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Nitzschia soratensis and N. inconspicua are two small diatoms that are extremely similar in the light microscope though separable in subtle aspects of valve and girdle ultrastructure. They are not closely related in molecular phylogenies and differ in their ecological preferences, though they sometimes co-occur in the same communities. To test further their functional equivalence, we investigated the reproductive biology of N. soratensis, for comparison with a previously published account of N. inconspicua. Both species are automictic, lacking pairing between gametangia and gamete exchange. Nuclear staining shows the presence of two nuclei in some auxospores of N. soratensis, which are smaller than the nuclei of vegetative cells and appear to be haploid, indicating prior meiosis. These auxospores, surrounded by incunabula containing tangles of silica strips, give rise to uninucleate initial cells 18–21 µm long. Frequently, however, small N. soratensis cells produce two spherical 'pseudogametes', some of which abort while others expand and form initial valves shorter than those produced by binucleate auxospores (maximum length 14.5 µm). Similar uniparental auxosporulation, with silica strip formation, occurs in N. aff. hantzschiana, N. acidoclinata, N. fonticola and N. angustata, which are close relatives of N. soratensis according to morphological and/or molecular evidence. This group and the N. inconspicua complex may be the diatom equivalents of apomictic angiosperms, e.g. dandelions, and likely contain a multitude of microspecies. [ABSTRACT FROM AUTHOR]

Ophiocordyceps sinensis is a famous traditional Chinese medicine adapted to the alpine environment of the Qinghai-Tibet Plateau and adjacent regions. Clarification of the species diversity of Ophiocordyceps sinensis and its relatives could expand the traditional medicinal resources and provide insights into the speciation and adaptation. The study is prompted by the discovery of a new species, O. megala, described here from a biodiversity hotspot in the Hengduan Mountains, China. Combined morphological, ecological, and phylogenetic evidence supports its distinctiveness from O. sinensis, O. xuefengensis, and O. macroacicularis. Additionally, based on the phylogenetic construction of Ophiocordyceps, a special clade was focused phylogenetically on the more closely related O. sinensis complex, which was defined as the O. sinensis- species complex lineage. A total of 10 species were currently confirmed in this lineage. We made a comprehensive comparison of the sexual/asexual morphological structures among this species complex, distinguishing their common and distinctive features. Furthermore, using the method of species distribution modelling, we studied the species ocurrences in relation to climatic, edaphic, and altitudinal variables for the eight species in the O. sinensis-species complex, and determined that their potential distribution could extend from the southeastern Qinghai-Tibet Plateau to the Xuefeng Mountains without isolating barrier. Thus, the biodiversity corridor hypothesis was proposed around the O. sinensis-species complex. Our study highlights the phylogeny, species diversity, and suitable distribution of the O. sinensis-species complex lineage, which should have a positive implication for the resource discovery and adaptive evolution of this unique and valuable group. [ABSTRACT FROM AUTHOR]

This document explores the taxonomic status of the butterfly species Amathuxidia morishitai found in Hainan, China. The study utilizes various methods, including external characteristics and genital structures, to determine the relationship between A. morishitai and Amathuxidia amythaon. The findings suggest that A. morishitai should be considered a subspecies of A. amythaon, and the study identifies two subspecies groups within A. amythaon. The document acknowledges the need for further research, particularly regarding the female of A. morishitai. The study was conducted with proper authorization and highlights the legal protection of the rare butterfly in China. [Extracted from the article]

The article assess the genetic diversity of Typhlodromus bagdasarjani, a predatory mite belonging to the Phytoseiidae family, based on molecular markers. It aims to understand the population variations of this mite species in different climate zones within Iran. It is reported that Typhlodromus bagdasarjani is known for its role as a generalist predator, feeding on various pests in orchards, making it an essential contributor to biological pest control.

Previous phylogenetic analyses indicated that Polygonoideae, the largest subfamily in the Polygonaceae, is monophyletic. Phylogenetic relationships within the Polygonoideae have been substantially controversial. We collected 160 samples representing all currently recognized tribes for a more comprehensive phylogenetic analysis of the subfamily. Here, we reconstructed phylogenetic relationships of the Polygonoideae, inferred ancestral character states, and estimated the divergence time with a dense taxon sampling. This study corroborated and expanded previous results regarding the phylogenetic relationships of the Polygonoideae clade, and resolved the phylogenetic status of some controversial taxa by integrating molecular and morphological evidence. Phylogenetic analyses based on the complete plastomes suggested strong support for six primary clades that correspond to the most recent circumscription of tribes: Polygoneae, Rumiceae, Calligoneae, Pteroxygoneae, Fagopyreae, and Persicarieae. In addition, we provided further morphological data and assessed characters that supported different clades. The 3‐colpate pollen, 5‐parted perianth, and 3 styles were inferred to be the ancestral states of Polygonoideae. Divergence time estimation revealed that Polygonoideae originated around the late Cretaceous, and diversification was concentrated in the Eocene and Miocene. Time estimation indicated that the rapid uplift of the Tibetan Plateau and the intensification of the Asian monsoons might be potential driving forces for the diversification of Polygonoideae. Overall, this study advances our understanding of the phylogeny and diversification of the Polygonoideae and highlights the adaptive evolution of the taxa. [ABSTRACT FROM AUTHOR]

The extant marine mussels which belong to the Mytiloidea are widespread species inhabiting mostly coastal waters, with some distributed in the deep sea. To clarify the classification systems and phylogenetic relationships range from genus to family level within Mytiloidea, new sequence was used in a phylogenetic analysis including all the available Mytiloidea mitochondrial genomes. In this study, the complete mitochondrial genome of Vignadula atrata is 15,624 bp in length and contains 12 protein-coding genes (PCGs, atp8 is absent), two ribosomal RNA genes, and 22 transfer RNA genes. Phylogenetic analysis based on 12 PCGs showed that it has a close relationship to Bathymodiolus. The analysis of gene rearrangements in the Pteriomorphia showed that the arrangements are highly variable across species, novel gene rearrangements were found within Mytiloidea. The V. atrata mitogenome was provided in detail, with notes on the sequence and a key to the species of Vignadula. This study provides a perspective on the taxonomic histories of the marine mussels and refines the unclear relationship between the origin and evolution of species in Mytiloidea within Bivalvia. [ABSTRACT FROM AUTHOR]

Gene trees and species trees: Molecular systematics as one-character taxonomy. Comprehensive taxon sampling, congruent data, gene trees, incomplete lineage sorting, plant molecular systematics, plant taxonomy, species trees, phylogenomic analysis Keywords: comprehensive taxon sampling; congruent data; gene trees; incomplete lineage sorting; phylogenomic analysis; plant molecular systematics; plant taxonomy; species trees EN comprehensive taxon sampling congruent data gene trees incomplete lineage sorting phylogenomic analysis plant molecular systematics plant taxonomy species trees 1 4 4 08/31/23 20230801 NES 230801 In the process of compiling a flora for Montana (Lesica, [21], [21]), we came to realize that many published nomenclatural changes are only weakly supported by the data presented which has often been based on recent findings in the field of molecular evolution. Taxonomists and non-taxonomic botanists should also realize that another source of discordance between gene trees and species trees is transfer of mitochondria or chloroplasts across species boundaries. [Extracted from the article]

Aedes aegypti (L., 1762) (Diptera: Culicidae) is an important pest for human health. It vectors many diseases, including yellow fever (YF), dengue (DENV), and chikungunya (CHIKV). This species has invaded numerous countries including Balkan and Caucasian countries few past decades. The established populations of species were found in Turkey in 2015. We investigated the genetic variation, molecular phylogenetics, and differences between samples from Turkey and Georgia using four mitochondrial and one genomic DNA markers. The possible origin of the species was determined separately for each gene region using maximum likelihood trees. The ML analysis showed a close relation with the Caucasian samples, and some haplotypes are specific to this region. Our results suggest that Turkish Ae. aegypti strains might have been a mix of Asian and American strains. The differences between Turkish and Georgian samples were statistically insignificant and values of difference were very low according to AMOVA. Pairwise difference values between the two countries indicated that populations may have the same origin and variation value between two countries is very low. As a conclusion, our results revealed that our region (Turkey and Georgia) samples were most probably a new invasion rather than an ancient one. [ABSTRACT FROM AUTHOR]

