Bayesian Concordance Analysis Research Articles

Genome sequence for the blue-flowered Andean shrub Iochroma cyaneum reveals extensive discordance across the berry clade of Solanaceae.

The tomato (Solanum lycopersicum L.) family, Solanaceae, is a model clade for a wide range of applied and basic research questions. Currently, reference-quality genomes are available for over 30 species from seven genera, and these include numerous crops as well as wild species [e.g., Jaltomata sinuosa (Miers) Mione and Nicotiana attenuata Torr. ex S. Watson]. Here we present the genome of the showy-flowered Andean shrub Iochroma cyaneum (Lindl.) M. L. Green, a woody lineage from the tomatillo (Physalis philadelphica Lam.) subfamily Physalideae. The assembled size of the genome (2.7 Gb) is more similar in size to pepper (Capsicum annuum L.) (2.6 Gb) than to other sequenced diploid members of the berry clade of Solanaceae [e.g., potato (Solanum tuberosum L.), tomato, and Jaltomata]. Our assembly recovers 92% of the conserved orthologous set, suggesting a nearly complete genome for this species. Most of the genomic content is repetitive (69%), with Gypsy elements alone accounting for 52% of the genome. Despite the large amount of repetitive content, most of the 12 I. cyaneum chromosomes are highly syntenic with tomato. Bayesian concordance analysis provides strong support for the berry clade, including I. cyaneum, but reveals extensive discordance along the backbone, with placement of chili pepper and Jaltomata being highly variable across gene trees. The I. cyaneum genome contributes to a growing wealth of genomic resources in Solanaceae and underscores the need for expanded sampling of diverse berry genomes to dissect major morphological transitions.

Optimal markers for the identification of Colletotrichum species

Colletotrichum is among the most important genera of fungal plant pathogens. Molecular phylogenetic studies over the last decade have resulted in a much better understanding of the evolutionary relationships and species boundaries within the genus. There are now approximately 200 species accepted, most of which are distributed among 13 species complexes. Given their prominence on agricultural crops around the world, rapid identification of a large collection of Colletotrichum isolates is routinely needed by plant pathologists, regulatory officials, and fungal biologists. However, there is no agreement on the best molecular markers to discriminate species in each species complex. Here we calculate the barcode gap distance and intra/inter-specific distance overlap to evaluate each of the most commonly applied molecular markers for their utility as a barcode for species identification. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), histone-3 (HIS3), DNA lyase (APN2), intergenic spacer between DNA lyase and the mating-type locus MAT1-2-1 (APN2/MAT-IGS), and intergenic spacer between GAPDH and a hypothetical protein (GAP2-IGS) have the properties of good barcodes, whereas sequences of actin (ACT), chitin synthase (CHS-1) and nuclear rDNA internal transcribed spacers (nrITS) are not able to distinguish most species. Finally, we assessed the utility of these markers for phylogenetic studies using phylogenetic informativeness profiling, the genealogical sorting index (GSI), and Bayesian concordance analyses (BCA). Although GAPDH, HIS3 and β-tubulin (TUB2) were frequently among the best markers, there was not a single set of markers that were best for all species complexes. Eliminating markers with low phylogenetic signal tends to decrease uncertainty in the topology, regardless of species complex, and leads to a larger proportion of markers that support each lineage in the Bayesian concordance analyses. Finally, we reconstruct the phylogeny of each species complex using a minimal set of phylogenetic markers with the strongest phylogenetic signal and find the majority of species are strongly supported as monophyletic.

A Malvaceae mystery: A mallow maelstrom of genome multiplications and maybe misleading methods?

