Parsimony Optimality Research Articles

Molecular phylogenetics of tribe Synandreae, a North American lineage of lamioid mints (Lamiaceae)

The five mint genera Brazoria, Macbridea, Physostegia, Synandra and Warnockia (Lamioideae: Lamiaceae) are all North American endemics. Together with the monotypic European genus Melittis and the Asian genus Chelonopsis, these taxa have been classified as subtribe Melittidinae. Previous morphological studies have failed to uncover synapomorphic characters for this group. We sequenced the plastid trnL-trnF region and trnS-trnG spacer and the nuclear ribosomal 5S non-transcribed spacer (5S-NTS) to assess phylogenetic relationships within Melittidinae. Standard parsimony and direct optimization (POY) analyses show Melittis, the type genus of the subtribe, as sister to Stachys. Thus, the monophyly of subtribe Melittidinae is not supported either by molecular or morphological data. However, the North American endemics form a monophyletic group that can be recognized as the recircumscribed tribe Synandreae. The molecular relationships among these genera are corroborated by both morphological and cytological data. The expected close relationship between the south-central endemics Warnockia and Brazoria and their sister relationship to the widespread genus Physostegia is confirmed. Nevertheless, most of the North American endemics are restricted to the south-east of the continent. Dispersal westwards and northwards is correlated with an increase in chromosome numbers. No specific Eurasian origin (i.e., transatlantic or transpacific) can be determined, but Synandreae are clearly distinct from the large Stachys clade, and therefore represent a separate migration into North America. © The Willi Hennig Society 2007.

Reproduction in Brevicipitid Frogs (Amphibia: Anura: Brevicipitidae)—Evidence from Probreviceps M. Macrodactylus

An egg clutch of the Tanzanian brevicipitid frog, Probreviceps m. macrodactylus, is described for the first time. The single clutch consists of 32 eggs and 21 infertile, jelly-filled capsules, tightly bound together by a thin, tough outer layer. The infertile capsules are concentrated toward the top of the clutch. The eggs were found in a dry season, and were perhaps likely to hatch at the onset of the short rains. The specific identification is confirmed through analysis of mitochondrial DNA sequence data. Eggs are yolky and large, about 8 mm in diameter (including capsule), suggesting that P. m. macrodactylus has a direct mode of development. The embryos observed were in an early developmental stage and showed the early division of the brain and anlagen of three pairs of visceral arches. Brevicipitid reproduction and development are poorly known, but a review of the existing literature and parsimonious optimization of simple characters onto a phylogenetic framework suggest that direct development is a derived condition characterizing the whole clade.

Bone histological correlates of high-frequency flapping flight and body mass in the furculae of birds: a phylogenetic approach

A parsimony optimization of the presence of high-frequency flapping flight onto a phylogeny of 29 species of birds shows that this is a derived character state that has been acquired at least four independent times: by the last common ancestor of Alcidae, that of Podicipedidae, that of Anatidae, and that of Rallidae. Cineradiographic analysis has shown that the furculae of birds underwent extraordinary deformations during the wingbeat cycle. Cyclical deformations are known to produce microfractures in the bone tissue, which may be a stimulus for Haversian remodelling, a mechanism of resorption and reconstruction of bone tissue that may repair bone microdamage. In the present study, we performed a comparative analysis in a phylogenetic context to test the effect of the frequency of cyclical deformations and body mass on the rate of Haversian remodelling in the furculae of birds. A variation partitioning analysis showed that the type of flight (high-frequency flapping flight vs. other kinds of flight of lower wing beat frequency) and body mass explained a significant portion of Haversian bone density (the outcome of Haversian remodelling) and that the phylogeny also explained a significant part of this variation. This phylogenetic signal on Haversian bone density variation may be the outcome of phylogenetic signal on the proximate causes producing Haversian remodelling. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society, 2007, 91, 729–738.

