Previously apparently undescribed syndrome: shallow orbits, ptosis, coloboma, trigonocephaly, gyral malformations, and mental and growth retardation

Baraitser-Winter cerebrofrontofacial syndrome: Report of two adult siblings

Baraitser-Winter cerebrofrontofacial syndrome (BWCS) is a rare, autosomal dominant condition that is characterized by intellectual disability, distinctive craniofacial features, structural brain abnormalities, seizures, microcephaly, hearing loss, and ocular colobomas. The first three cases were described in 1988 by Baraitser and Winter and included two siblings and an unrelated third patient. Subsequently, causative missense variants in the ACTB and ACTG1 genes were identified, with de novo occurrence in patients with the condition. Herein, we describe two adult siblings who were born to unaffected parents and who were diagnosed with BWCS in their fourth and sixth decade of life following exome sequencing performed for intellectual disability. We review the literature reports of adult patients with BWCS to document the clinical features and phenotypic variability that can occur later in life. This is the first molecularly confirmed report of germline mosaicism in BWCS and one of only a few reports to describe two BWCS patients belonging to the same family.

Previously undescribed phenotypic findings and novel ACTG1 gene pathogenic variants in Baraitser-Winter cerebrofrontofacial syndrome

Baraitser-Winter cerebrofrontofacial syndrome is an autosomal dominant disease characterized by multiple congenital abnormalities and intellectual disability, which is caused by mutations in either the ACTB or ACTG1 genes. In this report, we described novel phenotypic findings in two Mexican patients with the disorder in whom two novel ACTG1 mutations (c.176A > G, p.Gln59Arg; and c.608C > T, p.Thr203Met) were identified.

Our experience on Bentall procedure in an adult patient with Baraitser-Winter syndrome

Baraitser-Winter syndrome is a very rare genetic disorder caused by cytoplasmic actin-encoding genes defects. Although most patients have similar phenotype, concomitant cardiac anomalies widely vary. In addition to well-described congenital heart diseases, aortic aneurysms occur due to underlying actin gene mutation in these patients in the further years. Herein, we present a 26-year-old male case who underwent Bentall procedure with the diagnosis of new-onset aortic valve regurgitation and an ascending aorta aneurysm.

Child with cerebral malformations and epilepsy

PURPOSE

Baraitser-Winter cerebrofrontofacial syndrome (BWCFF) is a rare autosomal dominant genetic disorder involving multiple organ systems and primarily characterized by structural brain abnormalities and a distinctive facial appearance.

METHODS

To study the clinical characteristics, gene types and seizures of BWCFF. The natural history, clinical data and peripheral blood sample were collected in the child and his patients. To screen the β-actin gene (ACTB) of a newly diagnosed child, hoping to find the gene mutation.

RESULTS

The child had left ptosis, ocular hypertelorism, arched eyebrows, only 30% of the left ear hearing, a slight hypotonia, normal muscle strength, walking instability. The seizures were difficult to control with antiepileptic drugs and presented some degree of psychomotor development delay. Genetic screening showed De Novo in ACTB gene (c.484A> G, p.Thr162Ala). Parents did not detect related gene mutations.

CONCLUSIONS

Patients with typical facial features and cerebral cortical malformations associated with refractory epilepsy should be highly suspected BWCFF. Patients are advised to carry out genetic screening to confirm the diagnosis.

Could Dissimilar Phenotypic Effects of ACTB Missense Mutations Reflect the Actin Conformational Change? Two Novel Mutations and Literature Review

The beta-actin gene encodes 1 of 6 different actin proteins. De novo heterozygous missense mutations in ACTB have been identified in patients with Baraitser-Winter syndrome (BRWS) and also in patients with developmental disorders other than BRWS, such as deafness, dystonia, and neutrophil dysfunction. We describe 2 different novel de novo missense ACTB mutations, c.208C>G (p.Pro70Ala) and c.511C>T (p.Leu171Phe), found by trio exome sequencing analysis of 2 unrelated patients: an 8-year-old boy with a suspected BRWS and a 4-year-old girl with unclear developmental disorder. The mutated residue in the first case is situated in the actin H-loop, which is involved in actin polymerization. The mutated residue in the second case (p.Leu171Phe) is found at the actin barbed end in the W-loop, important for binding to profilin and other actin-binding molecules. While the boy presented with a typical BRWS facial appearance, the girl showed facial features not recognizable as a BRWS gestalt as well as ventricular arrhythmia, cleft palate, thrombocytopenia, and gray matter heterotopia. We reviewed previously published ACTB missense mutations and ascertained that a number of them do not cause typical BRWS. By comparing clinical and molecular data, we speculate that the phenotypic differences found in ACTB missense mutation carriers might supposedly be dependent on the conformational change of ACTB.

Language continuity despite population replacement in Remote Oceania

Recent genomic analyses show that the earliest peoples reaching Remote Oceania-associated with Austronesian-speaking Lapita culture-were almost completely East Asian, without detectable Papuan ancestry. However, Papuan-related genetic ancestry is found across present-day Pacific populations, indicating that peoples from Near Oceania have played a significant, but largely unknown, ancestral role. Here, new genome-wide data from 19 ancient South Pacific individuals provide direct evidence of a so-far undescribed Papuan expansion into Remote Oceania starting ~2,500 yr BP, far earlier than previously estimated and supporting a model from historical linguistics. New genome-wide data from 27 contemporary ni-Vanuatu demonstrate a subsequent and almost complete replacement of Lapita-Austronesian by Near Oceanian ancestry. Despite this massive demographic change, incoming Papuan languages did not replace Austronesian languages. Population replacement with language continuity is extremely rare-if not unprecedented-in human history. Our analyses show that rather than one large-scale event, the process was incremental and complex, with repeated migrations and sex-biased admixture with peoples from the Bismarck Archipelago.

