The relationships of the hyline tribe Dendropsophini remain poorly studied, with most published analyses dealing with few of the species groups of Dendropsophus. In order to test the monophyly of Dendropsophini, its genera, and the species groups currently recognized in Dendropsophus, we performed a total evidence phylogenetic analysis. The molecular dataset included sequences of three mitochondrial

Burmese amber and amber from other periods and regions became a rich source of new extinct insect species and yielded important insights in insect evolution in the dimension of time. Amber fossils have contributed to the understanding of the phylogeny, biology, and biogeography of insects and other groups, and have also gained great importance for dating molecular trees. Another major potential is

Within the hyperdiverse beetle family Staphylinidae, Dasycerinae is one of the smallest and most cryptic subfamilies, comprising a sole extant genus characterized by a latridiid beetle‐like body form. Little has been known about their early diversification, character evolution, phylogeny and historical biogeography because of limited fossil material and lack of a phylogeny integrating extant and extinct

In the rush to understand the coronaviruses that threaten human health, authors of many prominent papers have not performed phylogenetic analyses to the standard of the field today. Errors include faulty placement of the root of the phylogeny, outdated methods of reconstruction, poor taxon sampling, inappropriate emphasis on selected functional elements, and inadequate consideration of ambiguity. As

What are considered fundamental principles within the Willi Hennig Society and published in their journal are not always fully appreciated by many other biological fields that have not been schooled in these disciplines of systematics principles and the reasons for why these principles are important (Wenzel, Cladistics, 2020, in press). Natural history museums and their associated programs have been

Here, we publish Lepisorus sect. Paragramma (Blume) C.F. Zhao, R. Wei & X.C. Zhang as a combinatio nova to replace the section name in Zhao et al. (2020), which was published as a status nova and turned out to be an invalid name, because we cited an incorrect basionym. A revised infrageneric classification of Lepisorus also is proposed.

Freshwater mussels are a species‐rich group with biodiversity patterns strongly shaped by a life history strategy that includes an obligate parasitic larval stage. In this study, we set out to reconstruct the life history evolution and systematics in a clade of freshwater mussels adapted to parasitizing a molluscivorous host fish. Anchored hybrid enrichment and ancestral character reconstruction revealed

With the advent of high‐resolution and cost‐effective genomics and bioinformatics tools and methods contributing to a large database of both human (HAdV) and simian (SAdV) adenoviruses, a genomics‐based re‐evaluation of their taxonomy is warranted. Interest in these particular adenoviruses is growing in part due to the applications of both in gene transfer protocols, including gene therapy and vaccines

Chaetonotidae is the most diverse and widely distributed family of the order Chaetonotida (Gastrotricha) and includes both marine and freshwater species. Although the family is regarded as a sister taxon to the exclusively marine Xenotrichulidae, the type of environment, marine or freshwater, where Chaetonotidae originated is still not known. Here, we reconstructed the phylogeny of the family based

In the trapdoor spider genus Euoplos Rainbow & Pulleine (tribe Euoplini), it was discovered recently that two divergent lineages occur in sympatry in eastern Australia. This challenged the monogeneric classification of the tribe and, in combination with inadequate taxonomic descriptions of some species, precluded comprehensive taxonomic revision. To resolve these issues, we conducted a total‐evidence

The eusporangiate marattialean ferns represent an ancient radiation with a rich fossil record but limited modern diversity in the tropics. The long evolutionary history without close extant relatives has confounded studies of the phylogenetic origin, rooting and timing of marattialean ferns. Here we present new complete plastid genomes of six marattialean species and compiled a plastid genome dataset

Recent technical advances combined with novel computational approaches have promised the acceleration of our understanding of the tree of life. However, when it comes to hyperdiverse and poorly known groups of invertebrates, studies are still scarce. As published phylogenies will be rarely challenged by future taxonomists, careful attention must be paid to potential analytical bias. We present the

