Australopithecines: Ancestors of the African Apes?

Since australopithecines display humanlike traits such as short ilia, relatively small front teeth and thick molar enamel, they are usually assumed to be related toHomo rather than toPan orGorilla. However, this assumption is not supported by many other of their features. This paper briefly surveys the literature concerning craniodental comparisons of australopith species with those of bonobos, common chimps, humans and gorillas, adult and immature. It will be argued, albeit on fragmentary data, that the large australopiths of East Africa were in many instances anatomically and therefore possibly also evolutionarily nearer toGorilla than toPan orHomo, and the South African australopiths nearer toPan andHomo than toGorilla. An example of a possible evolutionary tree is provided. It is suggested that the evidence concerning the relation of the different australopithecines with humans, chimpanzees and gorillas should be re-evaluated.     

Engineering aspects of biological ion channels—from biosensors to computational models for permeation

Molecular sequencing has helped resolve the phylogenetic relationships amongst the diverse groups of algal, fungal-like and protist organisms that constitute the Chromalveolate “superkingdom” clade. It is thought that the whole clade evolved from a photosynthetic ancestor and that there have been at least three independent plastid losses during their evolutionary history. The fungal-like oomycetes and hyphochytrids, together with the marine flagellates Pirsonia and Developayella, form part of the clade defined by Cavalier-Smith and Chao (2006) as the phylum “Pseudofungi”, which is a sister to the photosynthetic chromistan algae (phylum Ochrophyta). Within the oomycetes, a number of predominantly marine holocarpic genera appear to diverge before the main “saprolegnian” and “peronosporalean” lines, into which all oomycetes had been traditionally placed. It is now clear that oomycetes have their evolutionary roots in the sea. The earliest diverging oomycete genera so far documented, Eurychasma and Haptoglossa, are both obligate parasites that show a high degree of complexity and sophistication in their host parasite interactions and infection structures. Key morphological and cytological features of the oomycetes will be reviewed in the context of our revised understanding of their likely phylogeny. Recent genomic studies have revealed a number of intriguing similarities in host–pathogen interactions between the oomycetes with their distant apicocomplexan cousins. Therefore, the earlier view that oomycetes evolved from the largely saprotrophic “saprolegnian line” is not supported and current evidence shows these organisms evolved from simple holocarpic marine parasites. Both the hyphal-like pattern of growth and the acquisition of oogamous sexual reproduction probably developed largely after the migration of these organisms from the sea to land.     

Following phylogenetic tracks of <Emphasis Type="Italic">Astragalus cicer</Emphasis> microsymbionts

A multilocus phylogenetic approach was applied to elucidate the phylogeny of Astragalus cicer rhizobia derived from Poland, Ukraine, and Canada. The strains selected for the studies represented three main geographically different phenons of these bacteria. Phylogenetic analyses were performed with three chromosomal housekeeping loci (16S rRNA, atpD, glnII) and three symbiotic genes located on a plasmid (nodA, nodC, nifH). The “core” and “auxiliary” gene trees revealed that A. cicer nodule isolates were intermingled with the strains of Mesorhizobium species, which implies that they are descendents of the same ancestor as mesorhizobia and fall into the Mesorhizobium genus. The noted congruence of the housekeeping and symbiotic gene phylogenies of A. cicer microsymbionts indicates that sym loci are transferred to these bacteria through vertical transmission without a significant participation of intergeneric horizontal gene spread. All the three sym gene sequences of the Polish and Ukrainian A. cicer nodule isolates were more closely related to one another than to the corresponding sequences of the Canadian isolates. The phylogeographic patterns of the sym genes of intercontinental strains point to their relatively long, separate, evolutionary history.     

