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See detailSpeciation slowing down in widespread and long-living tree taxa : insights from the tropical timber tree genus Milicia (Moraceae)
Daïnou, Kasso ULg; Mahy, Grégory ULg; Duminil, Jérôme et al

in Heredity (2014)

The long generation time and large effective size of widespread forest tree species can result in slow evolutionary rate and incomplete lineage sorting, complicating species delimitation. We addressed ... [more ▼]

The long generation time and large effective size of widespread forest tree species can result in slow evolutionary rate and incomplete lineage sorting, complicating species delimitation. We addressed this issue with the African timber tree genus Milicia that comprises two morphologically similar and often confounded species: M. excelsa, widespread from West to East Africa, and M. regia, endemic to West Africa. We combined information from nuclear microsatellites (nSSRs), nuclear and plastid DNA sequences, and morphological systematics to identify significant evolutionary units and infer their evolutionary and biogeographical history. We detected five geographically coherent genetic clusters using nSSRs and three levels of genetic differentiation. First, one West African cluster matched perfectly with the morphospecies M. regia that formed a monophyletic clade at both DNA sequences. Second, a West African M. excelsa cluster formed a monophyletic group at plastid DNA and was more related to M. regia than to Central African M. excelsa, but shared many haplotypes with the latter at nuclear DNA. Third, three Central African clusters appeared little differentiated and shared most of their haplotypes. Although gene tree paraphyly could suggest a single species in Milicia following the phylogenetic species concept, the existence of mutual haplotypic exclusivity and nonadmixed genetic clusters in the contact area of the two taxa indicate strong reproductive isolation and, thus, two species following the biological species concept. Molecular dating of the first divergence events showed that speciation in Milicia is ancient (Tertiary), indicating that long-living tree taxa exhibiting genetic speciation may remain similar morphologically. [less ▲]

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See detailToward genomic prediction from whole-genome sequence data: impact of sequencing design on genotype imputation and accuracy of predictions.
Druet, Tom ULg; Macleod, I. M.; Hayes, B. J.

in Heredity (2014), 112(1), 39-47

Genomic prediction from whole-genome sequence data is attractive, as the accuracy of genomic prediction is no longer bounded by extent of linkage disequilibrium between DNA markers and causal mutations ... [more ▼]

Genomic prediction from whole-genome sequence data is attractive, as the accuracy of genomic prediction is no longer bounded by extent of linkage disequilibrium between DNA markers and causal mutations affecting the trait, given the causal mutations are in the data set. A cost-effective strategy could be to sequence a small proportion of the population, and impute sequence data to the rest of the reference population. Here, we describe strategies for selecting individuals for sequencing, based on either pedigree relationships or haplotype diversity. Performance of these strategies (number of variants detected and accuracy of imputation) were evaluated in sequence data simulated through a real Belgian Blue cattle pedigree. A strategy (AHAP), which selected a subset of individuals for sequencing that maximized the number of unique haplotypes (from single-nucleotide polymorphism panel data) sequenced gave good performance across a range of variant minor allele frequencies. We then investigated the optimum number of individuals to sequence by fold coverage given a maximum total sequencing effort. At 600 total fold coverage (x 600), the optimum strategy was to sequence 75 individuals at eightfold coverage. Finally, we investigated the accuracy of genomic predictions that could be achieved. The advantage of using imputed sequence data compared with dense SNP array genotypes was highly dependent on the allele frequency spectrum of the causative mutations affecting the trait. When this followed a neutral distribution, the advantage of the imputed sequence data was small; however, when the causal mutations all had low minor allele frequencies, using the sequence data improved the accuracy of genomic prediction by up to 30%.Heredity advance online publication, 3 April 2013; doi:10.1038/hdy.2013.13. [less ▲]

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See detailPopulation history and gene dispersal inferred from spatial genetic structure of a Central African timber tree, Distemonanthus benthamianus (Caesalpinioideae)
Debout, G. D. G.; Doucet, Jean-Louis ULg; Hardy, O. J.

in Heredity (2011), 106

African rainforests have undergone major distribution range shifts during the Quaternary, but few studies have investigated their impact on the genetic diversity of plant species and we lack knowledge on ... [more ▼]

African rainforests have undergone major distribution range shifts during the Quaternary, but few studies have investigated their impact on the genetic diversity of plant species and we lack knowledge on the extent of gene flow to predict how plant species can cope with such environmental changes. Analysis of the spatial genetic structure (SGS) of a species is an effective method to determine major directions of the demographic history of its populations and to estimate the extent of gene dispersal. This study characterises the SGS of an African tropical timber tree species, Distemonanthus benthamianus, at various spatial scales in Cameroon and Gabon. Displaying a large continuous distribution in the Lower Guinea domain, this is a model species to detect signs of past population fragmentation and recolonization, and to estimate the extent of gene dispersal. Ten microsatellite loci were used to genotype 295 adult trees sampled from eight populations. Three clearly differentiated gene pools were resolved at this regional scale and could be linked to the biogeographical history of the region, rather than to physical barriers to gene flow. A comparison with the distribution of gene pools observed for two other tree species living in the same region invalidates the basic assumption that all species share the same Quaternary refuges and recolonization pathways. In four populations, significant and similar patterns of SGS were detected. Indirect estimates of gene dispersal distances (sigma) obtained for three populations ranged from 400 to 1200m, whereas neighbourhood size estimates ranged from 50 to 110. [less ▲]

