Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia

Were molecular data available for extinct taxa, questions regarding the origins of many groups could be settled in short order. As this is not the case, various strategies have been proposed to combine paleontological and neontological data sets. The use of fossil dates as node age calibrations for divergence time estimation from molecular phylogenies is commonplace. In addition, simulations suggest that the addition of morphological data from extinct taxa may improve phylogenetic estimation when combined with molecular data for extant species, and some studies have merged morphological and molecular data to estimate combined evidence phylogenies containing both extinct and extant taxa. However, few, if any, studies have attempted to estimate divergence times using phylogenies containing both fossil and living taxa sampled for both molecular and morphological data. Here, I infer both the phylogeny and the time of origin for Lissamphibia and a number of stem tetrapods using Bayesian methods based on a data set containing morphological data for extinct taxa, molecular data for extant taxa, and molecular and morphological data for a subset of extant taxa. The results suggest that Lissamphibia is monophyletic, nested within Lepospondyli, and originated in the late Carboniferous at the earliest. This research illustrates potential pitfalls for the use of fossils as post hoc age constraints on internal nodes and highlights the importance of explicit phylogenetic analysis of extinct taxa. These results suggest that the application of fossils as minima or maxima on molecular phylogenies should be supplemented or supplanted by combined evidence analyses whenever possible.     

Phylogeny of extant and fossil Juglandaceae inferred from the integration of molecular and morphological data sets

It is widely acknowledged that integrating fossils into data sets of extant taxa is imperative for proper placement of fossils, resolution of relationships, and a better understanding of character evolution. The importance of this process has been further magnified because of the crucial role of fossils in dating divergence times. Outstanding issues remain, including appropriate methods to place fossils in phylogenetic trees, the importance of molecules versus morphology in these analyses, as well as the impact of potentially large amounts of missing data for fossil taxa. In this study we used the angiosperm clade Juglandaceae as a model for investigating methods of integrating fossils into a phylogenetic framework of extant taxa. The clade has a rich fossil record relative to low extant diversity, as well as a robust molecular phylogeny and morphological database for extant taxa. After combining fossil organ genera into composite and terminal taxa, our objectives were to (1) compare multiple methods for the integration of the fossils and extant taxa (including total evidence, molecular scaffolds, and molecular matrix representation with parsimony [MRP]); (2) explore the impact of missing data (incomplete taxa and characters) and the evidence for placing fossils on the topology; (3) simulate the phylogenetic effect of missing data by creating "artificial fossils"; and (4) place fossils and compare the impact of single and multiple fossil constraints in estimating the age of clades. Despite large and variable amounts of missing data, each of the methods provided reasonable placement of both fossils and simulated "artificial fossils" in the phylogeny previously inferred only from extant taxa. Our results clearly show that the amount of missing data in any given taxon is not by itself an operational guideline for excluding fossils from analysis. Three fossil taxa (Cruciptera simsonii, Paleoplatycarya wingii, and Platycarya americana) were placed within crown clades containing living taxa for which relationships previously had been suggested based on morphology, whereas Polyptera manningii, a mosaic taxon with equivocal affinities, was placed firmly as sister to two modern crown clades. The position of Paleooreomunnea stoneana was ambiguous with total evidence but conclusive with DNA scaffolds and MRP. There was less disturbance of relationships among extant taxa using a total evidence approach, and the DNA scaffold approach did not provide improved resolution or internal support for clades compared to total evidence, whereas weighted MRP retained comparable levels of support but lost crown clade resolution. Multiple internal minimum age constraints generally provided reasonable age estimates, but the use of single constraints provided by extinct genera tended to underestimate clade ages.     

