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.     

The position of Cetacea within mammalia: phylogenetic analysis of morphological data from extinct and extant taxa

Knowledge of the phylogenetic position of the order Cetacea (whales, dolphins, and porpoises) within Mammalia is of central importance to evolutionary biologists studying the transformations of biological form and function that accompanied the shift from fully terrestrial to fully aquatic life in this clade. Phylogenies based on molecular data and those based on morphological data both place cetaceans among ungulates but are incongruent in other respects. Morphologists argue that cetaceans are most closely related to mesonychians, an extinct group of terrestrial ungulates. They have disagreed, however, as to whether Perissodactyla (odd-toed ungulates) or Artiodactyla (even-toed ungulates) is the extant clade most closely related to Cetacea, and have long maintained that each of these orders is monophyletic. The great majority of molecule-based phylogenies show, by contrast, not only that artiodactyls are the closest extant relatives of Cetacea, but also that Artiodactyla is paraphyletic unless cetaceans are nested within it, often as the sister group of hippopotamids. We tested morphological evidence for several hypotheses concerning the sister taxon relationships of Cetacea in a maximum parsimony analysis of 123 morphological characters from 10 extant and 30 extinct taxa. We advocate treating certain multistate characters as ordered because such a procedure incorporates information about hierarchical morphological transformation. In all most-parsimonious trees, whether multistate characters are ordered or unordered, Artiodactyla is the extant sister taxon of Cetacea. With certain multistate characters ordered, the extinct clade Mesonychia (Mesonychidae + Hapalodectidae) is the sister taxon of Cetacea, and Artiodactyla is monophyletic. When all fossils are removed from the analysis, Artiodactyla is paraphyletic with Cetacea nested inside, indicating that inclusion of mesonychians and other extinct stem taxa in a phylogenetic analysis of the ungulate clade is integral to the recovery of artiodactyl monophyly. Phylogenies derived from molecular data alone may risk recovering inconsistent branches because of an inability to sample extinct clades, which by a conservative estimate, amount to 89% of the ingroup. Addition of data from recently described astragali attributed to cetaceans does not overturn artiodactyl monophyly.     

The phylogenetic relationships of lampridiform fishes (Teleostei: acanthomorpha), based on a total-evidence analysis of morphological and molecular data

We investigated the phylogenetic relationships among five species of lampridiform fishes, three basal outgroup species (two aulopiforms and one myctophiform), and two species of non-lampridiform acanthomorphs (Polymixia and Percopsis) using a combined parsimony analysis of morphological and molecular data. Morphological characters included 28 transformation series obtained from the literature. Molecular characters included 223 informative transformation series from an aligned 854-base pair fragment of 12S mtDNA and 139 informative transformation series from an aligned 561-base pair fragment of 16S mtDNA. A total-evidence analysis using the aulopiforms Synodus and Aulopus and the myctophiform Hygophum as outgroups corroborates the monophyly of Lampridiformes and unites Polymixia with Percopsis. Among the lampridiform fishes we examined, Metavelifer is basal, followed in ascending order by Lampris, Lophotus, Regalecus, and Trachipterus. This hypothesis is congruent with the most recent morphological analysis of the Lampridiformes and rejects a diphyletic origin of elongate body form within the clade. Analysis of a combined matrix of 12S and 16S mtDNA data yielded a phylogenetic hypothesis isomorphic with the total-evidence phylogeny. Analyses of partitioned DNA data sets reveals that single gene regions are poor predictors of the total-evidence phylogeny while combined analyses of both DNA data sets are good predictors of the total-evidence phylogeny.     

