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      Phylogenetic nomenclature and evolution of mannose-binding lectin ( MBL2) haplotypes


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          Polymorphisms of the mannose-binding lectin gene ( MBL2) affect the concentration and functional efficiency of the protein. We recently used haplotype-specific sequencing to identify 23 MBL2 haplotypes, associated with enhanced susceptibility to several diseases.


          In this work, we applied the same method in 288 and 470 chromosomes from Gabonese and European adults, respectively, and found three new haplotypes in the last group. We propose a phylogenetic nomenclature to standardize MBL2 studies and found two major phylogenetic branches due to six strongly linked polymorphisms associated with high MBL production. They presented high Fst values and were imbedded in regions with high nucleotide diversity and significant Tajima's D values. Compared to others using small sample sizes and unphased genotypic data, we found differences in haplotyping, frequency estimation, Fu and Li's D* and Fst results.


          Using extensive testing for selective neutrality, we confirmed that stochastic evolutionary factors have had a major role in shaping this polymorphic gene worldwide.

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          Most cited references41

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          Arlequin (version 3.0): An integrated software package for population genetics data analysis

          Arlequin ver 3.0 is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework. Arlequin 3 introduces a completely new graphical interface written in C++, a more robust semantic analysis of input files, and two new methods: a Bayesian estimation of gametic phase from multi-locus genotypes, and an estimation of the parameters of an instantaneous spatial expansion from DNA sequence polymorphism. Arlequin can handle several data types like DNA sequences, microsatellite data, or standard multi-locus genotypes. A Windows version of the software is freely available on http://cmpg.unibe.ch/software/arlequin3.
            • Record: found
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            An Exact Test for Population Differentiation

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              Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population.

              Molecular techniques allow the survey of a large number of linked polymorphic loci in random samples from diploid populations. However, the gametic phase of haplotypes is usually unknown when diploid individuals are heterozygous at more than one locus. To overcome this difficulty, we implement an expectation-maximization (EM) algorithm leading to maximum-likelihood estimates of molecular haplotype frequencies under the assumption of Hardy-Weinberg proportions. The performance of the algorithm is evaluated for simulated data representing both DNA sequences and highly polymorphic loci with different levels of recombination. As expected, the EM algorithm is found to perform best for large samples, regardless of recombination rates among loci. To ensure finding the global maximum likelihood estimate, the EM algorithm should be started from several initial conditions. The present approach appears to be useful for the analysis of nuclear DNA sequences or highly variable loci. Although the algorithm, in principle, can accommodate an arbitrary number of loci, there are practical limitations because the computing time grows exponentially with the number of polymorphic loci. Although the algorithm, in principle, can accommodate an arbitrary number of loci, there are practical limitations because the computing time grows exponentially with the number of polymorphic loci.

                Author and article information

                BMC Genet
                BMC Genetics
                BioMed Central
                14 May 2010
                : 11
                : 38
                [1 ]Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
                [2 ]Laboratory of Molecular Immunopathology, Hospital de Clínicas, Federal University of Paraná, Curitiba, Brazil
                [3 ]Department of Genetics and Evolutionary Biology, Institute of Bioscience, University of São Paulo, São Paulo, Brazil
                [4 ]Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
                [5 ]Institute of Physiology I, University of Tübingen, Germany
                [6 ]Medical Research Unit, Albert Schweitzer Hospital, Lambaréné, Gabon
                [7 ]Department of Medical Biometry, University of Tübingen, Tübingen, Germany
                [8 ]Laboratory of Human Molecular Genetics, Federal University of Paraná, Brazil
                Copyright ©2010 Boldt et al; licensee BioMed Central Ltd.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                : 23 October 2009
                : 14 May 2010
                Research article



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