Homeotic change in segment identity derives the human vertebral formula from a chimpanzee-like one.

OBJECTIVES: One of the most contentious issues in paleoanthropology is the nature of the last common ancestor of humans and our closest living relatives, chimpanzees and bonobos (panins). The numerical composition of the vertebral column has featured prominently, with multiple models predicting distinct patterns of evolution and contexts from which bipedalism evolved. Here, we study total numbers of vertebrae from a large sample of hominoids to quantify variation in and patterns of regional and total numbers of vertebrae in hominoids. MATERIALS AND METHODS: We compile and study a large sample (N = 893) of hominoid vertebral formulae (numbers of cervical, thoracic, lumbar, sacral, caudal segments in each specimen) and analyze full vertebral formulae, total numbers of vertebrae, and super-regional numbers of vertebrae: presacral (cervical, thoracic, lumbar) vertebrae and sacrococcygeal vertebrae. We quantify within- and between-taxon variation using heterogeneity and similarity measures derived from population genetics. RESULTS: We find that humans are most similar to African apes in total and super-regional numbers of vertebrae. Additionally, our analyses demonstrate that selection for bipedalism reduced variation in numbers of vertebrae relative to other hominoids. DISCUSSION: The only proposed ancestral vertebral configuration for the last common ancestor of hominins and panins that is consistent with our results is the modal formula demonstrated by chimpanzees and bonobos (7 cervical-13 thoracic-4 lumbar-6 sacral-3 coccygeal). Hox gene expression boundaries suggest that a rostral shift in Hox10/Hox11-mediated complexes could produce the human modal formula from the proposal ancestral and panin modal formula.

Breeding crops for improved mineral nutrition under climate change conditions.

Improvements in understanding how climate change may influence chemical and physical processes in soils, how this may affect nutrient availability, and how plants may respond to changed availability of nutrients will influence crop breeding programmes. The effects of increased atmospheric CO2 and warmer temperatures, both individually and combined, on soil microbial activity, including mycorrhizas and N-fixing organisms, are evaluated, together with their implications for nutrient availability. Potential changes to plant growth, and the combined effects of soil and plant changes on nutrient uptake, are discussed. The organization of research on the efficient use of macro- and micronutrients by crops under climate change conditions is outlined, including analysis of QTLs for nutrient efficiency. Suggestions for how the information gained can be used in plant breeding programmes are given.

A partial hominoid innominate from the Miocene of Pakistan: description and preliminary analyses.

We describe a partial innominate, YGSP 41216, from a 12.3 Ma locality in the Siwalik Group of the Potwar Plateau in Pakistan, assigned to the Middle Miocene ape species Sivapithecus indicus. We investigate the implications of its morphology for reconstructing positional behavior of this ape. Postcranial anatomy of extant catarrhines falls into two distinct groups, particularly for torso shape. To an extent this reflects different although variable and overlapping positional repertoires: pronograde quadrupedalism for cercopithecoids and orthogrady for hominoids. The YGSP innominate (hipbone) is from a primate with a narrow torso, resembling most extant monkeys and differing from the broader torsos of extant apes. Other postcranial material of S. indicus and its younger and similar congener Sivapithecus sivalensis also supports reconstruction of a hominoid with a positional repertoire more similar to the pronograde quadrupedal patterns of most monkeys than to the orthograde patterns of apes. However, Sivapithecus postcranial morphology differs in many details from any extant species. We reconstruct a slow-moving, deliberate, arboreal animal, primarily traveling above supports but also frequently engaging in antipronograde behaviors. There are no obvious synapomorphic postcranial features shared exclusively with any extant crown hominid, including Pongo.

Stability of quantitative trait loci for growth and wood properties across multiple pedigrees and environments in Eucalyptus globulus.

· Eucalypts are one of the most planted tree genera worldwide, and there is increasing interest in marker-assisted selection for tree improvement. Implementation of marker-assisted selection requires a knowledge of the stability of quantitative trait loci (QTLs). This study aims to investigate the stability of QTLs for wood properties and growth across contrasting sites and multiple pedigrees of Eucalyptus globulus. · Saturated linkage maps were constructed using 663 genotypes from four separate families, grown at three widely separated sites, and were employed to construct a consensus map. This map was used for QTL analysis of growth, wood density and wood chemical traits, including pulp yield. · Ninety-eight QTLs were identified across families and sites: 87 for wood properties and 11 for growth. These QTLs mapped to 38 discrete regions, some of which co-located with candidate genes. Although 16% of QTLs were verified across different families, 24% of wood property QTLs and 38% of growth QTLs exhibited significant genotype-by-environment interaction. · This study provides the most detailed assessment of the effect of environment and pedigree on QTL detection in the genus. Despite markedly different environments and pedigrees, many QTLs were stable, providing promising targets for the application of marker-assisted selection.