Tooth development and histology patterns in lamniform sharks (Elasmobranchii,Lamniformes) revisited

The dentition of lamniforme sharks exhibits several characters that have been used extensively to resolve the phylogenetic relationships of extant taxa, yet some uncertainties remain. Also, the development of different teeth of a tooth file within the jaws of most extant lamniforms has not been documented to date. High‐resolution micro‐computed tomography is used here to re‐evaluate the importance of two dental characters within the order Lamniformes, which were considered not to be phylogenetically informative, the histotype and the number of teeth per tooth file. Additionally, the development and mineralization patterns of the teeth of the two osteodont lamniforms Lamna nasus and Alopias superciliosus were compared. We discuss the importance of these dental characters for phylogenetic interpretations to assess the quality of these characters in resolving lamniform relationships. The dental characters suggest that (1) Lamniformes are the only modern‐level sharks exhibiting the osteodont histotype, (2) the osteodont histotype in lamniform sharks is a derived state in modern‐level sharks (Elasmobranchii), (3) the osteodont type, conversely is convergently achieved when the clade Chondrichthyes is considered and thus might comprise a functional rather than a phylogenetic signal, and (4) there is an increase in the number of teeth per file throughout lamniform phylogeny. Structural development of the teeth of L. nasus and A. superciliosus is congruent with a previous investigation of the lamniform shark Carcharodon carcharias. J. Morphol. 277:1584–1598, 2016. © 2016 Wiley Periodicals, Inc.     

Systematics and evolution of the Pan‐Alcidae (Aves,Charadriiformes)

Puffins, auks and their allies in the wing‐propelled diving seabird clade Pan‐Alcidae (Charadriiformes) have been proposed to be key pelagic indicators of faunal shifts in Northern Hemisphere oceans. However, most previous phylogenetic analyses of the clade have focused only on the 23 extant alcid species. Here we undertake a combined phylogenetic analysis of all previously published molecular sequence data (～ 12 kb) and morphological data (n = 353 characters) with dense species level sampling that also includes 28 extinct taxa. We present a new estimate of the patterns of diversification in the clade based on divergence time estimates that include a previously vetted set of twelve fossil calibrations. The resultant time trees are also used in the evaluation of previously hypothesized paleoclimatic drivers of pan‐alcid evolution. Our divergence dating results estimate the split of Alcidae from its sister taxon Stercorariidae during the late Eocene (～ 35 Ma), an evolutionary hypothesis for clade origination that agrees with the fossil record and that does not require the inference of extensive ghost lineages. The extant dovekie Alle alle is identified as the sole extant member of a clade including four extinct Miocene species. Furthermore, whereas an Uria + Alle clade has been previously recovered from molecular analyses, the extinct diversity of closely related Miocepphus species yields morphological support for this clade. Our results suggest that extant alcid diversity is a function of Miocene diversification and differential extinction at the Pliocene–Pleistocene boundary. The relative timing of the Middle Miocene climatic optimum and the Pliocene–Pleistocene climatic transition and major diversification and extinction events in Pan‐Alcidae, respectively, are consistent with a potential link between major paleoclimatic events and pan‐alcid cladogenesis.     

Timing of deep‐sea adaptation in dogfish sharks: insights from a supertree of extinct and extant taxa

Klug, S. & Kriwet, J. (2010). Timing of deep‐sea adaptation in dogfish sharks: insights from a supertree of extinct and extant taxa. —Zoologica Scripta, 39, 331–342. Dogfish sharks (Squaliformes) constitute a monophyletic group of predominantly deep‐water neoselachians, but the reasons and timing of their adaptation to this hostile environment remain ambiguous. Late Cretaceous dogfish sharks, which generally would be associated with deep‐water occur predominantly in shallow water environments. Did the end‐Cretaceous mass extinction event that eliminated large numbers of both terrestrial and aquatic taxa and clades including sharks trigger the evolutionary adaptation of present deep‐water dogfish sharks? Here, we construct, date, and analyse a genus‐level phylogeny of extinct and living dogfish sharks to bring a new perspective to this question. For this, eleven partial source trees of dogfish shark interrelationships were merged to create a comprehensive phylogenetic hypothesis. The resulting supertree is the most inclusive estimate of squaliform interrelationships that has been proposed to date containing 23 fossil and extant members of all major groups. ?Eoetmopterus represents the oldest dalatoid. ?Microetmopterus, ?Paraphorosoides, ?Proetmopterus and ?Squaliogaleus are stem‐group dalatoids in which bioluminescence most likely was not developed. According to our analyses, bioluminescence in dogfish sharks was already developed in the early Late Cretaceous indicating that these sharks adapted to deep‐water conditions most likely at about 100 Mya. The advantage of this reconstruction is that the fossil record is used directly for age node estimates rather than employing molecular clock approaches.     

