| 1. |
- Plomion, Christophe, et al.
(författare)
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Oak genome reveals facets of long lifespan
- 2018
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Ingår i: NATURE PLANTS. - : Springer Science and Business Media LLC. - 2055-026X .- 2055-0278. ; 4:7, s. 440-452
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Tidskriftsartikel (refereegranskat)abstract
- Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes' but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times(2). With 450 species spread throughout Asia, Europe and America(3), oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associated with such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical(4) and modelling(5) approaches have shown that intra-organismal genetic heterogeneity can be selected for(6) and provides direct fitness benefits in the arms race with short-lived pests and pathogens through a patchwork of intra-organismal phenotypes(7). However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.
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| 2. |
- Fuchs, Jérôme, et al.
(författare)
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A multi-locus phylogeny suggests an ancient hybridization event between Campephilus and melanerpine woodpeckers (Aves : Picidae).
- 2013
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 67:3, s. 578-88
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Tidskriftsartikel (refereegranskat)abstract
- The ever increasing number of analysed loci in phylogenetics has not only allowed resolution of some parts of the Tree of Life but has also highlighted parts of the tree where incongruent signals among loci were detected. Previous molecular studies suggested conflicting relationships for the New World genus Campephilus, being either associated to the Megapicini or Dendropocini. Yet, the limited number of analysed loci and the use of the concatenation approach to reconstruct the phylogeny prevented the disentanglement of lineage sorting and introgression as causal explanation of this topological conflict. We sequenced four mitochondrial, nine autosomal and three Z-linked loci and used a method that incorporates population level processes into the phylogenetic framework to understand which process (lineage sorting of genetic polymorphism or hybridization/introgression) best explains this conflict. Our analyses revealed that the autosomal FGB intron-7 and to a lesser extent the Z-linked loci have a different phylogenetic history from the mitochondrial loci and some other nuclear loci we analysed. We suggest that this conflicting pattern is the result of introgression consecutive to a hybridization event at the time when members of the Campephilus and melanerpine (Melanerpes and Sphyrapicus) lineages colonized the New World. The case of Campephilus highlights that the mitochondrial genome does not always carry the 'wrong' phylogenetic signal after a past hybridization event. Indeed, we here emphasise that the signature of such event can also be detected in the nuclear genome. With the ongoing increase in the number of loci analysed in phylogenetic studies, it is very likely that further cases will be discovered. Our current results indicate that (1) the genus Campephilus is related to the Asian genera Blythipicus, Chrysocolaptes and Reinwardtipicus, in accordance with morphological data and (2) that the nuclear genome of Campephilus is likely the mixture of two unrelated lineages. Yet, further work with a denser sampling of loci is necessary to evaluate the extant of the Sphyrapicus/Melanerpes lineage nuclear genome that introgressed into the Campephilus genome.
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| 3. |
- Fuchs, Jérôme, et al.
(författare)
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Molecular support for a rapid cladogenesis of the woodpecker clade Malarpicini, with further insights into the genus Picus (Piciformes : Picinae).
- 2008
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 48:1, s. 34-46
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Tidskriftsartikel (refereegranskat)abstract
- Previous studies have suggested that the woodpecker genus Picus (Aves: Picidae) may not be monophyletic. In order to evaluate this hypothesis, we analyzed DNA sequences from all but two species of Picus, as well as from representatives of all genera in the tribe Malarpicini, within which Picus is nested. We sequenced seven loci (four autosomal, one Z-linked and two mitochondrial) with different evolutionary dynamics. The species currently placed in Picus fall into two subclades that may not form a monophyletic assemblage. Consequently, we propose to place miniaceus Pennant 1769, flavinucha Gould 1834 and mentalis Temminck 1825 in the genus Chrysophlegma Gould, 1850, while the remaining species are retained in Picus. The inclusion in our study of representatives of all genera included in the tribe Malarpicini, a group of woodpeckers which has proven difficult to resolve in several previous molecular studies, also allowed us to determine the earliest divergences within this clade. The results suggest that the low level of basal resolution in Malarpicini is attributable to multiple cladogenetic events in a short period of time rather than insufficient character sampling. This conclusion is supported by the observation of nucleotide insertion-deletions that support mutually exclusive phylogenetic hypotheses in different gene trees. We attribute this pattern of incongruent indels, together with short internodes in the tree, to incomplete lineage sorting.