Genetic control of interactions among individuals: contrasting outcomes of indirect genetic effects arising from neighbour disease infection and competition in a forest tree.

Indirect genetic effects (IGEs) are heritable effects of individuals on trait values of their conspecifics. IGEs may substantially affect response to selection, but empirical studies on IGEs are sparse and their magnitude and correlation with direct genetic effects are largely unknown in plants. Here we used linear mixed models to estimate genetic (co)variances attributable to direct and indirect effects for growth and foliar disease damage in a large pedigreed population of Eucalyptus globulus. We found significant IGEs for growth and disease damage, which increased with age for growth. The correlation between direct and indirect genetic effects was highly negative for growth, but highly positive for disease damage, consistent with neighbour competition and infection, respectively. IGEs increased heritable variation by 71% for disease damage, but reduced heritable variation by 85% for growth, leaving nonsignificant heritable variation for later age growth. Thus, IGEs are likely to prevent response to selection in growth, despite a considerable ordinary heritability. IGEs change our perspective on the genetic architecture and potential response to selection. Depending on the correlation between direct and indirect genetic effects, IGEs may enhance or diminish the response to natural or artificial selection compared with that predicted from ordinary heritability.

Sources of variation in self-incompatibility in the Australian forest tree, Eucalyptus globulus.

BACKGROUND AND AIMS: One of the major factors affecting the outcrossing rate in Eucalyptus globulus is thought to be the inherent self-incompatibility (SI) level of the female tree. SI in this species is mainly due to late-acting pre- and post-zygotic mechanisms operating in the ovary, and not S alleles. This study aimed to assess the phenotypic variation in SI levels within E. globulus and determine its genetic control and stability across pollination techniques, sites and seasons. METHODS: SI levels were estimated for 105 genotypes originating from across the geographical range of E. globulus over multiple years of crossing. Separate grafted trees of some genotypes growing at the same and different sites allowed the genetic basis of the variation in SI to be tested and its stability across sites and seasons to be determined. The SI level of a tree was measured as the relative reduction in seeds obtained per flower pollinated following selfing compared with outcross pollinations. Thus, if seed set is the same, SI is 0 %, and if no self seed is set, SI is 100 %. KEY RESULTS: The average SI in E. globulus was 91 % and genotypes ranged from 8 to 100 % SI. Most genotypes (>75 %) had SI levels >90 %. There were highly significant differences between genotypes and the within-site broad-sense heritability of percentage SI was high (H(2) = 0.80 +/- 0.13). However, there was evidence that growing site, and to a lesser extent season, can affect the expression of SI levels. Trees with low reproductive loads produced relatively more seed from selfed flowers. CONCLUSIONS: There is a strong genetic basis to the phenotypic variation in SI in E. globulus within a site. However, the level of SI was affected, but to a lesser extent, by the environment, which in part may reflect the higher probability of selfed zygotes surviving on sites or in seasons where competition for resources is less.

Isotopic ecology and dietary profiles of Liberian chimpanzees.

An extensive suite of isotopic data (delta(13)C, delta(15)N, and delta(18)O) from enamel apatite and bone collagen of adult male and female wild chimpanzees establishes baseline values for Pan troglodytes verus in a primary rainforest setting. The Ganta chimpanzee sample derives from a restricted region in northern Liberia. Diet is examined using stable light isotopes at three life stages-infant, young juvenile, and adult-and developmental differences are investigated within and between individual males and females. The isotopic data are very homogeneous with few exceptions. Juvenile females show consistent enrichment in (13)C relative to infants, while juvenile males do not. These data suggest that age at weaning may be more variable for male offspring who survive to adulthood than for female offspring. Alternatively, or additionally, the weaning diet of males and females may differ, with greater consumption of technologically extracted insects and/or nuts by young females. Metabolic differences, including growth and hormone-mediated responses, may also contribute to the observed variation. The Ganta chimpanzee data offer an independent and objective line of evidence to primatologists interested in the dietary strategies of the great apes and to paleoanthropologists seeking comparative models for reconstructing early hominin subsistence patterns. Despite the high diversity of dietary items consumed by chimpanzees, isotopic signatures of chimpanzees from a primary rainforest setting exhibit narrow ranges of variation similar to chimpanzees in more open habitats.

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.

Ecological changes in Miocene mammalian record show impact of prolonged climatic forcing.

