Fitch Parsimony Research Articles

Dollo-CDP: a polynomial-time algorithm for the clade-constrained large Dollo parsimony problem

The last decade of phylogenetics has seen the development of many methods that leverage constraints plus dynamic programming. The goal of this algorithmic technique is to produce a phylogeny that is optimal with respect to some objective function and that lies within a constrained version of tree space. The popular species tree estimation method ASTRAL, for example, returns a tree that (1) maximizes the quartet score computed with respect to the input gene trees and that (2) draws its branches (bipartitions) from the input constraint set. This technique has yet to be used for parsimony problems where the input are binary characters, sometimes with missing values. Here, we introduce the clade-constrained character parsimony problem and present an algorithm that solves this problem for the Dollo criterion score in O(|Sigma |^{3.726}(n+k) + |Sigma |^{1.726}nk) time, where n is the number of leaves, k is the number of characters, and Sigma is the set of clades used as constraints. Dollo parsimony, which requires traits/mutations to be gained at most once but allows them to be lost any number of times, is widely used for tumor phylogenetics as well as species phylogenetics, for example analyses of low-homoplasy retroelement insertions across the vertebrate tree of life. This motivated us to implement our algorithm in a software package, called Dollo-CDP, and evaluate its utility for analyzing retroelement insertion presence / absence patterns for bats, birds, toothed whales as well as simulated data. Our results show that Dollo-CDP can improve upon heuristic search from a single starting tree, often recovering a better scoring tree. Moreover, Dollo-CDP scales to data sets with much larger numbers of taxa than branch-and-bound while still having an optimality guarantee, albeit a more restricted one. Lastly, we show that our algorithm for Dollo parsimony can easily be adapted to Camin-Sokal parsimony but not Fitch parsimony.

Combinatorial perspectives on Dollo-k characters in phylogenetics

Recently, the perfect phylogeny model with persistent characters has attracted great attention in the literature. It is based on the assumption that complex traits or characters can only be gained once and lost once in the course of evolution. Here, we consider a generalization of this model, namely Dollo parsimony, that allows for multiple character losses. More precisely, we take a combinatorial perspective on the notion of Dollo-k characters, i.e. traits that are gained at most once and lost precisely k times throughout evolution. We first introduce an algorithm based on the notion of spanning subtrees for finding a Dollo-k labelling for a given character and a given tree in linear time. We then compare persistent characters (consisting of the union of Dollo-0 and Dollo-1 characters) and general Dollo-k characters. While it is known that there is a strong connection between Fitch parsimony and persistent characters, we show that Dollo parsimony and Fitch parsimony are in general very different. Moreover, while it is known that there is a direct relationship between the number of persistent characters and the Sackin index of a tree, a popular index of tree balance, we show that this relationship does not generalize to Dollo-k characters. In fact, determining the number of Dollo-k characters for a given tree is much more involved than counting persistent characters, and we end this manuscript by introducing a recursive approach for the former. This approach leads to a polynomial time algorithm for counting the number of Dollo-k characters, and both this algorithm as well as the algorithm for computing Dollo-k labellings are publicly available in the Babel package for BEAST 2.

Phylogenetic relationships of Manonychus Moser among the Neotropical Melolonthinae (Coleoptera: Scarabaeidae)

Manonychus Moser, 1919 is composed by seven species, all endemic from Brazil, and it is placed in incertae sedis of Melolonthinae (Coleoptera: Scarabaeoidea: Scarabaeidae). This study aimed to test the monophyly of Manonychus and its position among the other genera of the subfamily. Around 184 specimens belonging to seven melolontine tribes and one orphnine were analysed. A total of 66 morphological characters of adults, including mouthparts and male genitalia were built, and 15 are a new contribution to the subfamily. Equal and implied weighting analyses were carried out using TNT program and Fitch parsimony as optimization criteria. From the equal weighting analysis a consensus of two trees was obtained with 340 steps length (ci = 0.221; ri = 0.483); and in the implied weighting analysis one tree was obtained with k = 18.920.302 steps length, and 56.28 of adjusted fit (ci = 0.245; ri = 0.550). Manonychus is monophyletic, its sister clade is composed by Ovomanonychus + (Apterodemidea + Sericoides). All these genera are nested in Sericoidini, subsidising the inclusion of Manonychus and the confirmation of Ovomanonychus in this tribe. The placement of Manonychus rufinus and Manonychus ovalis in Manonychus is corroborated.

