Testing morphological concepts of orders of pleurocarpous mosses (Bryophyta) using phylogenetic reconstructions based on TRNL-TRNF and RPS4 sequences

The ordinal classification of pleurocarpous mosses rests on characters such as branching mode and architecture of the peristome teeth that line the mouth of the capsule. The Leucodontales comprise mainly epiphytic taxa, characterized by sympodial branching and reduced peristomes, whereas the Hypnales are primarily terricolous and monopodially branching. The third order, the Hookeriales, is defined by a unique architecture of the endostome. We sampled 78 exemplar taxa representing most families of these orders and sequenced two chloroplast loci, the trnL-trnF region and the rps4 gene, to test the monophyly and relationships of these orders of pleurocarpous mosses. Estimates of levels of saturation suggest that the trnL-trnF spacer and the third codon position of the rps4 gene have reached saturation, in at least the transitions. Analyses of the combined data set were performed under three optimality criteria with different sets of assumptions, such as excluding hypervariable positions, downweighting the most likely transformations, and indirect weighting of rps4 codon positions by including amino acid translations. Multiple parallelism in nonsynonymous mutations led to little or no improvement in various indices upon inclusion of amino acid sequences. Trees obtained under likelihood were significantly better under likelihood than the trees derived from the same matrix under parsimony. Our phylogenetic analyses suggest that (1) the pleurocarpous mosses, with the exception of the Cyrtopodaceae, form a monophyletic group which is here given formal recognition as the Hypnidae; (2) the Leucodontales are at least paraphyletic; and (3) the Hypnales form, with most members of the Leucodontalean grade, a monophyletic group sister to a Hookerialean lineage. The Hypopterygiaceae, Hookeriales, and a clade composed of Neorutenbergia, Pseudocryphaea, and Trachyloma likely represent a basal clade or grade within the Hypnidae. These results suggest that mode of branching and reduced peristomes are homoplastic at the ordinal level in pleurocarpous mosses.     

Phylogeny of the Polytrichales (Bryophyta) based on simultaneous analysis of molecular and morphological data

Phylogenetic analyses of Polytrichales were conducted using morphology and sequence data from the chloroplast genes rbcL and rps4 plus the trnL-F gene region, part of the mitochondrial nad5 and the nuclear-encoded 18S rDNA. Our analyses included 46 species representing all genera of Polytrichales. Phylogenetic trees were constructed with simultaneous parsimony analyses of all sequences plus morphology and separate combinations of sequence data only. Results lend support for recognition of Polytrichales as a monophyletic entity. Oedipodium griffithianum appears as a sister taxon to Polytrichales or as a sister taxon of all mosses excluding Sphagnales and Andreaeles. Within Polytrichales, Alophosia and Atrichopsis, species without the adaxial lamellae (in Atrichopsis present but poorly developed on male gametophyte) otherwise typical of the group are sister to the remaining species followed by a clade including Bartramiopsis and Lyellia, species with adaxial lamellae covering only the central portion of the leaves. Six taxa with an exclusively Southern Hemisphere distribution form a grade between the basal lineages and a clade including genera that are mostly confined to the Northern Hemisphere.     

Subtribe Vellinae (Brassiceae, Brassicaceae): a Combined Analysis of ITS nrDNA Sequences and Morphological Data

Phylogenetic relationships in subtribe Vellinae (Brassiceae,Brassicaceae) were studied using combined parsimony analysisof nucleotide sequences of nuclear ribosomal internal transcribedspacers (ITS) and morphology. Analyses of 17 taxa of Vellinae,Zillinae and Savignyinae, plus two outgroups from Brassicinae,reveal a main clade consisting of Vella plus Boleum. This groupis sister to Euzomodendron, to which Carrichtera and Succowiaare successive sisters. Although Euzomodendron, a morphologicallydistinctive genus, is embedded inVella in the ITS analysis,it is placed as sister to Vella in the combined analysis. Boleum,however, is included in the Vella clade in all cases, and itssegregation at the genus rank is inappropriate. Psychine, agenus thought by some authors to be related to Vellinae, issister to Savignya(Savignyinae). Zillinae and Savignyinae aresister groups in the combined analysis, and the pair is sisterto Vellinae. Biogeographical features can be inferred from thecombined analysis. The annual representatives of Vellinae (Succowiaand Carrichtera) are widespread in the Mediterranean and Irano–Turanianterritories. Conversely, the woody taxa are narrow endemicsgrowing in either high-elevation environments or dry, steppehabitats of central and southern Spain, northern Morocco andAlgeria. A combination of molecular data, morphology, cytologyand biogeographical patterns are used for estimating the generalevolutionary patterns of the subtribe.Copyright 2000 Annalsof Botany Company Brassicaceae, Cruciferae, Mediterranean, parsimony analysis, phylogeny, ITS sequences, systematics, Vellinae     