Impact of increased character sampling on the phylogeny of Cetartiodactyla (Mammalia): combined analysis including fossils

The phylogenetic position of Cetacea (whales, dolphins and porpoises) is an important exemplar problem for combined data parsimony analyses because the clade is ancient and includes many well‐known and relatively complete fossil species. We combined data for 71 terminal taxa (43 extinct/28 extant) to test where Cetacea fits within Cetartiodactyla, and where various fossil hoofed mammals (e.g., ?entelodonts, “?anthracotheriids” and ?mesonychians) are positioned. We scored 635 phenotypic characters (osteology, dentition, soft tissue, behavior), approximately three times the number of characters in the last major analysis of this clade, and combined these with > 40 000 molecular characters, including new data from 10 genes. The analysis supported a topology consistent with the majority of recently published molecular studies. Cetacea was the extant sister taxon of Hippopotamidae, followed successively by Ruminantia, Suina and Camelidae. Several extinct taxa were phylogenetically unstable, upsetting resolution of the strict consensus and limiting branch support, but the positions of several key fossils were consistently resolved. The wholly extinct ?Mesonychia was more closely related to Cetacea than was any “artiodactylan.”“?Anthracotheriids” were paraphyletic, and, with the exception of one species, were more closely related to Hippopotamidae than to any other living taxon. The total evidence analysis overturned a highly nested position for Moschus supported by molecular data alone. The character partition that could be scored for the fossil taxa (osteological and dental characters) included more informative characters than most molecular partitions in our analysis, and had the fewest missing data. The osteological–dental data alone, however, did not support inclusion of cetaceans within crown “Artiodactyla.” Recently discovered ankle bones from fossil whales reinforced the monophyly of Cetartiodactyla but provided no particular evidence of derived similarities between hippopotamids and fossil cetaceans that were not shared with other “artiodactylans”. © The Willi Hennig Society 2007.     

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.     

The female reproductive unit of Ephedra (Gnetales): comparative morphology and evolutionary perspectives

Morphological variation in Ephedra (Gnetales) is limited and confusing from an evolutionary perspective, with parallelisms and intraspecific variation. However, recent analyses of molecular data provide a phylogenetic framework for investigations of morphological traits, albeit with few informative characters in the investigated gene regions. We document morphological, anatomical and histological variation patterns in the female reproductive unit and test the hypothesis that some Early Cretaceous fossils, which share synapomorphies with Ephedra, are members of the extant clade. Results indicate that some morphological features are evolutionarily informative although intraspecific variation is evident. Histology and anatomy of cone bracts and seed envelopes show clade‐specific variation patterns. There is little evidence for an inclusion of the Cretaceous fossils in the extant clade. Rather, a hypothesized general pattern of reduction of the vasculature in the ephedran seed envelope, probably from four vascular bundles in the fossils, to ancestrally three in the living clade, and later to two, is consistent with phylogenetic and temporal analyses, which indicate that extant diversity evolved after the Cretaceous–Tertiary boundary. Notwithstanding striking similarities between living and Cretaceous Ephedra, available data indicate that the Mesozoic diversity went almost entirely extinct in the late Cretaceous causing a bottleneck effect in Ephedra, still reflected today by an extraordinarily low level of genetic and structural diversity. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 163 , 387–430.     

The phylogeny of charadriiform birds (shorebirds and allies) – reassessing the conflict between morphology and molecules

Multiple molecular analyses provide a congruent and well‐supported phylogeny of the charadriiform family‐level taxa, which conflicts with previous hypotheses based on osteological data. In order to revise the latter and to identify new characters of phylogenetic significance, skeletons of most charadriiform family‐level taxa were examined and 49 characters analysed. Tree topology was sensitive to outgroup choice, but the result of the analysis rooted with Columbidae (doves and pigeons) recovered a monophyletic Scolopaci, Charadrii, and nonturnicid Lari. With regard to the inclusion of Alcidae and Glareolidae in the Lari, the results of the present study are also in better concordance with the new molecular phylogenies than previous analyses of morphological data. Furthermore, for the first time an apomorphy of a clade including Thinocoridae, Pedionomidae, Rostratulidae, and Jacanidae was identified. Inclusion of Turnicidae in the Lari could not be supported, but there is no strong morphological evidence for an alternative placement. Pluvianus shares derived osteological features with the Burhinidae, and its position in the molecular analyses likewise cannot be corroborated with morphological data. Based on the topology of the molecular consensus tree, the ancestral state of selected characters is reconstructed. It is finally noted that recent calibrations of molecular analyses, which indicate an origin of extant charadriiform lineages in the Cretaceous, are based on incorrectly identified fossils. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 161 , 916–934.     