Evolution of Angiosperm Pollen: 8. Lamiids

Lamiids, a clade composed of approximately 15% of all flowering plants, contains more than 50,000 species dispersed across 49 families and eight orders (APG IV, 2016). This paper is the eighth in a series that analyzes pollen characters across angiosperms. We reconstructed a maximum likelihood tree based on the most recent phylogenetic studies for the Lamiids, comprising 150 terminal genera (including six outgroups) and covering all eight orders and 49 families within the clade. To illustrate pollen diversity across the Lamiids, pollen grains from 22 species (22 genera in 14 families) were imaged under light, scanning, and transmission electron microscopy. Eighteen pollen characters that were documented from previous publications, websites, and our new observations were coded and optimized onto the reconstructed phylogenetic tree using Fitch parsimony, maximum likelihood, and hierarchical Bayesian analysis. Pollen morphology of the Lamiids is highly diverse, particularly in shape class, pollen size, aperture number, endoaperture shape, supratectal element shape, and tectum sculpture. In addition, some genera show relatively high infrageneric pollen variation within the Lamiids: i.e., Coffea L., Jacquemontia Choisy, Justicia L., Pedicularis L., Psychotria L. nom. cons., Sesamum L., Stachytarpheta Vahl, and Veronica L. The plesiomorphic states for 16 pollen characters were inferred unambiguously, and 10 of them displayed consistent plesiomorphic states under all optimization methods. Seventy-one lineages at or above the family level are characterized by pollen character state transitions. We identified diagnostic character states for monophyletic clades and explored palynological evidence to shed light on unresolved relationships. For example, palynological evidence supports the monophyly of Garryales and Metteniusaceae, and sister relationships between Icacinaceae and Oncothecaceae, as well as between Vahliales and Solanales. The evolutionary patterns of pollen morphology found in this study reconfirm several previously postulated evolutionary trends, which include an increase in aperture number, a transition from equatorially arranged apertures to globally distributed ones, and an increase in exine ornamentation complexity. Furthermore, there is a significant correlation between pollen characters and a number of ecological factors, e.g., pollen size and pollination type, pollen ornamentation and pollination type, and shape class and plant growth form. Our results provide insight into the ecological, environmental, and evolutionary mechanisms driving pollen character state changes in the Lamiids.

Evolution of Angiosperm Pollen. 7. Nitrogen-fixing Clade

Nitrogen-fixing symbiosis in root nodules is known in only 10 families, which are distributed among a clade of four orders and delimited as the nitrogen-fixing clade. As the seventh in a series that examines pollen morphological distribution and evolution in the angiosperms, this paper focuses on pollen morphological character states of the nitrogen-fixing clade. To illustrate the palynological diversity of the clade, we first examined pollen grains from 26 species with light electron, scanning electron, and transmission electron microscopy. Second, we used a reduced data matrix from Li et al. (2015) to reconstruct a maximum likelihood tree and then optimized 18 pollen character states onto the tree using Fitch parsimony, maximum likelihood, and hierarchical Bayesian inference. Finally, 12 plesiomorphic states for the nitrogen-fixing clade were inferred unambiguously under all methods, and more than 40 clades (or lineages) at or above familial level were characterized by unambiguous pollen character state changes in at least one of the optimizations. We found a number of evolutionary trends for changes in pollen character states. These include increasing grain size, increasing aperture number accompanied by concomitant changes in aperture position (from equatorial to global) and aperture shape (from colpate to colporate), and increasing complexity of tectum ornamentation. There was a strong correlation between some pollen characters (prolate shape class, lobe outline in polar view, colpate ectoaperture, lalongate and lolongate endoaperture, absent supratectal element, reticulate tectum) and insect pollination, while other pollen characters—simple aperture structure, porate ectoaperture, circular endoaperture, present and gemmate or echinate supratectal element, and imperforate tectum—were strongly correlated with wind pollination. In addition, rugulate tectum was significantly correlated with shrub habit while larger pollen size was significantly correlated with vine habit; the helophytic habitat was significantly correlated with having two apertures. Our study provides rich evidence for the phylogenetic significance of pollen morphological diversity in the nitrogen-fixing clade.