Previous research suggests that Gossypium has undergone a 5- to 6-fold multiplication following its divergence from Theobroma. However, the number of events, or where they occurred in the Malvaceae phylogeny remains unknown. We analyzed transcriptomic and genomic data from representatives of eight of the nine Malvaceae subfamilies. Phylogenetic analysis of nuclear data placed Dombeya (Dombeyoideae) as sister to the rest of Malvadendrina clade, but the plastid DNA tree strongly supported Durio (Helicteroideae) in this position. Intraspecific Ks plots indicated that all sampled taxa, except Theobroma (Byttnerioideae), Corchorus (Grewioideae), and Dombeya (Dombeyoideae), have experienced whole genome multiplications (WGMs). Quartet analysis suggested WGMs were shared by Malvoideae-Bombacoideae and Sterculioideae-Tilioideae, but did not resolve whether these are shared with each other or Helicteroideae (Durio). Gene tree reconciliation and Bayesian concordance analysis suggested a complex history. Alternative hypotheses are suggested, each involving two independent autotetraploid and one allopolyploid event. They differ in that one entails an allopolyploid origin for the Durio lineage, whereas the other invokes an allopolyploid origin for Malvoideae-Bombacoideae. We highlight the need for more genomic information in the Malvaceae and improved methods to resolve complex evolutionary histories that may include allopolyploidy, incomplete lineage sorting, and variable rates of gene and genome evolution.

Resolving Deep Nodes in an Ancient Radiation of Neotropical Fishes in the Presence of Conflicting Signals from Incomplete Lineage Sorting.

Resolving patterns of ancient and rapid diversifications is one of the most challenging tasks in evolutionary biology. These difficulties arise from confusing phylogenetic signals that are associated with the interplay of incomplete lineage sorting (ILS) and homoplasy. Phylogenomic analyses of hundreds, or even thousands, of loci offer the potential to resolve such contentious relationships. Yet, how much useful phylogenetic information these large data sets contain remains uncertain and often goes untested. Here, we assess the utility of different data filtering approaches to maximize phylogenetic information and minimize noise when reconstructing an ancient radiation of Neotropical electric knifefishes (Order Gymnotiformes) using ultraconserved elements. We found two contrasting hypotheses of gymnotiform evolutionary relationships depending on whether phylogenetic inferences were based on concatenation or coalescent methods. In the first case, all analyses inferred a previously-and commonly-proposed hypothesis, where the family Apteronotidae was found as the sister group to all other gymnotiform families. In contrast, coalescent-based analyses suggested a novel hypothesis where families producing pulse-type (viz., Gymnotidae, Hypopomidae, and Rhamphichthyidae) and wave-type electric signals (viz., Apteronotidae, Sternopygidae) were reciprocally monophyletic. Nodal support for this second hypothesis increased when analyzing loci with the highest phylogenetic information content and further increased when data were pruned using targeted filtering methods that maximized phylogenetic informativeness at the deepest nodes of the Gymnotiformes. Bayesian concordance analyses and topology tests of individual gene genealogies demonstrated that the difficulty of resolving this radiation was likely due to high gene-tree incongruences that resulted from ILS. We show that data filtering reduces gene-tree heterogeneity and increases nodal support and consistency of species trees using coalescent methods; however, we failed to observe the same effect when using concatenation methods. Furthermore, the targeted filtering strategies applied here support the use of "gene data interrogation" rather than "gene genealogy interrogation" approaches in phylogenomic analyses, to extract phylogenetic signal from intractable portions of the Tree of Life.

Phylogeny with introgression in Habronattus jumping spiders (Araneae: Salticidae)

BackgroundHabronattus is a diverse clade of jumping spiders with complex courtship displays and repeated evolution of Y chromosomes. A well-resolved species phylogeny would provide an important framework to study these traits, but has not yet been achieved, in part because the few genes available in past studies gave conflicting signals. Such discordant gene trees could be the result of incomplete lineage sorting (ILS) in recently diverged parts of the phylogeny, but there are indications that introgression could be a source of conflict.ResultsTo infer Habronattus phylogeny and investigate the cause of gene tree discordance, we assembled transcriptomes for 34 Habronattus species and 2 outgroups. The concatenated 2.41 Mb of nuclear data (1877 loci) resolved phylogeny by Maximum Likelihood (ML) with high bootstrap support (95-100%) at most nodes, with some uncertainty surrounding the relationships of H. icenoglei, H. cambridgei, H. oregonensis, and Pellenes canadensis. Species tree analyses by ASTRAL and SVDQuartets gave almost completely congruent results. Several nodes in the ML phylogeny from 12.33 kb of mitochondrial data are incongruent with the nuclear phylogeny and indicate possible mitochondrial introgression: the internal relationships of the americanus and the coecatus groups, the relationship between the altanus, decorus, banksi, and americanus group, and between H. clypeatus and the coecatus group. To determine the relative contributions of ILS and introgression, we analyzed gene tree discordance for nuclear loci longer than 1 kb using Bayesian Concordance Analysis (BCA) for the americanus group (679 loci) and the VCCR clade (viridipes/clypeatus/coecatus/roberti groups) (517 loci) and found signals of introgression in both. Finally, we tested specifically for introgression in the concatenated nuclear matrix with Patterson’s D statistics and DFOIL. We found nuclear introgression resulting in substantial admixture between americanus group species, between H. roberti and the clypeatus group, and between the clypeatus and coecatus groups.ConclusionsOur results indicate that the phylogenetic history of Habronattus is predominantly a diverging tree, but that hybridization may have been common between phylogenetically distant species, especially in subgroups with complex courtship displays.