Monophyly, phylogeny and systematic position of the †Synechodontiformes (Chondrichthyes, Neoselachii)

Klug, S. (2009). Monophyly, phylogeny and systematic position of the †Synechodontiformes (Chondrichthyes, Neoselachii). — Zoologica Scripta, 39 , 37–49.
Identifying the monophyly and systematic position of extinct sharks is one of the major challenges in reconstructing the phylogeny and evolutionary history of sharks in general. Although great progress has been accomplished in the last few decades with regard to resolving the interrelationships of living sharks, a comprehensive phylogeny identifying the systematic position of problematic or exclusively fossil taxa is still lacking. Fossil taxa traditionally assigned to synechodontiform sharks are very diverse with a fossil record extending back into the Palaeozoic but with uncertain inter- and intrarelationships. Here, phylogenetic analyses using robust cladistic principles are presented for the first time to evaluate the monophyly of this group, their intrarelationships and their systematic position within Neoselachii. According to the results of this study, taxa assigned to this group form a monophyletic clade, the †Synechodontiformes. This group is sister to all living sharks and displays a suite of neoselachian characters. Consequently, the concept of neoselachian systematics needs to be enlarged to include this completely extinct group, which is considered to represent stem-group neoselachians. The origin of modern sharks can be traced back into the Late Permian (250 Mya) based on the fossil record of †Synechodontiformes. The systematic position of batoids remains contradictory, which relates to the use of different data (molecular vs. morphological) in phylogentic analyses.     

Geometric morphometric analyses of worn cheek teeth help identify extant and extinct gophers (Rodentia,Geomyidae)

Studies of the biostratigraphy and palaeoecology of fossil vertebrate assemblages require large samples of accurately identified specimens. Such analyses can be hampered by the inability to assign isolated and worn remains to specific taxa. Entoptychine gophers are a diverse group of burrowing rodents found in Oligo‐Miocene deposits of the western United States. In both entoptychines and their extant relatives the geomyines, diagnostic characters of the occlusal surface of the teeth are modified with wear, making difficult the identification of many isolated fossil teeth. We use geometric morphometrics to test the hypothesis that tooth shape informs taxonomic affinities and expected levels of morphological variation across gopher taxa. We also incorporate data from microcomputer tomography to investigate changes in occlusal surface shape through wear within individuals. Our analyses demonstrate the usefulness of our approach in identifying extant geomyines to the genus, subgenus and species levels, and fossil entoptychines to the genus and, in some cases, the species level. Our results cast doubt on the validity of some species within Entoptychus and suggest future revisions to entoptychine taxonomy. The amounts of morphological divergence observed among fossil and extant genera are similar. Fossil species do not differ greatly from extant ones in that regard either. Further work evaluating the morphological variation within and across entoptychine species, including unworn teeth and osteological material, will allow revised analyses of the biostratigraphy and palaeoecology of important Oligo‐Miocene mammalian assemblages of the western United States and help to infer the phylogenetic relationships and evolution of gophers.     

A phylogeny of the fossil and extant zeiform-like fishes, Upper Cretaceous to Recent, with comments on the putative zeomorph clade (Acanthomorpha)