Lissencephaly: Expanded imaging and clinical classification

Lissencephaly ("smooth brain," LIS) is a malformation of cortical development associated with deficient neuronal migration and abnormal formation of cerebral convolutions or gyri. The LIS spectrum includes agyria, pachygyria, and subcortical band heterotopia. Our first classification of LIS and subcortical band heterotopia (SBH) was developed to distinguish between the first two genetic causes of LIS-LIS1 (PAFAH1B1) and DCX. However, progress in molecular genetics has led to identification of 19 LIS-associated genes, leaving the existing classification system insufficient to distinguish the increasingly diverse patterns of LIS. To address this challenge, we reviewed clinical, imaging and molecular data on 188 patients with LIS-SBH ascertained during the last 5 years, and reviewed selected archival data on another ∼1,400 patients. Using these data plus published reports, we constructed a new imaging based classification system with 21 recognizable patterns that reliably predict the most likely causative genes. These patterns do not correlate consistently with the clinical outcome, leading us to also develop a new scale useful for predicting clinical severity and outcome. Taken together, our work provides new tools that should prove useful for clinical management and genetic counselling of patients with LIS-SBH (imaging and severity based classifications), and guidance for prioritizing and interpreting genetic testing results (imaging based- classification).

Generalized epilepsy in Baraitser-Winter cerebrofrontofacial syndrome

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Baraitser–Winter cerebrofrontofacial syndrome (BWMS) is caused by actin gene mutations.

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Key features of BWMS are ptosis, hypertelorism, iris colobomata, and mental retardation.

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Generalized epilepsy is seen in half of those with BWMS.

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Seizures in BWMS can be absence, myoclonic, tonic, or tonic–clonic.

Baraitser-Winter cerebrofrontofacial syndrome

Baraitser-Winter cerebrofrontofacial syndrome (BWCFF) (BRWS; MIM #243310, 614583) is a rare developmental disorder affecting multiple organ systems. It is characterised by intellectual disability (mild to severe) and distinctive facial appearance (metopic ridging/trigonocephaly, bilateral ptosis, hypertelorism). The additional presence of cortical malformations (pachygyria/lissencephaly) and ocular colobomata are also suggestive of this syndrome. Other features include moderate short stature, contractures, congenital cardiac disease and genitourinary malformations. BWCFF is caused by missense mutations in the cytoplasmic beta- and gamma-actin genes ACTB and ACTG1. We provide an overview of the clinical characteristics (including some novel findings in four recently diagnosed patients), diagnosis, management, mutation spectrum and genetic counselling.

Genomic insights into the peopling of the Southwest Pacific

The appearance of people associated with the Lapita culture in the South Pacific around 3,000 years ago marked the beginning of the last major human dispersal to unpopulated lands. However, the relationship of these pioneers to the long-established Papuan people of the New Guinea region is unclear. Here we present genome-wide ancient DNA data from three individuals from Vanuatu (about 3,100-2,700 years before present) and one from Tonga (about 2,700-2,300 years before present), and analyse them with data from 778 present-day East Asians and Oceanians. Today, indigenous people of the South Pacific harbour a mixture of ancestry from Papuans and a population of East Asian origin that no longer exists in unmixed form, but is a match to the ancient individuals. Most analyses have interpreted the minimum of twenty-five per cent Papuan ancestry in the region today as evidence that the first humans to reach Remote Oceania, including Polynesia, were derived from population mixtures near New Guinea, before their further expansion into Remote Oceania. However, our finding that the ancient individuals had little to no Papuan ancestry implies that later human population movements spread Papuan ancestry through the South Pacific after the first peopling of the islands.

Update on the ACTG1-associated Baraitser-Winter cerebrofrontofacial syndrome

Baraitser-Winter cerebrofrontofacial syndrome is caused by heterozygous missense mutations in one of the two ubiquitous cytoplasmic actin-encoding genes ACTB and ACTG1. Recently, we characterized the large cohort of 41 patients presenting with this condition. Our series contained 34 patients with mutations in ACTB and only nine with ACTG1 mutations. Here, we report on seven unrelated patients with six mutations in ACTG1-four novel and two previously reported. Only one of seven patients was clinically diagnosed with this disorder and underwent ACTB/ACTG1 targeted sequencing, four patients were screened as a part of the large lissencephaly cohort and two were tested with exome sequencing. Retrospectively, facial features were compatible with the diagnosis but significantly milder than previously reported in four patients, and non-specific in one. The pattern of malformations of cortical development was highly similar in four of six patients with available MRI images and encompassed frontal predominant pachygyria merging with the posterior predominant band heterotopia. Two remaining patients showed mild involvement consistent with bilaterally simplified gyration over the frontal lobes. Taken together, we expand the clinical spectrum of the ACTG1-associated Baraitser-Winter cerebrofrontofacial syndrome demonstrating the mild end of the facial and brain manifestations. © 2016 Wiley Periodicals, Inc.

A novel mutation in ACTG1 causing Baraitser-Winter syndrome with extremely variable expressivity in three generations

Baraitser-Winter syndrome (cerebrofrontofacial syndrome, type 3) is a rare developmental disorder typified by hypertelorism, ptosis, high-arched eyebrows, ocular coloboma, and brain malformations. Other common manifestations include hearing loss, short stature, seizures, intellectual impairment, muscle dysfunction, and abnormalities of the kidney and urinary system. This syndrome is caused by missense mutations in the genes ACTB or ACTG1, both of which encode for cytoplasmic actin proteins crucial for proper development of many organs in the human body. There are no reports of familial transmission; all reported cases have been new mutations. However, different mutations in ACTG1 have been reported to cause isolated non-syndromic hearing loss, with many reported cases of autosomal dominant (AD) inheritance. We have identified a three-generation pedigree segregating a novel mutation in the ACTG1 gene that causes Baraitser-Winter Syndrome with extremely variable expressivity, leading to an initial diagnosis of isolated AD hearing loss in two members. Subtle optic nerve signs not previously reported in this syndrome are also documented in one patient.

Resolving the ancestry of Austronesian-speaking populations

There are two very different interpretations of the prehistory of Island Southeast Asia (ISEA), with genetic evidence invoked in support of both. The "out-of-Taiwan" model proposes a major Late Holocene expansion of Neolithic Austronesian speakers from Taiwan. An alternative, proposing that Late Glacial/postglacial sea-level rises triggered largely autochthonous dispersals, accounts for some otherwise enigmatic genetic patterns, but fails to explain the Austronesian language dispersal. Combining mitochondrial DNA (mtDNA), Y-chromosome and genome-wide data, we performed the most comprehensive analysis of the region to date, obtaining highly consistent results across all three systems and allowing us to reconcile the models. We infer a primarily common ancestry for Taiwan/ISEA populations established before the Neolithic, but also detected clear signals of two minor Late Holocene migrations, probably representing Neolithic input from both Mainland Southeast Asia and South China, via Taiwan. This latter may therefore have mediated the Austronesian language dispersal, implying small-scale migration and language shift rather than large-scale expansion.

