The Eastern Asia (EA) – North America (NA) disjunction is a well-known biogeographic pattern of the Tertiary relict flora; however, few studies have investigated the evolutionary history of this disjunction using a phylogenomic approach. Here, we used 2369 single copy nuclear genes and nearly full plastomes to reconstruct the evolutionary history of the small Tertiary relict genus Thuja, which consists

Halting biodiversity decline is one of the most critical challenges for humanity, but monitoring biodiversity is hampered by taxonomic impediments. One impediment is the large number of undescribed species (here called “dark taxon impediment”) whereas another is caused by the large number of superficial species descriptions, that can only be resolved by consulting type specimens (“superficial description

The genus Thuridilla Bergh, 1872 comprises mostly tropical sap-sucking sea slugs species with flamboyantly coloured forms. However, the potential for cryptic or pseudocryptic species masked by convergent or polymorphic colour patterns has not been tested using molecular characters. In this study, we sampled 20 of the 23 recognized worldwide species and performed the most comprehensive molecular phylogenetic

Calaphidinae is the second-largest subfamily in the family Aphididae. Despite their species diversity and some taxonomic controversy, no phylogenetic studies have been conducted on them thus far. Herein, we report the first molecular phylogeny of Calaphidinae and two related lineages, Phyllaphidinae and Saltusaphidinae, based on five genes (3418 bp) for 126 taxa. Maximum parsimony, maximum-likelihood

The systematics of Megalopodidae is not adequately known, in spite of it being a relatively small group of phytophagous beetles. The first phylogenetic analysis of Megalopodidae with a comprehensive generic representation (25 genera of 30 described, 10 subgenera and 77 species) is undertaken. A parsimony analysis under equal and implied weights was carried out based on 147 adult and larval morphological

Pollen, the microgametophyte of seed plants, has an important role in plant reproduction and, therefore, evolution. Pollen is variable in, for example, size, shape, aperture number; these features are particularly diverse in some plant taxa and can be diagnostic. In one family, Boraginaceae, the range of pollen diversity suggests the potential utility of this family as a model for integrative studies

Baripus is a ground beetle genus endemic to southern South America, currently distributed across grassland and shrub habitats in mountain and lowland regions. The species of this genus are known to have been affected by the Andean orogeny and the climate changes that occurred during this process. In this study, we seek to understand how the orogeny of the Andes may have led to changes in the climatic

Phylogenetic graph structures used in empirical and theoretical analysis have expanded beyond trees to more general directed acyclic graphs including networks and forests. Several methods to reconcile multiple such graphs are presented and discussed here, extending existing consensus and supertree techniques to form a set of phylogenetic supergraph methods. These graphs can be used as the summary of

A new troodontid (LH PV39) recovered from the Upper Cretaceous Wulansuhai Formation, Inner Mongolia, China, is described, highlighting the dorsoventrally compressed sacral centra. The completely fused neurocentral junctions indicate that LH PV39 had reached adulthood at the time of death, but its size is nevertheless 20% smaller than that of the sympatric Philovenator, demonstrating that it is the

Using Lauraceae as a study case, we aimed in this article to: (i) delimit areas of endemism in the Espinhaço Range, Brazil; (ii) compare these areas of endemism with those previously delimited, as well as with the centres of endemism; (iii) evaluate the association between areas of endemism and vegetation types; and (iv) classify the areas of endemism according to the International Code of Area Nomenclature

We analyzed patterns of complexity and simplicity in holometabolan insects using parsimony and maximum-likelihood. By contrast with other groups of arthropods (and most other groups of animals), insects have undergone a stepwise process of structural simplification in their evolution. The megadiverse Holometabola are characterized mainly by structurally simplified larvae, which differ strongly from

