Gene genealogies and population variation in plants (original) (raw)
Related papers
The genic view of plant speciation: recent progress and emerging questions
Philosophical Transactions of the Royal Society B: Biological Sciences, 2008
The genic view of the process of speciation is based on the notion that species isolation may be achieved by a modest number of genes. Although great strides have been made to characterize 'speciation genes' in some groups of animals, little is known about the nature of genic barriers to gene flow in plants. We review recent progress in the characterization of genic species barriers in plants with a focus on five 'model' genera: Mimulus (monkey flowers); Iris (irises); Helianthus (sunflowers); Silene (campions); and Populus (poplars, aspens, cottonwoods). The study species in all five genera are diploid in terms of meiotic behaviour, and chromosomal rearrangements are assumed to play a minor role in species isolation, with the exception of Helianthus for which data on the relative roles of chromosomal and genic isolation factors are available. Our review identifies the following key topics as being of special interest for future research: the role of intraspecific variation in speciation; the detection of balancing versus directional selection in speciation genetic studies; the timing of fixation of alleles of major versus minor effects during plant speciation; the likelihood of adaptive trait introgression; and the identification and characterization of speciation genes and speciation gene networks.
Plant phylogeography based on organelle genes: an introduction
Phylogeography of Southern European Refugia, 2007
Plants have unique biological attributes of great interest to researchers investigating population dynamics. Yet, until recently, organelle DNA had been seldom utilized for phylogeographic studies in plants. While cpDNA variation has been used extensively to construct interspecific phylogenies, many researchers have considered that the relatively low levels of intraspecific variation revealed by early studies of plant organelle DNA render these genomes of little use for intraspecific studies. In this review we introduce the field of plant phylogeography based on organelle polymorphisms by providing a detailed discussion of the processes underlying this variation. Progress in molecular organelle genetics has provided insights into the structure, variation, inheritance, vegetative segregation and recombination of organelle genomes. While some of these features (e.g. low substitution rates) may complicate phylogeographic studies, others (e.g. presence of two genomes and frequency of atypical modes of transmission) offer unique opportunities, many of which are virtually unexplored. , 23 -Allen JF, Raven JA (1996) Free-radical induced mutation vs redox regulation: costs and benefits of genes in organelles. Journal of Molecular Evolution 42, 482-492. Amoatey HM, Tilney-Bassett RAE (1994) A test of the complementary gene model for the control of bi-parental plastid inheritance in zonal pelargoniums. Heredity 72, 69-77. Andersson H (1999) Female and hermaphrodite flowers on a chimeric gynomonoecious Silene vulgaris plant produce offspring with different genders: a case of heteroplasmic sex determination? Journal of Heredity 90, 563-565. Asmussen A, Arnold J (1991) The effects of admixture and population subdivision on cytonuclear disequilibria. Theoretical Population Biology 39, 273-300. Atchison BA, Whitfeld PR, Bottomley W (1976) Comparison of chloroplast DNAs by specific fragmentation with EcoR1 endonuclease. Molecular and General Genetics 148, 263-269. Avise JC (2000) Phylogeography: The History and Formation of Species. Harvard University Press, Cambridge. Avise JC, Giblin-Davidson C, Laerm J, Patton JC, Lansman RA (1979) Mitochondrial DNA clones and matriarchal phylogeny within and among geographic populations of the pocket gopher, Geomys pinetis. Proceedings of the National Academy of Sciences, USA 76, 6694-6698. Avise JC, Shapira JF, Daniel SW, Aquadro CF, Lansman RA (1983) Mitochondrial-DNA differentiation during the speciation process in Peromyscus. Molecular Biology and Evolution 1, 38-56. Avise JC, Arnold J, Ball RM, Bermingham E, Lamb T, Neigel JE, Reeb CA, Saunders NC (1987) Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annual Review of Ecology and Systematics 18, 489-522. Bacilieri R, Ducousso A, Petit RJ, Kremer A (1996) Mating system and asymmetric hybridization in a mixed stand of European oaks. Evolution 50, 900-908. Backert S, Lurz R, Börner T (1996) Electron microscopic investigation of mitochondrial DNA from Chenopodium album (L.) Current Genetics 29, 427-436. Backert S, Lurz R, Oyarzabal OA, Börner T (1997) High content, size and distribution of single-stranded DNA in the mitochondria of Chenopodium album (L.). Plant Molecular Biology 33, 1037-1050. Baker HG (1959) The contribution of autecological and genecological studies to our knowledge of the past migration of plants. American Naturalist 93, 255-271. Balfourier F, Imbert C, Charmet G (2000) Evidence for phylogeographic structure in Lolium species related to the spread of agriculture in Europe: a cpDNA study. Theoretical and Applied Genetics 101, 131-138. Banks JA, Birky, CW Jr (1985) Chloroplast DNA diversity is low in a wild plant, Lupinus texensis.