Genome-wide insights into the genetic history of human populations

Although mtDNA and the non-recombining Y chromosome (NRY) studies continue to provide valuable insights into the genetic history of human populations, recent technical, methodological and computational advances and the increasing availability of large-scale, genome-wide data from contemporary human populations around the world promise to reveal new aspects, resolve finer points, and provide a more detailed look at our past demographic history. Genome-wide data are particularly useful for inferring migrations, admixture, and fine structure, as well as for estimating population divergence and admixture times and fluctuations in effective population sizes. In this review, we highlight some of the stories that have emerged from the analyses of genome-wide SNP genotyping data concerning the human history of Southern Africa, India, Oceania, Island South East Asia, Europe and the Americas and comment on possible future study directions. We also discuss advantages and drawbacks of using SNP-arrays, with a particular focus on the ascertainment bias, and ways to circumvent it.

Congenital eyelid ptosis: onset and prevalence of amblyopia, associations with systemic disorders, and treatment outcomes

OBJECTIVES

To determine the age at onset of amblyopia, the response to occlusion therapy, and the association with systemic disorders in children with congenital eyelid ptosis.

STUDY DESIGN

Retrospective chart review of children seen at Seattle Children's Hospital with moderate or severe congenital ptosis. Assessments were longitudinal visual acuity development using objective methods, definition of ptosis severity by eyelid margin to pupillary light reflex distance (margin reflex distance [MRD]), age at amblyopia diagnosis, correlation between amblyopia and MRD, and associated systemic disorders.

RESULTS

Eighty-four children with moderate-to-severe congenital ptosis met inclusion criteria; the mean longitudinal follow-up was 49.1 months. Fifteen (18%) of these children had amblyopia, of which 9 had deprivation amblyopia (mean age 17.3 months ± 11.2) and 6 had anisometropic or strabismic amblyopia (mean age 60 months ± 11.8). Eleven (73%) of the children with amblyopia were successfully treated with occlusion therapy. Amblyopia was not correlated with MRD. A systemic disorder was identified in 29 (35%) of the children, the most common being genetic, chromosomal, or neurologic conditions. Patients with systemic disorders and developmental delay have significantly lower visual acuity bilaterally compared with patients without systemic disorders (P ≤ .003).

CONCLUSIONS

Using longitudinal and objective visual acuity assessments, the incidence of amblyopia was 18% in children with moderate to severe congenital ptosis. Visual deprivation was the predominant risk factor that was reliably distinguished by its earlier onset in young children. The best indicator of amblyopia in children is visual acuity rather than MRD measurements. Systemic disorders are frequent in children with moderate to severe congenital ptosis.

Global analysis of saliva as a source of bacterial genes for insights into human population structure and migration studies

BACKGROUND

The genetic diversity of the human microbiome holds great potential for shedding light on the history of our ancestors. Helicobacter pylori is the most prominent example as its analysis allowed a fine-scale resolution of past migration patterns including some that could not be distinguished using human genetic markers. However studies of H. pylori require stomach biopsies, which severely limits the number of samples that can be analysed. By focussing on the house-keeping gene gdh (coding for the glucose-6-phosphate dehydrogenase), on the virulence gene gtf (coding for the glucosyltransferase) of mitis-streptococci and on the 16S-23S rRNA internal transcribed spacer (ITS) region of the Fusobacterium nucleatum/periodonticum-group we here tested the hypothesis that bacterial genes from human saliva have the potential for distinguishing human populations.

RESULTS

Analysis of 10 individuals from each of seven geographic regions, encompassing Africa, Asia and Europe, revealed that the genes gdh and ITS exhibited the highest number of polymorphic sites (59% and 79%, respectively) and most OTUs (defined at 99% identity) were unique to a given country. In contrast, the gene gtf had the lowest number of polymorphic sites (21%), and most OTUs were shared among countries. Most of the variation in the gdh and ITS genes was explained by the high clonal diversity within individuals (around 80%) followed by inter-individual variation of around 20%, leaving the geographic region as providing virtually no source of sequence variation. Conversely, for gtf the variation within individuals accounted for 32%, between individuals for 57% and among geographic regions for 11%. This geographic signature persisted upon extension of the analysis to four additional locations from the American continent. Pearson correlation analysis, pairwise Fst-cluster analysis as well as UniFrac analyses consistently supported a tree structure in which the European countries clustered tightly together and branched with American countries and South Africa, to the exclusion of Asian countries and the Congo.

CONCLUSION

This study shows that saliva harbours protein-coding bacterial genes that are geographically structured, and which could potentially be used for addressing previously unresolved human migration events.

Reconstructing Austronesian population history in Island Southeast Asia

Austronesian languages are spread across half the globe, from Easter Island to Madagascar. Evidence from linguistics and archaeology indicates that the ‘Austronesian expansion,’ which began 4,000–5,000 years ago, likely had roots in Taiwan, but the ancestry of present-day Austronesian-speaking populations remains controversial. Here, we analyse genome-wide data from 56 populations using new methods for tracing ancestral gene flow, focusing primarily on Island Southeast Asia. We show that all sampled Austronesian groups harbour ancestry that is more closely related to aboriginal Taiwanese than to any present-day mainland population. Surprisingly, western Island Southeast Asian populations have also inherited ancestry from a source nested within the variation of present-day populations speaking Austro-Asiatic languages, which have historically been nearly exclusive to the mainland. Thus, either there was once a substantial Austro-Asiatic presence in Island Southeast Asia, or Austronesian speakers migrated to and through the mainland, admixing there before continuing to western Indonesia.

Populations speaking Austronesian languages are numerous and widespread, but their history remains controversial. Here, the authors analyse genetic data from Southeast Asia and show that all populations harbour ancestry most closely related to aboriginal Taiwanese, while some also contain a component closest to Austro-Asiatic speakers.

