Putative Ancestral Species Research Articles

A Recent Expansion of the RXLR Effector Gene Avrblb2 Is Maintained in Global Populations of Phytophthora infestans Indicating Different Contributions to Virulence.

The introgression of disease resistance (R) genes encoding immunoreceptors with broad-spectrum recognition into cultivated potato appears to be the most promising approach to achieve sustainable management of late blight caused by the oomycete pathogen Phytophthora infestans. Rpi-blb2 from Solanum bulbocastanum shows great potential for use in agriculture based on preliminary potato disease trials. Rpi-blb2 confers immunity by recognizing the P. infestans avirulence effector protein AVRblb2 after it is translocated inside the plant cell. This effector belongs to the RXLR class of effectors and is under strong positive selection. Structure-function analyses revealed a key polymorphic amino acid (position 69) in AVRblb2 effector that is critical for activation of Rpi-blb2. In this study, we reconstructed the evolutionary history of the Avrblb2 gene family and further characterized its genetic structure in worldwide populations. Our data indicate that Avrblb2 evolved as a single-copy gene in a putative ancestral species of P. infestans and has recently expanded in the Phytophthora spp. that infect solanaceous hosts. As a consequence, at least four variants of AVRblb2 arose in P. infestans. One of these variants, with a Phe residue at position 69, evades recognition by the cognate resistance gene. Surprisingly, all Avrblb2 variants are maintained in pathogen populations. This suggests a potential benefit for the pathogen in preserving duplicated versions of AVRblb2, possibly because the variants may have different contributions to pathogen fitness in a diversified solanaceous host environment.

Relationship between amino acid changes in mitochondrial ATP6 and life-history variation in anguillid eels.

Mitochondrial genes are part of the oxidative phosphorylation pathway and important for energy production. Although evidence for positive selection at the mitochondrial level exists, few studies have investigated the link between amino acid changes and phenotype. Here we test the hypothesis that differences in two life-history related traits, migratory distance between spawning and foraging areas and larval phase duration, are associated with divergent selection within the mitochondrial ATP6 gene in anguillid eels. We compare amino acid changes among 18 species with the sequence of the putative ancestral species, believed to have shown short migratory distance and larval phase duration. We find positive correlations between both life-history related traits and (i) the number of amino acid changes and (ii) the strength of the combined physico-chemical and structural changes at positions previously identified as candidates for positive selection. This supports a link between genotype and phenotype driven by positive selection at ATP6.

A phylogeographic investigation of the hybrid origin of a species of swordtail fish from Mexico

Hybrid speciation may contribute significantly to generating biodiversity, but only a few well-documented examples for it exist so far that do not involve polyploidization as a mechanism. The swordtail fish, Xiphophorus clemenciae, shows common hallmarks of a hybrid origin and still overlaps in its current geographic distribution with its putative ancestral species (Xiphophorus hellerii and Xiphophorus maculatus). Xiphophorus clemenciae provides an ideal system for investigating the possible continued genetic interactions between a hybrid and its parental species. Here, we use microsatellite and mitochondrial markers to investigate the population structure of these species of swordtails and search for signs of recent hybridization. Individuals were sampled from 21 localities across the known range of X.clemenciae- the Isthmus of Tehuantepec (IT) Mexico, and several environmental parameters that might represent barriers to dispersal were recorded. The hybridization event that gave rise to X.clemenciae appears to be rather ancient, and a single origin is likely. We find negligible evidence for ongoing hybridization and introgression between the putative ancestral species, because they now occupy distinct ecological niches, and a common haplotype is shared by most populations of X.clemenciae. The population structure within these species shows an isolation-by-distance (IBD) pattern and genetic differentiation between most populations is significant and high. We infer that tectonic evolution in the Isthmus has greatly restricted gene flow between the southern and central IT populations of X.clemenciae and X.helleriii and provide preliminary information to aid in conservation management of this geographically restricted hybrid species, X.clemenciae.