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See detailSo close and so different: comparative phylogeography of two small mammal species, the yellow-necked fieldmouse (Apodemus flavicollis) and the woodmouse (Apodemus sylvaticus) in the Western Palearctic region.
Michaux, Johan ULg; Libois, Roland ULg; Filippucci, M*-G

in Heredity (2005), 94(1), 52-63

In Europe, concordant geographical distribution among genetic lineages within different species is rare, which suggests distinct reactions to Quaternary ice ages. This study aims to determine whether such ... [more ▼]

In Europe, concordant geographical distribution among genetic lineages within different species is rare, which suggests distinct reactions to Quaternary ice ages. This study aims to determine whether such a discrepancy also affects a pair of sympatric species, which are morphologically and taxonomically closely related but which have slight differences in their ecological habits. The phylogeographic structures of two European rodents, the Yellow-necked fieldmouse (A. flavicollis) and the woodmouse (Apodemus sylvaticus) were, therefore, compared on the basis of mitochondrial DNA cytochrome b (mtDNA cyt b) sequences (965 base pairs) from 196 specimens collected from 59 European localities spread throughout the species distributions. The results indicate that the two species survived in different ways through the Quaternary glaciations. A. sylvaticus survived in the Iberian Peninsula from where it recolonized almost all Europe at the end of the last glaciation. Conversely, the refuge from which A. flavicollis recolonized Europe, including northern Spain, during the Holocene corresponds to the Italo-Balkan area, where A. sylvaticus suffered a serious genetic bottleneck. This study confirms that even closely related species may have highly different phylogeographic histories and shows the importance of ecological plasticity of the species for their survival through climate change. Finally, it suggests that phylogeographic distinctiveness may be a general feature of European species. [less ▲]

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See detailMating System Of Wild Phaseolus Lunatus L. And Its Relationship To Population Size
Zoro Bi, I.; Maquet, A.; Baudoin, Jean-Pierre ULg

in Heredity (2005), 94(2), 153-158

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See detailIncreased fecundity of malathion-specific resistant beetles in absence of insecticide pressure
Arnaud, Ludovic; Brostaux, Yves ULg; Assie, Lazare Komenan et al

in Heredity (2002), 89(6), 425-429

Despite that resistance frequency is assumed to decline when selective pressure is relaxed, the stability of resistance frequency has been observed in some insects in the absence of insecticide. In the ... [more ▼]

Despite that resistance frequency is assumed to decline when selective pressure is relaxed, the stability of resistance frequency has been observed in some insects in the absence of insecticide. In the red flour beetle, Tribolium castaneum, the first case of malathion-resistance was reported in the early 1960s. The malathion-specific resistant phenotype has now almost completely replaced the susceptible one in red flour beetle populations. In the present study, several life-history traits that could influence the fitness of the insects were compared between insecticide-susceptible and malathion-specific resistant populations of the red flour beetle. On average, egg fertility and egg-to-adult development time did not differ between susceptible and resistant populations. However, the fecundity of resistant females was greater than that of susceptible ones. Generally, differences in development time between insecticide resistant and susceptible populations are considered as having more effect on fitness than do differences in fecundity. However, the observed increased female fecundity may participate, in combination with the previously observed increased male reproductive success, to the development and the stability of malathion-specific resistance in T. castaneum. [less ▲]

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See detailAllozymic variation and genetic structure of Scottish Calluna vulgaris populations the effect of postglacial recolonization
Mahy, Grégory ULg; Ennos, Richard; Jacquemart, Anne Laure

in Heredity (1999), 82

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See detailPatterns of allozymic variation within Calluna vulgaris populations at seed bank and adult stages
Mahy, Grégory ULg; Vekemans, Xavier; Jacquemart, Anne Laure

in Heredity (1999), 82

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See detailBiogeography and taxonomy of Apodemus sylvaticus (the woodmouse) in the Tyrrhenian region: Enzymatic variations and mitochondrial DNA restriction pattern analysis
Michaux, Johan ULg; Filippucci, M. G.; Libois, Roland ULg et al

in Heredity (1996), 76(Part 3), 267-277

In the western Mediterranean area, the taxonomic status of the various forms of Apodemus sylvaticus is quite unclear. Moreover, though anthropogenic, the origins of the island populations remain unknown ... [more ▼]

In the western Mediterranean area, the taxonomic status of the various forms of Apodemus sylvaticus is quite unclear. Moreover, though anthropogenic, the origins of the island populations remain unknown in geographical terms. In order to examine the level of genetic relatedness of insular and continental woodmice, 258 animals were caught in 24 localities distributed in Belgium, France, mainland Italy, Sardinia, Corsica and Elba. Electrophoresis of 33 allozymes and mtDNA restriction fragments were performed and a UPGMA dendrogram built from the indices of genetic divergence. The dendrogram based on restriction patterns shows two main groups: 'Tyrrhenian', comprising all the Italian and Corsican animals and 'North-western', corresponding to all the other mice trapped from the Pyrenees to Belgium. Since all the Tyrrhenian mice are similar and well isolated from their relatives living on the western edge of the Alpine chain, they must share a common origin. The insular populations are consequently derived from peninsular Italian ones. From a taxonomic point of view and taking the priority rules into account, we have to invalidate A. s. clanceyi Harrison, 1948 and to consider the Tyrrhenian woodmice as belonging to A. s. milleri de Beaux, 1926, whereas the North-western ones must be referred to as the nominal subspecies. As far as the Elban woodmouse is concerned, at the moment we prefer to keep its present subspecific status because we only studied one animal. [less ▲]

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