A molecular phylogenetic analysis of the Scarabaeinae (dung beetles)

The dung beetles (Scarabaeinae) include ca. 5000 species and exhibit a diverse array of morphologies and behaviors. This variation presumably reflects the adaptation to a diversity of food types and the different strategies used to avoid competition for vertebrate dung, which is the primary breeding environment for most species. The current classification gives great weight to the major behavioral types, separating the ball rollers and the tunnelers, but existing phylogenetic studies have been based on limited taxonomic or biogeographic sampling and have been contradictory. Here, we present a molecular phylogenetic analysis of 214 species of Scarabaeinae, representing all 12 traditionally recognized tribes and six biogeographical regions, using partial gene sequences from one nuclear (28S) and two mitochondrial (cox1, rrnL) genes. Length variation in 28S (588–621bp) and rrnL (514–523bp) was subjected to a thorough evaluation of alternative alignments, gap-coding methods, and tree searches using model-based (Bayesian and likelihood), maximum parsimony, and direct optimization analyses. The small-bodied, non-dung-feeding Sarophorus+Coptorhina were basal in all reconstructions. These were closely related to rolling Odontoloma+Dicranocara, suggesting an early acquisition of rolling behavior. Smaller tribes and most genera were monophyletic, while Canthonini and Dichotomiini each consisted of multiple paraphyletic lineages at hierarchical levels equivalent to the smaller tribes. Plasticity of rolling and tunneling was evidenced by a lack of monophyly (S-H test, p>0.05) and several reversals within clades. The majority of previously unrecognized clades were geographical, including the well-supported Neotropical Phanaeini+Eucraniini, and a large Australian clade of rollers as well as tunneling Coptodactyla and Demarziella. Only three lineages, Gymnopleurini, Copris+Microcopris and Onthophagus, were widespread and therefore appear to be dispersive at a global scale. A reconstruction of biogeographical characters recovered 38–48 transitions between regions and an African origin for most lineages. Dispersal–vicariance analysis supported an African origin with links to all other regions and little back-migration. Our results provide a new synthesis of global-scale dung beetle evolution, demonstrating the great plasticity of behavioral and morphological traits and the importance of biogeographic distributions as the basis for a new classification.

Biogeography and evolution of flower color in Veratrum (Melanthiaceae) through inference of a phylogeny based on multiple DNA markers

Veratrum (Melanthiaceae) comprises ca. 27 species with highly variable morphology. This study aims to construct the molecular phylogeny of this genus to infer its floral evolution and historical biogeography, which have not been examined in detail before. Maximum parsimony, maximum likelihood, and Bayesian analyses were performed on the separate and combined ITS, trnL-F, and atpB-rbcL sequences to reconstruct the phylogenetic tree of the genus. All Veratrum taxa formed a monophyletic group, within which two distinct clades were distinguished: species with white-to-green perianth formed one highly supported clade, and the species with black-purple perianth constituted another highly supported clade. Phylogenetic inference on flower color evolution suggested that white-to-green perianth was a plesiomorphic state and black-purple perianth was apomorphic for Veratrum. When species distribution areas were traced as a multi-state character, parsimonious optimization inferred that Veratrum possibly originated in East Asia. Our study confirmed previous phylogenetic and taxonomic suggestions on this genus and provided a typical example of plant radiation across the Northern Hemisphere.

EVOLUTIONARY DYNAMICS OF HOST-PLANT SPECIALIZATION: A CASE STUDY OF THE TRIBE NYMPHALINI

Abstract Two general patterns that have emerged from the intense studies on insect‐host plant associations are a predominance of specialists over generalists and a taxonomic conservatism in host‐plant use. In most insect‐host plant systems, explanations for these patterns must be based on biases in the processes of host colonizations, host shifts, and specialization, rather than cospeciation. In the present paper, we investigate changes in host range in the nymphalid butterfly tribe Nymphalini, using parsimony optimizations of host‐plant data on the butterfly phylogeny. In addition, we performed larval establishment tests to search for larval capacity to feed and survive on plants that have been lost from the female egg‐laying repertoire. Optimizations suggested an ancestral association with Urticaceae, and most of the tested species showed a capacity to feed on Urtica dioica regardless of actual host‐plant use. In addition, there was a bias among the successful establishments on nonhosts toward plants that are used as hosts by other species in the Nymphalini. An increased likelihood of colonizing ancestral or related plants could also provide an alternative explanation for the observed pattern that some plant families appear to have been colonized independently several times in the tribe. We also show that there is no directionality in host range evolution toward increased specialization, that is, specialization is not a dead end. Instead, changes in host range show a very dynamic pattern.