Geohistorical records reveal the long-term impacts of climate change on ecosystem structure. A 5-myr record of mammalian faunas from floodplain ecosystems of South Asia shows substantial change in species richness and ecological structure in relation to vegetation change as documented by stable isotopes of C and O from paleosols. Between 8.5 and 6.0 Ma, C(4) savannah replaced C(3) forest and woodland. Isotopic historical trends for 27 mammalian herbivore species, in combination with ecomorphological data from teeth, show three patterns of response. Most forest frugivores and browsers maintained their dietary habits and disappeared. Other herbivores altered their dietary habits to include increasing amounts of C(4) plants and persisted for >1 myr during the vegetation transition. The few lineages that persisted through the vegetation transition show isotopic enrichment of delta(13)C values over time. These results are evidence for long-term climatic forcing of vegetation structure and mammalian ecological diversity at the subcontinental scale.

Hybrid weakness controlled by the dosage-dependent lethal (DL) gene system in common bean (Phaseolus vulgaris) is caused by a shoot-derived inhibitory signal leading to salicylic acid-associated root death.

Certain crosses of common bean (Phaseolus vulgaris) result in temperature-dependent hybrid weakness associated with a severe root phenotype. This is controlled by the interaction of the root- and shoot-expressed semidominant alleles dosage-dependent lethal 1 (DL(1)) and DL(2), which communicate via long-distance signaling. Previously, apparent reciprocal effects on root growth and the restoration of normal root growth by exogenous sucrose led to the hypothesis that the dosage-dependent lethal (DL) system may control root-shoot carbon partitioning. Here, recombinant inbred lines were used to map the DL loci and physiological and biochemical analysis, including metabolite profiling, was used to gain new insights into the signaling interaction and the root phenotype. It is shown that the DL system does not control root-shoot carbon partitioning and that roots are unlikely to die from carbon starvation. Instead, root death likely occurs by defense-related programmed cell death, as indicated by salicylic acid accumulation. DL(2)-expressing cotyledons supply a potent inhibitory signal that is sufficient to cause such death in DL(1)-expressing roots. These data implicate the DL system in defense-related signaling and provide support for the recent hypothesis of defense-related autoimmunity as a potential isolating mechanism in plant speciation, in particular, setting a precedence for the potential roles of long-distance signaling and temperature dependence.

Signalling mechanisms underlying the morphological responses of the root system to nitrogen in Arabidopsis thaliana.

Plants display considerable developmental plasticity in response to changing environmental conditions. The adaptations of the root system to variations in N supply are an excellent example of such developmental plasticity. In Arabidopsis, four morphological adaptations to the N supply have been characterized: (i) a localized stimulatory effect of external nitrate on lateral root elongation; (ii) a systemic inhibitory effect of high tissue nitrate concentrations on the activation of lateral root meristems; (iii) a suppression of lateral root initiation by high C:N ratios, and (iv) an inhibition of primary root growth and stimulation of root branching by external L-glutamate. These responses have provided valuable experimental systems for the study of N signalling in plants. This article will highlight some recent progress made in this direction from studies using the Arabidopsis root system. One recent development of note has been the emerging evidence of a regulatory role of nitrate transporters in some of the responses. It has been reported that the AtNRT1.1 (CHL1) dual-affinity nitrate transporter acts upstream of the ANR1 MADS box gene in mediating the stimulatory effect of a localized nitrate supply on lateral root proliferation. The AtNRT2.1 high-affinity nitrate transporter seems to be involved in the repression of lateral root initiation by high C:N ratios. The systemic inhibitory effect of high nitrate supply on lateral root development, which is mediated by abscisic acid (ABA), may be linked to the recently identified ABA receptor, FCA. The newly discovered root architectural response to external L-glutamate potentially offers a valuable experimental tool for studying the biological function of plant glutamate receptors and amino acid signalling.

Morphological affinities of the Sahelanthropus tchadensis (Late Miocene hominid from Chad) cranium.

The recent reconstruction of the Sahelanthropus tchadensis cranium (TM 266-01-60-1) provides an opportunity to examine in detail differences in cranial shape between this earliest-known hominid, African apes, and other hominid taxa. Here we compare the reconstruction of TM 266-01-60-1 with crania of African apes, humans, and several Pliocene hominids. The results not only confirm that TM 266-01-60-1 is a hominid but also reveal a unique mosaic of characters. The TM 266-01-60-1 reconstruction shares many primitive features with chimpanzees but overall is most similar to Australopithecus, particularly in the basicranium. However, TM 266-01-60-1 is distinctive in having the combination of a short subnasal region associated with a vertical upper face that projects substantially in front of the neurocranium. Further research is needed to determine the evolutionary relationships between Sahelanthropus and the known Miocene and Pliocene hominids.

New material of the earliest hominid from the Upper Miocene of Chad.

