Papers by Maarten Larmuseau
Microarray Analysis of Copy Number Variants on the Human Y Chromosome Reveals Novel and Frequent Duplications Overrepresented in Specific Haplogroups
PLOS ONE, 2015
The human Y chromosome is almost always excluded from genome-wide investigations of copy number v... more The human Y chromosome is almost always excluded from genome-wide investigations of copy number variants (CNVs) due to its highly repetitive structure. This chromosome should not be forgotten, not only for its well-known relevance in male fertility, but also for its involvement in clinical phenotypes such as cancers, heart failure and sex specific effects on brain and behaviour. We analysed Y chromosome data from Affymetrix 6.0 SNP arrays and found that the signal intensities for most of 8179 SNP/CN probes in the male specific region (MSY) discriminated between a male, background signals in a female and an isodicentric male containing a large deletion of the q-arm and a duplication of the p-arm of the Y chromosome. Therefore, this SNP/CN platform is suitable for identification of gain and loss of Y chromosome sequences. In a set of 1718 males, we found 25 different CNV patterns, many of which are novel. We confirmed some of these variants by PCR or qPCR. The total frequency of individuals with CNVs was 14.7%, including 9.5% with duplications, 4.5% with deletions and 0.7% exhibiting both. Hence, a novel observation is that the frequency of duplications was more than twice the frequency of deletions. Another striking result was that 10 of the 25 detected variants were significantly overrepresented in one or more haplogroups, demonstrating the importance to control for haplogroups in genome-wide investigations to avoid stratification. NO-M214(xM175) individuals presented the highest percentage (95%) of CNVs. If they were not counted, 12.4% of the rest included CNVs, and the difference between duplications (8.9%) and deletions (2.8%) was even larger. Our results demonstrate that currently available genome-wide SNP platforms can be used to identify duplications and deletions in the human Y chromosome. Future association studies of the full spectrum of Y chromosome variants will demonstrate the potential involvement of gain or loss of Y chromosome sequence in different human phenotypes.
PLoS neglected tropical diseases, 2015
Anthropogenic environmental changes may lead to ecosystem destabilization and the unintentional c... more Anthropogenic environmental changes may lead to ecosystem destabilization and the unintentional colonization of new habitats by parasite populations. A remarkable example is the outbreak of intestinal schistosomiasis in Northwest Senegal following the construction of two dams in the '80s. While many studies have investigated the epidemiological, immunological and geographical patterns of Schistosoma mansoni infections in this region, little is known about its colonization history. Parasites were collected at several time points after the disease outbreak and genotyped using a 420 bp fragment of the mitochondrial cytochrome c oxidase subunit 1 gene (cox1) and nine nuclear DNA microsatellite markers. Phylogeographic and population genetic analyses revealed the presence of (i) many genetically different haplotypes at the non-recombining mitochondrial marker and (ii) one homogenous S. mansoni genetic group at the recombining microsatellite markers. These results suggest that the S. ...
Gobiidae (gobies) is one of the most species-rich fish families. Several lineages underwent radia... more Gobiidae (gobies) is one of the most species-rich fish families. Several lineages underwent radiation. Since this is a major mechanism underlying biological diversity, gobies can be considered a prime target for research into speciation, evolution and biogeography. As the family contains many small and often cryptic species, a multidisciplinary approach is crucial to describe and understand the actual diversity of gobies. Here we present molecular genetics and evolutionary parasitology as additional tools to reach this goal. Nucleotide sequence data can indicate populations that should be managed as separate units or deserve species status. Furthermore, they can support morphological species descriptions and provide a reliable means for non-specialists to identify gobies to species level. Besides species identification, these data can help to clarify phylogenetic relationships and biogeographic affinities. In case of protein-coding genes, sequence data can shed some light on selection processes and functional adaptation to the (local) environment. A European case study concerns the sand gobies (including the smallest European freshwater fish Economidichthys trichonis). In terms of diversity and endemicity, their freshwater stronghold is the eastern Mediterranean Basin. Indeed, its role as glacial refugium together with a dynamic biogeographic history stimulated the maintenance and diversification of this region's freshwater fauna. Many uncertainties remain regarding the taxonomy, phylogeny and biogeography of the endemic gobies. This poses urgent assessment and management difficulties, as several gobies (including, in all probability, undiscovered populations and species) endemic to the region are severely endangered as a result of anthropogenic impact. Apart from sand gobies, we will touch upon American seven-spined gobies (Elacatinus) and Millerigobius. Both neutral (mitochondrial) and functional (opsin) genes are used for phylogeny reconstruction.
Biological Journal of the Linnean Society, 2012
Within the Atlantic-Mediterranean region, the 'sand gobies' are abundant and widespread, and play... more Within the Atlantic-Mediterranean region, the 'sand gobies' are abundant and widespread, and play an important role in marine, brackish, and freshwater ecosystems. They include the smallest European freshwater fish, Economidichthys trichonis, which is threatened by habitat loss and pollution, as are several other sand gobies. Key to good conservation management is an accurate account of the number of evolutionary significant units. Nevertheless, many taxonomic and evolutionary questions remain unresolved within the clade, and molecular studies are lacking, especially in the Balkans. Using partial 12S and 16S mitochondrial ribosomal DNA sequences of 96 specimens of at least eight nominal species (both freshwater and marine populations), we assess species relationships and compare molecular and morphological data. The results obtained do not support the monophyly of Economidichthys, suggesting the perianal organ to be a shared adaptation to hole-brooding rather than a synapomorphy, and urge for a taxonomic revision of Knipowitschia. The recently described Knipowitschia montenegrina seems to belong to a separate South-East Adriatic lineage. Knipowitschia milleri, an alleged endemic of the Acheron River, and Knipowitschia cf. panizzae, are shown to be very closely related to other western Greek Knipowitschia populations, and appear conspecific. A distinct Macedonian-Thessalian lineage is formed by Knipowitschia thessala, whereas Knipowitschia caucasica appears as an eastern lineage, with populations in Thrace and the Aegean. The present study combines the phylogeny of a goby radiation with insights on the historical biogeography of the eastern Mediterranean, and identifies evolutionary units meriting conservation attention.
