Incomplete Taxon Sampling Research Articles

Multilocus phylogenetic analysis of the first molecular data from the rare and monotypic Amarsipidae places the family within the Pelagia and highlights limitations of existing data sets in resolving pelagian interrelationships

The Pelagia is a recently delineated group of fishes, comprising fifteen families formerly placed in six perciform suborders. The Pelagia was lately recognized as it encompasses huge morphological diversity and only in the last few years have large-scale molecular phylogenetic studies been undertaken that could unite such morphologically disparate lineages. Due to the recent erection of Pelagia, the composition of the taxon is not entirely certain. Five families of the former perciform suborder Stromateoidei have been identified as pelagians. However, the sixth stromateoid subfamily Amarsipidae is a rare monotypic family that has distinctive meristic and morphological characteristics from that of other stromateoids such as the lack of a pharyngeal sac. We examine molecular data generated from the sole species in Amarsipidae, Amarsipus carlsbergi, and demonstrate that it is clearly nested within Pelagia. As with two previous studies that have the breadth of sampling to evaluate pelagian intra-relationships, we find high support for monophyly of most family-level taxonomic units but statistical support for early-branching nodes in the pelagian tree is very low. We conduct the first analyses of Pelagia incorporating the multispecies coalescent and are limited by a high degree of missing loci, or, incomplete taxon sampling. The high degree of missing data across a complete sampling of pelagian lineages along with the deep time scale and rapid radiation of the lineage contribute to poor resolution of early-branching relationships within Pelagia that cannot be resolved with current data sets. Currently available data are either mitochondrial genomes or a super matrix of relatively few loci with a high degree of missing data. A new and independent dataset of numerous phylogenetic loci derived from high-throughput sequencing technology may reduce uncertainty within the Pelagia and provide insights into this adaptive radiation.

Phylogenomic analysis of the Chilean clade of Liolaemus lizards (Squamata: Liolaemidae) based on sequence capture data.

The genus Liolaemus is one of the most ecologically diverse and species-rich genera of lizards worldwide. It currently includes more than 250 recognized species, which have been subject to many ecological and evolutionary studies. Nevertheless, Liolaemus lizards have a complex taxonomic history, mainly due to the incongruence between morphological and genetic data, incomplete taxon sampling, incomplete lineage sorting and hybridization. In addition, as many species have restricted and remote distributions, this has hampered their examination and inclusion in molecular systematic studies. The aims of this study are to infer a robust phylogeny for a subsample of lizards representing the Chilean clade (subgenus Liolaemus sensu stricto), and to test the monophyly of several of the major species groups. We use a phylogenomic approach, targeting 541 ultra-conserved elements (UCEs) and 44 protein-coding genes for 16 taxa. We conduct a comparison of phylogenetic analyses using maximum-likelihood and several species tree inference methods. The UCEs provide stronger support for phylogenetic relationships compared to the protein-coding genes; however, the UCEs outnumber the protein-coding genes by 10-fold. On average, the protein-coding genes contain over twice the number of informative sites. Based on our phylogenomic analyses, all the groups sampled are polyphyletic. Liolaemus tenuis tenuis is difficult to place in the phylogeny, because only a few loci (nine) were recovered for this species. Topologies or support values did not change dramatically upon exclusion of L. t. tenuis from analyses, suggesting that missing data did not had a significant impact on phylogenetic inference in this data set. The phylogenomic analyses provide strong support for sister group relationships between L. fuscus, L. monticola, L. nigroviridis and L. nitidus, and L. platei and L. velosoi. Despite our limited taxon sampling, we have provided a reliable starting hypothesis for the relationships among many major groups of the Chilean clade of Liolaemus that will help future work aimed at resolving the Liolaemus phylogeny.

