Showing papers by "Michael F. Fay published in 2007"
TL;DR: The potential for successful cross‐species transfer appears highest in species with long generation times, mixed or outcrossing breeding systems, and where genome size in the target species is small compared to the source.
Abstract: Molecular ecologists increasingly require 'universal' genetic markers that can easily be transferred between species. The distribution of cross-species transferability of nuclear microsatellite loci is highly uneven across taxa, being greater in animals and highly variable in flowering plants. The potential for successful cross-species transfer appears highest in species with long generation times, mixed or outcrossing breeding systems, and where genome size in the target species is small compared to the source. We discuss the implications of these findings and close with an outlook on potential alternative sources of cross-species transferable markers.
437 citations
TL;DR: The results indicate a high potential for inselbergs as venues for studies of the molecular ecology and genetics of continental radiations, such as the one that gave rise to the extraordinary diversity of adaptive strategies and phenotypes seen in Bromeliaceae.
Abstract: Isolated granitic rock outcrops or ‘inselbergs’ may provide a window into the molecular ecology and genetics of continental radiations under simplified conditions, in analogy to the use of oceanic islands in studies of species radiations. Patterns of variability and gene flow in inselberg species have never been thoroughly evaluated in comparison to related taxa with more continuous distribution ranges, or to other species in the same kingdom in general. We use nuclear microsatellites to study population differentiation and gene flow in two diploid, perennial plants adapted to high-altitude neotropical inselbergs, Alcantarea imperialis and Alcantarea geniculata (Bromeliaceae). Population differentiation is pronounced in both taxa, especially in A. imperialis. Gene flow in this species is considerably lower than expected from the literature on plants in general and Bromeliaceae in particular, and too low to prevent differentiation due to drift (Nem < 1), unless selection coefficients/effect sizes of favourable alleles are great enough to maintain species cohesion. Low gene flow in A. imperialis indicates that the ability of pollinating bats to promote gene exchange between inselbergs is smaller than previously assumed. Population subdivision in one inselberg population of A. imperialis appears to be associated with the presence of two colour morphs that differ in the coloration of rosettes and bracts. Our results indicate a high potential for inselbergs as venues for studies of the molecular ecology and genetics of continental radiations, such as the one that gave rise to the extraordinary diversity of adaptive strategies and phenotypes seen in Bromeliaceae.
140 citations
TL;DR: Heterogeneous copies of the nuclear ITS region show that some putative Ophrys species arose through hybridization rather than divergent speciation, suggesting that the genus has been substantially over-divided at the species level.
126 citations
TL;DR: Several major lineages with geographical coherence, as identified in previous studies based on smaller data sets, are supported and others with either geographical or ecological correspondence are recognized for the first time.
122 citations
TL;DR: Although important advances have been made in understanding genomic responses to allopolyploidized genomes, further insights are still expected to be gained in the near future, such as the direction and nature of the diploidization process, functional relevance of gene expression alterations, molecular mechanisms that result in adaptation to different ecologies/habitats, and ecological and evolutionary implications of recurrent polyploidsization.
Abstract: Hybridization and polyploidization are now recognized as major phenomena in the evolution of plants, promoting genetic diversity, adaptive radiation and speciation. Modern molecular techniques have recently provided evidence that allopolyploidy can induce several types of genetic and epigenetic events that are of critical importance for the evolutionary success of hybrids: (1) chromosomal rearrangements within one or both parental genomes contribute toward proper meiotic pairing and isolation of the hybrid from its progenitors; (2) demethylation and activation of dormant transposable elements may trigger insertional mutagenesis and changes in local patterns of gene expression, facilitating rapid genomic reorganisation; (3) rapid and reproducible loss of low copy DNA sequence appears to result in further differentiation of homoeologous chromosomes; and (4) organ-specific up- or down-regulation of one of the duplicated genes, resulting in unequal expression or silencing one copy. All these alterations also have the potential, while stabilizing allopolyploid genomes, to produce novel expression patterns and new phenotypes, which together with increased heterozygosity and gene redundancy might confer on hybrids an elevated evolutionary potential, with effects at scales ranging from molecular to ecological. Although important advances have been made in understanding genomic responses to allopolyploidization, further insights are still expected to be gained in the near future, such as the direction and nature of the diploidization process, functional relevance of gene expression alterations, molecular mechanisms that result in adaptation to different ecologies/habitats, and ecological and evolutionary implications of recurrent polyploidization.