Molecular Phylogenetic Relationships Among Crested-tailed Mice (Genus Habromys)

We examined genealogical relationships among six of seven species of crested-tailed mice (Habromys chinanteco, H. delicatulus, H. ixtlani, H. lepturus, H. lophurus, and H. simulatus) using DNA sequence data from the cytochrome-b gene. Gene trees based on maximum likelihood, Bayesian inference and maximum parsimony were largely congruent in that H. lepturus and H. ixtlani were closely related and formed the sister group to H. lophurus. All analyses also arranged H. chinanteco and H. simulatus as sister taxa. These results are concordant with the phenetic groupings of Carleton et al. (2002) based on morphology. Our unweighted maximum parsimony trees did not resolve placement of H. delicatulus relative to other taxa. However, analyses using weighted maximum parsimony, maximum likelihood and Bayesian inference optimality criteria recovered a sister group relationship between H. delicatulus and the clade comprised of ((H. lepturus H. ixtlani)(H. lophurus)). This relationship differs from the overall phenetic similarity of H. delicatulus with H. simulatus and H. chinanteco, influenced by the small size of these three taxa, but is consistent with some derived features of the phallus (Carleton et al., 2002). Based on our sequence data, a specimen from Michoacan, Mexico, recently assigned to Peromyscus sagax likely was inadvertently misidentified (Tiemann-Boege et al., 2000) and actually represents a new locality record for H. delicatulus. Finally, we comment on the conservation status of species of Habromys.

Molecular phylogeny of the genus Stereocaulon ( Stereocaulaceae, lichenized ascomycetes)

In the present study phylogenetic relationships of the genus Stereocaulon (lichenized ascomycetes) were examined using DNA sequences from the ITS1–5.8 S–ITS2 rDNA gene cluster and from the protein-coding β-tubulin gene. In addition to the fruticose species traditionally classified in Stereocaulon, representatives of the crustose species that have recently been transferred to the genus were included. Muhria, a monotypic genus that is morphologically similar to Stereocaulon, differing only in apothecia ontogeny, was also incorporated. The analyses included 101 specimens from the ingroup representing 49 taxa. Sequences from both DNA regions were analysed simultaneously using direct optimization under the parsimony optimality criterion. The results support the inclusion of the crustose species and Muhria in Stereocaulon, while the current infrageneric classification is not supported. As Muhria is securely nested within Stereocaulon the new combination Stereocaulon urceolatum comb. nov. (syn. Muhria urceolata) is made. Further, species concepts need to be re-examined, as some species do not appear as monophyletic entities in the phylogeny.

Phlogeny and Biogeography of the Prayer Plant Family

Marantaceae are the second largest family in the order Zingiberales, with approximately 31 genera and 535 species. Earlier studies based on morphological and molecular characters could not confidently determine the relationships among major lineages of the family, nor could they identify the basal branch of the family tree. Phylogenetic analyses of DNA sequence data from all three genomic compartments (chloroplast: matK, ndhF, rbcL, rps16 intron, and trnL-trnF intergenic spacer; mitochondrion: cox1; nucleus: ITS region and the 5'-end of 26S) for a restricted set of taxa were conducted under parsimony criteria to define the root node and to assess geographical distribution patterns. Our results support the recognition of five major lineages, most of which are restricted to a single geographical region (tropical America, tropical Africa, or tropical Asia). The phylogenies and character reconstructions (Fitch parsimony optimization, Bremer ancestral areas, and DIVA) support an African origin for the family, followed by a minimum of two dispersal events to the New World tropics and four or more dispersal events to the Asian tropics. Less likely are two alternative hypotheses: (1) vicariance of a western Gondwanan group (the Americas and Africa) followed by several dispersals to Asia and Africa, or (2) an American origin followed by several dispersals to Africa and Asia. The low specific diversity in Africa may be due to higher extinction rates as a result of shrinking lowland tropical forests during the Tertiary.

