Rooting molecular trees: problems and strategies

Revised phylogeny from complete mitochondrial genomes of phyllostomid bats resolves subfamilial classification

Classically, molecular phylogenetic trees of Phyllostomidae have been inferred using a combination of a few mitochondrial and nuclear markers. However, there is still uncertainty in the relationships, especially among deep clades within the family. In this study, we provide newly sequenced complete mitochondrial genomes from 26 bat species, including genomes of 23 species reported here for the first time. By carefully analysing these genomes using maximum likelihood and Bayesian methods and different ingroup and outgroup samples, partition schemes and data types, we investigated the robustness and sensitivity of our phylogenetic results. The optimal topologies were those inferred from the complete data matrix of nucleotides, with complex and highly parameterized substitution models and partition schemes. Our results show a statistically robust picture of the evolutionary relationships between phyllostomid subfamilies and clarify hitherto uncertain relationships of Lonchorhininae and Macrotinae.

Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Non-Reversible Models for Mammals

Using time-reversible Markov models is a very common practice in phylogenetic analysis, because although we expect many of their assumptions to be violated by empirical data, they provide high computational efficiency. However, these models lack the ability to infer the root placement of the estimated phylogeny. In order to compensate for the inability of these models to root the tree, many researchers use external information such as using outgroup taxa or additional assumptions such as molecular clocks. In this study, we investigate the utility of nonreversible models to root empirical phylogenies and introduce a new bootstrap measure, the rootstrap, which provides information on the statistical support for any given root position. [Bootstrap; nonreversible models; phylogenetic inference; root estimation.]

Spectral neighbor joining for reconstruction of latent tree Models

A common assumption in multiple scientific applications is that the distribution of observed data can be modeled by a latent tree graphical model. An important example is phylogenetics, where the tree models the evolutionary lineages of a set of observed organisms. Given a set of independent realizations of the random variables at the leaves of the tree, a key challenge is to infer the underlying tree topology. In this work we develop Spectral Neighbor Joining (SNJ), a novel method to recover the structure of latent tree graphical models. Given a matrix that contains a measure of similarity between all pairs of observed variables, SNJ computes a spectral measure of cohesion between groups of observed variables. We prove that SNJ is consistent, and derive a sufficient condition for correct tree recovery from an estimated similarity matrix. Combining this condition with a concentration of measure result on the similarity matrix, we bound the number of samples required to recover the tree with high probability. We illustrate via extensive simulations that in comparison to several other reconstruction methods, SNJ requires fewer samples to accurately recover trees with a large number of leaves or long edges.

Dinosaur diversification rates were not in decline prior to the K-Pg boundary

Determining the tempo and mode of non-avian dinosaur extinction is one of the most contentious issues in palaeobiology. Extensive disagreements remain over whether their extinction was catastrophic and geologically instantaneous or the culmination of long-term evolutionary trends. These conflicts have arisen due to numerous hierarchical sampling biases in the fossil record and differences in analytical methodology, with some studies identifying long-term declines in dinosaur richness prior to the Cretaceous-Palaeogene (K-Pg) boundary and others proposing continued diversification. Here, we use Bayesian phylogenetic generalized linear mixed models to assess the fit of 12 dinosaur phylogenies to three speciation models (null, slowdown to asymptote, downturn). We do not find strong support for the downturn model in our analyses, which suggests that dinosaur speciation rates were not in terminal decline prior to the K-Pg boundary and that the clade was still capable of generating new taxa. Nevertheless, we advocate caution in interpreting the results of such models, as they may not accurately reflect the complexities of the underlying data. Indeed, current phylogenetic methods may not provide the best test for hypotheses of dinosaur extinction; the collection of more dinosaur occurrence data will be essential to test these ideas further.

Characterization of the Complete Genome and P0 Protein for a Previously Unreported Genotype of Cotton Leafroll Dwarf Virus, an Introduced Polerovirus in the United States

Virus-like disease symptoms consisting of leaf cupping, shortened internodes, and overall stunting were observed in commercial cotton fields in Alabama in 2017 to 2018. To determine the complete genome sequence of the suspected causal polerovirus, symptomatic leaf samples were collected in Macon County, Alabama, and subjected to Illumina RNA sequencing. Based on BLASTn analysis, the Illumina contig of 5,771 nt shared the highest nucleotide identity (approximately 95%) with members of the species Cotton leafroll dwarf virus (CLRDV) (genus Polerovirus; family Luteoviridae) from Argentina and Brazil. The full-length viral genome sequence was verified by reverse transcription (RT)-PCR amplification, cloning, and Sanger sequencing. The complete CLRDV genome of 5,865 nt in length shared 94.8 to 95.2% nucleotide identity with six previously reported CLRDV isolates. The genome of the CLRDV isolate amplified from Alabama samples (CLRDV-AL) has seven predicted open reading frames (ORFs). Viral proteins 1 to 5 (P1 to P5) shared 91.9 to 99.5% amino acid identity with the six CLRDV isolates from Argentina and Brazil. However, P0, the suppressor of host gene silencing, shared 82.4 to 88.5% pairwise amino acid identity with the latter CLRDV isolates. Phylogenetic analysis of the seven full-length CLRDV genomes resolved three sister clades: CLRDV-AL, CLRDV-typical, and CLRDV-atypical, respectively. Three recombination events were detected by the recombination detection program among the seven CLRDV isolates with breakpoints occurring along the genome. Pairwise nucleotide identity comparisons of ORF0 sequences for the three CLRDV-AL field isolates indicated that they were >99% identical, suggesting that this previously unknown CLRDV genotype represents a single introduction to Alabama.