116 citations
TL;DR: DNA microsatellites are used to assess the feasibility of admixture mapping in hybrid zones between two members of the ‘model tree’ genus Populus and validate a modified approach of studying genotypic clines in ‘mosaic’ hybrid zones.
Abstract: Admixture in European Populus hybrid zones makes feasible the mapping of loci that contribute to reproductive isolation and trait differences
112 citations
TL;DR: Combining the degree of concerted evolution in ITS alleles (thought to reflect gene conversion) with inferred parentage provides support for a quadripartite classification of western European allopolyploid dactylorchids according to their respective parentage and relative dates of origin.
Abstract: Patterns of polyploid evolution in the taxonomically controversial Dactylorhiza incarnata/maculata groups were inferred genetically by analyzing 399 individuals from 177 localities for (1) four polymorphic plastid regions yielding aggregate haplotypes and (2) nuclear ribosomal ITS allele frequencies. Concordance between patterns observed in distributions of plastid haplotypes and ITS alleles renders ancestral polymorphism an unlikely cause of genetic variation in diploids and allopolyploids. Combining the degree of concerted evolution in ITS alleles (thought to reflect gene conversion) with inferred parentage provides support for a quadripartite classification of western European allopolyploid dactylorchids according to their respective parentage and relative dates of origin. The older allotetraploids that generally exhibit only one parental ITS allele can be divided into those derived via hybridization between the divergent complexes we now call D. incarnata s.l. and D. fuchsii (e.g., D. majalis) and those derived via hybridization between D. incarnata s.l. and D. maculata (e.g., D. elata). Similarly, the younger allotetraploids that maintain evidence of both parental ITS alleles can be divided into those derived from hybridization between D. incarnata s.l. and D. fuchsii, or perhaps in some cases a diploid species resembling D. saccifera (e.g., D. praetermissa, D. purpurella, D. traunsteineri s.l., D. baltica), and those derived from hybridization between the D. incarnata s.l. and D. maculata groups (e.g., D. occidentalis, D. sphagnicola). Older allotetraploids are inferred to have passed through glacially induced migration bottlenecks in southern Eurasia, whereas at least some younger allotetraploids now occupying northern Europe are inferred to have originated post-glacially and remain sympatric with their parents, a scenario that is largely in agreement with the morphology and ecology of these allotetraploids. ITS conversion is in most cases biased toward the maternal parent, eventually obscuring evidence of the original allopolyploidization event because plastid haplotypes also reflect the maternal contribution. Gene flow appears unexpectedly low among allotetraploids relative to diploids, whereas several mechanisms may assist the gene flow observed across ploidy levels. There is good concordance between (1) the genetically delimited species that are required to accurately represent the inferred evolutionary events and processes and (2) morphologically based species recognized in certain moderately conservative morphological classifications previously proposed for the genus. Further research will seek to improve sampling, especially in eastern Eurasia, and to develop more sensitive markers for distinguishing different lineages within (1) the remarkably genetically uniform D. incarnata group (diploids) and (2) locally differentiated populations of (in some cases unnamed) allotetraploids. (Less)
97 citations
TL;DR: It is considered that the large genome sizes of Liliaceae may have emerged passively rather than being driven primarily by selection.