We newly sequenced complete mitochondrial genomes (mitogenome) of two gudgeon species Saurogobio dabryi and S. punctatus, and we downloaded 49 gudgeon mitogenomes from GenBank to investigate the phylogeny of the Pseudogobionini group and analyze selection pressure of the genes. With genera Gobio, Acanthogobio, and Romanogobio as outgroups, the phylogeny of the Pseudogobionini group was revealed as ((Xenophysogobio + Gobiobotia) + (Saurogobio + (Abbottina + (Pseudogobio + Biwia complex)))) based on the concatenated nucleotide sequences of 13 protein-coding genes (PCGs). Based on the molecular phylogeny and morphological or osteological characters, we proposed a classification system of the Pseudogobionini group. Moreover, five pairs of sister taxa were selected for gene selection pressure analyses to explore the link of mitochondrial gene evolution to group differentiation and adaptations. We detected significantly different dN/dS values in 11 out of 13 (excluding ND3 and ND4L) PCGs in five pairs of clades, significantly different mean dN/dS, dN, and/or dS values in 8 out of 13 PCGs (excluding ND2, ATP8, ND3, ND4L, and ND6) in three pairs of sub-clades and seven positively selected sites in another three pairs of sub-clades. These results indicated that mitochondrial gene evolution might have contributed to group differentiation and adaptations especially for river or lake environments. [ABSTRACT FROM AUTHOR]

The discovery of the Aleurocanthus cf. Aleurocanthus spiniferus (Tea spiny whitefly spiniferus morphotype; previously found in Tokyo) for the first time in Shizuoka Prefecture raised the possibility that this species had invaded Honshu Island, Japan. Unlike the allied species, Aleurocanthus spiniferus and A. camelliae, which have been intercepted from China to Japan, the origin of the current species remains unclear. Despite the status of this species as a minor pest on the ornamental plant, Eurya japonica, the cryptic diversity among the black spiny whitefly is fascinating to be elucidated, specifically how the primary endosymbiont of whiteflies, Portiera aleyrodidarum, coevolved and contributed to the classification of whiteflies. The current study examines the taxonomic status of five species of whiteflies, i.e., A. spiniferus (Quaintance), Aleurocanthus aff. A. camelliae, Aleurocanthus cf. A. spiniferus, A. camelliae Kanmiya and Kasai, Aleurotrachelus camelliae Kuwana, and A. ishigakiensis Takahashi. Using consortium molecular typing targeting mitochondrial DNA (COI and 16S of mitoribosome), the nuclear gene (ITS1), and the ribosomal gene of Portiera, the phylogenetic clustering analysis has been conducted and revealed that the genus Aleurotrachelus sensu lato was clustered together with Aleurocanthini Takahashi, 1954 stat. rev. and reinstated Crenidorsum ishigakiensis comb. nov. due to crescent-shaped scallops being clearly defined. The current study also unveiled several putative species in the A. spiniferus species complex, molecularly. In addition, the recombination event was not detected in Portiera but has been detected in the mtCOI genes of the A. spiniferus cryptic species and the A. woglumi sequences deposited in the NCBI database. The mitochondrial recombination gives an insight into the speciation process among this species complex. [ABSTRACT FROM AUTHOR]

The mitochondrial (mt) genome is an important tool when studying the evolution of metazoan animals. The oyster family Gryphaeidae, together with Ostreidae, is one of the two extant taxa of superfamily Ostreoidea. Up until now, the available mitochondrial genomes of oysters were all limited to family Ostreidae. In the present study, the first complete mtDNA of family Gryphaeidae represented by Hyotissa hyotis was sequenced and compared with other available ostreoid mtDNA. The mtDNA of H. hyotis is 22,185 bp in length, encoding 13 protein-coding-genes (PCGs), two ribosomal RNA (rRNA) and 23 transfer RNA (tRNA) genes. Within all the intergenic regions that range from 2 to 1528 bp, two large non-coding regions were identified. The first large non-coding region, located between Cox1 and trnA, contains 1528 nucleotides, while the second one is 1191 bp in length and positioned between Cytb and Nad2. The nucleotide composition of the whole mtDNA is A + T biased, accounting for 59.2%, with a negative AT skew value of −0.20 and a positive GC skew value of 0.33. In contrast to the mtDNA of Ostreidae, neither the split of rrnL nor rrnS was detected in that of H. hyotis. The duplication of trnW of H. hyotis was also discovered for the first time within Ostreoidea. The gene order of H. hyotis is quite different from those of ostreids, indicating extensive rearrangements within superfamily Ostreoidea. The reconstructed phylogeny supported H. hyotis as sister to Ostreidae, with the latter clade formed by Ostrea + (Saccostrea + Crassostrea). This study could provide important information for further understanding the mitochondrial evolution of oysters. [ABSTRACT FROM AUTHOR]

The emergence and subsequent evolution of pectoral fins is a key point in vertebrate evolution, as pectoral fins are dominant control surfaces for locomotion in extant fishes. 1,2,3 However, major gaps remain in our understanding of the diversity and evolution of pectoral fins among cartilaginous fishes (Chondrichthyes), a group with an evolutionary history spanning over 400 million years with current selachians (modern sharks) appearing about 200 million years ago. 4,5,6 Modern sharks are a charismatic group of vertebrates often thought to be predators roaming the open ocean and coastal areas, but most extant species occupy the seafloor. 4 Here we use an integrative approach to understand what facilitated the expansion to the pelagic realm and what morphological changes accompanied this shift. On the basis of comparative analyses in the framework of a time-calibrated molecular phylogeny, 7 we show that modern sharks expanded to the pelagic realm no later than the Early Cretaceous (Barremian). The pattern of pectoral fin aspect ratios across selachians is congruent with adaptive evolution, and we identify an increase of the subclade disparity of aspect ratio at a time when sea surface temperatures were at their highest. 8 The expansion to open ocean habitats likely involved extended bouts of sustained fast swimming, which led to the selection for efficient movement via higher aspect ratio pectoral fins. Swimming performance was likely enhanced in pelagic sharks during this time due to the elevated temperatures in the sea, highlighting that shark evolution has been greatly impacted by climate change. • Modern sharks were likely benthic or benthopelagic in origin • Sharks have independently expanded to the pelagic zone several times • Pectoral fin shape shows signatures of adaptive evolution • Sea surface temperature impacts shark evolution Sternes et al. use an integrative approach to show that sharks first expanded to the pelagic zone during the Cretaceous, linked with adaptive evolution of their pectoral fin shape. The mid-Cretaceous, a time with very high sea surface temperatures, emerges as a critical phase in shark evolution. [ABSTRACT FROM AUTHOR]

Situated at the junction of three continents, Europe, Asia and Africa, the Eastern Mediterranean is an ideal region to study the effects of palaeogeography, ecology and long human presence on animal evolution. Laudakia stellio (Squamata: Agamidae) is found across this region and offers an excellent opportunity for such studies. The high morphological variation across their range suggests that these lizards might represent a species complex. This is the first study exploring their evolutionary history, using molecular markers and individuals from all described subspecies. We employed the latest phylogenetic and species-delimitation methods to identify all distinct evolutionary lineages, their genetic variation and divergence times. The phenotypical diversity of L. stellio matches its genetic differentiation: almost all subspecies correspond to well-supported retrieved subclades and additional distinct lineages representing intermediate morphs have been retrieved. ' Laudakia stellio ' represents three distinct evolutionary entities that diverged during the Plio-Pleistocene transition, which we propose as distinct species. One includes Greek and Turkish populations, as well as cryptic Anatolian lineages. The second comprises all other Near East populations and the third is endemic to Cyprus. Our results indicate a role of humans in shaping present distribution patterns, and highlight the importance of the Aegean, Anatolia and the Levant as glacial refugia and diversity hotspots. [ABSTRACT FROM AUTHOR]

The distinction of the annual Sagina apetala and S. micropetala (= S. apetala subsp. erecta, S. filicaulis) is based mainly on the position of sepals in fruit and shape and colour of the sepals, but identification of the two species is difficult. A molecular phylogeny of material identified as S. apetala and S. micropetala as well as other species of the genus using two nuclear and two plastid markers showed that there exist two lineages that are sister to each other and can be unambiguously distinguished molecularly. Although many of the morphological characters used in the literature proved useful in distinguishing these two lineages, sepal indumentum is the most reliable character to discriminate between them in Germany. Whereas S. micropetala usually has glabrous sepals, the sepals of S. apetala usually are glandular-pubescent. The chromosome number of 2n = 12 for S. micropetala, here determined for the first time, is identical to that of S. apetala, supporting the close relationship between the two species. Sagina apetala and S. micropetala are sister to S. maritima, an annual species from European coasts, which may imply a coastal origin of the two species. A brief review of the possible origin of other European ruderals from coastal relatives is provided. [ABSTRACT FROM AUTHOR]