Origin and diversification of Xanthomonas citri subsp. citri pathotypes revealed by inclusive phylogenomic, dating, and biogeographic analyses

BACKGROUND

Xanthomonas citri subsp. citri pathotypes cause bacterial citrus canker, being responsible for severe agricultural losses worldwide. The A pathotype has a broad host spectrum, while A* and Aw are more restricted both in hosts and in geography. Two previous phylogenomic studies led to contrasting well-supported clades for sequenced genomes of these pathotypes. No extensive biogeographical or divergence dating analytic approaches have been so far applied to available genomes.

RESULTS

Based on a larger sampling of genomes than in previous studies (including six new genomes sequenced by our group, adding to a total of 95 genomes), phylogenomic analyses resulted in different resolutions, though overall indicating that A + AW is the most likely true clade. Our results suggest the high degree of recombination at some branches and the fast diversification of lineages are probable causes for this phylogenetic blurring effect. One of the genomes analyzed, X. campestris pv. durantae, was shown to be an A* strain; this strain has been reported to infect a plant of the family Verbenaceae, though there are no reports of any X. citri subsp. citri pathotypes infecting any plant outside the Citrus genus. Host reconstruction indicated the pathotype ancestor likely had plant hosts in the family Fabaceae, implying an ancient jump to the current Rutaceae hosts. Extensive dating analyses indicated that the origin of X. citri subsp. citri occurred more recently than the main phylogenetic splits of Citrus plants, suggesting dispersion rather than host-directed vicariance as the main driver of geographic expansion. An analysis of 120 pathogenic-related genes revealed pathotype-associated patterns of presence/absence.

CONCLUSIONS

Our results provide novel insights into the evolutionary history of X. citri subsp. citri as well as a sound phylogenetic foundation for future evolutionary and genomic studies of its pathotypes.

Molecular identification of Andricus species (Hymenoptera: Cynipidae) inducing various oak galls in Central Zagros of Iran

This study uses an integrated approach to address the taxonomic status of six different and problematic oak galls and their inducing wasps sampled from two sites in the Central Zagros Mountains (Lorestan province) in western Iran. Our aim was to establish whether morphologically similar but different galls are induced by the same or distinct gall-inducers. The gall wasp specimens were identified morphologically to species level, and their genomic DNA was extracted. We used PCR and Sanger sequencing to amplify three fragments comprising cytochrome oxidase subunit I (COI), cytochrome b (cytB), and a multi-gene fragment of ribosomal DNA (rDNA) including partial 5.8S, complete internal transcribed spacer 2 (ITS2), and partial 28S rRNA. We found that a pair of structurally similar but differently coloured galls are induced by the sexual generation of Andricus grossulariae, while another similar pair are induced by the asexual generation of A. sternlichti. In contrast, we found that two similar galls that differ in some structural details and in developmental phenology are induced by two closely related but different gall wasps; one is the sexual generation of A. cecconii, while the second is a new but closely related sexual generation Andricus sp.

Molecular identification of Rhipicephalus species (Acari: Ixodidae) parasitizing livestock from Iran

This study was designed to identify populations of Rhipicephalus sanguineus collected from Iran and also to study molecular taxonomy of Rhipicephalus species using cytochrome C oxidase subunit 1 (COI) and internal transcribed spacer 2 (ITS2) sequences. Tick specimens were collected from livestock (sheep and goat) in 14 Iranian provinces. DNA of individual specimens was extracted and PCR was done on these samples. So, 62 sequencing (33 COI and 29 ITS2) were done, successfully. Morphologically, we identified four Rhipicephalus species, namely R. bursa, R. sanguineus (s.l.), R. sanguineus (s.s.), and R. turanicus based on taxonomic keys. The data obtained from the phylogenetic analyses of COI and ITS2 fragments present a possible conflict regarding the identity of R. sanguineus species. Thus, the molecular identification of R. sanguineus group might be different according to mitochondrial and nuclear DNA. The results show a phylogenic conflict based on COI and ITS2 phylogeny in a tree topology. We dealt with three genetic entities in R. sanguineus group (i.e. R. sanguineus (s.s.), R. sanguineus (s.l.), and R. turanicus) based on COI phylogeny and two genetic clades (i.e. R. sanguineus (s.s.) and R. sanguineus (s.l.)/R. turanicus) according to ITS2 phylogeny.

Synthesizing large-scale species trees using the strict consensus approach

Supertree problems are a standard tool for synthesizing large-scale species trees from a given collection of gene trees under some problem-specific objective. Unfortunately, these problems are typically NP-hard, and often remain so when their instances are restricted to rooted gene trees sampled from the same species. While a class of restricted supertree problems has been effectively addressed by the parameterized strict consensus approach, in practice, most gene trees are unrooted and sampled from different species. Here, we overcome this stringent limitation by describing efficient algorithms that are adopting the strict consensus approach to also handle unrestricted supertree problems. Finally, we demonstrate the performance of our algorithms in a comparative study with classic supertree heuristics using simulated and empirical data sets.