Evolution of Angiosperm Pollen. 6. The Celastrales, Oxalidales, and Malpighiales (Com) Clade and Zygophyllales

Analyzing pollen morphological data on a contemporary phylogenetic framework can enhance our understanding of the distribution, diversity, and evolution of palynological characters. In this paper, the sixth in a series detailing pollen morphological characters across angiosperms, we focus on the Celastrales, Oxalidales, and Malpighiales (COM) clade and Zygophyllales, together comprising ca. 20,000 species in 47 families within fabids. We first examined pollen grains from 21 species with light, scanning electron, and transmission electron microscopy, to illustrate pollen diversity within the COM clade and Zygophyllales. Second, based on a reexamination of previously published pollen data and our new observations, we optimized 21 pollen characters on a maximum likelihood (ML) tree of 169 genera in 45 families representing all four orders, using Fitch parsimony, ML, and hierarchical Bayesian inference. The pollen morphology of this group displays great diversity, particularly in size, aperture number, supratectal element shape, and tectum sculpture. Plesiomorphic states for 18 characters were inferred unambiguously under all methods for the COM clade, and over 300 character state changes were hypothesized by each analysis on lineages at different levels within the group. Changes of state were found to occur most frequently in the characters outline in polar view, pollen size, and tectum sculpture; changes of state occurred least frequently in the characters dispersal unit, symmetry, and tectum presence/absence. We identified diagnostic character states for several monophyletic clades and explored palynological evidence to shed light on some unresolved relationships. For example, the previously poorly resolved Malpighiales were found to be distinguished by a single pollen character state change (from annulus absent to present). Patterns of evolutionary change in several notable pollen characters, such as the number of pollen apertures (from three to other states) and tectum sculpture (from perforate to reticulate), were further confirmed, and their possible adaptive functions are proposed. Reflecting current interest in the relationship between pollen morphology and pollination syndrome, we conducted tests of correlated evolution between pollen morphology and pollination syndrome, with results demonstrating significant correlations between a thin exine and anemophily and, unexpectedly, between presence of supratectal elements and anemophily. Evidence for previously postulated evolutionary trends in aperture number (increasing), tectum sculpture (from perforate to reticulate), and infratectum structure (from columellate to granulate) is discussed. The relatively high frequency of state changes in presence or absence of supratectal elements may be linked to switches in pollination syndrome within this group.

On the Accuracy of Ancestral Sequence Reconstruction for Ultrametric Trees with Parsimony.

We examine a mathematical question concerning the reconstruction accuracy of the Fitch algorithm for reconstructing the ancestral sequence of the most recent common ancestor given a phylogenetic tree and sequence data for all taxa under consideration. In particular, for the symmetric four-state substitution model which is also known as Jukes-Cantor model, we answer affirmatively a conjecture of Li, Steel and Zhang which states that for any ultrametric phylogenetic tree and a symmetric model, the Fitch parsimony method using all terminal taxa is more accurate, or at least as accurate, for ancestral state reconstruction than using any particular terminal taxon or any particular pair of taxa. This conjecture had so far only been answered for two-state data by Fischer and Thatte. Here, we focus on answering the biologically more relevant case with four states, which corresponds to ancestral sequence reconstruction from DNA or RNA data.

Evolution of Angiosperm Pollen: 4. Basal Eudicots

In this paper, the fourth in a series documenting palynological characters across angiosperms using a contemporary phylogenetic framework, we deal with the basal eudicots, a group which includes Buxales, Proteales, Ranunculales, Sabiaceae, and Trochodendrales. Using available molecular sequences of matK and rbcL from previous studies, we reconstructed a maximum likelihood tree for a total of 196 genera (including nine outgroups), representing 13 families and all four orders of basal eudicots. Across the 196 genera, 20 pollen characters were documented from prior publications and new observations. These were coded using two strategies and optimized onto the reconstructed phylogenetic tree using Fitch parsimony, maximum likelihood, and hierarchical Bayesian inference to infer ancestral states. Pollen samples of 24 species from 24 genera in eight families were imaged under LM and SEM to illustrate the diversity of basal eudicot pollen. In addition, we tested for correlated evolution between plant growth form and pollen shape class, and between anemophily and pollen aperture number, using maximum likelihood and Markov chain Monte Carlo analyses. Basal eudicot pollen showed high morphological diversity, especially in characters including tectum sculpture, aperture number, and ectoaperture shape. Depending upon the method of reconstruction, 14 to 18 plesiomorphic palynological states were unequivocally inferred, and a total number of 357 character state transitions were found at or above tribal level. These provide palynological support for at least 58 of the clades discovered by molecular phylogenetic estimation. For example, using hierarchical Bayesian inference with comprehensive data coding, 222 state changes were inferred. Pollen size, tectum sculpture, and pollen shape class changed the most frequently among the 20 studied characters. The most concentrated character state changes in basal eudicot pollen are estimated to have occurred around the Barremian to Albian stages of the Early Cretaceous. Tests of correlated evolution suggest that the herbaceous growth form is significantly associated with spheroidal pollen shape and the arborescent growth form with oblate pollen shape. However, no significant correlations were found between anemophily and aperture number. Patterns of evolutionary change in pollen size and tectum sculpture, and their adaptive functions, are discussed. Based on previous evidence and our data, pollination syndrome is the most likely factor associated with the high frequency of state changes in these two characters.

