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Luísa Pereira

Publications and source records attributed to Luísa Pereira.

At least 19 recordsLinked to original sources
PubMed2007

No evidence for an mtDNA role in sperm motility: data from complete sequencing of asthenozoospermic males.

The first complete mitochondrial DNA (mtDNA) sequences (approximately 16,569 bp) in 20 patients with asthenozoospermia and a comparison with 23 new complete mtDNA sequences in teratoasthenozoospermic individuals, confirmed no sharing of specific polymorphisms or specific mitochondrial lineages between these individuals. This is strong evidence against the accepted claim of a major role played by mtDNA in male fertility, once supported by haplogroup association studies based on the screening of hypervariable region I. The hypothesis of maternally driven selection acting in male reproductive success must thus be treated with caution.

Analysis of Variance↗
PubMed2006

RepeatAround: a software tool for finding and visualizing repeats in circular genomes and its application to a human mtDNA database.

RepeatAround is a Windows based software tool designed to find "direct repeats", "inverted repeats", "mirror repeats" and "complementary repeats", from 3 to 64 bp length, in circular genomes. It processes input files directly extracted from GenBank database, providing visualisation of the repeats location in the genomic structure, so that for instance, in most mtDNAs the user can check if the repeats are located in coding or non-coding region (and in the first case in which gene), and how far apart the repeat pair(s) are. Besides the visual tool, it provides other outputs in a spreadsheet containing information on the number and location of the repeats, facilitating graphic analyses. Several genomes can be inputed simultaneously, for phylogenetic comparison purposes. Other capabilities of the software are the generation of random circular genomes, for statistical evaluation of comparison between observed repeats distributions with their shuffled counterparts, as well as the search for specific motifs, allowing an easy confirmation of repeats flanking a newly detected rearrangement. As an example of the programme's applications we analysed the Direct Repeats distribution in a large human mtDNA database. Results showed that Direct Repeats, even the larger ones, are evenly distributed among the human mtDNA haplogroups, enabling us to state that, based only on the repetitive motifs, no haplogroup is particularly more or less prone to mtDNA macrodeletions.

Computational Biology↗
PubMed2006

Genetic signatures of a Mediterranean influence in Iberian Peninsula sheep husbandry.

Highly adaptable and versatile populations of domestic sheep, the result of millennia of intense husbandry, are found in almost every corner of the world. Here we describe a genetic survey of sheep from the western fringe of its European distribution. We studied the mitochondrial DNA control region sequences from 161 individuals belonging to 7 Portuguese sheep breeds. Our study revealed a high level of genetic diversity, with an average breed haplotype diversity of 0.983, substantially above that observed in central European breeds, as well as the presence of maternal lineages until now only found in the Middle East and Asia. A broad north-south pattern describes the most important trend in the Portuguese sheep population with a southern population clearly distinct from most other breeds. A recurrent influx of new genetic diversity, probably via the Mediterranean Sea, may explain these patterns and appears to corroborate the importance of this maritime route in the history of both mankind and livestock. Zooarchaeological studies of sheep bones from southern Portugal indicate a marked size increase during the Moslem period that may reflect an improvement of this animal--perhaps part of the well known "Arab agricultural revolution" in Andalusia. This could have been a time when the gene pool of Iberian sheep was substantially enriched and may help to explain the history of modern sheep breeds in this peninsula.

Animal Husbandry↗
PubMed2006

Islands inside an island: reproductive isolates on Jerba island.

