Cladonia rubrotincta, a new species distinct from C. norvegica

Reappraising adaptive radiation

BackgroundMatrices of morphological characters are frequently used for dating species divergence times in systematics. In some studies, morphological and molecular character data from living taxa are combined, whereas others use morphological characters from extinct taxa as well. We investigated whether morphological data produce time estimates that are concordant with molecular data. If true, it will justify the use of morphological characters alongside molecular data in divergence time inference.ResultsWe systematically analyzed three empirical datasets from different species groups to test the concordance of species divergence dates inferred using molecular and discrete morphological data from extant taxa as test cases. We found a high correlation between their divergence time estimates, despite a poor linear relationship between branch lengths for morphological and molecular data mapped onto the same phylogeny. This was because node-to-tip distances showed a much higher correlation than branch lengths due to an averaging effect over multiple branches. We found that nodes with a large number of taxa often benefit from such averaging. However, considerable discordance between time estimates from molecules and morphology may still occur as some intermediate nodes may show large time differences between these two types of data.ConclusionsOur findings suggest that node- and tip-calibration approaches may be better suited for nodes with many taxa. Nevertheless, we highlight the importance of evaluating the concordance of intrinsic time structure in morphological and molecular data before any dating analysis using combined datasets.

A major challenge in the post-genomics era will be to integrate molecular sequence data from extant organisms with morphological data from fossil and extant taxa into a single, coherent picture of phylogenetic relationships; only then will these phylogenetic hypotheses be effectively applied to the study of morphological character evolution. At least two analytical approaches to solving this problem have been utilized: (1) simultaneous analysis of molecular sequence and morphological data with fossil taxa included as terminals in the analysis, and (2) the molecular scaffold approach, in which morphological data are analyzed over a molecular backbone (with constraints that force extant taxa into positions suggested by sequence data). The perceived obstacles to including fossil taxa directly in simultaneous analyses of morphological and molecular sequence data with extant taxa include: (1) that fossil taxa are missing the molecular sequence portion of the character data; (2) that morphological characters might be misleading due to convergence; and (3) character weighting, specifically how and whether to weight characters in the morphological partition relative to characters in the molecular sequence data partition. The molecular scaffold has been put forward as a potential solution to at least some of these problems. Using examples of simultaneous analyses from the literature, as well as new analyses of previously published morphological and molecular sequence data matrices for extant and fossil Chiroptera (bats), we argue that the simultaneous analysis approach is superior to the molecular scaffold approach, specifically addressing the problems to which the molecular scaffold has been suggested as a solution. Finally, the application of phylogenetic hypotheses including fossil taxa (whatever their derivation) to the study of morphological character evolution is discussed, with special emphasis on scenarios in which fossil taxa are likely to be most enlightening: (1) in determining the sequence of character evolution; (2) in determining the timing of character evolution; and (3) in making inferences about the presence or absence of characteristics in fossil taxa that may not be directly observable in the fossil record.

A cladistic analysis is performed using 94 morphological and biochemical characters for 42 genera to compare a phylogeny based on morphological data with those obtained using different genes (rbcL, atpB, 18S RNA, matK) or their combination with morphological data, and to understand the floral evolution within the expanded Brassicales (Capparales) relative to Sapindales and Malvales. The tree produced with morphological data is congruent with those obtained from macromolecular studies in obtaining a well-supported glucosinolate-producing clade and an expanded Sapindales. The combined analysis of the morphological and molecular characters is generally well resolved with support for many of the relationships. The inclusion of the fossil taxon Dressiantha demonstrates the value of inserting fossil evidence in phylogenetic analyses. However, the fossil appears to be related to the Anacardiaceae and not to the Brassicales. The core Brassicales are well supported by a number of synapomorphies, although the internal position of Tovariaceae and Pentadiplandraceae is not well resolved. Emblingiaceae appears to be related to Bataceae and Salvadoraceae. Several significant morphological characters are mapped on the combined trees and their evolutionary significance is discussed. Within Brassicales and Sapindales several well supported clades can be recognized which merit ordinal or subordinal status, putting the present orders at a higher level; these include: Tropaeolales, Setchellanthales, Batidales, Brassicales (Brassiciflorae), Burserales, Sapindales and Rutales (Sapindiflorae). The present scheme of affinities within the Brassicales corresponds well with a gradual morphological evolution in the order. © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society, 2006, 151, 453–494.

