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The northern North American Cordillera is a globally significant center of endemism. In western North America, imperiled arid steppe habitats support a number of unique species, including several endemic lichens. However, processes driving diversification and endemism in this region remain unclear. In this study, we investigate diversity and phylogeography of the threatened wanderlust lichens (mycobiont = Rhizoplaca species) which occur unattached on calcareous soils in steppe habitats. Wanderlust lichens comprise three species of lichen-forming fungi (LFF) - Rhizoplaca arbuscula, R. haydenii, and R. idahoensis (endangered, IUCN Red List) - which occur in fragmented populations in Idaho and Wyoming, with more limited populations in southern Montana and northern Utah. These lichens reproduce almost exclusively via large, asexual vegetative propagules. Here, our aims were to (i) assess the evolutionary origin of this group and identify phylogeographic structure, (ii) infer ancestral geographic distributions for lineages within this clade, and (iii) use species distribution modeling to better understand the distribution of contemporary populations. Using a genome-skimming approach, we generated a 19.1Mb alignment, spanning ca. half of the complete LFF genome, from specimens collected throughout the entire range of wanderlust lichens. Based on this phylogeny, we investigated phylogeographic patterns using RASP. Finally, we used MaxEnt to estimate species distribution models for R. arbuscula and R. haydenii. We inferred a highly structured topology, with clades corresponding to distinct geographic regions and morphologies collected throughout the group's distribution. We found that R. robusta, a sexually reproducing taxon, is clearly nested within the vagrant Rhizoplaca clade. Phylogeographic analyses suggest that both dispersal and vicariance played significant roles throughout the evolutionary history of the vagrant Rhizoplaca clade, with most of the dispersal events originating from the Salmon Basin in eastern Idaho - the center of diversity for this group. Despite the fact that wanderlust lichens are dispersal limited due to large, unspecialized vegetative propagules, we inferred multiple dispersal events crossing the Continental Divide. Comparing herbarium records with species distribution models suggests that wanderlust lichens don't fully occupy the areas of highest distribution probability. In fact, documented records often occur in areas predicted to be only marginally suitable. These data suggest a potential mismatch between contemporary habitats outside of the center of diversity in eastern Idaho with the most suitable habitat, adding to the vulnerability of this imperiled complex of endemic lichens., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Abiotic variables can influence species distributions, often restricting taxa to an acquired climatic signature or conversely, related species are conserved in the same ecological space over millions of years. An investigation into how abiotic change has shaped geographic distributions of taxa may be key to understanding diversification of lineages, and in the absence of reliable morphological characteristics, such information may support taxonomic units at multiple scales. Here, we examine the historical biogeography and patterns of habitat preference within the North American solifuge family, Eremobatidae. A previous study demonstrated that a major taxonomic revision of Eremobatidae is warranted, however recent studies demonstrate high levels of morphological convergence within the group, thus a re-classification of generic boundaries using additional information must be prioritized before we can formally begin solid revisionary efforts. In this study, we aimed to reconstruct a well-resolved phylogenetic hypothesis of Eremobatidae by filtering UCE loci based on informativeness, by mitigating the effect of cogenic UCE on phylogenetic estimation, and by supplementing our curated UCE loci with mitochondrial information. Using our preferred topology, in conjunction with published estimated divergence dates for Eremobatidae, we inferred a time-calibrated phylogenetic hypothesis to inform the historical biogeography and patterns of habitat preference. The two major habitat types that were observed for Eremobatidae were warm deserts for early diverging taxa and a subsequent evolution to cold deserts and Mediterranean California ecoregions for later diverging taxa. Eremobatid niche space, determined by temperature and precipitation, has been conserved for at least 25 million years in North America, supporting a warm desert origin, and thus supporting high species richness in the Sonoran and Mexican Plateau. Overall, our study provides support for new generic level designations within Eremobatidae., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Three novel crayfish-infecting nudiviruses from crayfish in North America represent the first genomic confirmation of nudiviruses in crayfish: Faxonius propinquus nudivirus (FpNV), Faxonius rusticus nudivirus (FrNV), and Faxonius virilis nudivirus (FvNV). Histopathology and electron microscopy revealed nuclear infections, including nuclear hypertrophy in hepatopancreatic epithelial cells and the presence of membrane-bound bacilliform virions. Metagenomic sequencing resulted in complete circular genome assembly, and phylogenetic analyses (based on nudivirus core genes) placed these viruses within the unofficial Epsilonnudivirus genus. One of the nudiviruses was detected in the antennal gland of its host, and another is correlated with invasive crayfish decline in one infected lake ecosystem - suggesting a potential route for viral transmission through water, and possible population level impact. This study highlights the importance of genomic and ecological data in elucidating the diversity and evolutionary relationships of the Nudiviridae, while expanding their known diversity and range of host species., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