Baraitser-Winter cerebrofrontofacial syndrome: delineation of the spectrum in 42 cases

Baraitser-Winter, Fryns-Aftimos and cerebrofrontofacial syndrome types 1 and 3 have recently been associated with heterozygous gain-of-function mutations in one of the two ubiquitous cytoplasmic actin-encoding genes ACTB and ACTG1 that encode β- and γ-actins. We present detailed phenotypic descriptions and neuroimaging on 36 patients analyzed by our group and six cases from the literature with a molecularly proven actinopathy (9 ACTG1 and 33 ACTB). The major clinical anomalies are striking dysmorphic facial features with hypertelorism, broad nose with large tip and prominent root, congenital non-myopathic ptosis, ridged metopic suture and arched eyebrows. Iris or retinal coloboma is present in many cases, as is sensorineural deafness. Cleft lip and palate, hallux duplex, congenital heart defects and renal tract anomalies are seen in some cases. Microcephaly may develop with time. Nearly all patients with ACTG1 mutations, and around 60% of those with ACTB mutations have some degree of pachygyria with anteroposterior severity gradient, rarely lissencephaly or neuronal heterotopia. Reduction of shoulder girdle muscle bulk and progressive joint stiffness is common. Early muscular involvement, occasionally with congenital arthrogryposis, may be present. Progressive, severe dystonia was seen in one family. Intellectual disability and epilepsy are variable in severity and largely correlate with CNS anomalies. One patient developed acute lymphocytic leukemia, and another a cutaneous lymphoma, indicating that actinopathies may be cancer-predisposing disorders. Considering the multifaceted role of actins in cell physiology, we hypothesize that some clinical manifestations may be partially mutation specific. Baraitser-Winter cerebrofrontofacial syndrome is our suggested designation for this clinical entity.

Mitochondrial DNA association study of type 2 diabetes with or without ischemic stroke in Taiwan

Background

The importance of mitochondrial DNA (mtDNA) polymorphism in the prediction of type 2 diabetes (T2D) in men and women is not well understood. We questioned whether mtDNA polymorphism, mitochondrial functions, age and gender influenced the occurrence of T2D with or without ischemic stroke (IS).

Methods

We first designed a matched case–control study of 373 T2D patients and 327 healthy unrelated individuals without history of IS. MtDNA haplogroups were determined on all participants using sequencing of the control region and relevant SNPs from the coding region. Mitochondria functional tests, systemic biochemical measurements and complete genomic mtDNA sequencing were further determined on 239 participants (73 healthy controls, 33 T2D with IS, 70 T2D only and 63 IS patients without T2D).

Results

MtDNA haplogroups B4a1a, and E2b1 showed significant association with T2D (P <0.05), and haplogroup D4 indicated resistance (P <0.05). Mitochondrial and systemic functional tests showed significantly less variance within groups bearing the same mtDNA haplotypes. There was a pronounced male excess among all T2D patients and prevalence of IS was seen only in the older population. Finally, nucleotide variant np 15746, a determinant of haplogroup G3 seen in Japanese and of B4a1a prevalent in Taiwanese was associated with T2D in both populations.

Conclusions

Men appeared more susceptible to T2D than women. Although the significant association of B4a1a and E2b1 with T2D ceased when corrected for multiple testings, these haplogroups are seen only among Taiwan Aborigines, Southeast Asian and the Pacific Ocean islanders where T2D is predominant. The data further suggested that physiological and biochemical measurements were influenced by the mtDNA genetic profile of the individual. More understanding of the function of the mitochondrion in the development of T2D might indicate ways of influencing the early course of the disease.

Human genetics of the Kula Ring: Y-chromosome and mitochondrial DNA variation in the Massim of Papua New Guinea

The island region at the southeastern-most tip of New Guinea and its inhabitants known as Massim are well known for a unique traditional inter-island trading system, called Kula or Kula Ring. To characterize the Massim genetically, and to evaluate the influence of the Kula Ring on patterns of human genetic variation, we analyzed paternally inherited Y-chromosome (NRY) and maternally inherited mitochondrial (mt) DNA polymorphisms in >400 individuals from this region. We found that the nearly exclusively Austronesian-speaking Massim people harbor genetic ancestry components of both Asian (AS) and Near Oceanian (NO) origin, with a proportionally larger NO NRY component versus a larger AS mtDNA component. This is similar to previous observations in other Austronesian-speaking populations from Near and Remote Oceania and suggests sex-biased genetic admixture between Asians and Near Oceanians before the occupation of Remote Oceania, in line with the Slow Boat from Asia hypothesis on the expansion of Austronesians into the Pacific. Contrary to linguistic expectations, Rossel Islanders, the only Papuan speakers of the Massim, showed a lower amount of NO genetic ancestry than their Austronesian-speaking Massim neighbors. For the islands traditionally involved in the Kula Ring, a significant correlation between inter-island travelling distances and genetic distances was observed for mtDNA, but not for NRY, suggesting more male- than female-mediated gene flow. As traditionally only males take part in the Kula voyages, this finding may indicate a genetic signature of the Kula Ring, serving as another example of how cultural tradition has shaped human genetic diversity.

Cerebro-fronto-facial syndrome type 3 with polymicrogyria: a clinical presentation of Baraitser-Winter syndrome

Baraitser-Winter syndrome (BRWS) is a rare condition affecting the development of the brain and the face. The most common characteristics are unusual facial appearance including hypertelorism and ptosis, ocular colobomas, hearing loss, impaired neuronal migration and intellectual disability. BRWS is caused by mutations in the ACTB and ACTG1 genes. Cerebro-fronto-facial syndrome (CFFS) is a clinically heterogeneous condition with distinct facial dysmorphism, and brain abnormalities. Three subtypes are identified. We report a female infant with striking facial features and brain anomalies (included polymicrogyria) that fit into the spectrum of the CFFS type 3 (CFFS3). She also had minor anomalies on her hands and feet, heart and kidney malformations, and recurrent infections. DNA investigations revealed c.586C>T mutation (p.Arg196Cys) in ACTB. This mutation places this patient in the spectrum of BRWS. The same mutation has been detected in a polymicrogyric patient reported previously in literature. We expand the malformation spectrum of BRWS/CFFS3, and present preliminary findings for phenotype-genotype correlation in this spectrum.

Trees, thickets, or something in between? Recent theoretical and empirical work in cultural phylogeny

Anthropology has always had as one of its goals the explanation of human cultural diversity across space and through time. Over the past several decades, there has been a growing appreciation among anthropologists and other social scientists that the phylogenetic approaches that biologists have developed to reconstruct the evolutionary relationships of species are useful tools for building and explaining patterns of human diversity. Phylogenetic methods offer a means of creating testable propositions of heritable continuity – how one thing is related to another in terms of descent. Such methods have now been applied to a wide range of cultural phenomena, including languages, projectile points, textiles, marital customs, and political organization. Here we discuss several cultural phylogenies and demonstrate how they were used to address long-standing anthropological issues. Even keeping in mind that phylogenetic trees are nothing more than hypotheses about evolutionary relationships, some researchers have argued that when it comes to cultural behaviors and their products, tree building is theoretically unwarranted. We examine the issues that critics raise and find that they in no way sound the death knell for cultural phylogenetic work.

