Rodent phylogeny and a timescale for the evolution of Glires: evidence from an extensive taxon sampling using three nuclear genes

Rodentia is the largest order of placental mammals, with approximately 2,050 species divided into 28 families. It is also one of the most controversial with respect to its monophyly, relationships between families, and divergence dates. Here, we have analyzed and compared the performance of three nuclear genes (von Willebrand Factor, interphotoreceptor retinoid-binding protein, and Alpha 2B adrenergic receptor) for a large taxonomic sampling, covering the whole rodent and placental diversity. The phylogenetic results significantly support rodent monophyly, the association of Rodentia with Lagomorpha (the Glires clade), and a Glires + Euarchonta (Primates, Dermoptera, and Scandentia) clade. The resolution of relationships among rodents is also greatly improved. The currently recognized families are divided here into seven well-defined clades (Anomaluromorpha, Castoridae, Ctenohystrica, Geomyoidea, Gliridae, Myodonta, and Sciuroidea) that can be grouped into three major clades: Ctenohystrica, Gliridae + Sciuroidea, and a mouse-related clade (Anomaluromorpha, Castoridae + Geomyoidea, and Myodonta). Molecular datings based on these three genes suggest that the rodent radiation took place at the transition between Paleocene and Eocene. The divergence between rodents and lagomorphs is placed just at the K-T boundary and the first splits among placentals in the Late Cretaceous. Our results thus tend to reconcile molecular and morphological-paleontological insights.     

Molecular phylogeny and divergence times of Malagasy tenrecs: Influence of data partitioning and taxon sampling on dating analyses

Background  

Malagasy tenrecs belong to the Afrotherian clade of placental mammals and comprise three subfamilies divided in eight genera (Tenrecinae: Tenrec, Echinops, Setifer and Hemicentetes; Oryzorictinae: Oryzorictes, Limnogale and Microgale; Geogalinae: Geogale). The diversity of their morphology and incomplete taxon sampling made it difficult until now to resolve phylogenies based on either morphology or molecular data for this group. Therefore, in order to delineate the evolutionary history of this family, phylogenetic and dating analyses were performed on a four nuclear genes dataset (ADRA2B, AR, GHR and vWF) including all Malagasy tenrec genera. Moreover, the influence of both taxon sampling and data partitioning on the accuracy of the estimated ages were assessed.     

Molecular phylogeny of living xenarthrans and the impact of character and taxon sampling on the placental tree rooting

Extant xenarthrans (armadillos, anteaters and sloths) are among the most derived placental mammals ever evolved. South America was the cradle of their evolutionary history. During the Tertiary, xenarthrans experienced an extraordinary radiation, whereas South America remained isolated from other continents. The 13 living genera are relics of this earlier diversification and represent one of the four major clades of placental mammals. Sequences of the three independent protein-coding nuclear markers alpha2B adrenergic receptor (ADRA2B), breast cancer susceptibility (BRCA1), and von Willebrand Factor (VWF) were determined for 12 of the 13 living xenarthran genera. Comparative evolutionary dynamics of these nuclear exons using a likelihood framework revealed contrasting patterns of molecular evolution. All codon positions of BRCA1 were shown to evolve in a strikingly similar manner, and third codon positions appeared less saturated within placentals than those of ADRA2B and VWF. Maximum likelihood and Bayesian phylogenetic analyses of a 47 placental taxa data set rooted by three marsupial outgroups resolved the phylogeny of Xenarthra with some evidence for two radiation events in armadillos and provided a strongly supported picture of placental interordinal relationships. This topology was fully compatible with recent studies, dividing placentals into the Southern Hemisphere clades Afrotheria and Xenarthra and a monophyletic Northern Hemisphere clade (Boreoeutheria) composed of Laurasiatheria and Euarchontoglires. Partitioned likelihood statistical tests of the position of the root, under different character partition schemes, identified three almost equally likely hypotheses for early placental divergences: a basal Afrotheria, an Afrotheria + Xenarthra clade, or a basal Xenarthra (Epitheria hypothesis). We took advantage of the extensive sampling realized within Xenarthra to assess its impact on the location of the root on the placental tree. By resampling taxa within Xenarthra, the conservative Shimodaira-Hasegawa likelihood-based test of alternative topologies was shown to be sensitive to both character and taxon sampling.     