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| 4. |
- Fuchs, Jerome, et al.
(författare)
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The complex phylogeography of the Indo-Malayan Alophoixus bulbuls with the description of a putativenew ring species complex
- 2015
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 24, s. 5460-5474
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Tidskriftsartikel (refereegranskat)abstract
- The Indo-Malayan bioregion has provided some of the most spectacular discoveries of new vertebrate species (e.g. saola, khanyou, bare-faced bulbul) over the last 25 years. Yet, very little is known about the processes that led to the current biodiversity in this region. We reconstructed the phylogeographic history of a group of closely related passerines, the Alophoixus bulbuls. These birds are continuously distributed in Indo-Malaya around the Thailand lowlands such that their distribution resembles a ring. Our analyses revealed a single colonization event of the mainland from Sundaland with sequential divergence of taxa from southwest to northeast characterized by significant gene flow between parapatric taxa, and reduced or ancient gene flow involving the two taxa at the extremities of the ring. We detected evidence of population expansion in two subspecies, including one that was involved in the closing of the ring. Hence, our analyses indicate that the diversification pattern of Alophoixus bulbuls fits a ring species model driven by geographic isolation. To our knowledge, the Alophoixus bulbuls represent the first case of a putative broken ring species complex in Indo-Malaya. We also discuss the implications of our results on our understanding of the biogeography in Indo-Malaya.
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| 5. |
- Normand, Philippe, et al.
(författare)
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Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography.
- 2007
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Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051. ; 17:1, s. 7-15
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Tidskriftsartikel (refereegranskat)abstract
- Soil bacteria that also form mutualistic symbioses in plants encounter two major levels of selection. One occurs during adaptation to and survival in soil, and the other occurs in concert with host plant speciation and adaptation. Actinobacteria from the genus Frankia are facultative symbionts that form N2-fixing root nodules on diverse and globally distributed angiosperms in the "actinorhizal" symbioses. Three closely related clades of Frankia sp. strains are recognized; members of each clade infect a subset of plants from among eight angiosperm families. We sequenced the genomes from three strains; their sizes varied from 5.43 Mbp for a narrow host range strain (Frankia sp. strain HFPCcI3) to 7.50 Mbp for a medium host range strain (Frankia alni strain ACN14a) to 9.04 Mbp for a broad host range strain (Frankia sp. strain EAN1pec.) This size divergence is the largest yet reported for such closely related soil bacteria (97.8%–98.9% identity of 16S rRNA genes). The extent of gene deletion, duplication, and acquisition is in concert with the biogeographic history of the symbioses and host plant speciation. Host plant isolation favored genome contraction, whereas host plant diversification favored genome expansion. The results support the idea that major genome expansions as well as reductions can occur in facultative symbiotic soil bacteria as they respond to new environments in the context of their symbioses.
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| 6. |
- Razafimandimbison, Sylvain G., et al.
(författare)
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Implications of a molecular phylogenetic study of the Malagasy genus Cedrelopsis and its relatives (Ptaeroxylaceae)
- 2010
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 57:1, s. 258-265
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Tidskriftsartikel (refereegranskat)abstract
- Ptaeroxylaceae is an Afro-Malagasy family containing three genera, Bottegoa. Cedrelopsis, and Ptaeroxylon. Although the family is morphologically well delimited, it is currently considered part of the subfamily Spathelioideae in a broadly circumscribed orange family (Rutaceae). The Malagasy Cedrelopsis has traditionally been associated with different families of the order Sapindales and its phylogenetic placement in Rutaceae sensu lato has yet to be tested with molecular data. The present molecular phylogenetic study reaffirms the monophyly of Ptaeroxylaceae and its placement in Spathelioideae. Therefore, molecules and morphology support close affinities between Bottegoa, Cedrelopsis, and Ptaeroxylon and also their current generic circumscriptions. We report a case of an evolutionary change from one-seeded to two-seeded carpels within the Harrisonia-Cneorum-Ptaeroxylaceae clade of Spathelioideae. Finally, the sister-group relationship between the African Bottegoa and the Afro-Malagasy Ptaeroxylon-Cedrelopsis clade suggests an African origin of Cedrelopsis.
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