Experimental evidence for the ancestry of allotetraploid Trifolium repens and creation of synthetic forms with value for plant breeding

BackgroundWhite clover (Trifolium repens) is a ubiquitous weed of the temperate world that through use of improved cultivars has also become the most important legume of grazed pastures world-wide. It has long been suspected to be allotetraploid, but the diploid ancestral species have remained elusive. Putative diploid ancestors were indicated by DNA sequence phylogeny to be T. pallescens and T. occidentale. Here, we use further DNA evidence as well as a combination of molecular cytogenetics (FISH and GISH) and experimental hybridization to test the hypothesis that white clover originated as a hybrid between T. pallescens and T. occidentale.ResultsT. pallescens plants were identified with chloroplast trnL intron DNA sequences identical to those of white clover. Similarly, T. occidentale plants with nuclear ITS sequences identical to white clover were also identified. Reciprocal GISH experiments, alternately using labeled genomic DNA probes from each of the putative ancestral species on the same white clover cells, showed that half of the chromosomes hybridized with each probe. F1 hybrids were generated by embryo rescue and these showed strong interspecific chromosome pairing and produced a significant frequency of unreduced gametes, indicating the likely mode of polyploidization. The F1 hybrids are inter-fertile with white clover and function as synthetic white clovers, a valuable new resource for the re-incorporation of ancestral genomes into modern white clover for future plant breeding.ConclusionsEvidence from DNA sequence analyses, molecular cytogenetics, interspecific hybridization and breeding experiments supports the hypothesis that a diploid alpine species (T. pallescens) hybridized with a diploid coastal species (T. occidentale) to generate tetraploid T. repens. The coming together of these two narrowly adapted species (one alpine and the other maritime), along with allotetraploidy, has led to a transgressive hybrid with a broad adaptive range.

Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires

BackgroundGenome size and complexity, as measured by the number of genes or protein domains, is remarkably similar in most extant eukaryotes and generally exhibits no correlation with their morphological complexity. Underlying trends in the evolution of the functional content and capabilities of different eukaryotic genomes might be hidden by simultaneous gains and losses of genes.ResultsWe reconstructed the domain repertoires of putative ancestral species at major divergence points, including the last eukaryotic common ancestor (LECA). We show that, surprisingly, during eukaryotic evolution domain losses in general outnumber domain gains. Only at the base of the animal and the vertebrate sub-trees do domain gains outnumber domain losses. The observed gain/loss balance has a distinct functional bias, most strikingly seen during animal evolution, where most of the gains represent domains involved in regulation and most of the losses represent domains with metabolic functions. This trend is so consistent that clustering of genomes according to their functional profiles results in an organization similar to the tree of life. Furthermore, our results indicate that metabolic functions lost during animal evolution are likely being replaced by the metabolic capabilities of symbiotic organisms such as gut microbes.ConclusionsWhile protein domain gains and losses are common throughout eukaryote evolution, losses oftentimes outweigh gains and lead to significant differences in functional profiles. Results presented here provide additional arguments for a complex last eukaryotic common ancestor, but also show a general trend of losses in metabolic capabilities and gain in regulatory complexity during the rise of animals.

Genetic tests of rapid parallel speciation of flightless birds from an extant volant ancestor

Prior to the extinction wave that followed the human colonization of Oceania, flightless rails (Aves: Rallidae) were among the largest radiations of island birds, and perhaps the most species-rich example of convergent evolution in vertebrates. Insular flightless species are thought to have evolved from extant, volant species that colonized from continental sources and rapidly followed parallel adaptive pathways to flightlessness. The present study provides the first test of this model of speciation using genetic data sampled throughout the range of a putative ancestral species. Mitochondrial control region sequences from 71 individuals of the Gallirallus philippensis species complex reveal essentially no geographic structure within archipelagos and only weak structure among archipelagos, with no major genetic breaks except for birds sampled in the Philippines. Demographic tests of coalescent models support a recent rapid expansion into Oceania (including Australia) out of the Philippines approximately 20 000 years ago. The estimated coalescence of G. philippensis mitochondrial alleles approximately 33 000 years ago closely corresponds to the expansion of humans into the archipelagoes of Near Oceania, suggesting that humans may have facilitated its colonization by exterminating flightless competitors and clearing lowland forests. Phylogenetic analyses that included all G. philippensis haplotypes and samples from 11 single-island endemic flightless species of Gallirallus indicate that G. philippensis is polyphyletic, but is not the ancestor of most of its flightless congeners, as previously thought. Nuclear gene sequences (β-actin inron 3) suggest that G. philippensis polyphyly is at least partly due to hybridization. The flightless condition evolves in rails before reproductive isolation is complete. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 96, 601–616.