De novo mutations in the actin genes ACTB and ACTG1 cause Baraitser-Winter syndrome

Brain malformations are individually rare but collectively common causes of developmental disabilities^1–3. Many forms occur sporadically and have reduced reproductive fitness, pointing towards a causative role for de novo mutations^4,5. Here we report our studies of Baraitser-Winter syndrome, a well-defined syndrome characterized by distinct craniofacial features, ocular colobomata and a neuronal migration defect^6,7. By using whole-exome sequencing in three proband-parent trios, we identified de novo missense changes in the cytoplasmic actin genes ACTB and ACTG1 in one and two probands, respectively. Sequencing of both genes in fifteen additional patients revealed disease-causing mutations in all probands, including two recurrent de novo mutations (ACTB p.Arg196His and ACTG1 p.Ser155Phe). Our results confirm that trio-based exome sequencing is a powerful approach to discover the genes causing sporadic developmental disorders, emphasize the overlapping roles of cytoplasmic actins in development, and suggest that Baraitser-Winter syndrome is the predominant phenotype associated with mutations of these two genes.

Developmental differences of the major forebrain commissures in lissencephalies

BACKGROUND AND PURPOSE

Changes of the major forebrain commissures in lissencephaly have not been systematically studied. We investigated the developmental differences of the commissures in patients with varying types of lissencephaly to determine whether specific commissural features may help in distinguishing lissencephaly phenotypes.

MATERIALS AND METHODS

MR imaging of 124 patients was retrospectively reviewed. Patients were classified as having cLIS, vLIS, and CBSC, according to cortical phenotype; few patients had genetic diagnoses. Abnormalities of the CC, AC, and HC were recorded, and the overall shape was regarded as hypogenetic, hypoplastic, dysmorphic, a thin flat callosal body with a vertical splenium, and a convex upward callosal body, compared with age-matched controls. Correlations between commissural characteristics and cortical patterns were analyzed by using the Monte Carlo simulation of χ(2), extension to m × n table, and Fisher exact tests as appropriate (P < .05).

RESULTS

Patients were classified as having cLIS (57.4%), vLIS (38.4%), or CBSC (4.2%). The most common callosal developmental anomaly was hypogenesis with an absent rostrum, a small inferior genu, and a small splenium. An angled (90°) splenium was found to be significantly associated with cLIS, as was an excessively convex upward callosal body with VLDLR. ACC with an enlarged AC was found in all cases of ARX.

CONCLUSIONS

Specific patterns of the commissure anomalies were associated with certain types of lissencephaly. Callosal anomalies were more common than those of the AC or HC. Developmental variations of commissures may be useful as an imaging criterion in differentiating the groups of lissencephalies and may give insight into the processes causing these malformations.

A case of Baraitser-Winter syndrome with unusual brain MRI findings: pachygyria, subcortical-band heterotopia, and periventricular heterotopia

Baraitser-Winter syndrome (BaWS) is characterized by iris coloboma, ptosis, hypertelorism, and mental retardation; it is a rare multiple congenital anomaly or a mental-retardation syndrome of unknown etiology. Patients suffering from this syndrome have been also found to show brain anomalies such as pachygyria, subcortical-band heterotopia (SBH), and hippocampal malformations; therefore, these anomalies have been included in the phenotypic spectrum of this syndrome. We report the case of a Japanese boy suffering from BaWS; the patient's brain magnetic resonance imaging scan revealed pachygyria, SBH, and periventricular heterotopia. However, the results of the genome-wide array comparative genomic hybridization did not reveal any chromosomal rearrangements.

Complete mitochondrial DNA sequences provide new insights into the Polynesian motif and the peopling of Madagascar

More than a decade of mitochondrial DNA (mtDNA) studies have given the 'Polynesian motif' renowned status as a marker for tracing the late-Holocene expansion of Austronesian speaking populations. Despite considerable research on the Polynesian motif in Oceania, there has been little equivalent work on the western edge of its expansion - leaving major issues unresolved regarding the motif's evolutionary history. This has also led to considerable uncertainty regarding the settlement of Madagascar. In this study, we assess mtDNA variation in 266 individuals from three Malagasy ethnic groups: the Mikea, Vezo, and Merina. Complete mtDNA genome sequencing reveals a new variant of the Polynesian motif in Madagascar; two coding region mutations define a Malagasy-specific sub-branch. This newly defined 'Malagasy motif' occurs at high frequency in all three ethnic groups (13-50%), and its phylogenetic position, geographic distribution, and estimated age all support a recent origin, but without conclusively identifying a specific source region. Nevertheless, the haplotype's limited diversity, similar to those of other mtDNA haplogroups found in our Malagasy groups, best supports a small number of initial settlers arriving to Madagascar through the same migratory process. Finally, the discovery of this lineage provides a set of new polymorphic positions to help localize the Austronesian ancestors of the Malagasy, as well as uncover the origin and evolution of the Polynesian motif itself.

The peopling of the Pacific from a bacterial perspective

Two prehistoric migrations peopled the Pacific. One reached New Guinea and Australia, and a second, more recent, migration extended through Melanesia and from there to the Polynesian islands. These migrations were accompanied by two distinct populations of the specific human pathogen Helicobacter pylori, called hpSahul and hspMaori, respectively. hpSahul split from Asian populations of H. pylori 31,000 to 37,000 years ago, in concordance with archaeological history. The hpSahul populations in New Guinea and Australia have diverged sufficiently to indicate that they have remained isolated for the past 23,000 to 32,000 years. The second human expansion from Taiwan 5000 years ago dispersed one of several subgroups of the Austronesian language family along with one of several hspMaori clades into Melanesia and Polynesia, where both language and parasite have continued to diverge.