Molecular phylogeny of the palm genus Chamaedorea, based on the low-copy nuclear genes PRK and RPB2

Sequence data from the low-copy nuclear genes encoding phosphoribulokinase (PRK) and the second largest subunit of RNA polymerase II (RPB2) are used to generate the first phylogenetic analysis of Chamaedorea (Arecaceae: Arecoideae: Chamaedoreeae), the largest neotropical genus of palms. The prevailing current taxonomy of Chamaedorea recognizes approximately 100 species in eight subgenera, all delimited using floral characters, which provide a useful starting point to explore species-level systematics. Sequence data from 63 species, including representatives of all eight subgenera, were analyzed using maximum parsimony and Bayesian inference optimality criteria. Genus Chamaedorea is resolved as monophyletic with strong support in all separate and combined analyses. The less species-rich subgenera are convincingly monophyletic and can be diagnosed using morphological synapomorphies. In contrast, the two largest subgenera, Chamaedorea and Chamaedoropsis, which are supposedly distinguishable from each other by the degree of connation in the staminate petals, are both resolved as highly polyphyletic. Several well supported monophyletic groups resolved by these gene regions have never before been proposed within Chamaedorea and are challenging to delimit using morphological criteria. Although PRK proved more informative than RPB2, both regions have strong utility for interpreting species-level relationships among the palms, which are notoriously recalcitrant subjects for molecular phylogenetic studies. In addition, a paralog of the target copy of PRK identified during the analysis represents a potentially valuable source of phylogenetic information for future studies.

Phylogeny and Historical Biogeography of <I>Anaxagorea</I> (Annonaceae) Using Morphology and Non-Coding Chloroplast Sequence Data

The Annonaceae are a pantropical angiosperm family, in which Anaxagorea is sister to the rest of the family based on previous phylogenetic studies. Anaxagorea is the only genus of Annonaceae with a disjunct distribution in South and Central America and southeast Asia. Earlier arguments on the biogeographic history of Annonaceae led to the hypothesis of a Laurasian origin for Anaxagorea. A detailed phylogenetic study was conducted using 75 morphological characters and molecular sequences from the atpB-rbcL, psbA-trnH, and trnL-trnF spacer regions and the trnL intron. Molecular analyses alone do not support the monophyly of the Asian species, but the morphological and combined molecular and morphological analyses do. All analyses place most Central American species in a clade, but none support an Asian-Central American clade. South American species form a basal grade, thereby refuting the hypothesis of a Laurasian origin for the genus and indicating instead a Gondwanan origin. Parsimony optimizations and DIVA reconstructions of biogeographic data indicate separate dispersals from South America to Central America and to Asia. Molecular age estimates indicate an Eocene origin for the genus. The clade containing the Asian and Central American species is dated to be younger than the Oligocene climatic deterioration, which reduces support for the North Atlantic land bridge as a dispersal route from South America to Asia.

Molecular systematics of Middle American harvest mice Reithrodontomys (Muridae), estimated from mitochondrial cytochrome b gene sequences