The importance of even highly incomplete fossil taxa in reconstructing the phylogenetic relationships of the tetraodontiformes (acanthomorpha: pisces)

The use of fossils in the phylogenetics of extant clades traditionallyhas been a contentious issue. Fossils usually are relativelyincomplete, and their use commonly leads to an increase in thenumber of equally most parsimonious trees and a decrease inthe resolution of phylogenies. Fossils alone, however, providecertain kinds of information about the biological history ofa clade, and computer simulations have shown that even highlyincomplete material can, under certain circumstances, increasethe accuracy of a phylogeny, rather than decrease it. Because empirical data are still scarce on the effects of theinclusion of fossils on phylogenetic reconstructions, we attemptedto investigate this problem by using a relatively well-knowngroup of acanthomorph fishes, the Tetraodontiformes (triggerfishes,pufferfishes, and ocean sunfishes), for which robust phylogeniesusing extant taxa already exist and that has a well-studiedfossil record. Adding incomplete fossil taxa of tetraodontiformsusually increases the number of equally most parsimonious treesand often decreases the resolution of consensus trees. However,adding fossil taxa may help to correctly establish relationshipsamong lineages that have experienced high degrees of morphologicaldiversification by allowing for a reinterpretation of homologousand homoplastic features, increasing the resolution rather thandecreasing it. Furthermore, taxa that were scored for 25% ormore of their characters did not cause a significant loss ofresolution, while providing unique biological information.     

The male postabdomen and genital apparatus of †Mengea tertiaria,a strepsipteran amber fossil (Insecta)

The male genital apparatus of a fossil insect including internal soft parts is described in detail for the first time. The conditions found in an approximately 42‐My‐old specimen of ?Mengea tertiaria embedded in Baltic amber are compared to what is found in other extinct and extant strepsipterans, notably members of the basal ‘Mengenillidae’ (probably paraphyletic). The postabdomen of ?Mengea is very similar to what is present in other fossil and extant members of Strepsiptera. Only few structural features vary within the group, but it differs strongly from the apparatus in other holometabolan lineages. The slender, exposed tergite IX, the complete absence of parameres, a sperm pump formed by a strongly developed muscularis (layers of mainly circular muscle fibres) around the proximal part of the ejaculatory duct and the presence of four specific muscles are potential autapomorphies of the Strepsiptera. A presumptive strepsipteran ground plan feature found in ?Mengea is the nearly straight, simple penis, which is also present in ?Protoxenos, ?Cretostylops, Bahiaxenos, Mengenilla, Eoxenos and Congoxenos. This strongly suggests that males of ?Mengea (and other stem group strepsipterans) copulated in a very similar way as males of extant members of the group with free‐living females (e.g. Mengenilla). In contrast, the penis of stylopidian males, which copulate with females parasitizing in pterygote hosts, is hook shaped. A sister group relationship between ?Mengea and Strepsiptera s.s. (extant groups) is supported by a distinctly weaker sclerotization of the abdominal tergites, compared to the corresponding sternites. The study of other stem group strepsipterans using μ‐computer tomography should have high priority. This technique has a great potential to facilitate morphological reconstruction and phylogenetic placement of amber fossils.     

生花植物概念简介及其名称的商榷

在上个世纪最后的 2 0年里 ,系统学家应用形态性状对种子植物进行了大量的分支分析。其结果显示灭绝的五柱木属加上灭绝的本内苏铁目及尚存的买麻藤目是被子植物的姊妹群 ,形成一个强支 ,称之为生花植物支。生花植物假说对探讨被子植物起源有着重要影响 ,它激发人们讨论被子植物起源时间可能要提前到三叠纪甚至石炭纪 ,除了支持原有的真花学说外 ,还提出新恩格勒学说。但是 ,近年来对现存种子植物进行分子系统学研究的结果是 :(1)拒绝接受生花植物概念 ;(2 )买麻藤目并不是被子植物的姊妹群而是松柏目的姊妹群 ,甚至网结于松柏类而成为松科的姊妹群。这些结果并不使人惊讶 ,因为对探讨像包含许多灭绝类群的种子植物系统 ,决不可能是仅仅单独应用现代类群资料所能完成的。假如生花植物支是成立的 ,但其名称以AGPB支代替生花植物支可能较为合理。     

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.     