Antimicrobial resistance (AMR) in pathogenic strains of bacteria, such as Escherichia coli (E. coli), adversely impacts personal and public health. In this study, we examine competing hypotheses for the evolution of AMR including (i) ‘genetic capitalism’ in which genotypes that confer antibiotic resistance are gained and not often lost in lineages, and (ii) ‘stabilizing selection’ in which genotypes

We used a bi‐organellar phylogenomic approach to address higher‐order relationships in Pandanales, including the first molecular phylogenetic study of the panama‐hat family, Cyclanthaceae. Our genus‐level study of plastid and mitochondrial gene sets includes a comprehensive sampling of photosynthetic lineages across the order, and provides a framework for investigating clade ages, biogeographic hypotheses

In order to place a newly discovered species Antigracilus costatus gen. sp. n. from the Lower Cretaceous Yixian Formation (China) and to assess previously unplaced fossil taxa, we investigated the relationships of extant and extinct lineages of Histeridae based on three data sets: (i) 69 morphological characters belonging to 48 taxa (representing all 11 subfamilies and 15 of 17 tribes of modern Histeridae);

Temperate South American–Asian disjunct distributions are the most unusual in organisms, and challenging to explain. Here, we address the origin of this unusual disjunction in Lardizabalaceae using explicit models and molecular data. The family (c.40 species distributed in ten genera) also provides an opportunity to explore the historical assembly of East Asian subtropical evergreen broadleaved forests

The first two fossil species of the canthyloscelid genus Synneuron are described based on compression wings. Synneuron eomontana sp. nov. is described from the Middle Eocene Coal Creek Member of the Kishenehn Formation, in the USA, and Synneuron jelli sp. nov. is described from the Lower Cretaceous Koonwarra Fossil Bed of the Korumburra Group, in Australia. The wings are illustrated and compared to

The South American and West Indian Casque‐headed Treefrogs (Hylidae: Hylinae: Lophyohylini) include 85 species. These are notably diverse in morphology (e.g. disparate levels of cranial hyperossification) and life history (e.g. different reproductive modes, chemical defences), have a wide distribution, and occupy habitats from the tropical rainforests to semiarid scrubland. In this paper, we present

Variations of speciation and extinction rates determine the fate of clades through time. Periods of high diversification and extinction (possibly mass‐extinction events) can punctuate the evolutionary history of various clades, but they remain loosely defined for many biological groups, especially nonmarine invertebrates like insects. Here, we examine whether the cockroaches, mantises and termites

The connection between monophyly and efficient taxonomic diagnoses is elaborated. The inefficiency of nonmonophyletic groups is shown by reconstructing data matrices from hierarchical sets of diagnoses that are derived from apomorphies and read in order from highest to lowest rank. The practice of diagnosing nonmonophyletic groups either results in omitting data, resulting in errors in reconstructed

As an ancient lineage of ferns, Ophioglossaceae are evolutionarily among the most fascinating because they have the highest chromosome count of any known organism as well as the presence of sporophores, subterranean gametophytes, eusporangiate sporangia without annuli, and endophytic fungi. Previous studies have produced conflicting results, identifyingsome lineages with unresolved relationships, and

Alopoglossidae is a family of Neotropical lizards composed of 23 species allocated in two genera (Alopoglossus and Ptychoglossus). There is a lack of knowledge about the phylogenetic relationships and systematics of this family. Published phylogenies that include alopoglossid species have very low taxon coverage within the family, and are usually based on limited character sampling. Considering these

Contemporary phylogenomic studies frequently incorporate two‐step coalescent analyses wherein the first step is to infer individual‐gene trees, generally using maximum‐likelihood implemented in the popular programs PhyML or RAxML. Four concerns with this approach are that these programs only present a single fully resolved gene tree to the user despite potential for ambiguous support, insufficient

With approximately 3000 marine species, Tunicata represents the most disparate subtaxon of Chordata. Molecular phylogenetic studies support Tunicata as sister taxon to Craniota, rendering it pivotal to understanding craniate evolution. Although successively more molecular data have become available to resolve internal tunicate phylogenetic relationships, phenotypic data have not been utilized consistently