Jerba Island, located in South Eastern Tunisia, is inhabited by four ethnic groups: Berbers, Arabs, sub-Saharans, and Jews. All live in distinct areas, although the Arabs are also distributed all over the island. The first Arab settlement was founded in the 7th century A.D., so co-existence with Berbers has lasted for more than a millennium. Religious and cultural differences have represented an obstacle to the intermixing of these groups, and among both Arabs and Berbers marriages usually occur between members from the same extended family. Using new mtDNA data and previously described Y-chromosome STR-defined haplotypes, we tested whether this reported inbreeding would be reflected in the differentiation between Berber and Arab communities. Concerning mtDNA, the Berber group presented a greater Eurasian contribution (87%), and, surprisingly, no U6 haplotypes were found; in contrast, the Arabs showed a larger contribution of sub-Saharan lineages (24%) and the U6 haplogroup amounted to 10%. Another source of evidence for the reproductive isolation of the two groups was revealed through the analysis of haplotype matching (both mtDNA and Y-chromosome), showing that matching probabilities between them is of the same order of magnitude of that observed when contrasting samples from different European countries.

Arabs↗
PubMed2005

Y-chromosomal STR haplotypes in three ethnic groups and one cosmopolitan population from Tunisia.

The 11 Y-chromosomal short tandem repeats (STRs) included in the Promega Corporation PowerPlex Y System (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438 and DYS439) were typed in three ethnic groups ("Andalusians", Berber and Arab) and one cosmopolitan population (Tunis) from Tunisia, summing up 247 individuals, and 139 different haplotypes. Focusing the analysis on the seven Y-STRs of the YHRD Minimal Haplotype Core (DYS385 excepted), "Andalusians" showed no differences from the Cosmopolitan and the Arab samples previously published (our Arab sample presented an extremely low haplotype diversity), but were different from the Berbers. The Berbers from Tunisia were not different from those from Morocco.

Chromosomes, Human, Y↗
PubMed2005

Evaluating the forensic informativeness of mtDNA haplogroup H sub-typing on a Eurasian scale.

The impact of phylogeographic information on mtDNA forensics has been limited to the quality control of published sequences and databases. In this work we use the information already available on Eurasian mtDNA phylogeography to guide the choice of coding-region SNPs for haplogroup H. This sub-typing is particularly important in forensics since, even when sequencing both HVRI and HVRII, the discriminating power is low in some Eurasian populations. We show that a small set (eight) of coding-region SNPs resolves a substantial proportion of the identical haplotypes, as defined by control-region variation alone. Moreover, this SNP set, while substantially increasing the discriminating efficiency in most Eurasian populations by roughly equal amounts, discloses population-specific profiles.

Asia↗
PubMed2005

Data for Y-chromosome haplotypes defined by 17 STRs (AmpFLSTR Yfiler) in two Tunisian Berber communities.

The 17 Y-chromosomal short tandem repeats (STRs) included in the AmpFLSTR Yfiler PCR Amplification Kit (AB Applied Biosystems) (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4) were typed in two Berber communities, a small village (Takrouna) and a town (Sejenane), from North Tunisia. As expected, diversity was higher in the town, even when compared with a pool of three small Berber communities, probably due to the combination of different founder effects and genetic drifts operating in the small villages.

Chromosomes, Human, Y↗
PubMed2005

MtDNA diversity among four Portuguese autochthonous dog breeds: a fine-scale characterisation.

