Testing for correlation between traits under directional evolution

Being confounding factors, directional trends are likely to make two quantitative traits appear as spuriously correlated. By determining the probability distributions of independent contrasts when traits evolve following Brownian motions with linear trends, we show that the standard independent contrasts can not be used to test for correlation in this situation. We propose a multiple regression approach which corrects the bias caused by directional evolution. We show that our approach is equivalent to performing a Phylogenetic Generalized Least Squares (PGLS) analysis with tip times as covariables by providing a new and more general proof of the equivalence between PGLS and independent contrasts methods. Our approach is assessed and compared with three previous correlation tests on data simulated in various situations and overall outperforms all the other methods. The approach is next illustrated on a real dataset to test for correlation between hominin cranial capacity and body mass.

What do cranial bones of LB1 tell us about Homo floresiensis?

Cranial vault thickness (CVT) of Liang Bua 1, the specimen that is proposed to be the holotype of Homo floresiensis, has not yet been described in detail and compared with samples of fossil hominins, anatomically modern humans or microcephalic skulls. In addition, a complete description from a forensic and pathological point of view has not yet been carried out. It is important to evaluate scientifically if features related to CVT bring new information concerning the possible pathological status of LB1, and if it helps to recognize affinities with any hominin species and particularly if the specimen could belong to the species Homo sapiens. Medical examination of the skull based on a micro-CT examination clearly brings to light the presence of a sincipital T (a non-metrical variant of normal anatomy), a scar from an old frontal trauma without any evident functional consequence, and a severe bilateral hyperostosis frontalis interna that may have modified the anterior morphology of the endocranium of LB1. We also show that LB1 displays characteristics, related to the distribution of bone thickness and arrangements of cranial structures, that are plesiomorphic traits for hominins, at least for Homo erectus s.l. relative to Homo neanderthalensis and H. sapiens. All the microcephalic skulls analyzed here share the derived condition of anatomically modern H. sapiens. Cranial vault thickness does not help to clarify the definition of the species H. floresiensis but it also does not support an attribution of LB1 to H. sapiens. We conclude that there is no support for the attribution of LB1 to H. sapiens as there is no evidence of systemic pathology and because it does not have any of the apomorphic traits of our species.

Homo floresiensis contextualized: a geometric morphometric comparative analysis of fossil and pathological human samples

The origin of hominins found on the remote Indonesian island of Flores remains highly contentious. These specimens may represent a new hominin species, Homo floresiensis, descended from a local population of Homo erectus or from an earlier (pre-H. erectus) migration of a small-bodied and small-brained hominin out of Africa. Alternatively, some workers suggest that some or all of the specimens recovered from Liang Bua are pathological members of a small-bodied modern human population. Pathological conditions proposed to explain their documented anatomical features include microcephaly, myxoedematous endemic hypothyroidism (“cretinism”) and Laron syndrome (primary growth hormone insensitivity). This study evaluates evolutionary and pathological hypotheses through comparative analysis of cranial morphology. Geometric morphometric analyses of landmark data show that the sole Flores cranium (LB1) is clearly distinct from healthy modern humans and from those exhibiting hypothyroidism and Laron syndrome. Modern human microcephalic specimens converge, to some extent, on crania of extinct species of Homo. However in the features that distinguish these two groups, LB1 consistently groups with fossil hominins and is most similar to H. erectus. Our study provides further support for recognizing the Flores hominins as a distinct species, H. floresiensis, whose affinities lie with archaic Homo.