Tyler, J. C. & Santini, F. (2005). A phylogeny of the fossil and extant zeiform-like fishes, Upper Cretaceous to Recent, with comments on the putative zeomorph clade (Acanthomorpha). — Zoological Scripta , ** , ***–***.
A phylogenetic hypothesis based on 107 morphological characters is proposed for a data set of 43 taxa. Thirty-three are extant and belong to the orders Zeiformes (20 taxa), Caproiformes (2), Tetraodontiformes (2), Beryciformes (3), Stephanoberyciformes (3) and Perciformes (3). Ten are fossil taxa previously assigned to the Zeiformes (3), Caproiformes (1), Tetraodontiformes (2), Perciformes (1), and to two extinct Eocene families, the Sorbinipercidae (2) and the Zorzinichthyidae (1). This analysis indicates the existence of a previously undocumented clade formed by the families Sorbinipercidae + Zorzinichthyidae that may be related to the tetraodontiforms. It also shows that two uppermost Palaeocene species, Archaeozeus skamolensis and Protozeus kuehnei , sequentially represent the two most basal lineages of zeiforms, whereas the most ancient known zeiform, the Upper Cretaceous Cretazeus rinaldii , belongs within the clade of extant species in a polytomy with many other zeiform lineages. A reduced data set of 25 mostly zeiform taxa, after the removal of most outgroups, shows at least weak support for Cretazeus being nested deeply within the extant zeiforms; such a placement would indicate that at least six lineages of zeiforms were present during the Upper Cretaceous, and survived the Cretaceous/Tertiary (K/T) extinction to radiate in Cenozoic seas.     

The biology of extinct and extant sawfish (Batoidea: Sclerorhynchidae and Pristidae)

Sclerorhynchids (extinct sawfishes, Batoidea), pristids (extant sawfish, Batoidea) and pristiophorids (sawsharks, Squalomorphi) are the three elasmobranch families that possess an elongated rostrum with lateral teeth. Sclerorhynchids are the extinct sawfishes of the Cretaceous period, which reached maximum total lengths of 100 cm. The morphology of their rostral teeth is highly variable. Pristid sawfish occur circumtropically and can reach maximum total lengths of around 700 cm. All pristid species are globally endangered due to their restricted habitat inshore. Pristiophorid sawsharks are small sharks of maximum total lengths below 150 cm, which occur in depths of 70–900 m. Close examination of the morphology of pectoral fin basals and the internal structure of the rostrum reveals that sclerorhynchids and pristids evolved independently from rhinobatids, whereas pristiophorids are squalomorph sharks. The elongation of the rostrum may be an adaptation for feeding, as all marine vertebrate taxa that possess this structure are said to use it in the context of feeding.     

Bayesian phylogenetic estimation of fossil ages

Recent advances have allowed for both morphological fossil evidence and molecular sequences to be integrated into a single combined inference of divergence dates under the rule of Bayesian probability. In particular, the fossilized birth–death tree prior and the Lewis-Mk model of discrete morphological evolution allow for the estimation of both divergence times and phylogenetic relationships between fossil and extant taxa. We exploit this statistical framework to investigate the internal consistency of these models by producing phylogenetic estimates of the age of each fossil in turn, within two rich and well-characterized datasets of fossil and extant species (penguins and canids). We find that the estimation accuracy of fossil ages is generally high with credible intervals seldom excluding the true age and median relative error in the two datasets of 5.7% and 13.2%, respectively. The median relative standard error (RSD) was 9.2% and 7.2%, respectively, suggesting good precision, although with some outliers. In fact, in the two datasets we analyse, the phylogenetic estimate of fossil age is on average less than 2 Myr from the mid-point age of the geological strata from which it was excavated. The high level of internal consistency found in our analyses suggests that the Bayesian statistical model employed is an adequate fit for both the geological and morphological data, and provides evidence from real data that the framework used can accurately model the evolution of discrete morphological traits coded from fossil and extant taxa. We anticipate that this approach will have diverse applications beyond divergence time dating, including dating fossils that are temporally unconstrained, testing of the ‘morphological clock'', and for uncovering potential model misspecification and/or data errors when controversial phylogenetic hypotheses are obtained based on combined divergence dating analyses.This article is part of the themed issue ‘Dating species divergences using rocks and clocks’.     