Hybrid zones provide biologists with the opportunity to examine genetic and ecological interactions between differentiated populations. Accurate identification of hybrid genealogies is considered a necessary prerequisite to understanding observed patterns of hybridization-related phenomena. We analysed molecular and morphological data from individuals in a hybrid zone between two species of willows (Salix sericea Marshall and S. eriocephala Michaux) and report the use of randomly amplified polymorphic DNA (RAPD), chloroplast DNA (cpDNA), and ribosomal DNA (rDNA) markers, as well as vegetative morphology and foliar chemistry data to identify individuals in terms of hybrid genealogy and to infer the direction and extent of backcrossing and introgression within the hybrid zone. A novel version of a maximum likelihood estimate approach (developed for this study) was used to calculate hybrid index scores from RAPD marker data; this method produced results similar to those obtained using traditional arithmetic methods. Distribution of rDNA, cpDNA, and chemistry data were examined within the graphical context of RAPD-based hybrid index score histograms and principal component analyses (PCA) on RAPD and morphology data. Seven of the 21 plants classified as S. eriocephala in the field were possible introgressants. Another plant presented an unequivocal example of backcrossed S. sericea chemistry and RAPD markers. Inter- and intraspecific chloroplast diversity found within the hybrid zone suggests both historic introgression (perhaps in a glacial refugium), and contemporary hybridization. Patterns of inheritance and expression within the hybrid zone suggest that morphological characters are often not expressed in a simple additive fashion, and problems associated with both morphological and molecular data are considered.

The new species Hypocrea virens, has been found to be the teleomorph of Trichoderma virens, a species commonly used in biological control applications. This conclusion is based on the comparison of morphological and molecular data from four isolates of T. virens and a single collection and isolate of H. virens. Data for several morphological characters, including colony and growth characteristics, were collected. In addition, sequence data from ITS1, 5.8S, ITS2 rDNA and translation elongation factor (tef-1α) were analyzed for the five isolates. Analysis of phenotypic characters show that cultures and microscopic characters of the anamorph of H. virens are indistinguishable from those of T. virens. This is consistent with sequence data from ITS1, 5.8S, ITS2 rDNA which show that the sequence of H. virens is identical to that of the ex-type isolate of T. virens. Despite minor variation in tef-1α sequences, T. virens isolates and H. virens form a monophyletic group that is different from other examined species of Hypocrea; this clade is supported by a 100% bootstrap value. Molecular and morphological data confirm the connection between H. virens and T. virens.

It took almost a century until Schwendener’s (1867) finding that lichens belong to the fungi finally led mycologists and lichenologists to include them in the fungal system (Nannfeldt 1932; Santesson 1952). Trying to elucidate the phylogenetic relationships between lichenized and un-lichenized fungi and among lichen taxa, based solely on morphological and chemical data, has proven to be a frustrating endeavour. Lichens display few taxonomically useful characters, of which many are widely variable; the homology of character states within and between groups is difficult to assess. Often, even the interpretation of morphological characters, e.g. types of ascoma development or ascus type, proved difficult (see e.g. Henssen and Jahns 1974; Lumbsch 2000; Lumbsch et al. 2001c; Ott and Lumbsch 2001; Stenroos et al. 2002b; Lumbsch and Huhndorf 2007). In the absence of well-supported and uncontroversial phylogenetic reconstructions based on morphological data, molecular data have, therefore, gained great importance in lichen systematics. The impact of molecular data on the classification and taxonomy of lichenized ascomycetes has been summarized regularly in recent years (Lumbsch 2000, 2007; Grube and Winka 2002; DePriest 2004). This review is not an attempt to update these previous comprehensive reviews. It rather tries to shed light on the relationship between results based on molecular and morphological studies of lichens. In the late 1980s and early 1990s, morphology-based taxonomy and systematics and molecular phylogenetics of lichens more or less led their own separate lives. The first studies based on molecular data often concentrated on reconstructing phylogenetic relationships and were not so much concerned with character evolution or the reinterpretation of morphological characters in light of molecular results. Likewise, a critical evaluation of the results in light of morphological data was rarely attempted. This has changed profoundly in recent years. Most phylogenetic reconstructions of lichenized ascomycetes are now designed to test morphology-based classifications. As a result, the systematic value of morphological characters in diverse groups is now much better understood than previously and reconstructions of character evolution exist for many systematic groups. On the other hand, classical taxonomists make increasing use of molecular data because classical lichen taxonomy is riddled with problems that only independent data from molecular analyses are likely to solve. One very obvious problem that is relatively easy to solve with molecular data concerns the systematic placement of obligately sterile lichens (Stenroos and DePriest 1998; Arup and Grube 1999; Platt and Spatafora 2000; Ekman and Tonsberg 2002; Crespo et al. 2004a) or other species with doubtful systematic affinities (Printzen and Kantvilas 2004; Lucking et al. 2007; Spribille et al. 2009). Other such problems arise from the multiple description of morphologically variable species, doubtful circumscriptions of taxa and erroneous assignment of species to them, or misinterpretation of the systematic value of characters due to incorrect homology hypotheses. In all these cases, molecular analyses offer promising tools to test traditional hypotheses.