BACKGROUND: The picture of dog mtDNA diversity, as obtained from geographically wide samplings but from a small number of individuals per region or breed, has revealed weak geographic correlation and high degree of haplotype sharing between very distant breeds. We aimed at a more detailed picture through extensive sampling (n = 143) of four Portuguese autochthonous breeds - Castro Laboreiro Dog, Serra da Estrela Mountain Dog, Portuguese Sheepdog and Azores Cattle Dog-and comparatively reanalysing published worldwide data. RESULTS: Fifteen haplotypes belonging to four major haplogroups were found in these breeds, of which five are newly reported. The Castro Laboreiro Dog presented a 95% frequency of a new A haplotype, while all other breeds contained a diverse pool of existing lineages. The Serra da Estrela Mountain Dog, the most heterogeneous of the four Portuguese breeds, shared haplotypes with the other mainland breeds, while Azores Cattle Dog shared no haplotypes with the other Portuguese breeds.A review of mtDNA haplotypes in dogs across the world revealed that: (a) breeds tend to display haplotypes belonging to different haplogroups; (b) haplogroup A is present in all breeds, and even uncommon haplogroups are highly dispersed among breeds and continental areas; (c) haplotype sharing between breeds of the same region is lower than between breeds of different regions and (d) genetic distances between breeds do not correlate with geography. CONCLUSION: MtDNA haplotype sharing occurred between Serra da Estrela Mountain dogs (with putative origin in the centre of Portugal) and two breeds in the north and south of the country-with the Castro Laboreiro Dog (which behaves, at the mtDNA level, as a sub-sample of the Serra da Estrela Mountain Dog) and the southern Portuguese Sheepdog. In contrast, the Azores Cattle Dog did not share any haplotypes with the other Portuguese breeds, but with dogs sampled in Northern Europe. This suggested that the Azores Cattle Dog descended maternally from Northern European dogs rather than Portuguese mainland dogs. A review of published mtDNA haplotypes identified thirteen non-Portuguese breeds with sufficient data for comparison. Comparisons between these thirteen breeds, and the four Portuguese breeds, demonstrated widespread haplotype sharing, with the greatest diversity among Asian dogs, in accordance with the central role of Asia in canine domestication.

Animals↗
PubMed2005

Pros and cons in the use of SNPs in forensic kinship investigation: a comparative analysis with STRs.

Recent advances in single nucleotide polymorphisms (SNPs) research have raised the possibility that these markers could replace the forensically established short tandem repeats (STRs). In this work, we compare STRs and SNPs applicability for kinship investigation in terms of expected informative content and probability of occurrence of "difficult cases" (when isolated Mendelian incompatibilities between alleged father and child are found). Since SNPs have a much lower mutation rate than STRs, these difficulties were expected to occur less frequently if SNPs were used instead of STRs. The purpose of this paper is to make some simulations allowing the estimation of how often such difficult cases are expected to occur using both types of markers and how serious can be their impact in routine work. Our results demonstrate that a battery based exclusively on SNPs matching the informative power of current STR kits would be prone, if applied to routine paternity investigation, to the occurrence of cases where the statistical evidence would be inconclusive. We infer that the introduction of a SNP based strategy, as a substitute to the now classical STR approach poses statistical problems that must be carefully evaluated.

Adult↗
PubMed2005

High-resolution mtDNA evidence for the late-glacial resettlement of Europe from an Iberian refugium.

The advent of complete mitochondrial DNA (mtDNA) sequence data has ushered in a new phase of human evolutionary studies. Even quite limited volumes of complete mtDNA sequence data can now be used to identify the critical polymorphisms that define sub-clades within an mtDNA haplogroup, providing a springboard for large-scale high-resolution screening of human mtDNAs. This strategy has in the past been applied to mtDNA haplogroup V, which represents <5% of European mtDNAs. Here we adopted a similar approach to haplogroup H, by far the most common European haplogroup, which at lower resolution displayed a rather uninformative frequency distribution within Europe. Using polymorphism information derived from the growing complete mtDNA sequence database, we sequenced 1580 base pairs of targeted coding-region segments of the mtDNA genome in 649 individuals harboring mtDNA haplogroup H from populations throughout Europe, the Caucasus, and the Near East. The enhanced genealogical resolution clearly shows that sub-clades of haplogroup H have highly distinctive geographical distributions. The patterns of frequency and diversity suggest that haplogroup H entered Europe from the Near East approximately 20,000-25,000 years ago, around the time of the Last Glacial Maximum (LGM), and some sub-clades re-expanded from an Iberian refugium when the glaciers retreated approximately 15,000 years ago. This shows that a large fraction of the maternal ancestry of modern Europeans traces back to the expansion of hunter-gatherer populations at the end of the last Ice Age.

