Cladistics

Recent discoveries in Asia have greatly increased our understanding of the evolution of dinosaurs' integumentary structures, revealing a previously unexpected diversity of "protofeathers" and feathers. However, all theropod dinosaurs with preserved feathers reported so far are coelurosaurs. Evidence for filaments or feathers in noncoelurosaurian theropods is circumstantial and debated.

Cladistics Cladistics F o r P e e r R e v i e w TITLE First phylogeny of predatory hoverflies (Diptera, Syrphidae, Syrphinae) using mitochondrial COI and nuclear 28S rRNA genes: conflict and congruence with the current tribal classification. AUTHORS o r P e e r R e v i e w ABSTRACT The family Syrphidae (Diptera) is traditionally divided into three subfamilies. The aim of this study was to address the monophyly of the tribes within the subfamily Syrphinae (virtually all with predaceous habits), as well as the phylogenetic placement of particular genera using molecular characters. Sequence data from the mitochondrial protein-coding gene cytochrome c oxidase subunit I (COI) and the nuclear 28S ribosomal RNA gene of ninety eight Syrphinae taxa were analysed using optimization alignment to explore phylogenetic relationships among included taxa. Volucella pellucens was used as outgroup, and representatives of the tribe Pipizini (Eristalinae), with similar larval feeding mode, were also included. Congruence of our results with current tribal classification of Syrphinae is discussed. Our results include the tribe Toxomerini resolved as monophyletic but placed in a clade with genera Ocyptamus and Eosalpingogaster. Some genera traditionally placed into Syrphini were resolved outside of this tribe, as sister groups to other tribes or genera. The tribe Bacchini was resolved into several different clades. We recovered Paragini as a monophyletic group, and sister-group of the genus Allobaccha. The present results highlight the need of a reclassification of Syrphinae.

In the present study a character data set suitable for cladistic analysis at the family level was developed. A data matrix consisting of 50 morphological characters from 15 families of tardigrades was analyzed by maximum parsimony. Kinorhynchs, loriciferans, and gastrotrichs were used as outgroups. The results agree with the currently accepted hypothesis that Eutardigrada and Heterotardigrada are distinct monophyletic groups. Among the eutardigrades, Eohypsibiidae was found to be a sister group to Macrobioti-dae+Hypsibiidae, while Milnesiidae was the basal eutardigrade family. The basal heterotardigrade family was found to be Oreellidae. Echiniscoideans grouped with some traditional Arthrotardigrada (Renaudarctidae, Coronarctidae+Batillipedidae) suggesting that the arthrotardigrades are not monophyletic. The 18S rRNA gene sequence of Batillipes mirus Richters, 1909 and Calohypsibius schusteri Nelson & McGlothlin, 1996 were obtained and their addition to a previously published dataset supports the monophyly of Heterotardigrada and of Parachela versus Apochela within the Eutardigrada.

371 Introduction 372 Morphological and molecular data 373 Methods 375 Separate analyses 375 Combined parsimony analyses 375 Combined Bayesian analyses 375 Combined likelihood analyses 376 Results 378 Separate analyses 378 Combined analyses 380 Discussion 383 Weighting morphology and molecules in parsimony and likelihood 383 Snake phylogeny and taxonomy 387