Alveolar echinococcosis (AE) is a rare but severe disease that affects more than 18,000 people worldwide per year. The complete sequencing of the mitochondrial genome of Echinococcus multilocularis has made it possible to study the genetic diversity of the parasite and its spatial and temporal evolution. We amplified the whole mitochondrial genome by PCR, using one uniplex and two multiplex reactions to cover the 13,738 bp of the mitogenome, and then sequenced the amplicons with Illumina technology. In total, 113 samples from Europe, Asia, the Arctic and North America were analyzed. Three major haplogroups were found: HG1, which clustered samples from Alaska (including Saint-Lawrence Island), Yakutia (Russia) and Svalbard; HG2, with samples from Asia, North America and Europe; and HG3, subdivided into three micro-haplogroups. HG3a included samples from North America and Europe, whereas HG3b and HG3c only include samples from Europe. In France, HG3a included samples from patients more recently diagnosed in a region outside the historical endemic area. A fourth putative haplogroup, HG4, was represented by only one isolate from Olkhon Island (Russia). The increased discriminatory power of the complete sequencing of the E. multilocularis mitogenome has made it possible to highlight four distinct geographical clusters, one being divided into three micro-haplogroups in France., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Simple Summary: Black-winged fungus gnats (family Sciaridae) are one of the most species-rich groups of flies (Diptera), with about 3000 described species worldwide. Their taxonomy is notoriously challenging, as many genera are difficult to delimit and species identification relies almost exclusively on the male genitalia. Existing phylogenetic hypotheses based on DNA sequences are often contradictory, presumably due to low taxon or gene sampling. In this paper, a new multigene phylogenetic analysis is presented to support the concept and monophyly of a new genus, containing eight species, seven of them being described as new to science. The genus Spinopygina gen. nov. (type species Camptochaeta uniceps Hippa & Vilkamaa, 1994) from western North America is described. The genus includes the following eight species: Spinopygina acerfalx sp. nov.; S. aurifera sp. nov.; S. camura sp. nov.; S. edura sp. nov.; S. peltata sp. nov.; S. plena sp. nov.; S. quadracantha sp. nov.; and S. uniceps (Hippa & Vilkamaa, 1994) comb. nov., transferred from Corynoptera Winnertz. The new species are described and Spinopygina uniceps is re-diagnosed. The species are keyed and illustrated. In the maximum-likelihood phylogenetic hypothesis based on four gene fragments (28S, 18S, 16S and COI), Spinopygina gen. nov. appears as the sister group of Claustropyga Hippa, Vilkamaa & Mohrig, 2003. In the same analysis, a remarkable, undescribed species is placed within Camptochaeta Hippa & Vilkamaa clade. [ABSTRACT FROM AUTHOR]

Genomics has revolutionized our understanding of hybridization and introgression, but most of the early evidence for these processes came from studies of mitochondrial introgression. To expand these evolutionary insights from mitochondrial patterns, we evaluate phylogenetic discordance across the nuclear genomes of a hybridizing system, the Papilio machaon group of swallowtail butterflies. This species group contains three hybrid lineages (P. brevicauda, P. joanae, and P. m. kahli) that are geographically disjunct across North America and have complete fixation of a mitochondrial lineage that is otherwise primarily found in P. m. hudsonianus, a boreal subspecies of the Holarctic P. machaon. Genome-wide nuclear markers place the three hybrid lineages as a monophyletic group that is sister to P. polyxenes/P. zelicaon rather than P. machaon, although ancient hybridization between a subspecies of P. machaon and the ancestor of these three lineages is also shown by their greater nuclear affinity to P. m. hudsonianus than to other subspecies of P. machaon. Individuals from contemporary hybrid swarms in Alberta, where mitochondrial DNA fixation has not occurred, were more intermediate between their respective parent species, demonstrating diversity in mito-nuclear discordance following hybrid interactions. Our new phylogenetic findings for the P. machaon species group also include: subspecific paraphyly within P. machaon itself across its Holarctic distribution; paraphyly of P. zelicaon relative to P. polyxenes; and more divergent placement of a Mediterranean species, P. hospiton. These results provide the first comprehensive genomic evaluation of relationships within this species group and provide insight into the evolutionary dynamics of hybridization and mitochondrial introgression., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier Inc. All rights reserved.)

Background: The lake deposits of the informal Ruby Paper Shale unit, part of the Renova Formation of Montana, have yielded abundant plant fossils that document Late Eocene - Early Oligocene global cooling in western North America. A nearly complete small bird with feather impressions was recovered from this unit in in 1959, but has only been informally mentioned., Results: Here we describe this fossil and identify it as a new species of Zygodactylus, a stem lineage passerine with a zygodactyl foot. The new taxon shows morphological traits that are convergent on crown Passeriformes, including an elongate hallux, reduced body size, and a comparative shortening of proximal limb elements. The fossil documents the persistence of this lineage into the earliest Oligocene (~ 33 Ma) in North America. It is the latest occurring North American species of a group that persists in Europe until the Miocene., Conclusions: Eocene-Oligocene global cooling is known to have significantly remodeled both Palearctic and Nearctic mammal faunas but its impact on related avifaunas has remained poorly understood. The geographic and temporal range expansion provided by the new taxon together with avian other taxa with limited fossil records suggests a similar pattern of retraction in North America followed by Europe.