• Three diploid-containing sections of Enkianthus (Meisteria, Andromedina and Enkianthus) are monophyletic groups. • Sect. Enkiantella in China likely arose from allopolyploidy, their diploid progenitors may be members of sect. Meisteria and sect. Andromedina. • E. tubulatus may be a diploid species of hybrid origin. Enkianthus is a small genus of Ericaceae mostly in east Asia, most constituent species with important ornamental and ecological values. Due to limited sampling of Chinese species and neglect of the origin of polyploid species in previous studies, phylogenetic relationships within this genus remain elusive. Using six chloroplast DNA fragments (psb A- trn H, rpl 32- trn L, trn L- trn F, rps 16- trn Q, psb J- pet A and mat K), nuclear ribosomal internal transcribed spacer (nrITS) and one single-copy nuclear gene (OG9899), we reconstructed the phylogenetic relationships of most Enkianthus species, with a special attempt to decipher the origin of polyploids within the genus. The phylogenetic trees excluding polyploid species indicated that the sections of Meisteria, Andromedina and Enkianthus were all monophyletic groups, with sect. Enkianthus first branching out. The position of E. tubulatus was in conflict between cpDNA and nuclear gene trees, indicating that this species could be of hybrid origin. After the inclusion of polyploid species, we found that members of sect. Enkiantella clustered either with sect. Meisteria or with sect. Andromedina in nuclear gene trees , suggesting this section might be derived from allopolyploidy. The close affinity of sect. Enkiantella with sect. Meisteria in cpDNA tree implies that the members of sect. Meisteria might be the maternal progenitor of sect. Enkiantella. In addition, the octoploid species E. campanulatus might be either an autopolyploid or an allopolyploid with one of its progenitors originating from sect. Meisteria. Our findings provide a robust phylogenetic framework for the evolutionary study and the utility of germplasm resources of Enkianthus. The results of this study will also be helpful for the breeding of Enkianthus cultivars. [ABSTRACT FROM AUTHOR]

The evolution of nervous systems in animals has always fascinated biologists, and thus multiple evolutionary scenarios have been proposed to explain the appearance of neurons and complex neuronal centers. However, the absence of a robust phylogenetic framework for animal interrelationships, the lack of a mechanistic understanding of development, and a recapitulative view of animal ontogeny have traditionally limited these scenarios. Only recently, the integration of advanced molecular and morphological studies in a broad range of animals has allowed to trace the evolution of developmental and neuronal characters on a better-resolved animal phylogeny. This has falsified most traditional scenarios for nervous system evolution, paving the way for the emergence of new testable hypotheses. Here we summarize recent progress in studies of nervous system development in major animal lineages and formulate some of the arising questions. In particular, we focus on how lineage analyses of nervous system development and a comparative study of the expression of neural-related genes has influenced our understanding of the evolution of an elaborated central nervous system in Bilateria. We argue that a phylogeny-guided study of neural development combining thorough descriptive and functional analyses is key to establish more robust scenarios for the origin and evolution of animal nervous systems. • New trees and improved taxon sampling reject traditional views of neural evolution. • It is uncertain whether a nervous system evolved once or twice in animals. • Xenacoelomorpha sister to Nephrozoa supports a nerve net ancestral to Bilateria. • Nervous system development became restricted to the ectoderm in Bilateria. • AP and DV molecular arrangements were secondarily coopted into neural patterning. [ABSTRACT FROM AUTHOR]

Penicillium is one of the most important postharvest pathogens of citrus fruits worldwide. It induces blue or green mold disease, a decay that can lead to significant economic losses during storage. Based on internal transcribed spacer (ITS) sequences, seven Penicillium species and one closely related Talaromyces variabilis were identified from 30 rotten samples of citrus fruits marketed in Qena. Penicillium expansum was the most common species, recovered from 16.7% of the samples, followed by P. chrysogenum (10%) and P. polonicum (10%). Sixteen isolates were tested through inoculation on healthy citrus fruits; the data exhibited that 68.7% of isolates were highly virulent. A "Specific Gene Random Primer Polymerase Chain Reaction (SGRP-PCR)" marker technique indicated that the genetic similarity among P. expasum ranged from 49.4 to 85.7%, and a relatively correlation was found between SGRP band profile and species origin. Patulin was detected in 40% of P. expansum isolates. This study provided a useful molecular approach to identify different Penicillium species by sequencing ITS region, focus on the pathogenicity, compare between P. expansum isolates and their ability in patulin production. [ABSTRACT FROM AUTHOR]

There are considerable phylogenetic incongruencies between morphological and phylogenomic data for the deep evolution of animals. This has contributed to a heated debate over the earliest-branching lineage of the animal kingdom: the sister to all other Metazoa (SOM). Here, we use published phylogenomic data sets (⁠|$\sim $| 45,000–400,000 characters in size with |$\sim $| 15–100 taxa) that focus on early metazoan phylogeny to evaluate the impact of incorporating morphological data sets (⁠|$\sim $| 15–275 characters). We additionally use small exemplar data sets to quantify how increased taxon sampling can help stabilize phylogenetic inferences. We apply a plethora of common methods, that is, likelihood models and their "equivalent" under parsimony: character weighting schemes. Our results are at odds with the typical view of phylogenomics, that is, that genomic-scale data sets will swamp out inferences from morphological data. Instead, weighting morphological data 2–10 |$\times $| in both likelihood and parsimony can in some cases "flip" which phylum is inferred to be the SOM. This typically results in the molecular hypothesis of Ctenophora as the SOM flipping to Porifera (or occasionally Placozoa). However, greater taxon sampling improves phylogenetic stability, with some of the larger molecular data sets (⁠|$>$| 200,000 characters and up to |$\sim $| 100 taxa) showing node stability even with |$\geqq100\times $| upweighting of morphological data. Accordingly, our analyses have three strong messages. 1) The assumption that genomic data will automatically "swamp out" morphological data is not always true for the SOM question. Morphological data have a strong influence in our analyses of combined data sets, even when outnumbered thousands of times by molecular data. Morphology therefore should not be counted out a priori. 2) We here quantify for the first time how the stability of the SOM node improves for several genomic data sets when the taxon sampling is increased. 3) The patterns of "flipping points" (i.e. the weighting of morphological data it takes to change the inferred SOM) carry information about the phylogenetic stability of matrices. The weighting space is an innovative way to assess comparability of data sets that could be developed into a new sensitivity analysis tool. [Metazoa; Morphology; Phylogenomics; Weighting.] [ABSTRACT FROM AUTHOR]

Innovation is a key to evolutionary success and entrance into novel ecosystems. 1 Species that float freely at the ocean's surface, termed obligate neuston (also called pleuston , here referred to simply as neuston), include highly specialized taxa from distinct evolutionary lineages that evolved floating morphologies. 2 In 1958, Soviet scientist, A.I. Savilov, 3 stated that floating animal species are derived from benthic ancestors, rather than species from the adjacent pelagic zone, and that floating morphologies are homologous to benthic attachment structures. To test Savilov's hypothesis, we constructed molecular phylogenies and ancestral states for all major floating groups for which molecular data were available. Our results reveal that four of the five clades examined arose directly from a substrate-attached ancestor, although that substrate was not necessarily the benthos, as Savilov stated, and instead included epibiotic and rafting ancestors. Despite their diverse evolutionary origins, floating animals use gas-trapping mechanisms to remain at the surface, 4,5,6 and many of these gas-trapping structures appear to be homologous to substrate attachment structures. We also reconstruct the trophic habits of floating mollusks and their sister species, revealing that prey preference remains conserved upon entering the ocean's surface ecosystem. Colonization of the ocean's surface seems to have occurred through successive evolutionary steps from the seafloor. Our results suggest that these steps often included transitions through epibiotic (where species attach to other living organisms) or rafting (where species attach to floating debris) habits. The water-air interface, despite its unique properties, may, in some ways, be just another substrate. • We examine the evolutionary history of ocean surface-dwelling organisms • Most surface species evolved from ancestors that attached to a substrate • Floating animal diet and reproduction is similar to substrate-attached sister taxa • Floating morphologies likely evolved from ancestral attachment structures Anthony et al. test a 66-year-old assumption that animals living on the ocean's surface evolved from seafloor ancestors. Ancestral reconstructions reveal that surface animals largely evolved from substrate-attached ancestors, although not necessarily from the seafloor. This transition was likely facilitated by modifications of attachment structures. [ABSTRACT FROM AUTHOR]