We estimated phylogenetic relationships among 16 species of harvest mice using sequences from the mitochondrial cytochrome b (cyt b) gene. Gene phylogenies constructed using maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) optimality criteria were largely congruent and arranged taxa into two groups corresponding to the two recognized subgenera ( Aporodon and Reithrodontomys). All analyses also recovered R. mexicanus and R. microdon as polyphyletic, although greater resolution was obtained using ML and BI approaches. Within R. mexicanus, three clades were identified with high nodal support (MP and ML bootstrap, Bremer decay and Bayesian posterior probabilities). One represented a subspecies of R. mexicanus from Costa Rica ( R. m. cherrii) and a second was distributed in the Sierra Madre Oriental of Mexico. The third R. mexicanus clade consisted of mice from southern Mexico southward to South America. Polyphyly between the two moieties of R. microdon corresponded to the Isthmus of Tehuantepec in southern Mexico. Populations of R. microdon microdon to the east of the isthmus (Chiapas, Mexico) grouped with R. tenuirostris, whereas samples of R. m. albilabris to the west in Oaxaca, Mexico, formed a clade with R. bakeri. Within the subgenus Reithrodontomys, all analyses recovered R. montanus and R. raviventris as sister taxa, a finding consistent with earlier studies based on allozymes and cyt b data. There was also strong support (ML and BI criteria) for a clade consisting of (( R. megalotis, R. zacatecae) ( R. sumichrasti)). In addition, cyt b gene phylogenies (MP, ML, and BI) recovered R. fulvescens and R. hirsutus (ML and BI) as basal taxa within the subgenus Reithrodontomys. Constraint analyses demonstrated that tree topologies treating the two subgenera ( Aporodon and Reithrodontomys) as monophyletic (ML criterion) was significantly better ( p > 0.036) and supported polyphyly of R. mexicanus (both ML and MP criteria – p > 0.013) and R. microdon (MP criterion only for certain topologies; p > 0.02). Although several species-level taxa were identified based on multiple, independent data sets, we recommended a conservative approach which will involve thorough analyses of museum specimens including material from type localities together with additional sampling and data from multiple, nuclear gene markers.

Phylogeny of Meloidogyne spp. based on 18S rDNA and the intergenic region of mitochondrial DNA sequences

AbstractThe 18S rDNA of 19 populations of Meloidogyne spp. was amplified and directly sequenced. The region of mitochondrial DNA, located in the 3′ portion of the gene that codes for cytochrome oxidase subunit II (COII) through a portion of the 16S rRNA (lRNA) gene, from 16 of these populations was cloned and sequenced. Heteroplasmic sequences were identified from both rDNA and mtDNA regions for several taxa. Several sequences sampled from nominal taxa differed from previously published accounts. Phylogenetic trees based on alignments of these sequences were constructed using distance, parsimony and likelihood optimality criteria. For 18S rDNA data, three main clades were identified. One well supported clade (86–91% bootstrap) included the most common and widely disseminated species, e.g.,M. arenaria, M. javanica and M. incognita, some recently described or redescribed species (M. floridensis, M. paranaensis, and M. ethiopica) plus numerous unidentified isolates. All mitotic parthenogenetic species, except for M. oryzae, were included in this clade. Other, less well supported clades included the amphimictic and facultative meiotic species M. hapla, M. microtyla, M. maritima and M. duytsi. One such clade comprised three meiotic parthenogens (M. exigua, M. graminicola and M. chitwoodi) and M. oryzae. This clade was moderately supported (77% bootstrap) but the relationships within this clade were poor. For mitochondrial DNA data, only the species in clade I from rDNA analysis, and M. hapla were analysed. These species formed a well supported clade (100% bootstrap) to the exclusion of M. mayaguensis and M. hapla. The addition of taxa and mtDNA data to publicly available records improved the discrimination sensitivity of species and atypical, non-identified, isolates.

Phylogeny of Tragopogon L. (Asteraceae) Based on Internal and External Transcribed Spacer Sequence Data