The impact of phenotypic and molecular data on the inference of Colletotrichum diversity associated with Musa

ABSTRACTDeveloping a comprehensive and reliable taxonomy for the Colletotrichum gloeosporioides species complex will require adopting data standards on the basis of an understanding of how methodological choices impact morphological evaluations and phylogenetic inference. We explored the impact of methodological choices in a morphological and molecular evaluation of Colletotrichum species associated with banana in Brazil. The choice of alignment filtering algorithm has a significant impact on topological inference and the retention of phylogenetically informative sites. Similarly, the choice of phylogenetic marker affects the delimitation of species boundaries, particularly if low phylogenetic signal is confounded with strong discordance, and inference of the species tree from multiple-gene trees. According to both phylogenetic informativeness profiling and Bayesian concordance analyses, the most informative loci are DNA lyase (APN2), intergenic spacer (IGS) between DNA lyase and the mating-type locus MAT1-2-1 (APN2/MAT-IGS), calmodulin (CAL), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), glutamine synthetase (GS), β-tubulin (TUB2), and a new marker, the intergenic spacer between GAPDH and an hypothetical protein (GAP2-IGS). Cornmeal agar minimizes the variance in conidial dimensions compared with potato dextrose agar and synthetic nutrient-poor agar, such that species are more readily distinguishable based on phenotypic differences. We apply these insights to investigate the diversity of Colletotrichum species associated with banana anthracnose in Brazil and report C. musae, C. tropicale, C. theobromicola, and C. siamense in association with banana anthracnose. One lineage did not cluster with any previously described species and is described here as C. chrysophilum.

Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae)

Hybridization is a frequent and important force in plant evolution. Next-generation sequencing (NGS) methods offer new possibilities for clade resolution and ambitious sampling of gene genealogies, yet difficulty remains in detecting deep reticulation events using currently available methods. We reconstructed the phylogeny of diploid representatives of Amaryllidaceae tribe Hippeastreae to test the hypothesis of ancient hybridizations preceding the radiation of its major subclade, Hippeastrinae. Through hybrid enrichment of DNA libraries and NGS, we obtained data for 18 nuclear loci through a curated assembly approach and nearly complete plastid genomes for 35 ingroup taxa plus 5 outgroups. Additionally, we obtained alignments for 39 loci through an automated assembly algorithm. These data were analyzed with diverse phylogenetic methods, including concatenation, coalescence-based species tree estimation, Bayesian concordance analysis, and network reconstructions, to provide insights into the evolutionary relationships of Hippeastreae. Causes for gene tree heterogeneity and cytonuclear discordance were examined through a Bayesian posterior predictive approach (JML) and coalescent simulations. Two major clades were found, Hippeastrinae and Traubiinae, as previously reported. Our results suggest the presence of two major nuclear lineages in Hippeastrinae characterized by different chromosome numbers: (1) Tocantinia and Hippeastrum with 2n=22, and (2) Eithea, Habranthus, Rhodophiala, and Zephyranthes mostly with 2n=12, 14, and 18. Strong cytonuclear discordance was confirmed in Hippeastrinae, and a network scenario with at least six hybridization events is proposed to reconcile nuclear and plastid signals, along a backbone that may also have been affected by incomplete lineage sorting at the base of each major subclade.

Optimal data partitioning, multispecies coalescent and Bayesian concordance analyses resolve early divergences of the grape family (Vitaceae).