The freshwater-fish genus Laubuka contains ∼13 species distributed through the lowlands of tropical South and South-east Asia. Four of these species (Laubuka lankensis, L. varuna, L. ruhuna, and L. insularis) are reported as endemic to Sri Lanka, a remarkable datum given the island's small size. We sampled populations of Laubuka at 56 locations in 14 of the island's principal river basins and analysed their morphological, meristic, phylogenetic, and phylogeographic relationships using the mitochondrial genes cytochrome b and cytochrome c oxidase subunit 1 and the nuclear recombination activating protein 1. We investigated the geographic structure, and delineated species using molecular species delimitation methods and morphological analysis within the general lineage concept of species. Molecular and morphological analyses failed to identify L. ruhuna and L. insularis as distinct species; we show them to be synonyms of L. varuna and L. lankensis, respectively. Taxonomic inflation in previous literature is attributed as a result of limited sampling and negligence of size allometry. Additionally, a third, cryptic species discovered in this study is described as L. hema sp. nov. which is evidently confined to the headwaters of the Gal basin in eastern Sri Lanka. Phylogenetic and haplotype network analyses suggest phylogeographic structure within both the southwest-endemic L. varuna and the dry-zone endemic L. lankensis, but the former shows strong phylogeographic structure between adjacent basins. The Sri Lankan species of Laubuka do not form a monophyletic group: they stem from two dispersal or vicariance events, one involving the lineage that led to L. varuna in south-western Sri Lanka, and the other, of [L. lankensis + L. hema] in the dry zone. [ABSTRACT FROM AUTHOR]

Thismia is a genus of > 80 mycoheterotrophic species characterized by a peculiar appearance and complex floral morphology. A significant proportion of the species and morphological diversity of Thismia has only been uncovered in the past two decades, and new discoveries continue to be made. Given that many new data have recently become available, and the most comprehensive taxonomic revision of the genus from 1938 addresses less than half of the currently known species, previous hypotheses for species relationships and infrageneric taxonomic classification in Thismia was in need of review. Extensive molecular phylogenetic studies of Thismia at the genus level have never been presented. We investigate the phylogenetic relationships of 41 species (and one variety) of Thismia from the Old World. Our study comprises 68 specimens (for 28 of which the data were newly generated), including outgroup taxa broadly representing Thismiaceae (= Burmanniaceae p.p. sensu APG IV, 2016), and is based on two nuclear and one mitochondrial marker. We use maximum likelihood and Bayesian inference to infer relationships among the taxa. We also constructed a morphological dataset of 12 mostly floral characters, comparing these characters to hypotheses based on molecular evidence to identify putative synapomorphies for major clades and to discuss hypotheses regarding the evolution of structural traits in the genus. Our analyses indicate that the majority of currently accepted infrageneric taxa of Thismia are polyphyletic. We find support for the monophyly of the Old World group, in which we recognize five well-supported lineages (clades); the only New World species studied appears to be related to the Neotropical genus Tiputinia. Ancestral state reconstructions demonstrate that the evolution of most morphological characters was homoplastic, but we identify characters that provide each of the five clades of Old World Thismia with a unique morphological description. The geographical distribution of the species under study is also shown to be consistent with the major clades. Our investigation provides a phylogenetic basis for the development of a novel sectional classification of Thismia reflecting morphological and geographical traits. [ABSTRACT FROM AUTHOR]

Molecular techniques are currently the leading tools for reconstructing phylogenetic relationships, but our understanding of ancestral, plesiomorphic and apomorphic characters requires the study of the morphology of extant forms for testing these phylogenies and for reconstructing character evolution. This review highlights the potential of soft body morphology for inferring the evolution and phylogeny of the lophotrochozoan phylum Bryozoa. This colonial taxon comprises aquatic coelomate filter‐feeders that dominate many benthic communities, both marine and freshwater. Despite having a similar bauplan, bryozoans are morphologically highly diverse and are represented by three major taxa: Phylactolaemata, Stenolaemata and Gymnolaemata. Recent molecular studies resulted in a comprehensive phylogenetic tree with the Phylactolaemata sister to the remaining two taxa, and Stenolaemata (Cyclostomata) sister to Gymnolaemata. We plotted data of soft tissue morphology onto this phylogeny in order to gain further insights into the origin of morphological novelties and character evolution in the phylum. All three larger clades have morphological apomorphies assignable to the latest molecular phylogeny. Stenolaemata (Cyclostomata) and Gymnolaemata were united as monophyletic Myolaemata because of the apomorphic myoepithelial and triradiate pharynx. One of the main evolutionary changes in bryozoans is a change from a body wall with two well‐developed muscular layers and numerous retractor muscles in Phylactolaemata to a body wall with few specialized muscles and few retractors in the remaining bryozoans. Such a shift probably pre‐dated a body wall calcification that evolved independently at least twice in Bryozoa and resulted in the evolution of various hydrostatic mechanisms for polypide protrusion. In Cyclostomata, body wall calcification was accompanied by a unique detachment of the peritoneum from the epidermis to form the hydrostatic membraneous sac. The digestive tract of the Myolaemata differs from the phylactolaemate condition by a distinct ciliated pylorus not present in phylactolaemates. All bryozoans have a mesodermal funiculus, which is duplicated in Gymnolaemata. A colonial system of integration (CSI) of additional, sometimes branching, funicular cords connecting neighbouring zooids via pores with pore‐cell complexes evolved at least twice in Gymnolaemata. The nervous system in all bryozoans is subepithelial and concentrated at the lophophoral base and the tentacles. Tentacular nerves emerge intertentacularly in Phylactolaemata whereas they partially emanate directly from the cerebral ganglion or the circum‐oral nerve ring in myolaemates. Overall, morphological evidence shows that ancestral forms were small, colonial coelomates with a muscular body wall and a U‐shaped gut with ciliary tentacle crown, and were capable of asexual budding. Coloniality resulted in many novelties including the origin of zooidal polymorphism, an apomorphic landmark trait of the Myolaemata. [ABSTRACT FROM AUTHOR]

Recent molecular phylogeny of deer revealed that the characters of antlers previously focused on are homoplasious, and antlers tend to be considered problematic for classification. However, we think antlers are important tools and reconsidered and analysed the characters and structures to use them for classification. This study developed a method to describe the branching structure of antlers by using antler grooves, which are formed on the antlers by growth, and then projecting the position of the branching directions of tines on the burr circumference. By making diagrams, comparing the branching structure interspecifically, homologous elements (tines, beams, and processes) of the antlers of 25 species of 16 genera were determined. Subsequently, ancestral state reconstruction was performed on the fixed molecular phylogenetic tree. It was revealed that Capreolinae and Cervini gained respective three-pointed antlers independently, and their subclades gained synapomorphous tines. We found new homologous and synapomorphous characters, as the antler of Eld's deer, which has been classified in Rucervus, is structurally close to that of Elaphurus rather than that of Rucervus, consistent with molecular phylogeny. The methods of this study will contribute to the understanding of the branching structure and phylogeny of fossil species and uncover the evolutionary history of Cervidae. [ABSTRACT FROM AUTHOR]

Symbiotic relations and range of host usage are prominent in coral reefs and crucial to the stability of such systems. In order to explain how symbiotic relations are established and evolve, we used sponge-associated barnacles to ask three questions. (1) Does larval settlement on sponge hosts require novel adaptations facilitating symbiosis? (2) How do larvae settle and start life on their hosts? (3) How has this remarkable symbiotic lifestyle involving many barnacle species evolved? We found that the larvae (cyprids) of sponge-associated barnacles show a remarkably high level of interspecific variation compared with other barnacles. We document that variation in larval attachment devices are specifically related to properties of the surface on which they attach and metamorphose. Mapping of the larval and sponge surface features onto a molecular-based phylogeny showed that sponge symbiosis evolved separately at least three times within barnacles, with the same adaptive features being found in all larvae irrespective of phylogenetic relatedness. Furthermore, the metamorphosis of two species proceeded very differently, with one species remaining superficially on the host and developing a set of white calcareous structures, the other embedding itself into the live host tissue almost immediately after settlement. We argue that such a high degree of evolutionary flexibility of barnacle larvae played an important role in the successful evolution of complex symbiotic relationships in both coral reefs and other marine systems. [ABSTRACT FROM AUTHOR]