A new species of Linum (Linaceae) from Iran with a focus on description of Linum turcomanicum in view of morphological and molecular analyses

The genus Linum consists of 15 species in Iran. A new species as well as a new record from Iran is described and illustrated here as L. khorassanicum and L. turcomanicum, respectively. The original description of the latter species is incomplete and ambiguous, probably due to incomplete taxon sampling. In this work, after a comprehensive taxon sampling from the entire distribution range of the species in northeast of Iran, the taxonomic description of L. turcomanicum is completed. The present study considers morphological and molecular (the nrITS region) analyses of the both species. In phylogenetic analysis based on the molecular data, we included these species and some related Linum species to examine the phylogenetic relationship of the new species and L. turcomanicum with other members of the genus. Linum turcomanicum is morphologically almost similar to L. austriacum and L. perenne, but it can be distinguished from them on the basis of several traits such as fruiting-pedicel form and length of petal. Likewise, results obtained from the molecular phylogenetic tree are consistent with those obtained from the morphological data. Linum khorassanicum is well characterized morphologically by having erect fruiting pedicels and inflorescence with few flowers. Our results suggest that the morphological data are in agreement with the molecular phylogenetic tree in which the taxonomic status of L. khorassanicum is confirmed as a new species. Based on IUCN Red List categories and criteria, L. khorassanicum and L. turcomanicum are evaluated as Endangered and Near Threatened species, respectively.

New circumscription of the genus Gamochaeta (Asteraceae, Gnaphalieae) inferred from nuclear and plastid DNA sequences

Gamochaeta (tribe Gnaphalieae, Asteraceae) is composed of ca. 60 species primarily distributed in tropical and subtropical America. Within the tribe Gnaphalieae, the genus is characterized by capitula arranged in spikes or head-like clusters, few hermaphroditic central florets, truncate style branches with apical sweeping trichomes, pappus bristles connate at the base into a ring falling as a unit, and achenes with globose twin trichomes. Previous molecular phylogenetic studies have suggested the paraphyly of the genus, but have not provided a basis for redefining generic limits due to incomplete taxon sampling. To address this problem, DNA sequences from the plastid (trnL-F) and nuclear (ETS and ITS) genomes were analyzed from a broad taxon sample representing the full range of morphological variation known in the genus. Our results affirm that Gamochaeta is paraphyletic as presently circumscribed. Two clades can be recognized: one clade that includes the majority of the species currently assigned to Gamochaeta and a second clade that includes Gamochaetopsis, Stuckertiella and seven species of Gamochaeta. We present here a new circumscription of Gamochaeta, including two new combinations, Gamochaeta alpina and Gamochaeta peregrina, and the resurrection of Gamochaeta capitata. Our results also show Omalotheca supina, O. norvegica and O. sylvatica, which were placed by some authors in Gamochaeta or in Gnaphalium, form a monophyletic group distantly related to both genera.

Molecular phylogeny and genome size evolution of the genus Betula (Betulaceae).

Background and Aims Betula L. (birch) is a genus of approx. 60 species, subspecies or varieties with a wide distribution in the northern hemisphere, of ecological and economic importance. A new classification of Betula has recently been proposed based on morphological characters. This classification differs somewhat from previously published molecular phylogenies, which may be due to factors such as convergent evolution, hybridization, incomplete taxon sampling or misidentification of samples. While chromosome counts have been made for many species, few have had their genome size measured. The aim of this study is to produce a new phylogenetic and genome size analysis of the genus.Methods Internal transcribed spacer (ITS) regions of nuclear ribosomal DNA were sequenced for 76 Betula samples verified by taxonomic experts, representing approx. 60 taxa, of which approx. 24 taxa have not been included in previous phylogenetic analyses. A further 49 samples from other collections were also sequenced, and 108 ITS sequences were downloaded from GenBank. Phylogenetic trees were built for these sequences. The genome sizes of 103 accessions representing nearly all described species were estimated using flow cytometry.Key Results As expected for a gene tree of a genus where hybridization and allopolyploidy occur, the ITS tree shows clustering, but not resolved monophyly, for the morphological subgenera recently proposed. Most sections show some clustering, but species of the dwarf section Apterocaryon are unusually scattered. Betula corylifolia (subgenus Nipponobetula) unexpectedly clusters with species of subgenus Aspera. Unexpected placements are also found for B. maximowicziana, B. bomiensis, B. nigra and B. grossa. Biogeographical disjunctions were found within Betula between Europe and North America, and also disjunctions between North-east and South-west Asia. The 2C-values for Betula ranged from 0·88 to 5·33 pg, and polyploids are scattered widely throughout the ITS phylogeny. Species with large genomes tend to have narrow ranges.Conclusions Betula grossa may have formed via allopolyploidization between parents in subgenus Betula and subgenus Aspera. Betula bomiensis may also be a wide allopolyploid. Betula corylifolia may be a parental species of allopolyploids in the subsection Chinenses. Placements of B. maximowicziana, B. michauxii and B. nigra need further investigation. This analysis, in line with previous studies, suggests that section Apterocaryon is not monophyletic and thus dwarfism has evolved repeatedly in different lineages of Betula. Polyploidization has occurred many times independently in the evolution of Betula.