Language phylogenies reveal expansion pulses and pauses in Pacific settlement

Debates about human prehistory often center on the role that population expansions play in shaping biological and cultural diversity. Hypotheses on the origin of the Austronesian settlers of the Pacific are divided between a recent "pulse-pause" expansion from Taiwan and an older "slow-boat" diffusion from Wallacea. We used lexical data and Bayesian phylogenetic methods to construct a phylogeny of 400 languages. In agreement with the pulse-pause scenario, the language trees place the Austronesian origin in Taiwan approximately 5230 years ago and reveal a series of settlement pauses and expansion pulses linked to technological and social innovations. These results are robust to assumptions about the rooting and calibration of the trees and demonstrate the combined power of linguistic scholarship, database technologies, and computational phylogenetic methods for resolving questions about human prehistory.

Genetic change in the polynesian population of Easter Island: evidence from Alu insertion polymorphisms

The origin of Pacific islanders is still an open issue in human population genetics. To address this topic we analyzed a set of 18 Alu insertion polymorphisms in a total of 176 chromosomes from native Easter Island inhabitants (Rapanui). Available genealogical records allowed us to subdivide the total island sample into two groups, representative of the native population living in the island around 1900, and another formed by individuals with some ancestors of non-Rapanui origin. Significant genetic differentiation was found between these groups, allowing us to make some biodemographic and historical inferences about the origin and evolution of this geographically isolated island population. Our data are consistent with equivalent and recent contributions from Amerindian and European migrants to the 1900s Rapanui population, with an accelerated increase in the European gene flow during the 20(th) century, especially since the 1960s. Comparative analysis of our results with other available Alu variation data on neighbouring populations supports the "Voyaging Corridor" model of Polynesian human settlement, which indicates that pre-Polynesians are mainly derived from Southeast Asian and Wallacean populations rather than from Taiwan or the Philippines. This study underlines the importance of sampling and taking into account historical information in genetic studies to unravel the recent evolution of human populations.

Human population genetic structure and diversity inferred from polymorphic L1(LINE-1) and Alu insertions

BACKGROUND/AIMS

The L1 retrotransposable element family is the most successful self-replicating genomic parasite of the human genome. L1 elements drive replication of Alu elements, and both have had far-reaching impacts on the human genome. We use L1 and Alu insertion polymorphisms to analyze human population structure.

METHODS

We genotyped 75 recent, polymorphic L1 insertions in 317 individuals from 21 populations in sub-Saharan Africa, East Asia, Europe and the Indian subcontinent. This is the first sample of L1 loci large enough to support detailed population genetic inference. We analyzed these data in parallel with a set of 100 polymorphic Alu insertion loci previously genotyped in the same individuals.

RESULTS AND CONCLUSION

The data sets yield congruent results that support the recent African origin model of human ancestry. A genetic clustering algorithm detects clusters of individuals corresponding to continental regions. The number of loci sampled is critical: with fewer than 50 typical loci, structure cannot be reliably discerned in these populations. The inclusion of geographically intermediate populations (from India) reduces the distinctness of clustering. Our results indicate that human genetic variation is neither perfectly correlated with geographic distance (purely clinal) nor independent of distance (purely clustered), but a combination of both: stepped clinal.

Effect of SstI polymorphism of the apolipoprotein CIII gene and environmental factors on risks of hypertriglyceridemia in Taiwan aborigines

BACKGROUND

Hypertriglyceridemia (HTG) is a heterogeneous metabolic disorder. The aim of this study was to examine associations among genetic polymorphisms, SstI polymorphism of apolipoprotein CIII (ApoCIII) and Hind III polymorphism of lipoprotein lipase (LPL), environmental factors and risks of HTG.

METHODS AND RESULTS

Two hundred and forty-nine southern Taiwanese aborigines were recruited for a cross-sectional study, which included 90 subjects with triglyceride (TG)>150 mg/dl (HTG) and 159 with TG<or=150 mg/dl (NTG). The frequencies of SstI major allele (S1) and minor allele (S2) of ApoCIII were 66.1% and 33.9% in HTG and 73.6% and 26.4% in NTG (p<0.1). In female subjects, the frequencies of the S2 allele was significantly higher in HTG (0.38) than NTG (0.27) (p<0.04). The frequencies of the LPL HindIII major allele (H+) and minor allele (H-) were similar between HTG (H+ 84.3%; H- 15.7%) and NTG (H+ 78.9%; H- 21.1%). In a multivariate adjusted logistic model, education<or=6 year (odds ratio (OR)=3.71, 95% confidence interval (CI): 1.24-8.13), Amis tribe (OR=3.08, 95% CI: 1.41-6.77), body mass index (BMI)>or=25 (OR=2.22, 95% CI: 1.18-4.16), starchy food consumption>or=3 times/week (OR=1.89, 95% CI: 1.00-3.59) and ApoCIII S2S2 genotype (OR=3.35, 95% CI: 1.10-10.19) were independently (p<0.05) associated with HTG risks. Among ApoCIII S1S1, S1S2 and S2S2 genotypes, ApoCIII and TG concentrations increased (p<0.01) in a dose-responsive manner.

CONCLUSIONS

The ApoCIII S2 variant and environmental factors, including education, tribal background, BMI and starchy food intake, modulate the risks of HTG in aboriginal Taiwanese. Interaction between genetic and environmental factors warrants further investigation.

Sequence polymorphisms of the mtDNA control region in a human isolate: the Georgians from Swanetia

In this work, we analyzed the sequence diversity of the mtDNA control region (HVI and HVII) in a sample of 48 individuals from Swanetia (Georgia), using direct fluorescent-based sequencing methods. We identified 43 different mtDNA haplotypes resulting from 78 polymorphic sites (46 in HVI and 32 in HVII). Most of the variable positions identified in both HVI and HVII were transitions (82.6 and 71.9%, respectively). The frequency of length heteroplasmy in the homopolymeric C-stretch regions was the same for both segments (10.4%). The sequence diversity increased markedly when both hypervariable regions were analyzed jointly (HVI: 0.985, HVII: 0.975, HVI+HVII: 0.994). Accordingly, the probability of two randomly selected sequences matching (random match probability, RMP) decreased from 3.4% (HVI) to 2.6% (HVI+HVII), despite which the RMP values in Georgians remained higher than estimated in most Europeans. This suggests that the variability of maternal lineages tends to be lower in traditional human isolates and, therefore, the potential of discrimination of mtDNA in forensic analysis is more limited in this type of population. The incorporation of HVII data also contributed to the refinement of results regarding the genetic relationships among the samples included in the analyses, which stress the importance of considering HVII in both population and forensic genetics.