Riethia Kieffer, a genus of the non-biting midge subfamily Chironominae (Diptera: Chironomidae) is distributed in Australia, New Zealand, New Caledonia and South America. This austral distribution could be due to earth history (vicariance) or from Southern Hemisphere dispersal(s). We obtained samples from each area, most intensively from throughout Australia. We included putative sister genus Pseudochironomus Malloch, many genera from tribe Tanytarsini, enigmatic taxa in Chironomini and conventional outgroups from other subfamilies. We assembled a multilocus molecular dataset for four genetic regions from 107 individuals to reconstruct the first dated molecular phylogeny for the group. Four terminal clusters corresponded to unreared (thus unassociated) larvae. Monophyly was supported for 'core' Riethia , Pseudochironomus , putative tribe Pseudochironomini, tribe Tanytarsini (including enigmatic Nandeva Wiedenbrug, Reiss & Fittkau) and subfamily Chironominae. All species are monophyletic except for R. cinctipes Freeman, which includes R. neocaledonica Cranston. Riethia zeylandica Freeman, previously thought to be widespread in eastern Australia, now is a New Zealand endemic with Australian specimens allocated now to several regionally restricted species. The origin of Riethia was at 60.6 Ma ('core') or 52.1 Ma depending on the relationship of two South American species. Both dates are before the break-up of South America and Australia. Diversification within crown group Riethia started before the Cretaceous–Paleogene boundary, with subsequent separation at 52 Ma of an Australian 'clade I' from its sister 'clade II', which comprises Australian, New Zealand and New Caledonian species. Inferred dates for species origins of New Caledonia and New Zealand taxa imply transoceanic dispersals from eastern Australia. Western Australian species diverged during the mid to late Miocene from their eastern Australian sister taxa. This correlates with the onset of drying of Australia and the separation of mesic east from west by the formation of an arid proto-Nullarbor. Taken together, the inferred tempo of diversification in the group included both older ages reflecting earth history, yet with suggested recent intra-Pacific separations due to transoceanic dispersals. Several non-biting midges have exclusively austral (Southern Hemisphere) distributions, suggesting that their distribution and diversification was due to Mesozoic breakup of the megacontinent Gondwana. We estimated a dated phylogeny for Riethia (Kieffer) (Chironomidae), supporting an underlying earth history explanation for its austral distribution. However, dates involving New Zealand, New Caledonia and South America are too young and more likely arise from transoceanic dispersal. Miocene onset of aridification likely influenced two east–west disjunctions in Australia. Diversification in this clade evidently is more complex and nuanced than naively 'Gondwanan'. [ABSTRACT FROM AUTHOR]

Rhytidanthera is the only genus of Ochnaceae with compound leaves, and it forms sparse, small populations restricted to the primary forest of the Colombian and Venezuelan Andes and the sandstone hills of La Macarena and Chiribiquete. It has been suggested to be related to Godoya , Cespedesia and Krukoviella in taxonomic and phylogenetic studies. However, the relationships in this group remain poorly resolved, due to the lack of a wider molecular and taxonomic sampling. We present a phylogenetic study of tribe Sauvagesieae including three Rhytidanthera spp. and one species each of Godoya and Cespedesia , using sequences from one nuclear (ITS) and four plastid DNA regions (matK , ndhF , rbcL and trnL-F), in order to clarify the relationships among these four genera. We recover a new and well-supported phylogenetic hypothesis, with Rhytidanthera as sister to a clade comprising Godoya and the clade formed by Cespedesia and Krukoviella. This Neotropical clade was recovered as sister to the monotypic and African genus Fleurydora. The clade comprising Rhytidanthera , Godoya , Cespedesia and Krukoviella is supported by the presence of glandular structures (colleters) at the base of stipules and bracts. The colleters also evolved at the base of the sepals in this clade, with a secondary loss in Cespedesia and Krukoviella. We suggest that the combination of unequal-sized sepals enclosing the floral bud and the presence of colleters in members of this clade could have a role in the protection of leaves and flowers in the early stages of development, instead of acting in pollinator attraction. [ABSTRACT FROM AUTHOR]

Sequence type (ST) 398 is the most prevalent clone of livestock-associated methicillin-resistant Staphylococcus aureus (MRSA). To evaluate the molecular characteristics and phylogeny of Chinese ST398 isolates, 4 MRSA ST398 strains and 4 methicillin-susceptible S. aureus (MSSA) ST398 strains were collected from patients with bacteremia at 6 teaching hospitals in China between 1999 and 2016. Moreover, 689 ST398 genome sequences were downloaded from the GenBank database for comparison. The 4 MRSA ST398 strains were resistant to β-lactam antibiotics, and 2 strains were also resistant to erythromycin. Among the 4 MSSA ST398 strains, 2 strains displayed multidrug resistance (MDR) and were resistant to penicillin, erythromycin, tetracycline, and gentamicin. The accessory genome of MSSA ST398 was more diverse than that of MRSA ST398. All 4 MRSA ST398 strains carried type V staphylococcal cassette chromosome mec elements; however, MSSA ST398 carried more resistance genes than MRSA ST398. These 4 MRSA ST398 strains carried hemolysin, along with virulence genes associated with immune invasion and protease. Phylogenic analysis showed that the 4 MRSA ST398 strains clustered in 1 clade. The global ST398 phylogeny showed that ST398 was divided into an animal clade and a human clade, and the ST398 strains of this study clustered in the human clade. A small number of human strains were also present in the animal clade and vice versa, suggesting transmission of ST398 between animals and humans. In conclusion, livestock-associated MRSA ST398 has caused severe infections in Chinese hospitals, and it should therefore be paid more attention to and monitored. [ABSTRACT FROM AUTHOR]

Background: Most cinquefoils (Potentilla L., Rosaceae) are polyploids, ranging from tetraploid (4x) to dodecaploid (12x), diploids being a rare exception. Previous studies based on ribosomal and chloroplast data indicated that Norwegian cinquefoil (P. norvegica L.) has genetic material from two separate clades within Potentilla; the Argentea and the Ivesioid clades – and thus a possible history of hybridization and polyploidization (allopolyploidy). In order to trace the putative allopolyploid origin of the species, sequence data from low-copy, biparentally inherited, nuclear markers were used. Specimens covering the circumpolar distribution of P. norvegica and its two subspecies were included, along with the morphologically similar P. intermedia. Potentilla species of low ploidy level known to belong to other relevant clades were also included. Results: Gene trees based on three low-copy nuclear markers, obtained by Bayesian Inference and Maximum Likelihood analyses, showed slightly different topologies. This is likely due to genomic reorganizations following genome duplication, but the gene trees were not in conflict with a species tree of presumably diploid taxa obtained by Multispecies Coalescent analysis. The results show that both P. norvegica and P. intermedia are allopolyploids with a shared evolutionary history involving at least four parental lineages, three from the Argentea clade and one from the Ivesioid clade. Conclusions: This is the first time that reticulate evolution has been proven in the genus Potentilla, and shows the importance of continuing working with low-copy markers in order to properly resolve its evolutionary history. Several hybridization events between the Argentea and Ivesioid clades may have given rise to the species of Wolf's grex Rivales. To better estimate when and where these hybridizations occurred, other Argentea, Ivesioid and Rivales species should be included in future studies. [ABSTRACT FROM AUTHOR]

Premise of research. The Caribbean is an important area of species diversity within the large pantropical genus Phyllanthus. With the goal of illuminating the evolutionary origins of Caribbean Phyllanthus , we undertook a phylogenetic analysis significantly increasing previous samplings of the genus in the Neotropics. We reconstructed the evolution of selected morphological characters and evaluated the implications of our results in light of the representation of Caribbean and Neotropical species in the infrageneric classification of the genus. Methodology. We estimated phylogentic trees using parsimony, Bayesian, and likelihood approaches based on plastid and nuclear sequence data sets. These represented 78 taxa from the Neotropics, most of which were generated for this study, as well as most other subgenera and sections of Phyllanthus and other genera of Phyllanthaceae. Four vegetative and four floral morphological characters were assessed for the whole study group. Ancestral character states were reconstructed using BayesTraits. Pivotal results. Plastid and nuclear partitions agree on a highly supported Caribbean clade that contains the vast majority of the species from this region as being part of a large Neotropical clade. Another small Caribbean clade is found nested among African linages. Although morphological characters exhibit some level of homoplasy, some trends are evident, for example, in the large Neotropical clade. Conclusions. The majority of species in the Caribbean belong to a single clade that has evolved from Neotropical ancestors. This is well circumscribed with morphology and corresponds to subgenus Xylophylla , the concept of which is adjusted here to be monophyletic. The existence of a small Caribbean clade related to African species marks a noteworthy case of Caribbean plant origin. Although phyllanthoid branching is not a synapomorphy for Phyllanthus s.l. (including Breynia , Glochidion , and Sauropus), combinations of vegetative and floral characters allow a clear assignment to the Phyllanthus s.l. clade. [ABSTRACT FROM AUTHOR]