Bats (Chiroptera: Noctilionoidea) Challenge a Recent Origin of Extant Neotropical Diversity.

The mechanisms underlying the high extant biodiversity in the Neotropics have been controversial since the 19th century. Support for the influence of period-specific changes on diversification often rests on detecting more speciation events during a particular period. The timing of speciation events may reflect the influence of incomplete taxon sampling, protracted speciation, and null processes of lineage accumulation. Here we assess the influence of these factors on the timing of speciation with new multilocus data for New World noctilionoid bats (Chiroptera: Noctilionoidea). Biogeographic analyses revealed the importance of the Neotropics in noctilionoid diversification, and the critical role of dispersal. We detected no shift in speciation rate associated with the Quaternary or pre-Quaternary periods, and instead found an increase in speciation linked to the evolution of the subfamily Stenodermatinae (∼18 Ma). Simulations modeling constant speciation and extinction rates for the phylogeny systematically showed more speciation events in the Quaternary. Since recording more divergence events in the Quaternary can result from lineage accumulation, the age of extant sister species cannot be interpreted as supporting higher speciation rates during this period. Instead, analyzing the factors that influence speciation requires modeling lineage-specific traits and environmental, spatial, and ecological drivers of speciation.

Integrating Sequence Evolution into Probabilistic Orthology Analysis.

Orthology analysis, that is, finding out whether a pair of homologous genes are orthologs - stemming from a speciation - or paralogs - stemming from a gene duplication - is of central importance in computational biology, genome annotation, and phylogenetic inference. In particular, an orthologous relationship makes functional equivalence of the two genes highly likely. A major approach to orthology analysis is to reconcile a gene tree to the corresponding species tree, (most commonly performed using the most parsimonious reconciliation, MPR). However, most such phylogenetic orthology methods infer the gene tree without considering the constraints implied by the species tree and, perhaps even more importantly, only allow the gene sequences to influence the orthology analysis through the a priori reconstructed gene tree. We propose a sound, comprehensive Bayesian Markov chain Monte Carlo-based method, DLRSOrthology, to compute orthology probabilities. It efficiently sums over the possible gene trees and jointly takes into account the current gene tree, all possible reconciliations to the species tree, and the, typically strong, signal conveyed by the sequences. We compare our method with PrIME-GEM, a probabilistic orthology approach built on a probabilistic duplication-loss model, and MrBayesMPR, a probabilistic orthology approach that is based on conventional Bayesian inference coupled with MPR. We find that DLRSOrthology outperforms these competing approaches on synthetic data as well as on biological data sets and is robust to incomplete taxon sampling artifacts.

Evolutionary plant radiations: where, when, why and how?

Evolutionary plant radiations: where, when, why and how?

Diversification of North American natricine snakes

The phylogeny of thamnophiine snakes has not been fully resolved, largely because previous phylogenetic estimates have been based on incomplete taxon sampling or relied solely on mitochondrial sequence data. To address this deficiency, we collected data from multiple autosomal loci collected from 50 taxa before estimating the most robust phylogeny of Thamnophiini to date. Our findings clarify the relationships of taxa not previously included in molecular analyses and also lend evidence to previously recommended taxonomic revisions. Differences in topological estimates between competing models of evolution were minimal and not strongly supported; however, a multispecies coalescent model of evolution was highly favoured over a concatenated model based on marginal likelihood estimates. Additionally, we estimated the timing of divergence among the three major lineages to have occurred during the Miocene period (approximately 11–14 Mya), followed by a decline in speciation rates in all major lineages.