Evolutionary rate heterogeneity and rapid radiations are common phenomena in organismal evolution and represent major challenges for reconstructing deep-level phylogenies. Here we detected substantial conflicts in and among data sets as well as uncertainty concerning relationships among lineages of Vitaceae from individual gene trees, supernetworks and tree certainty values. Congruent deep-level relationships of Vitaceae were retrieved by comprehensive comparisons of results from optimal partitioning analyses, multispecies coalescent approaches and the Bayesian concordance method. We found that partitioning schemes selected by PartitionFinder were preferred over those by gene or by codon position, and the unpartitioned model usually performed the worst. For a data set with conflicting signals, however, the unpartitioned model outperformed models that included more partitions, demonstrating some limitations to the effectiveness of concatenation for these data. For a transcriptome data set, fast coalescent methods (STAR and MP-EST) and a Bayesian concordance approach yielded congruent topologies with trees from the concatenated analyses and previous studies. Our results highlight that well-resolved gene trees are critical for the effectiveness of coalescent-based methods. Future efforts to improve the accuracy of phylogenomic analyses should emphasize the development of newmethods that can accommodate multiple biological processes and tolerate missing data while remaining computationally tractable.

Chromosome 1 Sequence Analysis of C57BL/6J-Chr1KM Mouse Strain.

The Chinese Kunming (KM) mouse is a widely used outbred mouse stock in China. However, its genetic structure remains unclear. In this study, we sequenced the genome of the C57BL/6J-Chr1KM (B6-Chr1KM) strain, the chromosome 1 (Chr 1) of which was derived from one KM mouse. With 36.6× average coverage of the entire genome, 0.48 million single nucleotide polymorphisms (SNPs) and 96,679 indels were detected on Chr 1 through comparison with reference strain C57BL/6J. Moreover, 46,590 of them were classified as novel mutations. Further functional annotation identified 155 genes harboring potentially functional variants, among which 27 genes have been associated with human diseases. We then performed sequence similarity and Bayesian concordance analysis using the SNPs identified on Chr 1 and their counterparts in three subspecies, Mus musculus domesticus, M. m. musculus, and M. m. castaneus. Both analyses suggested that the Chr 1 sequence of B6-Chr1KM was predominantly derived from M. m. domesticus while 9.7% of the sequence was found to be from M. m. musculus. In conclusion, our analysis provided a detailed description of the genetic variations on Chr 1 of B6-Chr1KM and a new perspective on the subspecies origin of KM mouse which can be used to guide further genetic studies with this mouse strain.

Phylogenomics of tubeworms (Siboglinidae, Annelida) and comparative performance of different reconstruction methods

Deep‐sea tubeworms (Annelida, Siboglinidae) represent dominant species in deep‐sea chemosynthetic communities (e.g. hydrothermal vents and cold methane seeps) and occur in muddy sediments and organic falls. Siboglinids lack a functional digestive tract as adults, and they rely on endosymbiotic bacteria for energy, making them of evolutionary and physiological interest. Despite their importance, inferred evolutionary history of this group has been inconsistent among studies based on different molecular markers. In particular, placement of bone‐eating Osedax worms has been unclear in part because of their distinctive biology, including harbouring heterotrophic bacteria as endosymbionts, displaying extreme sexual dimorphism and exhibiting a distinct body plan. Here, we reconstructed siboglinid evolutionary history using 12 newly sequenced transcriptomes. We parsed data into three data sets that accommodated varying levels of missing data, and we evaluate effects of missing data on phylogenomic inference. Additionally, several multispecies‐coalescent approaches and Bayesian concordance analysis (BCA) were employed to allow for a comparison of results to a supermatrix approach. Every analysis conducted herein strongly supported Osedax being most closely related to the Vestimentifera and Sclerolinum clade, rather than Frenulata, as previously reported. Importantly, unlike previous studies, the alternative hypothesis that frenulates and Osedax are sister groups to one another was explicitly rejected by an approximately unbiased (AU) test. Furthermore, although different methods showed largely congruent results, we found that a supermatrix method using data partitioning with site‐homogenous models potentially outperformed a supermatrix method using the CAT‐GTR model and multispecies‐coalescent approaches when the amount of missing data varies in a data set and when taxa susceptible to LBA are included in the analyses.

