Megabase-scale inversion polymorphism in the wild ancestor of maize

Chromosomal inversions are thought to play a special role in local adaptation, through dramatic suppression of recombination, which favors the maintenance of locally adapted alleles. However, relatively few inversions have been characterized in population genomic data. On the basis of single-nucleotide polymorphism (SNP) genotyping across a large panel of Zea mays, we have identified an ～50-Mb region on the short arm of chromosome 1 where patterns of polymorphism are highly consistent with a polymorphic paracentric inversion that captures >700 genes. Comparison to other taxa in Zea and Tripsacum suggests that the derived, inverted state is present only in the wild Z. mays subspecies parviglumis and mexicana and is completely absent in domesticated maize. Patterns of polymorphism suggest that the inversion is ancient and geographically widespread in parviglumis. Cytological screens find little evidence for inversion loops, suggesting that inversion heterozygotes may suffer few crossover-induced fitness consequences. The inversion polymorphism shows evidence of adaptive evolution, including a strong altitudinal cline, a statistical association with environmental variables and phenotypic traits, and a skewed haplotype frequency spectrum for inverted alleles.     

Search for the wild ancestor of buckwheat III. The wild ancestor of cultivated common buckwheat, and of tatary buckwheat

By surveying wild Fagopyrum species and their distribution in southern China and the Himalayan hills, I arrived at the conclusion that the newly discovered subspecies F. esculentum ssp. ancestralis Ohnishi is the wild ancestor of cultivated common buckwheat, while previously known wild tatary buckwheat,F. tataricum ssp. potanini Batalin is the wild ancestor of tatary buckwheat. Their original birthplace is revealed to be northwestern corner of Yunnan province for common buckwheat judging from the distribution of wild ancestor, and to be the northwest part of Sichuan province for tatary buckwheat judging from allozyme variability in wild tatary buckwheat. F. cymosum is not the ancestor of cultivated buckwheat; it is only distantly related to cultivated buckwheat, in morphology, isozymes and cpDNA. Several genetic, ecological and taxonomic categories which should be taken into consideration in examining the origin of buckwheat were discussed. Key Words: Fagopyrum esculentum ssp. ancestralis; Fagopyrum tataricum ssp. potanini; southern China theory of origin of buckwheat. Contribution from Plant Germ-Plasm Institute, Faculty of Agriculture, Kyoto University. No. 78.     

Population genetics of foxtail millet and its wild ancestor

Background

The size of the vertebrate eye and the retina is likely to be controlled at several stages of embryogenesis by mechanisms that affect cell cycle length as well as cell survival. A mutation in the zebrafish out of sight (out) locus results in a particularly severe reduction of eye size. The goal of this study is to characterize the out ^m233 mutant, and to determine whether mutations in the out gene cause microphthalmia in humans.

Results

In this study, we show that the severe reduction of eye size in the out ^m233 mutant is caused by a mutation in the zebrafish gdf6a gene. Despite the small eye size, the overall retinal architecture appears largely intact, and immunohistochemical studies confirm that all major cell types are present in out ^m233 retinae. Subtle cell fate and patterning changes are present predominantly in amacrine interneurons. Acridine orange and TUNEL staining reveal that the levels of apoptosis are abnormally high in out ^m233 mutant eyes during early neurogenesis. Mutation analysis of the GDF6 gene in 200 patients with microphthalmia revealed amino acid substitutions in four of them. In two patients additional skeletal defects were observed.

Conclusions

This study confirms the essential role of GDF6 in the regulation of vertebrate eye size. The reduced eye size in the zebrafish out ^m233 mutant is likely to be caused by a transient wave of apoptosis at the onset of neurogenesis. Amino acid substitutions in GDF6 were detected in 4 (2%) of 200 patients with microphthalmia. In two patients different skeletal defects were also observed, suggesting pleitrophic effects of GDF6 variants. Parents carrying these variants are asymptomatic, suggesting that GDF6 sequence alterations are likely to contribute to the phenotype, but are not the sole cause of the disease. Variable expressivity and penetrance suggest a complex non-Mendelian inheritance pattern where other genetic factors may influence the outcome of the phenotype.     

