Oreopithecus bambolii: an unlikely case of hominid-like grip capability in a Miocene ape

Oreopithecus bambolii, an ape from the late Miocene of Italy, is said to possess a hand capable of a precision grip like that of humans. Relative hand length, proportions of the thumb, and morphological features of the thumb and wrist were adduced to support the idea that Oreopithecus had a hand that closely matched the pattern in Australopithecus. A reappraisal of earlier arguments and comparisons of Oreopithecus with humans, apes, and Old World monkeys, reveals that Oreopithecus had an essentially ape-like hand that emphasized ape-like power grasping over human-like precision grasping.     

Late Miocene insular mice from the Tusco-Sardinian palaeobioprovince provide new insights on the palaeoecology of the Oreopithecus faunas

Oreopithecus bambolii is one of the few hominoids that evolved under insular conditions, resulting in the development of unique adaptations that have fueled an intensive debate. The palaeoenvironment associated with this great ape has been the subject of great controversy as well. On the one hand, palaeobotanical data indicate that Oreopithecus likely inhabited mixed mesophytic forests interrupted by swamps; on the other hand, an abundance of hypsodont bovids points towards the existence of dry and open environments. Here, we provide a new approach based on the ecomorphology of the extinct endemic Muridae (rats and mice) of the so-called Oreopithecus faunas. Our results show that the successive species of endemic insular murids (Huerzelerimys and Anthracomys) evolved a number of adaptations observed only in extant family members that include significant proportions of grass in their diet. While this fits the pattern exhibited by large mammals, it contrasts with the available palaeobotanical information, which indicates that grasses were minor components of the vegetation. This contradiction may be explained because these endemic murids may have been adapted to the consumption of particular food items such as hard parts of aquatic plants (as shown by some extant murid species). However, because it is unlikely that the remaining herbivore mammals were adapted to this diet as well, we favour an alternative hypothesis that takes into account the peculiar ecological conditions of insular ecosystems leading to a density-dependent selective regime with strong competition. Such a regime would promote the selection of dental adaptations to increase feeding efficiency and durability of the dentition (such as hypsodonty) as seen in some fossil insular ruminants. This hypothesis requires further testing, but may partly account for parallel evolution of dental traits in phylogenetically unrelated insular mammals.     

The hominoid proximal radius: re-interpreting locomotor behaviors in early hominins

Studies of fossil hominins are traditionally taxonomically narrow and often exclude comparisons with hylobatids. Hence, results of functional analyses of postcrania, interpreted as indicating that early hominins are "African-ape-like" in their postcranial skeletons and positional behaviors, may reflect an artifact of inadequate taxonomic and morphological breadth of the comparative sample. To address this problem and better understand early hominin positional behaviors, this study included hylobatids in a comparative analysis, focusing on the hominoid elbow joint. Specifically, morphometric variables of the proximal radius were derived from measurements from a sample of all genera of extant hominoids and casts of extinct hominin species. Univariate and multivariate analyses were performed on these data. Results show that early hominins are morphologically diverse and are not, as a group, similar to any one extant group. Instead, the fossils resemble Pan, Gorilla, and Hylobates, and are not like modern Homo sapiens or Pongo. This suggests that the morphology of Hylobates may reflect a morphotype for all later hominoids, thus complicating the functional interpretations of fossil hominins. The implications of these results are that the proximal radius is not a sensitive indicator of locomotor behavior among hominoids since the morphology in hylobatids and Gorilla and Pan is similar despite widely varying positional repertoires. Furthermore, inferences of function from form in extinct hominins can be drastically affected by the comparative outgroup selection. A re-evaluation of the functional morphology of the proximal radius in early hominins is addressed.     

The peppered moth and industrial melanism: evolution of a natural selection case study

From the outset multiple causes have been suggested for changes in melanic gene frequency in the peppered moth Biston betularia and other industrial melanic moths. These have included higher intrinsic fitness of melanic forms and selective predation for camouflage. The possible existence and origin of heterozygote advantage has been debated. From the 1950s, as a result of experimental evidence, selective predation became the favoured explanation and is undoubtedly the major factor driving the frequency change. However, modelling and monitoring of declining melanic frequencies since the 1970s indicate either that migration rates are much higher than existing direct estimates suggested or else, or in addition, non-visual selection has a role. Recent molecular work on genetics has revealed that the melanic (carbonaria) allele had a single origin in Britain, and that the locus is orthologous to a major wing patterning locus in Heliconius butterflies. New methods of analysis should supply further information on the melanic system and on migration that will complete our understanding of this important example of rapid evolution.     