Ah.~/mcl Srvrral prominrnt cladists h a w qurstioiied thc importancc of fossils in phylogrnctic inference, and i t is becoming iiicreasingly popular to simply fit extinct forms, ifthcy are considered at all, 10 a cladogram ofReccnt taxa. ) arid Lovtrup's [ 1985 study ofamniote phylogeny rxcmplilirs this dilfrrrntial treatment, and we focuard on that group of organisms t o test the proposition that hssils c;mnot overturn a theory of'relatioiiships based only on the Recent biota. O u r parsimony analysis of amniotc phylogrny, special knowledge contributed by fossils being scrupulously avoided, led to the followiiig best fitting classification, which is similar to the novel hypothesis Gardiner published: (lcpidmaurs (turtles (mammals (birds, crocodiles)))). However, adding fossils resulted in a markedly dilfcrcnt most parsimonious cladogram or thc extant taxa: (mammals (turtles (lepidosaurs [birds, crocodilrs)))). 'l'hat classification is likr thr traditional hypothesis, and it provides a brttrr fit to the stratigraphic rrcord. '1.0 isolate thr extinct taxa rcsponsihle for the lattcr c,lassification, thr data wrrr succcssi~ely partitioned with each phylogenetic analysis, and wc coneluded that: ( 1 ) the ingroup, not the outgroup, fossils were important; (2) synapsid, not reptile, fossils wcrc pivotal; (3) certain syiiapsid fossils, not the rarliest or latrst, were responsible. 'Ihr critical nature of thr syiiapsid lossils sremcd to lir i n the particular comhinatioti of primitive arid derivrd c.haracter states they exhibited. Classifvirig those fossils, along with mammals, as the sistrr group to the lineage consisting of birds and crocodiles rrsultrd in a relatively poor fit to data; one involving a 2-4 fold increase in cvolutionary reversals! Thus, thc importance (~f t h r critic-al fossils, collectively or individually, seems to rcsidc in their rclalivc primilivcness, and the simplcst explanation for their more conservative nature is that they have had Irss timr to evolvr. While Ibssils may br important in phylogenrtic inferencr only undrr crrtain (wnditiona, thew is no comprlling rrason to prrjudge their contribution. LVc urge systrmatists to evaluate fairlv all of the available rvidencc.

The phylogenetic relationships among the penguins have received little attention, despite their well-known anatomy and the conspicuous nature of the group. Previous attempts have included datasets limited to few, mostly osteological characters, and one study was based on integumentary and breeding characters. We developed a morphological matrix comprising 159 morphological characters of osteology (70 characters), myology (15), digestive tract (1), integument (66), and breeding (7 characters), scored in 18 extant forms (all currently recognized species plus one distinct subspecies). A gaviiform was placed at the root, and 11 species of representative procellariiform groups completed the outgroup. A heuristic parsimony analysis under equal weights was performed. We also compiled DNA sequences available in GenBank for the mitochondrial genes 12S rDNA and cytochrome b. We included the two data partitions in a combined analysis under direct optimization. Both analyses recovered the monophyly of Sphenisciformes and all the traditional polytypic genera. Morphological characters performed optimally at the ordinal and generic nodes, also providing resolution and varying degrees of support at supra-and intrageneric nodes. The comparison of molecular and morphological results indicated that the most significant problem in the phylogeny of extant penguins is rooting the ingroup. The mutual interaction of molecular and morphological data decreases the ambiguity regarding the placement of the root, and provides a resolved, relatively well-supported phylogeny of extant penguins. Biogeographical patterns based on breeding ranges and derived from the combined analysis show that the major intercontinental vicariance events detected are consistent with cold marine current patterns of the Southern Hemisphere.

Phylogenetic relationships among marsupial taxa have proven to be more complex than the simple grouping of species by continent. Recent marsupials are distributed across the New World, Australia, New Guinea, and certain neighboring islands. Morphological characteristics of various groups bridge different geographical areas. We investigated the origin of these characteristics by assembling a morphological data matrix consisting of a new suite of 149 postcranial characters and incorporated a series of previously published data on the craniodental (76 characters) and soft tissue (5 characters) anatomy. Twenty-one marsupial terminal taxa representing all the major radiations of marsupials and 10 outgroups, most of which are exceptionally well-preserved fossils such as Vincelestes, Ukhaatherium, and a few basal metatherian taxa, were investigated. A maximum parsimony analysis was conducted, resulting in one most parsimonious tree. Relationships among outgroups are congruent with current understanding of mammalian phylogeny. All currently accepted marsupial orders were recovered by the analysis. We confirmed previous results showing the South American ''monito del monte'' Dromiciops nested within the Australasian radiation. Within this australidelphian clade, Dromiciops was closely allied with the Diprotodontia. The South American paucituberculates appeared more closely related to the Australidelphia than to the American Didelphimorphia. The marsupial mole Notoryctes and the Peramelia were closely allied to each other and in turn were the sister group of the Dromiciops plus Diprotodontia clade. This pattern of relationships left Dasyuromorphia as the most basal offshoot of the Australidelphia. Whereas this tree topology recovers some signal that had been detected by previous studies, morphological and/or molecular, some novel hypotheses are also supported.