A cladistic analysis of the Tegulinae (Turbinidae) is presented using 132 morphological characters and 41 taxa. Tegulinae is recovered and is sister to Prisogaster niger (Prisogasterinae) within the family Turbinidae. This scenario, with Tegulinae as a subfamily within Turbinidae, corroborates with the most molecular analyses. Tegulinae comprises >40 extant species, belonging to eight genera. Morphological

Luminescent bacteria in the family Vibrionaceae (Bacteria: γ-Proteobacteria) are commonly found in complex, bilobed light organs of sepiolid and loliginid squids. Although morphology of these organs in both families of squid is similar, the species of bacteria that inhabit each host has yet to be verified. We utilized sequences of 16S ribosomal RNA, luciferase α-subunit (luxA) and the glyceraldehyde-3-phosphate

The ordinal level phylogeny of the Arachnida and the suprafamilial level phylogeny of the Opiliones were studied on the basis of a combined analysis of 253 morphological characters, the complete sequence of the 18S rRNA gene, and the D3 region of the 28S rRNA gene. Molecular data were collected for 63 terminal taxa. Morphological data were collected for 35 exemplar taxa of Opiliones, but groundplans

The problem of determining the minimum cost hypothetical ancestral sequences for a given cladogram is known to be NP-complete (Wang and Jiang, 1994). Traditionally, point estimations of hypothetical ancestral sequences have been used to gain heuristic, upper bounds on cladogram cost. These include procedures with such diverse approaches as non-additive optimization of multiple sequence alignment, direct

A method to align sequence data based on parsimonious synapomorphy schemes generated by direct optimization (DO; earlier termed optimization alignment) is proposed. DO directly diagnoses sequence data on cladograms without an intervening multiple-alignment step, thereby creating topology-specific, dynamic homology statements. Hence, no multiple-alignment is required to generate cladograms. Unlike general

The problem of determining the minimum-cost hypothetical ancestral sequences for a given cladogram is known to be NP-complete. This "tree alignment" problem has motivated the considerable effort placed in multiple sequence alignment procedures. Wheeler in 1996 proposed a heuristic method, direct optimization, to calculate cladogram costs without the intervention of multiple sequence alignment. This

Tremendous progress has been made at the level of sequential computation in phylogenetics. However, little attention has been paid to parallel computation. Parallel computing is particularly suited to phylogenetics because of the many ways large computational problems can be broken into parts that can be analyzed concurrently. In this paper, we investigate the scaling factors and efficiency of random

The performance of the computer program for phylogenetic analysis, POY, and its two implemented methods, "optimization alignment" and "fixed-states optimization," are explored for four data sets. Four gap costs are analyzed for every partition; some of the partitions (the 18S rRNA) are treated as a single fragment or in increasing fragments of 3, 10, and 30. Comparisons within and among methods are

Three methods of nucleotide character analysis are discussed. Their implications for molecular sequence homology and phylogenetic analysis are compared. The criterion of inter-data set congruence, both character based and topological, are applied to two data sets to elucidate and potentially discriminate among these parsimony-based ideas.

Amino acid encoding genes contain character state information that may be useful for phylogenetic analysis on at least two levels. The nucleotide sequence and the translated amino acid sequences have both been employed separately as character states for cladistic studies of various taxa, including studies of the genealogy of genes in multigene families. In essence, amino acid sequences and nucleic

The fern genus Lepisorus represents one of the most complicated and controversial lineages in Polypodiaceae, with about 80 species which have been classified into several separate genera, and is notorious for its taxonomic difficulty. Despite progress in recent phylogenetic studies of the family Polypodiaceae involving Lepisorus and its allies, the deep phylogenetic relationship within this group of

Recent disease outbreaks have raised awareness of tropical pathogens, especially mosquito‐borne viruses. Dengue virus (DENV) is a widely studied mammalian pathogen transmitted by various species of mosquito in the genus Aedes, especially Aedes aegypti and Aedes albopictus. The prevailing view of the research community is that endemic viral lineages that cause epidemics of DENV in humans have emerged

