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

Cerebro-oculo-facial-lymphatic syndrome

We describe a boy whose prime features are severe-to-profound mental retardation, intractable complex seizures, lissencephaly, facial dysmorphism, and lymphatic abnormalities. To our knowledge, this is the fourth reported case of this syndrome. We propose the syndromic appellation of cerebro-oculo-facial-lymphatic syndrome, suggest cardinal diagnostic features, and discuss several possible overlapping syndromic diagnoses.

Mitochondrial DNA analysis reveals diverse histories of tribal populations from India

We analyzed 370 bp of the first hypervariable region of the mitochondrial DNA (mtDNA) control region in 752 individuals from 17 tribal and four nontribal groups from the Indian subcontinent, to address questions concerning the origins, genetic structure and relationships of these groups. Southern Indian tribes showed reduced diversity and large genetic distances, both among themselves and when compared with other groups, and no signal of prehistoric demographic expansions. These results probably reflect enhanced genetic drift because of small population sizes and/or bottlenecks in these groups. By contrast, northern groups exhibited more diversity and signals of prehistoric demographic expansions. Phylogenetic analyses revealed that southern and northern groups (except northeastern ones) have related mtDNA sequences albeit at different frequencies, further supporting the larger impact of drift on the genetic structure of southern groups. The Indian mtDNA gene pool appears to be more closely related to the east Eurasian gene pool (including central, east and southeast Asian populations) than the west Eurasian one (including European and Caucasian populations). Within India, northeastern tribes are quite distinct from other groups; they are more closely related to east Asians than to other Indians. This is consistent with linguistic evidence in that these populations speak Tibeto-Burman languages of east Asian origin. Otherwise, analyses of molecular variance suggested that caste and tribal groups are genetically similar with respect to mtDNA variation.

Mitochondrial DNA variability of West New Guinea populations

This paper reports human mitochondrial DNA variability in West New Guinea (the least known, western side of the island of New Guinea), not yet described from a molecular perspective. The study was carried out on 202 subjects from 12 ethnic groups, belonging to six different Papuan language families, representative of both mountain and coastal plain areas. Mitochondrial DNA hypervariable region 1 (HVS 1) and the presence of the 9-bp deletion (intergenic region COII-tRNA(Lys)) were investigated. HVS 1 sequencing identified 73 polymorphic sites defining 89 haplotypes; the 9-bp deletion, which is considered a marker of Austronesian migration in the Pacific, was found to be absent in the whole West New Guinea study sample. Statistical analysis applied to the resulting haplotypes reveal high heterogeneity and an intersecting distribution of genetic variability in these populations, despite their cultural and geographic diversity. The results of subsequent phylogenetic approaches subdivide mtDNA diversity in West New Guinea into three main clusters (groups I-III), defined by sets of polymorphisms which are also shared by some individuals from Papua New Guinea. Comparisons with worldwide HVS 1 sequences stored in the MitBASE database show the absence of these patterns outside Oceania and a few Indonesian subjects, who also lack the 9-bp deletion. This finding, which is consistent with the effects of genetic drift and prolonged isolation of West New Guinea populations, lead us to regard these patterns as New Guinea population markers, which may harbor the genetic memory of the earliest human migrations to the island.

Maori origins, Y-chromosome haplotypes and implications for human history in the Pacific

An assessment of 28 pertinent binary genetic markers on the non-recombining portion of the Y chromosome (NRY) in New Zealand Maori and other relevant populations has revealed a diverse genetic paternal heritage of extant Maori. A maximum parsimony phylogeny was constructed in which nine of the 25 possible binary haplotypes were observed. Although approximately 40% of the samples have haplotypes of unequivocal European origin, an equivalent number of samples have a single binary haplotype that is also observed in Indonesia and New Guinea, indicative of common indigenous Melanesian ancestry. The balance of the lineages has either typical East Asian signatures or alternative compositions consistent with their affinity to Melanesia or New Guinea. Molecular analysis of mtDNA variation confirms the presence of a single predominant characteristic Southeast Asian (9-bp deletion in the Region V) lineage. The Y-chromosome results support a pattern of complex interrelationships between Southeast Asia, Melanesia, and Polynesia, in contrast to mtDNA and linguistic data, which uphold a rapid and homogeneous Austronesian expansion. The Y-chromosome data highlight a distinctive gender-modulated pattern of differential gene flow in the history of Polynesia.