DNA, Mitochondrial↗
PubMed2005

Human mtDNA haplogroups and reduced male fertility: real association or hidden population substructuring.

A mitochondrial DNA (mtDNA) haplogroup association study carried out in 101 southern Portuguese males with oligozoospermia showed to be negative when comparing with a geographically matching control sample. Misleading positive association signs were however obtained when using other control samples from the same country. This shows that mtDNA population substructure can also introduce spurious signs in haplogroup association studies, as previously reported for Y-chromosome. However, our data do not exclude the probability that a particular mtDNA mutation contributes significantly to the reduction of sperm production, but indeed precludes the hypothesis of a significant association between such a mutation and specific haplogroup.

Complementarity Determining Regions↗
PubMed2005

Female gene pools of Berber and Arab neighboring communities in central Tunisia: microstructure of mtDNA variation in North Africa.

North African populations are considered genetically closer to Eurasians than to sub-Saharans. However, they display a considerably high mtDNA heterogeneity among them, namely in the frequencies of the U6, East African, and sub-Saharan haplogroups. In this study, we describe and compare the female gene pools of two neighboring Tunisian populations, Kesra (Berber) and Zriba (non-Berber), which have contrasting historical backgrounds. Both populations presented lower diversity values than those observed for other North African populations, and they were the only populations not showing significant negative Fu's F(S) values. Kesra displayed a much higher proportion of typical sub-Saharan haplotypes (49%, including 4.2% of M1 haplogroup) than Zriba (8%). With respect to U6 sequences, frequencies were low (2% in Kesra and 8% in Zriba), and all belonged to the subhaplogroup U6a. An analysis of these data in the context of North Africa reveals that the emerging picture is complex, because Zriba would match the profile of a Berber Moroccan population, whereas Kesra, which shows twice the frequency of sub-Saharan lineages normally observed in northern coastal populations, would match a western Saharan population except for the low U6 frequency. The North African patchy mtDNA landscape has no parallel in other regions of the world and increasing the number of sampled populations has not been accompanied by any substantial increase in our understanding of its phylogeography. Available data up to now rely on sampling small, scattered populations, although they are carefully characterized in terms of their ethnic, linguistic, and historical backgrounds. It is therefore doubtful that this picture truly represents the complex historical demography of the region rather than being just the result of the type of samplings performed so far.

Arabs↗
PubMed2005

African female heritage in Iberia: a reassessment of mtDNA lineage distribution in present times.

The Iberian peninsula is a peripheral region of Europe in close proximity to Africa. Its inhabitants have an overall mtDNA genetic landscape typical of European background, although with signs of some African influence, whose features we deemed to disclose by analyzing available mtDNA HVRI distributions and new data. We analyzed 1,045 sequences. The most relevant results are the following: (1) North African sequences (haplogroup U6) present an overall frequency of 2.39%, and sub-Saharan sequences reach 3.83%, values that are, in both cases, much higher than those generally observed in Europe; and (2) there is a substantial geographic heterogeneity in the distribution of these lineages (haplogroup L being the most frequent in the south, whereas haplogroup U6 is generally more common in the north). The analysis of the observed diversity within each haplogroup strongly suggests that both were recently introduced (in historical times). Although for haplogroup U6 the documented event that is demographically compatible is the Islamic period (beginning of the 8th century to the end of the 15th century), for haplogroup L the most probable origin is the modern slave trade (mid 15th century to the end of the 18th century). However, the observed geographic structuring for one of the haplogroups does not fit the expected distribution provided by simplistic historical considerations. In fact, although for haplogroup L the north-south increasing frequency is corroborated by historical data, the opposite trend, observed for haplogroup U6, is more difficult to reconcile with the magnitude and time span of the Islamic political and cultural influence, which lasted longer and was more intense in the south. To clarify this conundrum, we need not only a substantial increase in the amount of mtDNA data (particularly for North Africa) but also new historical data and interpretations.