A review of the systematics and taxonomy of Pythonidae: an ancient serpent lineage

Here we review research over the past quarter century regarding the systematics and taxonomy of an ancient, popular and economically valuable group of snakes referred to as pythons (Serpentes, Pythonidae). All recent phylogenetic studies recognize the pythons as monophyletic; however, the phylogenetic relationships at supraspecific levels are conflicting, and many of the relationships recovered are paraphyletic. We identify several taxonomic changes as necessary to clarify supraspecific relationships and which resolve the issue of paraphyly recovered in several studies. Overall, our review of the phylogenetic systematics of pythons points to considerable incongruence among recovered relationships. Instances of paraphyly emerge, low node support is detected, and terminal taxa are unstable across phylogenetic hypotheses. We thus recognize that pythonid gene trees have been unable, for various reasons, to reveal the true species tree. This occurrence is not unexpected and can arise from incomplete taxon sampling, long-branch attraction and repulsion, homoplasy, ancestral polymorphism, and, more notably, the anomaly zone. These phenomena ultimately yield incomplete lineage sorting, or the failure of lineages to coalesce over evolutionary time. We discuss future directions to resolve these troubling issues. Without resolution, adaptive hypotheses about pythons will be limited, including hypotheses of geographic origin. Analyses that recover the clade Python as sister to the Indo-Australian clade are interpreted to support a Laurasian origin of Pythonidae. In contrast, a Gondwanan origin is supported when the Indo-Australian clade is recovered as basal to the Python clade. We describe the morphology of two recently proposed genera. Finally, we designate and describe the neotype for Morelia azurea and offer a list of the currently accepted python species and their taxonomy.

Sympatric speciation in killer whales?

Sympatric speciation in killer whales?

Phylogenetic Relationships in <I>Echinocereus</I> (Cactaceae, Cactoideae)

Echinocereus is the third most species-rich genus in the Cactaceae. It is distributed in North America from Mexico to the central U. S. A. Previous molecular phylogenetic studies have indicated that the genus is polyphyletic, but incomplete taxon sampling and unclear resolution have hindered the formal re-evaluation of generic and infrageneric circumscriptions. To address this problem, we analyzed six plastid regions (matK, rbcL, psbA-trnH, trnQ-rps16, rpl16, and trnL-F) using maximum parsimony and Bayesian inference criteria for 59 species, including all previously proposed infrageneric entities and representing the full range of morphological variation known in the genus. Our results support the monophyly of Echinocereus if E. pensilis is excluded and reestablished as the monotypic genus Morangaya. Two additional morphological characters, erumpent flower buds and green stigma lobes, further support the circumscription of Echinocereus sensu stricto. Phylogenetic analyses recovered nine main clades in Echinocereus s. s., one of which corresponds to the Triglochidiati section; the remaining clades did not correspond to any other recognized sections. We suggest a re-evaluation of previously proposed infrageneric entities.

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

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

Likelihood Inference of Non-Constant Diversification Rates with Incomplete Taxon Sampling