Tragopogon L. (Lactuceae, Cichorioideae, Scorzonerinae) is an Old World genus of ca. 150 species. To elucidate relationships in this poorly understood genus, we analyzed internal and external transcribed spacer sequences (ITS and ETS, respectively) from 59 species from 14 of the 17 sections recognized by Borisova. Podospermum and Lactuca were used as outgroups. ITS and ETS sequence data provide strong support for the monophyly of Tragopogon under parsimony optimality criteria. Sequence data also support the monophyly of several of the recognized sections within Tragopogon, including the sections Tragopogon, Majores, Hebecarpus, Chromopappus, and Collini. However, the circumscriptions of these groups are often altered from the taxonomic treatment of Borisova. Most members of the recognized sections Brevirostres and Profundisulcati appear within the Brevirostres and Profundisulcati clades, respectively. Species of section Nikitinia are also included in the Brevirostres clade. Sequence data also provide evidence for an Angustissimi clade of T. pusillus, T. filifolius, diploid T. latifolius ($$2\mathrm{n}\,=12$$), T. segetum, T. acanthocarpus, T. serotinus, and T. charadzae, species not previously considered closely related. Our analyses also indicate possible relationships for 17 species that had not been previously placed in any section. The diploids T. porrifolius, T. pratensis, and T. dubius, which were introduced into North America and ultimately formed the recent alloploids T. mirus and T. miscellus, are not closely related within Tragopogon; T. dubius and T. porrifolius appear in sister clades, and T. pratensis is more distantly related. Characters often used to establish sectional groupings, such as the length of the achene beak, evolved multiple times in Tragopogon.

Ordinal relationships of pleurocarpous mosses, with special emphasis on the Hookeriales

Sequence data from four DNA regions, namely, chloroplast trnL‐trnF and rps4, mitochondrial nad5, and nuclear 26S rDNA, were surveyed from 89 taxa traditionally associated with the Hookeriales, five Hypnales and five outgroups. Phylogenetic reconstruction was performed using the maximum parsimony and maximum likelihood optimality criteria and by Bayesian phylogenetic inference. Thirteen morphological characters were optimized on the resulting phylogeny using maximum likelihood. Inferences of character evolution based on the molecular phylogeny suggest that (1) the core of pleurocarpous mosses (i.e. the Hypnanae) is best defined and thus distinguished from the Ptychomnianae by smooth rather than furrowed capsules, (2) a synapomorphy for the Ptychomnianae is the short and double (or absent) costa and (3) the Hookeriales are defined by undifferentiated alar cells. The Ptychomniaceae plus Garovagliaceae are recognized as a single family in its own order, the Ptychomniales ord. nov. and superorder, the Ptychomnianae, superord. nov. This superorder is sister to the combined Hypnales and Hookeriales, i.e. the Hypnanae. The Hookeriales are interpreted as consisting of seven families, the Hypopterygiaceae, Saulomataceae fam. nov., Daltoniaceae, Schimperobryaceae fam. nov., Hookeriaceae, Leucomiaceae and Pilotrichaceae. The Adelotheciaceae are embedded within the Daltoniaceae and considered synonymous with that family. Within the Ptychomniaceae, Ptychomniella is raised from a subgenus of Ptychomnion to generic status. Euptychium setigerum and its monospecific section, Crassisubulata, are transferred to Garovaglia. Callicostella diatomophila is transferred to Diploneuron. Additional alterations at the generic level await more data.