Integrated Molecular and Morphological Studies of the <I>Daucus guttatus</I> Complex (Apiaceae)

Abstract In a previous study using 94 nuclear orthologs, we reported the species status of the Daucus guttatus complex to be unresolved, partitioned into three clades. In the present study, a subset of ten of these 94 orthologs was used to infer the phylogeny of the D. guttatus complex and related species. A near parallel set of accessions, planted in a common garden, was used for morphological analyses. The molecular trees are highly resolved for most of the clades, grouping accessions of the D. guttatus complex into four clades. Bayesian concordance analysis and a coalescent approach gave slightly different topologies. Morphological data likewise support four taxa in the complex. Moreover, herbarium research from a companion study informs nomenclature for taxa of the complex. We identify these four clades as D. bicolor, D. conchitae, D. guttatus, and D. setulosus; internested in or among these segregates are the phenetically distinctive species D. glochidiatus, D. involucratus, D. littoralis, and D. pus...

Whole genome duplication in coast redwood (Sequoia sempervirens) and its implications for explaining the rarity of polyploidy in conifers.

Polyploidy is common and an important evolutionary factor in most land plant lineages, but it is rare in gymnosperms. Coast redwood (Sequoia sempervirens) is one of just two polyploid conifer species and the only hexaploid. Evidence from fossil guard cell size suggests that polyploidy in Sequoia dates to the Eocene. Numerous hypotheses about the mechanism of polyploidy and parental genome donors have been proposed, based primarily on morphological and cytological data, but it remains unclear how Sequoia became polyploid and why this lineage overcame an apparent gymnosperm barrier to whole-genome duplication (WGD). We sequenced transcriptomes and used phylogenetic inference, Bayesian concordance analysis and paralog age distributions to resolve relationships among gene copies in hexaploid coast redwood and close relatives. Our data show that hexaploidy in coast redwood is best explained by autopolyploidy or, if there was allopolyploidy, it happened within the Californian redwood clade. We found that duplicate genes have more similar sequences than expected, given the age of the inferred polyploidization. Conflict between molecular and fossil estimates of WGD can be explained if diploidization occurred very slowly following polyploidization. We extrapolate from this to suggest that the rarity of polyploidy in gymnosperms may be due to slow diploidization in this clade.

Thousands of RAD-seq Loci Fully Resolve the Phylogeny of the Highly Disjunct Arctic-Alpine Genus Diapensia (Diapensiaceae)

Restriction-site associated DNA sequencing (RAD-seq) has recently become an important method to generate genome-wide molecular data for species delimitation, phylogeography, and population genetic studies. However, very few empirical studies have so far tested its applicability in phylogenetic reconstruction. The alpine-arctic genus Diapensia was selected to study the origin of the disjunction between the Arctic and the Himalayan-Hengduan Mountains (HHM). However, a previous phylogenetic analysis based on one nuclear and four plastid DNA regions failed to resolve the oldest divergences in Diapensia as well as the relationship between the two HHM species. Here we reconstruct a fully resolved phylogeny of Diapensia and address the conflict between the currently accepted taxonomy and the gene trees in the HHM species using RAD-seq. Based on a data set containing 2,650 loci selected to maximize the number of parsimony informative sites and allowing for a high level of missing data (51%), the phylogeny of Diapensia was fully resolved and each of the four species was reciprocally monophyletic. Whereas the arctic D. lapponica was inferred as sister to the HHM clade in the previous study, the RAD-seq data resolved the two arctic species as sisters to the HHM clade. Similar relationships were inferred from a differently filtered data set with far fewer loci (114) and less missing data (21%), but with lower support and with one of the two HHM species as non-monophyletic. Bayesian concordance analysis and Patterson’s D-statistic tests suggested that admixture has occurred between the two HHM species.

An Expanded <I>Metrosideros</I> (Myrtaceae) to Include <I>Carpolepis</I> and <I>Tepualia</I> Based on Nuclear Genes

Abstract The genus Metrosideros (Myrtaceae) comprises 50–60 species found largely across the Pacific Islands. The relationships within this genus, including the circumscriptions of the subgenera Mearnsia and Metrosideros and their relationships with the other members of the tribe Metrosidereae (namely the New Caledonian endemic genus Carpolepis and the South American Tepualia), are poorly understood. Phylogenetic analyses were carried out using previously published ITS sequences, covering most species of the tribe, and new sequences of five single-copy nuclear genes with a reduced taxon sampling. The independent and combined analyses of the five nuclear genes using a range of approaches, including Bayesian single-gene, concatenated (MrBayes), concordance (BUCKy) and coalescent (*BEAST) analyses, yielded different topologies, indicating important conflicts among phylogenies based on individual genes. The deep relationships within the tribe Metrosidereae remain poorly resolved, but our results indicate that...