Are pollen fossils useful for calibrating relaxed molecular clock dating of phylogenies? A comparative study using Myrtaceae

The identification and application of reliable fossil calibrations represents a key component of many molecular studies of evolutionary timescales. In studies of plants, most paleontological calibrations are associated with macrofossils. However, the pollen record can also inform age calibrations if fossils matching extant pollen groups are found. Recent work has shown that pollen of the myrtle family, Myrtaceae, can be classified into a number of morphological groups that are synapomorphic with molecular groups. By assembling a data matrix of pollen morphological characters from extant and fossil Myrtaceae, we were able to measure the fit of 26 pollen fossils to a molecular phylogenetic tree using parsimony optimisation of characters. We identified eight Myrtaceidites fossils as appropriate for calibration based on the most parsimonious placements of these fossils on the tree. These fossils were used to inform age constraints in a Bayesian phylogenetic analysis of a sequence alignment comprising two sequences from the chloroplast genome (matK and ndhF) and one nuclear locus (ITS), sampled from 106 taxa representing 80 genera. Three additional analyses were calibrated by placing pollen fossils using geographic and morphological information (eight calibrations), macrofossils (five calibrations), and macrofossils and pollen fossils in combination (12 calibrations). The addition of new fossil pollen calibrations led to older crown ages than have previously been found for tribes such as Eucalypteae and Myrteae. Estimates of rate variation among lineages were affected by the choice of calibrations, suggesting that the use of multiple calibrations can improve estimates of rate heterogeneity among lineages. This study illustrates the potential of including pollen-based calibrations in molecular studies of divergence times.     

Of teeth and trees: A fossil tip‐dating approach to infer divergence times of extinct and extant squaliform sharks

Fossil tip‐dating allows for the inclusion of morphological data in divergence time estimates based on both extant and extinct taxa. Neoselachii have a cartilaginous skeleton, which is less prone to fossilization compared to skeletons of Osteichthyans. Therefore, the majority of the neoselachian fossil record is comprised of single teeth, which fossilize more easily. Neoselachian teeth can be found in large numbers as they are continuously replaced. Tooth morphologies are of major importance on multiple taxonomic levels for identification of shark and ray taxa. Here, we review dental morphological characters of squalomorph sharks and test these for their phylogenetic signal. Subsequently, we combine DNA sequence data (concatenated exon sequences) with dental morphological characters from 85 fossil and extant taxa to simultaneously infer the phylogeny and re‐estimate divergence times using information of 61 fossil tip‐dates as well as eight node age calibrations of squalomorph sharks. Our findings show that the phylogenetic placement of fossil taxa is mostly in accordance with their previous taxonomic allocation. An exception is the phylogenetic placement of the extinct genus ?Protospinax , which remains unclear. We conclude that the high number of fossil taxa as well as the comprehensive DNA sequence data for extant taxa may compensate for the limited number of morphological characters identifiable on teeth, serving as a backbone for reliably estimating the phylogeny of both extinct and extant taxa. In general, tip‐dating mostly estimates older node ages compared to previous studies based on calibrated molecular clocks.     

Genomic data reject the hypothesis of a prosimian primate clade

The phylogenetic position of tarsiers within the primates has been a controversial subject for over a century. Despite numerous morphological and molecular studies, there has been weak support for grouping tarsiers with either strepsirrhine primates in a prosimian clade or with anthropoids in a haplorrhine clade. Here, we take advantage of the recently released whole genome assembly of the Philippine tarsier, Tarsius syrichta, in order to infer the phylogenetic relationship of Tarsius within the order Primates. We also present estimates of divergence times within the primates. Using a 1.26 million base pair multiple sequence alignment derived from 1078 orthologous genes, we provide overwhelming statistical support for the presence of a haplorrhine clade. We also present divergence date estimates using local relaxed molecular clock methods. The estimated time of the most recent common ancestor of extant Primates ranged from 64.9 Ma to 72.6 Ma, and haplorrhines were estimated to have a most recent common ancestor between 58.9 Ma and 68.6 Ma. Examination of rates of nucleotide substitution in the three major extant primate clades show that anthropoids have a slower substitution rate than either strepsirrhines or tarsiers. Our results provide the framework on which primate morphological, reproductive, and genomic features can be reconstructed in the broader context of mammalian phylogeny.     