Bayesian Inference of Phylogeny: A Non-Technical Primer

methodology employed to estimate phylogeny. This is not to say that issues such as the use of morphological data versus molecular data or whether or not to combine data for phylogenetic analyses have not been debated in the past. Clearly, these and many other issues have received a considerable amount of debate in the phylogenetic literature. Possibly one of the most rigorously debated topics is the choice of an optimality criterion. In general, there are three basic methods that have been used to estimate phylogeny, including distance, maximum parsimony (MP), and maximum likelihood (ML). The relative merits and shortcomings of these methods have been debated for a number of years (e.g., Faith, 1985; Swofford & Olsen, 1990; Kunhner & Felsenstein, 1994; Huelsenbeck, 1995; Farris & al., 1996; Lewis, 1998; Steel & Penny, 2000), and it is not within the scope of this column to reiterate these discussions. However, it is noteworthy that numerous comparative studies employing both known phylogenies and simulated data have been very useful in determining under what set of conditions each of the methods performs the others. For example, it is now generally accepted that when rates of change along branches vary greatly, employing a parsimony optimality criterion may be misleading due to long branch attraction (Felsenstein, 1978; but see Siddall, 1998); whereas additional studies have shown that ML may be inconsistent in other situations, such as when the chosen model of evolution is inappropriate (e.g., Farris, 1999). Simulation studies indicate that distance methods (especially UPGMA) are highly susceptible to variations in evolutionary rates and typically perform more poorly than either MP or ML (e.g., Huelsenbeck & Hillis, 1993). Studies such as these have been important in laying a theoretical foundation for making decisions on how best to estimate phylogeny given the data in hand. However, under most sets of realistic conditions, comparison of ML and MP indicates that these methods perform similarly and often result in highly concordant topologies (e.g., Reed & al., 2002; Kimball & al., 2003). Recently, another round of comparative studies has begun to address a new approach for phylogeny reconstruction (e.g., Suzuki & al., 2002; Wilcox & al., 2002; Alfaro & al., 2003; Douady & al., 2003). This new approach, Bayesian analyses, was proposed in 1996 (Rannala & Yang, 1996; Mau, 1996; Li, 1996) and is now receiving much attention in the literature [e.g., see Systematic Biology 51 (5)]. Several excellent technical reviews have recently been provided by Huelsenbeck & al. (2001, 2002) and Lewis (2001). Although this approach is now a hot topic in systematics, Bayesian statistics actually dates back to the 18th century and its utility for reconstructing phylogeny was suggested initially in 1968 by Felsenstein (see Huelsenbeck & al., 2002). It is only recently, however, that these methods have become more widely known and that relevant computer programs have become available. Internet links for downloadable programs for Bayesian analyses (and other methods) are available from the websites of J. Felsenstein (http://evolution.genetics.washington.edu/ phylip/software.html), and P. Lewis (http://lewis. eeb.uconn.edu/lewishome/), or directly from the MrBayes (http://morphbank.ebc.uu.se/mrbayes/; Huelsenbeck & Ronquist, 2001) or BAMBE (http://www. mathcs.duq.edu/larget/bambe.html; Simon & Larget, 1998) websites. A helpful introduction on how to use MrBayes is provided by Hall (2001). Here we attempt to provide a basic introduction to Bayesian approaches to phylogeny reconstruction. In doing so, we point out what we feel are some of the most significant attributes of this new approach. It is important to note that we do not consider ourselves to be experts on this topic, but merely are interested in how this approach differs from other methods and how to implement this methodology into our own research, should we feel it appropriate. Thus, we hope this column will serve as a primer for those of you curious about Bayesian methods.

Phylogenetic relationships within the moss family Bryaceae based on chloroplast DNA evidence.

The Bryaceae are a large cosmopolitan family of mosses containing genera of considerable taxonomic difficulty. Phylogenetic relationships within the family were inferred using data from chloroplast DNA sequences (rps4 and trnL-trnF region). Parsimony and maximum likelihood optimality criteria, and Bayesian phylogenetic inference procedures were employed to reconstruct relationships. The genera Bryum and Brachymenium are not monophyletic groups. A clade comprising Plagiobryum, Acidodontium, Mielichhoferia macrocarpa, Bryum sects. Bryum, Apalodictyon, Limbata, Leucodontium, Caespiticia, Capillaria (in part: sect. Capillaria), and Brachymenium sect. Dicranobryum, is well supported in all analyses and represents a major lineage within the family. Section Dicranobryum of Brachymenium is more closely related to section Bryum than to the other sections of Brachymenium, as are Mielichhoferia macrocarpa and M. himalayana. Species of Acidodontium form a clade with Anomobryum julaceum. The grouping of species with a rosulate gametophytic growth form suggests the presence of a 'rosulate' clade similar in circumscription to the genus Rosulabryum. Mielichhoferia macrocarpa and M. himalayana are transferred to Bryum as B. porsildii and B. caucasicum, respectively.