Fast trains, slow boats, and the ancestry of the Polynesian islanders

The question of the origins of the Polynesians has, for over 200 years, been the subject of adventure science. Since Captain Cook's first speculations on these isolated Pacific islanders, their language affiliations have been seen as an essential clue to the solution. The geographic and numeric centre of gravity of the Austronesian language family is in island Southeast Asia, which was therefore originally seen as their dispersal homeland. However, another view has held sway for 15 years, the 'out of Taiwan' model, popularly known as the 'express train to Polynesia'. This model, based on the combined evidence of archaeology and linguistics, proposes a common origin for all Austronesian-speaking populations, in an expansion of rice agriculturalists from south China/Taiwan beginning around 6,000 years ago. However, it is becoming clear that there is, in fact, little supporting evidence in favour of this view. Alternative models suggest that the ancestors of the Polynesians achieved their maritime skills and horticultural Neolithic somewhere between island Southeast Asia and Melanesia, at an earlier date. Recent advances in human genetics now allow for an independent test of these models, lending support to the latter view rather than the former. Although local gene flow occurring between the bio-geographic regions may have been the means for the dramatic cultural spread out to the Pacific, the immediate genetic substrate for the Polynesian expansion came not from Taiwan, but from east of the Wallace line, probably in Wallacea itself.

Natives or immigrants: modern human origin in east Asia

East Asia is one of the few regions in the world where a relatively large number of human fossils have been unearthed--a discovery that has been taken as evidence for an independent local origin of modern humans outside of Africa. However, genetic studies conducted in the past ten years, especially using Y chromosomes, have provided unequivocal evidence for an African origin of East Asian populations. The genetic signatures present in diverse East Asian populations mark the footsteps of prehistoric migrations that occurred tens of thousands of years ago.

Polynesian origins: insights from the Y chromosome

The question surrounding the colonization of Polynesia has remained controversial. Two hypotheses, one postulating Taiwan as the putative homeland and the other asserting a Melanesian origin of the Polynesian people, have received considerable attention. In this work, we present haplotype data based on the distribution of 19 biallelic polymorphisms on the Y chromosome in a sample of 551 male individuals from 36 populations living in Southeast Asia, Taiwan, Micronesia, Melanesia, and Polynesia. Surprisingly, nearly none of the Taiwanese Y haplotypes were found in Micronesia and Polynesia. Likewise, a Melanesian-specific haplotype was not found among the Polynesians. However, all of the Polynesian, Micronesian, and Taiwanese haplotypes are present in the extant Southeast Asian populations. Evidently, the Y-chromosome data do not lend support to either of the prevailing hypotheses. Rather, we postulate that Southeast Asia provided a genetic source for two independent migrations, one toward Taiwan and the other toward Polynesia through island Southeast Asia.

Language trees support the express-train sequence of Austronesian expansion

Languages, like molecules, document evolutionary history. Darwin observed that evolutionary change in languages greatly resembled the processes of biological evolution: inheritance from a common ancestor and convergent evolution operate in both. Despite many suggestions, few attempts have been made to apply the phylogenetic methods used in biology to linguistic data. Here we report a parsimony analysis of a large language data set. We use this analysis to test competing hypotheses--the "express-train" and the "entangled-bank" models--for the colonization of the Pacific by Austronesian-speaking peoples. The parsimony analysis of a matrix of 77 Austronesian languages with 5,185 lexical items produced a single most-parsimonious tree. The express-train model was converted into an ordered geographical character and mapped onto the language tree. We found that the topology of the language tree was highly compatible with the express-train model.

