Henrik Lantz

The genomic landscape underlying phenotypic integrity in the face of gene flow in crows

Crows of a feather flock together Closely related species with overlapping ranges typically evolve genetic barriers to prevent crossbreeding. Poelstra et al. sequenced genes from two species of central European crows: gray-bodied hooded crows and black carrion crows (see the Perspective by de Knijff). Although most of the genomes shared genes between the two species, one region that affected coat color and color vision differed. The authors suggest that black and gray-coated crows prefer to mate with birds like themselves. Science, this issue p. 1410; see also p. 1345 Gray hooded crow and black carrion crow genomes reveal the effects of hybridization on keeping the species separate. [Also see Perspective by de Knijff] The importance, extent, and mode of interspecific gene flow for the evolution of species has long been debated. Characterization of genomic differentiation in a classic example of hybridization between all-black carrion crows and gray-coated hooded crows identified genome-wide introgression extending far beyond the morphological hybrid zone. Gene expression divergence was concentrated in pigmentation genes expressed in gray versus black feather follicles. Only a small number of narrow genomic islands exhibited resistance to gene flow. One prominent genomic region (<2 megabases) harbored 81 of all 82 fixed differences (of 8.4 million single-nucleotide polymorphisms in total) linking genes involved in pigmentation and in visual perception—a genomic signal reflecting color-mediated prezygotic isolation. Thus, localized genomic selection can cause marked heterogeneity in introgression landscapes while maintaining phenotypic divergence.

More characters or more taxa for a robust phylogeny--case study from the coffee family (Rubiaceae).

Using different data sets mainly from the plant family Rubiaceae, but in parts also from the Apocynaceae, Asteraceae, Lardizabalaceae, Saxifragaceae, and Solanaceae, we have investigated the effect of number of characters, number of taxa, and kind of data on bootstrap values within phylogenetic trees. The percentage of supported nodes within a tree is positively correlated with the number of characters, and negatively correlated with the number of taxa. The morphological analyses are based on few characters and weakly supported trees are expected. The percentage of supported nodes is also dependent on the kind of data analyzed. In analyses of Rubiaceae based on the same number of characters, RFLP data give trees with higher percentage of supported nodes than rbcL and morphological data. We also discuss the support values for particular nodes at the familial and subfamilial levels. Two new data sets of ndhF and rbcL sequences of Rubiaceae are analyzed and together with earlier studies of the family we can conclude that the monophyly of the Rubiaceae is supported and within the family there are three well supported, but not easily characterized, large subfamilies, Rubioideae, Cinchonoideae s.s. and Ixoroideae s.l. There are also a few genera (Luculia and Coptosapelta) unclassified to subfamily.

Molecular phylogeny reveals a core clade of Rhytismatales

Rhytismatales (Leotiomycetes, Pezizomycotina, Ascomycota) are an order of mostly plant-associated ascomycetes with a global distribution. Well known taxa include the Rhytisma tar spots on Acer spp. and several needle-cast pathogens in genera Lophodermium and Meloderma. Critical studies are lacking at all taxonomic ranks from order to species, and in particular the genus taxonomy in the order has been criticized for being unnatural. We used nuclear LSU and mitochondrial SSU sequences in Bayesian phylogenetic analyses to define a core clade of Rhytismatales sensu stricto. Some of the genera traditionally placed within the Rhytismatales, Ascodichaena, Marthamyces, Mellitiosporium, Potebniamyces, Propolis and Pseudophacidium, are shown to be phylogenetically distinct, all related to various other taxa at present placed in the polyphyletic Helotiales. Within the core clade only Cudonia, Spathularia and Terriera are supported as monophyletic. The large genera Coccomyces, Hypoderma and Lophodermium all are polyphyletic as are a few smaller genera. The traditionally used characters of ascoma and spore shape are shown to be unreliable for the delimitation of monophyletic genera but in some cases can be useful when combined with other characters. In this study we provide 72 new nrLSU and 64 new mtSSU sequences. Together withPUBLICly available sequences data for 103 specimens representing 91 species of Rhytismatales are now available. Despite this taxon sampling intensity is still too low to propose an alternative generic taxonomy.

Nuclear rDNA ITS sequence data used to construct the first phylogeny of Vanguerieae (Rubiaceae)

Abstract. The morphologically homogenous tribe Vanguerieae was investigated phylogenetically using sequence data from the Internal Transcribed Spacer (ITS) region in the nuclear ribosomal DNA. Sequences from 41 Vanguerieae species representing 19 genera were produced, and a parsimony analysis was performed. The phylogenetic analysis has several clades with strong support, among which three new informal groups are discussed, i.e. the Vangueria group, the Fadogia-Rytigynia group and the Spiny group. Also found monophyletic with strong support are Multidentia, Keetia, Lagynias, and Pyrostria. Canthium and Rytigynia are revealed as polyphyletic; Vangueria, Tapiphyllum, and Fadogia are paraphyletic. Results from this first phylogenetic analysis of the tribe clearly demonstrate a need for new circumscriptions of several genera. Morphological characters are discussed and putative synapomorphies are mentioned. Jackknife, bootstrap, and Bremer support are calculated and differences found in support are discussed.