Discoveries in Chad by the Mission Paleoanthropologique Franco-Tchadienne have substantially changed our understanding of early human evolution in Africa. In particular, the TM 266 locality in the Toros-Menalla fossiliferous area yielded a nearly complete cranium (TM 266-01-60-1), a mandible, and several isolated teeth assigned to Sahelanthropus tchadensis and biochronologically dated to the late Miocene epoch (about 7 million years ago). Despite the relative completeness of the TM 266 cranium, there has been some controversy about its morphology and its status in the hominid clade. Here we describe new dental and mandibular specimens from three Toros-Menalla (Chad) fossiliferous localities (TM 247, TM 266 and TM 292) of the same age. This new material, including a lower canine consistent with a non-honing C/P3 complex, post-canine teeth with primitive root morphology and intermediate radial enamel thickness, is attributed to S. tchadensis. It expands the hypodigm of the species and provides additional anatomical characters that confirm the morphological differences between S. tchadensis and African apes. S. tchadensis presents several key derived features consistent with its position in the hominid clade close to the last common ancestor of chimpanzees and humans.

Virtual cranial reconstruction of Sahelanthropus tchadensis.

Previous research in Chad at the Toros-Menalla 266 fossiliferous locality (about 7 million years old) uncovered a nearly complete cranium (TM 266-01-60-1), three mandibular fragments and several isolated teeth attributed to Sahelanthropus tchadensis. Of this material, the cranium is especially important for testing hypotheses about the systematics and behavioural characteristics of this species, but is partly distorted from fracturing, displacement and plastic deformation. Here we present a detailed virtual reconstruction of the TM 266 cranium that corrects these distortions. The reconstruction confirms that S. tchadensis is a hominid and is not more closely related to the African great apes. Analysis of the basicranium further indicates that S. tchadensis might have been an upright biped, suggesting that bipedalism was present in the earliest known hominids, and probably arose soon after the divergence of the chimpanzee and human lineages.

The anthropoid postcranial axial skeleton: comments on development, variation, and evolution.

Within-species phenotypic variation is the raw material on which natural selection acts to shape evolutionary change, and understanding more about the developmental genetics of intraspecific as well as interspecific phenotypic variation is an important component of the Evo-Devo agenda. The axial skeleton is a useful system to analyze from such a perspective. Its development is increasingly well understood, and between-species differences in functionally important developmental parameters are well documented. I present data on intraspecific variation in the axial postcranial skeleton of some Primates, including hominoids (apes and humans). Hominoid species are particularly valuable, because counts of total numbers of vertebrae, and hence original somite numbers, are available for large samples. Evolutionary changes in the axial skeleton of various primate lineages, including bipedal humans, are reviewed, and hypotheses presented to explain the changes in terms of developmental genetics. Further relevant experiments on model organisms are suggested in order to explore more fully the differences in developmental processes between primate species, and hence to test these hypotheses.

A new hominid from the Upper Miocene of Chad, Central Africa.

The search for the earliest fossil evidence of the human lineage has been concentrated in East Africa. Here we report the discovery of six hominid specimens from Chad, central Africa, 2,500 km from the East African Rift Valley. The fossils include a nearly complete cranium and fragmentary lower jaws. The associated fauna suggest the fossils are between 6 and 7 million years old. The fossils display a unique mosaic of primitive and derived characters, and constitute a new genus and species of hominid. The distance from the Rift Valley, and the great antiquity of the fossils, suggest that the earliest members of the hominid clade were more widely distributed than has been thought, and that the divergence between the human and chimpanzee lineages was earlier than indicated by most molecular studies.

New Sivapithecus postcranial specimens from the Siwaliks of Pakistan.

Several new postcranial elements of Sivapithecus from the Siwaliks of Pakistan are described. These include a distal femur from the U-level of the Dhok Pathan Formation, a navicular from the Chinji Formation, and seven manual and pedal phalanges from the Nagri Formation. The functional morphology of these elements adds new detail to the reconstruction of Sivapithecus positional behavior. Femoral cross-sectional geometry indicates that the shaft was adapted to support mediolaterally directed loading. Femoral condylar asymmetry and a broad but shallow trochlea are distinctly ape-like, revealing capabilities for both rotation and withstanding eccentric loading in the knee. The navicular is characterized by features relating to a broad mid-tarsus and broad distal articulations for the cuneiforms. It also lacks a navicular tubercle as in Pongo. These features suggest that the foot was capable of a powerful grip on large supports, with an inversion/supination capability that would permit foot placement in a variety of positions. The morphology of the new phalanges, including evidence for a relatively large pollex, similarly suggests powerful grasping, consistent with prior evidence from the hallux and tarsus. The functional features of the new specimens permit refinement of previous interpretations of Sivapithecus positional capabilities. They suggest a locomotor repertoire dominated by pronograde activities and also such antipronograde activities as vertical climbing and clambering, but not by antipronograde suspensory activities as practiced by extant apes.