Genetic relationships of endophytic Lophodermium nitens isolates from needles of Pinus strobus

The integration of morphological and molecular data is essential to understand the affinities of fossil taxa and spatio-temporal evolutionary processes of organisms. However, homoplastic morphological characters can mislead the placement of fossil taxa and impact downstream analyses. Here, we provide an example of how to mitigate effectively the effect of morphological homoplasy on the placement of fossil taxa and biogeographic inferences of Cissampelideae. We assembled three data types, morphological data only, morphological data with a molecular scaffold and combined morphological and molecular data. By removing high-level homoplastic morphological data or reweighting the morphological characters, we conducted 15 parsimony, 12 undated Bayesian and four dated Bayesian analyses. Our results show that the 14 selected Cissampelideae fossil taxa are placed poorly when based only on morphological data, but the addition of molecular scaffold and combination of morphological and molecular data greatly improve the resolution of fossil nodes. We raise the monotypic Stephania subg. Botryodiscia to generic status and discover that three fossils previously assigned to Stephania should be members of Diploclisia. The Bayesian tip-dated tree recovered by removing homoplastic morphological characters with a Rescaled Consistency Index <0.25 has the highest stratigraphic fit and consequently generates more reasonable biogeographic reconstruction for Cissampelideae. Cissampelideae began to diversify in Asia in the latest Cretaceous and subsequently dispersed to South America around the Cretaceous-Palaeogene boundary. Two dispersal events from Asia to Africa occurred in the Early Eocene and the Late Eocene-Late Oligocene, respectively. These findings provide guidelines and practical methods for mitigating the effects of homoplastic morphological characters on fossil placements and Bayesian tip-dating, as well as insights into the past tropical floristic exchanges among different continents.

Phylogeny of the ectomycorrhizal mushroom genus Alnicola (Basidiomycota, Cortinariaceae) based on rDNA sequences with special emphasis on host specificity and morphological characters

DNA fingerprinting based on SSR amplification profiles was applied to native species of Piper from the Atlantic Forest to compare the utility of this type of molecular marker with the morphological characters traditionally applied in Piper taxonomy and identification. Fifty-one SSR markers developed for four species of Piper native to Asia and Mesoamerica were applied to 16 species, together with 63 morphological characters, for species characterization. Molecular and morphological data were analysed by cluster analysis, followed by a cluster sharpness test and the construction of a heat map to visualize the association of characters with species groups. A multivariate regression tree determined the number of loci needed for species identification. Forty-five primers were transferable to at least four species. Molecular data were more efficient in detecting sharp groups than morphological data. Species groups delimited by a set of shared morphological characters were differentiated based on molecular data. The sixteen studied species could be separated by nine primers, demonstrating the cross-species transferability of SSR markers and the usefulness of DNA fingerprinting for both the delimitation and the identification of species of Piper.