All 37 Mitochondrial Genes of Aphid Aphis craccivora Obtained from Transcriptome Sequencing: Implications for the Evolution of Aphids

The availability of mitochondrial genome data for Aphididae, one of the economically important insect pest families, in public databases is limited. The advent of next generation sequencing technology provides the potential to generate mitochondrial genome data for many species timely and cost-effectively. In this report, we used transcriptome sequencing technology to determine all the 37 mitochondrial genes of the cowpea aphid, Aphis craccivora. This method avoids the necessity of finding suitable primers for long PCRs or primer-walking amplicons, and is proved to be effective in obtaining the whole set of mitochondrial gene data for insects with difficulty in sequencing mitochondrial genome by PCR-based strategies. Phylogenetic analyses of aphid mitochondrial genome data show clustering based on tribe level, and strongly support the monophyly of the family Aphididae. Within the monophyletic Aphidini, three samples from Aphis grouped together. In another major clade of Aphididae, Pterocomma pilosum was recovered as a potential sister-group of Cavariella salicicola, as part of Macrosiphini.

Phylogeny and Historical Biogeography of Asian Pterourus Butterflies (Lepidoptera: Papilionidae): A Case of Intercontinental Dispersal from North America to East Asia

The phylogenetic status of the well-known Asian butterflies often known as Agehana (a species group, often treated as a genus or a subgenus, within Papilio sensu lato) has long remained unresolved. Only two species are included, and one of them especially, Papilio maraho, is not only rare but near-threatened, being monophagous on its vulnerable hostplant, Sassafras randaiense (Lauraceae). Although the natural history and population conservation of "Agehana" has received much attention, the biogeographic origin of this group still remains enigmatic. To clarify these two questions, a total of 86 species representatives within Papilionidae were sampled, and four genes (concatenated length 3842 bp) were used to reconstruct their phylogenetic relationships and historical scenarios. Surprisingly, "Agehana" fell within the American Papilio subgenus Pterourus and not as previously suggested, phylogenetically close to the Asian Papilio subgenus Chilasa. We therefore formally synonymize Agehana with Pterourus. Dating and biogeographic analysis allow us to infer an intercontinental dispersal of an American ancestor of Asian Pterourus in the early Miocene, which was coincident with historical paleo-land bridge connections, resulting in the present "East Asia-America" disjunction distribution. We emphasize that species exchange between East Asia and America seems to be a quite frequent occurrence in butterflies during the Oligocene to Miocene climatic optima.

Phylogenetic analysis of HpnP reveals the origin of 2-methylhopanoid production in Alphaproteobacteria

Hopanoids are bacterial steroid-like lipids that can be preserved in the rock record on billion-year timescales. 2-Methylhopanoids are of particular interest to geobiologists because methylation is one of the few chemical modifications that remain after diagenesis and catagenesis. 2-Methylhopanes, the molecular fossils of 2-methylhopanoids, are episodically enriched in the rock record, but we do not have a robust interpretation for their abundance patterns. Here, we exploit the evolutionary record found in molecular sequences from extant organisms to reconstruct the biosynthetic history of 2-methylhopanoids using the C-2 hopanoid methylase, HpnP. Based on HpnP phylogenetic analysis, we find that 2-methylhopanoids originated in a subset of the Alphaproteobacteria. This conclusion is statistically robust and reproducible in multiple trials varying the outgroup, trimming stringency, and ingroup dataset used to infer the evolution of this protein family. The capacity for 2-methylhopanoid production was likely horizontally transferred from the Alphaproteobacteria into the Cyanobacteria after the Cyanobacteria's major divergences. Together, these results suggest that the ancestral function of 2-methylhopanoids was not related to oxygenic photosynthesis but instead to a trait already present in the Alphaproteobacteria. Moreover, given that early 2-methylhopane deposits could have been made solely by Alphaproteobacteria before the acquisition of hpnP by Cyanobacteria, and that the Alphaproteobacteria are thought to be ancestrally aerobic, we infer that 2-methylhopanoids likely arose after the oxygenation of the atmosphere. This finding is consistent with the geologic record-the oldest syngenetic 2-methylhopanes occur after the rise of oxygen, in middle Proterozoic strata of the Barney Creek Formation.

Long-branch attraction and the phylogeny of true water bugs (Hemiptera: Nepomorpha) as estimated from mitochondrial genomes

BACKGROUND

Most previous studies of morphological and molecular data have consistently supported the monophyly of the true water bugs (Hemiptera: Nepomorpha). An exception is a recent study by Hua et al. (BMC Evol Biol 9: 134, 2009) based on nine nepomorphan mitochondrial genomes. In the analysis of Hua et al. (BMC Evol Biol 9: 134, 2009), the water bugs in the group Pleoidea formed the sister group to a clade that consisted of Nepomorpha (the remaining true water bugs) + Leptopodomorpha (shore bugs) + Cimicomorpha (assassin bugs and relatives) + Pentatomomorpha (stink bugs and relatives), thereby suggesting that fully aquatic hemipterans evolved independently at least twice. Based on these results, Hua et al. (BMC Evol Biol 9: 134, 2009) elevated the Pleoidea to a new infraorder, the Plemorpha.