Molecular evidence for the origin of plastids from a cyanobacterium-like ancestor

Summary The origin of plastids by either a single or multiple endosymbiotic event(s) and the nature of the progenitor(s) of plastids have been the subjects of much controversy. The sequence of the small subunit rRNA (Ssu rRNA) from the plastid of the chlorophyllc-containing algaCryptomonas is presented, allowing for the first time a comparison of this molecule from all of the major land plant and algal lineages. Using a distance matrix method, the phylogenetic relationships among representatives of these lineages have been inferred and the results indicate a common origin of plastids from a cyanobacterium-like ancestor. Within the plastid line of descent, there is a deep dichotomy between the chlorophyte/land plant lineage and the rhodophyte/chromophyte lineage, with the cyanelle ofCyanophora paradoxa forming the deepest branch in the latter group. Interestingly,Euglena gracilis and its colorless relativeAstasia longa are more related to the chromophytes than to the chlorophytes, raising once again the question of the origin of the euglenoid plastids.     

In search of the last common ancestor: new findings on wild chimpanzees

Modelling the behaviour of extinct hominins is essential in order to devise useful hypotheses of our species'' evolutionary origins for testing in the palaeontological and archaeological records. One approach is to model the last common ancestor (LCA) of living apes and humans, based on current ethological and ecological knowledge of our closest living relations. Such referential modelling is based on rigorous, ongoing field studies of the chimpanzee (Pan troglodytes) and the bonobo (Pan paniscus). This paper reviews recent findings from nature, focusing on those with direct implications for hominin evolution, e.g. apes, using elementary technology to access basic resources such as food and water, or sheltering in caves or bathing as thermoregulatory adaptations. I give preference to studies that directly address key issues, such as whether stone artefacts are detectible before the Oldowan, based on the percussive technology of hammer and anvil use by living apes. Detailed comparative studies of chimpanzees living in varied habitats, from rainforest to savannah, reveal that some behavioural patterns are universal (e.g. shelter construction), while others show marked (e.g. extractive foraging) or nuanced (e.g. courtship) cross-populational variation. These findings allow us to distinguish between retained, primitive traits of the LCA versus derived ones in the human lineage.     

Phylogeography and origin of Indian domestic goats

The Indian subcontinent contains 20 well-characterized goat breeds, which vary in their genetic potential for the production of milk, meat, and fibre; disease resistance; heat tolerance; and fecundity. Indian goats make up 20% of the world's goat population, but there has been no extensive study of these economically important animals. Therefore, we have undertaken the present investigation of 363 goats belonging to 10 different breeds from different geographic regions of India using mtDNA sequence data from the HVRI region. We find evidence for population structure and novel lineages in Indian goats and cannot reconcile the genetic diversity found within the major lineage with domestication starting 10,000 years ago from a single mtDNA ancestor. Thus, we propose a more complex origin for domestic goats.     

Validation of yield-enhancing quantitative trait loci from a low-yielding wild ancestor of rice

A set of introgression lines (ILs) containing chromosomal segments from O. rufipogon (IRGC 105491), a wild relative of O. sativa, in the genetic background of an elite US variety, cv. Jefferson, was developed to confirm the performance of six yield-enhancing quantitative trait loci (QTL). Fifty BC3F3 ILs containing homozygous O. rufipogon introgressions at each of the target QTL regions, and as few background introgressions as possible, were selected for evaluation of yield and 14 yield-related traits in field studies conducted over 2 years at four locations in the southern USA. Performance of the IL families was compared with three commercial inbreds and one hybrid variety. IL families carrying introgressions from the low-yielding wild parent at the QTL yld2.1 and yld6.1 yielded 27.7 and 26.1 % more than Jefferson, respectively. IL yld2A, which possesses yld2.1, also performed well under alternate wetting and drying conditions in two field locations. After the first year of field trials, 10 of the top-performing BC3F4 families, representing five of the QTL targets, were genotyped with an Illumina 1,536 assay to define the size and location of the wild introgressions. BC3F4 families with the fewest background introgressions were backcrossed to Jefferson and selfed. The resulting BC4F2 families were screened with targeted single nucleotide polymorphism assays to identify individuals carrying homozygous introgressions across the target QTL. Twelve ILs, representing each of the six QTL targets, have been submitted to the Genetic Stocks Oryza Collection for studies on transgressive variation and as interspecific pre-breeding lines.     