Inferences from tip‐calibrated phylogenies: a review and a practical guide

Molecular dating of phylogenetic trees is a growing discipline using sequence data to co‐estimate the timing of evolutionary events and rates of molecular evolution. All molecular‐dating methods require converting genetic divergence between sequences into absolute time. Historically, this could only be achieved by associating externally derived dates obtained from fossil or biogeographical evidence to internal nodes of the tree. In some cases, notably for fast‐evolving genomes such as viruses and some bacteria, the time span over which samples were collected may cover a significant proportion of the time since they last shared a common ancestor. This situation allows phylogenetic trees to be calibrated by associating sampling dates directly to the sequences representing the tips (terminal nodes) of the tree. The increasing availability of genomic data from ancient DNA extends the applicability of such tip‐based calibration to a variety of taxa including humans, extinct megafauna and various microorganisms which typically have a scarce fossil record. The development of statistical models accounting for heterogeneity in different aspects of the evolutionary process while accommodating very large data sets (e.g. whole genomes) has allowed using tip‐dating methods to reach inferences on divergence times, substitution rates, past demography or the age of specific mutations on a variety of spatiotemporal scales. In this review, we summarize the current state of the art of tip dating, discuss some recent applications, highlight common pitfalls and provide a ‘how to’ guide to thoroughly perform such analyses.     

Incorporating phylogenetic uncertainty on phylogeny‐based palaeontological dating and the timing of turtle diversification

Methods improving the performance of molecular dating of divergence time of clades have improved dramatically in recent years. The calibration of molecular dating using the first appearance of a clade in the fossil record is a crucial step towards inferring the minimal diversification time of various groups and the choice of extinct taxa can strongly influence the molecular dates. Here, we evaluate the uncertainty on the phylogenetic position of extinct taxa through non‐parametric bootstrapping. The recognition of phylogenetic uncertainty resulted in the definition of the Bootstrap Uncertainty Range (BUR) for the age of first appearance of a given clade. The BUR is calculated as the interval of geological time in which the diversification of a given clade can be inferred to have occurred, based on the temporal information of the fossil record and the topologies of the bootstrap trees. Divergence times based on BUR analyses were calculated for three clades of turtles: Testudines, Pleurodira and Cryptodira. This resulted in extensive uncertainty ranges of topology‐dependent minimal divergence dates for these clades.     

A phylogeny of fossil and living neocoleoid cephalopods

Coleoid cephalopod phylogeny is well studied via both molecular and morphological data, yet although some agreement has been reached (e.g. that extant Decapodiformes and Octopoda are monophyletic) many details remain poorly resolved. Fossil coleoids, for which much data exists, have hitherto not been incorporated into analyses. Their inclusion is highly desirable for the support of neontological phylogenies, to better reconstruct character‐state histories, and to investigate the placement of the fossil groups themselves. In this study we present and analyse a morphological data matrix including both extinct and extant taxa. Homology assumptions in our data are discussed. Our results are presented both with and without the constraint of a monophyletic Decapodiformes imposed. When analysed with this constraint our results are strikingly congruent with those from molecular phylogeny, for instance placing Idiosepius in a basal position within Decapodiformes, and recovering Oegopsida and Bathyteuthoidea (although as grades). Our results support an Octopodiformes clade (“vampire squid” Vampyroteuthis as sister to Octopoda) and an octopodiform interpretation for most fossil coleoids. They suggest the fossil sister taxon to the octopods to be Plesioteuthididae. Most fossil higher taxa are supported, although many genera, especially within suborder Teudopseina, appear para‐ or polyphyletic.     

Inferring hominoid and early hominid phylogeny using craniodental characters: the role of fossil taxa