RESULTS

Our reanalysis suggests that the lack of support for the monophyly of the true water bugs (including Pleoidea) by Hua et al. (BMC Evol Biol 9: 134, 2009) likely resulted from inadequate taxon sampling. In particular, long-branch attraction (LBA) between the distant outgroup taxa and Pleoidea, as well as LBA among taxa in the ingroup, made Nepomorpha appear to be polyphyletic. We used three complementary strategies to test and alleviate the effects of LBA: (1) the removal of distant outgroups from the analysis; (2) the addition of closely related outgroups; and (3) the addition of a mitochondrial genome from a second family of Pleoidea. We also performed likelihood-ratio tests to examine the support for monophyly of Nepomorpha with different combinations of taxa included in the analysis. Furthermore, we found that specimens of Helotrephes sp. were misidentified as Paraplea frontalis (Fieber, 1844) by Hua et al. (BMC Evol Biol 9: 134, 2009).

CONCLUSIONS

All analyses that included the addition of more taxa significantly and consistently supported the placement of Pleoidea within the Nepomorpha (i.e., supported the monophyly of the traditional true water bugs). Our analyses further support a close relationship between Notonectoidea and Pleoidea within Nepomorpha, and the superfamilies Nepoidea, Ochteroidea, Naucoroidea, and Pleoidea are resolved as monophyletic in all trees with strong support. Our results also confirmed that monophyly of Nepomorpha clearly is not refuted by the mitochondrial genome data.

Seven-locus molecular phylogeny of Myctophiformes (Teleostei; Scopelomorpha) highlights the utility of the order for studies of deep-sea evolution

Fishes of the order Myctophiformes (Teleostei; Scopelomorpha) comprise over half of all deep-sea biomass, and are a critical component of marine ecosystems worldwide. Members of the family Myctophidae, within Myctophiformes, form the majority of species diversity within the order (∼250 species, 33 genera, 2 subfamilies), and are further known for their diverse bioluminescent traits, comprised of distinct cranial, postcranial, and caudal luminous systems that is perhaps the most elaborate among all vertebrates. These features make myctophids particularly compelling from both economic and scientific perspectives, yet no studies have sampled these fishes at a density appropriate for addressing any questions requiring a phylogenetic hypothesis as input. This study therefore presents a seven-locus molecular phylogeny of the order, sampling over 50% of all nominal myctophid species. This taxon sampling triples the representation of the next most comprehensive analysis, and reveals several new and well-supported hypotheses of relationships, in addition to supporting traditional hypotheses based on combined morphological data. This analysis shows that the slendertailed myctophids Gonichthys, Centrobranchus, Loweina, and Tarletonbeania are rendered non-monophyletic by a polyphyletic Myctophum; the enigmatic, monotypic genus Notolychnus valdiviae is nested within tribe Lampanyctini; the genus Diaphus is divided into at least two clades, with the suborbital (So) group recovered as monophyletic with strong support; and the genera Lampanyctus and Nannobrachium are recovered as non-monophyletic. These molecular results highlight the potential of myctophids as a premier model system for the application of modern comparative methods to studies of deep-sea evolution.

Evolution of lanthipeptide synthetases

Lanthionine-containing peptides (lanthipeptides) are a family of ribosomally synthesized and posttranslationally modified peptides containing (methyl)lanthionine residues. Here we present a phylogenomic study of the four currently known classes of lanthipeptide synthetases (LanB and LanC for class I, LanM for class II, LanKC for class III, and LanL for class IV). Although they possess very similar cyclase domains, class II-IV synthetases have evolved independently, and LanB and LanC enzymes appear to not always have coevolved. LanM enzymes from various phyla that have three cysteines ligated to a zinc ion (as opposed to the more common Cys-Cys-His ligand set) cluster together. Most importantly, the phylogenomic data suggest that for some scaffolds, the ring topology of the final lanthipeptides may be determined in part by the sequence of the precursor peptides and not just by the biosynthetic enzymes. This notion was supported by studies with two chimeric peptides, suggesting that the nisin and prochlorosin biosynthetic enzymes can produce the correct ring topologies of epilancin 15X and lacticin 481, respectively. These results highlight the potential of lanthipeptide synthetases for bioengineering and combinatorial biosynthesis. Our study also demonstrates unexplored areas of sequence space that may be fruitful for genome mining.

Fixed, free, and fixed: the fickle phylogeny of extant Crinoidea (Echinodermata) and their Permian-Triassic origin

Although the status of Crinoidea (sea lilies and featherstars) as sister group to all other living echinoderms is well-established, relationships among crinoids, particularly extant forms, are debated. All living species are currently placed in Articulata, which is generally accepted as the only crinoid group to survive the Permian-Triassic extinction event. Recent classifications have recognized five major extant taxa: Isocrinida, Hyocrinida, Bourgueticrinina, Comatulidina and Cyrtocrinida, plus several smaller groups with uncertain taxonomic status, e.g., Guillecrinus, Proisocrinus and Caledonicrinus. Here we infer the phylogeny of extant Crinoidea using three mitochondrial genes and two nuclear genes from 59 crinoid terminals that span the majority of extant crinoid diversity. Although there is poor support for some of the more basal nodes, and some tree topologies varied with the data used and mode of analysis, we obtain several robust results. Cyrtocrinida, Hyocrinida, Isocrinida are all recovered as clades, but two stalked crinoid groups, Bourgueticrinina and Guillecrinina, nest among the featherstars, lending support to an argument that they are paedomorphic forms. Hence, they are reduced to families within Comatulida. Proisocrinus is clearly shown to be part of Isocrinida, and Caledonicrinus may not be a bourgueticrinid. Among comatulids, tree topologies show little congruence with current taxonomy, indicating that much systematic revision is required. Relaxed molecular clock analyses with eight fossil calibration points recover Articulata with a median date to the most recent common ancestor at 231-252mya in the Middle to Upper Triassic. These analyses tend to support the hypothesis that the group is a radiation from a small clade that passed through the Permian-Triassic extinction event rather than several lineages that survived. Our tree topologies show various scenarios for the evolution of stalks and cirri in Articulata, so it is clear that further data and taxon sampling are needed to recover a more robust phylogeny of the group.