Darwin offered an intriguing answer to the species problem. He doubted the existence of the species category as a real category in nature, but he did not doubt the existence of those taxa called ''species''. And despite his scepticism of the species category, Darwin continued using the word ''species''. Many have said that Darwin did not understand the nature of species. Yet his answer to the species problem is both theoretically sound and practical. On the theoretical side, DarwinÕs answer is confirmed by contemporary biology, and it offers a more satisfactory answer to the species problem than recent attempts to save the species category. On the practical side, DarwinÕs answer frees us from the search for the correct theoretical definition of ''species''. But at the same time it does not require that we banish the word ''species'' from biology as some recent sceptics of the species category advocate.

This is the first study to use both molecular and fossil data to date the divergence of taxa within the coleoid cephalopods (octopus, squid, cuttlefish). A dataset including sequences from three nuclear and three mitochondrial genes (3415 bp in total) was used to investigate the evolutionary divergences within the group. Divergence time analyses were performed using the Thorne ⁄ Kishino method of analysis which allows multiple constraints from the fossil record and permits rates of molecular evolution to vary on different branches of a phylogenetic tree. The data support a Paleozoic origin of the Orders Vampyromorpha, Octopoda and the majority of the extant higher level decapodiform taxa. These estimated divergence times are considerably older than paleontological estimates. The major lineages within the Order Octopoda were estimated to have diverged in the Mesozoic, with a radiation of many taxa around the Cretaceous ⁄ Cenozoic boundary. Higher level decapodiform phylogenetic relationships appear to have been obscured due to an ancient diversification of this group.

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Relationships among six key dictyopteran taxa (Mantodea; Blattodea (excluding Cryptocercidae); Cryptocercidae; Mastotermes darwiniensis, Termopsidae and Kalotermitidae [Isoptera]) are analysed based on seventy morphological, developmental and behavioural characters. The fossil record and the 'living fossil' genera Cryptocercus, Mastotermes and Archotermopsis are discussed in detail. Exact analysis of the character state matrix by implicit enumeration (Hennig86) resulted in one cladogram, strongly supporting Blattodea + Cryptocercidae as a sister group to Mantodea, with the Isoptera as a sister group to that complex. Arrangements within the termites are equivocal, with Termopsidae and Mastotermes darwiniensis possible as the relatively most primitive element of Isoptera.

“This book is not a dusty compendium but a virtuoso performance. It is truly outstanding on account of its comprehensive coverage of the field, the depth of its analysis, the lucidity of its presentation, and the sheer sense of fun that is conveyed by many of its pages […]. It deserves to be read by every textual scholar” (Dániel Kiss, Exemplaria Classica, 20, 2016).

“A new book came out last October that I think deserves the attention of NT text critics, especially those working on all things stemmatic […]. Written with verve but also with a thorough knowledge of the subject, it should serve beginning students and seasoned scholars admirably” (Peter J. Gurry, http://evangelicaltextualcriticism.blogspot.it/2015/6/).

“This volume is a didactic tool and at the same time a passionate and combative pamphlet; it speaks to students and colleagues at the same time and with the same stance” (Nicola Morato, French Studies, 2015).

“A scholar said that before entering into an edition, one should first read Maas and Pasquali. This is a very good idea, but I think that Trovato’s book will do perhaps equally well. There is a clear presentation of problems, illustrated by a wealth of examples, there is fairness towards those who cherish another view, bringing forward what is good in what is considered mistaken. This is scholarship on a high level” (Bengt Alexanderson, Augustinianum, 2016).



Paolo Trovato is a scholarly editor and book historian working on the field of medieval and Renaissance Italian literature. Professor of the History of the Italian language at the University of Ferrara since 1994, he was a Fellow at the Harvard Center for Italian Renaissance Studies (VIT) and at the Newberry Library, Chicago, as well as Visiting Professor in Aix-en-Provence and at the Hebrew University of Jerusalem.
His books include: Con ogni diligenza corretto. La stampa e le revisoni editoriali dei testi letterari italiani, 1470-1570 (il Mulino 1991, repr. UnifePress 2009); Storia della lingua italiana. Il primo Cinquecento (il Mulino, 1994, repr. libreriauniversitaria.it 2012); critical editions of Machiavelli’s Discorso intorno alla nostra lingua (Antenore 1982, repr. libreriauniversitaria.it. 2014) and Aretino’s Cortigiana (Salerno ed. 2009).
Since 2002 he has been leading a small team on a critical edition of Dante's Commedia.

