Transcriptome data from silica-preserved leaf tissue reveal gene flow patterns in a Caribbean bromeliad.

BACKGROUND AND AIMS: Transcriptome sequencing is a cost-effective approach that allows researchers to study a broad range of questions. However, to preserve RNA for transcriptome sequencing, tissue is often kept in special conditions, such as immediate ultracold freezing. Here, we demonstrate that RNA can be obtained from 6-month-old, field-collected samples stored in silica gel at room temperature. Using these transcriptomes, we explore the evolutionary relationships of the genus Pitcairnia (Bromeliaceae) in the Dominican Republic and infer barriers to gene flow. METHODS: We extracted RNA from silica-dried leaf tissue from 19 Pitcairnia individuals collected across the Dominican Republic. We used a series of macro- and micro-evolutionary approaches to examine the relationships and patterns of gene flow among individuals. KEY RESULTS: We produced high-quality transcriptomes from silica-dried material and demonstrated that evolutionary relationships on the island match geography more closely than species delimitation methods. A population genetic examination indicates that a combination of ecological and geographical features presents barriers to gene flow in Pitcairnia. CONCLUSIONS: Transcriptomes can be obtained from silica-preserved tissue. The genetic diversity among Pitcairnia populations does not warrant classification as separate species, but the Dominican Republic contains several barriers to gene flow, notably the Cordillera Central mountain range.

The Origins of Coca: Museum Genomics Reveals Multiple Independent Domestications from Progenitor Erythroxylum gracilipes.

Coca is the natural source of cocaine as well as a sacred and medicinal plant farmed by South American Amerindians and mestizos. The coca crop comprises four closely related varieties classified into two species (Amazonian and Huánuco varieties within Erythroxylum coca Lam., and Colombian and Trujillo varieties within Erythroxylum novogranatense (D. Morris) Hieron.) but our understanding of the domestication and evolutionary history of these taxa is nominal. In this study, we use genomic data from natural history collections to estimate the geographic origins and genetic diversity of this economically and culturally important crop in the context of its wild relatives. Our phylogeographic analyses clearly demonstrate the four varieties of coca comprise two or three exclusive groups nested within the diverse lineages of the widespread, wild species Erythroxylum gracilipes; establishing a new and robust hypothesis of domestication wherein coca originated two or three times from this wild progenitor. The Colombian and Trujillo coca varieties are descended from a single, ancient domestication event in northwestern South America. Huánuco coca was domesticated more recently, possibly in southeastern Peru. Amazonian coca either shares a common domesticated ancestor with Huánuco coca, or it was the product of a third and most recent independent domestication event in the western Amazon basin. This chronology of coca domestication reveals different Holocene peoples in South America were able to independently transform the same natural resource to serve their needs; in this case, a workaday stimulant. [Erythroxylum; Erythroxylaceae; Holocene; Museomics; Neotropics; phylogeography; plant domestication; target-sequence capture.].

Mass estimation of extinct taxa and phylogenetic hypotheses both influence analyses of character evolution in a large clade of birds (Telluraves).

Incorporating extinct taxa in phylogenetic comparative methods is rapidly becoming invaluable in studies of character evolution. An increasing number of studies have evaluated the effects of extinct taxa, and different numbers of extinct taxa, on model selection and parameter estimation. Body mass is a well-studied phenotype, but individual mass estimates may vary dramatically depending on the particular measurement used. Here, we perform an analysis of body mass evolution in a large clade of principally arboreal birds, incorporating 76 extinct species. We evaluate how different methods for estimating body mass of extinct taxa, and different phylogenetic hypotheses, affect our understanding of the rate and pattern of body mass evolution. Our results show that model selection can vary dramatically depending on the phenotypic and phylogenetic hypothesis used in the reconstruction. Even small changes in phenotype estimates can lead to different model selection and, as a result, affect the inferred evolutionary history. The best-fit models support an increase in the rate of evolution following the K-Pg boundary, with variation accumulating linearly through the Cenozoic. These results provide additional insight into the application of comparative models of evolution, as well as the evolutionary history of one of the most spectacular vertebrate radiations.