Femoral neck structure and function in early hominins

All early (Pliocene–Early Pleistocene) hominins exhibit some differences in proximal femoral morphology from modern humans, including a long femoral neck and a low neck‐shaft angle. In addition, australopiths (Au. afarensis, Au. africanus, Au. boisei, Paranthropus boisei), but not early Homo, have an “anteroposteriorly compressed” femoral neck and a small femoral head relative to femoral shaft breadth. Superoinferior asymmetry of cortical bone in the femoral neck has been claimed to be human‐like in australopiths. In this study, we measured superior and inferior cortical thicknesses at the middle and base of the femoral neck using computed tomography in six Au. africanus and two P. robustus specimens. Cortical asymmetry in the fossils is closer overall to that of modern humans than to apes, although many values are intermediate between humans and apes, or even more ape‐like in the midneck. Comparisons of external femoral neck and head dimensions were carried out for a more comprehensive sample of South and East African australopiths (n = 17) and two early Homo specimens. These show that compared with modern humans, femoral neck superoinferior, but not anteroposterior breadth, is larger relative to femoral head breadth in australopiths, but not in early Homo. Both internal and external characteristics of the australopith femoral neck indicate adaptation to relatively increased superoinferior bending loads, compared with both modern humans and early Homo. These observations, and a relatively small femoral head, are consistent with a slightly altered gait pattern in australopiths, involving more lateral deviation of the body center of mass over the stance limb. Am J Phys Anthropol, 2013. © 2013 Wiley Periodicals, Inc.     

Sangiran 5,(“Pithecanthropus dubius”), homo erectus, “Meganthropus,” orPongo?

There are now eleven known mandibular remains from the Lower and Middle Pleistocene of Java, all but one being from the Sangiran site. All of these have been assigned toHomo erectus by most workers, while others have suggested as many as four different hominoid taxa. The author finds that the jaws cannot be a homogeneous sample. Morphologically, they are a mixture of undoubtedH. erectus, “H. meganthropus,” and possibly a pongid. If the jaws are allH. erectus then they have a sexual dimorphism exceeding that of modern gorillas. The case of“Pithecanthropus dubius” (Sangiran 5) is even less certain; even its hominid status is disputed. If it is indeedHomo it must be placed with the other“H. meganthropus” specimens. Its size and morphology are well beyond the known range anyH. erectus.     

The nature and evolution of intelligence in orangutans (Pongo pygmaeus)

Orangutans share many intellectual qualities with African great apes and humans, likely because of their recent common ancestry. They may also show unique intellectual adaptations because of their long evolutionary divergence from the African lineage. This paper assesses orangutan intelligence in light of this evolutionary history. Evidence derives from observations of juvenile ex-captive orangutans reintroduced to free forest life by the Wanariset Orangutan Reintroduction Project, East Kalimantan, Indonesia. The intellectual qualities shared by great apes and humans point to a distinct “great ape” intelligence with hierarchization as a pivotal cognitive mechanism. Evolutionary reconstructions jibe with this view and suggest that technically difficult foods may have been key selection pressures. Orangutans should then show hierarchical intelligence when obtaining difficult foods. Evidence on ex-captive orangutans' techniques for processing difficult foods concurs. Intellectual qualities distinct to orangutans may owe to arboreal travel pressures; in particular arboreality may aggravate foraging problems. Evidence confirms that ex-captive orangutans' techniques for accessing difficult foods located arboreally are intellectually complex—i.e. they show hierarchization. These findings suggest other factors probably important to understanding great ape and orangutan forms of intelligence and their evolutionary origins.     

Disproportionate Cochlear Length in Genus Homo Shows a High Phylogenetic Signal during Apes’ Hearing Evolution

Changes in lifestyles and body weight affected mammal life-history evolution but little is known about how they shaped species’ sensory systems. Since auditory sensitivity impacts communication tasks and environmental acoustic awareness, it may have represented a deciding factor during mammal evolution, including apes. Here, we statistically measure the influence of phylogeny and allometry on the variation of five cochlear morphological features associated with hearing capacities across 22 living and 5 fossil catarrhine species. We find high phylogenetic signals for absolute and relative cochlear length only. Comparisons between fossil cochleae and reconstructed ape ancestral morphotypes show that Australopithecus absolute and relative cochlear lengths are explicable by phylogeny and concordant with the hypothetized ((Pan,Homo),Gorilla) and (Pan,Homo) most recent common ancestors. Conversely, deviations of the Paranthropus oval window area from these most recent common ancestors are not explicable by phylogeny and body weight alone, but suggest instead rapid evolutionary changes (directional selection) of its hearing organ. Premodern (Homo erectus) and modern human cochleae set apart from living non-human catarrhines and australopiths. They show cochlear relative lengths and oval window areas larger than expected for their body mass, two features corresponding to increased low-frequency sensitivity more recent than 2 million years ago. The uniqueness of the “hypertrophied” cochlea in the genus Homo (as opposed to the australopiths) and the significantly high phylogenetic signal of this organ among apes indicate its usefulness to identify homologies and monophyletic groups in the hominid fossil record.     