Recent discoveries of new fossil hominid species have been accompanied by several phylogenetic hypotheses. All of these hypotheses are based on a consideration of hominid craniodental morphology. However, Collard and Wood (2000) suggested that cladograms derived from craniodental data are inconsistent with the prevailing hypothesis of ape phylogeny based on molecular data. The implication of their study is that craniodental characters are unreliable indicators of phylogeny in hominoids and fossil hominids but, notably, their analysis did not include extinct species. We report here on a cladistic analysis designed to test whether the inclusion of fossil taxa affects the ability of morphological characters to recover the molecular ape phylogeny. In the process of doing so, the study tests both Collard and Wood's (2000) hypothesis of character reliability, and the several recently proposed hypotheses of early hominid phylogeny. One hundred and ninety-eight craniodental characters were examined, including 109 traits that traditionally have been of interest in prior studies of hominoid and early hominid phylogeny, and 89 craniometric traits that represent size-corrected linear dimensions measured between standard cranial landmarks. The characters were partitioned into two data sets. One set contained all of the characters, and the other omitted the craniometric characters. Six parsimony analyses were performed; each data set was analyzed three times, once using an ingroup that consisted only of extant hominoids, a second time using an ingroup of extant hominoids and extinct early hominids, and a third time excluding Kenyanthropus platyops. Results suggest that the inclusion of fossil taxa can play a significant role in phylogenetic analysis. Analyses that examined only extant taxa produced most parsimonious cladograms that were inconsistent with the ape molecular tree. In contrast, analyses that included fossil hominids were consistent with that tree. This consistency refutes the basis for the hypothesis that craniodental characters are unreliable for reconstructing phylogenetic relationships. Regarding early hominids, the relationships of Sahelanthropus tchadensis and Ardipithecus ramidus were relatively unstable. However, there is tentative support for the hypotheses that S. tchadensis is the sister taxon of all other hominids. There is support for the hypothesis that A. anamensis is the sister taxon of all hominids except S. tchadensis and Ar. ramidus. There is no compelling support for the hypothesis that Kenyanthropus platyops shares especially close affinities with Homo rudolfensis. Rather, K. platyops is nested within the Homo + Paranthropus + Australopithecus africanus clade. If K. platyops is a valid species, these relationships suggest that Homo and Paranthropus are likely to have diverged from other hominids much earlier than previously supposed. There is no support for the hypothesis that A. garhi is either the sister taxon or direct ancestor of the genus Homo. Phylogenetic relationships indicate that Australopithecus is paraphyletic. Thus, A. anamensis and A. garhi should be allocated to new genera.     

Phylogenetic interrelationships of living and extinct Tinamidae,volant palaeognathous birds from the New World

Tinamous, one of the earliest diverging living avian lineages, consists of a Neotropical clade of palaeognathous birds with a fossil record limited to the early Miocene–Quaternary of southern South America. Here, we conduct a comprehensive, morphology‐based phylogenetic study of the interrelationships among extinct and living species of tinamous. Morphological data of fossil species are included in a matrix of 157 osteological and myological characters of 56 terminal taxa. The monophyly of most recognized genera is supported by the results of the analysis. The cladistic analysis also recovers the traditional subdivision between those tinamous specialized for open areas (Nothurinae) and those inhabiting forested environments (Tinaminae). Temporal calibration of the resultant phylogeny indicates that such a basal divergence had already taken place in the early Miocene, some 17 million years ago. The placement of the fossil species within the open‐area (Nothurinae) and the forest‐dwelling (Tinaminae) tinamous is also consistent with the palaeoenvironmental conditions inferred from the associated fauna. © 2014 The Linnean Society of London     

Morphological and molecular phylogenetic context of the angiosperms: contrasting the 'top-down' and 'bottom-up' approaches used to infer the likely characteristics of the first flowers

Recent attempts to address the long-debated 'origin' of the angiosperms depend on a phylogenetic framework derived from a matrix of taxa versus characters; most assume that empirical rigour is proportional to the size of the matrix. Sequence-based genotypic approaches increase the number of characters (nucleotides and indels) in the matrix but are confined to the highly restricted spectrum of extant species, whereas morphology-based approaches increase the number of phylogenetically informative taxa (including fossils) at the expense of accessing only a restricted spectrum of phenotypic characters. The two approaches are currently delivering strongly contrasting hypotheses of relationship. Most molecular studies indicate that all extant gymnosperms form a natural group, suggesting surprisingly early divergence of the lineage that led to angiosperms, whereas morphology-only phylogenies indicate that a succession of (mostly extinct) gymnosperms preceded a later angiosperm origin. Causes of this conflict include: (i) the vast phenotypic and genotypic lacuna, largely reflecting pre-Cenozoic extinctions, that separates early-divergent living angiosperms from their closest relatives among the living gymnosperms; (ii) profound uncertainty regarding which (a) extant and (b) extinct angiosperms are most closely related to gymnosperms; and (iii) profound uncertainty regarding which (a) extant and (b) extinct gymnosperms are most closely related to angiosperms, and thus best serve as 'outgroups' dictating the perceived evolutionary polarity of character transitions among the early-divergent angiosperms. These factors still permit a remarkable range of contrasting, yet credible, hypotheses regarding the order of acquisition of the many phenotypic characters, reproductive and vegetative, that distinguish 'classic' angiospermy from 'classic' gymnospermy. The flower remains ill-defined and its mode (or modes) of origin remains hotly disputed; some definitions and hypotheses of evolutionary relationships preclude a role for the flower in delimiting the angiosperms. We advocate maintenance of parallel, reciprocally illuminating programmes of morphological and molecular phylogeny reconstruction, respectively supported by homology testing through additional taxa (especially fossils) and evolutionary-developmental genetic studies that explore genes potentially responsible for major phenotypic transitions.     