Mitochondrial DNA variation is an indicator of austronesian influence in Island Melanesia

Past studies have shown a consistent association of a specific set of mitochondrial DNA 9 base pair (bp) deletion haplotypes with Polynesians and their Austronesian-speaking relatives, and the total lack of the deletion in a short series of New Guinea Highlanders. Utilizing plasma and DNA samples from various old laboratory collections, we have extended population screening for the 9-bp deletion into "Island Melanesia," an area notorious for its extreme population variation. While the 9-bp deletion is present in all Austronesian, and many non-Austronesian-speaking groups, it is absent in the more remote non-Austronesian populations in Bougainville and New Britain. These results are consistent with the hypothesis that this deletion was first introduced to this region about 3,500 years ago with the arrival of Austronesian-speaking peoples from the west, but has not yet diffused through all populations there. The pattern cannot be reconciled with the competing hypothesis of a primarily indigenous Melanesian origin for the ancestors of the Polynesians. Although selection clearly has operated on some other genetic systems in this region, both migration and random genetic drift primarily account for the remarkable degree of biological diversity in these small Southwest Pacific populations.

Analysis of five Y-specific microsatellite loci in Asian and Pacific populations

We have analyzed five Y-specific microsatellite loci (DYS388, DYS390, DYS391, DYS394, DYS395) in 17 Asian and Pacific populations representing a broad geographical area and different linguistic families, with an emphasis on populations from mainland and insular Southeast Asia. Analysis of gene diversity indicates that several of the studied populations have experienced substantial genetic isolation, and a reduction in male effective sizes (viz. the Northeast Indian populations Nishi, Adi and the Taiwanese aboriginals). The average values of the F(ST) and ((ST) statistics indicate a high degree of genetic differentiation among these populations at the five Y-specific markers (F(ST) =0.21 and ((ST) = 0.33, based on individual loci; F(ST) = 0.09 and ((ST) = 0.36, based on haplotypes), which conform to the expectation of a fourfold smaller effective size of the Y-linked loci compared with the autosomal loci. Dendrogram and principal coordinates analysis, with few exceptions, show a major separation between mainland and insular populations. Among the mainland populations, the Tibeto-Burman speakers from Northeast India cluster in a well-defined group, supported by high bootstrap values. The Southern Chinese, Northern Thai, So, and Cambodian also are integral to this cluster. The other major cluster is rather heterogeneous and includes, among others, the Austronesian-speaking populations. The Samoans of the Pacific, with a distinctive pattern of allelic distributions, stand as an outlier in the tree and PC representations. Although trends of genetic affinities among ethnically and geographically related populations are evident from the Y-specific microsatellite data, microsatellites are not optimal for deciphering complex migratory patterns of human populations, which could possibly be clarified by using additional and more stable genetic markers.

Differential contribution of indigenous men and women to the formation of an urban population in the Amazon region as revealed by mtDNA and Y-DNA

The human populations of the Brazilian Amazon were formed by interethnic crosses between Europeans, Africans, and Amerindians. The relative contribution of men and women of different ethnic groups was not homogeneous, since the social policies of the first three centuries of Brazilian colonization encouraged mating between European men and indigenous women and, later on, African women. In order to test this model based on historical data, we compared the relative contribution of the Y-DNA and mtDNA of Amerindian and non-Amerindian populations to the formation of the urban population of the town of Belém, in the Amazon region, on the basis of a C-->T mutation at locus DYS199 present in 90% of the Amerindian Y-DNA and of five markers that define 99% of the mitochondrial sequences of Amerindians. The contribution of indigenous men to the formation of this population was less than 5%, whereas the contribution of indigenous women was estimated at more than 50% of the mitochondrial sequences of the same population. Thus, the present results demonstrate that the contribution of indigenous women to the formation of the Belém population was 10 times higher than the contribution of indigenous men, a genetic consequence of social behavior and attitudes of the past; our results also help clarify the process of integration of indigenous communities into the urban societies in Brazil and possibly in other countries.