We present a phylogenetic analysis of the Dactyloa clade of Anolis lizards, based on morphological (66 characters of external morphology and osteology) and molecular (∼4,700 bases of mitochondrial and nuclear DNA) data. Our set of morphological characters includes some that exhibit continuous variation and others that exhibit polymorphism within species; we explored different coding methods for these classes of characters. We performed parsimony and Bayesian analyses on morphology-only and combined data sets. Additionally, we explicitly tested hypotheses of monophyly of: 1) Dactyloa including Phenacosaurus, 2) Dactyloa excluding Phenacosaurus (as traditionally circumscribed), 3) taxa previously ranked as series or species groups described based on morphological characters, and 4) clades inferred from molecular data. The morphological data alone did not yield Dactyloa or any of the previously recognized series described based on morphological characters; only the Phenacosaurus clade (as delimited ...

Alvarez, B., Crisp, M.D., Driver, F., Hooper, J.N.A. &amp; Van Soest, R.W.M. (2000). Phylogenetic relationships of the family Axinellidae (Porifera: Demospongiae) using morphological and molecular data. —Zoologica Scripta, 29, 169–198.Twenty‐seven species of marine sponges belonging to Axinellidae and related groups (Halichondriidae, Dictyonellidae, Agelasida) were selected to test the monophyly of Axinellidae and investigate their phylogenetic relationships using parsimony and maximum likelihood methods. Partial 28S rDNA sequences, including the D3 domain, and traditional morphological characters (mainly skeletal ones) were used independently to construct phylogenetic trees. Sequences were aligned using the appropriate model of secondary structure of the RNA and compared to that produced by the multiple sequence alignment program, ClustalW. The alignment using secondary structure constraints produced a better estimate of the phylogeny and was demonstrated to be an effective and objective method.Results of the cladistic analyses of the molecular and morphological data sets were not fully congruent; the morphological data suggest that Axinellidae is monophyletic, however, the molecular data suggest that it is nonmonophyletic. The single most‐parsimonious tree derived from the molecular data showed that species ofAxinella(exceptA. polypoides) are united in a clade that is more closely related to members of Agelasida than to other species of Axinellidae; the remaining members of Axinellidae form a monophyletic group that is closely related to the families Dictyonellidae and Halichondriidae. The consensus tree of 20 most‐parsimonious trees from the morphological analysis, on the other hand, showed that all the sampled species of Axinellidae belong to a monophyletic group which is closely related to the species of Dictyonellidae and Halichondriidae. Only two branches were identical in both cladograms, the one uniting the species ofPtilocaulisandReniochalinaand the one with the species of Dictyonellidae.The robustness of the molecular and morphological trees (or parts of the trees), was tested using bootstrap, jack‐knife, PTP and T‐PTP tests. The results of the PTP test were significant indicating significant cladistic structure in both data sets. The bootstrap and jack‐knife values indicate that the molecular tree is in general better supported than the morphological one. The lack of morphological characters and the homoplastic nature of some may explain the weak support of the morphological tree. A T‐PTP test of nonmonophyly showed that the nonmonophyly of Axinellidae, as indicated by the results of the molecular analysis, is not significant; however, a T‐PTP test of monophyly of Axinellidae, as indicated by the morphological tree, produced significant results. This indicates that the monophyly of Axinellidae based on morphological data cannot be rejected; the family however, cannot be defined in terms of a unique diagnostic character common to all members of the ingroup.Tests of heterogeneity (reciprocal T‐PTP and partition homogeneity test) indicated that the data partitions are heterogeneous, which could be due to sampling errors (in either data set) or differences in the underlying phylogenies; therefore data were not combined in a single analysis. Further, both data sets are unequally sized (95 informative molecular characters vs. 16 informative morphological characters), which means that the molecular signal could swamp the morphological signal if the data is combined.Nonmonophyly of Axinellidae is supported by chemical and genetic evidence available in the literature and DNA sequences data of axinellid species from New Zealand. However, this needs to be confirmed using independent evidence from different genes (or gene regions), biochemistry, histology or cell ultrastructure. Therefore, no changes to the taxonomic position of the family in the higher classification are proposed at this stage.