Asian and non-Asian origins of Mon-Khmer- and Mundari-speaking Austro-Asiatic populations of India

In the present study, we analyzed 1,686 samples from 31 tribal populations of India for the mitochondrial DNA 9-base-pair deletion/insertion polymorphism, and characterized them based on the relevant mitochondrial DNA coding-region single nucleotide polymorphisms and hypervariable region I motifs, to test the genetic origins of the ethnically and linguistically heterogeneous Austro-Asiatic tribes of India. A comparative analysis of our results with the existing data suggests multiple origins of Austro-Asiatic tribes in India, and particularly the Asian and non-Asian origins of the Mon-Khmer and the Mundari populations. We also identified a novel subclade of haplogroup B in the Mon-Khmer Khasi tribes that distinguishes them from the Nicobarese, indicating two different waves of migration of the Mon-Khmer tribes in India.

Brief communication: Mitochondrial DNA variation suggests extensive gene flow from Polynesian ancestors to indigenous Melanesians in the northwestern Bismarck Archipelago

Archaeological, linguistic, and genetic studies show that Austronesian (AN)-speaking Polynesian ancestors came from Asia/Taiwan to the Bismarck Archipelago in Near Oceania more than 3,600 years ago, and then expanded into Remote Oceania. However, it remains unclear whether they extensively mixed with indigenous Melanesians who had populated the Bismarck Archipelago before their arrival. To examine the extent of admixture between Polynesian ancestors and indigenous Melanesians, mitochondrial DNA (mtDNA) variations in the D-loop region and the cytochrome oxidase and lysine transfer RNA (COII/tRNA(Lys)) intergenic 9-bp deletion were analyzed in the following three Oceanian populations: 1) Balopa Islanders as AN-speaking Melanesians living in the northwestern end of the Bismarck Archipelago, 2) Tongans as AN-speaking Polynesians, and 3) Gidra as non-Austronesian-speaking Melanesians in the southwestern lowlands of Papua New Guinea. Phylogenetic analysis of mtDNA sequences revealed that more than 60% of mtDNA sequences in the Balopa Islanders were very similar to those in Tongans, suggesting an extensive gene flow from Polynesian ancestors to indigenous Melanesians. Furthermore, analysis of pairwise difference distributions for the D-loop sequences with the 9-bp deletion and the Polynesian motif (i.e., T16217C, A16247G, and C16261T) suggested that the expansion of Polynesian ancestors possessing these variations occurred approximately 7,000 years ago.

The phenotypic spectrum of baraitser-winter syndrome: a new case and review of literature

The syndrome of iris coloboma, ptosis, hypertelorism, and mental retardation (Online Mendelian Inheritance in Man -- OMIM # 243310), also known as the Baraitser-Winter syndrome, originally was described in a brother and sister and in an unrelated girl in 1988. Six additional individuals with a similar phenotype have been reported in the world literature. Microphthalmos, microcornea, and brain malformations were added to the phenotypic spectrum of this syndrome in 1995. We report a child who presented with the aforementioned findings. Eye examination revealed bilateral microphthalmos and typical iris, optic nerve, and choroidal colobomas. Magnetic resonance imaging of the brain demonstrated pachygyria and cortical atrophy.

Genotypically defined lissencephalies show distinct pathologies

Lissencephaly is traditionally divided into 2 distinct pathologic forms: classic (type I) and cobblestone (type II). To date, mutations in 4 genes, LIS1, DCX, RELN, and ARX, have been associated with distinct type I lissencephaly syndromes. Each of these genes has been shown to play a role in normal cell migration, consistent with the presumed pathogenesis of type I lissencephaly. Based on these data, we hypothesized that all forms of radiographically defined type I lissencephaly independent of genotype would be pathologically similar. To test this hypothesis, we examined brains from 16 patients, including 15 lissencephalic patients and one patient with subcortical band heterotopia. Of these 16 patients, 6 had LIS1 deletions, 2 had DCX mutations, and 2 had ARX mutations. In addition, 6 patients had no defined genetic defect, although the patient with subcortical band heterotopia exhibited the same pattern of malformation expected with an XLIS mutation. In all cases, the cortex was thickened; however, the topographic distribution of the cortical pathology varied, ranging from frontal- to occipital-biased pathology to diffuse involvement of the neocortex. Although brains with LIS1 deletions exhibited the classic 4-layer lissencephalic architecture, patients with DCX and ARX mutations each had unique cytoarchitectural findings distinct from LIS1. Furthermore, 2 of the 5 patients with no known genetic defect showed a fourth type of histopathology characterized by a 2-layered cortex. Interestingly, the 2 brains with the fourth type of lissencephaly showed profound brainstem and cerebellar abnormalities. In summary, we identified at least 4 distinct histopathologic subtypes of lissencephaly that stratify with the underlying genetic defect. Based on these data, a new classification for lissencephaly is proposed that incorporates both pathologic and genetic findings.

MITOCHONDRIAL DNA AND HUMAN EVOLUTION

Several unique properties of human mitochondrial DNA (mtDNA), including its high copy number, maternal inheritance, lack of recombination, and high mutation rate, have made it the molecule of choice for studies of human population history and evolution. Here we review the current state of knowledge concerning these properties, how mtDNA variation is studied, what we have learned, and what the future likely holds. We conclude that increasingly, mtDNA studies are (and should be) supplemented with analyses of the Y-chromosome and other nuclear DNA variation. Some serious issues need to be addressed concerning nuclear inserts, database quality, and the possible influence of selection on mtDNA variation. Nonetheless, mtDNA studies will continue to play an important role in such areas as examining socio-cultural influences on human genetic variation, ancient DNA, certain forensic DNA applications, and in tracing personal genetic history.