Relevant for various areas of human genetics, Y-chromosomal short tandem repeats (Y-STRs) are com... more Relevant for various areas of human genetics, Y-chromosomal short tandem repeats (Y-STRs) are commonly used for testing close paternal relationships among individuals and populations, and for male lineage identification. However, even the widely used 17-loci Yfiler set cannot resolve individuals and populations completely. Here, 52 centers generated quality-controlled data of 13 rapidly mutating (RM) Y-STRs in 14,644 related and unrelated males from 111 worldwide populations. Strikingly, >99% of the 12,272 unrelated males were completely individualized. Haplotype diversity was extremely high (global: 0.9999985, regional: 0.99836-0.9999988). Haplotype sharing between populations was almost absent except for six (0.05%) of the 12,156 haplotypes. Haplotype sharing within populations was generally rare (0.8% nonunique haplotypes), significantly lower in urban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). Analysis of molecular variance revealed 99.98% of variation within populations, 0.018% among populations within groups, and 0.002% among groups. Of the 2,372 newly and 156 previously typed male relative pairs, 29% were differentiated including 27% of the 2,378 father-son pairs. Relative to Yfiler, haplotype diversity was increased in 86% of the populations tested and overall male relative differentiation was raised by 23.5%. Our study demonstrates the value of RM Y-STRs in identifying and separating unrelated and related males and provides a reference database.
Pseudoautosomal Region 1 Length Polymorphism in the Human Population
PLoS Genetics, 2014
Recent Radiation within Y-chromosomal Haplogroup R-M269 Resulted in High Y-STR Haplotype Resemblance
The Y-chromosome tree bursts into leaf: 13,000 high-confidence SNPs covering the majority of known clades
Mol Biol Evol, 2014
A gene with major phenotypic effects as a target for selection vs. homogenizing gene flow
Molecular Ecology, 2014
Distributional and demographic consequences of Pleistocene climate fluctuations for a marine demersal fish in the north-eastern Atlantic
Journal of Biogeography, 2009
Mito-nuclear discordance in the degree of population differentiation in a marine goby
Heredity, 2010
A global analysis of Y-chromosomal haplotype diversity for 23 STR loci
Forensic Science International: Genetics, 2014
Genetic genealogy reveals true Y haplogroup of House of Bourbon contradicting recent identification of the presumed remains of two French Kings
European Journal of Human Genetics, 2014
Deep into the roots of the Libyan Tuareg: A genetic survey of their paternal heritage
American Journal of Physical Anthropology, 2011
Genetisch onderzoek van zoetwatervissen ten dienste van natuurbeheer
De Levende Natuur-maart 2011| 61 terug zodra de waterkwaliteit verbetert. Toch is het onjuist te ... more De Levende Natuur-maart 2011| 61 terug zodra de waterkwaliteit verbetert. Toch is het onjuist te beweren dat deze soorten vrij zijn van nefaste menselijke invloeden. Ten eerste gebeurt het nog veel te vaak dat geen van beide soorten voorkomen (trouwens geen enkele andere soort); op zulke plaatsen zijn er doorgaans ernstige problemen met de waterkwaliteit. Ten tweede liggen de Belgische en Nederlandse waterlopen bezaaid met vismigratieknelpunten die de verplaatsingen van vissen belemmeren. Het gaat hier vooral ...
Molecular Phylogenetics and Evolution, 2010
The spectral tuning mechanism of visual pigments is an excellent model to elucidate the mechanism... more The spectral tuning mechanism of visual pigments is an excellent model to elucidate the mechanisms of adaptive evolution and the importance of selection as an evolutionary force. Therefore, we use a phylogenetic approach to determine whether there is evidence for differential adaptive molecular evolution on the rhodopsin (RH1) gene among closely related 'sand goby' species (Teleostei, Gobiidae). Fragments of the RH1 gene (868 bp) were sequenced and analyzed for nine 'sand goby' species that inhabit different photic environments. A high level of interspecific polymorphism at the RH1 gene was observed, including non-synonymous mutations on amino acids known as spectral tuning sites. Clear indications for positive Darwinian selection were provided by three independent methods: (1) by linking functional variation on the RH1 gene to specific light environments of the different fish habitats; (2) by constructing and comparing phylogenies based on RH1 and the 'neutral' 12S and 16S mtDNA fragments; and (3) by performing statistical tests to detect signatures of directional selection on the RH1 gene. This study shows an unusual high variability in the gobiid visual RH1 pigment, and we therefore suggest a possible role for sensory genes in the adaptive radiation of 'sand goby' species.
conference Papers by Maarten Larmuseau
Archaeologia Mediaevalis, 2021
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Papers by Maarten Larmuseau
conference Papers by Maarten Larmuseau