence for a knuckle-walking origin of bipedalism. However, discrepancies in the literature concerning the taxa in which this scaphoid-centrale fusion occurs, as well as the timing and/or frequency of this fusion, have confounded the significance of this trait. This study provides an historical review of the literature on scaphoid-centrale fusion in primates and the first formal investigation into the timing and frequency of this character among primates, with a focus on extant hominoids. Results indicate that there is a significant difference in the timing and frequency of scaphoid-centrale fusion in African apes and humans compared to Asian apes, suggesting that prenatal or early postnatal fusion among hominines is a synapomorphy. Scaphoid-centrale fusion does not occur randomly within primates. Instead, only Homininae and some members of Lemuroidea show consistent and ontogenetically early fusion of these carpals. The consistent occurrence of this trait within only two primate clades and a clear heterochronic trend in timing and frequency of scaphoid-centrale fusion among hominines suggest that this character is primarily phylogenetically controlled. We could not falsify the hypothesis that scaphoid-centrale fusion in African apes is indeed related to midcarpal stability in knuckle-walking, but neither were we able to find direct biomechanical or kinematic evidence to support this hypothesis. A more definitive answer to the question of the functional significance of scaphoid-centrale fusion will have to await more detailed analyses of great ape wrist kinematics.     

Skeletal development in Pan paniscus with comparisons to Pan troglodytes

Fusion of skeletal elements provides markers for timing of growth and is one component of a chimpanzee's physical development. Epiphyseal closure defines bone growth and signals a mature skeleton. Most of what we know about timing of development in chimpanzees derives from dental studies on Pan troglodytes. Much less is known about the sister species, Pan paniscus, with few in captivity and a wild range restricted to central Africa. Here, we report on the timing of skeletal fusion for female captive P. paniscus (n = 5) whose known ages range from 0.83 to age 11.68 years. Observations on the skeletons were made after the individuals were dissected and bones cleaned. Comparisons with 10 female captive P. troglodytes confirm a generally uniform pattern in the sequence of skeletal fusion in the two captive species. We also compared the P. paniscus to a sample of three unknown‐aged female wild P. paniscus, and 10 female wild P. troglodytes of known age from the Taï National Park, Côte d'Ivoire. The sequence of teeth emergence to bone fusion is generally consistent between the two species, with slight variations in late juvenile and subadult stages. The direct‐age comparisons show that skeletal growth in captive P. paniscus is accelerated compared with both captive and wild P. troglodytes populations. The skeletal data combined with dental stages have implications for estimating the life stage of immature skeletal materials of wild P. paniscus and for more broadly comparing the skeletal growth rates among captive and wild chimpanzees (Pan), Homo sapiens, and fossil hominins. Am J Phys Anthropol 2012. © 2012 Wiley Periodicals, Inc.     

Evolution of locomotion in Anthropoidea: the semicircular canal evidence

Our understanding of locomotor evolution in anthropoid primates has been limited to those taxa for which good postcranial fossil material and appropriate modern analogues are available. We report the results of an analysis of semicircular canal size variation in 16 fossil anthropoid species dating from the Late Eocene to the Late Miocene, and use these data to reconstruct evolutionary changes in locomotor adaptations in anthropoid primates over the last 35 Ma. Phylogenetically informed regression analyses of semicircular canal size reveal three important aspects of anthropoid locomotor evolution: (i) the earliest anthropoid primates engaged in relatively slow locomotor behaviours, suggesting that this was the basal anthropoid pattern; (ii) platyrrhines from the Miocene of South America were relatively agile compared with earlier anthropoids; and (iii) while the last common ancestor of cercopithecoids and hominoids likely was relatively slow like earlier stem catarrhines, the results suggest that the basal crown catarrhine may have been a relatively agile animal. The latter scenario would indicate that hominoids of the later Miocene secondarily derived their relatively slow locomotor repertoires.     