The impact of fossils and taxon sampling on ancient molecular dating analyses

The number and complexity of molecular dating studies has increased over the past decade. Along with a broadening acceptance of their utility has come significant controversy over the methods and models that are appropriate, as well as the accuracy of the estimates yielded by molecular clock analyses. Radically different age estimates have been published for the same divergences from analyses of different datasets with different fossil constraints obtained with different methods, and the underlying explanation for these differences is often unclear. Here we utilize two previously published datasets to examine the effect of fossil calibrations and taxon sampling on the age estimates for two deep eukaryote divergences in an attempt to discern the relative impact of these factors. Penalized likelihood, non-parametric rate smoothing, and Bayesian methods were utilized to generate age estimates for the origin of the Metazoa from a 7-gene dataset and for the divergence of Eukaryotes from a 129-gene dataset. From these analyses, it is clear that the fossil calibrations chosen and the method for applying constraints to these nodes have a large impact on age estimates, while the degree of taxon sampling within a dataset is less important in terms of the resulting age estimates. Concerns and recommendations for addressing these two factors when initiating a dating analysis are discussed.     

Effect of taxon sampling on recovering the phylogeny of squamate reptiles based on complete mitochondrial genome and nuclear gene sequence data

The complete nucleotide sequences of the mitochondrial (mt) genomes of three species of squamate lizards: Blanus cinereus (Amphisbaenidae), Anguis fragilis (Anguidae), and Tarentola mauritanica (Geckkonidae) were determined anew. The deduced amino acid sequences of all 13 mt protein-coding genes were combined into a single data set and phylogenetic relationships among main squamate lineages were analyzed under maximum likelihood (ML) and Bayesian Inference (BI). Within Squamata, the monophyly of Iguanidae, Anguimorpha, Amphisbaenia, Gekkota, Serpentes, and Acrodonta received high statistical support with both methods. It is particularly striking that this is the first molecular analysis that recovers the monophyly of Scincomorpha (including Scincidae, Xantusiidae, Cordylidae, and Lacertidae), although it is only supported in the Bayesian analysis, and it is sensitive to changes in the outgroup (see below). Phylogenetic relationships among the main squamate lineages could not be resolved with ML but received strong support with BI (above 95%). The newly reconstructed phylogeny of squamates does not support the Iguania-Scleroglossa split. Acrodonta and Serpentes form a clade, which is the sister group of the remaining squamate lineages. Within these, Gekkota were the first branching out, followed by Amphisbaenia, and a clade including Anguimorpha as sister group of Scincomorpha + Iguanidae. The recovered topology differed substantially from previously reported hypotheses on squamate relationships, and the relative effect of using different outgroups, genes, and taxon samplings were explored. The sister group relationship of Serpentes + Acrodonta, and their relative basal position within Squamata could be due to a long-branch attraction artifact. Phylogenetic relationships among Scincomorpha, Amphisbaenia, and Anguimorpha were found to be rather unresolved. Future improving of squamate phylogenetic relationships would rely on finding snake and acrodont species with slower mt evolutionary rates, ensuring thorough taxon coverage of squamate diversity, and incorporating more nuclear genes with appropriate evolutionary rates.     

Combining molecular and morphological analyses of water strider phylogeny (Hemiptera–Heteroptera, Gerromorpha): effects of alignment and taxon sampling

Abstract. The semiaquatic bugs (Hemiptera–Heteroptera, infraorder Gerromorpha), comprising water striders and their allies (c. 1900 described species), are familiar inhabitants of water surfaces in all continents. Recent fossil evidence indicates that the evolutionary history of semiaquatic bugs spans more than 120 million years of geological time. At present, our insight into the phylogeny of higher taxa is based upon Andersen's manual cladistic analysis of a suite of morphological characters. The present work expands the phylogenetic insight with numerical cladistic analyses of morphological and molecular datasets (partial sequences of 16S and 28S rDNA) for forty species of Gerromorpha covering most higher taxa (families, subfamilies), estimates of branch support, character incongruence, and topological congruence (nodal stability). For the molecular data we apply different alignment options (manual vs numerical alignment; multiple alignment vs direct optimization), treat insertion–deletion events (indels) as either missing data or as a fifth character state, subject the data to a sensitivity analysis, and estimate topological congruence between different analysis trees. Relationships change considerably under different analysis conditions, which means that there is little node stability, and for selecting preferred analysis conditions there is conflicting evidence from rescaled incongruence length difference and the key node criterion. Based on the analysis of the combined morphological and molecular datasets, this study supports the close relationship between the families Gerridae, Hermatobatidae and Veliidae (superfamily Gerroidea), but not the monophyly of the family Veliidae. The results suggest that the genus Ocellovelia (Ocelloveliinae) should be excluded from this family and placed as a sister group to Gerridae + the remaining species of Veliidae. Our study also supports a close relationship between the subfamilies Halobatinae and Ptilomerinae (Gerridae), and that the subfamily Veliinae is probably nonmonophyletic.     