Vertebrate evolution reflected in the evolution of nuclear ribosomal internal transcribed spacer 2

In eukaryotes, mature rRNA sequences are produced from single large (45S) precursor (pre-rRNA) as the result of successive removal of spacers through a series of rapid and intricate actions of endo- and exonucleases. The excision of internal transcribed spacer (ITS2), a eukaryotic-specific insertion, remains the most elusive processing step. ITS2 is the element mandatory for all eukaryotic pre-rRNAs that contain at least three processing cleavage sites for precise 5.8S and 28S formation. Conserved core sequences (cis-elements) binding to trans-factors provide for precise rRNA processing, whereas rapidly diverging regions between the core sequences preserve internal complementarity, which guarantees the spatial integrity of ITS2. Characteristic differences in the formation of such insertions during evolution should reflect the relationships between taxa. The phylogeny of the reptiles and the relationships between taxa proposed by scientists are controversial. To delineate the structural and functional features preserved among reptilian ITS2s, we cloned and sequenced 58 ITS2s belonging to four reptile orders: Squamata, Crocodilians, Aves, and Testudines. We studied the subsequent alignment and folding of variable regions. The sizes and packing of the loop–stems between conserved consensus segments in reptiles vary considerably between taxa. Our phylogenetic trees constructed on the basis of the reptile ITS2s primary structural alignments revealed a split between Iguania clade and all other taxa. True lizards (suborder Scleroglossa) and snakes (suborder Serpentes) show sister relationships, as well as the two other reptilian orders, Crocodilia + Aves and Testudines. In summary, our phylogenetic trees exhibit a mix of specific features deduced or, to the contrary, rejected earlier by other authors.     

Host factors limiting monogenean infections: a case study

Comprehensive field data on polystomatid monogeneans record low prevalence and intensity of infection and suggest that worm burdens in this group are strongly regulated: thus, in the majority of Polystoma species infecting anuran amphibians mean abundance is typically less than one parasite/host. There is circumstantial evidence that the dominant control is attributable to host factors which over-ride variations in transmission success. This review provides a brief summary of information on Pseudodiplorchis americanus, a parasite of the desert toad, Scaphiopus couchii, and then focuses in detail on the spectrum of factors regulating infrapopulations of Protopolystoma xenopodis, a parasite of the aquatic Xenopus laevis. Infection levels of adult worms and their contribution to transmission are regulated by external environmental factors (especially temperature), by host factors (including behaviour and population density), and by a range of parasite factors including intra- and inter-specific competitive interactions and variations in intrinsic characters, especially survivorship and reproductive output. In addition to these factors whose primary effect is to modulate transmission rates, there is a major attrition in parasite numbers between invasion and maturity (3 months post-infection). Long-term laboratory experiments on the Xenopus laevis/Protopolystoma xenopodis interaction demonstrate a powerful acquired immune response. Primary infection is characterised by a high prevalence of established adult worms but the success of subsequent challenge infection is greatly reduced, leading to low prevalence and extended pre-patent period. In the small proportion of hosts supporting a second infection of adult parasites, surviving burdens are small (one to two worms/host) and show reduced egg production. These results provide an explanation for the low burdens encountered in field studies: a majority of adult X. laevis in natural populations are likely to exhibit strong, relatively long-term, post-infection immunity after the loss of a previous infection.     

The evolution of stability in a competitive system

The characteristics governing the dynamics of populations can evolve and this evolution can either be towards stability or chaos. Yet it is not obvious how or why such population characteristics can evolve through selection on individuals. In this paper we construct a mathematical model, inspired by experimental results, illustrating the dynamics of a population of competing Drosophila. We demonstrate how selection of life history characteristics and stability influence one another as a population interacts with its environment. We generalize this result and show that population stability can evolve as a consequence of selection on individuals.     