Phylogeny of marattioid ferns (Marattiaceae): inferring a root in the absence of a closely related outgroup

Closely related outgroups are optimal for rooting phylogenetic trees; however, such ideal outgroups are not always available. A phylogeny of the marattioid ferns (Marattiaceae), an ancient lineage with no close relatives, was reconstructed using nucleotide sequences of multiple chloroplast regions (rps4 + rps4-trnS spacer, trnS-trnG spacer + trnG intron, rbcL, atpB), from 88 collections, selected to cover the broadest possible range of morphologies and geographic distributions within the extant taxa. Because marattioid ferns are phylogenetically isolated from other lineages, and internal branches are relatively short, rooting was problematic. Root placement was strongly affected by long-branch attraction under maximum parsimony and by model choice under maximum likelihood. A multifaceted approach to rooting was employed to isolate the sources of bias and produce a consensus root position. In a statistical comparison of all possible root positions with three different outgroups, most root positions were not significantly less optimal than the maximum likelihood root position, including the consensus root position. This phylogeny has several important taxonomic implications for marattioid ferns: Marattia in the broad sense is paraphyletic; the Hawaiian endemic Marattia douglasii is most closely related to tropical American taxa; and Angiopteris is monophyletic only if Archangiopteris and Macroglossum are included.     

Molecular phylogenetics of Diseae (Orchidaceae): a contribution from nuclear ribosomal ITS sequences

We present here the first molecular phylogeny of tribe Diseae (Orchidoideae: Orchidaceae). Nuclear ribosomal ITS1, 5.8S rDNA, and ITS2 sequences were compared for 30 Diseae, 20 Orchideae, and four Cranichideae and Diurideae outgroups. ITS - rDNA sequences exhibited a transition:transversion ratio of 1.3 and extensive ITS length polymorphism. Phylogenetic analyses using maximum parsimony identified seven major core orchidoid groups. The branching order of the five Diseae and two Orchideae clades was weakly supported but indicated paraphyly of Diseae, with Disperis sister to the rest, followed by successive divergence of Brownleea, Disinae, Coryciinae sensu stricto (s.s.), Satyriinae, and terminated by Orchidinae plus Habenariinae. Within the monophyletic Disinae, Herschelia and Monadenia were nested within a paraphyletic Disa and clustered with D. sect. Micranthae. Within monophyletic Satyriinae, Satyridium rostratum plus Satyrium bicallosum was sister to the rest of Satyrium, and then Satyrium nepalense plus S. odorum was distinct from a cluster of six species. Coryciinae are paraphyletic because Disperis is sister to all other core orchidoids. Coryciinae s.s. are sister to Satyriinae plus Orchideae, with Pterygodium nested within Corycium. Maximum likelihood analysis supported possible affinities among Disinae, Brownleeinae, and Coryciinae but did not support monophyly of Diseae or an affinity between Disinae and Satyriinae. Morphological characters are fully congruent with the well-supported groups identified in the ITS phylogeny.     

A molecular phylogeny of celtidaceae and ulmaceae (Urticales) based onrbcL Nucleotide sequences

On the basis of 1,290 bp sequences of the chloroplast generbcL, a molecular phylogeny of seven of nine genera of the Celtidaceae and four of six genera of the Ulmaceae was produced. These data were analyzed together with some other urticalean genera using three methods (i.e., maximum parsimony, maximum likelihood, and neighbor joining methods). Maximum likelihood topology among 18 trees obtained indicated that the Urticales are monophyletic with its common clade splitting basally into two: one leading to a line comprisingAmpelocera (traditionally placed in Celtidaceae) and Ulmaceae, and the other leading to a line comprising the remaining genera of Celtidaceae, Moraceae, and other Urticales. Ulmaceae, to whichAmpelocera is a sister group, are monophyletic, as supported by many lines of morphological evidence. In contrast to Ulmaceae, the monophyly of Celtidaceae (excludingAmpelocera) was not supported, and resolution of relationships of Celtidaceae with other Urticales, as well as of those within the family, is left for future study.     