The phylogeny of the superfamily Coccoidea (Hemiptera: Sternorrhyncha) based on the morphology of extant and extinct macropterous males

Currently, 49 families of scale insects are recognised, 33 of which are extant. Despite more than a decade of DNA sequence‐based phylogenetic studies of scales insects, little is known with confidence about relationships among scale insects families. Multiple lines of evidence support the monophyly of a group of 18 scale insect families informally referred to as the neococcoids. Among neococcoid families, published DNA sequence‐based estimates have supported Eriococcidae paraphyly with respect to Beesoniidae, Dactylopiidae, and Stictococcidae. No other neococcoid interfamily relationship has been strongly supported in a published study that includes exemplars of more than ten families. Likewise, no well‐supported relationships among the 15 extant scale insect families that are not neococcoids (usually referred to as ‘archaeococcoids’) have been published. We use a Bayesian approach to estimate the scale insect phylogeny from 162 adult male morphological characters, scored from 269 extant and 29 fossil species representing 43/49 families. The result is the most taxonomically comprehensive, most resolved and best supported estimate of phylogenetic relationships among scale insect families to date. Notable results include strong support for (i) Ortheziidae sister to Matsucoccidae, (ii) a clade comprising all scale insects except for Margarodidae s.s., Ortheziidae and Matsucoccidae, (iii) Coelostomidiidae paraphyletic with respect to Monophlebidae, (iv) Eriococcidae paraphyletic with respect to Stictococcidae and Beesoniidae, and (v) Aclerdidae sister to Coccidae. We recover strong support for a clade comprising Phenacoleachiidae, Pityococcidae, Putoidae, Steingeliidae and the neococcoids, along with a sister relationship between this clade and Coelostomidiidae + Monophlebidae. In addition, we recover strong support for Pityococcidae + Steingeliidae as sister to the neococcoids. Data from fossils were incomplete, and the inclusion of extinct taxa in the data matrix reduced support and phylogenetic structure. Nonetheless, these fossil data will be invaluable in DNA sequence‐based and total evidence estimates of phylogenetic divergence times.     

Evolution of fossil and living spider flies based on morphological and molecular data (Diptera,Acroceridae)

The phylogeny of spider flies is presented based on an analysis of DNA sequence data combined with morphological characters for both living and fossil species. We sampled 40 extant and extinct genera across all major lineages of Acroceridae, which were compared with outgroup taxa from various lower brachyceran families. In all, 81 morphological characters of 60 extant and 10 extinct ingroup species were combined with 7.1 kb of DNA sequences of two nuclear (CAD and 28S rDNA) and two mitochondrial genes (COI and 16S rDNA). Results strongly support the monophyly of Acroceridae, with major clades contained within classified here in five extant subfamilies (Acrocerinae, Cyrtinae stat. rev. , Ogcodinae stat. rev. , Panopinae and Philopotinae) and one extinct subfamily, Archocyrtinae. The evolution of important spider fly traits is discussed, including genitalia and wing venation. The status of the enigmatic Psilodera Gray and Pterodontia Gray as members of the Panopinae is confirmed based on both molecular and morphological data.