Molecular Evidence of Transmission of Influenza A/H1N1 2009 on a University Campus.

BackgroundIn the recent years, the data on the molecular epidemiology of influenza viruses have expanded enormously because of the availability of cutting-edge sequencing technologies. However, much of the information is from the temperate regions with few studies from tropical regions such as South-east Asia. Despite the fact that influenza has been known to transmit rapidly within semi-closed communities, such as military camps and educational institutions, data are limited from these communities.ObjectivesTo determine the phylogeography of influenza viruses on a university campus, we examined the spatial distribution of influenza virus on the National University of Singapore (NUS) campus.MethodsConsenting students from the NUS who sought medical attention at the UHC provided two nasopharyngeal swabs and demographic data. PCR was used for detection of influenza viruses. 34 full-genomes of pH1N1/09 viruses were successfully sequenced by Sanger method and concatenated using Geneious R7. Phylogenetic analysis was conducted using these 34 sequences and 1518 global sequences. Phylogeographic analysis was done using BaTS software and Association index and Fitch parsimony scores were determined.ResultsIntegrating whole genome sequencing data with epidemiological data, we found strong evidence of influenza transmission on campus as isolates from students residing on-campus were highly similar to each other (AI, P value = 0.009; PS, P value = 0.04). There was also evidence of multiple introductions from the community.ConclusionsSuch data are useful in formulating pandemic preparedness plans which can use these communities as sentinel sites for detection and monitoring of emerging respiratory viral infections.

Evolution of Angiosperm Pollen. 3. Monocots1

Monocots, with ca. 65,000 species in 78 families and 12 orders as classified by the Angiosperm Phylogeny Group (Angiosperm Phylogeny Group III, 2009), have traditionally been known as a distinct assemblage from dicots within angiosperms and are now seen as a lineage that diverged from within the more basal of the angiosperm groupings. In this study, the third in a series analyzing pollen characters across the angiosperms, we illustrate the pollen morphological diversity of monocots and analyze 19 palynological and two ecological characters for 120 taxa in 71 families covering the 12 monocot orders and 16 taxa of nine orders in basal angiosperms. Pollen morphological data from previous works and our investigations were optimized onto a new maximum likelihood tree reconstructed from an existing DNA matrix of Chase et al. (2006) using Fitch parsimony, maximum likelihood, and hierarchical Bayesian analysis. From these analyses we infer evolutionary patterns in palynological characters, assess their systematic value, and investigate two aspects (pollination type and habitat moisture) of their ecological adaptation. The highest levels of pollen variation were shown to exist in the Alismatales and Commelinales, with lower levels seen in the Asparagales, Dasypogonales, and Zingiberales; the most variable characters across the phylogeny were found to be pollen outline in polar view, size, and tectum extent. We infer unambiguous plesiomorphic states for monocots and report significant transitions in character states at various levels within the monocot assemblage. Analyses of correlated evolution reconfirmed the hypothesis of an association between exine reduction (or complete loss) and habitat moisture and found significant correlations between various states of exine loss and habitat for hydrophytic–helophytic plants. The presence or absence of the exine itself was found to be more significantly correlated than individual structures, in terms of association with hydrophytic–helophytic plants. The most rapid rate of state changes in pollen characters, in the evolutionary history of monocots, is estimated to have occurred during the Albian-Turonian stage; our work may provide insights into the identification of enigmatic fossil pollen grains from this geological time.