Hybrid origin of Audubon's warbler

Several animal species have recently been shown to have hybrid origins, but no avian examples have been documented with molecular evidence. We investigate whether the Audubon’s warbler (Dendroica auduboni), one of four visually distinct species in the yellow‐rumped warbler complex, has originated through hybridization between two other species in this group, the myrtle warbler (D. coronata) and black‐fronted warbler (D. nigrifrons). Analysis of nuclear amplified fragment length polymorphism (AFLP) and sequence markers shows that Audubon’s warblers are genetically intermediate and carry a mixture of alleles otherwise found only in one or the other of their putative parental species. Audubon’s warblers also carry two deeply divergent mitochondrial DNA lineages, each shared with only one putative parental form. Broad clines between Audubon’s and black‐fronted warblers in AFLP markers call into question the validity of these two forms as full species; nevertheless, our results suggest that the Audubon’s warbler probably originated through hybridization between two long‐diverged species. It is likely that more cases of avian species of hybrid origin will be revealed by surveys of variation in nuclear DNA and other traits.     

Poinsettia's wild ancestor in the Mexican dry tropics: Historical, genetic, and environmental evidence

? Premise of the study: The poinsettia (Euphorbia pulcherrima) is the world's most economically important potted plant, but despite its preeminence it is not clear which wild populations are ancestral to the varieties cultivated around the world. Tradition holds that the U.S. envoy to Mexico J. R. Poinsett collected the progenitors of the over 300 varieties in global cultivation on an 1828 excursion to northern Guerrero State, Mexico. It is unknown whether the contemporary cultivars are descended from plants from Guerrero or whether germplasm from other parts of poinsettia's 2000 km long distribution entered into cultivation during the nearly 200 yr of subsequent poinsettia horticulture. ? Methods: To identify the wild populations that likely gave rise to the cultivars and test this historical account, we sequenced plastid and nuclear DNA regions and modeled poinsettia's potential distribution. ? Key results: The combination of nuclear and plastid haplotypes characterizing cultivars was found only in northern Guerrero. Distribution modeling indicated that suitable habitat conditions for wild poinsettias are present in this area, consistent with their likely wild status. ? Conclusions: Our data pinpoint the area of northern Guerrero as the cultivated poinsettia's probable ancestral region, congruent with the traditional account attributing the original collections to Poinsett. Abundant genetic variation likely offers raw material for improving the many shortcomings of cultivars, including vulnerability to cold, stem breakage, and pathogens such as Pythium and Phytophthora. However, genetic differences between populations make conservation of all of poinsettia's diversity difficult.     

Fine scale genetic structure in the wild ancestor of maize (Zea mays ssp. parviglumis)

Analysis of fine scale genetic structure in continuous populations of outcrossing plant species has traditionally been limited by the availability of sufficient markers. We used a set of 468 SNPs to characterize fine‐scale genetic structure within and between two dense stands of the wild ancestor of maize, teosinte (Zea mays ssp. parviglumis). Our analyses confirmed that teosinte is highly outcrossing and showed little population structure over short distances. We found that the two populations were clearly genetically differentiated, although the actual level of differentiation was low. Spatial autocorrelation of relatedness was observed within both sites but was somewhat stronger in one of the populations. Using principal component analysis, we found evidence for significant local differentiation in the population with stronger spatial autocorrelation. This differentiation was associated with pronounced shifts in the first two principal components along the field. These shifts corresponded to changes in allele frequencies, potentially due to local topographical features. There was little evidence for selection at individual loci as a contributing factor to differentiation. Our results demonstrate that significant local differentiation may, but need not, co‐occur with spatial autocorrelation of relatedness. The present study represents one of the most detailed analyses of local genetic structure to date and provides a benchmark for future studies dealing with fine scale patterns of genetic diversity in natural plant populations.     