The hydrozoan family Cladocorynidae inhabits tropical to temperate waters and comprises the two genera Pteroclava and Cladocoryne. Pteroclava lives in association with some octocorals and hydrozoans, whereas Cladocoryne is more generalist in terms of substrate choice. This work provides a thorough morpho-molecular reassessment of the Cladocorynidae by presenting the first well-supported phylogeny of

This paper examines the implementation of parsimony methods in the programs PAUP*, MEGA and MPBoot, and compares them with TNT. PAUP* implements standard, well-tested algorithms, and flexible search strategies and options for handling trees; its main drawback is the lack of advanced search algorithms, which makes it difficult to find most parsimonious trees for large and complex datasets. In addition

We discuss here the use of TNT (Tree Analysis using New Technology) for phylogenomic analysis. For such data, parsimony is a useful alternative to model-based analyses, which frequently utilize models that make unrealistic assumptions (e.g. low heterotachy), struggle with high levels of missing data, etc. Parsimony and model-based methods often yield trees with few topological differences, which can

The distance Wagner procedure of Farris (American Naturalist, 1972, 106, 645), in its original or random addition sequence form, is a rapid method of tree construction. The original formulation did not allow for refinement of tree hypotheses via common trajectory search operations (e.g. SPR, TBR). Here, the distance Wagner method is extended to allow for refinement of initial trees produced via the

Several taxa that are distributed in the Caucasus and/or the adjacent Pontic Mountains also have representatives in the East Mediterranean region. These disjunctions could have been caused by long-distance dispersal or be the result of extinctions in Central Anatolia caused by the aridification of the Anatolian Plateau during the Pliocene. We studied the Longiphallus–Hiramia group of Oxychilus as an

The Asian potamid subfamily Potamiscinae is the most species-rich group of primary freshwater crabs in the world, and a large number of these (318 species in 52 genera) are found in China where they exhibit a remarkably high rate of endemism. However, the evolutionary history and phylogenetic relationships of this subfamily is still poorly understood and the hypothesis that the Chinese potamids originated

“Candidatus Sulcia muelleri” (Sulcia) is a diverse lineage of intracellular nutritional endosymbiotic bacteria strictly associated with auchenorrhynchous hemipteran insects. Sulcia has undergone long-term codiversification with its insect hosts but the phylogeny of these endosymbionts, their relationships to other bacteria, and the extent of their occurrence within various groups of Auchenorrhyncha

Biodiversity exchanges across the Malesian region, linking the distinct biotas of Asia and Australia, have long attracted the curiosity of biologists. Tetrastigma (Vitaceae) has a wide distribution in Asia through the Sunda archipelago to Australia and provides a good case to elucidate floristic exchange between Asia and Australia. Tetrastigma species have fleshy fruits that are consumed by birds,

We recently published a method to infer ancestral landmark-based shape ontogenies that takes into account the possible existence of changes in developmental timing. Here we describe SPASOS, a software to perform that analysis. SPASOS is an open-source Windows program written in C. Input data include landmark coordinates for each specimen –with the corresponding information about developmental timing–

Several extinct species are known from the family Lacertidae, but due to poor preservation, many of them are based on single bones. Here, we compare phylogenetic signals of disarticulated premaxillae, maxillae and dentaries of lacertids from four French Oligocene localities (Coderet, La Colombière, Roqueprune 2, Mas de Got B). We identified five morphotypes among the premaxillae, six among the maxillae

The polygrammoids (Polypodiaceae) are the most species‐rich and diversified epiphytic fern lineages, and hold an important role to understand the deep diverging events and rapid adaptation to changing environments in the plant tree of life. Despite progress in the phylogeny of this group of ferns in previous multilocus phylogenetic studies, uncertainty remains especially in backbone relationships among

Pericopina is divided into 36 genera, with the greatest diversity recorded in the Neotropics. Studies on the taxonomy and systematics of pericopines are scarce, and one of the few phylogenetic hypotheses available in the literature places some Afro‐Indo‐Malayan lineages among the Neotropical representatives. Through a survey of adult morphological characters, we analyzed the phylogenetic relationships

The severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in humans in 2002. Despite reports showing Chiroptera as the original animal reservoir of SARS-CoV, many argue that Carnivora-hosted viruses are the most likely origin. The emergence of the Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012 also involves Chiroptera-hosted lineages. However, factors such as the lack of

Comprising about 82% of the extant fern species diversity, Polypodiales are generally believed to have diversified in the Late Cretaceous. We estimated the divergence times of Polypodiales using both penalized likelihood and Bayesian methods, based on a dataset consisting of 208 plastomes representing all 28 families and 14 fossil constraints reflecting current interpretations of fossil record. Our

Evidence for phylogenetic analysis comes in the form of observed similarities, and trees are selected to minimize the number of similarities that cannot be accounted for by homology (homoplasies). Thus, the classical argument for parsimony directly links homoplasy with explanatory power. When characters are hierarchically related, a first character may represent a primary structure such as tail absence/presence

The explosion of research on COVID-19 has resulted in an unprecedented pace of publication. Science magazine states that there were more than 23 000 papers published between January and May, 2020, and 4000 papers published in one week in May (https://www.sciencemag.org/news/2020/05/scientists-are-drowning-covid-19-papers-can-new-tools-keep-them-afloat). Retractionwatch has given COVID-19 literature

Species distribution patterns are constrained by historical and ecological processes in space and time, but very often the species range sizes are geographical sampling biases resulting from unequal sampling effort. One of the most common definitions of endemism is based on the “congruence of distributional areas” criterion, when two or more species have the same distributional limits. By acknowledging

The most ventral muscles of the head (the mm. submentalis, intermandibularis, and interhyoideus) provide support to the gular region and lift the buccal floor during ventilation and feeding. These muscles show limited variation in most gnathostomes, but in Anura they exhibit a surprising diversity. The few studies that have explored this character system highlighted its potential as a source of phylogenetic

A new phylogenetic comparative method called DUALCOR is presented to evaluate the evolutionary response of a character to non-evolving external factors, such as environmental variables. The method treats the character as a typical evolving feature of an organism that is reconstructed on a given tree, whereas the external factor is treated as unrelated to the phylogeny. DUALCOR first calculates the

The Sarcophagidae (flesh flies) comprise a large and widely distributed radiation within the Calyptratae (Diptera). Larval feeding habits are ecologically diverse and include sarcosaprophagy, coprophagy, herbivory, invertebrate and vertebrate predation, and kleptoparasitism. To elucidate the geographic origin and evolution of flesh fly life-history, we inferred a backbone phylogeny based on transcriptomic

Asian forest scorpions (Scorpionidae Latreille, 1802: Heterometrinae Simon, 1879) are distributed across South and Southeast Asia. All are fossorial, constructing burrows under stones or in open ground, in habitats differing in precipitation and vegetation cover, from rainforests and tropical deciduous forests to savanna and scrubland. The systematics of these scorpions has long been confused due to

Neotropical swarm-founding wasps are divided into 19 genera in the tribe Epiponini (Vespidae, Polistinae). They display extensive variation in several colony-level traits that make them an attractive model system for reconstructing the evolution of social phenotypes, including caste dimorphism and nest architecture. Epiponini has been upheld as a solid monophyletic group in most phylogenetic analyses

We analyzed 769 242 occurrence records for 115 424 species of terrestrial arthropods, from three biodiversity repositories (Global Biodiversity Information Facility (GBIF), Natural History Museum, London, and “Sistema de Informação Distribuído para Coleções Biológicas” (SpeciesLink)), to test the use of global-scale data points for quantitative assessments of areas of endemism. The data include Insecta

Phylogenetic studies of Aleocharinae rove beetles, arguably one of the least known and the largest insect lineages, are compromised by its enormous taxonomic diversity. DNA, a powerful resource for phylogenetics, is not available for numerous extant aleocharine species. We provide a broad comparative morphological study of Aleocharinae to frame molecular datasets for total-evidence analyses. Using

