Origin of the phyla and cancer

Multicelled animals with specialized cells (metazoans) emerged shortly after rising oxygen levels in the seas permitted formation of collagen-family molecules. Certain unicells then formed 3-D clusters, some with disc- or ball-like shapes that happened to resemble blastulas. These became unstable beyond a certain size due to contrasting metabolic styles among their component cells. For whereas cells near their exteriors could employ oxygen respiration, cells closer to the oxygen-deprived interiors were obliged to rely on anaerobic metabolism (fermentation), a process that produces waste molecules that, if retained within cells, cause disproportionate cell growth. Unstable blastula-like forms would either disintegrate or reorganize along surfaces of relative weakness in a process that may be likened to gastrulation. Initial cell-differentiation depended on the quantity and diversity of retained fermentation products and on the pumping of molecules from cell to cell by the consequent electro-chemical gradients. In subsequent contexts, oxygen deprivation, fermentation, excess cell growth, and disintegration or reorganization of tissues produce cancer.     

The developmental evolution of avian digit homology: An update

The identity of avian digits has been unresolved since the beginning of evolutionary morphology in the mid-19th century, i.e. as soon as questions of phylogenetic homology have been raised. The main source of concern is the persistent discrepancy between anatomical/paleontological and embryological evidence over the identity of avian digits. In this paper, recent evidence pertaining to the question of avian digit homology is reviewed and the various ideas of how to resolve the disagreement among developmental and phylogenetic evidence are evaluated. Paleontological evidence unequivocally supports the hypothesis that the fully formed digits of maniraptoran theropods are digits DI, DII, and DIII, because the phylogenetic position of Herrerasaurus is resolved, even when hand characters are excluded from the analysis. Regarding the developmental origin of the three digits of the avian hand the discovery of an anterior digit condensation in the limb bud of chickens and ostriches conclusively shows that these three digits are developing from condensations CII, CIII, and CIV. The existence of this additional anterior condensation has been confirmed in four different labs, using four different methods: Alcian blue staining, PNA affinity histochemistry, micro-capillary regression and Sox9 expression. Finally, recent evidence shows that the digit developing from condensation CII has a Hox gene expression pattern that is found in digit DI of mice forelimb and chick hind limbs. The sum of these data supports the idea that digit identity has shifted relative to the location of condensations, known as Frame Shift Hypothesis, such that condensation CII develops into digit DI and condensation CIII develops into digit DII, etc. A review of the literature on the digit identity of the Italian Three-toed Skink or Luscengola (Chalcides chalcides), shows that digit identity frame shifts may not be limited to the bird hand but may be characteristic of “adaptive” digit reduction in amniotes (sensu Steiner, H., Anders, G., 1946. Zur Frage der Entstehung von Rudimenten. Die Reduktion der Gliedmassen von Chalcides tridactylus Laur. Rev. Suisse Zool. 53, 537–546) in general. In this mode of evolution two digits are lost, in the course of the adaptation of the three anterior digits to a function that does not require the two posterior digits. This evidence suggests that the evolution of digits in tetrapods can proceed at least on two distinct levels of integration, the level of digit condensations and that of adult digits.     

Jaw-muscle electromyography during chewing in Belanger's treeshrews (Tupaia belangeri)

We examined masseter and temporalis recruitment and firing patterns during chewing in five male Belanger's treeshrews (Tupaia belangeri), using electromyography (EMG). During chewing, the working-side masseters tend to show almost three times more scaled EMG activity than the balancing-side masseters. Similarly, the working-side temporalis muscles have more than twice the scaled EMG activity of the balancing-side temporalis. The relatively higher activity in the working-side muscles suggests that treeshrews recruit less force from their balancing-side muscles during chewing. Most of the jaw-closing muscles in treeshrews can be sorted into an early-firing or late-firing group, based on occurrence of peak activity during the chewing cycle. Specifically, the first group of jaw-closing muscles to reach peak activity consists of the working-side anterior and posterior temporalis and the balancing-side superficial masseter. The balancing-side anterior and posterior temporalis and the working-side superficial masseter peak later in the power stroke. The working-side deep masseter peaks, on average, slightly before the working-side superficial masseter. The balancing-side deep masseter typically peaks early, at about the same time as the balancing-side superficial masseter. Thus, treeshrews are unlike nonhuman anthropoids that peak their working-side deep masseters early and their balancing-side deep masseters late in the power stroke. Because in anthropoids the late firing of the balancing-side deep masseter contributes to wishboning of the symphysis, the treeshrew EMG data suggest that treeshrews do not routinely wishbone their symphyses during chewing. Based on the treeshrew EMG data, we speculate that during chewing, primitive euprimates 1) recruited more force from the working-side jaw-closing muscles as compared to the balancing-side muscles, 2) fired an early group of jaw-closing muscles followed by a second group of muscles that peaked later in the power stroke, 3) did not fire their working-side deep masseter significantly earlier than their working-side superficial masseter, and 4) did not routinely fire their balancing-side deep masseter after the working-side superficial masseter.     