Fast local search for unrooted Robinson-Foulds supertrees

A Robinson-Foulds (RF) supertree for a collection of input trees is a tree containing all the species in the input trees that is at minimum total RF distance to the input trees. Thus, an RF supertree is consistent with the maximum number of splits in the input trees. Constructing RF supertrees for rooted and unrooted data is NP-hard. Nevertheless, effective local search heuristics have been developed for the restricted case where the input trees and the supertree are rooted. We describe new heuristics, based on the Edge Contract and Refine (ECR) operation, that remove this restriction, thereby expanding the utility of RF supertrees. Our experimental results on simulated and empirical data sets show that our unrooted local search algorithms yield better supertrees than those obtained from MRP and rooted RF heuristics in terms of total RF distance to the input trees and, for simulated data, in terms of RF distance to the true tree.

Molecular characterization of podoviral bacteriophages virulent for Clostridium perfringens and their comparison with members of the Picovirinae

Clostridium perfringens is a Gram-positive, spore-forming anaerobic bacterium responsible for human food-borne disease as well as non-food-borne human, animal and poultry diseases. Because bacteriophages or their gene products could be applied to control bacterial diseases in a species-specific manner, they are potential important alternatives to antibiotics. Consequently, poultry intestinal material, soil, sewage and poultry processing drainage water were screened for virulent bacteriophages that lysed C. perfringens. Two bacteriophages, designated ΦCPV4 and ΦZP2, were isolated in the Moscow Region of the Russian Federation while another closely related virus, named ΦCP7R, was isolated in the southeastern USA. The viruses were identified as members of the order Caudovirales in the family Podoviridae with short, non-contractile tails of the C1 morphotype. The genomes of the three bacteriophages were 17.972, 18.078 and 18.397 kbp respectively; encoding twenty-six to twenty-eight ORF's with inverted terminal repeats and an average GC content of 34.6%. Structural proteins identified by mass spectrometry in the purified ΦCP7R virion included a pre-neck/appendage with putative lyase activity, major head, tail, connector/upper collar, lower collar and a structural protein with putative lysozyme-peptidase activity. All three podoviral bacteriophage genomes encoded a predicted N-acetylmuramoyl-L-alanine amidase and a putative stage V sporulation protein. Each putative amidase contained a predicted bacterial SH3 domain at the C-terminal end of the protein, presumably involved with binding the C. perfringens cell wall. The predicted DNA polymerase type B protein sequences were closely related to other members of the Podoviridae including Bacillus phage Φ29. Whole-genome comparisons supported this relationship, but also indicated that the Russian and USA viruses may be unique members of the sub-family Picovirinae.

Cenozoic extinctions account for the low diversity of extant gymnosperms compared with angiosperms

We test the widely held notion that living gymnosperms are 'ancient' and 'living fossils' by comparing them with their sister group, the angiosperms. This perception derives partly from the lack of gross morphological differences between some Mesozoic gymnosperm fossils and their living relatives (e.g. Ginkgo, cycads and dawn redwood), suggesting that the rate of evolution of gymnosperms has been slow. We estimated the ages and diversification rates of gymnosperm lineages using Bayesian relaxed molecular clock dating calibrated with 21 fossils, based on the phylogenetic analysis of alignments of matK chloroplast DNA (cpDNA) and 26S nuclear ribosomal DNA (nrDNA) sequences, and compared these with published estimates for angiosperms. Gymnosperm crown groups of Cenozoic age are significantly younger than their angiosperm counterparts (median age: 32 Ma vs 50 Ma) and have long unbranched stems, indicating major extinctions in the Cenozoic, in contrast with angiosperms. Surviving gymnosperm genera have diversified more slowly than angiosperms during the Neogene as a result of their higher extinction rate. Compared with angiosperms, living gymnosperm groups are not ancient. The fossil record also indicates that gymnosperms suffered major extinctions when climate changed in the Oligocene and Miocene. Extant gymnosperm groups occupy diverse habitats and some probably survived after making adaptive shifts.

Sequential Rift Valley fever outbreaks in eastern Africa caused by multiple lineages of the virus

BACKGROUND

During the Rift Valley fever (RVF) epidemic of 2006-2007 in eastern Africa, spatial mapping of the outbreaks across Kenya, Somalia, and Tanzania was performed and the RVF viruses were isolated and genetically characterized.

METHODS

Following confirmation of the RVF epidemic in Kenya on 19 December 2006 and in Tanzania on 2 February 2007, teams were sent to the field for case finding. Human, livestock, and mosquito specimens were collected and viruses isolated. The World Health Organization response team in Kenya worked with the WHO's polio surveillance team inside Somalia to collect information and specimens from Somalia.