Premise: Despite intensive research, the pathways and driving forces behind the evolution of derived woodiness on oceanic islands remain obscure. The genus Daucus comprises mostly herbs (therophytes, hemicryptophytes) with few rosette treelets (chamaephytes) endemic to various Macaronesian archipelagos, suggesting their independent evolution. To elucidate the evolutionary pathways to derived woodiness, we examined phylogenetic relationships and the habit and secondary xylem evolution in Daucus and related taxa. Methods: Sixty taxa were surveyed for molecular markers, life history, and habit traits. Twenty‐one species were considered for wood anatomical characters. A dated phylogeny was estimated using Bayesian methods. The evolution of selected traits was reconstructed using parsimony and maximum likelihood. Results: Daucus dispersed independently to the Canary Islands (and subsequently to Madeira), Cape Verde, and the Azores in the late Miocene and Pleistocene. Life span, reproductive strategy, and life form were highly homoplastic; the ancestor of Daucus was probably a monocarpic, biennial hemicryptophyte. Rosette treelets evolved independently in the Canarian‐Madeiran lineage and in Cape Verde, the latter within the last 0.13 Myr. Treelets and hemicryptophytes did not differ in wood anatomy. Pervasive axial parenchyma in wood occurred more often in polycarpic rather than monocarpic species. Conclusions: Life span and life form in Daucus are evolutionarily labile and may change independently of wood anatomy, which is related to plant reproductive strategy rather than to life form. Insular woodiness may evolve rapidly (as demonstrated in D. bischoffii), and in Daucus, it does not seem to be an adaptation to lower the risk of xylem embolism. [ABSTRACT FROM AUTHOR]

In Apiaceae, embryos of most species have two cotyledons, but some species are consistently monocotylar. Traditionally, the monocotyly has been considered as taxonomically important at the generic level, despite its presumably multiple origins in the family. In this study, a survey of the published literature and our new findings on cotyledon number, embryo and seedling morphology and nrDNA ITS sequence data are presented to provide modern insights into the taxonomic distribution and phylogenetic relationships of monocotylar taxa. A molecular phylogenetic tree representing much of the diversity of monocotylar Apiaceae was produced to re-evaluate the potential implication of monocotyly for systematics and to elucidate its evolutionary significance in the family. Our data document the presence of monocotylar seedlings in 59 species representing 15 genera, in three species and one genus (Postiella) of which monocotylar seedlings are reported for the first time. Analysis of ITS sequence data indicates that monocotyly in Apiaceae has arisen independently in at least seven different lineages encompassing five of 41 major clades of subfamily Apioideae, but not in early-diverging lineages. Parallel evolution has resulted in a remarkable morphological similarity in monocotylar embryo and seedling organization, especially in the proportion of the cotyledon length to the axis of the embryo and the multifunctional cotyledonary tube in the seedling. These features could be considered as adaptations to a geophilic life form, as all monocotylar species are perennial herbs with tuberous underground organs distributed mainly in the Ancient Mediterranean region. The single cotyledon in Apiaceae, as in most other monocotyledonous eudicots, could be interpreted as two united cotyledons (syncotyly), but further developmental studies are needed to test this hypothesis. [ABSTRACT FROM AUTHOR]

Our ability to correctly reconstruct a phylogenetic tree is strongly affected by both systematic errors and the amount of phylogenetic signal in the data. Current approaches to tackle tree reconstruction artifacts, such as the use of parameter-rich models, do not translate readily to single-gene alignments. This, coupled with the limited amount of phylogenetic information contained in single-gene alignments, makes gene trees particularly difficult to reconstruct. Opsin phylogeny illustrates this problem clearly. Opsins are G-protein coupled receptors utilized in photoreceptive processes across Metazoa and their protein sequences are roughly 300 amino acids long. A number of incongruent opsin phylogenies have been published and opsin evolution remains poorly understood. Here, we present a novel approach, the canary sequence approach, to investigate and potentially circumvent errors in single-gene phylogenies. First, we demonstrate our approach using two well-understood cases of long-branch attraction in single-gene data sets, and simulations. After that, we apply our approach to a large collection of well-characterized opsins to clarify the relationships of the three main opsin subfamilies. [ABSTRACT FROM AUTHOR]

The eight‐eyed haplogyne spider family Plectreuridae Simon, 1893 is one of the oldest of spider families, currently comprising two genera (Kibramoa and Plectreurys), 30 extant species and one subspecies. Plectreuridae have not been rigorously examined since 1958, with only three new species added to Plectreurys. This study revisited a subset of taxa from the genus Kibramoa using a combined morphological and multilocus phylogenetic analysis. Species distribution modeling (SDM) was used to investigate the current and paleo distributional patterns of the genus Kibramoa throughout the biodiverse region of the California Floristic Province (CFP). A reexamination of genitalic morphology reflected cryptic species, yet multilocus Bayesian and maximum likelihood analyses of mitochondrial (COI, 16S) and nuclear (ITS1, 28S) markers consistently suggested several divergent lineages. A time‐calibrated phylogeny indicated that the most recent common ancestor of Kibramoa appeared in the Mid‐Miocene and continued to diversify throughout the Plio‐Pleistocene. Xerophilic Kibramoa, as inferred by SDM, had a much wider distribution during the Mid‐Holocene, when climate was at its warmest. This body of work uncovered novel findings regarding the evolution of plectreurids, provided the first phylogeny of the family, and demonstrated similar biogeographic patterns displayed in other CFP taxa. [ABSTRACT FROM AUTHOR]

Dietary shifts can alter the relative availability of different nutrients and are therefore associated with metabolic adaptation in animals. The Coccinellidae (ladybirds) exhibits three major types of feeding habits and provides a useful model to study the effects of dietary changes on the evolution of mitogenomes, which encode proteins directly involved in energy metabolism. Here, mitogenomes of three coccinellid species were newly sequenced. These data were combined with other ten previously sequenced coccinellid mitogenomes to explore the relationship between mitogenome evolution and diets. Our results indicate that mitogenomic data can be effectively used to resolve phylogenetic relationships of Coccinellidae. Strong codon usage bias in coccinellid mitogenomes was predominantly determined by nucleotide composition. The 13 mitochondrial protein‐coding genes (PCGs) globally evolved under negative constraints, with some PCGs showing a stronger purifying selection. Six PCGs (nad3, nad4L, and nad5 from Complex I; cox1 and cox3 from Complex IV; and atp6 from Complex V) displayed signs of positive selection. Of these, adaptive changes in cox3 were potentially associated with metabolic differences resulting from dietary shifts in Coccinellidae. Our results provide insights into the adaptive evolution of coccinellid mitogenomes in response to both dietary shifts and other life history traits. [ABSTRACT FROM AUTHOR]

Staphylinidae, or rove beetles, are a megadiverse family known for their typically very short elytra exposing most of the abdomen, but the putatively early‐derived subfamily Omaliinae and its relatives have been known to include multiple taxa with unusually long elytra. The ancestral elytral length of the family and of this subfamily have long been debated. We present a phylogenetic analysis of Omaliinae based on partial mitochondrial COI (1488 bp), COII (366 bp), 12S rDNA (353 bp), nuclear 18S rDNA (1814 bp), 28S rDNA (876 bp) and CAD (869 bp) data. In all, 51 species in 31 genera and four outgroup species were included. The concatenated sequences were analysed by both parsimony‐ and model‐based (Bayesian and maximum likelihood) methods. The subfamily Omaliinae was not supported as a monophyletic group. The model‐based analyses (Bayesian and maximum likelihood trees) showed Empelinae nested within Omaliinae (excluding Corneolabiini), whereas parsimony analysis found all three putative ingroup subfamilies, Empelinae, Glypholomatinae and Microsilphinae, grouped within Omaliinae. Within the Omaliinae, the tribes Coryphiini and Eusphalerini were each supported as monophyletic, whereas Anthophagini and Omaliini were each nonmonophyletic. We hypothesize that there have been at least four independent origins of long elytra from short elytra in the omaliine lineage. [ABSTRACT FROM AUTHOR]

Melanism in the cat family has been associated with functions including camouflage, thermoregulation and parasite resistance. Here we investigate a new hypothesis proposing that the evolution of melanism in cats has additionally been influenced by communication functions of body markings. To evaluate this hypothesis, we assembled a species-level data set of morphological (body marks: white marks on the backs of ears) and ecological (circadian activity: arrhythmic/nocturnal, and environmental preference: open/closed) characteristics that could be associated with communication via body markings, and combined these data with a dated molecular phylogeny. Next, we tested the association between melanism and communication, first by relating species' body marks with their ecological conditions, using a Bayesian implementation of the threshold model. Second, to explore the evolution of characteristics potentially influencing melanism in cat species, we modeled their evolution relative to melanism using models of coordinated vs. independent character changes. Our results suggest that white marks are associated with intraspecific communication between individuals that have non-melanistic phenotypes, as well as towards melanistic individuals (without white marks). The absence of white marks in a melanistic individual tends to be a limiting condition for intraspecific visual communication at night, resulting in an evolutionary dilemma for these species, i.e. to be almost invisible at night, but not to communicate visually. The comparative analysis of several evolutionary models indicated more support for the evolution of melanism being coordinated with the evolution of arrhythmic activity and white marks on the backs of ears. [ABSTRACT FROM AUTHOR]