Homology in cladistics is reviewed. The definition of important terms is explicated in historical context. Homology is not synonymous with synapomorphy: it includes symplesiomorphy, and Hennig clearly included both plesiomorphy and synapomorphy
as types of homology. Homoplasy is error, in coding, and is analogous to residual error in simple regression. If parallelism and convergence are to be distinguished, homoplasy would be evidence of the former and analogy evidence of the latter. We discuss
whether there is a difference between molecular homology and morphological homology, character state homology, nested homology (additive characters), and serial homology. We conclude by proposing a global definition of homology.

The semiaquatic bugs (Hemiptera:Heteroptera, infraorder Gerromorpha), comprising water striders and their allies, are familiar inhabitants of water surfaces in all continents. Currently, the world fauna has more than 1900 described species classified in eight families and 165 genera. A phylogenetic analysis using maximum parsimony was performed on a dataset comprising 56 morphological characters scored for 24 exemplar genera covering all families and subfamilies of Gerromorpha. The phylogenetic relationships found concur with those presented by except that the relationships between some subfamilies of Veliidae and Gerridae are unresolved. The Australian fauna of Gerromorpha comprises six families, 30 genera, and 123 species. One-third of the genera and more than 80% of the species are endemic to Australia. Previously, we have covered all Australian species of the families Gerridae, Hermatobatidae and Veliidae. The present paper deals with the families Hebridae, Hydrometridae, and Mesoveliidae. We offer redescriptions or descriptive notes on all previously described species, describe Mesovelia ebbenielseni , sp. nov. (Mesoveliidae), Austrohebrus apterus , gen. et sp. nov., and Hebrus pilosus , sp. nov. (Hebridae), and synonymise Hebrus woodwardi Lansbury, syn. nov. (Hebridae) and Hydrometra halei Hungerford and Evans, syn. nov. (Hydrometridae). We present keys for the identification of genera and species, and map the distribution of all species. We also give a key for the identification of the families of Gerromorpha known from Australia.

Echinodorus is the second largest genus in the aquatic plant family Alismataceae. The genus is naturally distributed in the New World, but many species are known world-wide as popular aquarium plants. The views upon species delimitation and infrageneric classification of the genus have been controversial. Phenotypic plasticity of aquatic plants combined with reduced and presumably convergent morphological structures pose serious problems to classification, emphasizing the need for molecular-level data. A simultaneous cladistic analysis of molecular and morphological data was conducted to resolve the phylogeny of the genus. The results showed Echinodorus (as it is currently circumscribed) to be polyphyletic. None of the currently proposed infrageneric classifications of the genus were supported in the light of phylogenetic evidence. Also, many species and subspecies level rankings were found to be unnatural. Monophyly of Echinodorus is ascertained by separating Helanthium and the monotypic genus Albidella from Echinodorus. As a result, two new combinations (Helanthium bolivianum and H. zombiense) are made, and a detailed description of the genus Helanthium is provided.

Nine decades after the discovery of the Clovis type site, Blackwater Draw Locality No. 1, we are getting closer to solving the perplexing mystery of Clovis origins. Working together, geneticists and archeologists are closing in on the ancestral Northeast Asian and Beringian homelands. We can anticipate that future archaeology will fill in the details about the emergence of Clovis lithic technology, south of the ice sheets, from its Beringian precursors. Morphometric analysis of fluted points is increasingly used to address the origins of Clovis and the "mutation" of the Clovis form into other fluted point types. Since the early 2000s, cladistics, a technique borrowed from biology, has been employed in such analyses; the results are computer-constructed cladograms that purport to illustrate pseudo-genetic phylogenies of fluted points. Here, I critically examine the utility of cladistics for addressing the issue of Clovis origins and the stylistic or functional evolution of fluted points.