Unsupervised genome-wide recognition of local relationship patterns

BackgroundPhenomena such as incomplete lineage sorting, horizontal gene transfer, gene duplication and subsequent sub- and neo-functionalisation can result in distinct local phylogenetic relationships that are discordant with species phylogeny. In order to assess the possible biological roles for these subdivisions, they must first be identified and characterised, preferably on a large scale and in an automated fashion.ResultsWe developed Saguaro, a combination of a Hidden Markov Model (HMM) and a Self Organising Map (SOM), to characterise local phylogenetic relationships among aligned sequences using cacti, matrices of pair-wise distance measures. While the HMM determines the genomic boundaries from aligned sequences, the SOM hypothesises new cacti in an unsupervised and iterative fashion based on the regions that were modelled least well by existing cacti. After testing the software on simulated data, we demonstrate the utility of Saguaro by testing two different data sets: (i) 181 Dengue virus strains, and (ii) 5 primate genomes. Saguaro identifies regions under lineage-specific constraint for the first set, and genomic segments that we attribute to incomplete lineage sorting in the second dataset. Intriguingly for the primate data, Saguaro also classified an additional ~3% of the genome as most incompatible with the expected species phylogeny. A substantial fraction of these regions was found to overlap genes associated with both the innate and adaptive immune systems.ConclusionsSaguaro detects distinct cacti describing local phylogenetic relationships without requiring any a priori hypotheses. We have successfully demonstrated Saguaro’s utility with two contrasting data sets, one containing many members with short sequences (Dengue viral strains: n = 181, genome size = 10,700 nt), and the other with few members but complex genomes (related primate species: n = 5, genome size = 3 Gb), suggesting that the software is applicable to a wide variety of experimental populations. Saguaro is written in C++, runs on the Linux operating system, and can be downloaded from http://saguarogw.sourceforge.net/.

Evolutionary trends, major lineages, and new generic limits in the dioecious group of the tribe Vanguerieae (Rubiaceae): Insights into the evolution of functional dioecy

Abstract New generic circumscriptions of the Paleotropical tribe Vanguerieae in the subfamily Ixoroideae s.l. (Rubiaceae) have recently been established as a result of a series of phylogenetic studies conducted by Lantz and Bremer. The genus Canthium Lam. was shown in their study to be highly polyphyletic, and a largely dioecious group was for the first time identified within Vanguerieae. The dioecious group sensu Lantz and Bremer comprises about 140 species classified in eight genera: Canthium (Canthium subg. Bullockia Bridson), Dinocanthium Bremek., Leroya Cavaco, Neoleroya Cavaco, Peponidium (Baill.) Arènes, Pseudopeponidium Homolles ex Arènes, Pyrostria Comm. ex Juss., and Scyphochlamys Balf. f. We sequenced 79 Vanguerieae taxa and performed phylogenetic analyses based on sequence data from two nuclear (ETS and ITS) markers to: (1) pinpoint the phylogenetic positions of the Comorean and Indian Ocean Canthium and the Southeast Asian Canthium confertum Korth. group in Vanguerieae; (2) evaluate the phylogenetic utility of three taxonomic characters (bract type, locule number, and fruit shape) previously and currently used for delimiting genera in the dioecious group; and (3) assess the evolution of functional dioecy in Vanguerieae. The results support a further disintegration of Canthium s.l., as the Comorean and Malagasy Canthium species are shown for the first time to be closely related to Peponidium. Similarly, C. confertum appears to have a close affinity with Cyclophyllum Hook. f. The combined analyses show that the dioecious group can be subdivided into four morphologically distinct clades formally recognized as genera: Bullockia (Bridson) Razafim., Lantz & B. Bremer, here elevated from Canthium subgen. Bullockia Bridson, as well as Cyclophyllum, Peponidium (including all Comorean, Malagasy, and Seychellean Canthium species), and Pyrostria (including Dinocanthium, Leroya, Neoleroya, Pseudopeponidium, and Scyphochlamys). All described species of Canthium subgen. Bullockia are transferred to Bullockia: B. dyscriton (Bullock) Razafim., Lantz & B. Bremer, B. fadenii (Bridson) Razafim., Lantz & B. Bremer, B. impressinervia (Bridson) Razafim., Lantz & B. Bremer, B. mombazensis (Baill.) Razafim., Lantz & B. Bremer, B. pseudosetiflora (Bridson) Razafim., Lantz & B. Bremer, and B. setiflora (Hiern) Razafim., Lantz & B. Bremer. Furthermore, the results seem to point to a single origin of functional dioecy followed by subsequent reversals back to the hermaphroditic conditions at least within the Cyclophyllum–Canthium confertum clade and Pyrostria s.l. The Malagasy Bullockia species seem to have an African ancestor, whereas the Comorean Peponidium and the African Pyrostria appear to have originated from Malagasy progenitors.