A mitochondrial genome phylogeny of the Neuropterida (lace-wings, alderflies and snakeflies) and their relationship to the other holometabolous insect orders

We present a mitochondrial (mt) genome phylogeny inferring relationships within Neuropterida (lacewings, alderflies and camel flies) and between Neuropterida and other holometabolous insect orders. Whole mt genomes were sequenced for Sialis hamata (Megaloptera: Sialidae), Ditaxis latistyla (Neuroptera: Mantispidae), Mongoloraphidia harmandi (Raphidioptera: Raphidiidae), Macrogyrus oblongus (Coleoptera: Gyrinidae), Rhopaea magnicornis (Coleoptera: Scarabaeidae), and Mordella atrata (Coleoptera: Mordellidae) and compared against representatives of other holometabolous orders in phylogenetic analyses. Additionally, we test the sensitivity of phylogenetic inferences to four analytical approaches: inclusion vs. exclusion of RNA genes, manual vs. algorithmic alignments, arbitrary vs. algorithmic approaches to excluding variable gene regions and how each approach interacts with phylogenetic inference methods (parsimony vs. Bayesian inference). Of these factors, phylogenetic inference method had the most influence on interordinal relationships. Bayesian analyses inferred topologies largely congruent with morphologically‐based hypotheses of neuropterid relationships, a monophyletic Neuropterida whose sister group is Coleoptera. In contrast, parsimony analyses failed to support a monophyletic Neuropterida as Raphidioptera was the sister group of the entire Holometabola excluding Hymenoptera, and Neuroptera + Megaloptera is the sister group of Diptera, a relationship which has not previously been proposed based on either molecular or morphological data sets. These differences between analytical methods are due to the high among site rate heterogeneity found in insect mt genomes which is properly modelled by Bayesian methods but results in artifactual relationships under parsimony. Properly analysed, the mt genomic data set presented here is among the first molecular data to support traditional, morphology‐based interpretations of relationships between the three neuropterid orders and their grouping with Coleoptera.     

Generic relationships among the baccate-fruited Amaryllidaceae (tribe Haemantheae) inferred from plastid and nuclear non-coding DNA sequences

Using sequences from the plastid trnL-F region and nrDNA ITS, we investigated the phylogeny of the fleshy-fruited African tribe Haemantheae of the Amaryllidaceae across 19 species representing all genera of the tribe. ITS and a combined matrix produce the most resolute and well-supported tree with parsimony analysis. Two main clades are resolved, one comprising the monophyletic rhizomatous genera Clivia and Cryptostephanus, and a larger clade that unites Haemanthus and Scadoxus as sister genera to an Apodolirion/Gethyllis subclade. One of four included Gethyllis species, G. lanuginosa, resolves as sister to Apodolirion with ITS. Relationships among the Clivia species are not in agreement with a previous published phylogeny. Biogeographic analysis using the divergence/vicariance method roots the tribe in Eastern South Africa, with several subsequent dispersals to the winter rainfall Western Cape region. Chromosomal change from an ancestral 2n=22 (characteristic of Clivia) is associated with each main clade. Reduction in number has occurred in all but Cryptostephanus, which has 2n=24 chromosomes. Increasing the sampling across all of the species in the tribe will allow a more detailed understanding of the biogeographic patterns inherent in the parsimony topology, which undoubtedly reflect Quaternary climatic changes in Southern Africa.     

Phylogenetics of Quiinaceae (Malpighiales): evidence from trnL-trnF sequence data and morphology

We present the first parsimony analyses of the Neotropical family Quiinaceae using nucleotide sequence data from the non-coding trnL intron and trnL-trnF intergenic spacer of the plastid genome, analysed separately as well as in combination with morphology. Both molecules and combined data recover Quiinaceae as a well-supported monophyletic group. Quiinaceae form a polytomy together with their potential sister groups, the monophyletic Ochnaceae s.str. and the monotypic Medusagynaceae from the Seychelles in the Indian Ocean. Froesia is resolved as sister to the rest of the family. Other members of the family, Lacunaria, Quiina, and Touroulia, are all recovered as monophyletic despite the inclusion of strikingly distinctive representatives (L. oppositifolia and Q. pteridophylla). Relationships among the last three genera, however, are yet uncertain. Optimising characters of breeding system onto the molecular phylogeny reveals that bisexual flowers (Froesia) are the ancestral state in Quiinaceae, whereas androdioecy (Quiina, Touroulia) and dioecy (Lacunaria) are derived breeding systems.     