Leaf epidermal character variation and evolution in Gaultherieae (Ericaceae)

The taxonomic value and evolutionary significance of 30 leaf epidermal characters from 238 samples representing 127 species of all seven genera in the tribe Gaultherieae (Ericaceae) and two outgroup genera were investigated by scanning electron microscopy. The character states were coded and optimized onto a maximum-likelihood tree based on previous molecular data with Fitch parsimony and hierarchical Bayesian analysis to trace the evolution of character states throughout all internodes in the phylogenetic tree for Gaultherieae. Leaf epidermal characters were found to be largely consistent within species, but highly variable at interspecific and higher taxonomic levels. The most recent common ancestral states of 15 characters diagnosed various lineages recovered from prior studies, some with no prior morphological support. Relatively high frequencies of state change occur in the eastern Asian clade Gaultheria series Gymnobotrys + Diplycosia, the American clade G. subsection Dasyphyta p.p., the core East Asian clade and the Australia/New Zealand clade. The characters with the highest frequencies of state change are the outer stomatal ledge ornamentation type, the stomatal apparatus level, stomatal density and area, and the type of abaxial trichomes. These character state change patterns may provide insight into the ecological adaptions of Gaultherieae during their evolutionary history.

Evolution of Angiosperm Pollen. 2. The Basal Angiosperms1

Recently, evolutionary relationships among the five major lineages of the basal angiosperms, i.e., Amborellanae, Nymphaeanae, Austrobaileyanae, Magnolianae, and Ceratophyllanae, still remain incompletely or controversially resolved. This study reviews and reevaluates the origin, evolution, and systematic significance of pollen morphology in basal angiosperms. Pollen grains from 34 species of 31 genera in 23 families of the basal angiosperms are investigated, using light microscopy (LM) and scanning electron microscopy (SEM), to illustrate the pollen diversity across the grade. Pollen data for 57 genera, representing all nine orders and 28 families of the basal angiosperms, were obtained from previous work and new investigations and were used to optimize character states onto recent molecular phylogenetic estimates. Two 18-character datasets were generated: a comprehensively coded dataset optimized with Fitch parsimony onto 12 recent phylogenies with differing topologies to evaluate the degree of pollen systematic significance of each topology, and a democratically coded dataset optimized by using Fitch parsimony, maximum likelihood, and hierarchical Bayesian inference onto a single recent phylogeny based on molecular data from Soltis et al. to evaluate the disparity of pollen evolutionary patterns among the three methods. Pollen morphology of the basal angiosperms is highly diverse, particularly in terms of pollen size, aperture number, aperture position, ectoaperture shape, tectum sculpture, and infratectal structure. Based on both datasets, the plesiomorphic pollen type for angiosperms was inferred to comprise monads of heteropolar, spheroidal, mono-apertural grains, with distal, colpate apertures, sculptured aperture membranes, and an infratectum and foot layer. Of the basal angiosperm phylogenies considered, when taxon sampling is taken into account, pollen characters provide greatest support for the topology represented in the three-mitochondrial-gene study from Qiu et al., in terms of number of synapomorphies plus what we term “likely synapomorphies” in which the subtending node is ambiguous and, therefore, the exact position of the synapomorphy is ambiguous. Thirty-six various lineages above family level are supported by pollen morphological synapomorphies or likely synapomorphies. We discuss the systematic significance of pollen morphology in basal angiosperm clades including the ANITA group (Amborellaceae, Nymphaeaceae, Schisandraceae, Trimeniaceae, and Austrobaileyaceae), Ceratophyllales, Chloranthales, and magnoliids, as well as in related lineages, i.e., monocots and basal eudicots. We also discuss present limitations in inferring the evolutionary history of pollen morphology in basal angiosperms.

A phylogenetic analysis of the grape genus (Vitis L.) reveals broad reticulation and concurrent diversification during neogene and quaternary climate change.