Classifications in the world's tropics often involve an early and sustained adoption of Holarctic‐based patterns. Such is the case of the megadiverse subtribe Philonthina and its Neotropical (NT) members, for which generic limits are ill‐defined due to an alleged high level of homoplasy. Although a recent total‐evidence study confirmed the monophyly of a NT lineage, most of its species are assigned

A cladistic analysis of the Tegulinae (Turbinidae) is presented using 132 morphological characters and 41 taxa. Tegulinae is recovered and is sister to Prisogaster niger (Prisogasterinae) within the family Turbinidae. This scenario, with Tegulinae as a subfamily within Turbinidae, corroborates most molecular analyses. Tegulinae comprises >40 extant species belonging to eight genera. Morphological studies

A new generic name, Rexiella, is published to replace the recently published name Rexia S. Stenroos, Pino‐Bodas and Ahti, which turned out to be an illegitimate later homonym of the cyanobacterial genus Rexia D. A. Casamatta, S. R. Gomez and J. R. Johansen.

Ronald Brady was the first philosopher to defend pattern cladistics as an independent scientific field. That independence was achieved through the decoupling of biological systematics from phylogenetics––that is, inferred evolutionary processes (e.g. character transformation). Brady saw parallels between biological systematics and Wolfgang von Goethe's Morphology, an empirical scientific field that

The thelypteroid fern genus Stegnogramma s.l. contains around 18–35 species and has a global, cross‐continental distribution ranging from tropical to temperate regions. Several genera and infrageneric sections have been recognized previously in Stegnogramma s.l., but their phylogenetic relationships are still unclear. In this study, we present a global phylogeny of Stegnogramma s.l. with the most comprehensive

As one of the four main lineages diverging from the early diversification of land plants, the phylogeny of liverworts holds the information about nearly 500 Myr of independent adaptation to changing environments. Thus, resolving the phylogenetic history of liverworts will provide unique insights into the successful diversification of early land plants in terrestrial ecosystems. However, the deep diverging

Archaeognatha (Machilida plus †Monura), with ~450 extant species worldwide, represent a key lineage for the understanding of insect evolution. In a recently published phylogenetic analysis on Archaeognatha, based on a total‐evidence approach, a Machilidae key fossil (Gigamachilis triassicus) from the Middle Triassic Lagerstätte of Monte San Giorgio and a representative of †Monura (Dasyleptus triassicus)

The infrageneric relationships and taxonomy of the largest fern genus, Asplenium (Aspleniaceae), have remained poorly understood. Previous studies have focused mainly on specific species complexes involving a few or dozens of species only, or have achieved a large taxon sampling but only one plastid marker was used. In the present study, DNA sequences from six plastid markers (atpB, rbcL, rps4, rps4‐trnS

Major geological processes have shaped biogeographical patterns of riverine biota. The Edwards Plateau of central Texas, USA, exhibits unique aquatic communities and endemism, including several species of freshwater mussels. Lampsilis bracteata (Gould, 1855) is endemic to the Edwards Plateau region; however, its phylogenetic relationship with other species in the Gulf coastal rivers and Mississippi

Climate fluctuations and tectonic reconfigurations associated with environmental changes play large roles in determining patterns of adaptation and diversification, but studies documenting how such drivers have shaped the evolutionary history and diversification dynamics of limnic organisms during the Mesozoic are scarce. Members of the heteropteran infraorder Nepomorpha, or aquatic bugs, are ideal

We present a new phylogeny of the spider family Araneidae based on five genes (28S, 18S, COI, H3 and 16S) for 158 taxa, identified and mainly sequenced by us. This includes 25 outgroups and 133 araneid ingroups representing the subfamilies Zygiellinae Simon, 1929, Nephilinae Simon, 1894, and the typical araneids, here informally named the “ARA Clade”. The araneid genera analysed here include roughly