Deuterostome phylogeny and the sister group of the chordates: evidence from molecules and morphology

Complete coding regions of the 18S rRNA gene of an enteropneust hemichordate and an echinoid and ophiuroid echinoderm were obtained and aligned with 18S rRNA gene sequences of all major chordate clades and four outgroups. Gene sequences were analyzed to test morphological character phylogenies and to assess the strength of the signal. Maximum- parsimony analysis of the sequences fails to support a monophyletic Chordata; the urochordates form the sister taxon to the hemichordates, and together this clade plus the echinoderms forms the sister taxon to the cephalochordates plus craniates. Decay, bootstrap, and tree-length distribution analyses suggest that the signal for inference of dueterostome phylogeny is weak in this molecule. Parsimony analysis of morphological plus molecular characters supports both monophyly of echinoderms plus enteropneust hemichordates and a sister group relationship of this clade to chordates. Evolutionary parsimony does not support chordate monophyly. Neighbor-joining, Fitch-Margoliash, and maximum-likelihood analyses support a chordate lineage that is the sister group to an echinoderm-plus-hemichordate lineage. The results illustrate both the limitations of the 18S rRNA molecule alone for high- level phylogeny inference and the importance of considering both molecular and morphological data in phylogeny reconstruction.      

基于mtDNA和rDNA基因序列的中国按蚊属塞蚊亚属种类的系统发育研究（双翅目：蚊科）

【目的】应用mtDNA和rDNA基因特征重建中国按蚊属塞蚊亚属已知种类的系统发育关系, 以阐明亚属内各蚊种的亲缘关系。【方法】对采自中国的按蚊属塞蚊亚属Anopheles (Cellia) 20种蚊的mtDNA-COⅡ和 rDNA-28S-D3序列进行测定和分析, 以按蚊属按蚊亚属Anopheles (Anopheles)的中华按蚊An. (An.) sinensis和赫坎按蚊An. (An.) hyrcanus为外群, 采用COⅡ和D3单基因, 以及“COⅡ+D3”联合数据组以邻接法（NJ）、 最大简约法（MP）、 最大似然法（ML）和贝叶斯法（BI）等重建这些种类的系统发育树。【结果】 mtDNA-COⅡ和rDNA-28S-D3序列的长度范围分别为685 bp和375～410 bp, 在塞蚊亚属蚊种间的遗传距离分别为0.015～0.117和0.003～0.111。各系统树显示外群被合理分开,除在COⅡ树中新塞蚊系为并系外,各系均聚为单系群,新迈蚊系和迈蚊系亲缘关系最近。联合数据组构建的系统合意树显示中国塞蚊亚属各蚊种形成4支,除伪威氏按蚊与多斑按蚊种团未聚为单系群外,其他各种团和复合体成员种均分别聚在一起,各分支的置信值均大于50%。【结论】本研究获得的分子系统发育树清楚地显示了中国按蚊属塞蚊亚属各种类及系之间的系统发育关系, 对其分类和防治研究具有参考价值。     

Phylogeny of Ptychostomum （Bryaceae,Musci） inferred from sequences of nuclear ribosomal DNA internal transcribed spacer （ITS） and chloroplast rps4

The phylogeny of Ptychostomum was first spacer （ITS） region of the nuclear ribosomal （nr） DNA DNA rps4 sequences. Maximum parsimony, maximum undertaken based on analysis of the internal transcribed and by combining data from nrDNA ITS and chloroplast likelihood, and Bayesian analyses all support the conclusion that the reinstated genus Ptychostomum is not monophyletic. Ptychostomum funkii （Schwagr.） J. R. Spence （≡ Bryum funkii Schwaigr.） is placed within a clade containing the type species of Bryum, B. argenteum Hedw. The remaining members of Ptychostomum investigated in the present study constitute another well-supported clade. The results are congruent with previous molecular analyses. On the basis of phylogenetic evidence, we agree with transferring B. amblyodon Mull. Hal. （≡ B. inclinatum （Brid.） Turton≡ Bryum archangelicum Bruch ＆ Schimp.）, Bryum lonchocaulon Mull. Hal., Bryum pallescens Schleich. ex Schwaigr., and Bryum pallens Sw. to Ptychostomum.     