Sulcal patterns of fossilTheropithecus baboons: Phylogenetic and functional implications

Sulcal patterns were determined from endocasts of fossilTheropithecus (T. oswaldi andT. darti) and compared to the sulcal pattern of extant geladas (T. gelada). A comparison of the configurations of central and arcuate sulci suggests that the cortical motor face representation is relatively enlarged in extantTheropithecus, whereas the cortical motor and sensory face representations were enlarged inT. oswaldi. A relatively expanded sensory and/or motor cortical face representation may be related to masticatory (e.g., “seed-eating”) and gestural (e.g., “lipflip”) functions. SinceT. oswaidi is more derived (expanded) in sensory face representation thanT. gelada, it seems unlikely that it was a direct ancestor of modern geladas. Rather, the two groups were separate by 1.8 million years ago and may have had a most recent common ancestor similar toT. darti from the Hadar Formation of Ethiopia between 2 and 3 million years ago.     

Characterizing the Evolutionary Path(s) to Early Homo

Numerous studies suggest that the transition from Australopithecus to Homo was characterized by evolutionary innovation, resulting in the emergence and coexistence of a diversity of forms. However, the evolutionary processes necessary to drive such a transition have not been examined. Here, we apply statistical tests developed from quantitative evolutionary theory to assess whether morphological differences among late australopith and early Homo species in Africa have been shaped by natural selection. Where selection is demonstrated, we identify aspects of morphology that were most likely under selective pressure, and determine the nature (type, rate) of that selection. Results demonstrate that selection must be invoked to explain an Au. africanus—Au. sediba—Homo transition, while transitions from late australopiths to various early Homo species that exclude Au. sediba can be achieved through drift alone. Rate tests indicate that selection is largely directional, acting to rapidly differentiate these taxa. Reconstructions of patterns of directional selection needed to drive the Au. africanus—Au. sediba—Homo transition suggest that selection would have affected all regions of the skull. These results may indicate that an evolutionary path to Homo without Au. sediba is the simpler path and/or provide evidence that this pathway involved more reliance on cultural adaptations to cope with environmental change.     

Homology as a relation of correspondence between parts of individuals

The recognition of correspondences has long been a fundamental activity among systematists. Advocates ofNaturphilosophie, such as Lorenz Oken, drew far-fetched analogies between taxonomic groups and all sorts of other things, including the Persons of the Trinity. They treated change through time either as analogous to an ontogeny or as the product of divinely instituted laws of nature. Darwin changed things by making the taxonomic units strictly historical, implying that they are not classes but rather individuals in a broad metaphysical sense. That means that taxa are concrete, particular things, or wholes made up of parts which are themselves individuals, and that there are no laws of nature for them. Homology is a relationship of correspondence between parts of organisms that are also parts of populations and lineages. It is not a relationship of similarity, and unlike similarity it is transitive. Analogy is a relationship of correspondence between parts of organisms that are members of classes, and is not necessarily due to function. Taxa, like other individuals, can change indefinitely, and the only thing that they must share is a common ancestor. They do not share an essence, Platonic Idea orBauplan, although “conservative characters” may be widespread in them. Iterative homology likewise is a relationship of correspondence, but the nature of that correspondence remains unclear. The difficulties of the homology concept can be overcome by treating phylogenetics and comparative biology in general as historical narrative. From the 46th “Phylogenetisches Symposium”, Jena, Germany, November 20–21, 2004. Theme of the symposium: “Evolutionary developmental biology—new challenges to the homology concept”.     