RESULTS

Seven geographical foci that reported hundreds of livestock and >25 cases in humans between December 2006 and June 2007 were identified. The onset of RVF cases in each epidemic focus was preceded by heavy rainfall and flooding for at least 10 days. Full-length genome analysis of 16 RVF virus isolates recovered from humans, livestock, and mosquitoes in 5 of the 7 outbreak foci revealed 3 distinct lineages of the viruses within and across outbreak foci.

CONCLUSION

The findings indicate that the sequential RVF epidemics in the region were caused by multiple lineages of the RVF virus, sometimes independently activated or introduced in distinct outbreak foci.

Identification of a methylase required for 2-methylhopanoid production and implications for the interpretation of sedimentary hopanes

The rise of atmospheric oxygen has driven environmental change and biological evolution throughout much of Earth's history and was enabled by the evolution of oxygenic photosynthesis in the cyanobacteria. Dating this metabolic innovation using inorganic proxies from sedimentary rocks has been difficult and one important approach has been to study the distributions of fossil lipids, such as steranes and 2-methylhopanes, as biomarkers for this process. 2-methylhopanes arise from degradation of 2-methylbacteriohopanepolyols (2-MeBHPs), lipids thought to be synthesized primarily by cyanobacteria. The discovery that 2-MeBHPs are produced by an anoxygenic phototroph, however, challenged both their taxonomic link with cyanobacteria and their functional link with oxygenic photosynthesis. Here, we identify a radical SAM methylase encoded by the hpnP gene that is required for methylation at the C-2 position in hopanoids. This gene is found in several, but not all, cyanobacteria and also in alpha -proteobacteria and acidobacteria. Thus, one cannot extrapolate from the presence of 2-methylhopanes alone, in modern environments or ancient sedimentary rocks, to a particular taxonomic group or metabolism. To understand the origin of this gene, we reconstructed the evolutionary history of HpnP. HpnP proteins from cyanobacteria, Methylobacterium species, and other alpha-proteobacteria form distinct phylogenetic clusters, but the branching order of these clades could not be confidently resolved. Hence,it is unclear whether HpnP, and 2-methylhopanoids, originated first in the cyanobacteria. In summary, existing evidence does not support the use of 2-methylhopanes as biomarkers for oxygenic photosynthesis.

Molecular systematics: A synthesis of the common methods and the state of knowledge

The comparative and evolutionary analysis of molecular data has allowed researchers to tackle biological questions that have long remained unresolved. The evolution of DNA and amino acid sequences can now be modeled accurately enough that the information conveyed can be used to reconstruct the past. The methods to infer phylogeny (the pattern of historical relationships among lineages of organisms and/or sequences) range from the simplest, based on parsimony, to more sophisticated and highly parametric ones based on likelihood and Bayesian approaches. In general, molecular systematics provides a powerful statistical framework for hypothesis testing and the estimation of evolutionary processes, including the estimation of divergence times among taxa. The field of molecular systematics has experienced a revolution in recent years, and, although there are still methodological problems and pitfalls, it has become an essential tool for the study of evolutionary patterns and processes at different levels of biological organization. This review aims to present a brief synthesis of the approaches and methodologies that are most widely used in the field of molecular systematics today, as well as indications of future trends and state-of-the-art approaches.

Comparison of methods for rooting phylogenetic trees: a case study using Orcuttieae (Poaceae: Chloridoideae)

DNA sequence data (cpDNA trnL intron and nrDNA ITS1 and ITS2) were analyzed to identify relationships within Orcuttieae, a small tribe of endangered grasses endemic to vernal pools in California and Baja California. The tribe includes three genera: Orcuttia, Tuctoria, and Neostapfia. All three genera carry out C(4) photosynthesis but aquatic taxa of Orcuttia lack Kranz anatomy. The unusual habitat preference of the tribe is coupled with the atypical development of C(4) photosynthesis without Kranz anatomy. Furthermore, the tribe has no known close relatives and has been noted to be phylogenetically isolated within the subfamily Chloridoideae. In this study we examine the problem of inferring the root of the tribe in the absence of an identified outgroup, analyze the phylogenetic relationships of the constituent taxa, and evaluate the evolutionary development of C(4) photosynthesis. We compare four methods for inferring the root of the tree: (1) the outgroup method, (2) midpoint rooting, the imposition of a molecular clock for both (3) maximum likelihood (ML) and (4) Bayesian analysis. We examine the consequences of each method for the inferred phylogenetic relationships. Three of the methods (outgroup rooting and the ML and Bayesian molecular clock analyses) suggest that the root of Orcuttieae is between Neostapfia and the Tuctoria/Orcuttia lineage, while midpoint rooting gives a different root. The Bayesian method additionally provides information about probabilities associated with other possible root locations. Assuming that the true root of Orcuttieae is between Neostapfia and the Tuctoria/Orcuttia lineage, our data indicate Neostapfia and Orcuttia are both monophyletic, while Tuctoria is paraphyletic (with no synapomorphies in either dataset) and forming a grade between the other two genera and needs taxonomic revision. Our data support the hypothesis that Orcuttieae was derived from a terrestrial ancestor and evolved specializations to an aquatic environment, including C(4) photosynthesis without Kranz anatomy.