Allometric scaling and locomotor function in the primate pelvis

Identification of positional behavior adaptation in the pelvis of primates is complicated by possible confounding effects of body size and phylogeny. Previous work on primate pelvic allometry has focused primarily on sexual dimorphism and its relationship to obstetric constraints in species with large fetal size relative to maternal size. This study investigates patterns of pelvic scaling with a specific aim to understand how pelvic scaling relates to locomotor function. Patterns of scaling of nine pelvic dimensions were examined in a broad comparative sample of 40 species of primates, covering both haplorhines and strepsirrhines, while accounting for phylogenetic nonindependence. Phylogenetic reduced major axis regressions on pelvic scaling patterns suggest that primate-wide patterns are reflected in haplorhine- and strepsirrhine-specific analyses. Many measures scale isometrically with pelvis size, but notably, features of the ilium tend to scale allometrically. As predicted, ilium width and lower ilium cross-sectional area scale with positive allometry, while lower iliac height scales with negative allometry. Further regression analyses by locomotor group suggest that these ilium measures, as well as pubic symphysis and ischium lengths, differ in their scaling patterns according to locomotor mode. These results suggest that scaling differences within primates, when present, are related to functional differences in locomotor behavior and mechanics. This study supports recent work that identifies adaptations to locomotor loading in the ilium and highlights the need for a better understanding of the relationship between pelvic structural mechanics and the mechanical requirements of primate locomotion. Am J Phys Anthropol 156:511–530, 2015. © 2015 Wiley Periodicals, Inc.     

Transmembrane helix dimerization: beyond the search for sequence motifs

Studies of the dimerization of transmembrane (TM) helices have been ongoing for many years now, and have provided clues to the fundamental principles behind membrane protein (MP) folding. Our understanding of TM helix dimerization has been dominated by the idea that sequence motifs, simple recognizable amino acid sequences that drive lateral interaction, can be used to explain and predict the lateral interactions between TM helices in membrane proteins. But as more and more unique interacting helices are characterized, it is becoming clear that the sequence motif paradigm is incomplete. Experimental evidence suggests that the search for sequence motifs, as mediators of TM helix dimerization, cannot solve the membrane protein folding problem alone. Here we review the current understanding in the field, as it has evolved from the paradigm of sequence motifs into a view in which the interactions between TM helices are much more complex. This article is part of a Special Issue entitled: Membrane protein structure and function.     

Multimodal phylogeny for taxonomy: integrating information from nucleotide and amino acid sequences

The crucial role played by the analysis of microbial diversity in biotechnology-based innovations has increased the interest in the microbial taxonomy research area. Phylogenetic sequence analyses have contributed significantly to the advances in this field, also in the view of the large amount of sequence data collected in recent years. Phylogenetic analyses could be realized on the basis of protein-encoding nucleotide sequences or encoded amino acid molecules: these two mechanisms present different peculiarities, still starting from two alternative representations of the same information. This complementarity could be exploited to achieve a multimodal phylogenetic scheme that is able to integrate gene and protein information in order to realize a single final tree. This aspect has been poorly addressed in the literature. In this paper, we propose to integrate the two phylogenetic analyses using basic schemes derived from the multimodality fusion theory (or multiclassifier systems theory), a well-founded and rigorous branch for which its powerfulness has already been demonstrated in other pattern recognition contexts. The proposed approach could be applied to distance matrix-based phylogenetic techniques (like neighbor joining), resulting in a smart and fast method. The proposed methodology has been tested in a real case involving sequences of some species of lactic acid bacteria. With this dataset, both nucleotide sequence- and amino acid sequence-based phylogenetic analyses present some drawbacks, which are overcome with the multimodal analysis.     

Is There Selection for the Pace of Successive Inactivation of the arpAT Gene in Primates?

Pseudogenes have classically been considered inactive sequences evolving under neutrality. In recent years, however, a growing body of evidence is favoring the appearance of hypotheses attributing a functional role to pseudogenes. One of these hypotheses is that the silencing of a gene could produce a loss of function that could have been favored by natural selection. Here, we analyzed the pace of pseudogenization of arpAT, an L-DOPA transporter related to the neurotransmitter function of this amino acid in the brain. While active in rodent, dog, and chicken, arpAT has been silenced during primate evolution. Given the high number of inactivating mutations described in humans, it is possible that there have been selective pressures favoring this silencing. Through analysis of orthologous sequences in several primate species, we show that the silencing of arpAT occurred approximately 77 million to 90 million years ago, and that the observed mutation pattern is likely a consequence of its antiquity.     

Myoblast fusion in Drosophila

Somatic muscle formation is an unusual process as it requires the cells involved, the myoblasts, to relinquish their individual state and fuse with one another to form a syncitial muscle fiber. The potential use of myoblast fusion therapies to rebuild damaged muscles has generated continuing interest in elucidating the molecular basis of the fusion process. Yet, until recently, few of the molecular players involved in this process had been identified. Now, however, it has been possible to couple a detailed understanding of the cellular basis of the fusion process with powerful classical and molecular genetic strategies in the Drosophila embryo. We review the cellular studies, and the recent genetic and biochemical analyses that uncovered interacting extracellular molecules present on fusing myoblasts and the intracellular effectors that facilitate fusion. With the conservation of proteins and protein functions across species, it is likely that these findings in Drosophila will benefit understanding of the myoblast fusion process in higher organisms.     