A small skull from Flores dated to the 20th century

A human skull with mandible from the Ngada District on the island of Flores, Indonesia, is described in order to contribute to the knowledge of variation in cranial architecture, which is important in interpretations of evolutionary cerebralisation. The skull was excavated in 1924 and sent to the National Museum in Copenhagen. The "Copenhagen Flores" (CF) male skull is radiocarbon-dated and of modern age. The cranium is small, but larger than e.g. Liang Bua skull (LB1) in every measurement. The (CT-scan based) cranial capacity of 1258 ml is normal for modern humans, but somewhat lower than values from the middle or upper Palaeolithics. The metric cranial data analysed in FORDISC, characterize the skull as a male Vietnamese rather than a Chinese or White individual. Tooth morphology shows the sundadont pattern and tooth size corresponds to that of teeth from Bali, Java and Malayan Orang Asli. Remarkable are the marked asymmetries in the dentition with rotation of an upper premolar and congenital absence of a third molar. In these respects the CF skull is similar to dentitions belonging to the pygmoid villagers of Rampasasa, a village not far from the Liang Bua cave, and to LB1.

Craniometric ratios of microcephaly and LB1, Homo floresiensis, using MRI and endocasts

The designation of Homo floresiensis as a new species derived from an ancient population is controversial, because the type specimen, LB1, might represent a pathological microcephalic modern Homo sapiens. Accordingly, two specific craniometric ratios (relative frontal breadth and cerebellar protrusion) were ascertained in 21 microcephalic infants and children by using MRI. Data on 118 age-equivalent control (normocephalic) subjects were collected for comparative purposes. In addition, the same craniometric ratios were determined on the endocasts of 10 microcephalic individuals, 79 normal controls (anatomically modern humans), and 17 Homo erectus specimens. These ratios were then compared with those of two LB1 endocasts. The findings showed that the calculated cerebral/cerebellar ratios of the LB1 endocast [Falk D, et al. (2007) Proc Natl Acad Sci USA 104:2513-2518] fall outside the range of living normocephalic individuals. The ratios derived from two LB1 endocasts also fall largely outside the range of modern normal human and H. erectus endocasts and within the range of microcephalic endocasts. The findings support but do not prove the contention that LB1 represents a pathological microcephalic Homo sapiens rather than a new species, (i.e., H. floresiensis).

Five years of Homo floresiensis

Since Homo floresiensis was first described in October 2004 there has been a lively debate over its status. Is it a late surviving species of early Homo or merely a modern individual afflicted with disordered growth and one of the many syndromes resulting in microchephaly? Recently the discovery team has published a series of articles providing detailed descriptions of the hominin material, its geomorphological context, and the associated archaeology and faunal material (Morwood and Jungers: J Hum Evol 57 (2009) 437-648). In addition, other researchers have put forward new hypotheses for possible pathologies including Laron's Syndrome and Myxoedematous Endemic (ME) Cretinism. Here I review this new information and conclude that the evidence supports the hypothesis that Homo floresiensis is a late-surviving species of early Homo with its closest morphological affinities to early African pre-erectus/ergaster hominins. Although this hypothesis requires fundamental paradigm changes in our understanding of human evolution, it provides a more economical explanation for H. floresiensis than do the alternatives. None of the current explanations for microcephaly and disordered growth account for the range of features observed in H. floresiensis. Neither do they provide explanations for why a pathological condition in modern humans would mimic so closely the morphology observed in earlier hominins. This conclusion is based on the current evidence for H. floresiensis and on the particular pathological explanations that have appeared in the literature. There is no doubt that controversy over H. floresiensis will continue until new and conclusive evidence is available to settle the debate one way or another.

Reconstructing the ups and downs of primate brain evolution: implications for adaptive hypotheses and Homo floresiensis

Background

Brain size is a key adaptive trait. It is often assumed that increasing brain size was a general evolutionary trend in primates, yet recent fossil discoveries have documented brain size decreases in some lineages, raising the question of how general a trend there was for brains to increase in mass over evolutionary time. We present the first systematic phylogenetic analysis designed to answer this question.