Primate sociality in evolutionary context

Much work has been done to further our understanding of the mechanisms that underlie the diversity of primate social organizations, but none has addressed the limits to that diversity or the question of what causes species to either form or not form social networks. The fact that all living primates typically live in social networks makes it highly likely that the last common ancestor of living primates already lived in social networks, and that sociality formed an integral part of the adaptive nature of primate origins. A characterization of primate sociality within the wider mammalian context is therefore essential to further our understanding of the adaptive nature of primate origins. Here we determine correlates of sociality and nonsociality in rodents as a model to infer causes of sociality in primates. We found sociality to be most strongly associated with large-bodied arboreal species that include a significant portion of fruit in their diet. Fruits and other plant products, such as flowers, seeds, and young leaves, are patchily distributed in time and space and are therefore difficult to find. These food resources are, however, predictable and dependable when their location is known. Hence, membership in a social unit can maximize food exploitation if information on feeding sites is shared. Whether sociality evolved in the primate stem lineage or whether it was already present earlier in the evolution of Euarchontoglires remains uncertain, although tentative evidence points to the former scenario. In either case, frugivory is likely to have played an important role in maintaining the presence of a social lifestyle throughout primate evolution.     

GENOMICS IN THE LIGHT OF EVOLUTIONARY TRANSITIONS

Molecular biology has entrenched the gene as the basic hereditary unit and genomes are often considered little more than collections of genes. However, new concepts and genomic data have emerged, which suggest that the genome has a unique place in the hierarchy of life. Despite this, a framework for the genome as a major evolutionary transition has not been fully developed. Instead, genome origin and evolution are frequently considered as a series of neutral or nonadaptive events. In this article, we argue for a Darwinian multilevel selection interpretation for the origin of the genome. We base our arguments on the multilevel selection theory of hypercycles of cooperative interacting genes and predictions that gene‐level trade‐offs in viability and reproduction can help drive evolutionary transitions. We consider genomic data involving mobile genetic elements as a test case of our view. A new concept of the genome as a discrete evolutionary unit emerges and the gene–genome juncture is positioned as a major evolutionary transition in individuality. This framework offers a fresh perspective on the origin of macromolecular life and sets the scene for a new, emerging line of inquiry—the evolutionary ecology of the genome.     

Heterotachy and tree building: a case study with plastids and eubacteria

The nature of heterotachy at the center of recent controversy over the relative performance of tree-building methods is different from the form of heterotachy that has been inferred in empirical studies. The latter have suggested that proportions of variable sites (p(var)) vary among orthologues and among paralogues. However, the strength of this inference, describing what may be one of the most important evolutionary properties of sequence data, has remained weak. Consequently, other models of sequence evolution have been proposed to explain some long-branch attraction (LBA) problems that could be attributed to differences in p(var). For an empirical case with plastid and eubacterial RNA polymerase sequences, we confirm using capture-recapture estimates and simulations that p(var) can differ among orthologues in anciently diverged evolutionary lineages. We find that parsimony and a least squares distance method that implements an overly simple model of sequence evolution are susceptible to LBA induced by this form of heterotachy. Although homogeneous maximum likelihood inference was found to be robust to model misspecification in our specific example, we caution against assuming that it will always be so.     