Are Cirripedia hopeful monsters? Cytogenetic approach and evidence for a Hox gene cluster in the cirripede crustacean Sacculina carcini

The “hopeful monster” has haunted evolutionary thinking since Richard Goldschmidt coined the phrase in 1933. The phrase is directly related to genetic mechanisms in development and evolution. Cirripedes are peculiar crustaceans in that they all lack abdomens as adults. In a previous study aimed at describing the repertoire of Hox genes of the Cirripedia, we failed to isolate the abdominal-A gene in three species representative of all three cirripede orders. To address the question of whether the cirripede ancestor could have been a “hopeful monster” arising from a rearrangement of the Hox complex, we have performed a cytogenetic analysis of the Hox complex of the cirripede Sacculina carcini. We present here molecular and cytogenetic evidence for the grouping of the Hox genes on a single chromosome. This is the first direct evidence reported for the grouping of Hox genes on the same chromosome in a non-insect arthropod species.     

A New Extinct Genus of Cavioidea (Rodentia,Hystricognathi) from the Miocene of Patagonia (Argentina) and the Evolution of Cavioid Mandibular Morphology

The family Caviidae is represented in modern faunas by cavies and maras, whereas the family Hydrochoeridae is represented by capybaras. The evolutionary origin of these families has been related to a diversity of plesiomorphic fossil forms (recorded from the late Oligocene up to the middle Miocene) traditionally grouped in the family “Eocardiidae”. These fossil forms were included, together with Caviidae and Hydrochoeridae, within the Cavioidea s.s. (sensu stricto), because they share high crowned cheek teeth, double-hearted occlusal surface, short lower incisors, and moderate hystricognathy. Within Cavioidea s.s., caviids and hydrochoerids were interpreted as forming its crown group, because they have unique craniomandibular and dental features. In this contribution, a new taxon of Cavioidea s.s. from the middle Miocene of central Patagonia, Argentina, is described, and its phylogenetic position is determined on the basis of a morphological cladistic analysis in which “eocardiids” were included. The study permits the understanding of the sequence of appearance of characters that originated the highly divergent morphology of crown-group cavioids. The analysis of the sequence of appearance of the characters that traditionally diagnosed the crown group indicates that these changes did not occur at the same time. On the contrary, many of these features seem to have appeared at different nodes of the evolutionary history of Cavioidea s.s. The remarkably derived morphology of modern cavioids is the result of a stepwise appearance of a mosaic of evolutionary innovations that originated gradually along the history of Cavioidea during the late-middle Miocene.     

Serial allocations of isolated mandibular molars of unknown taxonomic affinities from the Shungura and Unso Formations,Ethiopia, a combined method approach

The early hominid dental remains from the Omo succession represent a fragmentary but important source of information regarding hominid evolution during the 2 to 3 myr time period. As an initial step toward the evaluation of taxonomic affinities and evolutionary significance, the present study attempts serial allocations of 21 isolated mandibular molars from the Shungura and Usno Formations. A comparative sample consisting of 250 mandibular molars ofA.afarensis, A.africanus, A.robustus, A.boisei and earlyHomo was used to compile the baseline data for allocating the isolated Omo molars to serial positions. The methods employed in the present study include morphometric analyses of 5 cusp areas, 8 linear variables reflecting crown shape, and 4 measurements of fissure pattern. It was found that by combining morphological observations with both “restricted” and “non-restricted” applications of discriminant function analyses (sensu Albrecht, 1992), sufficiently reliable serial allocations could be attained.     

Ontogeny of the appendicularian <Emphasis Type="Italic">Oikopleura dioica</Emphasis> (Tunicata,Chordata) reveals characters similar to ascidian larvae with sessile adults