Phylogenetic inference in section Archerythroxylum informs taxonomy, biogeography, and the domestication of coca (Erythroxylum species).

PREMISE OF THE STUDY: This investigation establishes the first DNA-sequence-based phylogenetic hypothesis of species relationships in the coca family (Erythroxylaceae) and presents its implications for the intrageneric taxonomy and neotropical biogeography of Erythroxylum. We also identify the closest wild relatives and evolutionary relationships of the cultivated coca taxa. METHODS: We focused our phylogenomic inference on the largest taxonomic section in the genus Erythroxylum (Archerythroxylum O.E.Schulz) using concatenation and gene tree reconciliation methods from hybridization-based target capture of 427 genes. KEY RESULTS: We show that neotropical Erythroxylum are monophyletic within the paleotropical lineages, yet Archerythroxylum and all of the other taxonomic sections from which we sampled multiple species lack monophyly. We mapped phytogeographic states onto the tree and found some concordance between these regions and clades. The wild species E. gracilipes and E. cataractarum are most closely related to the cultivated E. coca and E. novogranatense, but relationships within this "coca" clade remain equivocal. CONCLUSIONS: Our results point to the difficulty of morphology-based intrageneric classification in this clade and highlight the importance of integrative taxonomy in future systematic revisions. We can confidently identify E. gracilipes and E. cataractarum as the closest wild relatives of the coca taxa, but understanding the domestication history of this crop will require more thorough phylogeographic analysis.

Oligocene origin and drivers of diversification in the genus Sticta (Lobariaceae, Ascomycota).

A major challenge to evolutionary biologists is to understand how biodiversity is distributed through space and time and across the tree of life. Diversification of organisms is influenced by many factors that act at different times and geographic locations but it is still not clear which have a significant impact and how drivers interact. To study diversification, we chose the lichen genus Sticta, by sampling through most of the global range and producing a time tree. We estimate that Sticta originated about 30 million years ago, but biogoegraphic analysis was unclear in estimating the origin of the genus. Furthermore, we investigated the effect of dispersal ability finding that Sticta has a high dispersal rate, as collections from Hawaii showed that divergent lineages colonized the islands at least four times. Symbiont interactions were investigated using BiSSE to understand if green-algal or cyanobacterial symbiont interactions influenced diversification, only to find that the positive results were driven almost completely by Type I error. On the other hand, another BiSSE analysis found that an association with Andean tectonic activity increases the speciation rate of species.

Transcriptional activity of PIF and Pong-like Class II transposable elements in Triticeae.

BACKGROUND: Transposable elements are major contributors to genome size and variability, accounting for approximately 70-80% of the maize, barley, and wheat genomes. PIF and Pong-like elements belong to two closely-related element families within the PIF/Harbinger superfamily of Class II (DNA) transposons. Both elements contain two open reading frames; one encodes a transposase (ORF2) that catalyzes transposition of the functional elements and their related non-autonomous elements, while the function of the second is still debated. In this work, we surveyed for PIF- and Pong-related transcriptional activity in 13 diploid Triticeae species, all of which have been previously shown to harbor extensive within-genome diversity of both groups of elements. RESULTS: The results revealed that PIF elements have considerable transcriptional activity in Triticeae, suggesting that they can escape the initial levels of plant cell control and are regulated at the post-transcriptional level. Phylogenetic analysis of 156 PIF cDNA transposase fragments along with 240 genomic partial transposase sequences showed that most, if not all, PIF clades are transcriptionally competent, and that multiple transposases coexisting within a single genome have the potential to act simultaneously. In contrast, we did not detect any transcriptional activity of Pong elements in any sample. CONCLUSIONS: The lack of Pong element transcription shows that even closely related transposon families can exhibit wide variation in their transposase transcriptional activity within the same genome.

Diversity, abundance, and evolutionary dynamics of Pong-like transposable elements in Triticeae.