Broken fingers: retesting locomotor hypotheses for fossil hominoids using fragmentary proximal phalanges and high-resolution polynomial curve fitting (HR-PCF)

Phalangeal curvature has frequently been used as a proxy indicator of fossil hominoid and hominin positional behavior and locomotor adaptations, both independently and within the context of broader discussions of the postcranium as a whole. This study used high-resolution polynomial curve fitting (HR-PCF) to measure the shaft curvature of fragmentary proximal phalanges that have previously been excluded from analyses of phalangeal curvature owing to design limitations of existing methods. In doing so, the available sample of fossil specimens was increased substantially, making it possible to test prevailing locomotor hypotheses for many taxa with new specimens. The results generated from the HR-PCF analysis of extant primate manual and pedal phalangeal samples suggest that, although capable of identifying suspensory hominoids with some degree of accuracy, phalangeal curvature values reported for extant terrestrial and arboreal quadrupeds overlap considerably. Consequently, it is difficult to reliably predict the locomotor adaptations for fossil taxa with phalangeal curvatures similar to these groups, although the curvature values reported for most taxa were broadly consistent with existing locomotor hypotheses. Only the curvature values reported for Pierolapithecus, which are most similar to those of suspensory hominoids, are inconsistent with previously published locomotor hypotheses. Likewise, although not inconsistent with bipedality, curvature values reported for Australopithecus confirm earlier conclusions that, despite a general reduction in phalangeal length relative to Pan, these taxa have similar and overlapping ranges of phalangeal curvature.     

Indonesian mitochondrial DNA and its opposition to a Pleistocene era origin of proto-Polynesians in island southeast Asia

The origin of modern Polynesians, the route of their expansion into the Pacific Ocean, and the timing of their movements all remain contentious topics in modern anthropology. Numerous studies have used molecular data to elucidate settlement patterns in the Indo-Pacific region, but the same evidence is often interpreted in opposing ways by different researchers. Above all, mitochondrial DNA (mtDNA) diversity has been used to discriminate between competing migration models and has narrowed the probable source of proto-Polynesian peoples to southern China and Taiwan or eastern Indonesia. Richards et al. (1998) used a dating method employing the p statistic to argue for an origin of Polynesian peoples in eastern Indonesia during the Pleistocene (> 10,000 years ago). Here, the time to the most recent common ancestor (TMRCA) is recalculated for a new series of Indonesian mtDNA sequences with Polynesian affinities. These data, which incorporate additional sequences published after 1998, produce dates that cannot rule out the possibility of a common ancestor for these sequences during the Holocene (< 10,000 years ago). This implies that previous estimates of TMRCA dates for Indonesian sequences lacked the statistical robustness necessary for replicability. The extant mtDNA evidence can no longer be viewed as favoring a Polynesian origin in eastern Indonesia, but instead remains consistent with an origin of proto-Polynesian peoples in southern China and Taiwan.     

The origins of music in auditory scene analysis and the roles of evolution and culture in musical creation

Whether music was an evolutionary adaptation that conferred survival advantages or a cultural creation has generated much debate. Consistent with an evolutionary hypothesis, music is unique to humans, emerges early in development and is universal across societies. However, the adaptive benefit of music is far from obvious. Music is highly flexible, generative and changes rapidly over time, consistent with a cultural creation hypothesis. In this paper, it is proposed that much of musical pitch and timing structure adapted to preexisting features of auditory processing that evolved for auditory scene analysis (ASA). Thus, music may have emerged initially as a cultural creation made possible by preexisting adaptations for ASA. However, some aspects of music, such as its emotional and social power, may have subsequently proved beneficial for survival and led to adaptations that enhanced musical behaviour. Ontogenetic and phylogenetic evidence is considered in this regard. In particular, enhanced auditory–motor pathways in humans that enable movement entrainment to music and consequent increases in social cohesion, and pathways enabling music to affect reward centres in the brain should be investigated as possible musical adaptations. It is concluded that the origins of music are complex and probably involved exaptation, cultural creation and evolutionary adaptation.