“I have mentioned that my first essay on editorial methodology concerned the number of branches in family trees, and my latest concerned editing with the aid of computer programmes. On these topics and many another, Paolo Trovato’s combative and richly instructive book leaves me far behind, and it is a privilege to have the opportunity of commending it” (from M.D. Reeve’s foreword)
"It is a didactic tool and at the same time a passionate and combative pamphlet; it speaks to students and colleagues at the same time and with the same stance" (Morato, French Studies) - Available in both a print edition and an e-book, the book is distributed  by major online retailers, such as  libreriauniversitaria.it and Amazon.

In view of the progress made in recent decades in the fields of stemmatology and the analysis of geometric diagrams, the present article explores the possibility of establishing the stemma codicum of a handwritten tradition from geometric diagrams alone. This exploratory method is tested on Ibn al-Haytham’s Epistle on the Shape of the Eclipse, because this work has not yet been issued in a critical edition. Separate stemmata were constructed on the basis of the diagrams and the text, and a comparison showed no major differences. The greater reliability of a stemma codicum constructed on the basis of the diagrams rather than the text of a mathematical work is discussed and preliminary conclusions are drawn.

Most taxonomists agree on the need to adapt current classifications to recognize monophyletic units. However, delineations between higher taxonomic units can be based on the relative ages of different lineages and ⁄ or the level of morphological differentiation. In this paper, we address these issues in considering the species-rich Polyommatus section, a group of butterflies whose taxonomy has been highly controversial. We propose a taxonomy-friendly, flexible temporal scheme for higher-level classification. Using molecular data from nine markers (6666 bp) for 104 representatives of the Polyommatus section, representing all but two of the 81 described genera ⁄ subgenera and five outgroups, we obtained a complete and well resolved phylogeny for this clade. We use this to revise the systematics of the Polyommatus blues, and to define criteria that best accommodate the described genera within a phylogenetic framework. First, we normalize the concept of section (Polyommatus) and propose the use of subtribe (Polyommatina) instead. To preserve taxonomic stability and traditionally recognized taxa, we designate an age interval (4-5 Myr) instead of a fixed minimum age to define genera. The application of these criteria results in the retention of 31 genera of the 81 formally described generic names, and necessitates the description of one new genus (Rueckbeilia gen. nov.). We note that while classifications should be based on phylogenetic data, applying a rigid universal scheme is rarely feasible. Ideally, taxon age limits should be applied according to the particularities and pre-existing taxonomy of each group. We demonstrate that the concept of a morphological gap may be misleading at the genus level and can produce polyphyletic genera, and we propose that recognition of the existence of cryptic genera may be useful in taxonomy.

Despite recent progress on the higher-level relationships of Cichlidae and its Indian, Malagasy, and Greater Antillean components, conflict and uncertainty remain within the species-rich African, South American, and Middle American assemblages. Herein, we combine morphological and nucleotide characters from the mitochondrial large ribosomal subunit, cytochrome c oxidase subunit I, NADH dehydrogenase four, and cytochrome b genes and from the nuclear histone H3, recombination activating gene two, Tmo-4C4, Tmo-M27, and ribosomal S7 loci to analyse relationships within the Neotropical cichlid subfamily Cichlinae. The simultaneous analysis of 6309 characters for 90 terminals, including representatives of all major cichlid lineages and all Neotropical genera, resulted in the first well-supported and resolved generic-level phylogeny for Neotropical cichlids. The Neotropical subfamily Cichlinae was recovered as monophyletic and partitioned into seven tribes: Astronotini, Chaetobranchini, Cichlasomatini, Cichlini, Geophagini, Heroini, and Retroculini. Chaetobranchini + Geophagini (including the ''crenicichlines'') was resolved as the sister group of Heroini + Cichlasomatini (including Acaronia). The monogeneric Astronotini was recovered as the sister group of these four tribes. Finally, a clade composed of Cichlini + Retroculini was resolved as the sister group to all other cichlines. The analysis included the recently described Proterocara argentina, the oldest known cichlid fossil (Eocene), which was placed in an apical position within Geophagini, further supporting a Gondwanan origin for Cichlidae. These phylogenetic results were used as the basis for generating a monophyletic cichline taxonomy.