Results

We performed ancestral state reconstructions of three traits (absolute brain mass, absolute body mass, relative brain mass) using 37 extant and 23 extinct primate species and three approaches to ancestral state reconstruction: parsimony, maximum likelihood and Bayesian Markov-chain Monte Carlo. Both absolute and relative brain mass generally increased over evolutionary time, but body mass did not. Nevertheless both absolute and relative brain mass decreased along several branches. Applying these results to the contentious case of Homo floresiensis, we find a number of scenarios under which the proposed evolution of Homo floresiensis' small brain appears to be consistent with patterns observed along other lineages, dependent on body mass and phylogenetic position.

Conclusions

Our results confirm that brain expansion began early in primate evolution and show that increases occurred in all major clades. Only in terms of an increase in absolute mass does the human lineage appear particularly striking, with both the rate of proportional change in mass and relative brain size having episodes of greater expansion elsewhere on the primate phylogeny. However, decreases in brain mass also occurred along branches in all major clades, and we conclude that, while selection has acted to enlarge primate brains, in some lineages this trend has been reversed. Further analyses of the phylogenetic position of Homo floresiensis and better body mass estimates are required to confirm the plausibility of the evolution of its small brain mass. We find that for our dataset the Bayesian analysis for ancestral state reconstruction is least affected by inclusion of fossil data suggesting that this approach might be preferable for future studies on other taxa with a poor fossil record.

Preface: research at Liang Bua, Flores, Indonesia

Excavations at Liang Bua, Flores, Indonesia, have yielded evidence for an endemic human species, Homo floresiensis, a population that occupied the cave between approximately 95-17ka. This discovery has major implications for early hominin evolution and dispersal in Africa and Asia, attracting worldwide interest. This preface describes the rationale for the excavations in historical, geographical, and wider research contexts, as well as the methods used. It also introduces the other papers on aspects of Liang Bua research that feature in this edition of the Journal of Human Evolution.

Two interpretations of human evolution: Essentialism and Darwinism

Despite intensive studies of a large number of fossils discovered during the 20th century there is no consensus as to the interpretation of the process of hominin evolution. Some authors see as many as six genera and some 17 species, while others argue for a single lineage from Plio/Pleistocene until today. Such diversity of interpretations of the same facts indicates lack of a uniform theoretical basis underlying studies of human evolution. Debates can be resolved using basic principles of scientific inquiry - parsimony and falsification of null hypotheses. Hypothesis testing is now possible with respect to the evolution of basic hominin characteristics such as brain size, body size and the size of the dentition that have sample sizes of a few hundred individual data points each. These characters display a continuous change with time. Analyses of variance do not falsify the null hypothesis of the existence of only one species at any time - variances around regression lines on time do not differ from the variance observed in the single species of Homo sapiens - distributions of residuals are normal. Thus, splitting of the hominin lineage into coeval species can only be based on descriptive characteristics that are liable to errors of subjective judgment.

Who Is LB1? Discriminant Analysis for the Classification of Specimens

Many problems in paleontology reduce to finding those features that best discriminate among a set of classes. A clear example is the classification of new specimens. However, these classifications are generally challenging because the number of discriminant features and the number of samples are limited. This has been the fate of LB1, a new specimen found in the Liang Bua Cave of Flores. Several authors have attributed LB1 to a new species of Homo, H. floresiensis. According to this hypothesis, LB1 is either a member of the early Homo group or a descendent of an ancestor of the Asian H. erectus. Detractors have put forward an alternate hypothesis, which stipulates that LB1 is in fact a microcephalic modern human. In this paper, we show how we can employ a new Bayes optimal discriminant feature extraction technique to help resolve this type of issues. In this process, we present three types of experiments. First, we use this Bayes optimal discriminant technique to develop a model of morphological (shape) evolution from Australopiths to H. sapiens. LB1 fits perfectly in this model as a member of the early Homo group. Second, we build a classifier based on the available cranial and mandibular data appropriately normalized for size and volume. Again, LB1 is most similar to early Homo. Third, we build a brain endocast classifier to show that LB1 is not within the normal range of variation in H. sapiens. These results combined support the hypothesis of a very early shared ancestor for LB1 and H. erectus, and illustrate how discriminant analysis approaches can be successfully used to help classify newly discovered specimens.