Origin and diversification ofHibiscus glaber, species endemic to the oceanic Bonin Islands, revealed by chloroplast DNA polymorphism

Abstract Two woody Hibiscus species co-occur in the Bonin Islands of the northwestern Pacific Ocean: Hibiscus glaber Matsum. is endemic to the islands, and its putative ancestral species, Hibiscus tiliaceus L., is widely distributed in coastal areas of the tropics and subtropics. To infer isolating mechanisms that led to speciation of H. glaber and the processes that resulted in co-occurrence of the two closely related species on the Bonin Islands, we conducted molecular phylogenetic analyses on chloroplast DNA (cpDNA) sequences. Materials collected from a wide area of the Pacific and Indian Oceans were used, and two closely related species, Hibiscus hamabo Siebold Zucc. and Hibiscus macrophyllus Roxb., were also included in the analyses. The constructed tree suggested that H. glaber has been derived from H. tiliaceus, and that most of the modern Bonin populations of H. tiliaceus did not share most recent ancestry with H. glaber. Geographic isolation appears to be the most important mechanism in the speciation of H. glaber. The co-occurrence of the two species can be attributed to multiple migrations of different lineages into the islands. While a wide and overlapping geographical distribution of haplotypes was found in H. tiliaceus, localized geographical distribution of haplotypes was detected in H. glaber. It is hypothesized that a shift to inland habitats may have affected the mode of seed dispersal from ocean currents to gravity and hence resulted in geographical structuring of H. glaber haplotypes.

Evaluation of several wild tuber-bearingSolanum species for scab resistance

One hundred accessions of 18 wild diploid potato species were screened for resistance to scab through three cycles of selection, from which a total of 322 clones were selected as resistant. The putative ancestral species of the cultivated potatoes (Solanum bukasovii, S. canasense andS. multidissectum) produced resistant clones with significantly higher rates. Thus, these are primary gene sources for conferring scab resistance to cultivated potatoes.

Discriminating the ancestral progenitors of hexaploid Festuca arundinacea using genomic in situ hybridization

The phylogeny of Festuca arundinacea Schreb. (2n = 6x = 42) was determined using GISH. Total genomic DNA of putative ancestral species was labelled with rhodamine and hybridized to chromosome preparations of hybrids involving these species and F. arundinacea. The degree of hybridization to chromosomes known to be homologous to the probe DNA was compared with that found simultaneously on chromosomes of the genome of F. arundinacea. It was concluded that the tetraploid species Festuca arundinacea var. glaucescens contributed two genomes and the diploid species Festuca pratensis one, to create the allohexaploid species F. arundinacea.

Origin of the rose-scented Pelargonium cultivar grown on Réunion Island

The Pelargonium cultivar grown on Reunion for the production of rose-scented geranium oil is locally known as the cv. Rose. The origin of the cv. Rose is demonstrated by comparing its morphology, chromosome number and essential oil with those of putative ancestral species. It is concluded that P. capitatum (L.) L’Herit. and P. radens H.E. Moore can be considered as the parent species. A comparison of the characters of the cv. Rose and those of artificial hybrids between P. capitatum and P. radens , confirmed the assumption.

Allozyme Differentiation and Biosystematics of the Californian Closed-Cone Pines (Pinus subsect. Oocarpae)