Pong-like elements are members of the PIF/Harbinger superfamily of DNA transposons that has been described in many plants, animals, and fungi. Most Pong elements contain two open reading frames (ORFs). One encodes a transposase (ORF2) that catalyzes transposition of Pong and related non-autonomous elements, while the function of the second is unknown. Little is known about the evolutionary history of Pong elements in flowering plants. In this work, we present the first comprehensive analysis of the diversity, abundance, and evolution of the Pong-like transposase gene in the genomes of 21 diploid species from the wheat tribe, Triticeae, and we present the first convincing evidence of horizontal transfer of nuclear-encoded Pong elements in any organism. A phylogenetic analysis of nearly 300 Pong sequences based on a conserved region of the transposase domain revealed a complex evolutionary history of Pong elements that can be best explained by ancestral polymorphism, followed by differential evolutionary success of some transposase lineages, and by occasional horizontal transfer between phylogenetically distant genera. In addition, we used transposon display to estimate the abundance of the transposase gene within Triticeae genomes, and our results revealed varying levels of Pong proliferation, with numbers of transposase copies ranging from 22 to 92. Comparisons of Pong transposase abundance to flow cytometry estimates of genome size revealed that larger Triticeae genome size was not correlated with transposase abundance.

Evolution of the beta-amylase gene in the temperate grasses: Non-purifying selection, recombination, semiparalogy, homeology and phylogenetic signal.

Low-copy nuclear genes (LCNGs) have complex genetic architectures and evolutionary dynamics. However, unlike multicopy nuclear genes, LCNGs are rarely subject to gene conversion or concerted evolution, and they have higher mutation rates than organellar or nuclear ribosomal DNA markers, so they have great potential for improving the robustness of phylogenetic reconstructions at all taxonomic levels. In this study, our first objective is to evaluate the evolutionary dynamics of the LCNG ß-amylase by testing for potential pseudogenization, paralogy, homeology, recombination, and phylogenetic incongruence within a broad representation of the main Pooideae lineages. Our second objective is to determine whether ß-amylase shows sufficient phylogenetic signal to reconstruct the evolutionary history of the Pooid grasses. A multigenic (ITS, matK, ndhF, trnTL, and trnLF) tree of the study group provided a framework for assessing the ß-amylase phylogeny. Eight accessions showed complete absence of selection, suggesting putative pseudogenic copies or other relaxed selection pressures; resolution of Vulpia alopecuros 2x clones indicated its potential (semi) paralogy; and homeologous copies of allopolyploid species Festuca simensis, F. fenas, and F. arundinacea tracked their Mediterranean origin. Two recombination events were found within early-diverged Pooideae lineages, and five within the PACCMAD clade. The unexpected phylogenetic relationships of 37 grass species (26% of the sampled species) highlight the frequent occurrence of non-treelike evolutionary events, so this LCNG should be used with caution as a phylogenetic marker. However, once the pitfalls are identified and removed, the phylogenetic reconstruction of the grasses based on the ß-amylase exon+intron positions is optimal at all taxonomic levels.

Distribution and evolutionary dynamics of Stowaway Miniature Inverted repeat Transposable Elements (MITEs) in grasses.

The occurrence of Stowaway MITEs and their potential footprints in the grasses was assessed within an explicit phylogenetic framework. An organismal tree was used to analyze the distribution and evolutionary dynamics of these elements and their potential excision footprints in the fourth intron of the ß-amylase gene and in other introns of several nuclear genes across the Poaceae. Megablast and discontiguous megablast searches in the Entrez nucleotide database were performed for the ß-amylase, blz-1, dmc1, nuc, and xly genes MITEs. These elements and their potential footprints were distributed in introns and intergenic spacers of many other nuclear genes throughout the BEP lineages; however, they were absent in the studied PACCMAD lineages. A plausible underlying dynamic of successive acquisitions and deletions of ß-amylase Stowaway MITEs in the temperate grasses could be explained by three alternative hypotheses: (i) a single early acquisition of a palindrome element, similar to Tc1-Mariner, in the fourth intron of the ß-amylase gene in the ancestor of the Pooideae, followed by multiple independent losses, (ii) multiple independent acquisitions of MITEs in non-related pooid lineages or (iii) different waves of acquisition of MITEs, followed by multiple losses and horizontal transfers in the temperate grasses. This last hypothesis seems to fit best with the evidence found to date.