Are the small human-like fossils found on Flores human endemic cretins?

Fossils from Liang Bua (LB) on Flores, Indonesia, including a nearly complete skeleton (LB1) dated to 18kyr BP, were assigned to a new species, Homo floresiensis. We hypothesize that these individuals are myxoedematous endemic (ME) cretins, part of an inland population of (mostly unaffected) Homo sapiens. ME cretins are born without a functioning thyroid; their congenital hypothyroidism leads to severe dwarfism and reduced brain size, but less severe mental retardation and motor disability than neurological endemic cretins. We show that the fossils display many signs of congenital hypothyroidism, including enlarged pituitary fossa, and that distinctive primitive features of LB1 such as the double rooted lower premolar and the primitive wrist morphology are consistent with the hypothesis. We find that the null hypothesis (that LB1 is not a cretin) is rejected by the pituitary fossa size of LB1, and by multivariate analyses of cranial measures. We show that critical environmental factors were potentially present on Flores, how remains of cretins but not of unaffected individuals could be preserved in caves, and that extant oral traditions may provide a record of cretinism.

The Homo floresiensis cranium (LB1): size, scaling, and early Homo affinities

The skeletal remains of a diminutive small-brained hominin found in Late Pleistocene cave deposits on the island of Flores, Indonesia were assigned to a new species, Homo floresiensis [Brown P, et al. (2004) A new small-bodied hominin from the Late Pleistocene of Flores, Indonesia. Nature 431: 1055-1061]. A dramatically different interpretation is that this material belongs not to a novel hominin taxon but to a population of small-bodied modern humans affected, or unaffected, by microcephaly. The debate has primarily focused on the size and shape of the endocranial cavity of the type specimen, LB1, with less attention being paid to the morphological evidence provided by the rest of the LB1 cranium and postcranium, and no study thus far has addressed the problem of how scaling would affect shape comparisons between a diminutive cranium like LB1 and the much larger crania of modern humans. We show that whether or not the effects of its small cranial size are accounted for, the external cranial morphology of the LB1 cranium cannot be accommodated within a large global sample of normal modern human crania. Instead, the shape of LB1, which is shown by multivariate analysis to differ significantly from that of modern humans, is similar to that of Homo erectus sensu lato, and, to a lesser extent, Homo habilis. Our results are consistent with hypotheses that suggest the Liang Bua specimens represent a diminutive population closely related to either early H. erectus s. l. from East Africa and/or Dmanisi or to H. habilis.

Homo floresiensis and the evolution of the hominin shoulder

The holotype of Homo floresiensis, diminutive hominins with tiny brains living until 12,000 years ago on the island of Flores, is a partial skeleton (LB1) that includes a partial clavicle (LB1/5) and a nearly complete right humerus (LB1/50). Although the humerus appears fairly modern in most regards, it is remarkable in displaying only 110 degrees of humeral torsion, well below modern human average values. Assuming a modern human shoulder configuration, such a low degree of humeral torsion would result in a lateral set to the elbow. Such an elbow joint would function more nearly in a frontal than in a sagittal plane, and this is certainly not what anyone would have predicted for a tool-making Pleistocene hominin. We argue that Homo floresiensis probably did not have a modern human shoulder configuration: the clavicle was relatively short, and we suggest that the scapula was more protracted, resulting in a glenoid fossa that faced anteriorly rather than laterally. A posteriorly directed humeral head was therefore appropriate for maintaining a normally functioning elbow joint. Similar morphology in the Homo erectus Nariokotome boy (KNM-WT 15000) suggests that this shoulder configuration may represent a transitional stage in pectoral girdle evolution in the human lineage.