A hominoid distal tibia from the Miocene of Pakistan

A distal tibia, YGSP 1656, from the early Late Miocene portion of the Chinji Formation in Pakistan is described. The fossil is 11.4 million years old and is one of only six postcranial elements now assigned to Sivapithecus indicus. Aspects of the articular surface are cercopithecoid-like, suggesting some pronograde locomotor activities. However, YGSP 1656 possesses an anteroposteriorly compressed metaphysis and a mediolaterally thick medial malleolus, ape-like features functionally related to orthograde body postures and vertical climbing. YGSP 1656 lacks specializations found in the ankle of terrestrial cercopithecoids and thus Sivapithecus may have been primarily arboreal. Nevertheless, the morphology of this tibia is unique, consistent with other interpretations of Sivapithecus postcranial functional morphology that suggest the locomotion of this ape lacks a modern analog. Based on the limited postcranial remains from S. indicus, we hypothesize that this taxon exhibited substantial body size dimorphism.     

基于生物多样性保护的兴安落叶松与白桦最佳混交比例——以阿尔山林区为例

选取内蒙古阿尔山林区7种不同混交比例的松桦混交林,包括落叶松纯林、白桦纯林及5种不同比例的混交林为研究对象。对植物和昆虫种群丰富度、多样性进行了研究,并对种群在乔木层混交状况梯度下的分布进行了分析。结果表明:植物和昆虫种群分布受乔木层混交状况影响显著。同时,郁闭度能改变其分布状况及决定于松桦比例。兴安落叶松和白桦混交比例介于5∶5和7∶3之间时最有利于森林多样性,是进行林分疏伐的理想模式。     

Molecular evolution of the actin-like MreB protein gene family in wall-less bacteria

The mreB gene family encodes actin-like proteins that determine cell shape by directing cell wall synthesis and often exists in one to three copies in the genomes of non-spherical bacteria. Intriguingly, while most wall-less bacteria do not have this gene, five to seven mreB homologs are found in Spiroplasma and Haloplasma, which are both characterized by cell contractility. To investigate the molecular evolution of this gene family in wall-less bacteria, we sampled the available genome sequences from these two genera and other related lineages for comparative analysis. The gene phylogenies indicated that the mreB homologs in Haloplasma are more closely related to those in Firmicutes, whereas those in Spiroplasma form a separate clade. This finding suggests that the gene family expansions in these two lineages are the results of independent ancient duplications. Moreover, the Spiroplasma mreB homologs can be classified into five clades, of which the genomic positions are largely conserved. The inference of gene gains and losses suggests that there has been an overall trend to retain only one homolog from each of the five mreB clades in the evolutionary history of Spiroplasma.     

Morphological affinities of the Australopithecus afarensis hand on the basis of manual proportions and relative thumb length

The hands of apes and humans differ considerably with regard to proportions between several bones. Of critical significance is the long thumb relative to other fingers, which is the basis for human-like pad-to-pad precision grip capability, and has been considered by some as evidence of tool-making. The nature and timing of the evolutionary transition from ape-like to human-like manual proportions, however, have remained unclear as a result of the lack of appropriate fossil material. In this article, the manual proportions of Australopithecus afarensis from locality AL 333/333w (Hadar, Ethiopia) are investigated by means of bivariate and multivariate morphometric analyses, in order to test the hypothesis that human-like proportions, including an enhanced thumb/hand relationship, originally evolved as an adaptation to stone tool-making. Although some evidence for human-like manual proportions had been previously proposed for this taxon, conclusive evidence was lacking. Our results indicate that A. afarensis possessed overall manual proportions, including an increased thumb/hand relationship that, contrary to previous reports, is fully human and would have permitted pad-to-pad human-like precision grip capability. We show that these human-like proportions in A. afarensis mainly result from hand shortening, as in modern humans, and that these conclusions are robust enough as to be non-dependent on whether the bones belong to a single individual or not. Since A. afarensis predates the appearance of stone tools in the archeological record, the above-mentioned conclusions permit a confident refutation of the null hypothesis that human-like manual proportions are an adaptation to stone tool-making, and thus alternative explanations must be therefore sought. One hypothesis would consider manipulative behaviors (including tool-use and/or non-lithic tool-making) in early hominines exceeding those reported among extant non-human primates. Alternatively, on the basis of the many adaptations to committed bipedalism in A. afarensis, we propose the hypothesis that once arboreal behaviors became adaptively insignificant and forelimb-dominated locomotor selection pressures were relaxed with the adoption of terrestrial bipedalism, human-like manual proportions could have merely evolved as a result of the complex manipulation selection pressures already present in extant non-human primates.Both hypotheses are not mutually exclusive, and even other factors such as pleiotropy cannot be currently discarded.     