Is a robust phylogeny of the enterobacterial plant pathogens attainable?

Sequences from gapA, gyrA and ompA were used to evaluate the relationships of the enterobacterial plant pathogens, and assess whether a robust phylogeny can be ascertained using this group of housekeeping genes. Up to 48 taxa were included in a combined phylogenetic analysis to explore the evolutionary distribution of plant pathogenic species across the family Enterobacteriaceae. Phylogenies were reconstructed from gapA, gyrA and ompA gene sequences using maximum parsimony and maximum likelihood algorithms, and phylogenetic congruence was evaluated by the incongruence length difference test and the partition addition bootstrap alteration approach. The resulting gene trees were found to be incongruent, with gapA supporting a monophyletic origin for the plant pathogenic species. In contrast, gyrA and ompA supported multiple polyphyletic origins of Erwinia, Brenneria, Pectobacterium and Pantoea in conjunction with a previously published 16S rDNA phylogeny. However, none of the trees (not even the published 16S rDNA gene tree) supports the current taxonomic classification of these genera into four clades, with Pantoea forming the only monophyletic group in the gapA, gyrA and 16S rDNA trees. Finally, the gapA, gyrA and previously published 16S rDNA phylogenies differ in the taxonomic placement of several bacterial strains which are separated in the three trees. The observed incongruence among the four gene histories is likely to be the result of horizontal transfer events, confounding the search for a robust set of housekeeping genes with a shared evolutionary history that could be used to confidently characterize the relationships of the plant pathogenic enterobacteria. © The Willi Hennig Society 2010.

Phylogenetic relationships and reticulation among Asian Elymus (Poaceae) allotetraploids: analyses of three nuclear gene trees.

This phylogenetic study focuses on a subset of the species in Elymus-specifically, the endemic Asian tetraploids presumed to combine the St genome from Pseudoroegneria with the Y genome from an unknown donor. The primary goals were to (1) determine whether the St and Y genomes are derived from phylogenetically distinct donors; (2) identify the closest relative, and potentially the likely donor, of the Y genome; and (3) interpret variation among StStYY species in terms of multiple origins and/or introgression. The goals were addressed using phylogenetic analyses of sequences from three low-copy nuclear genes: phosphoenolpyruvate carboxylase, beta-amylase, and granule-bound starch synthase I. Data sets include 16 StStYY individuals representing nine species, along with a broad sample of representatives from most of the monogenomic (i.e., non-allopolyploid) genera in the tribe. To briefly summarize the results: (1) the data clearly support an allopolyploid origin for the Asian tetraploids, involving two distinct donors; (2) the Y genome was contributed by a single donor, or multiple closely-related donors; (3) the phylogenetic position of the ElymusY genome varies among the three trees and its position is not strongly supported, so the identity of the donor remains a mystery; and (4) conflicts among the gene trees with regard to the St-genome sequences suggest introgression involving both Elymus and Pseudoroegneria.

Multiple historical processes obscure phylogenetic relationships in a taxonomically difficult group (Lobariaceae, Ascomycota).

In the age of next-generation sequencing, the number of loci available for phylogenetic analyses has increased by orders of magnitude. But despite this dramatic increase in the amount of data, some phylogenomic studies have revealed rampant gene-tree discordance that can be caused by many historical processes, such as rapid diversification, gene duplication, or reticulate evolution. We used a target enrichment approach to sample 400 single-copy nuclear genes and estimate the phylogenetic relationships of 13 genera in the lichen-forming family Lobariaceae to address the effect of data type (nucleotides and amino acids) and phylogenetic reconstruction method (concatenation and species tree approaches). Furthermore, we examined datasets for evidence of historical processes, such as rapid diversification and reticulate evolution. We found incongruence associated with sequence data types (nucleotide vs. amino acid sequences) and with different methods of phylogenetic reconstruction (species tree vs. concatenation). The resulting phylogenetic trees provided evidence for rapid and reticulate evolution based on extremely short branches in the backbone of the phylogenies. The observed rapid and reticulate diversifications may explain conflicts among gene trees and the challenges to resolving evolutionary relationships. Based on divergence times, the diversification at the backbone occurred near the Cretaceous-Paleogene (K-Pg) boundary (65 Mya) which is consistent with other rapid diversifications in the tree of life. Although some phylogenetic relationships within the Lobariaceae family remain with low support, even with our powerful phylogenomic dataset of up to 376 genes, our use of target-capturing data allowed for the novel exploration of the mechanisms underlying phylogenetic and systematic incongruence.