Ontogeny and homology of the paranasal sinuses in Platyrrhini (Mammalia: Primates)

The identity and taxonomic distribution of paranasal sinuses among living platyrrhines has remained a contentious issue (e.g., Cave [1967] Am J Phys Anthropol 26:277-288 vs. Hershkovitz [1977] Chicago: University of Chicago Press) largely because the ontogenetic data required for their detection and identification (e.g., Cave [1967]; Maier [2000] Cambridge, UK: Cambridge University Press, 99-132.) were not attainable without sacrificing valuable juvenile and subadult specimens. Non-invasive computed tomography (CT) scanning of ontogenetic series of skulls for 10 platyrrhine genera demonstrates the presence of maxillary and ethmoid sinuses, as well as homologs of the human sphenoid and frontal sinuses. Differences in the latter two sinuses between platyrrhines and hominoids highlight the need for early developmental data in establishing sinus homology. In particular, the identification of homologous recesses in the cartilaginous nasal capsule, from which sinuses later develop, emerges as the critical step. This developmental approach also reveals that the anterior and posterior ethmoid sinuses are each sets of serial homologs, a point which reconciles previous difficulties in establishing sinus homologies across mammalian orders (e.g., Paulli [1900] Gegenbaurs Morphol Jahrb 28:147-178, 179-251, 483-564).     

New primate first metatarsals from the Paleogene of Egypt and the origin of the anthropoid big toe

The specialized grasping feet of primates, and in particular the nature of the hallucal grasping capabilities of living strepsirrhines and tarsiers (i.e., ‘prosimians’), have played central roles in the study of primate origins. Prior comparative studies of first metatarsal (Mt1) morphology have documented specialized characters in living prosimians that are indicative of a more abducted hallux, which in turn is often inferred to be related to an increased ability for powerful grasping. These include a well-developed peroneal process and a greater angle of the proximal articular surface relative to the long axis of the diaphysis. Although known Mt1s of fossil prosimians share these characters with living non-anthropoid primates, Mt1 morphology in the earliest crown group anthropoids is not well known. Here we describe two Mt1s from the Fayum Depression of Egypt - one from the latest Eocene (from the ∼34 Ma Quarry L-41), and one from the later early Oligocene (from the ∼29-30 Ma Quarry M) - and compare them with a sample of extant and fossil primate Mt1s. Multivariate analyses of Mt1 shape variables indicate that the Fayum specimens are most similar to those of crown group anthropoids, and likely belong to the stem catarrhines Catopithecus and Aegyptopithecus specifically, based on analyses of size. Also, phylogenetic analyses with 16 newly defined Mt1 characters support the hypotheses that “prosimian”-like Mt1 features evolved along the primate stem lineage, while crown anthropoid Mt1 morphology and function is derived among primates, and likely differed from that of basal stem anthropoids. The derived loss of powerful hallucal grasping as reflected in the Mt1 morphology of crown anthropoids may reflect long-term selection for improved navigation of large-diameter, more horizontal branches at the expense of movement in smaller, more variably inclined branches in the arboreal environment.     

Allotetraploid Mimulus sookensis are highly interfertile despite independent origins

Polyploidy (whole‐genome duplication) has contributed significantly to angiosperm evolution and diversification. To date, it has been found that most polyploids are the result of multiple formation events, which may contribute to genetic diversity and affect interfertility among polyploid lineages of independent origin. A recently discovered allotetraploid derivative of Mimulus guttatus and M. nasutus, Mimulus sookensis, is found throughout the valleys of western Oregon and Vancouver Island. Here, we analyse the patterns of nucleotide diversity at three chloroplast and six nuclear loci in M. guttatus, M. nasutus and M. sookensis, to gain insight into the formation of M. sookensis. By analysing the patterns of genetic variation seen in the diploid progenitors in comparison with the variation seen in M. sookensis, we are able to show that M. sookensis has recurrently formed. We also observed that most M. sookensis individuals are fixed heterozygotes at all of the nuclear loci examined, suggesting that duplicate gene loss is not extensive in M. sookensis. To assess the possibility that hybridization among M. sookensis has contributed to genetic diversity, we conducted crossing experiments within M. sookensis. We found that M. sookensis of independent origin are highly interfertile, suggesting that crossing barriers do not exist within M. sookensis, and that hybridization among M. sookensis may result in new recombinant genotypes. Together, the data suggest that although recurrent origins may be common, they can contribute to genetic diversity without contributing to reproductive isolation among independently arisen polyploid lineages.