Abstract: Most angiosperms possess small genomes (mode 1C = 0.6 pg, median 1C = 2.9 pg). Those with truly enormous genomes (i.e. ≥ 35 pg) are phylogenetically restricted to a few families and include Liliaceae – with species possessing some of the largest genomes so far reported for any plant as well as including species with much smaller genomes. To gain insights into when and where genome size expansion took place during the evolution of Liliaceae and the mode and tempo of this change, data for 78 species were superimposed onto a phylogenetic tree and analysed. Results suggest that genome size in Liliaceae followed a punctuated rather than gradual mode of evolution and that most of the diversification evolved recently rather than early in the evolution of the family. We consider that the large genome sizes of Liliaceae may have emerged passively rather than being driven primarily by selection.
91 citations
TL;DR: The circumscription of Coffeeae (Rubiaceae) and phylogenetic relationships within the tribe were evaluated using sequence data from four plastid regions and a morphological data set and support an enlarged circumscription for Coffeeae, containing 11 genera.
Abstract: The circumscription of Coffeeae (Rubiaceae) and phylogenetic relationships within the tribe were evaluated using sequence data from four plastid regions (trnL-F intron, trnL-F intergenic spacer [IGS], rpl16 intron, and accD-psa1 IGS) and a morphological data set. Eleven candidates for inclusion in Coffeeae were examined using plastid data, and a further three were investigated using morphology alone. Based on previous phylogenetic analysis of the subfamily Ixoroideae, nine genera representing five tribes were used as outgroups. Our results support an enlarged circumscription for Coffeeae, containing 11 genera, viz. Argocoffeopsis, Belonophora, Calycosiphonia, Coffea, Diplospora, Discospermum, Nostolachma, Psilanthus, Tricalysia, Sericanthe, and Xantonnea. The inclusion of Diplospora and Tricalysia within Coffeeae, based on published molecular data, and the inclusion of Argocoffeopsis, Belonophora, Calycosiphonia, Discospermum, and Sericanthe, based on morphological evidence, are well supported. Nostolachma is newly transferred from Gardenieae subtribe Diplosporinae to Coffeeae, and Xantonnea from Octotropideae to Coffeeae. The exclusion of Bertiera from Coffeeae and placement in tribe Bertiereae is supported on the basis of molecular and morphological data. The removal of Diplospora and all other genera from Gardenieae subtribe Diplosporinae to Coffeeae and Octotropideae renders Diplosporinae superfluous. It is proposed that Xantonneopsis be transferred to Octotropideae; Petitiocodon is tentatively placed in Gardenieae. The monophyly of seven genera is supported, but Coffea is identified as paraphyletic in relation to Psilanthus on the basis of molecular and combined molecular and morphological data.
74 citations
TL;DR: The parentage of polyploid Sorbus species in the British Isles was investigated using plastid DNA microsatellites and indicated that the hybridization events that led to the formation of species inThe S. anglica and S.latifolia groups usually did so with S. l.
60 citations
TL;DR: It was found that despite critically small population sizes there was considerable genetic diversity within populations, and that ecologically and or geographically distinct populations were genetically distinct.
TL;DR: The gene pools detected within an overall pattern of clinal variation suggest distinct episodes of gene flow, possibly correlated with past humid forest expansions, and reinforce the importance of conserving the endangered brejo forests.
TL;DR: The phylogenetic position and taxonomy of tribe Gilliesieae (Alliaceae) and Gethyum atropurpureum Phil.
Abstract: Summary The phylogenetic position and taxonomy of tribe Gilliesieae (Alliaceae) and Gethyum atropurpureum Phil. and the cultivation requirements of G. atropurpureum are discussed. A synonymy, description, colour plate and line drawing are given.
TL;DR: The distinctive Tulipa sprengeri Baker (Liliaceae) is illustrated and described, including the results of recent research at Kew that establishes its position within the genus.
Abstract: Summary The distinctive Tulipa sprengeri Baker (Liliaceae) is illustrated and described. Its history, classification and cultivation requirements are discussed, including the results of recent research at Kew that establishes its position within the genus.