Convergent evolution of morphological and ecological traits in the open-habitat chat complex (Aves, Muscicapidae: Saxicolinae)

Snails in the closely related trochid genera Phorcus Risso, 1826 and Osilinus Philippi, 1847 are ecologically important algal grazers in the intertidal zone of the northeastern Atlantic Ocean and Mediterranean Sea. Here we present the first complete molecular phylogeny for these genera, based on the nuclear 28S rRNA gene and the mitochondrial 16S rRNA and COI genes, and show that the current classification is erroneous. We recognize nine species in a single genus, Phorcus: estimated by BEAST analysis, this arose 30 (±10) Ma; it consists of two subgenera, Phorcus and Osilinus, which we estimate diverged 14 (±4.5) Ma. Osilinus kotschyi, from the Arabian and Red Seas, is not closely related and is tentatively referred to Priotrochus Fischer, 1879. Our phylogeny allows us to address biogeographical questions concerning the origins of the Mediterranean and Macaronesian species of this group. The former appear to have evolved from Atlantic ancestors that invaded the Mediterranean on several occasions after the Zanclean Flood, which ended the Messinian Salinity Crisis 5.3 Ma; whereas the latter arose from several colonizations of mainland Atlantic ancestors within the last 3 (±1.5) Ma.     

Divergence of cofactor recognition across evolution: coenzyme A binding in a prokaryotic arylamine N-acetyltransferase

Arylamine N-acetyltransferase (NAT) enzymes are widespread in nature. They serve to acetylate xenobiotics and/or endogenous substrates using acetyl coenzyme A (CoA) as a cofactor. Conservation of the architecture of the NAT enzyme family from mammals to bacteria has been demonstrated by a series of prokaryotic NAT structures, together with the recently reported structure of human NAT1. We report here the cloning, purification, kinetic characterisation and crystallographic structure determination of NAT from Mycobacterium marinum, a close relative of the pathogenic Mycobacterium tuberculosis. We have also determined the structure of M. marinum NAT in complex with CoA, shedding the first light on cofactor recognition in prokaryotic NATs. Surprisingly, the principal CoA recognition site in M. marinum NAT is located some 30 Å from the site of CoA recognition in the recently deposited structure of human NAT2 bound to CoA. The structure explains the Ping-Pong Bi-Bi reaction mechanism of NAT enzymes and suggests mechanisms by which the acetylated enzyme intermediate may be protected. Recognition of CoA in a much wider groove in prokaryotic NATs suggests that this subfamily may accommodate larger substrates than is the case for human NATs and may assist in the identification of potential endogenous substrates. It also suggests the cofactor-binding site as a unique subsite to target in drug design directed against NAT in mycobacteria.     

Evolutionary history of frogfishes (Teleostei: Lophiiformes: Antennariidae): a molecular approach

Fishes of the family Antennariidae (order Lophiiformes) are primarily shallow-water benthic forms found in nearly all tropical and subtropical oceans and seas of the world, with some taxa extending into temperate waters. Despite an earlier attempt based on morphology, no previous hypothesis of intergeneric relationships of the Antennariidae exists. To resolve phylogenetic relationships within the Antennariidae, and to test the validity of species groups within Antennarius, DNA sequences from the mitochondrial 16S and cytochrome oxidase c subunit 1 (COI) genes, and nuclear recombination activating gene 2 (RAG2), for 25 described and four undescribed antennariid species, representing 10 of 12 known genera and one undescribed genus, were unambiguously aligned and analyzed using Bayesian and maximum likelihood methods. The markers were partitioned and analyzed for substitution saturation and only the third codon position of COI (COI-3) was found to have reached saturation. However, analysis of both datasets, one with the saturated data and one without, differed only slightly. All molecular analyses recovered two major clades, one comprised of Fowlerichthys, Antennarius, Histrio, and Antennatus; and another containing Rhycherus, Antennariidae gen. et sp. nov., Kuiterichthys, Phyllophryne, Echinophryne, Tathicarpus, Lophiocharon, and Histiophryne. Evidence is presented to illustrate a correlation between phylogeny, geographic distribution, and reproductive life history. The results of these analyses provide the first hypothesis of evolutionary relationships within the Antennariidae.     