Support patterns from different outgroups provide a strong phylogenetic signal

It is known that the accuracy of phylogenetic reconstruction decreases when more distant outgroups are used. We quantify this phenomenon with a novel scoring method, the outgroup score pOG. This score expresses if the support for a particular branch of a tree decreases with increasingly distant outgroups. Large-scale simulations confirmed that the outgroup support follows this expectation and that the pOG score captures this pattern. The score often identifies the correct topology even when the primary reconstruction methods fail, particularly in the presence of model violations. In simulations of problematic phylogenetic scenarios such as rate variation among lineages (which can lead to long-branch attraction artifacts) and quartet-based reconstruction, the pOG analysis outperformed the primary reconstruction methods. Because the pOG method does not make any assumptions about the evolutionary model (besides the decreasing support from increasingly distant outgroups), it can detect cases of violations not treated by a specific model or too strong to be fully corrected. When used as an optimization criterion in the construction of a tree of 23 mammals, the outgroup signal confirmed many well-accepted mammalian orders and superorders. It supports Atlantogenata, a clade of Afrotheria and Xenarthra, and suggests an Artiodactyla-Chiroptera clade.

Tree thinking for all biology: the problem with reading phylogenies as ladders of progress

Phylogenies are increasingly prominent across all of biology, especially as DNA sequencing makes more and more trees available. However, their utility is compromised by widespread misconceptions about what phylogenies can tell us, and improved "tree thinking" is crucial. The most-serious problem comes from reading trees as ladders from "left to right"--many biologists assume that species-poor lineages that appear "early branching" or "basal" are ancestral--we call this the "primitive lineage fallacy". This mistake causes misleading inferences about changes in individual characteristics and leads to misrepresentation of the evolutionary process. The problem can be rectified by considering that modern phylogenies of present-day species and genes show relationships among evolutionary cousins. Emphasizing that these are extant entities in the 21(st) century will help correct inferences about ancestral characteristics, and will enable us to leave behind 19(th) century notions about the ladder of progress driving evolution.

A molecular phylogeny of the Sylvia cantillans complex: cryptic species within the Mediterranean basin

The subalpine warbler Sylvia cantillans is formally considered a polytypic species, with four subspecies, European S. c. cantillans, albistriata, moltonii (recently resumed name: subalpina) and North African S. c.inornata. They are very similar in external morphology but clearly differ in their vocalizations. We evaluated their uncertain taxonomic status reconstructing the phylogenetic and phylogeographic relationships among populations sampled across major biogeographical areas in the European species' range, using nucleotide sequences of the mitochondrial cytochrome b gene (mtDNA cyt b). A variety of phylogenetic analyses concordantly led to identify four major groups, only partially corresponding to the three European nominal subspecies. Phylogenetic trees showed a monophyletic group including all moltonii individuals, well diverged from all other taxa. Populations taxonomically assigned to cantillans were polyphyletic being split into two distinct clades (western and southern cantillans), with monophyletic albistriata closely related to southern cantillans. Individuals of moltonii and southern cantillans sampled in sites of sympatry in central Italy were assigned to their respective groups, with perfect concordance between phenotypic and genetic identifications. All findings indicate that moltonii should be ranked as a distinct species. Former subspecies cantillans is polyphyletic, but additional data are needed to define the taxonomic status of its two clades. Albistriata is phylogenetically related to southern cantillans and should be provisionally kept as a subspecies of S. cantillans. The cantillans complex thus provides an interesting case-study illustrating geographical structuring across small geographical ranges, and it exemplifies speciation through differentiation in allopatry leading to reproductive isolation after a secondary contact.

Molecular phylogenetics of cixiid planthoppers (Hemiptera: Fulgoromorpha): new insights from combined analyses of mitochondrial and nuclear genes

The planthopper family Cixiidae (Hemiptera: Fulgoromorpha) comprises approximately 160 genera and 2000 species divided in three subfamilies: Borystheninae, Bothriocerinae and Cixiinae, the later with 16 tribes. The current paper represents the first attempt to estimate phylogenetic relationships within Cixiidae based on molecular data. We use a total of 3652bp sequence alignment of four genes: the mitochondrial coding genes Cytochrome c Oxidase subunit 1 (Cox1) and Cytochrome b (Cytb), a portion of the nuclear 18S rDNA and two non-contiguous portions of the nuclear 28S rDNA. The phylogenetic relationships of 72 terminal specimens were reconstructed using both maximum parsimony and Bayesian inference methods. Through the analysis of this empirical dataset, we also provide comparisons among different a priori partitioning strategies and the use of mixture models in a Bayesian framework. Our comparisons suggest that mixture models overcome the benefits obtained by partitioning the data according to codon position and gene identity, as they provide better accuracy in phylogenetic reconstructions. The recovered maximum parsimony and Bayesian inference phylogenies suggest that the family Cixiidae is paraphyletic in respect with Delphacidae. The paraphyly of the subfamily Cixiinae is also recovered by both approaches. In contrast to a morphological phylogeny recently proposed for cixiids, subfamilies Borystheninae and Bothriocerinae form a monophyletic group.