Traces of archaic mitochondrial lineages persist in Austronesian-speaking Formosan populations

Genetic affinities between aboriginal Taiwanese and populations from Oceania and Southeast Asia have previously been explored through analyses of mitochondrial DNA (mtDNA), Y chromosomal DNA, and human leukocyte antigen loci. Recent genetic studies have supported the "slow boat" and "entangled bank" models according to which the Polynesian migration can be seen as an expansion from Melanesia without any major direct genetic thread leading back to its initiation from Taiwan. We assessed mtDNA variation in 640 individuals from nine tribes of the central mountain ranges and east coast regions of Taiwan. In contrast to the Han populations, the tribes showed a low frequency of haplogroups D4 and G, and an absence of haplogroups A, C, Z, M9, and M10. Also, more than 85% of the maternal lineages were nested within haplogroups B4, B5a, F1a, F3b, E, and M7. Although indicating a common origin of the populations of insular Southeast Asia and Oceania, most mtDNA lineages in Taiwanese aboriginal populations are grouped separately from those found in China and the Taiwan general (Han) population, suggesting a prevalence in the Taiwanese aboriginal gene pool of its initial late Pleistocene settlers. Interestingly, from complete mtDNA sequencing information, most B4a lineages were associated with three coding region substitutions, defining a new subclade, B4a1a, that endorses the origin of Polynesian migration from Taiwan. Coalescence times of B4a1a were 13.2 +/- 3.8 thousand years (or 9.3 +/- 2.5 thousand years in Papuans and Polynesians). Considering the lack of a common specific Y chromosomal element shared by the Taiwanese aboriginals and Polynesians, the mtDNA evidence provided here is also consistent with the suggestion that the proto-Oceanic societies would have been mainly matrilocal.

Origins and dispersals of Pacific peoples: evidence from mtDNA phylogenies of the Pacific rat

The human settlement of the Pacific in general, and the origin of the Polynesians in particular, have been topics of debate for over two centuries. Polynesian origins are most immediately traced to people who arrived in the Fiji, Tonga, and Samoa region approximately 3,000 B.P. and are clearly associated with the Lapita Cultural Complex. Although this scenario of the immediate origins of the Polynesians is generally accepted, the debate on the ultimate origin of the Polynesians and the Lapita cultural complex continues. Our previous research has shown that analyses of mtDNA variation in the Pacific rat (Rattus exulans), often transported as a food item in the colonizing canoes, are valuable for tracing prehistoric human migration within Polynesia. Here we present mtDNA phylogenies based on approximately 240 base pairs of the d-loop from both archaeological and modern samples collected from Island Southeast Asia and the Pacific. We identify three major haplogroups, two of which occur in the Pacific. Comparing our results with Lapita models of Oceanic settlement, we are able to reject two often cited but simplistic models, finding support instead for multifaceted models incorporating a more complex view of the Lapita intrusion. This study is unique and valuable in that R. exulans is the only organism associated with the Lapita dispersal for which there are sufficient ancient and extant populations available for genetic analysis. By tracking population changes through time, we can understand more fully the settlement process and population interactions in both Near and Remote Oceania.

Eleven human platelet systems studied in the Vietnamese and Ma'ohis Polynesian populations

The frequencies of human platelet antigens (HPA) are variable among different ethnic groups. Platelet phenotyping and genotyping in different populations are important to the clinical implications of antiplatelet alloimmunization. No report on HPA prevalence has been published concerning the Vietnamese Kinh and Ma'ohis Polynesian populations. Recent anthropological and genetic marker studies suggest that these two groups have a common origin in East Asia, so we have conducted a combined study concerning the frequency of HPA-1 to HPA-11w systems (excluding HPA-8w) and Gov in these two populations. The results demonstrate a similar pattern of prevalence between Ma'ohis and most of the Asian populations. However, it should be noted that the frequency of HPA-2 is closer to northern Caucasian frequencies than to Asian frequencies. The population of Kinh shows an HPA distribution that is closer to the Chinese population than to the northeastern Thais except for HPA-3, closer to the Indonesian population. Given HPA-3 gene frequency distribution fetomaternal incompatibility could occur more frequently with the risk of alloantibody production.

Dispersal ghosts in Oceania

Anthropological genetics helps expand our understanding of human phenotypes in the Pacific, in part because of its focus on gene genealogies to infer past episodes of dispersal and to differentiate these events from adaptations due to long-duration directional selection. Sewall Wright's 1949 seminal paper on population structure emphasized that there were two strong forces that exerted systematic and therefore determinant pressure on the gene pool: recurrent immigration and gene flow. These are important topics to all discussions of human dispersal in any region of the world. Furthermore, Wright listed five unique kinds of events that produced indeterminate or unpredictable changes that could lead to phenotypic and genotypic effects. In this category, he placed unique selective incidents, unique hybridization events, unique reductions in number, swamping by mass immigration, and mutational drive due to an allele always being favored since its origin or introduction. This discussion of human dispersal in the Pacific will touch on these topics, since they provide a second level of complexity in knowing who moved about a region of the world found already settled when rediscovered by colonial explorers during the 16-18th centuries.

Mitochondrial DNA polymorphisms in nine aboriginal groups of Taiwan: implications for the population history of aboriginal Taiwanese

Mitochondrial DNA (mtDNA) polymorphisms in the D-loop region and the intergenic COII/tRNA(Lys) 9-bp deletion were examined in 180 individuals from all nine aboriginal Taiwanese groups: Atayal, Saisiat, Bunun, Tsou, Rukai, Paiwan, Ami, Puyuma, and Yami. A comparison of 563-bp sequences showed that there were 61 different sequence types, of which 42 types were specific to respective aboriginal groups. D-loop sequence variation and phylogenetic analysis enabled the 180 aboriginal lineages to be classified into eight monophyletic clusters (designated C1-C8). Phylogeographic analysis revealed that two (C2 and C4) of the eight clusters were new characteristic clusters of aboriginal Taiwanese and accounted for 8.3% and 13.9% of the aboriginal lineages, respectively. From the estimated coalescent times for the two unique clusters, the mtDNA lineages leading to such clusters were inferred to have been introduced into Taiwan approximately 11,000-26,000 years ago, suggesting ancient immigrations of the two mtDNA lineages. Genetic distances, based on net nucleotide diversities between populations, revealed three distinct clusters that were comprised of northern mountain (Atayal and Saisiat), southern mountain (Rukai and Paiwan), and middle mountain/east coast (Bunun, Tsou, Ami, Puyuma, and Yami) groups, respectively. Furthermore, phylogenetic analysis of 16 human populations (including six other Asian populations and one African population) confirmed that the three clusters for aboriginal Taiwanese had remained largely intact. Each of the clusters (north, south, and middle-east coast) was characterized by a high frequency of a particular lineage (C4, C2, and 9-bp deletion, respectively). This may result from random genetic drift among the aboriginal groups after a single introduction of all the mtDNA lineages into Taiwan, but another plausible explanation is that at least three genetically distinct ancestral populations have contributed to the maternal gene pool of aboriginal Taiwanese.