Large-scale phylogenies provide a valuable source to study background diversification rates and investigate if the rates have changed over time. Unfortunately most large-scale, dated phylogenies are sparsely sampled (fewer than 5% of the described species) and taxon sampling is not uniform. Instead, taxa are frequently sampled to obtain at least one representative per subgroup (e.g. family) and thus to maximize diversity (diversified sampling). So far, such complications have been ignored, potentially biasing the conclusions that have been reached. In this study I derive the likelihood of a birth-death process with non-constant (time-dependent) diversification rates and diversified taxon sampling. Using simulations I test if the true parameters and the sampling method can be recovered when the trees are small or medium sized (fewer than 200 taxa). The results show that the diversification rates can be inferred and the estimates are unbiased for large trees but are biased for small trees (fewer than 50 taxa). Furthermore, model selection by means of Akaike's Information Criterion favors the true model if the true rates differ sufficiently from alternative models (e.g. the birth-death model is recovered if the extinction rate is large and compared to a pure-birth model). Finally, I applied six different diversification rate models – ranging from a constant-rate pure birth process to a decreasing speciation rate birth-death process but excluding any rate shift models – on three large-scale empirical phylogenies (ants, mammals and snakes with respectively 149, 164 and 41 sampled species). All three phylogenies were constructed by diversified taxon sampling, as stated by the authors. However only the snake phylogeny supported diversified taxon sampling. Moreover, a parametric bootstrap test revealed that none of the tested models provided a good fit to the observed data. The model assumptions, such as homogeneous rates across species or no rate shifts, appear to be violated.

Ecological Opportunity and Incumbency in the Diversification of Repeated Continental Colonizations by Muroid Rodents

Why some clades are more species-rich than others is a central question in macroevolution. Most hypotheses explaining exceptionally diverse clades involve the emergence of an ecological opportunity caused by a major biogeographic transition or evolution of a key innovation. The radiation of muroid rodents is an ideal model for testing theories of diversification rates in relation to biogeography and ecological opportunity because the group is exceptionally species-rich (comprising nearly one-third of all mammal species), it is ecologically diverse, and it has colonized every major landmass except New Zealand and Antarctica, thus providing multiple replicate radiations. We present an extension of the conventional ecological opportunity model to include a geographic incumbency effect, develop the largest muroid phylogeny to date, and use this phylogeny to test the new model. The nearly 300-species phylogeny based on four nuclear genes is robustly resolved throughout. Consistent with the fossil record, we identified Eurasia as the most likely origin of the group and reconstructed five to seven colonizations of Africa, five of North America, four of Southeast Asia, two of South America, two of Sahul, one of Madagascar, and eight to ten recolonizations of Eurasia. We accounted for incomplete taxon sampling by using multiple statistical methods and identified three corroborated regions of the tree with significant shifts in diversification rates. In several cases, higher rates were associated with the first colonization of a continental area, but most colonizations were not followed by bursts of speciation. We found strong evidence for diversification consistent with the ecological opportunity model (initial burst followed by density-dependent slowdown) in the first colonization of South America and partial support for this model in the first colonization of Sahul. Primary colonizers appear to inhibit the ultimate diversity of secondary colonizers, a pattern of incumbency that is consistent with ecological opportunity, but they did not inhibit initial diversification rates of secondary colonizers. These results indicate that ecological opportunity may be a general but weak process in muroids and one that requires specific circumstances to lead to an adaptive radiation. The total land area, length of time between colonizations, and rank of colonizations did not influence the diversification rates of primary colonizers. Models currently employed to test ecological opportunity do a poor job of explaining muroid diversity. In addition, the various rate-shift metrics identified different clades, suggesting that caution should be used when only one is applied, and we discuss which methods are most appropriate to address different questions of diversification.

Phylogeny of the Oenanthe lugens complex (Aves, Muscicapidae: Saxicolinae): Paraphyly of a morphologically cohesive group within a recent radiation of open-habitat chats