PHYLOGENETICS OF THE GRASS GENUS EHRHARTA: EVIDENCE FOR RADIATION IN THE SUMMER-ARID ZONE OF THE SOUTH AFRICAN CAPE

Climatic and geological change may play a key role in stimulating biological radiations. Here, we use phylogenetic data to test whether the comparatively high diversity of ehrharteoid grasses in the Cape region of South Africa is the result of rapid radiation associated with the onset of a seasonally arid climate during the late Miocene. A phylogenetic hypothesis based on morphological and nucleotide sequence (nuclear ITS1 and plastid trnL-F) data confirms the monophyly of the African Ehrharta species and shows that the diversification of this lineage was centered in the Cape region. Sequence divergence data (ITS1 trnL-F) indicate a pulse of rapid speciation, which may explain poor phylogenetic resolution within the African Ehrharta clade. Alternative calibrations yield a broad range of time estimates for the start and end of this radiation, most of which indicate a radiation inside the last 11 million years. A calibration based on the age of Ehrhartoideae suggests that radiation started 9.82 ± 0.20 million years ago and ended 8.74 ± 0.21 million years ago. Under alternative calibrations, estimated speciation rates during the period of radiation range between 0.87 and 4.18 species per million years. Parsimony optimization of habitat parameters reveals that radiation was correlated with the occupation of seasonally arid succulent karoo environments, wet heathy (fynbos) environments being ancestral. These data support earlier suggestions that late Miocene climatic change stimulated floristic radiation at the Cape, and highlight the potential importance of environmental change in powering diversification in continental floras.

Phylogeny of the Macaronesian endemic Crambe section Dendrocrambe (Brassicaceae) based on internal transcribed spacer sequences of nuclear ribosomal DNA

The 14 species of Crambe L. sect. Dendrocrambe DC. (Brassicaceae) form a monophyletic group endemic to the Canary and Madeira archipelagos. Both parsimony and maximum likelihood analyses of sequence data from the two internal transcribed spacer regions of nuclear ribosomal DNA were used to estimate phylogenetic relationships within this section. These analyses support the monophyly of three major clades. No clade is restricted to a single island, and therefore it appears that inter-island colonization has been the main avenue for speciation in these two archipelagos. The two species endemic to Fuerteventura (C. sventenii) and Madeira (C. fruticosa) comprise a clade, providing the first evidence for a floristic link between the Eastern Canary Islands and the archipelago of Madeira. Both maximum likelihood and weighted parsimony analyses show that this clade is sister to the two other clades, although bootstrap support for this relationship is weak. Parsimony optimizations of ecological zones and island distribution suggest a colonization route from the low-altitude areas of the lowland scrub toward the high-elevation areas of the laurel and pine forests. In addition, Tenerife is likely the ancestral island for species endemic to the five westernmost islands of Gran Canaria, La Gomera, El Hierro, La Palma, and Tenerife.

Rate acceleration and long-branch attraction in a conserved gene of cryptic daphniid (Crustacea) species.

The nuclear large subunit (LSU) rRNA gene is a rich source of phylogenetic characters because of its large size, mosaic of slowly and rapidly evolving regions, and complex secondary structure variation. Nevertheless, many studies have indicated that inconsistency, bias, and gene-specific error (e.g., within-individual gene family variation, cryptic sequence simplicity, and sequence coevolution) can complicate animal phylogenies based on LSU rDNA sequences. However, most of these studies sampled small gene fragments from expansion segments--among animals only five nonchordate complete LSU sequences are published. In this study, we sequenced near-complete nuclear LSU genes from 11 representative daphniids (Crustacea). The daphniid expansion segment V6 was larger and showed more length variation (90-351 bp) than is found in all other reported LSU V6 sequences. Daphniid LSU (without the V6 region) phylogenies generally agreed with the existing phylogenies based on morphology and mtDNA sequences. Nevertheless, a major disagreement between the LSU and the expected trees involved a positively misleading association between the two taxa with the longest branches, Daphnia laevis and D. occidentalis. Both maximum parsimony (MP) and maximum likelihood (ML) optimality criteria recovered this association, but parametric simulations indicated that MP was markedly more sensitive to this bias than ML. Examination of data partitions indicated that the inconsistency was caused by increased nucleotide substitution rates in the branches leading to D. laevis and D. occidentalis rather than among-taxon differences in base composition or distribution of sites that are free to vary. These results suggest that lineage-specific rate acceleration can lead to long-branch attraction even in the conserved genes of animal species that are almost morphologically indistinguishable.