Species-Level Phylogeny and Polyploid Relationships in Hordeum (Poaceae) Inferred by Next-Generation Sequencing and In Silico Cloning of Multiple Nuclear Loci.

Polyploidization is an important speciation mechanism in the barley genus Hordeum. To analyze evolutionary changes after allopolyploidization, knowledge of parental relationships is essential. One chloroplast and 12 nuclear single-copy loci were amplified by polymerase chain reaction (PCR) in all Hordeum plus six out-group species. Amplicons from each of 96 individuals were pooled, sheared, labeled with individual-specific barcodes and sequenced in a single run on a 454 platform. Reference sequences were obtained by cloning and Sanger sequencing of all loci for nine supplementary individuals. The 454 reads were assembled into contigs representing the 13 loci and, for polyploids, also homoeologues. Phylogenetic analyses were conducted for all loci separately and for a concatenated data matrix of all loci. For diploid taxa, a Bayesian concordance analysis and a coalescent-based dated species tree was inferred from all gene trees. Chloroplast matK was used to determine the maternal parent in allopolyploid taxa. The relative performance of different multilocus analyses in the presence of incomplete lineage sorting and hybridization was also assessed. The resulting multilocus phylogeny reveals for the first time species phylogeny and progenitor-derivative relationships of all di- and polyploid Hordeum taxa within a single analysis. Our study proves that it is possible to obtain a multilocus species-level phylogeny for di- and polyploid taxa by combining PCR with next-generation sequencing, without cloning and without creating a heavy load of sequence data.

Re-evaluating the phylogeny of allopolyploid Gossypium L.

The formation of allopolyploid cotton precipitated a rapid diversification and colonization of dry coastal American tropical and subtropical regions. Previous phylogenetic analyses, combined with molecular divergence analyses, have offered a temporal framework for this radiation, but provide only weak support for some of the resolved branches. Moreover, these earlier analyses did not include the recently recognized sixth polyploid species, G. ekmanianum Wittmack. Here we use targeted sequence capture of multiple loci in conjunction with both concatenated and Bayesian concordance analyses to reevaluate the phylogeny of allopolyploid cotton species. Although phylogenetic resolution afforded by individual genes is often low, sufficient signal was attained both through the concatenated and concordance analyses to provide robust support for the Gossypium polyploid clade, which is reported here.

A tribal level phylogeny of Lake Tanganyika cichlid fishes based on a genomic multi-marker approach

The species-flocks of cichlid fishes in the East African Great Lakes Victoria, Malawi and Tanganyika constitute the most diverse extant adaptive radiations in vertebrates. Lake Tanganyika, the oldest of the lakes, harbors the morphologically and genetically most diverse assemblage of cichlids and contains the highest number of endemic cichlid genera of all African lakes. Based on morphological grounds, the Tanganyikan cichlid species have been grouped into 12–16 distinct lineages, so-called tribes. While the monophyly of most of the tribes is well established, the phylogenetic relationships among the tribes remain largely elusive. Here, we present a new tribal level phylogenetic hypothesis for the cichlid fishes of Lake Tanganyika that is based on the so far largest set of nuclear markers and a total alignment length of close to 18kb. Using next-generation amplicon sequencing with the 454 pyrosequencing technology, we compiled a dataset consisting of 42 nuclear loci in 45 East African cichlid species, which we subjected to maximum likelihood and Bayesian inference phylogenetic analyses. We analyzed the entire concatenated dataset and each marker individually, and performed a Bayesian concordance analysis and gene tree discordance tests. Overall, we find strong support for a position of the Oreochromini, Boulengerochromini, Bathybatini and Trematocarini outside of a clade combining the substrate spawning Lamprologini and the mouthbrooding tribes of the ‘H-lineage’, which are both strongly supported to be monophyletic. The Eretmodini are firmly placed within the ‘H-lineage’, as sister-group to the most species-rich tribe of cichlids, the Haplochromini. The phylogenetic relationships at the base of the ‘H-lineage’ received less support, which is likely due to high speciation rates in the early phase of the radiation. Discordance among gene trees and marker sets further suggests the occurrence of past hybridization and/or incomplete lineage sorting in the cichlid fishes of Lake Tanganyika.