BackgroundGrapes are one of the most economically important fruit crops. There are about 60 species in the genus Vitis. The phylogenetic relationships among these species are of keen interest for the conservation and use of this germplasm. We selected 309 accessions from 48 Vitis species,varieties, and outgroups, examined ~11 kb (~3.4 Mb total) of aligned nuclear DNA sequences from 27 unlinked genes in a phylogenetic context, and estimated divergence times based on fossil calibrations.ResultsVitis formed a strongly supported clade. There was substantial support for species and less for the higher-level groupings (series). As estimated from extant taxa, the crown age of Vitis was 28 Ma and the divergence of subgenera (Vitis and Muscadinia) occurred at ~18 Ma. Higher clades in subgenus Vitis diverged 16 – 5 Ma with overlapping confidence intervals, and ongoing divergence formed extant species at 12 – 1.3 Ma. Several species had species-specific SNPs. NeighborNet analysis showed extensive reticulation at the core of subgenus Vitis representing the deeper nodes, with extensive reticulation radiating outward. Fitch Parsimony identified North America as the origin of the most recent common ancestor of extant Vitis species.ConclusionsPhylogenetic patterns suggested origination of the genus in North America, fragmentation of an ancestral range during the Miocene, formation of extant species in the late Miocene-Pleistocene, and differentiation of species in the context of Pliocene-Quaternary tectonic and climatic change. Nuclear SNPs effectively resolved relationships at and below the species level in grapes and rectified several misclassifications of accessions in the repositories. Our results challenge current higher-level classifications, reveal the abundance of genetic diversity in the genus that is potentially available for crop improvement, and provide a valuable resource for species delineation, germplasm conservation and use.

Model uncertainty in ancestral area reconstruction: A parsimonious solution?

AbstractIncreasingly complex likelihood–based methods are being developed to infer biogeographic history. The results of these methods are highly dependent on the underlying model which should be appropriate for the scenario under investigation. Our example concerns the dispersal among the southern continents of the grass subfamily Danthonioideae (Poaceae). We infer ancestral areas and dispersals using likelihood–based Bayesian methods and show the results to be indecisive (reversible–jump Markov chain Monte Carlo; RJ–MCMC) or contradictory (continuous–time Markov chain with Bayesian stochastic search variable selection; BSSVS) compared to those obtained under Fitch parsimony (FP), in which the number of dispersals is minimised. The RJ–MCMC and BSSVS results differed because of the differing (and not equally appropriate) treatments of model uncertainty under these methods. Such uncertainty may be unavoidable when attempting to infer a complex likelihood model with limited data, but we show with simulated data that it is not necessarily a meaningful reflection of the credibility of a result. At higher overall rates of dispersal FP does become increasingly inaccurate. However, at and below the rate observed in Danthonioideae multiple dispersals along branches are not observed and the correct root state can be inferred reliably. Under these conditions parsimony is a more appropriate model.

Evolution of Pollen in the Family Berberidaceae

In the APG III, the family Berberidaceae is placed in the Ranunculales within the basal Eudicots. Here, the phylogenetic relationships within Berberidaceae were reconstructed using the Maximum Likelihood method on sequence data from four genomic regions (nuclear ribosomal 26S rDNA and plastid rbcL, matK, and trnL-F). Based on previously reported phylogenetic tree and pollen observation, the pollen morphologies of 16 genera of this family were investigated. Pollen plesiomorphy,synapomorphy, and evolutionary pattern were revealed by Fitch Parsimony analysis. Ten pollen characters, including dispersal unit, polarity, shape class, size, aperture number, aperture position, ectoaperture shape, supratectal elements, tectum sculpture, and exine thickness, were evaluated to reassess phylogenetic relationships. Tracing pollen character evolution showed that Berberidaceae possessed a series of plesiomorphies, such as the monad pollen unit, isopolarity, spheroidal shape and medium size. Apolarity, multiple apertures and global aperture state were found to be synapomorphies for the Berberidoideae, strongly supporting the monophyly of this subfamily. Triaperture was a synapomorphy for both Podophylloideae and Nandinoideae, respectively. Berberidoideae and Nandinoideae shared the synapomorphy supratectal elements absent, which distinguished them from Podophylloideae, and supported the sister relationship between Berberidoideae and Nandinoideae. Pollen evolutionary significance of some genera was discussed, and several pollen characters were suggested to be used for defining certain genera, such as Bongardia and Ranzania.