Appendicularians have always occupied a central role in considerations of tunicate and chordate evolution. Two hypotheses have been proposed – one holds that appendicularia represents the sister taxon to the remaining tunicates, the other suggests that appendicularians were derived from an ascidian-like ancestor. In the present study I report results from electron microscopic investigation of larval tunicates including the first electron microscopic investigation of the tail of the early ontogenetic appendicularian “Streckform” and discuss their phylogenetic implications. The early “Streckform” of Oikopleura dioica Fol, 1872 is invested with an extracellular covering that consists of an inner electron-light layer and an electron-dense outermost layer. In addition, the extracellular covering forms fin blades. Because these traits are shown to be similar to the tunic of different ascidian larvae, the extracellular covering in early appendicularian embryos is suggested to be homologous to the larval tunic of ascidian larvae. Overall, the tail of early developmental stages of appendicularians consists of a mosaic of apomorphic and plesiomorphic features. The straight, continuous endodermal strand was inherited from a common chordate ancestor whereas the finlets of larvae, consisting of extracellular material, were inherited from a common tunicate ancestor. The horizontal orientation of the tail as a whole was inherited from the last common ancestor of appendicularians and aplousobranch ascidians, and the discovered floating extension at the posterior tip of the tail is unique to the holoplanktonic Oikopleura dioica. These findings support the hypothesis that Appendicularia is derived from a sessile, ascidian-like ancestor.     

Circumscription of Malvaceae (Malvales) as determined by a preliminary cladistic analysis of morphological, anatomical, palynological, and chemical characters

We report a phylogenetic analysis of “core” Malvales (Tiliaceae, Sterculiaceae, Bombacaceae, and Malvaceae) based on morphological, anatomical, palynological, and chemical features. The results of the analyses lead to the conclusion that Tiliaceae, Sterculiaceae, and Bombacaceae, as variously delimited, are paraphyletic; only the Malvaceae are likely monophyletic. The genera of “core” Malvales form a well-defined clade. Genera of “Tiliaceae” constitute the basal complex within “core” Malvales. The “Sterculiaceae” (most genera)+ “Bombacaceae” + Malvaceae form a clade on the basis of a monadelphous androecium; “Bombacaceae”+ Malvaceae also form a clade, which is diagnosable on the basis of monoloculate anthers. It is clear that the traditional classification, with its arbitrarily delimited evolutionary grades, is unsatisfactory, especially if one seeks to reflect phylogeny accurately. Thus, Malvaceae is redefined to refer to the most recent common ancestor of plants previously considered to be “Tiliaceae,” “Sterculiaceae,” “Bombacaceae,” and Malvaceae, and all of the descendants of that ancestor. This broadly circumscribed Malvaceae can be diagnosed by several presumed synapomorphies, but we draw special attention to the unusual floral nectaries that are composed of densely packed, multicellular, glandular hairs on the sepals (or less commonly on the petals or androgynophore).     

Autotrophic,sulfur-oxidizing actinobacteria in acidic environments

Some novel actinobacteria from geothermal environments were shown to grow autotrophically with sulfur as an energy source. These bacteria have not been formally named and are referred to here as “Acidithiomicrobium” species, as the first of the acidophilic actinobacteria observed to grow on sulfur. They are related to Acidimicrobium ferrooxidans with which they share a capacity for ferrous iron oxidation. Ribulose bisphosphate carboxylase/oxygenase (RuBisCO) is active in CO₂ fixation by Acidimicrobium ferrooxidans, which appears to have acquired its RuBisCO-encoding genes from the proteobacterium Acidithiobacillus ferrooxidans or its ancestor. This lateral transfer of RuBisCO genes between a proteobacterium and an actinobacterium would add to those noted previously among proteobacteria, between proteobacteria and cyanobacteria and between proteobacteria and plastids. “Acidithiomicrobium” has RuBisCO-encoding genes which are most closely related to those of Acidimicrobium ferrooxidans and Acidithiobacillus ferrooxidans, and has additional RuBisCO genes of a different lineage. 16S rRNA gene sequences from “Acidithiomicrobium” species dominated clone banks of the genes extracted from mixed cultures of moderate thermophiles growing on copper sulfide and polymetallic sulfide ores in ore leaching columns.     