Genes of cyanobacterial origin in plant nuclear genomes point to a heterocyst-forming plastid ancestor

Plastids are descended from a cyanobacterial symbiosis which occurred over 1.2 billion years ago. During the course of endosymbiosis, most genes were lost from the cyanobacterium's genome and many were relocated to the host nucleus through endosymbiotic gene transfer (EGT). The issue of how many genes were acquired through EGT in different plant lineages is unresolved. Here, we report the genome-wide frequency of gene acquisitions from cyanobacteria in 4 photosynthetic eukaryotes--Arabidopsis, rice, Chlamydomonas, and the red alga Cyanidioschyzon--by comparison of the 83,138 proteins encoded in their genomes with 851,607 proteins encoded in 9 sequenced cyanobacterial genomes, 215 other reference prokaryotic genomes, and 13 reference eukaryotic genomes. The analyses entail 11,569 phylogenies inferred with both maximum likelihood and Neighbor-Joining approaches. Because each phylogenetic result is dependent not only upon the reconstruction method but also upon the site patterns in the underlying alignment, we investigated how the reliability of site pattern generation via alignment affects our results: if the site patterns in an alignment differ depending upon the order in which amino acids are introduced into multiple sequence alignment--N- to C-terminal versus C- to N-terminal--then the phylogenetic result is likely to be artifactual. Excluding unreliable alignments by this means, we obtain a conservative estimate, wherein about 14% of the proteins examined in each plant genome indicate a cyanobacterial origin for the corresponding nuclear gene, with higher proportions (17-25%) observed among the more reliable alignments. The identification of cyanobacterial genes in plant genomes affords access to an important question: from which type of cyanobacterium did the ancestor of plastids arise? Among the 9 cyanobacterial genomes sampled, Nostoc sp. PCC7120 and Anabaena variabilis ATCC29143 were found to harbor collections of genes which are-in terms of presence/absence and sequence similarity-more like those possessed by the plastid ancestor than those of the other 7 cyanobacterial genomes sampled here. This suggests that the ancestor of plastids might have been an organism more similar to filamentous, heterocyst-forming (nitrogen-fixing) representatives of section IV recognized in Stanier's cyanobacterial classification. Members of section IV are very common partners in contemporary symbiotic associations involving endosymbiotic cyanobacteria, which generally provide nitrogen to their host, consistent with suggestions that fixed nitrogen supplied by the endosymbiont might have played an important role during the origin of plastids.     

The non-monophyletic origin of the tRNA molecule and the origin of genes only after the evolutionary stage of the last universal common ancestor (LUCA)

A model has been proposed suggesting that the tRNA molecule must have originated by direct duplication of an RNA hairpin structure [Di Giulio, M., 1992. On the origin of the transfer RNA molecule. J. Theor. Biol. 159, 199-214]. A non-monophyletic origin of this molecule has also been theorized [Di Giulio, M., 1999. The non-monophyletic origin of tRNA molecule. J. Theor. Biol. 197, 403-414]. In other words, the tRNA genes evolved only after the evolutionary stage of the last universal common ancestor (LUCA) through the assembly of two minigenes codifying for different RNA hairpin structures, which is what the exon theory of genes suggests when it is applied to the model of tRNA origin. Recent observations strongly corroborate this theorization because it has been found that some tRNA genes are completely separate in two minigenes codifying for the 5' and 3' halves of this molecule [Randau, L., et al., 2005a. Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5'- and 3'-halves. Nature 433, 537-541]. In this paper it is shown that these tRNA genes codifying for the 5' and 3' halves of this molecule are the ancestral form from which the tRNA genes continuously codifying for the complete tRNA molecule are thought to have evolved. This, together with the very existence of completely separate tRNA genes codifying for their 5' and 3' halves, proves a non-monophyletic origin for tRNA genes, as a monophyletic origin would exclude the existence of these genes which have, on the contrary, been observed. Here the polyphyletic origin of genes codifying for proteins is also suggested and discussed. Moreover, a hypothesis is advanced to suggest that the LUCA might have had a fragmented genome made up of RNA and the possibility that 'Paleokaryotes' may exist is outlined. Finally, the characteristic of the indivisibility of homology that these polyphyletic origins seem to remove at the sequence level is discussed.     