DCAMKL1, a brain-specific transmembrane protein on 13q12.3 that is similar to doublecortin (DCX)

Mutations in the human doublecortin (DCX), a brain-specific putative signaling protein, cause X-linked lissencephaly and subcortical band heterotopia. A predicted 740-amino-acid protein from human brain has two distinct regions, an N-terminal 345-amino-acid region 78% similar to the DCX protein and a C-terminal 427-amino-acid region that contains two transmembrane domains and is 98% homologous to a rat Ca2+/calmodulin-dependent protein kinase. We have designated this protein DCAMKL1. It maps to chromosome 13q12.3-q13, within a 540-kb YAC clone containing markers D13S805 and D13S1164. Northern analysis detected three major transcript isoforms of the DCAMKL1 gene expressed differentially and predominantly in human fetal and adult brain and during mouse embryogenesis (11-17 dpc). These results and its homology with the DCX and Ca2+/calmodulin dependent kinase proteins suggest a likely role for DCAMKL1 transmembrane protein in developing and adult brain, possibly in a pathway of cortical development.

Fluorescence in situ hybridization analysis with LIS1 specific probes reveals a high deletion mutation rate in isolated lissencephaly sequence

PURPOSE

Recent revision of the lissencephaly critical region on chromosome 17p13.3 and confirmation of LIS1 as the causative gene for classical lissencephaly has allowed the development and application of fluorescence in situ hybridization (FISH) probes corresponding directly to this gene.

METHOD

We have analyzed patients with isolated lissencephaly sequence (ILS) by FISH with probes at D17S379, an anonymous locus distal to LIS1, and with LIS1 specific probes.

RESULTS

In 110 patients with ILS, a deletion at D17S379 was detected in 23.6%. Of those patients without a deletion, 32 were available for further study with LIS1 probes. Deletions were found in eight additional individuals.

CONCLUSION

The overall deletion mutation rate detectable by FISH with LIS1 probes is approximately 40%. This rate is significantly higher than the deletion rate observed at D17S379. This indicates that FISH studies using probes specific to LIS1 should be undertaken as the initial diagnostic assay for the evaluation of patients with ILS, and the high frequency of deletions raises the possibility of "hotspots" for chromosome breakage in this region.

mtDNA and language support a common origin of Micronesians and Polynesians in Island Southeast Asia

The origins and relationships among Micronesians, Polynesians, and Melanesians were investigated. Five different mtDNA region V length polymorphisms from 873 individuals representing 24 Oceanic and Asian populations were analyzed. The frequency cline of a common deletion and the distributions of a rare expanded length polymorphism support the origin of both Micronesians and Polynesians in Island Southeast Asia. Genetic, linguistic, and geographic distances were compared to assess the relative importance of isolation and gene flow during the prehistory of 19 Austronesian-speaking populations subdivided into five potential spheres of interaction. We observed significant correlations (P < 0.05) between genetic and linguistic distances in four of five comparisons. These data indicate extensive gene flow throughout much of Micronesia, but substantial isolation in other Pacific regions. Although recent advancements in our understanding of intentional voyaging within Remote Oceania have challenged the existence of the "myth of the primitive isolate," we caution against the adoption of panmictic alternatives.

Dominant coloboma-microphthalmos syndrome associated with sensorineural hearing loss, hematuria, and cleft lip/palate

Ocular colobomas and microphthalmos, isolated or as part of a syndrome, are usually sporadic and only rarely found in large families. A 4-generation family with autosomal dominant uveal coloboma and microphthalmos associated with cleft lip and palate was re-evaluated. Wide variability in expression is evident and more recently recognized manifestations include a complete spectrum of eye involvement, impairment of extraocular movement, mid-frequency sensorineural hearing loss, and hematuria. Learning difficulties requiring remedial teaching were present in one third of those affected and a neural tube defect has occurred in one presumed affected member. This family appears to present a unique phenotype, which provides an opportunity to identify a genetic locus involved in eye, ear, renal, primary palate, and brain development.

The founding mitochondrial DNA lineages of Tristan da Cunha Islanders

Genealogical histories show that the inhabitants of Tristan da Cunha are derived from a known number of founders. Using the transmission of mitochondrial DNA (mtDNA) from mother to offspring pairs, we traced the mtDNA types found in 161 extant individuals to five female founders. Although the historical data claimed that two pairs of sisters were among the founding females, mtDNA data showed support for only one pair of sisters. We also studied the fidelity of mtDNA transmission in conjunction with the genealogical data. We did not detect any mutations from 698 base pairs of sequence data from 75 individuals, which together accounted for 108 independent transmissions of mtDNA from mother to offspring. Based on this observation, we estimate that the mtDNA mutation rate is no more than one new mutation every 36 transmissions. These results indicate a high fidelity of maternal mtDNA transmission and support the utility of mtDNA in evolutionary and forensic studies.