This review begins by setting out the context and the scope of human evolution. Several classes of evidence, morphological, molecular, and genetic, support a particularly close relationship between modern humans and the species within the genus Pan, the chimpanzee. Thus human evolution is the study of the lineage, or clade, comprising species more closely related to modern humans than to chimpanzees. Its stem species is the so-called ' common hominin ancestor ', and its only extant member is Homo sapiens. This clade contains all the species more closely-related to modern humans than to any other living primate. Until recently, these species were all subsumed into a family, Hominidae, but this group is now more usually recognised as a tribe, the Hominini. The rest of the review sets out the formal nomenclature, history of discovery, and information about the characteristic morphology, and its behavioural implications, of the species presently included in the human clade. The taxa are considered within their assigned genera, beginning with the most primitive and finishing with Homo. Within genera, species are presented in order of geological age. The entries conclude with a list of the more important items of fossil evidence, and a summary of relevant taxonomic issues.

Tool design is a cultural trait—a term long used in anthropology as a unit of transmittable information that encodes particular behavioral characteristics of individuals or groups. After they are transmitted, cultural traits serve as units of replication in that they can be modified as part of a cultural repertoire through processes such as recombination, loss, or partial alteration. Artifacts and other components of the archaeological record serve as proxies for studying the transmission (and modification) of cultural traits, provided there is analytical clarity in defining and measuring whatever it is that is being transmitted. Our interest here is in tool design, and we illustrate how to create analytical units that allow us to map tool-design space and to begin to understand how that space was used at different points in time. We first introduce the concept of fitness landscape and impose a model of cultural learning over it, then turn to four methods that are useful for the analysis of design space: paradigmatic classification, phylogenetic analysis, distance graphs, and geometric morphometrics. Each method builds on the others in logical fashion, which allows creation of testable hypotheses concerning cultural transmission and the evolutionary processes that shape it, including invention (mutation), selection, and drift. For examples, we turn to several case studies that focus on Early Paleoindian–period projectile points from eastern North America, the earliest widespread and currently recognizable remains of hunter–gatherers in late Pleistocene North America.

Middle Miocene chalicotheriine remains from France have played an important part in the palaeontological history of chalicotheres. For example, both the first known skull and first complete individual come from Sansan (MN 6, Gers, France). Nevertheless, these remains have never been described in detail until now. Firstly, cranial remains of Anisodon grande from Sansan are described. A review of nomenclatural problems supports Anisodon Lartet, 1851 as the appropriate genus name for this species and a new lectotype is designated. Secondly, the description of new remains of Chalicotherium goldfussi from Saint-Gaudens (MN 8, Haute-Garonne, France) considerably increases knowledge of this taxon. Thirdly, a skull from La Grive Saint-Alban (MN 7-8, Isère, France) is reassessed. A new cladistic analysis of the Chalicotheriinae is proposed incorporating these new data. This analysis, including 12 taxa and 51 cranio-mandibular and dental characters, supports the division of Middle and Late Miocene chalicotheriines into two clades. A novel pattern of relationships is proposed and the systematics is revised. However, chalicotheriine relationships remain labile because of the need for both a revision of pre-Middle Miocene taxa and the addition of postcranial data.

Marine file clams of family Limidae d'Orbigny, 1846 (+ Radulidae Adams & Adams), characterised by their often colourful mantle and pallial tentacles and by swimming behaviour, are commonly collected and illustrated bivalves. Based on new material from an extensive Florida Keys biodiversity survey plus museum and literature data, western Atlantic species of Lima Bruguière, 1797 (+ Mantellum Röding; Radula Mörch; Limaria Rafinesque; Austrolima Iredale; Meotolima Oyama) and Ctenoides Mörch, 1853 (+ Divaricolima Rovereto) are revised. Lima includes L. marioni Fischer, 1882 (+ L. lata Smith; lectotype selected), and L. caribaea d'Orbigny, 1842 (lectotype selected), distinguished from eastern Atlantic L. lima (Linné) and other species by shell rib number.