Allozyme differentiation at 32 loci was studied in the three Californian species of Pinus subsect. Oocarpae: P. attenuata, P. muricata, and P. radiata, and in a small sample of a Latin American species of the subsection, P. oocarpa. The Californian species were previously known to comprise highly differentiated, disjunct populations, but with uncertain phylogenetic relationships among several populations and species. All populations had clear affinities for single species. The controversial Channel Islands (Santa Cruz Island) population of P. muricata and the Mexican Island (Guadalupe and Cedros islands) populations of P. radiata were distinct within their respective species, but clearly fell within each species complex. Con- to evidence from other traits, the Californian species were equally differentiated from one another allozymically, with no evidence of close relationships among pairwise comparisons of the three species. Pinus oocorpa, the putative ancestral species, was about two times more variable, and at substantial and approximately equal genetic distance from each of the three Californian species. Divergence of populations within species was generally clinal. The initial radiation of P. attenuata was in the Sierra Nevada, and subsequent divergence was toward the coast in the Siskiyou Mountains, and then south through the coast range to southern California. Divergence in both P. muricata and P. radiata occurred northward along the coast, with the southern island populations retaining ancestral alleles, and differentiation from P. oocarpa increasing northward within species. Genetic differentiation among species was twice that among populations within species.

DOES ASYMMETRICAL MATING PREFERENCE SHOW THE DIRECTION OF EVOLUTION?

The analysis of present behavior patterns is often a useful tool in our attempts to decipher the past. Studies of reproductive behavior have proven particularly fruitful in this regard, for the extent and type(s) of ethological barriers between two or more species can sometimes offer clues concerning key events in their evolutionary history. The usual approach is to obtain data on the relative willingness of individuals to mate, indicated by some type of isolation index. This index may actually be a function of both sex drive and discrimination. The strength of the isolation present-as measured by the isolation index-together with other relevant information, is then used to determine evolutionary patterns. Such investigations have shown that certain species pairs exhibit asymmetrical isolation. Asymmetrical isolation is said to exist when sexual isolation between the females of one population (population A) and the males of another population (population B) is greater than that found in the reciprocal crosses (females of population B with males of population A). One might expect that the rate of the development of sexual isolation between two populations would, by chance, occasionally be asymmetrical. Indeed, where isolation is not complete, equality of isolation between populations may be the exception rather than the rule. On the other hand, since the development of reproductive isolation is crucial to the speciation process, the presence of asymmetrical mating preferences may actually reflect the mechanism by which speciation has occurred. Toward this end, Kaneshiro (1976) and Watanabe and Kawanishi (1979) proposed models whereby they suggested that the direction of evolution can be determined by the examination of patterns of asymmetrical isolation. Kaneshiro (1976) and later Ohta (1978) uncovered asymmetry in mating preferences among several Hawaiian Drosophila species. Kaneshiro's model, upon which Ohta elaborated, suggested that the females of the putative ancestral species are more isolated from males of the putative derived species than are the derived females from the ancestral males. In 1979 Watanabe and Kawanishi offered a contrasting model based on their experimental work with the Drosophila melanogaster species group (Watanabe and Kawanishi, 1979). Here they had found an asymmetrical mating preference whereby the females of the putative derived species were more isolated from the males of the putative ancestral species than were the ancestral females from the derived males. This seemed also to be true of the published work on the virilis group. Thus, for any given set of asymmetrical isolation indices, the direction of evolution proposed by Watanabe and Kawanishi is exactly opposite to that suggested by Kaneshiro. If either of these two models is generally correct, a very powerful tool is available to researchers. Both are adequate to explain the data for which they were designed. A good test of these models would be to apply them to new data. For this purpose we will use the results of a study made on the Drosophila arizonensis-Drosophila majavensis species pair in which we investigated the reproductive relationships between various allopatric and sympatric populations of the two species (Wasserman and Koepfer, 1977). We found a much higher level of sexual isolation between sympatric populations

Crossability between a diploidPelargonium × hortorum Bailey cultivar and some of its putative ancestral species

Crosses were made between ‘Mme. Buchner’, a diploid cultivar ofPelargonium × hortorum and four of its putative ancestral speciesP. zonale, P, inquinans, P. scandens andP. stenopetalum. Hybrids derived from these crosses were selfed and records kept of their self-fertility. Crosses between ‘Mme. Buchner’ andP. inquinans andP. zonale were the most successful.Pelargonium scandens andP. stenopetalum were difficult to cross with the cultivar. Lack of cross- and/or self-fertility appears as low seed set, low germination and, in the hybrids particularly, as partial or complete male-sterility. Partial male-sterility often appears in semi-double florets, a characteristic which seems linked to spurlessness.