Ancient and modern mitochondrial DNA sequences and the colonization of the Pacific

Mitochondrial DNA (mtDNA) is a valuable tool for the study of recent human evolution because it is easy to analyse, is inherited uniparentally and has a relatively rapid rate of evolution. mtDNA analysis has been used extensively for the elucidation of the pattern of migrations of human populations. Several studies have focused on the Pacific because Polynesia was settled by humans for the first time relatively recently and there is a wealth of archaeological and linguistic data to complement genetic data on the region. Results of mtDNA analyses on modern-day Pacific populations indicate reduced genetic variability, and suggest that the Polynesians descend from people who migrated relatively recently from island Southeast Asia and that a population bottleneck occurred during the settlement of the central Pacific. Several informative polymorphisms have been identified in the hypervariable control region of mtDNA in modern-day Pacific populations that are helpful in tracing the ancestral affinities of these people. Studies of these mtDNA polymorphisms in ancient bones of prehistoric Pacific islanders indicate that the proto-Polynesian colonizers may have descended from the early settlers of island Melanesia. Although fraught with technical difficulties, studies of ancient DNA can provide valuable evidence on the genetic affinities of past peoples.

Applications of microsatellite-based Y chromosome haplotyping

Y-chromosomal microsatellites have been investigated for the purposes of application to male identification, population genetics and population history. With nine markers, every male in a German population sample (n = 70) could be identified by an individual-specific Y microsatellite haplotype. The analysis of 474 unrelated males of nine human populations with seven markers revealed 301 different Y haplotypes. The analysis of molecular variance (AMOVA) approach was used to detect male population characteristics of Y microsatellite haplotypes. With pairwise comparisons of inter-population variance, most of the populations could be distinguished significantly. Sixty individuals from different male populations in Asia and Northern Europe carrying a novel Y-chromosomal T-->C transition show reduced microsatellite variability together with haplotype similarities. Microsatellite data suggest that the mutation occurred recently in Asia, supporting the hypothesis of Asian ancestry of some northern European populations.

Multiplex DNA typing of short-tandem-repeat loci on the Y chromosome

To facilitate evolutionary and forensic studies of DNA polymorphisms on the Y chromosome, we devised a multiplex amplification procedure for short-tandem-repeat (STR) loci. Four tetranucleotide STR loci (DYS19, DYS390, DYS391, and DYS393) were simultaneously amplified with FAM-labeled primers and genotypes were determined with an automated DNA sequencer. We typed 162 males from three U.S. populations (African-Americans, European-Americans and Hispanics) and found that the haplotype diversities range from 0.920 to 0.969. This quadruplex system provides a facile means of genotyping these Y chromosome STRs, and should be useful in population genetic and forensic applications.

Genetic relationship between the Canary Islanders and their African and Spanish ancestors inferred from mitochondrial DNA sequences

Nucleotide sequences of the hypervariable segment I of the control region of the mtDNA were determined in 101 individuals: 54 Canary Islanders, 18 North African Berbers, 18 Spanish mainlanders and 11 sub-Saharan Guineans. In spite of the fact that only members of the Fang tribe were analysed, nucleotide diversity in Guineans (theta x 100 = 2.33) is one of the highest found in African populations. Estimates of genetic contribution to the Canarians from their putative parental populations based on mtDNA (43.25 +/- 1.38% Berbers, 35.54 +/- 0.55% Spanish, 21.21 +/- 1.92% Guineans) showed an important North African substrate. These mtDNA results, when compared with data based on nuclear markers, point to a strong male female asymmetry, 75% of the Spanish nuclear contribution was due to males and practically all the Berber and Guinean was due to females. These results are in agreement with the way that the Canary Islands were conquered. Pairwise difference distributions in Guineans and Berbers are compatible with the model of populations in expansion. Departures from a Poisson distribution for the Canarians and Spanish can be explained by admixture and the way of sampling respectively.