Identification of non-taster Japanese macaques for a specific bitter taste

Bitter taste perception evolved as a key detection mechanism against the ingestion of bioactive substances, and is mediated by TAS2R gene family members in vertebrates. The most widely known and best studied bitter substance is phenylthiocarbamide (PTC), which is recognized by TAS2R38 and has a molecular structure similar to that of glucosinolates contained in Brassica plants. The “non-taster” phenotypic polymorphism (i.e., not sensitive to PTC-containing foods) has been identified in many primates, including humans. Here, we report genetic and behavioral evidence for the existence of “non-taster” Japanese macaques, which originated from a restricted region of Japan. Comparison of the sequences of the TAS2R38 gene of 333 Japanese and 55 rhesus macaques suggested that this genotype appeared after the divergence of these two species, independently of the appearance of human and chimpanzee “non-tasters”. This finding might give a clue for elucidating the ecological, evolutionary, and neurobiological aspects of bitter taste perception of primates, as related to the plants that they sometimes use as foods in their habitats.     

Ecological dominance and the final sprint in hominid evolution

In contrast to many other models of human evolution the “balance of power” theory of Alexander has a clear answer to the question why a runaway selection process for unique social and moral capacities occurred in our ancestry only and not in other species: “ecological dominance” is hypothesized to have diminished the effects of “extrinsic” forces of natural selection such that withinspecies, intergroup competition increased (Alexander, 1989). Alexander seems to be wrong, however, in his claim that already the common HUCHIBO (Humans, Chimps, Bonobo's)-ancestor has crossed the ecological dominance barrier. In this paper an adapted version of Alexander's model is presented and several different ways are proposed to make this adapted version testable. A preliminary survey of the available paleontological and paleoecological data suggests that there is some evidence of a less vulnerable position towards predators in earlyHomo and that there are clear signs related to a crossing of the ecological dominance barrier inHomo sapiens sapiens.     

Actin Gene Family Dynamics in Cryptomonads and Red Algae

Here we present evidence for a complex evolutionary history of actin genes in red algae and cryptomonads, a group that acquired photosynthesis secondarily through the engulfment of a red algal endosymbiont. Four actin genes were found in the nuclear genome of the cryptomonad, Guillardia theta, and in the genome of the red alga, Galdieria sulphuraria, a member of the Cyanidiophytina. Phylogenetic analyses reveal that the both organisms possess two distinct sequence types, designated “type-1” and “type-2.” A weak but consistent phylogenetic affinity between the cryptomonad type-2 sequences and the type-2 sequences of G. sulphuraria and red algae belonging to the Rhodophytina was observed. This is consistent with the possibility that the cryptomonad type-2 sequences are derived from the red algal endosymbiont that gave rise to the cryptomonad nucleomorph and plastid. Red algae as a whole possess two very different actin sequence types, with G. sulphuraria being the only organism thus far known to possess both. The common ancestor of Rhodophytina and Cyanidiophytina may have had two actin genes, with differential loss explaining the distribution of these genes in modern-day groups. Our study provides new insight into the evolution and divergence of actin genes in cryptomonads and red algae, and in doing so underscores the challenges associated with heterogeneity in actin sequence evolution and ortholog/paralog detection.     

Enzyme-Driven Speciation: Crystallizing Archaea via Lipid Capture

As the origin(s) of life on Earth remains an open question, detailed characteristics about the “last universal ancestor” (LUA) continue to be obscured. Here we provide arguments that strengthen the bacterial-like nature of the LUA. Our view attempts to recreate the evolution of archaeal lipids, the major components of the distinctive membrane that encapsulates these ancient prokaryotes. We show that (S)- 3-O-geranylgeranylglyceryl phosphate synthase (GGGPS), a TIM-barrel protein that performs the committed step in archaeal lipid synthesis, likely evolved from the duplication and fusion of a (βα)₄ half-barrel ancestor. By comparison to the well-characterized HisA and HisF TIM-barrel proteins, we propose a time line for the invention of this diagnostic archaeal biosynthetic pathway. After excluding the possibility of horizontal gene transfer, we conclude that the evolutionary history of GGGPS mirrors the emergence of Archaea from the LUA. We illustrate aspects of this “lipid capture” model that support its likelihood in recreating key evolutionary events and, as our hypothesis is built on a single initiating event, we suggest that the appearance of GGGPS represents an example of enzyme-driven speciation. Reviewing Editor: Dr. Niles Lehman