Phylogeny of the complex Vanguerieae (Rubiaceae) genera Fadogia, Rytigynia, and Vangueria with close relatives and a new circumscription of Vangueria

The phylogeny of the Vanguerieae genera Fadogia, Rytigynia, Vangueria, and closely related genera is investigated using nuclear rDNA ITS sequences and plastid trnT-F and rpl16 sequences. Individual and combined analyses reveal several strongly supported clades. There are indications that Fadogia, Rytigynia, Tapiphyllum, and Vangueria are para- or polyphyletic and only Multidentia is strongly supported as monophyletic. Several taxa are found to have incongruent positions in the ITS and chloroplast phylogenies, and possible reasons behind these incongruencies are discussed. For Ancylanthos rubiginosus a chloroplast capture event can explain the incongruent position. In the Fadogia-Rytigynia group the incongruence is more widespread and cannot be attributed to a single taxon or a few taxa, but hybridization and introgression is the most likely explanation for the incongruence. It is concluded that the genera Ancylanthos, Lagynias, Pachystigma, and Tapiphyllum and the three species Fadogia agrestis, Rytigynia fuscosetulosa, and Rytigynia induta should be transferred to Vangueria.

Xerochrysium gen. nov. and Bettsia, genera encompassing xerophilic species of Chrysosporium

On the basis of a study of ITS sequences, Vidal et al. (Rev. Iber. Micol. 17: 22, 2000) recommended that the genus Chrysosporium be restricted to species belonging to Onygenales. Using nrLSU genes, we studied the majority of clades examined by Vidal et al. and showed that currently accepted species in Chrysosporium phylogenetically belong in six clades in three orders. Surprisingly, the xerophilic species of Chrysosporium, long thought to be a single grouping away from the majority of Chrysosporium species, occupy two clades, one in Leotiales, the other in Eurotiales. Species accepted in Leotiales are related to the sexual genus Bettsia. One is the type species B. alvei, and related asexual strains classified as C. farinicola, the second is C. fastidium transferred to Bettsia as B. fastidia. Species in the Eurotiales are transferred to Xerochrysium gen. nov., where the accepted species are X. xerophilum and X. dermatitidis, the correct name for C. inops on transfer to Xerochrysium. All accepted species are extreme xerophiles, found in dried and concentrated foods.

Serendipitous meta-transcriptomics: the fungal community of Norway Spruce (Picea abies)

After performing de novo transcript assembly of >1 billion RNA-Sequencing reads obtained from 22 samples of different Norway spruce (Picea abies) tissues that were not surface sterilized, we found that assembled sequences captured a mix of plant, lichen, and fungal transcripts. The latter were likely expressed by endophytic and epiphytic symbionts, indicating that these organisms were present, alive, and metabolically active. Here, we show that these serendipitously sequenced transcripts need not be considered merely as contamination, as is common, but that they provide insight into the plant’s phyllosphere. Notably, we could classify these transcripts as originating predominantly from Dothideomycetes and Leotiomycetes species, with functional annotation of gene families indicating active growth and metabolism, with particular regards to glucose intake and processing, as well as gene regulation.

Quantitative proteogenomics of human pathogens using DIA-MS.

The increasing number of bacterial genomes in combination with reproducible quantitative proteome measurements provides new opportunities to explore how genetic differences modulate proteome composition and virulence. It is challenging to combine genome and proteome data as the underlying genome influences the proteome. We present a strategy to facilitate the integration of genome data from several genetically similar bacterial strains with data-independent analysis mass spectrometry (DIA-MS) for rapid interrogation of the combined data sets. The strategy relies on the construction of a composite genome combining all genetic data in a compact format, which can accommodate the fusion with quantitative peptide and protein information determined via DIA-MS. We demonstrate the method by combining data sets from whole genome sequencing, shotgun MS and DIA-MS from 34 clinical isolates of Streptococcus pyogenes. The data structure allows for fast exploration of the data showing that undetected proteins are on average more amenable to amino acid substitution than expressed proteins. We identified several significantly differentially expressed proteins between invasive and non-invasive strains. The work underlines how integration of whole genome sequencing with accurately quantified proteomes can further advance the interpretation of the relationship between genomes, proteomes and virulence. This article is part of a Special Issue entitled: Computational Proteomics.