Structural equation modeling as a tool to investigate correlates of extra-pair paternity in birds.

Identifying relationships between variables in ecological systems is challenging due to the large number of interacting factors. One system studied in detail is avian reproduction, where molecular analyses have revealed dramatic variation in rates of extra-pair paternity-the frequency with which broods contain individuals sired by different males. Despite the attention the topic has received, identification of ecological predictors of the observed variation remains elusive. In this study we evaluate how structural equation modeling-which allows for simultaneous estimation of covariation between all variables in a model-can help identify significant relationships between ecological variables and extra-pair paternity. We estimated the correlation of eight different variables using data from 36 species of passerines by including them in six different models of varying complexity. We recover strong support for species with lower rates of male care having higher rates of extra-pair paternity. Our results also suggest that testes size, range size, and longevity all potentially have a relationship with rates of extra-pair paternity; however, interpretation of this result is more challenging. More generally, these results demonstrate the utility of applying structural equation modeling to understanding correlations among interacting variables in complex biological systems.

Multiple homoplasious insertions and deletions of a Triticeae (Poaceae) DNA transposon: a phylogenetic perspective.

BACKGROUND: Stowaway elements are short, non-autonomous DNA transposons categorized as miniature inverted-repeat transposable elements (MITEs). The high MITE copy number in grass genomes suggests an active history of amplification and insertion, but ongoing MITE activity has only rarely been seen, and ongoing Stowaway activity has never been observed. Thus, a phylogenetic perspective on presence vs. absence of elements in an aligned data set can provide valuable historical insights into the dynamics of MITE acquisition and loss. RESULTS: A Stowaway-like element resides within the fourth intron of a beta-amylase gene in representatives of five genera in the wheat tribe, Triticeae. Its presence vs. absence was examined with reference to the beta-amylase gene tree topology, and in light of sequence comparisons of the beta-amylase elements to Triticeae Stowaway elements in the Entrez nucleotide database. Among the sequences lacking the element, there are five distinct putative excision footprints (one widespread and four restricted to unrelated lineages) and two flanking deletions. The sequences that do contain elements are polyphyletic on the beta-amylase tree, and their elements are divergent at the sequence level. The beta-amylase elements do not form a monophyletic group relative to other Stowaway elements in Entrez; most are more similar to elements from other loci in other Triticeae genomes than they are to one another. CONCLUSION: Combined, the phylogenetic distribution, sequence variation, and Entrez database comparisons indicate that a Stowaway-like element has undergone multiple deletions from and insertions into the same site in beta-amylase intron 4 during the history of the tribe. The elements currently at the site represent multiple, distinct lineages that transcend generic boundaries. While patterns of Stowaway polymorphism across a phylogenetic data set do not allow evolutionary mechanisms to be inferred with certainty, they do provide insights into the dynamics of element evolution over an extended time scale. The historical perspective provided by a phylogenetic approach is complementary to the few studies in which ongoing MITE activity has been documented.

Phylogenetic analysis of Sec7-domain-containing Arf nucleotide exchangers.