Patterns of co-evolution between trypanosomes and their hosts deduced from ribosomal RNA and protein-coding gene phylogenies

Trypanosomes (genus Trypanosoma) are widespread blood parasites of vertebrates, usually transmitted by arthropod or leech vectors. Most trypanosomes have lifecycles that alternate between a vertebrate host, where they exist in the bloodstream, and an invertebrate host, where they develop in the alimentary tract. This raises the question of whether one type of host has had greater influence on the evolution of the genus. Working from the generally accepted view that trypanosomes are monophyletic, here we examine relationships between trypanosomes using phylogenies based on the genes for the small subunit ribosomal RNA (SSU rRNA) and the glycosomal glyceraldehyde phosphate dehydrogenase (gGAPDH). New analysis of a combined dataset of both these genes provides strong support for many known clades of trypanosomes. It also resolves the deepest split within the genus between the Aquatic clade, which mainly contains trypanosomes of aquatic and amphibious vertebrates, and a clade of trypanosomes from terrestrial vertebrates. There is also strengthened support for two deep clades, one comprising a wide selection of mammalian trypanosomes and a tsetse fly-transmitted reptilian trypanosome, and the other combining two bird trypanosome subclades. Considering the vertebrate and invertebrate hosts of each clade, it is apparent that co-speciation played little role in trypanosome evolution. However most clades are associated with a type of vertebrate or invertebrate host, or both, indicating that 'host fitting' has been the principal mechanism for evolution of trypanosomes.

A Molecular Evaluation of the North American “Grassland” Sparrow Clade

Because they share several morphological and ecological characters, the North American sparrow (Emberizidae) genera Ammodramus, Passerculus, and Xenospiza have historically been considered members of a well-defined “grassland” sparrow assemblage. Relationships among the 11 members of this group have been the subject of much taxonomic debate, yet no comprehensive molecular assessment of relationships has been done. We investigated these relationships using mitochondrial DNA sequence data that included complete cytochrome-b and ND2 genes. Phylogenetic reconstructions derived via parsimony, likelihood, and Bayesian methods were congruent. The grassland sparrows, as presently configured, are polyphyletic. Pooecetes gramineus, Amphispiza belli (but not A. quinquestriata and A. bilineata), Oriturus superciliosus, and all three species of Melospiza are included in a reconfigured clade, whereas the traditional forms of Ammodramus savannarum, humeralis, and aurifons are placed well outside of these. Within the clade of interest, Ammodramus remains polyphyletic, with leconteii, maritimus, nelsoni, and caudacutus forming a well-resolved clade apart from henslowii and bairdii. The latter are in another strongly supported clade that also includes Passerculus and a Xenospiza-Melozpiza sister pairing. Pooecetes, Amphispiza (belli), and Oriturus represent early lineages in this clade that today have no close living relatives. The polyphyly of the genus Ammodramus is likely the result of morphological convergence attributable to similar adaptive responses to the occupation of similar habitats. In general, the morphological and ecological factors that have defined the grassland sparrows are poor indicators of relatedness. Taxonomic revisions are suggested.

Evaluación Molecular del Clado de Gorriones de Pastizales de Norte América

Phylogeography illuminates maternal origins of exotic Coptotermes gestroi (Isoptera: Rhinotermitidae)

Coptotermes gestroi, the Asian subterranean termite (AST), is an economically important structural and agricultural pest that has become established in many areas of the world. For the first time, phylogeography was used to illuminate the origins of new found C. gestroi in the US Commonwealth of Puerto Rico; Ohio, USA; Florida, USA; and Brisbane, Australia. Phylogenetic relationships of C. gestroi collected in indigenous locations within Malaysia, Thailand, and Singapore as well as from the four areas of introduction were investigated using three genes (16S rRNA, COII, and ITS) under three optimality criteria encompassing phenetic and cladistic assumptions (maximum parsimony, maximum likelihood, and neighbor-joining). All three genes showed consistent support for a close genetic relationship between C. gestroi samples from Singapore and Ohio, whereas termite samples from Australia, Puerto Rico, and Key West, FL were more closely related to those from Malaysia. Shipping records further substantiated that Singapore and Malaysia were the likely origin of the Ohio and Australia C. gestroi, respectively. These data provide support for using phylogeography to understand the dispersal history of exotic termites. Serendipitously, we also gained insights into concerted evolution in an ITS cluster from rhinotermitid species in two genera.

Phylogenetic analyses of parasites in the new millennium

Phylogenetic analysis has changed greatly in the last decade, and the most important themes in that change are reviewed here. Sequence data have become the most common source of phylogenetic information. This means that explicit models for evolutionary processes have been developed in a likelihood context, which allow more realistic data analyses. These models are becoming increasingly complex, both for nucleotides and for amino acid sequences, and so all such models need to be quantitatively assessed for each data set, to find the most appropriate one for use in any particular tree-building analysis. Bayesian analysis has been developed for tree-building and is greatly increasing in popularity. This is because a good heuristic strategy exists, which allows large data sets to be analyzed with complex evolutionary models in a practical time. Perhaps the most disappointing aspect of tree interpretation is the ongoing confusion between rooted and unrooted trees, while the effect of taxon and character sampling is often overlooked when constructing a phylogeny (especially in parasitology). The review finishes with a detailed consideration of the analysis of a multi-gene data set for several dozen taxa of Cryptosporidium (Apicomplexa), illustrating many of the theoretical and practical points highlighted in the review.