Africa South of the Sahara↗
PubMed2004

[Sliding tracheoplasty: a good choice for the treatment of congenital tracheal stenosis].

When infants with recurrent wheezing have a clinical course inconsistent with a common diagnosis, anatomic malformations should be considered in diagnostic workup, followed by medical stabilization and early therapy. A careful history and physical examination could reveal important diagnostic clues that indicate the need to perform a fiberoptic bronchoscopy, which in the reported case showed tracheal stenosis in the transition between the first and second third of the trachea. Chest CT scan revealed a long funnel-shaped tracheal stenosis and along with an echocardiogram, excluded associated cardiovascular malformations. Surgical correction by sliding tracheoplasty under extra-corporeal circulation was successfully performed at the Hospital Gregório Marañon in Madrid. The surgical complications that have occurred (mediastinitis and pulmonary embolism) were resolved. After a two-year follow-up, that included endoscopic control, the patient was found to be free of symptoms of wheezing or post-surgical complications. The authors emphasize the need for early diagnosis and surgical treatment to be performed in an experienced reference center.

Humans↗
PubMed2004

Predicting sampling saturation of mtDNA haplotypes: an application to an enlarged Portuguese database.

An enlarged mtDNA database ( n=549) for the Portuguese population, comprising HVRI and HVRII regions is reported. This database was used to test the effect of sample size on the estimation of relevant parameters such as haplotype diversity, number of different haplotypes, nucleotide diversity and number of polymorphic positions. Simulations were performed generating sets of random subsamples of variable sizes ( n=50, 100, 200, 300 and 400). The results show that while haplotype and nucleotide diversities do not vary significantly with sample size, the numbers of haplotypes and polymorphic positions rise continuously inside the tested interval. These trends are interpretable by the evolution of the proportions of sequences that are found once or twice, which drop dramatically as sample size increases, with the corresponding rise in the frequency of those encountered 3 times or more. The generated data were also used to extrapolate saturation curves for the referred parameters. When considering for instance the number of haplotypes, it is shown that a sample size of 1,000 individuals is required for practical saturation (defined as the point where a sample size increase of 100 individuals corresponds to an increment in the diversity measure below 5%). For HVRII the same level is reached at n=900 and n=1,300 is needed when both regions are analysed simultaneously. Consequently, we can infer that currently used sample sizes are still rather inadequate for both anthropological and forensic purposes.

DNA, Mitochondrial↗
PubMed2003

Mitochondrial portraits of the Madeira and Açores archipelagos witness different genetic pools of its settlers.

We have studied the matrilineal genetic composition of the Madeira and Açores north Atlantic archipelagos, which were settled by the Portuguese in the 15th century. Both archipelagos, and particularly Madeira, were involved in a complex commercial network established by the Portuguese, which included the trading of slaves across the Atlantic. One hundred and fifty-five mtDNAs sampled from the Madeira and 179 from the Açores archipelagos were analysed for the hypervariable segment I (HVS-I), and for haplogroup-diagnostic coding-region RFLPs. The different settlement histories of both groups of islands are well reflected in their present day mtDNA pool. Although both archipelagos show identical diversity values, they are clearly different in their haplogroup content. Madeira displays a stronger sub-Saharan imprint, with haplogroups L1-L3 constituting about 13% of the lineages. Also, the relative frequencies of L sub-clusters in Madeira and mainland Portugal suggests that, at least in part, African presence in Madeira can be attributed to a direct gene flow from West Africa and not via Portugal. A comparison of the genetic composition of these two archipelagos with the Canary Islands, specially taking into account that their European source population was essentially from the Iberian Peninsula, testifies the stronger impact of the North African U6 cluster in the Canaries. This group is present in Madeira at a moderate frequency, but very reduced in the Açores. Nevertheless the recorded introduction of Canary native Guanches, who are characterized by the presence of particular sub-clade U6b1, has left no detectable imprints in the present day population of Madeira.

DNA↗