Data concatenation, Bayesian concordance and coalescent-based analyses of the species tree for the rapid radiation of Triturus newts.

The phylogenetic relationships for rapid species radiations are difficult to disentangle. Here we study one such case, namely the genus Triturus, which is composed of the marbled and crested newts. We analyze data for 38 genetic markers, positioned in 3-prime untranslated regions of protein-coding genes, obtained with 454 sequencing. Our dataset includes twenty Triturus newts and represents all nine species. Bayesian analysis of population structure allocates all individuals to their respective species. The branching patterns obtained by data concatenation, Bayesian concordance analysis and coalescent-based estimations of the species tree differ from one another. The data concatenation based species tree shows high branch support but branching order is considerably affected by allele choice in the case of heterozygotes in the concatenation process. Bayesian concordance analysis expresses the conflict between individual gene trees for part of the Triturus species tree as low concordance factors. The coalescent-based species tree is relatively similar to a previously published species tree based upon morphology and full mtDNA and any conflicting internal branches are not highly supported. Our findings reflect high gene tree discordance due to incomplete lineage sorting (possibly aggravated by hybridization) in combination with low information content of the markers employed (as can be expected for relatively recent species radiations). This case study highlights the complexity of resolving rapid radiations and we acknowledge that to convincingly resolve the Triturus species tree even more genes will have to be consulted.

Phylogenomics of the carrot genus (Daucus, Apiaceae).

• We explored the utility of multiple nuclear orthologs for the taxonomic resolution of wild and cultivated carrot, Daucus species.• We studied the phylogeny of 92 accessions of 13 species and two subspecies of Daucus and 15 accessions of related genera (107 accessions total) with DNA sequences of 94 nuclear orthologs. Reiterative analyses examined data of both alleles using ambiguity codes or a single allele with the highest coverage, trimmed vs. untrimmed homopolymers; pure exonic vs. pure intronic data; the use of all 94 markers vs. a reduced subset of markers; and analysis of a concatenated data set vs. a coalescent (species tree) approach.• Our maximum parsimony and maximum likelihood trees were highly resolved, with 100% bootstrap support for most of the external and many of the internal clades. They resolved multiple accessions of many different species as monophyletic with strong support, but failed to support other species. The single allele analysis gave slightly better topological resolution; trimming homopolymers failed to increase taxonomic resolution; the exonic data had a smaller proportion of parsimony-informative characters. Similar results demonstrating the same dominant topology can be obtained with many fewer markers. A Bayesian concordance analysis provided an overall similar phylogeny, but the coalescent analysis provided drastic changes in topology to all the above.• Our research highlights some difficult species groups in Daucus and misidentifications in germplasm collections. It highlights a useful subset of markers and approaches for future studies of dominant topologies in Daucus.

Evaluating evolutionary history in the face of high gene tree discordance in Australian Gehyra (Reptilia: Gekkonidae).

Species tree methods have provided improvements for estimating species relationships and the timing of diversification in recent radiations by allowing for gene tree discordance. Although gene tree discordance is often observed, most discordance is attributed to incomplete lineage sorting rather than other biological phenomena, and the causes of discordance are rarely investigated. We use species trees from multi-locus data to estimate the species relationships, evolutionary history and timing of diversification among Australian Gehyra-a group renowned for taxonomic uncertainty and showing a large degree of gene tree discordance. We find support for a recent Asian origin and two major clades: a tropically adapted clade and an arid adapted clade, with some exceptions, but no support for allopatric speciation driven by chromosomal rearrangement in the group. Bayesian concordance analysis revealed high gene tree discordance and comparisons of Robinson-Foulds distances showed that discordance between gene trees was significantly higher than that generated by topological uncertainty within each gene. Analysis of gene tree discordance and incomplete taxon sampling revealed that gene tree discordance was high whether terminal taxon or gene sampling was maximized, indicating discordance is due to biological processes, which may be important in contributing to gene tree discordance in many recently diversified organisms.