A molecular phylogeny of Planorboidea (Gastropoda, Pulmonata): insights from enhanced taxon sampling

Planorbid gastropods are the most diverse group of limnic pulmonates, with both discoidal and highspired taxa. Phylogenetic relationships among these genera are confused and controversial. In particular, the monophyly of the limpet‐like taxa (traditionally Ancylidae) is disputed. Even recent molecular studies have concluded that substantially more work is necessary to solve the remaining issues concerning intergeneric phylogenetic relationships and higher taxa systematics. Planorbid snails are of great significance for humans as several members of this group are intermediate hosts of blood flukes (schistosomes) causing a chronic disease, schistosomiasis. We used the two independent molecular markers COI and 18S (concatenated dataset of 2837 nucleotide bp) to infer phylogenetic relationships of 26 genera (27 species) of Planorboidea, represented mostly by type species from mainly topotypical populations. With the majority of the taxa discussed not having been studied previously, this study attempted to test several hypotheses on planorbid phylogenetic relationships using Bayesian inference techniques. The monophyly of Planorboidea (= ‘Ancyloplanorbidae’) is strongly suggested on the basis of our extensive molecular analysis. Besides a distinct Burnupia clade, two major clades were recovered that correspond to family level taxa (traditional Bulinidae and Planorbidae). Considerable rearrangements of suprageneric taxa are evident from the phylogeny inferred. Therefore, the only clades recognized by current classifications and supported by our analysis are Planorbini and Segmentinini. The present study found that Ancylidae as traditionally understood, i.e. covering most freshwater limpet gastropods, is paraphyletic, as the genera of Burnupia and Protancylus have been shown to lie phylogenetically outside the Ancylini. Chromosome numbers and levels of polyploidy are discussed in the light of the new phylogeny. An earlier theory of shell shape evolution, i.e. that of patelliform taxa being most advanced, was not supported by this study; a limpet‐shaped taxon is most basal within Planorboidea. Although many taxa still remain to be studied, our results will hopefully contribute towards a better understanding of this very important group of freshwater organisms. Some taxonomic implications are discussed.     

Molecular phylogeny of the superfamily Tephritoidea (Insecta: Diptera) reanalysed based on expanded taxon sampling and sequence data

Phylogenenetic relationships of the superfamily Tephritoidea (Diptera: Tephritidae) were reanalysed based upon four mitochondrial gene fragments (12S, 16S, cytochrome c oxidase I and cytochrome c oxidase II) from 53 tephritoid (10 families) and 30 outgroup (14 families) species. The data set of Han and Ro (Mol Phylogenet Evol, 39, 2005, 416) was expanded in terms of the number of taxa as well as molecular characters. We were able to sample the enigmatic families Ctenostylidae and Eurygnathomyiidae for the first time. Based on increased taxon sampling (from 49 to 83 species) and additional sequences (combined length of DNA fragments increased from 2451 to 4490 bp), the inferred phylogenetic trees suggest a number of interesting phylogenetic relationships, some of which were not recovered from the previous study. Some of the important findings are as follows: (1) monophyly of the superfamily Tephritoidea; (2) all the included tephritoid families except for Tephritidae were recovered as monophyletic groups; (3) Tephritoidea can be divided into two monophyletic groups – the Piophilidae Family Group (Pallopteridae, Circumphallidae?, Lonchaeidae, Piophilidae and Eurygnathomyiidae) and the Tephritidae Family Group (Richardiidae, Ulidiidae, Platystomatidae, Tephritidae, Ctenostylidae and Pyrgotidae); (4) Eurygnathomyiidae is recognized as an independent monophyletic family apart from Pallopteridae; (5) the enigmatic family Ctenostylidae is a member of the superfamily Tephritoidea; (6) parasitic Pyrgotidae + Ctenostylidae + Tachiniscinae and mostly phytophagous Tephritidae are recovered within a monophyletic group; and (7) according to an inferred chronogram, the first Tephritoidea might have evolved around the middle of Paleocene Epoch [~59 Million years ago (mya)] and the family Tephritidae around the late Eocene (~36 mya).     