Tracking ancient polyploids: a retroposon insertion reveals an extinct diploid ancestor in the polyploid origin of belladonna

Polyploidy is a prominent process in plant evolution and adaptation, but molecular phylogenetic studies of polyploids based on DNA sequences have often been confounded by their complex gene and genome histories. We report here a retroposon insertion in the nuclear gene granule-bound starch synthase I (GBSSI or "waxy") that clearly reveals the ancient hybrid history of the medically important polyploid species belladonna (Atropa belladonna) and resolves the controversy over the taxonomic group to which it belongs, the tribe Hyoscyameae (Solanaceae). Our inferences based on the pattern of presence or absence of the retroposon insertion are corroborated by phylogenetic analyses of the GBSSI gene sequences. This case may suggest that retroposons are promising molecular markers to study polyploid evolution.     

Beta-2 microglobulin types in mice of wild origin

To determine the distribution of beta-2 microglobulin (B2m) alleles in wild mice we have typed mice derived from natural populations in Europe, North Africa, South America, and East Asia. Mus musculus domesticus mice from Germany, France, Italy, and Peru were all B2m ^a as were most from the United Kingdom. M.m. musculus mice from Denmark and Czechoslovakia, several stocks of M.m. molossinus from Japan, and M.m. castaneus from China, Thailand, and the Philippines were of B2m ^b type. This is consistent with the notion that C57BL/6 may have obtained some of its genes, including B2m, from Eastern mice. A BgII restriction site characteristic of B2m ^b was also found in mice from Czechoslovakia and Japan, confirming that B2m ^b is a naturally occurring allele of B2m. A new type of ₂m ( ₂m^w1) was found in four stocks of M. spretus from Portugal, Spain, and Morocco. This molecule differs in apparent size and charge from the a and b types. ₂m^w2 was found together with ₂ ma in one stock of M.m. domesticus (brevirostris) from Morocco. ₂m^w3 and ₂m^w4 were found in a few M. m. bactrianus from Pakistan. In all cases tested, these new ₂m molecules associate with class I histocompatibility antigens.Abbreviations used in this paper ₂m beta-2 microglobulin - B2m gene for beta-2 microglobulin - IEF isoelectric focusing - SDS-PAGE polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate - MHC major histocompatibility complex - T. E. Tris-EDTA buffer     

Single, ancient origin of a plastid metabolite translocator family in Plantae from an endomembrane-derived ancestor

Phylogenetic analyses show the single origin of a plastid metabolite translocator family in the Plantae from a gene encoding an existing endomembrane-derived protein. Red algal secondary endosymbiosis has spread a translocator gene into the ancestor of the "chromalveolate" protists, where it has diversified into a novel clade of proteins.     

Sexual size dimorphism in domestic goats,sheep, and their wild relatives

Sexual size dimorphism (SSD) is a widespread phenomenon in different animal taxa, including the subfamily of goats and sheep (Caprinae), which belongs to the most dimorphic mammalian groups. Rensch's rule describes the pattern of SSD, claiming that larger species generally exhibits higher male to female body size ratio. Agreement with Rensch's rule is manifested by slope of the allometric relationship between male and female body size exceeding one. To test this rule, we analysed the data available in the literature on adult body mass of males and females in domestic goat and sheep breeds (169 and 303, respectively) and 37 wild species/subspecies of the subfamily Caprinae. According to the current phylogenetical hypotheses, there are six distinct monophyletic groups with different levels of SSD (expressed as M/F): (1) wild goats (1.83); (2) wild sheep (1.67); (3) non‐European chamoises, including Ovibos moschatus (1.18); (4) European chamoises (1.27); (5) Budorcas taxicolor (1.01); and (6) Pantholops hodgsonii (1.65). Domestication has led to a remarkable decline in SSD of both domestic goats (1.36) and sheep (1.41). The highest regression slope of the relationship between male and female body size is that estimated for wild goats (1.32), followed by wild sheep (1.24), non‐European chamoises (1.14), domestic sheep (1.13), and domestic goats (1.10). Nevertheless, only the last two values are statistically different from one and thus corroborate Rensch's rule. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98 , 872–883.