A new Transantarctic relationship: morphological evidence for a Rheidae–Dromaiidae–Casuariidae clade (Aves,Palaeognathae, Ratitae)

Although ratites have been studied in considerable detail, avian systematists have been unable to reach a consensus regarding their relationships. Morphological studies indicate a basal split separating Apterygidae from all other extant ratites, and a sister‐group relationship between Rheidae and Struthionidae. Molecular studies have provided evidence for the paraphyly of the Struthionidae and Rheidae, with respect to a clade of Australasian extant ratites. The position of the extinct Dinornithidae and Aepyornithidae also remains hotly debated. A novel pattern of diversification of ratites is presented herein. The phylogenetic analysis is based on 17 taxa and 129 morphological characters, including 77 new characters. The resultant tree yields a sister‐group relationship between New Zealand ratites (Apterygidae plus Dinornithidae) and all other ratites. Within this clade, the Aepyornithidae and Struthionidae are successive sister taxa to a new, strongly supported clade comprising the Rheidae, Dromaiidae, and Casuariidae. The link between South American and Australian biotas proposed here is congruent with numerous studies that have evidenced closely related taxa on opposite sides of the Southern Pacific. These repeated patterns of area relationships agree with current knowledge on Gondwana break‐up, which indicates that Australia and South America remained in contact across Antarctica until the earliest Tertiary. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 156 , 641–663.     

A combined evidence phylogenetic analysis of Anguimorpha (Reptilia: Squamata)

Anguimorpha is a clade of limbed and limbless squamates with ca. 196 extant species and a known fossil record spanning the past 130 million years. Morphology‐based and molecule‐based phylogenetic analyses disagree on several key points. The analyses differ consistently in the placements of monstersaurs (e.g. Gila Monsters), shinisaurs (Crocodile Lizards), the anguid Anniella (American Legless Lizards), carusioids (Knobby Lizards), and the major clades within Varanus (Monitor Lizards). Given different data sources with such different phylogenetic hypotheses, Anguimorpha is an excellent candidate for a combined phylogenetic analysis. We constructed a data matrix consisting of 175 fossil and extant anguimorphs, and 2281 parsimony‐informative characters (315 morphological characters and 1969 molecular characters). We analysed these data using the computer program TNT using the “new technology search” with the ratchet. Our result is novel and shows similarities with both morphological and molecular trees, but is identical to neither. We find that a global combined evidence analysis (GCA) does not recover a holophyletic Varanoidea, but omission of fossil taxa reveals cryptic molecular support for that group. We describe these results and others from global morphological analysis, extant‐only morphological analysis, molecular data‐only analyses, combined evidence analysis of extant taxa, and GCA. © The Willi Hennig Society 2010.     

Morphology, fossils, divergence timing, and the phylogenetic relationships of Gavialis

Although morphological data have historically favored a basal position for the Indian gharial (Gavialis gangeticus) within Crocodylia and a Mesozoic divergence between Gavialis and all other crocodylians, several recent molecular data sets have argued for a sister-group relationship between Gavialis and the Indonesian false gharial (Tomistoma schlegelii) and a divergence between them no earlier than the Late Tertiary. Fossils were added to a matrix of 164 discrete morphological characters and subjected to parsimony analysis. When morphology was analyzed alone, Gavialis was the sister taxon of all other extant crocodylians whether or not fossil ingroup taxa were included, and a sister-group relationship between Gavialis and Tomistoma was significantly less parsimonious. In combination with published sequence and restriction site fragment data, Gavialis was the sister taxon of all other living crocodylians, but the position of Tomistoma depended on the inclusion of fossil ingroup taxa; with or without fossils, preferred morphological and molecular topologies were not significantly different. Fossils closer to Gavialis than to Tomistoma can be recognized in the Late Cretaceous, and fossil relatives of Tomistoma are known from the basal Eocene, strongly indicating a divergence long before the Late Tertiary. Comparison of minimum divergence time from the fossil record with different measures of molecular distance indicates evolutionary rate heterogeneity within Crocodylia. Fossils strongly contradict a post-Oligocene divergence between Gavialis and any other living crocodylian, but the phylogenetic placement of Gavialis is best viewed as unresolved.     