Taxonomic studies in Chiloscyphus Corda (Jungermanniales: Lophocoleaceae) based on nrITS sequences and morphology

Maximum parsimony and likelihood analyses of 40 Lophocoleaceae nrITS sequences and 6 Plagiochilaceae sequences (outgroup) lead to a robust phylogeny of Chiloscyphus. Four main lineages are assigned to as Chiloscyphus subgenera Chiloscyphus, Lophocolea, Connati and Notholophocolea. Chiloscyphus subgen. Connati is resolved sister to the remainder of this genus. Chiloscyphus subgenus Lophocolea is subdivided into sections Heterophylli (incl. sect. Semiteretes, syn. nov.), Lophocolea, Microlophocolea, and Novae-Zeelandiae. Five accessions of Chiloscyphus pallescens with a chromosome number of n = 18 form a robust monophyletic lineage that is placed sister to a well supported clade with 4 accessions of C. polyanthos [n = 9]. Chiloscyphus mandonii is placed in the synonymy of C. latifolius.     

PHYLOGENY OF THE DASYCLADALES (CHLOROPHYTA,ULVOPHYCEAE) BASED ON ANALYSES OF RUBISCO LARGE SUBUNIT (rbcL) GENE SEQUENCES1

The phylogeny of the green algal Order Dasycladales was inferred by maximum parsimony and Bayesian analyses of chloroplast‐encoded rbcL sequence data. Bayesian analysis suggested that the tribe Acetabularieae is monophyletic but that some genera within the tribe, such as Acetabularia Lamouroux and Polyphysa Lamouroux, are not. Bayesian analysis placed Halicoryne Harvey as the sister group of the Acetabularieae, a result consistent with limited fossil evidence and monophyly of the family Acetabulariaceae but was not supported by significant posterior probability. Bayesian analysis further suggested that the family Dasycladaceae is a paraphyletic assemblage at the base of the Dasycladales radiation, casting doubt on the current family‐level classification. The genus Cymopolia Lamouroux was inferred to be the basal‐most dasycladalean genus, which is also consistent with limited fossil evidence. Unweighted parsimony analyses provided similar results but primarily differed by the sister relationship between Halicoryne Lamouroux and Bornetella Munier‐Chalmas, thus supporting the monophyly of neither the families Acetabulariaceae nor Dasycladaceae. This result, however, was supported by low bootstrap values. Low transition‐to‐transversion ratios, potential loss of phylogenetic signal in third codon positions, and the 550 million year old Dasycladalean lineage suggest that dasyclad rbcL sequences may be saturated due to deep time divergences. Such factors may have contributed to inaccurate reconstruction of phylogeny, particularly with respect to potential inconsistency of parsimony analyses. Regardless, strongly negative g₁ values were obtained in analyses including all codon positions, indicating the presence of considerable phylogenetic signal in dasyclad rbcL sequence data. Morphological features relevant to the separation of taxa within the Dasycladales and the possible effects of extinction on phylogeny reconstruction are discussed relative to the inferred phylogenies.     

Nucleotide Sequence of a 28-kbp Portion of Rice Mitochondrial DNA: the Existence of Many Sequences That Correspond to Parts of Mitochondrial Genes in Intergenic Regions

The nucleotide sequence of a 27,588-bp region of rice mitochondrialDNA was determined. This sequence contains putative genes thatencode initiator methionine tRNA (trnfM), subunits III (nad3)and IV (nad4) of the NADH dehydrogenase complex, and ribosomalproteins S3 (rps3), S12 (rps12) and L16 (rp116). An open readingframe that contains sequences homologous to parts of rps2 andatpA is also present. In addition to these regions, there aremany short sequences with homology to fragments of mitochondrialDNAs from rice or other plants. These sequences may be remnantsof multiple rearrangements of the genome and their presenceseems to explain, in part, the large sizes of the mitochondrialgenomes of higher plants. (Received July 15, 1994; Accepted September 26, 1994)     

Phylogeny of the genus Aleochara inferred from mitochondrial cytochrome oxidase sequences (Coleoptera: Staphylinidae)