Mickevich, M. F., and M. S. Johnson (Ceutre de Recherches Mathe6matiques, Universit' de Montr6al, Montreal, P.Q., Canada and Department of Ecology and Evolution, State University of New York, Stony Brook, N. Y. 11794) 1976. Congruence between morphological and allozyme data in evolutionary inference and character evolution. Syst. Zool. 25:260-270. -In view of the growing concern that evolutionary information obtained from morphological data may differ in content from evolutionary information from molecular data, we have asked whether morphological data yield phyletic interpretations consistent with those inferred from allozymes. Minimum length Wagner trees were calculated from sets of morphometric and allozyme data on sixteen populations representing five nominal species of Menidia (Teleostel, Atherinidae). The two sets of characters yield nearly perfectly congruent evolutionary trees, despite the fact that phenetic analyses reveal very great disparity between the similarity structures of the morphometrics and the allozymes. A quantitative method for estimating convergence and parallelism was developed and revealed no significant differences in the proportions of these types of homoplasy for the two data sets. This cladistical method for estimating convergence is contrasted with partially phenetic methods used in the past; the later are shown to be incorrect. Mosaic evolution between morphometrics and allozymes is demonstrated statistically, and shown to result from heterogeneous rates of apomorphy, rather than from a preponderance of plesiomorphy in one data set. This mosaicism is the probable source of the large phenetic disparity. We conclude that 1) cladistical, rather than phenetic, methods are required for the analysis of character evolution, and 2) that the ease of obtaining sufficient information, rather than presumed inherent differences between characters, should determine which characters are used for evolutionary taxonomic inference. [Cladistical character analysis; taxonomic congruence; morphometrics; allozymes; Menidia.] During the past decade, studies of proteins have had an increasingly important influence on evolutionary biology and systematics. An important question arising from these studies is whether molecular characters are evolutionarily concordant with anatomical characters. The impression of some authors has been that proteins and morphological characters have evolved concordantly (summaries in Lewontin, 1974; Avise, 1974). Recently, however, several studies have indicated a high degree of evolutionary independence of molecular and morphological evolution (Turner, 1974; Gould et al., 1974; Maxson and Wilson, 1974, 1975; Johnson, 1974, 1975; Avise et al., 1975; King and Wilson, 1975; Kornfield and Koehn, 1975; Johnson et al., 1976). These 1Present address: Department of Zoology, University of Western Australia, Nedlands, Western Australia 6009. examples of disparity add to the already substantial evidence against the non-specificity hypothesis (Rohlf, 1965; Sneath and Sokal, 1973). It is not clear from such studies, however, whether there are differences between proteins and morphological characters in their reliability as indicators of evolutionary relationships, because characters which are completely independent genetically, and highly disparate in their rates of divergence, may be perfectly concordant in their indications of phylogenies. In other words, phenetically disparate characters may show taxonomic congruence (Farris, 1971). Either explicitly or implicitly, the suggestion has been made that molecular data are more reliable as phyletic indicators than are morphological data (Anonymous, 1974; Avise, 1974; Maxson and Wilson, 1974, 1975; Nei, 1975). However, to answer the

:This study evaluated the species level taxonomy and phylogenetic relationships among species of the section Virescentia of the genus Batrachospermum focusing on specimens from Brazil and other regions of the world. Molecular data (sequences of the plastid-encoded RuBisCO large-subunit gene, rbcL; and the barcode region of the mitochondrial encoded cytochrome c oxidase subunit 1, cox1) were generated, and morphological characters described for 13 populations. Molecular analyses of rbcL sequences revealed the existence of three well-supported clades with evident biogeographic trends, containing sequences of specimens of either North America (USA), Asia (Japan) or Brazil. Similarly, analysis of cox1 sequences (slightly different taxon sampling) also revealed three clades, containing specimens of either North America (USA), Europe (Norway) or Brazil. The three species recognized from Brazil in a previous study based on morphological data (Batrachospermum helminthosum, B. sirodotii and B. vogesiacum) could not be distinguished by molecular or morphological data. A new species was proposed for Brazilian specimens based on molecular and morphological evidence. Batrachospermum viride-brasiliense differed from the European species of the section Virescentia (B. bruziense, B. coerulescens, B. elegans, B. sirodotii and B. vogesiacum) by the longer carpogonia (≥ 40 μm) and larger carposporophytes (≥ 200 μm in diameter and ≥ 100 μm high) and carposporangia (≥ 19 μm long and ≥ 10 μm in diameter).