The eukaryotic family of ADP-ribosylation factor (Arf) GTPases plays a key role in the regulation of protein trafficking, and guanine-nucleotide exchange is crucial for Arf function. Exchange is stimulated by members of another family of proteins characterized by a 200-amino acid Sec7 domain, which alone is sufficient to catalyze exchange on Arf. Here, we analyzed the phylogeny of Sec7-domain-containing proteins in seven model organisms, representing fungi, plants, and animals. The phylogenetic tree has seven main groups, of which two include members from all seven model systems. Three groups are specific for animals, whereas two are specific for fungi. Based on this grouping, we propose a phylogenetically consistent set of names for members of the Sec7-domain family. Each group, except for one, contains proteins with known Arf exchange activity, implying that all members of this family have this activity. Contrary to the current convention, the sensitivity of Arf exchange activity to the inhibitor brefeldin A probably cannot be predicted by group membership. Multiple alignment reveals group-specific domains outside the Sec7 domain and a set of highly conserved amino acids within it. Determination of the importance of these conserved elements in Arf exchange activity and other cellular functions is now possible.

The Role of Vertical and Horizontal Transfer in the Evolutionary Dynamics of PIF-Like Transposable Elements in Triticeae.

PIF-like transposable elements are members of the PIF/Harbinger superfamily of DNA transposons found in the genomes of many plants, animals, and fungi. The evolution of the gene that encodes the transposase responsible for mobilizing PIF-like elements has been studied in both plants and animals, but the elements' history in flowering plants remains poorly known. In this work, we describe the phylogenetic distribution and evolution of PIF-like elements in the genomes of 21 diploid species from the wheat tribe, Triticeae, and we present the first convincing evidence of horizontal transfer of PIF elements in plant genomes. A phylogenetic analysis of 240 PIF sequences based on the conserved region of the transposase domain revealed at least four main transposase lineages. Their complex evolutionary history can be best explained by a combination of vertical transmission with differential evolutionary success among lineages, and occasional horizontal transfer between phylogenetically distant Triticeae genera. In addition, we identified 127 potentially functional transposase sequences indicating possible recent activity of PIF.

Phylogeny of a genomically diverse group of elymus (poaceae) allopolyploids reveals multiple levels of reticulation.

The grass tribe Triticeae (=Hordeeae) comprises only about 300 species, but it is well known for the economically important crop plants wheat, barley, and rye. The group is also recognized as a fascinating example of evolutionary complexity, with a history shaped by numerous events of auto- and allopolyploidy and apparent introgression involving diploids and polyploids. The genus Elymus comprises a heterogeneous collection of allopolyploid genome combinations, all of which include at least one set of homoeologs, designated St, derived from Pseudoroegneria. The current analysis includes a geographically and genomically diverse collection of 21 tetraploid Elymus species, and a single hexaploid species. Diploid and polyploid relationships were estimated using four molecular data sets, including one that combines two regions of the chloroplast genome, and three from unlinked nuclear genes: phosphoenolpyruvate carboxylase, ß-amylase, and granule-bound starch synthase I. Four gene trees were generated using maximum likelihood, and the phylogenetic placement of the polyploid sequences reveals extensive reticulation beyond allopolyploidy alone. The trees were interpreted with reference to numerous phenomena known to complicate allopolyploid phylogenies, and introgression was identified as a major factor in their history. The work illustrates the interpretation of complicated phylogenetic results through the sequential consideration of numerous possible explanations, and the results highlight the value of careful inspection of multiple independent molecular phylogenetic estimates, with particular focus on the differences among them.

Reticulate evolutionary history of a complex group of grasses: phylogeny of Elymus StStHH allotetraploids based on three nuclear genes.