The morphologically inferred Oenanthe lugens complex comprises nine taxa of open-habitat chats which occur in rocky and/or mountainous areas adjacent to the Saharo-Sindian desert belt. It has traditionally been divided into the lugubris group of north-east Africa, the lugentoides group of the southern part of the Arabian Peninsula and the lugens group of North Africa and the Middle East. Previous molecular phylogenetic studies have shown that the O. lugens complex might not be monophyletic. However, it remained unclear how this result might have been affected by incomplete taxon sampling, as the lugentoides group and two out of three taxa of the lugubris group have not been analyzed so far. In this study, we present a phylogenetic hypothesis of the O. lugens complex based on two mitochondrial genes and one nuclear intron using, for the first time, a complete taxon sampling. The application of a multispecies coalescent approach allowed us to simultaneously estimate the sequence and timing of speciation events. The O. lugens complex was consistently revealed as a polyphyletic assemblage and the traditionally recognized groups should be treated as at least three different species: O. lugens, Oenanthelugubris, and Oenanthelugentoides. While O. lugubris and O. lugentoides were revealed to be sister groups, O. lugens was found to be closely related to the species pair Oenanthechrysopygia/Oenanthexanthoprymna. The latter differ quite strongly in morphology and have traditionally not been associated with members of the lugens complex. We thus corroborate the results of previous studies, which demonstrated that morphology seems to be a poor predictor of phylogenetic relationships in Oenanthe. In contrast to the mtDNA markers analyzed, it was revealed that differences among taxa were not fixed in the nuclear intron. In the case of the taxa persica of the lugens group, an influence of introgression in autosomal markers cannot be excluded and deserves further study. The three species O. lugens, O. lugubris, and O. lugentoides and their associated taxa comprise a comparatively young radiation, which started to diversify in the Pliocene with major diversification events during the Pleistocene. The different taxa seem to have evolved during periods of increased aridity in isolation in rocky mountainous areas adjacent to hyper arid regions.

The rise of the Himalaya enforced the diversification of SE Asian ferns by altering the monsoon regimes

BackgroundThe rise of high mountain chains is widely seen as one of the factors driving rapid diversification of land plants and the formation of biodiversity hotspots. Supporting evidence was reported for the impact of the rapid rise of the Andean mountains but this hypothesis has so far been less explored for the impact of the “roof of the world”. The formation of the Himalaya, and especially the rise of the Qinghai–Tibetan Plateau in the recent 20 million years, altered the monsoon regimes that dominate the current climates of South East Asia. Here, we infer the hypothesis that the rise of Himalaya had a strong impact on the plant diversity in the biodiversity hotspot of the Southwest Chinese Mountains.ResultsOur analyses of the diversification pattern of the derived fern genus Lepisorus recovered evidence for changes in plant diversity that correlated with the strengthening of South East Asian monsoon. Southwest China or Southwest China and Japan was recovered as the putative area of origin of Lepisorus and enhancing monsoon regime were found to shape the early diversification of the genus as well as subsequent radiations during the late Miocene and Pliocene.ConclusionsWe report new evidence for a coincidence of plant diversification and changes of the climate caused by the uplift of the Himalaya. These results are discussed in the context of the impact of incomplete taxon sampling, uncertainty of divergence time estimates, and limitations of current methods used to assess diversification rates.

Phylogenetic analyses of Tolpis Adans. (Asteraceae) reveal patterns of adaptive radiation, multiple colonization and interspecific hybridization.

The plant genus Tolpis (Asteraceae) has been the subject of several investigations on the evolution of oceanic island plants. Its insular species were utilized in studies of artificial hybrid fertility, testing the validity of Baker's law, the application of DNA barcodes, and the phylogenetic utility of inter-simple sequence repeat markers. Despite this considerable interest in Tolpis, little is known about its phylogenetic history. Past investigations were unable to resolve most of the interspecific relationships, especially within the Canary Islands, where the genus is particularly diverse. Incomplete taxon sampling, the use of ambiguous outgroups and the limited utility of slowly evolving chloroplast DNA markers precluded detailed reconstructions. The present investigation presents a comprehensive molecular phylogeny of Tolpis. By utilizing highly variable nuclear DNA markers and a comprehensive taxon set, we have resolved the majority of interspecific relationships in the genus. Evaluations of competing tree topologies and ancestral area reconstructions complemented the analyses. Our results highlight the presence of three dominant mechanisms of island plant evolution-island colonization, adaptive radiation and interspecific hybridization-in Tolpis: (i) the extant distribution of the genus is the result of two independent colonization pathways, (ii) Tolpis has colonized at least one archipelago multiple times, (iii) the present insular diversity is the product of adaptive radiation, (iv) potential hybridization was detected between species now inhabiting different islands and archipelagoes, indicating sympatric historical distributions, and (v) several undescribed species await taxonomic recognition.