We present the largest comparative biogeographical analysis that has complete coverage of Australia's geography (20 phytogeographical subregions), using the most complete published molecular phylogenies to date of large Australian plant clades (Acacia, Banksia and the eucalypts). Two distinct sets of areas within the Australian flora were recovered, using distributional data from the Australasian Virtual

A likelihood method that approximates the behaviour of implied weighting is described. This approach provides a likelihood perspective on several aspects of implied weighting, such as guidance for the choice of concavity values, a justification to use different concavities for different numbers of taxa, and a natural basis for extended implied weighting. In this approach, the number of free parameters

The genus Echiniscus C.A.S. Schultze, 1840, one of the earliest established and speciose tardigrade genera, has been hypothesized to be polyphyletic. Moreover, the presence or absence of trunk appendages, the type of cuticular sculpturing and body colour have been argued to hold taxonomic significance at the genus level in Echiniscus‐line taxa. Here, by combining morphological and genetic analyses

This paper reviews the ontogeny of pattern cladistics from the 1970s and 1980s, rebuts criticisms by contemporary anti‐cladists, and endeavours to clarify persistent misunderstandings about the philosophical foundations of the approach.

If a community and its substrate are raised by tectonic uplift, the species present can either die out in the area, survive in situ unchanged, or survive in situ with adaptation and differentiation. The large‐scale passive uplift of plant and animal populations during mountain‐building is accepted in a growing number of studies, but the idea has seldom been examined critically. If passive uplift does

The general problem of representing collections of trees as a single graph has led to many tree summary techniques. Many consensus approaches take sets of trees (either inferred as separate gene trees or gleaned from the posterior of a Bayesian analysis) and produce a single “best” tree. In scenarios where horizontal gene transfer or hybridization are suspected, networks may be preferred, which allow

The Calyptratae, one of the most species‐rich fly clades, only originated and diversified after the Cretaceous–Palaeogene extinction event and yet exhibit high species diversity and a diverse array of life history strategies including predation, phytophagy, saprophagy, haematophagy and parasitism. We present the first phylogenomic analysis of calyptrate relationships. The analysis is based on 40 species

The origin of the amniotic egg was a major event in vertebrate evolution and is thought to have contributed to the spectacular evolutionary radiation of amniotes. We test one of the most popular scenarios proposed by Carroll in 1970 to explain the origin of the amniotic egg using a novel method based on an asymmetric version of linear parsimony (aka Wagner parsimony) for identifying the most parsimonious

Here, we define a sequence file format that allows for multi‐character elements (FASTC). The format is derived from the FASTA format and the custom alphabet format of POY4/5. The format is more general than either of these formats and can represent a broad variety of sequence‐type data. This format should be useful for analyses involving datasets encoded as linear streams such as gene synteny, comparative

We present a novel phylogenetic approach to infer ancestral ontogenies of shape characters described as landmark configurations. The method is rooted in previously published theoretical developments to analyse landmark data in a phylogenetic context with parsimony as the optimality criterion, in this case using the minimization of differences in landmark position to define not only ancestral shapes

The Neotropical hylid genus Sphaenorhynchus includes 15 species of small, greenish treefrogs widespread in the Amazon and Orinoco basins, and in the Atlantic Forest of Brazil. Although some studies have addressed the phylogenetic relationships of the genus with other hylids using a few exemplar species, its internal relationships remain poorly understood. In order to test its monophyly and the relationships

Crocodylian systematics has long been confounded by conflicting hypotheses of higher level relationships—although molecular data sets strongly supported the sister‐taxon relationship of Tomistoma and Gavialis, morphological data sets placed Gavialis as sister to all other living taxa. One of the perceived difficulties in interpreting morphological character evolution on the molecular tree is the extensive

Since its introduction, the genus Philine has epitomized numerous mollusc snails with strong morphological convergence. Recently, a molecular analysis including a wide taxon sampling split this group into four non‐sister families. Although they are especially diverse in cold and deep waters, no comprehensive studies are available for the Antarctic counterparts. Here, our morpho‐anatomical and molecular