Inferring plant evolutionary history from molecular data
New Zealand Journal of Botany, 1993
The rapid development of molecular methods during the 1980s has had a profound effect on the study of plant evolution. Molecular data have accumulated very rapidly, and this abundance of data poses new problems for data analysis. We illustrate three problem areas that arise in plant evolutionary inference. The first problem concerns the use of molecular data to analyse closely related plant species linked through reticulate evolution. The second problem arises from our ability to sample DNA sequences from alleles of a single genetic locus within plant species. We show how cumulative information on selection and random genetic drift can be extracted from such data. The third problem area concerns the limitations of current algorithms for phylogenetic inference when confronted with large sets of DNA sequence data. Based on a consideration of these problem areas, we conclude that: (1) asymmetric transmission of cpDNA markers is useful in resolving the parentage of hybrid plant taxa; (2) simple clustering algorithms can provide B93022 useful information on cultivar or variety relationships, despite intervarietal hybridisation, if genetic similarities are averaged over sufficient loci; (3) samples of complete DNA sequence data from plant nuclear genes can provide a new dimension of information on historical effective population sizes and on the mechanisms that generate allelic diversity; (4) analyses of the chloroplast gene rbcL, sampled from across the monocotyledon class, reveal large variation in relative rates of nucleotide substitution-these variations, in turn, have important consequences for phylogeny estimation algorithms; and (5) the combined use of algorithms like parsimony and maximum likelihood may represent a more efficient approach to the phylogenetic analysis of very large (>100) sets of DNA sequences.
Genesis of phenotypic and genotypic diversity in land plants: the present as the key to the past
Systematics and Biodiversity, 2003
The evolutionary history of vascular plants is reviewed by extrapolation back through time from a wide range of data recently derived from the present flora, using as the central theme evolutionary inferences gained from phylogenies reconstructed as cladograms. Any region of the genome can be used to infer relationships, but only a combination of knowledge of morphology and the developmental genes broader systematic perspective -one that better encompasses the remarkable diversity of evolutionary processes that together generated the present diversity of life.
Molecular Population Genetics and the Search for Adaptive Evolution In Plants
Molecular Biology and Evolution, 2004
The first papers on plant molecular population genetics were published approximately 10 years ago. Since that time, well over 50 additional studies of plant nucleotide polymorphism have been published, and many of these studies focused on detecting the signature of balancing or positive selection at a locus. In this review, we discuss some of the theoretical and statistical issues surrounding
Contributions of domesticated plant studies to our understanding of plant evolution
Annals of botany, 2005
Plant evolutionary theory has been greatly enriched by studies on crop species. Over the last century, important information has been generated on many aspects of population biology, speciation and polyploid genetics. Searches for quantitative trait loci (QTL) in crop species have uncovered numerous blocks of genes that have dramatic effects on adaptation, particularly during the domestication process. Many of these QTL have epistatic and pleiotropic effects making rapid evolutionary change possible. Most of the pioneering work on the molecular basis of self-incompatibility has been conducted on crop species, along with the sequencing of the phytopathogenic resistance genes (R genes) responsible for the 'gene-to-gene' relations of coevolution observed in host-pathogen relationships. Some of the better examples of co-adaptation and early acting inbreeding depression have also been elucidated in crops. Crop-wild progenitor interactions have provided rich opportunities to study...
Using Molecular Marker Order to compare Genetic Structure in Plant Populations undergoing Selection
Many ecological studies compare the genetic structure of populations undergoing natural or artificial selection across different environments. High-throughput molecular markers are now commonly used for these comparisons and provide information on the adaptation of the populations to their environments. The genetic structure reflects the history of selection, mutation, migration, and the reproductive breeding system of the populations in their environments. This can be investigated by comparing the ordering of markers obtained from the population with that provided by a recombination or physical map. In populations undergoing selection many genes (markers) have low or zero frequency and commonly used disequilibrium coefficients become unstable under these conditions. A method is presented for ordering bi-allelic markers for populations of self-fertilizing plant species which consist of mixtures of related homozygous genotypes. This provides stable pair-wise marker similarity measures even when marker frequencies are low, identification of marker combinations that reflect phenomena that cause differentiation (such as selection and migration), and genetic information on the adaptation of the populations to the environments. The method is illustrated using data from a plant breeding program and inferences are made about accumulation of desirable genes (such as for disease resistance). Keywords: plant breeding and natural populations, haplotype disequilibrium.
Biological Journal of The Linnean Society, 2012
In the last decade a number of studies has illustrated quite different phylogeographical patterns amongst plants with a northern present-day geographical distribution, spanning the entire circumboreal region and/or circumarctic region and southern mountains. These works, employing several marker systems, have brought to light the complex evolutionary histories of this group. Here I focus on one circumboreal plant species, Chamaedaphne calyculata (leatherleaf), to unravel its phylogeographical history and patterns of genetic diversity across its geographical range. A survey of 29 populations with combined analyses of chloroplast DNA (cpDNA), internal transcribed spacer (ITS) and AFLP markers revealed structuring into two groups: Eurasian/north-western North American, and northeastern North American. The present geographical distribution of C. calyculata has resulted from colonization from two putative refugial areas: east Beringia and southeastern North America. The variation of chloroplast DNA (cpDNA) and ITS sequences strongly indicated that the evolutionary histories of the Eurasian/ northwestern North American and the northeastern North American populations were independent of each other because of a geographical disjunction in the distribution area and ice-sheet history between northeastern and northwestern North America. Mismatch analysis using ITS confirmed that the present-day population structure is the result of rapid expansion, probably since the last glacial maximum. The AFLP data revealed low genetic diversity of C. calyculata (P = 19.5%, H = 0.085) over the whole geographical range, and there was no evidence of loss of genetic diversity within populations in the continuous range, either at the margins or in formerly glaciated and nonglaciated regions.