Brain shape in human microcephalics and Homo floresiensis

Because the cranial capacity of LB1 (Homo floresiensis) is only 417 cm(3), some workers propose that it represents a microcephalic Homo sapiens rather than a new species. This hypothesis is difficult to assess, however, without a clear understanding of how brain shape of microcephalics compares with that of normal humans. We compare three-dimensional computed tomographic reconstructions of the internal braincases (virtual endocasts that reproduce details of external brain morphology, including cranial capacities and shape) from a sample of 9 microcephalic humans and 10 normal humans. Discriminant and canonical analyses are used to identify two variables that classify normal and microcephalic humans with 100% success. The classification functions classify the virtual endocast from LB1 with normal humans rather than microcephalics. On the other hand, our classification functions classify a pathological H. sapiens specimen that, like LB1, represents an approximately 3-foot-tall adult female and an adult Basuto microcephalic woman that is alleged to have an endocast similar to LB1's with the microcephalic humans. Although microcephaly is genetically and clinically variable, virtual endocasts from our highly heterogeneous sample share similarities in protruding and proportionately large cerebella and relatively narrow, flattened orbital surfaces compared with normal humans. These findings have relevance for hypotheses regarding the genetic substrates of hominin brain evolution and may have medical diagnostic value. Despite LB1's having brain shape features that sort it with normal humans rather than microcephalics, other shape features and its small brain size are consistent with its assignment to a separate species.

Brains, islands and evolution: breaking all the rules

The announcement in 2004 that a small-brained hominin, Homo floresiensis, had been discovered on the island of Flores, Indonesia, was hailed as a major scientific breakthrough because it challenged preconceptions about the evolution of our closest relatives. Now, just over two years later, questions raised by the interpretation of the fossil abound. In a series of recent papers, critics have questioned the interpretation of the small brain volume of the fossil as that of a new hominin species, suggesting instead that it was due to microcephaly. The arguments raised by critics and advocates alike prompt a re-examination of ideas about what is possible during the evolution of the brain.

Genetic, physiologic and ecogeographic factors contributing to variation in Homo sapiens: Homo floresiensis reconsidered

A new species, Homo floresiensis, was recently named for Pleistocene hominid remains on Flores, Indonesia. Significant controversy has arisen regarding this species. To address controversial issues and refocus investigations, I examine the affinities of these remains with Homo sapiens. Clarification of problematic issues is sought through an integration of genetic and physiological data on brain ontogeny and evolution. Clarification of the taxonomic value of various 'primitive' traits is possible given these data. Based on this evidence and using a H. sapiens morphological template, models are developed to account for the combination of features displayed in the Flores fossils. Given this overview, I find substantial support for the hypothesis that the remains represent a variant of H. sapiens possessing a combined growth hormone-insulin-like growth factor I axis modification and mutation of the MCPH gene family. Further work will be required to determine the extent to which this variant characterized the population.

Homo floresiensis: Microcephalic, pygmoid, Australopithecus, or Homo?

The remarkable partial adult skeleton (LB1) excavated from Liang Bua cave on the island of Flores, Indonesia, has been attributed to a new species, Homo floresiensis, based upon a unique mosaic of primitive and derived features compared to any other hominin. The announcement precipitated widespread interest, and attention quickly focused on its possible affinities. LB1 is a small-bodied hominin with an endocranial volume of 380-410 cm3, a stature of 1m, and an approximate geological age of 18,000 years. The describers [Brown, P., Sutikna, T., Morwood, M.J., Soejono, R.P., Jatmiko, Wayhu Saptomo, E., Awe Due, R., 2004. A new small-bodied hominin from the Late Pleistocene of Flores, Indonesia. Nature 431, 1055-1061] originally proposed that H. floresiensis was the end product of a long period of isolation of H. erectus or early Homo on a small island, a process known as insular dwarfism. More recently Morwood, Brown, and colleagues [Morwood, M.J., Brown, P., Jatmiko, Sutikna, T., Wahyu Saptomo, E., Westaway, K.E., Awe Due, R., Roberts, R.G., Maeda, T., Wasisto, S., Djubiantono, T., 2005. Further evidence for small-bodied hominins from the Late Pleistocene of Flores, Indonesia. Nature 437, 1012-1017] reviewed this assessment in light of new material from the site and concluded that H. floresiensis is not likely to be descended from H. erectus, with the genealogy of the species remaining uncertain. Other interpretations, namely that LB1 is a pygmy or afflicted with microcephaly, have also been put forward. We explore the affinities of LB1 using cranial and postcranial metric and non-metric analyses. LB1 is compared to early Homo, two microcephalic humans, a 'pygmoid' excavated from another cave on Flores, H. sapiens (including African pygmies and Andaman Islanders), Australopithecus, and Paranthropus. Based on these comparisons, we conclude that it is unlikely that LB1 is a microcephalic human, and it cannot be attributed to any known species. Its attribution to a new species, Homo floresiensis, is supported.