Premise of research. Spores and pollen often exhibit distinctive morphology, resulting from the structure of the exine (spore wall), and elaborate external ornamentation, known as perine. Spore-dispersed plants, particularly ferns, exhibit remarkable variation in the surface structure of their spores and provide an excellent model for the study of morphological trait evolution. Our goal is to assess the utility of spore morphology for characterizing clades and taxa. For this study, we chose Thelypteridaceae, a family of ferns with over 1000 species and exceptionally diverse spore morphology. Methodology. We generated a 200-species molecular phylogeny representing family diversity. We assigned discrete states for seven morphological characters of spores based on images from scanning electron microscopy (SEM). We then optimized these seven characters and their states on our molecular phylogeny, which represented about 10% of the species diversity in the family, including members of all 27 currently recognized genera, with the exception of the monotypic Menisorus and Nannothelypteris , which includes three species. We quantify phylogenetic signal and homoplasy for morphological traits and test for pairwise correlated evolution of traits. Finally, we provide a synoptic description of spore morphology for genera in the family, synthesizing our current findings with previous work. Pivotal results. Reticulate perine and perforate perine, which show high phylogenetic signal and low homoplasy, characterized genera and major clades. Microstructure, or fine superficial sculpturing, was not synapomorphic for any group and varied at fine phylogenetic scales. Certain genera, such as Amauropelta and Stegnogramma , exhibit uniform morphology among their species, whereas others, such as Christella , are highly variable. Our phylogenetic analyses indicate that Christella and Pronephrium are nonmonophyletic, whereas infrageneric sections of these genera are largely corroborated. Conclusions. Characters pertaining to perine macrostructure and perforations, in particular, were reconstructed as synapomorphic for genera or sections in the Thelypteridaceae. High variability of perine characters within the christelloid clade suggests that it is a promising group on which to focus further sampling. Our approach provides explicit statements of character evolution for perine morphology that can be used as a framework for further studies. We demonstrated that the repository of high-quality SEM images of spores in the literature serves as a rich source of morphological data. [ABSTRACT FROM AUTHOR]

Phylogenetic hypotheses of the relationships of Diptera: Anthomyzidae (61 taxa) are discussed with special reference to the genera Fungomyza Roháček, 1999, Anthomyza Fallén, 1810, Epischnomyia Roháček, 2006 and Arganthomyza Roháček, 2009 based on the analysis of 7 combined mitochondrial + nuclear gene markers in comparison with results of the most recent cladistic analysis of morphological characters. The majority of revealed inter‐ and intrageneric relationships of these genera in both analyses were largely congruent except for the topology of Fungomyza and Arganthomyza being equivocal because of different topologies in phylograms generated by alternative molecular methods and Epischnomyia forming a branch within Anthomyza in the molecular data hypothesis. The formerly unsettled Anthomyza drachma proved to be the sister species of the A. umbrosa group while the affinity of A. flavosterna to the A. bellatrix group has not been confirmed. The first phylogenetic hypothesis of Anthomyzinae to include timing of the nodes of divergence is presented. The origin of the subfamily is dated into the Eocene, ca 37.5 (30.6–45.3) MYA, and agrees with the age of the oldest known fossils from Baltic amber. The analysed members of the Anthomyza group of genera were found to have already evolved in the upper Oligocene. The divergences of the Palaearctic and Nearctic sister species in Arganthomyza and Anthomyza were found to occur at several different times during the Neogene (upper Miocene) to lower Quaternary (Pleistocene), from about 7 to 0.7 MYA. These were likely the result of fragmentation of widespread (Holarctic or Sino‐Japanese–Nearctic) ranges of ancestral taxa by vicariance events that were, in turn, caused by multiple interruptions of Beringia Land Bridges or cooling of climate and seem to be consistent with the times of multiple disjunctions of the flora. [ABSTRACT FROM AUTHOR]

Extrafloral nectaries (EFNs) mediating ecologically important ant–plant protection mutualisms are especially common and unusually diverse in the Leguminosae. We present the first comprehensively curated list of legume genera with EFNs, detailing and illustrating their systematic and phylogenetic distributions, locations on the plant, morphology and anatomy, on the basis of a unified classification of EFN categories and a time-calibrated phylogeny, incorporating 710 of the 768 genera. This new synthesis, the first since Mckey (1989)'s seminal paper, increases the number of genera with EFNs to 153 (20% of legumes), distributed across subfamilies Cercidoideae (1), Detarioideae (19), Caesalpinioideae (87) and Papilionoideae (46). EFNs occur at nine locations, and are most prevalent on vegetative plant parts, especially leaves (74%) and inflorescence axes (26%). Four main categories (with eight subcategories) are recognised and include the following: formless, trichomatic (exposed, hollow), parenchymatic (embedded, pit, flat, elevated) and abscission zone EFNs (non-differentiated, swollen scars). Phylogenetic reconstruction of EFNs suggests independent evolutionary trajectories of different EFN types, with elevated EFNs restricted almost exclusively to Caesalpinioideae (where they underwent spectacular morphological disparification), flat EFNs in Detarioideae, swollen scar EFNs in Papilionoideae, and Cercidoideae is the only subfamily bearing intrastipular EFNs. We discuss the complex evolutionary history of EFNs and highlight future research directions. [ABSTRACT FROM AUTHOR]

Mitochondrial genes are placed on one molecule, which implies that they should carry consistent phylogenetic information. Following this advantage, we present a well-supported phylogeny based on mitochondrial genomes from almost 300 representatives of Passeriformes, the most numerous and differentiated Aves order. The analyses resolved the phylogenetic position of paraphyletic Basal and Transitional Oscines. Passerida occurred divided into two groups, one containing Paroidea and Sylvioidea, whereas the other, Passeroidea and Muscicapoidea. Analyses of mitogenomes showed four types of rearrangements including a duplicated control region (CR) with adjacent genes. Mapping the presence and absence of duplications onto the phylogenetic tree revealed that the duplication was the ancestral state for passerines and was maintained in early diverged lineages. Next, the duplication could be lost and occurred independently at least four times according to the most parsimonious scenario. In some lineages, two CR copies have been inherited from an ancient duplication and highly diverged, whereas in others, the second copy became similar to the first one due to concerted evolution. The second CR copies accumulated over twice as many substitutions as the first ones. However, the second CRs were not completely eliminated and were retained for a long time, which suggests that both regions can fulfill an important role in mitogenomes. Phylogenetic analyses based on CR sequences subjected to the complex evolution can produce tree topologies inconsistent with real evolutionary relationships between species. Passerines with two CRs showed a higher metabolic rate in relation to their body mass. [ABSTRACT FROM AUTHOR]

Extrafloral nectaries (EFNs) mediating ecologically important ant–plant protection mutualisms are especially common and unusually diverse in the Leguminosae. We present the first comprehensively curated list of legume genera with EFNs, detailing and illustrating their systematic and phylogenetic distributions, locations on the plant, morphology and anatomy, on the basis of a unified classification of EFN categories and a time-calibrated phylogeny, incorporating 710 of the 768 genera. This new synthesis, the first since Mckey (1989)'s seminal paper, increases the number of genera with EFNs to 153 (20% of legumes), distributed across subfamilies Cercidoideae (1), Detarioideae (19), Caesalpinioideae (87) and Papilionoideae (46). EFNs occur at nine locations, and are most prevalent on vegetative plant parts, especially leaves (74%) and inflorescence axes (26%). Four main categories (with eight subcategories) are recognised and include the following: formless, trichomatic (exposed, hollow), parenchymatic (embedded, pit, flat, elevated) and abscission zone EFNs (non-differentiated, swollen scars). Phylogenetic reconstruction of EFNs suggests independent evolutionary trajectories of different EFN types, with elevated EFNs restricted almost exclusively to Caesalpinioideae (where they underwent spectacular morphological disparification), flat EFNs in Detarioideae, swollen scar EFNs in Papilionoideae, and Cercidoideae is the only subfamily bearing intrastipular EFNs. We discuss the complex evolutionary history of EFNs and highlight future research directions. [ABSTRACT FROM AUTHOR]