On the phylogenetic position and systematics of extant and fossil Aclopinae (Coleoptera: Scarabaeidae)

The Aclopinae is a small subfamily within the family Scarabaeidae. It currently comprises five extant genera with 28 species, and eight fossil genera with 25 species. The systematic position of Aclopinae within the family Scarabaeidae is uncertain, particularly because representative species of Aclopinae have been absent in previous phylogenetic studies. Here we performed phylogenetic analyses using morphological and molecular data to investigate the phylogenetic position of fossil and extant Aclopinae. For this objective, we expanded and revised a former morphological data matrix (composed of 68 characters) including all extant genera of Aclopinae. We complemented our morphological investigations with a molecular phylogenetic analysis based on four genes of several extant taxa of Aclopinae and a wide sample of diverse Scarabaeoidea. Our phylogenetic analyses show that all the type species of the fossil genera formerly included within Aclopinae do not belong within the extant Aclopinae clade and support both the exclusion of those fossil taxa and the monophyly of the extant genera of Aclopinae: Aclopus Erichson, Desertaclopus Ocampo & Mondaca, Gracilaclopus Ocampo & Mondaca, Neophanaeognatha Allsopp and Phanaeognatha Hope. Our results also show that the fossil taxa Prophaenognatha robusta Bai et al. and Ceafornotensis archratiras Woolley are closely related to Ochodaeidae, while the remaining type species of fossils formerly included in Aclopinae (Cretaclopus longipes (Ponomarenko), Holcorobeus vittatus Nikritin, Juraclopus rodhendorfi Nikolajev, Mesaclopus mongolicus (Nikolajev), and Mongolrobeus zherikhini Nikolajev) belong to a distinct lineage closely related to Diphyllostomatidae. Based on these results, the subfamily Aclopinae appears monophyletic and sister to the ‘pleurostict’ lineage. Consequently, we propose the following changes to the current classification of the fossil taxa: Holcorobeus monreali (Gómez‐Pallerola) belongs to Carabidae (incertae sedis) as proposed by the original author, and we place Ceafornotensis Woolley, Cretaclopus Nikolajev, Holcorobeus Nikritin, Juraclopus Nikolajev, Mesaclopus Nikolajev, Mongolrobeus Nikolajev and Prophaenognatha Bai et al. in Scarabaeoidea (incertae sedis). Furthermore, we provide an identification key to, and diagnoses of, the genera, illustrations of diagnostic characters and checklists of their included species. The evolutionary perspective presented provides new insights into the evolution of the pleurostict condition in Scarabaeoidea and the biogeography of this group, which is now regarded as Gondwanan, probably evolving during the Cretaceous and not from the upper Jurassic as previously assumed.     

Turtle origins: insights from phylogenetic retrofitting and molecular scaffolds

Adding new taxa to morphological phylogenetic analyses without substantially revising the set of included characters is a common practice, with drawbacks (undersampling of relevant characters) and potential benefits (character selection is not biased by preconceptions over the affinities of the ‘retrofitted’ taxon). Retrofitting turtles (Testudines) and other taxa to recent reptile phylogenies consistently places turtles with anapsid‐grade parareptiles (especially Eunotosaurus and/or pareiasauromorphs), under both Bayesian and parsimony analyses. This morphological evidence for turtle–parareptile affinities appears to contradict the robust genomic evidence that extant (living) turtles are nested within diapsids as sister to extant archosaurs (birds and crocodilians). However, the morphological data are almost equally consistent with a turtle–archosaur clade: enforcing this molecular scaffold onto the morphological data does not greatly increase tree length (parsimony) or reduce likelihood (Bayesian inference). Moreover, under certain analytic conditions, Eunotosaurus groups with turtles and thus also falls within the turtle–archosaur clade. This result raises the possibility that turtles could simultaneously be most closely related to a taxon traditionally considered a parareptile (Eunotosaurus) and still have archosaurs as their closest extant sister group.