The ascidian mouth opening is derived from the anterior neuropore: Reassessing the mouth/neural tube relationship in chordate evolution

The relative positions of the brain and mouth are of central importance for models of chordate evolution. The dorsal hollow neural tube and the mouth have often been thought of as developmentally distinct structures that may have followed independent evolutionary paths. In most chordates however, including vertebrates and ascidians, the mouth primordia have been shown to fate to the anterior neural boundary. In ascidians such as Ciona there is a particularly intimate relationship between brain and mouth development, with a thin canal connecting the neural tube lumen to the mouth primordium at larval stages. This so-called neurohypophyseal canal was previously thought to be a secondary connection that formed relatively late, after the independent formation of the mouth primordium and the neural tube. Here we show that the Ciona neurohypophyseal canal is present from the end of neurulation and represents the anteriormost neural tube, and that the future mouth opening is actually derived from the anterior neuropore. The mouth thus forms at the anterior midline transition between neural tube and surface ectoderm. In the vertebrate Xenopus, we find that although the mouth primordium is not topologically continuous with the neural tube lumen, it nonetheless forms at this same transition point. This close association between the mouth primordium and the anterior neural tube in both ascidians and amphibians suggests that the evolution of these two structures may be more closely linked than previously appreciated.     

Concerted evolution between duplicated genetic elements in Helicobacter pylori

The Helicobacter pylori genome includes a family of outer membrane proteins (OMPs) with substantial N and C-terminal identity. To better understand their evolution, the nucleotide sequences for two members, babA and babB, were determined from a worldwide group of 23 strains. The geographic origin of each strain was found to be the major determinant of phylogenetic structure, with strains of Eastern and Western origin showing greatest divergence. For strains 96-10 (Japan) and 96-74 (USA), the 5' regions of babB are replaced with babA sequences, demonstrating that recombination occurs between the two loci. babA and babB have nearly equivalent variation in nucleotide and amino acid identity, and frequencies of synonymous and non-synonymous substitutions. Both genes have segmental conservation but within the 3' segment, substitution patterns are nearly identical. Although babA and babB 5' and midregion segment phylogenies show strong interstrain similarity, the 3' segments show strong intrastrain similarity, indicative of concerted evolution. Within these 3' segments, the lower intrastrain than interstrain frequencies of nucleotide substitutions, which are below mean background H. pylori substitution frequencies, indicate selection against intrastrain diversification. Since babA/babB gene conversions likely underlie the concerted evolution of the 3' segments, in an experimental system, we demonstrate that gene conversions can frequently (10(-3)) occur in H. pylori. That these events are recA-dependent and DNase-resistant indicates their likely cause is intragenomic recombination.     

Sequence of mammalian fossils, including hominoid teeth, from the Bubing Basin caves, South China

A Plio-Pleistocene to Holocene faunal sequence has been recovered from four carefully excavated caves in the Bubing Basin, adjacent to the larger Bose Basin of South China. The caves vary in elevation; we suggest that the higher caves were formed and filled with sediments prior to the lower caves. The highest deposits, which are from Mohui Cave, contain hominoid teeth and other fossilized remains of mammalian taxa most similar to late Pliocene and early Pleistocene faunas. Wuyun Cave ( approximately 50m lower in elevation than Mohui) contains a late middle Pleistocene fauna, which is supported by U-series age constraints from 350 to 200ka. Lower Pubu Cave ( approximately 23m below Wuyun) is assigned to the late Pleistocene, while the Cunkong Cave (the lowest, approximately 2m lower elevation than Lower Pubu) preserves a Holocene fauna. The four faunal assemblages indicate species-level changes in Ailuropoda, Stegodon, and Sus, the appearance of Elephas, the local disappearance of Stegodon, and the migration of Equus hemionus to South China. These initial results of our work call into question the continued value of the Stegodon/Ailuropoda Fauna, a category long used to characterize the Pleistocene faunas of South China. Excavation of karstic caves of varying elevation within the basins of South China holds promise for defining local sequences of mammalian fossils that can be used to investigate faunal variations related to climate change, biogeographic events, and evolutionary change over the past two million years. Stable isotopic analysis of a small sample of mammalian teeth from Bubing Basin caves is consistent with 100% C(3) vegetation in the Bubing/Bose region, with certain delta(13)C values consistent with a canopied woodland or forest. A preliminary assessment of the hominoid teeth indicates the presence of diverse molar and premolar morphologies including dental remains of Gigantopithecus blacki and a sample with similarities to the teeth reported from Longgupo.