Intra‐ and inter‐specific variation in size and habitus of two sibling spider species (Araneae: Lycosidae): taxonomic and biogeographic insights from sampling across Europe

Discriminating closely related species can become a taxonomical challenge if a clear morphological diagnosis is lacking. Two subspecies have been recognized in Pardosa agrestis (Westring, 1861); however, their validity is still debated. To resolve this dilemma, quantitative and qualitative traits were measured for 30 females and 30 males per site from ten localities throughout Western Europe (11 measurements on each individual) and compared between subspecies. Mean annual temperature and geographical coordinates from all sites were also included in the statistical models in order to test for variations in size over the distribution range of each subspecies. We found significant differences in body size and size of copulatory organs as well as accurate criteria of discrimination between P. a. agrestis and P. a. purbeckensis F.O.P. Cambridge, 1895, suggesting that these taxa are two valid morphological species, occurring sympatrically. We also showed that temperatures did not directly influence the size of individuals, but that one species had smaller individuals at higher latitudes (following the converse Bergmann's rule), and that both species had larger individuals in centrally sampled populations (fitting to the centre hypothesis). © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113, 85–96.     

Poor taxon sampling, poor character sampling, and non-repeatable analyses of a contrived dataset do not provide a more credible estimate of insect phylogeny: a reply to Kjer

The wealth of data available for phylogenetic analysis of the insect orders, from both morphological and molecular sources, is steadily increasing. However, controversy exists among the methodologies one can use to reconstruct ordinal relationships. Recently, Kjer (2004 ) presented an analysis of insect ordinal relationships based exclusively on a single source of information: 18S rDNA sequence data. Kjer claims that his analysis resulted in a more “credible” phylogeny for the insect orders and strongly criticized our previous phylogenetic results. However, Kjer only used a subset of the data that are currently available for insect ordinal phylogeny, misrepresented our analyses, and omitted other analyses we have published on insect ordinal phylogeny. In our estimation, Kjer did a poor job of representing the current state of affairs in insect ordinal phylogenetics. Furthermore, we examine a number of analytical issues that are relevant not only for insect phylogeny, but systematics as a science, such as: repeatability and objectivity, locating alignment boundaries, secondary structure, goodness of fit measure, epistemological coherence, practicality and homology. © The Willi Hennig Society 2005.     

300 million years of diversification: elucidating the patterns of orthopteran evolution based on comprehensive taxon and gene sampling

Orthoptera is the most diverse order among the polyneopteran groups and includes familiar insects, such as grasshoppers, crickets, katydids, and their kin. Due to a long history of conflicting classification schemes based on different interpretations of morphological characters, the phylogenetic relationships within Orthoptera are poorly understood and its higher classification has remained unstable. In this study, we establish a robust phylogeny of Orthoptera including 36 of 40 families representing all 15 currently recognized superfamilies and based on complete mitochondrial genomes and four nuclear loci, in order to test previous phylogenetic hypotheses and to provide a framework for a natural classification and a reference for studying the pattern of divergence and diversification. We find strong support for monophyletic suborders (Ensifera and Caelifera) as well as major superfamilies. Our results corroborate most of the higher‐level relationships previously proposed for Caelifera, but suggest some novel relationships for Ensifera. Using fossil calibrations, we provide divergence time estimates for major orthopteran lineages and show that the current diversity has been shaped by dynamic shifts of diversification rates at different geological times across different lineages. We also show that mitochondrial tRNA gene orders have been relatively stable throughout the evolutionary history of Orthoptera, but a major tRNA gene rearrangement occurred in the common ancestor of Tetrigoidea and Acridomorpha, thereby representing a robust molecular synapomorphy, which has persisted for 250 Myr.     

Functional evolution of ADAMTS genes: Evidence from analyses of phylogeny and gene organization

Background  

The ADAMTS (A Disintegrin-like and Metalloprotease with Thrombospondin motifs) proteins are a family of metalloproteases with sequence similarity to the ADAM proteases, that contain the thrombospondin type 1 sequence repeat motifs (TSRs) common to extracellular matrix proteins. ADAMTS proteins have recently gained attention with the discovery of their role in a variety of diseases, including tissue and blood disorders, cancer, osteoarthritis, Alzheimer's and the genetic syndromes Weill-Marchesani syndrome (ADAMTS10), thrombotic thrombocytopenic purpura (ADAMTS13), and Ehlers-Danlos syndrome type VIIC (ADAMTS2) in humans and belted white-spotting mutation in mice (ADAMTS20).     