BACKGROUND: Elymus (Poaceae) is a large genus of polyploid species in the wheat tribe Triticeae. It is polyphyletic, exhibiting many distinct allopolyploid genome combinations, and its history might be further complicated by introgression and lineage sorting. We focus on a subset of Elymus species with a tetraploid genome complement derived from Pseudoroegneria (genome St) and Hordeum (H). We confirm the species' allopolyploidy, identify possible genome donors, and pinpoint instances of apparent introgression or incomplete lineage sorting. METHODOLOGY/PRINCIPAL FINDINGS: We sequenced portions of three unlinked nuclear genes-phosphoenolpyruvate carboxylase, beta-amylase, and granule-bound starch synthase I-from 27 individuals, representing 14 Eurasian and North American StStHHElymus species. Elymus sequences were combined with existing data from monogenomic representatives of the tribe, and gene trees were estimated separately for each data set using maximum likelihood. Trees were examined for evidence of allopolyploidy and additional reticulate patterns. All trees confirm the StStHH genome configuration of the Elymus species. They suggest that the StStHH group originated in North America, and do not support separate North American and European origins. Our results point to North American Pseudoroegneria and Hordeum species as potential genome donors to Elymus. Diploid P. spicata is a prospective St-genome donor, though conflict among trees involving P. spicata and the Eurasian P. strigosa suggests either introgression of GBSSI sequences from P. strigosa into North American Elymus and Pseudoroegneria, or incomplete lineage sorting of ancestral GBSSI polymorphism. Diploid H. californicum and/or allotetraploid H. jubatum are possible H-genome donors; direct involvement of an allotetraploid Hordeum species would simultaneously introduce two distinct H genomes to Elymus, consistent with some of the relationships among H-genome sequences in Hordeum and Elymus. CONCLUSIONS/SIGNIFICANCE: Comparisons among molecular phylogenetic trees confirm allopolyploidy, identify potential genome donors, and highlight cases of apparent introgression or incomplete lineage sorting. The complicated history of this group emphasizes an inherent problem with interpreting conflicts among bifurcating trees-identifying introgression and determining its direction depend on which tree is chosen as a starting point of comparison. In spite of difficulties with interpretation, differences among gene trees allow us to identify reticulate species and develop hypotheses about underlying evolutionary processes.

Phylogenetic evidence for extensive horizontal gene transfer of type III secretion system genes among enterobacterial plant pathogens.

This study uses sequences from four genes, which are involved in the formation of the type III secretion apparatus, to determine the role of horizontal gene transfer in the evolution of virulence genes for the enterobacterial plant pathogens. Sequences of Erwinia, Brenneria, Pectobacterium, Dickeya and Pantoea were compared (a) with one another, (b) with sequences of enterobacterial animal pathogens, and (c) with sequences of plant pathogenic gamma and beta proteobacteria, to evaluate probable paths of lateral exchange leading to the current distribution of virulence determinants among these micro-organisms. Phylogenies were reconstructed based on hrcC, hrcR, hrcJ and hrcV gene sequences using parsimony and maximum-likelihood algorithms. Virulence gene phylogenies were also compared with several housekeeping gene loci in order to evaluate patterns of lateral versus vertical acquisition. The resulting phylogenies suggest that multiple horizontal gene transfer events have occurred both within and among the enterobacterial plant pathogens and plant pathogenic gamma and beta proteobacteria. hrcJ sequences are the most similar, exhibiting anywhere from 2 to 50 % variation at the nucleotide level, with the highest degree of variation present between plant and animal pathogen sequences. hrcV sequences are conserved among plant and animal pathogens at the N terminus. The C-terminal domain is conserved only among the enterobacterial plant pathogens, as are the hrcC and hrcR sequences. Additionally, hrcJ and hrcV sequence phylogenies suggest that at least some type III secretion system virulence genes from enterobacterial plant pathogens are related more closely to those of the genus Pseudomonas, a conclusion neither supported nor refuted by hrcC or hrcR.

Allohexaploidy, introgression, and the complex phylogenetic history of Elymus repens (Poaceae).

The phylogenetic position of hexaploid Elymus repens within the tribe Triticeae (Poaceae) was examined using cloned sequences from the low-copy nuclear genes encoding phosphoenolpyruvate carboxylase (pepC) and beta-amylase. A previous analysis of E. repens using data from the nuclear granule-bound starch synthase I (GBSSI) gene had yielded five phylogenetically distinct gene copies, two more than expected from hexaploidy alone. The three gene trees share three distinct E. repens clades, suggesting that E. repens contains three phylogenetically divergent genomes, contributed by Hordeum, Pseudoroegneria, and an unknown donor. The two additional GBSSI sequences, including one that was apparently derived from outside of the tribe, appear to reflect past introgression of GBSSI sequences into the E. repens genome. On all three trees, the Hordeum-like E. repens sequences are polyphyletic within Hordeum, and the trees are in conflict with regard to the placement of these sequences within Hordeum, highlighting multiple contributions from Hordeum to E. repens.