The phylogeny of the genus Aleochara was previously poorly understood due to difficulties with phylogenetic reconstruction by morphological characters. We present here a phylogeny based on the sequences of a 2022-bp fragment of the COI/II genes; 50 Aleochara and 10 outgroup species were included in the analysis. We used parsimony, minimum-evolution, and maximum-likelihood analyses to infer the phylogeny of the group. Our data do not support the commonly assumed sister group relationship between Aleocharini and Hoplandriini. Aleochara is resolved as a monophylum, although A. clavicornis might not belong to the genus. Within Aleochara, there are two large monophyletic clades. Many of the existing subgenera are shown to be para- or polyphyletic; others are likely to be monophyletic. Tinotus morion, previously assigned to the Hoplandriini, is strongly supported as belonging to Aleochara. According to our data, the mesosternal carina that has been used as an important character for classification has arisen and been reduced independently in several clades within Aleochara.     

A global plastid phylogeny of the fern genus Asplenium (Aspleniaceae)

The infrageneric relationships and taxonomy of the largest fern genus, Asplenium (Aspleniaceae), have remained poorly understood. Previous studies have focused mainly on specific species complexes involving a few or dozens of species only, or have achieved a large taxon sampling but only one plastid marker was used. In the present study, DNA sequences from six plastid markers (atpB, rbcL, rps4, rps4-trnS, trnL and trnL-F) of 1030 accessions (616 of them newly sequenced here) representing c. 420 species of Asplenium (60% of estimated species diversity), 16 species of Hymenasplenium, three Diplaziopsidaceae, and four Rhachidosoraceae were used to produce the largest genus-level phylogeny yet for ferns. Our major results include: (i) Asplenium as broadly circumscribed is monophyletic based on our inclusion of representatives of 32 of 38 named segregate genera; (ii) 11 major clades in Asplenium are identified, and their relationships are mostly well-resolved and strongly supported; (iii) numerous species, unsampled in previous studies, suggest new relationships and numerous cryptic species and species complexes in Asplenium; and (iv) the accrued molecular evidence provides an essential foundation for further investigations of complex patterns of geographical diversification, speciation and reticulate evolution in this family.     

基部藓类分子系统学研究

基部藓类是稳定地处于藓类系统发育树基部的类群.它包括7纲,2亚纲,10目,10科,34属,637种.基部藓类虽然只占藓类种类的5％,但由于其内部各类群孢子体形态极为丰富,因此对于理解整个藓类植物的系统发育具有重要意义.通过对48个种(36个藓类、4个维管植物、2个角苔、4个苔类和2个藻类)的9个DNA片段(NU:26S,18S; MT:nad5,cox1; CP:rbcL,rps4,cp-LSU,cp-SSU,atpB)进行分子系统学分析,综合最大似然法(maximum likelihood)、最大简约法(most parsimony)和贝叶斯分析(Bayesian inference)方法的建树结果,理清了前人研究中存在冲突的类群之间的关系并为已确定的关系提供了更高的支持率.研究结果如下:(1)藻苔纲和泥炭藓纲互为姐妹类群,处于整个藓类的最基部;(2)黑藓纲与黑真藓纲互为姐妹类群(3)长台藓纲和具齿藓类组成单系;(4)四齿藓纲是所有具齿藓类的基部类群;(5)烟杆藓亚纲处于真藓纲的最基部,其次是短颈藓亚纲.以上结论在分子系统树上得到了很高的支持率.     

Phylogeny of Cidaroida (Echinodermata: Echinoidea) based on mitochondrial and nuclear markers

We present the first molecular phylogeny of Cidaroida, one of the most problematic groups within the echinoids. Two genes??the nuclear ribosomal gene 28?S rRNA and the mitochondrial protein-encoding gene COI??were obtained from 21 specimens representing 17 genera and 20 species, among which 13 species belong to Cidaroida. Phylogenetic analyses of the combined molecular data using parsimony and maximum likelihood optimality criteria resulted in a well-resolved phylogeny. Our results are broadly compatible (with the notable exception of Cidaris cidaris) with previous results obtained from morphological data. We find that Cidaroida represent a monophyletic group sister to the non-cidaroid Echinoidea. The family Cidaridae sensu Mortensen (1928) and Fell (1966) is paraphyletic because of the placement of Psychocidaris ohshimai as sister-group to Histocidaris elegans. Inside the Stylocidarina, we show that the two Atlantic species Stylocidaris affinis and Stylocidaris lineata constitute a well-supported clade. However, these two taxa could also represent two morphotypes within a single species showing high morphological variation.