We study the phylogenetic relationships of egg-brooding frogs, a group of 118 neotropical species, unique among anurans by having embryos with large bell-shaped gills and females carrying their eggs on the dorsum, exposed or inside a pouch. We assembled a total evidence dataset of published and newly generated data containing 51 phenotypic characters and DNA sequences of 20 loci for 143 hemiphractids

Brazil has high levels of biodiversity and has received strong criticism for the increasing country-wide deforestation that threatens it. Although a significant percentage of land area in Brazil is protected, the areas are insufficient and unevenly distributed. Many studies have contributed to the biogeographical knowledge of Brazilian flora, but no endemicity analysis (EA) has been conducted including

Despite many attempts in the Sanger sequencing era, the phylogeny of fig trees remains unresolved, which limits our ability to analyze the evolution of key traits that may have contributed to their evolutionary and ecological success. We used restriction-site-associated DNA sequencing (c. 420 kb) and 102 morphological characters to elucidate the relationships between 70 species of Ficus. To increase

Bombyliidae is a very species-rich and widespread family of parasitoid flies with more than 250 genera classified into 17 extant subfamilies. However, little is known about their evolutionary history or how their present-day diversity was shaped. Transcriptomes of 15 species and anchored hybrid enrichment (AHE) sequence captures of 86 species, representing 94 bee fly species and 14 subfamilies, were

In recent years, the use of extensive molecular and morphological datasets has clarified the phylogenetic relationships among the orders of complex thalloid liverworts (Marchantiidae). However, previous studies excluded extinct taxa; thereby, undersampling the actual taxonomic diversity of the group. Here, we conducted a total-evidence analysis of Marchantiidae incorporating fossils. The combined dataset

Phylogenetic analyses based on molecular and morphological data were conducted to shed light on relationships within the mostly Palaearctic/Oriental centipede family Lithobiidae, with a particular focus on the Palaearctic genus Lithobius Leach, 1814 (Lithobiidae, Lithobiomorpha), which contains >500 species and subspecies. Previous studies based on morphological data resolved Lithobius as nonmonophyletic

Currently comprising only about 430 species, Dipsocoromorpha or minute litter bugs are one of the small infraorders of Heteroptera. They are classified into five morphologically distinct families––Ceratocombidae, Dipsocoridae, Hypsipterygidae, Schizopteridae and Stemmocryptidae––but relationships among and within these families are poorly understood owing to the lack of phylogenetic studies. A phylogenetic

The Geomitrini is the most species‐rich group of land snails in the Madeiran Archipelago. The phylogeny of the group is reconstructed based on mitochondrial and nuclear genetic markers. The timing of diversification, the colonisation history of the islands of the Madeiran Archipelago and the evolution of characters of the dart apparatus are studied. The results of the phylogenetic analyses confirm

Direct optimization of unaligned sequence characters provides a natural framework to explore the sensitivity of phylogenetic hypotheses to variation in analytical parameters. Phenotypic data, when combined into such analyses, are typically analyzed with static homology correspondences unlike the dynamic homology sequence data. Static homology characters may be expected to constrain the direct optimization

High throughput sequencing and phylogenomic analyses focusing on relationships among spiders have both reinforced and upturned long-standing hypotheses. Likewise, the evolution of spider webs—perhaps their most emblematic attribute—is being understood in new ways. With a matrix including 272 spider species and close arachnid relatives, we analyze and evaluate the relationships among these lineages

We report on the colonization and diversification of linyphiid spiders in the Pacific oceanic archipelago of Juan Fernandez. About 50 spider species occur naturally in these islands, most of them endemic and about half of them are linyphiids. Linyphiidae includes no fewer than 15 species of Laminacauda and three of Neomaso (with several additional undescribed species in the latter genus), all of them

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

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

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

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

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

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

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);

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