The placement of South African strains of Beauveria in a phylogeny inferred from rDNA ITS1-5.8S-ITS2 sequences

This study aimed to confirm the identity of three strains of the entomopathogenic fungus Beauveria bassiana from South African soils and to investigate their phylogenetic relationship with non-indigenous strains from other geographic regions. Sequences of the rDNA ITS1-5.8S-ITS2 region of 23 strains were compared with the Genbank reference sequences of 20 other cosmopolitan strains. Fitch parsimony and neighbor-joining analyses of the ITS1-5.8S-ITS2 regions resolved the strains into two distinct clades and matched them to four species groups/lineages: Beauveria bassiana, B. cf. bassiana (pseudobassiana), B. brongniartii and B. caledonica. Two of the South African strains initially identified as B. bassiana grouped with B. caledonica, whereas the third strain was confirmed as B. bassiana. Because of the paucity of Genbank references for B. caledonica, we have designated the two South African B. caledonica strains as B. sp. aff. caledonica. Other reassignments included two strains from Norway, originally classified as B. bassiana, being grouped with B. brongniartii, and three of the B. brongniartii reference taxa from Brazil which were clearly placed in the B. bassiana clade. The study provides a first report of the presence of the B. caledonica lineage in Africa and confirms current Beauveria phylogenies inferred from molecular data.

A re-evaluation of Secernosaurus koerneri and Kritosaurus australis (Dinosauria, Hadrosauridae) from the Late Cretaceous of Argentina

ABSTRACT Hadrosaurids form the most diverse and derived clade of ornithopod dinosaurs. Although well represented in Asia and North America, its presence in South America is known only from rare and fragmentary remains that are poorly documented and mostly unstudied. As a result, the impact of these animals on the phylogenetics and biogeography of hadrosaurids as a whole is poorly known. Here, we provide a revised and complete osteology of the type specimens and hypodigms for the only two taxa known from South America, Secernosaurus koerneri and Kritosaurus australis. Likewise, we infer the phylogenetic position and historical biogeography of South American hadrosaurids using a nearly complete taxonomic sampling of hadrosaurid species. Parsimony methods were used to infer phylogenetic relationships, whereas Fitch parsimony and Dispersal-Vicariance analyses were implemented to reconstruct ancestral areas. Kritosaurus australis is regarded as a junior synonym of Secernosaurus koerneri, based on a combination of iliac and pubic characters unique to these two taxa. Inclusion of S. koerneri within the genus Kritosaurus is not supported by the phylogenetic analysis. S. koerneri is inferred to be a member of the Kritosaurus-Gryposaurus clade within Saurolophinae, as the sister taxon to the Argentinean unnamed hadrosaurid from Salitral Moreno. Another unnamed hadrosaurid from Big Bend National Park, Texas, is positioned as the closest outgroup to the South American clade. The results of this biogeographical analysis supports the hypothesis that the Secernosaurus clade originated in South America during the late Campanian after a dispersal event (probably followed by vicariance) from southern North America before the end of that geologic stage.

Pararhabdodon isonensis and Tsintaosaurus spinorhinus: a new clade of lambeosaurine hadrosaurids from Eurasia

We present new anatomical information showing that Koutalisaurus kohlerorum, from the Maastrichtian of Lleida Province, northeastern Spain, is most probably the junior synonym of Pararhabdodon isonensis from the same region. Dentary and maxillary characters previously considered as autapomorphies of K. kohlerorum and P. isonensis, respectively, are shown to be synapomorphies uniting the latter with Tsintaosaurus spinorhinus from the Campanian of the Wangshi Group, Shandong Province, China. This study provided conclusive evidence of the presence of the Lambeosaurinae in Europe. Tsintaosaurus spinorhinus and Pararhabdodon isonensis were inferred to form a clade of basal lambeosaurines characterized by a maxilla with an elevated articular facet for the jugal (continuous with the ectopterygoid ridge) and an extremely medially projected symphyseal region of the dentary. This clade originated in Asia during the middle or late Campanian. Pararhabdodon isonensis or its ancestors migrated from Asia to the Iberian island of the European archipelago. Reconstruction of ancestral areas by Fitch parsimony attributes the European occurrence of P. isonensis to a single dispersal event from Asia no later than middle to late Campanian.