The ontogeny of personality traits in the desert funnel‐web spider,Agelenopsis lisa (Araneae: Agelenidae)

Trait consistency over time is one of the cornerstones of animal personality. Behavioral syndromes are the result of correlations between behaviors. While repeatability in behavior is not a requirement for behavioral syndromes, the two concepts studied together provide a more comprehensive understanding of how behavior can change over ontogeny. The roles of ontogenetic processes in the emergence of personality and behavioral syndromes have received much individual attention. However, the characterization of both individual trait consistency and behavioral syndromes across both sexes, as in our study, has been relatively rare. Ontogeny refers to changes that occur from conception to maturation, and juveniles might be expected to undergo different selection pressures than sexually mature individuals and also will experience profound changes in hormones, morphology, and environment during this period. In this study, we test for behavioral trait consistency and behavioral syndromes across six time points during ontogenetic development in the desert funnel‐web spider (Agelenopsis lisa). Our results indicate behavioral traits generally lack consistency (repeatability) within life stages and across ontogeny. However, penultimate males and mature females do exhibit noticeable mean‐level changes, with greater aggressive responses toward prey, shorter latencies to explore their environment and in the exhibition of risk‐averse responses to predatory cues. These traits also show high repeatability. Some trait correlations do exist as well. In particular, a strong correlation between aggressiveness toward prey and exploration factors is observed in mature males. However, because correlations among these factors are unstable across ontogeny and vary in strength over time, we conclude that behavioral syndromes do not exist in this species. Nevertheless, our results indicate that increased consistency, increasing average trait values, and varying correlations between traits may coincide with developmentally important changes associated with sexual maturation, albeit at different time points in males and females. This period of the life cycle merits systematic examination across taxa.     

The mega‐matrix tree of life: using genome‐scale horizontal gene transfer and sequence evolution data as information about the vertical history of life

Because horizontal gene transfer can confound the recovery of the largely prokaryotic tree of life (ToL), most genome‐based techniques seek to eliminate horizontal signal from ToL analyses, commonly by sieving out incongruent genes and data. This approach greatly limits the number of gene families analysed to a subset thought to be representative of vertical evolutionary history. However, formalized tests have not been performed to determine whether combining the massive amounts of information available in fully sequenced genomes can recover a reasonable ToL. Consequently, we used empirically defined gene homology definitions from a previous study that delineate xenologous gene families (gene families derived from a common transfer event) to generate a massively concatenated, combined‐data ToL matrix derived from 323 404 translated open reading frames arranged into 12 381 gene homologue groups coded as amino acid data and 63 336, 64 105, 65 153, 66 922 and 67 109 gene homologue groups coded as gene presence/absence data for 166 fully sequenced genomes. This whole‐genome gene presence/absence and amino acid sequence ToL data matrix is composed of 4867 184 characters (a combined data‐type mega‐matrix). Phylogenetic analysis of this mega‐matrix yielded a fully resolved ToL that classifies all three commonly accepted domains of life as monophyletic and groups most taxa in traditionally recognized locations with high support. Most importantly, these results corroborate the existence of a common evolutionary history for these taxa present in both data types that is evident only when these data are analysed in combination.
© The Willi Hennig Society 2010.     

Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids

Background  

The Vitaceae (grape) is an economically important family of angiosperms whose phylogenetic placement is currently unresolved. Recent phylogenetic analyses based on one to several genes have suggested several alternative placements of this family, including sister to Caryophyllales, asterids, Saxifragales, Dilleniaceae or to rest of rosids, though support for these different results has been weak. There has been a recent interest in using complete chloroplast genome sequences for resolving phylogenetic relationships among angiosperms. These studies have clarified relationships among several major lineages but they have also emphasized the importance of taxon sampling and the effects of different phylogenetic methods for obtaining accurate phylogenies. We sequenced the complete chloroplast genome of Vitis vinifera and used these data to assess relationships among 27 angiosperms, including nine taxa of rosids.     

Incorporating functional dissimilarities into sample‐based rarefaction curves: from taxon resampling to functional resampling

Question: Indices of functional diversity have been seen as the key for integrating information on species richness with measures that focus on those components of community composition related to ecosystem functioning. For comparing species richness among habitats on an equal‐effort basis, so‐called sample‐based rarefaction curves may be used. Given a study area that is sampled for species presence and absence in N plots, sample‐based rarefaction generates the expected number of accumulated species as the number of sampled plots increases from 1 to N. Accordingly, the question for this study is: can we construct a ‘functional rarefaction curve’ that summarizes the expected functional dissimilarity between species when n plots are drawn at random from a larger pool of N plots? Methods: In this paper, we propose a parametric measure of functional diversity that is obtained by combining sample‐based rarefaction techniques that are usually applied to species richness with Rao's quadratic diversity. For a given set of N presence/absence plots, the resulting measure summarizes the expected functional dissimilarity at an increasingly larger cumulative number of plots n (n≤N). Results and Conclusions: Due to its parametric nature, the proposed measure is progressively more sensitive to rare species with increasing plot number, thus rendering this measure adequate for comparing the functional diversity of species assemblages that have been sampled with variable effort.     