Eriocaulon is a genus of c. 470 aquatic and wetland species of the monocot plant family Eriocaulaceae. It is widely distributed in Africa, Asia and America, with centres of species richness in the tropics. Most species of Eriocaulon grow in wetlands although some inhabit shallow rivers and streams with an apparent adaptive morphology of elongated submerged stems. In a previous molecular phylogenetic hypothesis, Eriocaulon was recovered as sister of the African endemic genus Mesanthemum. Several regional infrageneric classifications have been proposed for Eriocaulon. This study aims to critically assess the existing infrageneric classifications through phylogenetic reconstruction of infrageneric relationships, based on DNA sequence data of four chloroplast markers and one nuclear marker. There is little congruence between our molecular results and previous morphology-based infrageneric classifications. However, some similarities can be found, including Fyson's sect. Leucantherae and Zhang's sect. Apoda. Further phylogenetic studies, particularly focusing on less well sampled regions such as the Neotropics, will help provide a more global overview of the relationships in Eriocaulon and may enable suggesting the first global infrageneric classification. [ABSTRACT FROM AUTHOR]

Panorpidae is the most species‐rich family in Mecoptera with ca. 470 species in the Northern Hemisphere. However, the intergeneric phylogenetic relationships of Panorpidae remain unsatisfactorily resolved to date. Here, we used molecular and cytogenetic approaches to determine the phylogenetic relationships of Panorpidae in the evolutionary scenario of chromosomes, and estimated their divergence times using fossil‐calibrated Bayesian analysis. In total, 89 species representing all seven genera of Panorpidae were used to reconstruct the phylogenetic trees using maximum parsimony, maximum likelihood and Bayesian inference based on the nuclear 28S rRNA and mitochondrial cox1 and cox2 genes. The results reveal that Panorpidae is a well‐supported monophyletic group that can be categorized into two major clades. Major Clade I comprises Neopanorpa and Leptopanorpa, and Major Clade II consists of all the other genera (Cerapanorpa, Dicerapanorpa, Furcatopanorpa, Panorpa and Sinopanorpa). Neopanorpa and Cerapanorpa are regarded as paraphyletic groups for the first time. BEAST analysis indicates that Panorpidae originated in the Lower Cretaceous approximately 122.5 Ma (96.8–149.3 Ma), and that most diversification occurred from the Selandian (59.8 Ma) to the Middle Pleistocene (0.6 Ma) in the Cenozoic. Cytogenetic data plotted on the cladogram show that the lineage differentiation of Panorpidae is closely related to the chromosomal evolution, especially the reduction of chromosome number. Our study suggests that a taxonomic revision of Panorpidae is urgently needed at the generic level. [ABSTRACT FROM AUTHOR]

• Astragalus is probably originated in middle Miocene in W Asia. • Major Astragalus clades diversified probably in Miocene-Pliocene under changing climates. • Annual Astragalus species diversified probably between 8.6 and 2.98 Ma. • Three rapid and recent diversification events are identified in Astragalus. • The processes and factors shaping diversifications in Astragalus are complex. Astragalus , a highly diverse genus of flowering plants with its highest center of diversity in West Asia, is a classic example of rapid species-level radiation and adaptation to a diversity of habitats throughout the world. We examined the historical biogeography of Astragalus using molecular dating and ancestral area reconstruction to understand how past climate changes, geographical patterns and transition in life history have provoked diversification of Astragalus. Our results suggest that Astragalus probably originated during the middle Miocene in West Asia, underwent rapid diversification, subsequently and repeatedly expanded its range in the Mediterranean region, and later to North America through West Europe. This distribution range was also extended toward central and eastern Asia from the Middle Miocene to Pleistocene. Several climatic and geological processes during the Miocene-Pliocene may be implicated in the diversification of the major Astragalus clades. In particular, the annual lineages, which are important elements in the Mediterranean flora of Africa and Europe and in the deserts of southwest to central Asia, have arisen in response to progressing aridity from the late Miocene onwards (between 8.6 Ma and 2.98 Ma). Diversification rate analyses indicate three rapid and recent diversification events, one at c. 11 Ma in the clade that groups most of the Astragalus s.s. (all except the Ophiocarpus sister lineage), one at c. 5 Ma in the crown group of the Hypoglottis clade, including herbaceous annual and perennial species, and the most recent one at c. 3 Ma in the spiny cushion forming Astracantha clade. Our study highlights the complexity of processes and factors shaping diversifications in Astragalus ; a complex interaction among climatic modifications providing opportunities for diversification and likely coincident with the evolution of key morphological and physiological adaptations. [ABSTRACT FROM AUTHOR]

• This is the most comprehensive molecular phylogenetic study of the genus Turnera. • Turnera is not monophyletic and is recircumscribed here. • Oxossia , a new genus with 15 spp. from Atlantic forest, is proposed. • The ancestral flower of Turnera was solitary, yellow, and heterostylous. • Turnera infrageneric classification is revised based on morphological synapomrphies. With 145 species, Turnera is the largest genus of Turneraceae (Malpighiales). Despite several morphotaxonomic and cytogenetic studies, our knowledge about the phylogenetic relationships in Turnera remains mainly based on morphological data. Here, we reconstruct the most comprehensive phylogeny of Turnera with molecular data to understand the morphological evolution within this group and to assess its circumscription and infrageneric classification. We analyzed two nuclear and six plastid markers and 112 taxa, including species and infraspecific taxa, 97 from Turnera , covering the 11 series of the genus. Bayesian inference, maximum parsimony and maximum likelihood analyses show that Turnera , as traditionally circumscribed, is not monophyletic. The genus is divided into two well-supported independent clades; one of them is sister to the genus Piriqueta and is here segregated as the new genus Oxossia. According to our reconstructions, Turnera probably evolved from an ancestor without extrafloral nectaries and with solitary, homostylous flowers with yellow petals. The emergences of extrafloral nectaries and distyly, both common in extant taxa, played an important role in the diversification of the genus. An updated infrageneric classification reflecting the relationships within Turnera is now possible based on morphological synapomorphies and is here designed for further studies. [ABSTRACT FROM AUTHOR]

Seventy years have passed since Ernest H. Runyon presented a phenotypic classification approach for nontuberculous mycobacteria (NTM), primarily as a starting point in trying to understand their clinical relevance. From numerical taxonomy (biochemical testing) to 16S rRNA gene sequencing to whole genome sequencing (WGS), our understanding of NTM has also evolved. Novel species are described at a rapid pace, while taxonomical relationships are re-defined in large part due to the accessibility of WGS. The evolutionary course of clonal complexes within species is better known for some NTM and less for others. In contrast with M. tuberculosis , much is left to learn about NTM as a whole. • Nontuberculous mycobacteria, a monophyletic lineage within Actinomycetales , contain pathogenic and opportunistic species of human and animals. • NTM are typically environmental organisms with extensive genetic variability, some of which contain host-adapted clonal lineages. • The 16S rRNA gene provides a phylogenetic framework while genome sequencing helps resolve taxonomical relationships of closely related taxa. • Caution must be applied in genomic analyses due to occasional mislabeling of strains. • Proper NTM classification increases knowledge on the epidemiology, improves research, and ultimately impacts on the clinical care of diseases caused by NTMs. [ABSTRACT FROM AUTHOR]

For their survival from hatching or birth, snakes depend on their ability to eat other animals. Thus, ontogeny and reproduction occur only if eating other animals is successful. Determining the degree to which feeding is successful must be studied at a variety of levels. I briefly review past and recent studies of feeding mechanics, focusing on those clades I have observed, and outline some features of feeding that puzzle me. The questions arise partly from unusual features of snakes, but the answers, when found, might have broader potential application. The questions focus primarily on how cells and tissues perform behaviors that are extreme in either space or time. When they become available, I anticipate that the answers will reveal aspects of evolutionary processes underlying the differentiation of species-specific or clade-specific traits. In the process, I reflect on how studies of feeding have paralleled some patterns of scientific progress, and how current fads might either inhibit or promote that progress. [ABSTRACT FROM AUTHOR]

The subfamily Saprininae is a group of moderately large histerid beetles that exhibits remarkable morphological and biological diversity. Although all species are predaceous, feeding on larvae of flies and other arthropods, numerous ecologically diverse lineages appeared during the evolution of the group, including taxa adapted for life in sand. These psammophiles conquered the Earth's arid and sandy desert regions. They are endowed with profound morphological adaptations, and the beginning of their radiation largely coincides with the Palaeocene–Eocene Thermal Maximum, which constituted the peak of the long-term early Cenozoic global warming. Earth's temperature during that time was believed to be globally ~8 °C warmer than it is today, and the aridification played an important role in the desertification of the planet. Here, we present the first comprehensive phylogenetic analysis of Saprininae to date, based on 115 taxa of 37 (sub)genera, which represent all major Saprininae genera. Our analyses resulted in a well-resolved phylogeny of the group, partly congruent with earlier phylogenetic hypotheses. We find support for the monophyly of the Saprininae and four major clades within it. Ultra-psammophily has evolved at least three times independently, with convergent morphological features arising in different desert regions, as a response to similar selective pressures. [ABSTRACT FROM AUTHOR]