A Comparative Study in Ancestral Range Reconstruction Methods: Retracing the Uncertain Histories of Insular Lineages

Island systems have long been useful models for understanding lineage diversification in a geographic context, especially pertaining to the importance of dispersal in the origin of new clades. Here we use a well-resolved phylogeny of the flowering plant genus Cyrtandra (Gesneriaceae) from the Pacific Islands to compare four methods of inferring ancestral geographic ranges in islands: two developed for character-state reconstruction that allow only single-island ranges and do not explicitly associate speciation with range evolution (Fitch parsimony [FP; parsimony-based] and stochastic mapping [SM; likelihood-based]) and two methods developed specifically for ancestral range reconstruction, in which widespread ranges (spanning islands) are integral to inferences about speciation scenarios (dispersal-vicariance analysis [DIVA; parsimony-based] and dispersal-extinction-cladogenesis [DEC; likelihood-based]). The methods yield conflicting results, which we interpret in light of their respective assumptions. FP exhibits the least power to unequivocally reconstruct ranges, likely due to a combination of having flat (uninformative) transition costs and not using branch length information. SM reconstructions generally agree with a prior hypothesis about dispersal-driven speciation across the Pacific, despite the conceptual mismatch between its character-based model and this mode of range evolution. In contrast with narrow extant ranges for species of Cyrtandra, DIVA reconstructs broad ancestral ranges at many nodes. DIVA results also conflict with geological information on island ages; we attribute these conflicts to the parsimony criterion not considering branch lengths or time, as well as vicariance being the sole means of divergence for widespread ancestors. DEC analyses incorporated geological information on island ages and allowed prior hypotheses about range size and dispersal rates to be evaluated in a likelihood framework and gave more nuanced inferences about range evolution and the geography of speciation than other methods tested. However, ancestral ranges at several nodes could not be conclusively resolved, due possibly to uncertainty in the phylogeny or the relative complexity of the underlying model. Of the methods tested, SM and DEC both converge on plausible hypotheses for area range histories in Cyrtandra, due in part to the consideration of branch lengths and/or timing of events. We suggest that DEC model-based methods for ancestral range inference could be improved by adopting a Bayesian SM approach, in which stochastic sampling of complete geographic histories could be integrated over alternative phylogenetic topologies. Likelihood-based estimates of ancestral ranges for Cyrtandra suggest a major dispersal route into the Pacific through the islands of Fiji and Samoa, motivating future biogeographic investigation of this poorly known region.

Reconstructing the biogeographical history of two plant genera with different dispersion capabilities

AbstractAim The pappus is one of the most distinctive features of the genera belonging to the sunflower family, and is an efficient mechanism for dispersion by wind. The pappose Holocheilus (seven species) and the non‐pappose Panphalea (nine species) are two genera of the monophyletic subtribe Nassauviinae (Asteraceae, Mutisieae), which overlap in their areas of distribution. This paper aims to reconstruct the biogeographical histories that shaped the distribution of these two genera, which are phylogenetically and geographically related, but differ in their means of dispersion. Our initial expectation was that the dispersion capability of the pappus should be reflected in more dispersal events in Holocheilus than in Panphalea.Location South‐eastern Brazil, Paraguay, Uruguay and Argentina.Methods Morphological data were acquired from the literature and by analysis of specimens. Two cladistic analyses, one for Holocheilus and one for Panphalea, were based on morphological characters, and data matrices were analysed with the Fitch parsimony algorithm of paup. The ancestral distributions were reconstructed using diva ver. 1.1 according to the dispersal–vicariance optimization method.Results The Paranense‐fields were identified as the most likely ancestral area of Holocheilus and Panphalea. Biogeographical reconstruction of Holocheilus shows several dispersal events from the Paranense‐fields: two ancestral dispersal events to the Yungas, followed by vicariance events (Paranense‐fields/Yungas) and numerous terminal dispersals to the surrounding areas such as Chacoan, Pampean and Espinal. diva reconstruction of Panphalea distribution also shows frequent terminal dispersals, with no vicariant events, from the Paranense‐fields to the other areas: (1) to Espinal, Pampean‐Uruguayan, Pampean‐oriental; (2) to Paranense‐hills; (3) to Pampean‐Uruguayan; and (4) to Paranense‐pine lands.Main conclusions In the past, both genera probably originated in the Paranense‐fields area, which was subject to the dry and humid cycles of the Quaternary glaciations. Dispersal was the process that predominantly shaped the distribution of Panphalea and Holocheilus, with approximately the same number of dispersal events in both genera, despite differing ranges of dispersion. The main barriers to dispersal were the dry Cerrado and Chaco, the latter promoting vicariance in Holocheilus. The lack of a pappus in Panphalea was a limitation for its dispersion compared with Holocheilus.