To elucidate the evolutionary relationships of the major lineages within the moth family Nolidae, we analysed a molecular dataset comprising eight independent gene regions (6.4 kbp), cytochrome c oxidase subunit I (COI) from the mitochondrial genome, and elongation factor-1a (EF-1a), ribosomal protein S5 (RpS5), carbamoylphosphate synthase domain protein (CAD), cytosolic malate dehydrogenase (MDH), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), isocitrate dehydrogenase (IDH) and wingless genes from the nuclear genome, using parsimony and model-based evolutionary methods (maximum likelihood and Bayesian inference). Our analyses revealed a well-resolved phylogenetic hypothesis, again recovering the six previously recognized families within Noctuoidea (i.e. Oenosandridae, Notodontidae, Euteliidae, Erebidae, Nolidae and Noctuidae), and monophyly of the quadrifid Noctuoidea (i.e. Euteliidae, Erebidae, Nolidae and Noctuidae). The family Nolidae is diagnosed and characterized by two synapomorphies from morphology: construction of a ridged boat-shaped cocoon that bears a vertical exit slit at one end; and two other morphological character states: elongation of the forewing retinaculum into a bar-like or digitate condition and possession of a postpiracular counter-tympanal hood. We present a new phylogenetic hypothesis for Nolidae consisting of eight strongly supported subfamilies, two of which are erected here: Diphtherinae, Risobinae, Collomeninae subfam. nov., Beaninae subfam. nov., Eligminae, Westermanniinae, Nolinae and Chloephorinae. Where we are able, each monophyletic lineage is diagnosed by morphological autapomorphies and within each subfamily, monophyletic tribes and subtribes are circumscribed, most of which are also diagnosable by morphological apomorphies. We also describe two new taxa: Gelastocerini trib. nov. and Etannina subtrib. nov. The Neotropical subfamily Diphtherinae, here newly circumscribed, is considered to be the plesiomorphic sister lineage to the rest of Nolidae. Diphtherinae are characterized by loss of the proximal pair of metatibial spurs in males and by the presence of a frontal tubercle, which is presumably associated with a derived strategy of emergence from the cocoon.

All diploid sexual organisms have two distinct haploid genomes, one from each parent. There is the male derived haploid genome and the female derived haploid genome. Each genome contains a distinct developmental control network that directs the development of the embryo to an adult. Run separately, independent of the influence of the other network, the each haploid genome produces a morphologically different organism. The interrelationship of the male and female haploid genome networks is governed by an interaction protocol that determines which parental network is in control in any given cell at any given point in development. The protocol consists of two interacting half-protocols, one for each parental hap-loid genome. The full interaction protocol is itself a higher-level, meta-network, or internetwork between the two lower-level, parental developmental control networks. Computer simulations show that if the interaction protocol is random then there is a loss of bilateral symmetry in the generated organism. Therefore, for all bilaterally symmetric organisms, the interaction protocol between the two parental genomes cannot be random. This implies that a nonrandom ur-protocol must have evolved with the first diploid bilaterians in the Precambrian more than 570 million years ago. Nonrandom protocols partition the embryo and adult into dynamic sections that are variably controlled by one or the other parental haploid genome network. Developmental networks and their meta-network protocols provide fundamentally new insights into embryonic and post-embryonic development, developmental pathologies, animal and plant hybrids, heterosis, and evolutionary dynamics.

We present SequenceMatrix, software that is designed to facilitate the assembly and analysis of multi-gene datasets. Genes are concatenated by dragging and dropping FASTA, NEXUS, or TNT files with aligned sequences into the program window. A multigene dataset is concatenated and displayed in a spreadsheet; each sequence is represented by a cell that provides information on sequence length, number of indels, the number of ambiguous bases (''Ns''), and the availability of codon information. Alternatively, GenBank numbers for the sequences can be displayed and exported. Matrices with hundreds of genes and taxa can be concatenated within minutes and exported in TNT, NEXUS, or PHYLIP formats, preserving both character set and codon information for TNT and NEXUS files. SequenceMatrix also creates taxon sets listing taxa with a minimum number of characters or gene fragments, which helps assess preliminary datasets. Entire taxa, whole gene fragments, or individual sequences for a particular gene and species can be excluded from export. Data matrices can be re-split into their component genes and the gene fragments can be exported as individual gene files. SequenceMatrix also includes two tools that help to identify sequences that may have been compromised through laboratory contamination or data management error. One tool lists identical or near-identical sequences within genes, while the other compares the pairwise distance pattern of one gene against the pattern for all remaining genes combined. SequenceMatrix is Java-based and compatible with the Microsoft Windows, Apple MacOS X and Linux operating systems. The software is freely available from