The phylogeny of the Neuropterida: long lasting and current controversies and challenges (Insecta: Endopterygota)

Despite numerous efforts to establish a sound phylogeny of Neuropterida and to trace their position within the tree of Endopterygota these questions up to now still appear far from being solved. The evidence for the sister group relationships among the three orders of Neuropterida is contradictory (i.e., Raphidioptera as sister group of Megaloptera + Neuroptera versus Neuroptera as sister group of Megaloptera + Raphidioptera) and recently even the monophyly of Megaloptera was challenged. Also the phylogenetic relationships among neuropteran families deduced from various studies differ basically in all aspects concerning the number and composition of suborders as well as the basal dichotomies. The morphology based division of Neuroptera into the three suborders Nevrorthiformia, Myrmeleontiformia and Hemerobiiformia with the latter two being sister groups is not recovered by molecular but also some morphology based analyses – as all of them lack monophyletic Hemerobiiformia. Possible methodological problems contributing to this lack of unambiguous resolution of the phylogeny of Neuropterida are sequence saturation, lack of information in DNA marker sequences, incomplete taxon sampling and data matrices, as well as – concerning morphological characters – convergence and interpretation of ambiguous character polarity. The phylogenetic relationships of Neuropterida and their position within Endopterygota are of interest with respect to the reconstruction of character evolution and the evolution of life styles of the larvae (terrestrial in Raphidioptera, aquatic in Megaloptera and in two families of Neuroptera).

Molecular Phylogeny and Redefined Generic Limits of <I>Calathea</I> (Marantaceae)

Calathea, with an estimated 285 species, is the largest genus of Marantaceae and an important component of Neotropical herbaceous diversity. The genus is also of high importance for horticulture as species are cultivated for their showy, patterned leaves. Previous molecular phylogenetic studies indicated that the genus is polyphyletic, but have not provided a basis for redefining generic limits due to incomplete taxon sampling. To address this problem we analyzed DNA sequence data from three plastid markers (matK with flanking 30 trnK intron, trnL intron and trnL-trnF intergenic spacer) and one nuclear marker (ITS) under a maximum parsimony criterion for a large and representative taxon sample covering all previously proposed infrageneric entities, and representing the full range of morphological variation known in the genus. Our results confirm that Calathea is polyphyletic. One clade, including subgenus Calathea ,t heC. lanicaulis group, and the genus Sanblasia, is sister to a clade formed by Ischnosiphon and Pleiostachya .T he genusMonotagma is placed as sister to this clade. The remaining species form a second strongly supported clade as sister to a clade containing these other genera. Based on these findings Calathea is recircumscribed in a narrow sense and Sanblasia is placed in synonymy. The genus Goeppertia is resurrected and redefined to include all members of the second Calathea clade. Morphological characters defining each genus are provided. A total of 246 new combinations are made. Keywords—Goeppertia, ITS, matK, maximum parsimony, Sanblasia, trnL-F region. Marantaceae, with approximately 550 species, is the sec- ond largest family in the Zingiberales. The family is particu- larly diverse in the Neotropics where it is represented by an estimated 450 species. Phylogenetic studies at the family level (Andersson and Chase 2001; Prince and Kress 2006a) have shown Neotropical diversity to primarily involve two large groups: the Maranta clade with nine genera and ca. 70 species is concentrated in southeastern Brazil; and the Calathea clade with five genera and ca. 370 species is distrib- uted throughout the Neotropics but with highest diversity in northwestern South America. Within the Calathea clade, Calathea G. Mey. is by far the largest genus with an esti- mated 300 species (Andersson 1998). Govaerts and Kennedy (2012) list 285 accepted names. These numbers clearly make Calathea the largest genus in the family. The genus is also important for horticulture as indoor plants and in tropical garden landscaping due to their variegated leaves with spots or bands of white, orange, or red, and often bright purple underside. Several species have been used as model organisms for studies of reproductive ecology, plant phys- iology, and demography (e.g. Kennedy 1978; Horvitz and Schemske 2002; Clasen-Bockhoff and Heller 2008; Matlaga and Sternberg, 2009; Swenson 2009; Maron et al. 2010). Other