Pygmoid Australomelanesian Homo sapiens skeletal remains from Liang Bua, Flores: population affinities and pathological abnormalities

Liang Bua 1 (LB1) exhibits marked craniofacial and postcranial asymmetries and other indicators of abnormal growth and development. Anomalies aside, 140 cranial features place LB1 within modern human ranges of variation, resembling Australomelanesian populations. Mandibular and dental features of LB1 and LB6/1 either show no substantial deviation from modern Homo sapiens or share features (receding chins and rotated premolars) with Rampasasa pygmies now living near Liang Bua Cave. We propose that LB1 is drawn from an earlier pygmy H. sapiens population but individually shows signs of a developmental abnormality, including microcephaly. Additional mandibular and postcranial remains from the site share small body size but not microcephaly.

Direct dating of human fossils

The methods that can be used for the direct dating of human remains comprise of radiocarbon, U-series, electron spin resonance (ESR), and amino acid racemization (AAR). This review gives an introduction to these methods in the context of dating human bones and teeth. Recent advances in ultrafiltration techniques have expanded the dating range of radiocarbon. It now seems feasible to reliably date bones up to 55,000 years. New developments in laser ablation mass spectrometry permit the in situ analysis of U-series isotopes, thus providing a rapid and virtually non-destructive dating method back to about 300,000 years. This is of particular importance when used in conjunction with non-destructive ESR analysis. New approaches in AAR analysis may lead to a renaissance of this method. The potential and present limitations of these direct dating techniques are discussed for sites relevant to the reconstruction of modern human evolution, including Florisbad, Border Cave, Tabun, Skhul, Qafzeh, Vindija, Banyoles, and Lake Mungo.

Flores hominid: New species or microcephalic dwarf?

The proposed new hominid "Homo floresiensis" is based on specimens from cave deposits on the Indonesian island Flores. The primary evidence, dated at approximately 18,000 y, is a skull and partial skeleton of a very small but dentally adult individual (LB1). Incomplete specimens are attributed to eight additional individuals. Stone tools at the site are also attributed to H. floresiensis. The discoverers interpreted H. floresiensis as an insular dwarf derived from Homo erectus, but others see LB1 as a small-bodied microcephalic Homo sapiens. Study of virtual endocasts, including LB1 and a European microcephalic, purportedly excluded microcephaly, but reconsideration reveals several problems. The cranial capacity of LB1 ( approximately 400 cc) is smaller than in any other known hominid < 3.5 Ma and is far too small to derive from Homo erectus by normal dwarfing. By contrast, some associated tools were generated with a prepared-core technique previously unknown for H. erectus, including bladelets otherwise associated exclusively with H. sapiens. The single European microcephalic skull used in comparing virtual endocasts was particularly unsuitable. The specimen was a cast, not the original skull (traced to Stuttgart), from a 10-year-old child with massive pathology. Moreover, the calotte does not fit well with the rest of the cast, probably being a later addition of unknown history. Consideration of various forms of human microcephaly and of two adult specimens indicates that LB1 could well be a microcephalic Homo sapiens. This is the most likely explanation for the incongruous association of a small-brained recent hominid with advanced stone tools.