Evolutionary relationships among scyphozoan jellyfish families based on complete taxon sampling and phylogenetic analyses of 18S and 28S ribosomal DNA

A stable phylogenetic hypothesis for families within jellyfish class Scyphozoa has been elusive. Reasons for the lack of resolution of scyphozoan familial relationships include a dearth of morphological characters that reliably distinguish taxa and incomplete taxonomic sampling in molecular studies. Here, we address the latter issue by using maximum likelihood and Bayesian methods to reconstruct the phylogenetic relationships among all 19 currently valid scyphozoan families, using sequence data from two nuclear genes: 18S and 28S rDNA. Consistent with prior morphological hypotheses, we find strong evidence for monophyly of subclass Discomedusae, order Coronatae, rhizostome suborder Kolpophorae and superfamilies Actinomyariae, Kampylomyariae, Krikomyariae, and Scapulatae. Eleven of the 19 currently recognized scyphozoan families are robustly monophyletic, and we suggest recognition of two new families pending further analyses. In contrast to long-standing morphological hypotheses, the phylogeny shows coronate family Nausithoidae, semaeostome family Cyaneidae, and rhizostome suborder Daktyliophorae to be nonmonophyletic. Our analyses neither strongly support nor strongly refute monophyly of order Rhizostomeae, superfamily Inscapulatae, and families Ulmaridae, Catostylidae, Lychnorhizidae, and Rhizostomatidae. These taxa, as well as familial relationships within Coronatae and within rhizostome superfamily Inscapulatae, remain unclear and may be resolved by additional genomic and taxonomic sampling. In addition to clarifying some historically difficult taxonomic questions and highlighting nodes in particular need of further attention, the molecular phylogeny presented here will facilitate more robust study of phenotypic evolution in the Scyphozoa, including the evolution characters associated with mass occurrences of jellyfish.     

Rounding up the usual suspects: a standard target‐gene approach for resolving the interfamilial phylogenetic relationships of ecribellate orb‐weaving spiders with a new family‐rank classification (Araneae,Araneoidea)

We test the limits of the spider superfamily Araneoidea and reconstruct its interfamilial relationships using standard molecular markers. The taxon sample (363 terminals) comprises for the first time representatives of all araneoid families, including the first molecular data of the family Synaphridae. We use the resulting phylogenetic framework to study web evolution in araneoids. Araneoidea is monophyletic and sister to Nicodamoidea rank. n. Orbiculariae are not monophyletic and also include the RTA clade, Oecobiidae and Hersiliidae. Deinopoidea is paraphyletic with respect to a lineage that includes the RTA clade, Hersiliidae and Oecobiidae. The cribellate orb‐weaving family Uloboridae is monophyletic and is sister group to a lineage that includes the RTA Clade, Hersiliidae and Oecobiidae. The monophyly of most Araneoidea families is well supported, with a few exceptions. Anapidae includes holarchaeids but the family remains diphyletic even if Holarchaea is considered an anapid. The orb‐web is ancient, having evolved by the early Jurassic; a single origin of the orb with multiple “losses” is implied by our analyses. By the late Jurassic, the orb‐web had already been transformed into different architectures, but the ancestors of the RTA clade probably built orb‐webs. We also find further support for a single origin of the cribellum and multiple independent losses. The following taxonomic and nomenclatural changes are proposed: the cribellate and ecribellate nicodamids are grouped in the superfamily Nicodamoidea rank n. (Megadictynidae rank res. and Nicodamidae stat. n. ). Araneoidea includes 17 families with the following changes: Araneidae is re‐circumscribed to include nephilines , Nephilinae rank res., Arkyidae rank n. , Physoglenidae rank n. , Synotaxidae is limited to the genus Synotaxus, Pararchaeidae is a junior synonym of Malkaridae ( syn. n. ), Holarchaeidae of Anapidae ( syn. n. ) and Sinopimoidae of Linyphiidae ( syn. n. ).