Molecular data have been increasingly used to study the phylogenetic relationships among many taxa, including scrophs. Sometimes they have provided phylogenetic reconstructions that are in conflict with morphological data leading to a re-evaluation of long-standing evolutionary hypotheses. In this paper, we review reports of the recent knowledge of the phylogenetic relationships within Scrophularieae (2011–2017). The results of these analyses led to the following conclusions. (1) Species of Scrophularia have undergone one or more Miocene migration events occurred from eastern Asia to the North America with subsequent long dispersal and diversification in three main directions. (2) Allopolyploid and aneuploid hybrid speciation between Scrophularia species can occur, so hybridization and polyploidy have an important role for history of diversification. (3) The ancestral staminode type for the genus Scrophularia seems to be a large staminode. (4) Monophyly of the genus Verbascum with respect to the genus Scrophularia is strongly supported. (5) Oreosolen, is not monophyletic, because all accessions of Oreosolen were nested within Scrophularia. We discuss methods of data collection and analysis, and we describe the areas of conflict and agreement between molecular phylogenies. [ABSTRACT FROM AUTHOR]

This paper summarizes currently available morphological data on larval stages of representatives of the 'Opatrinoid' clade (Tenebrionidae: Tenebrioninae). Literature research revealed that larval morphology of approximately 6% of described species representing this lineage is currently known (139 out of ~ 2325 spp.). Larvae of the five following species are described and illustrated: Zadenos mulsanti (Dendarini: Melambiina; South Africa), Blapstinus histricus, Blapstinus longulus, Trichoton sordidum (Opatrini: Blapstinina; North America), and Eurynotus rudebecki (Platynotini: Eurynotina; South Africa). The majority of studied larvae were associated with adults using molecular tools, resulting in an updated phylogeny of the 'Opatrinoid' clade. This revised phylogeny provides an evolutionary context for discussion of larval morphology. Based on the morphological and molecular evidence, the following synonym is proposed within Blapstinina: Trichoton Hope, 1841 (= Bycrea Pascoe, 1868 syn. nov.). Based on this decision, a new combination is introduced: Trichoton villosum Pascoe, 1868 comb. nov. The economic importance of the 'Opatrinoid' clade larvae is also briefly discussed, as well as potential future avenues of research. [ABSTRACT FROM AUTHOR]

Copyright of Canadian Journal of Earth Sciences is the property of Canadian Science Publishing and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Canadian Journal of Fisheries & Aquatic Sciences is the property of Canadian Science Publishing and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Haminoea japonica is a species of opisthobranch sea slug native to Japan and Korea. Non-native populations have spread unnoticed for decades due to difficulties in the taxonomy of Haminoea species. Haminoea japonica is associated with a schistosome parasite in San Francisco Bay, thus further spread could have consequence to human health and economies. Anecdotal evidence suggests that H. japonica has displaced native species of Haminoea in North America and Europe, becoming locally dominant in estuaries and coastal lagoons. In this paper we study the population genetics of native and non-native populations of H. japonica based on mt-DNA data including newly discovered populations in Italy and France. The conclusions of this study further corroborate a Northeastern Japan origin for the non-native populations and suggest possible independent introductions into North America and Europe. Additionally, the data obtained revealed possible secondary introductions within Japan. Although non-native populations have experienced severe genetic bottlenecks they have colonized different regions with a broad range of water temperatures and other environmental conditions. The environmental tolerance of this species, along with its ability to become dominant in invaded areas and its association with a schistosome parasite, suggest H. japonica could be a dangerous invasive species.

Characeae ( Charophyceae, Charophyta) contains two tribes with six genera: tribe Chareae with four genera and tribe Nitelleae, which includes Tolypella and Nitella. This paper uses molecular and morphological data to elucidate the phylogeny of Tolypella species in North America. In the most comprehensive taxonomic treatment of Characeae, 16 Tolypella species worldwide were subsumed into two species, T. intricata and T. nidifica, in two sections, Rothia and Tolypella respectively. It was further suggested that Tolypella might be a derived group within Nitella. In this investigation into species diversity and relationships in North American Tolypella, sequence data from the plastid genes atpB, psbC, and rbcL were assembled for a broad range of charophycean and land plant taxa. Molecular data were used in conjunction with morphology to test monophyly of the genus and species within it. Phylogenetic analyses of the sequence data showed that Characeae is monophyletic but that Nitelleae is paraphyletic with Tolypella sister to a monophyletic Nitella + Chareae. The results also supported the monophyly of Tolypella and the sections Rothia and Tolypella. Morphologically defined species were supported as clades with little or no DNA sequence differences. In addition, molecular data revealed several lineages and a new species ( T. ramosissima sp. nov.), which suggests greater species diversity in Tolypella than previously recognized. [ABSTRACT FROM AUTHOR]

Background: Infectious salmon anemia (ISA) virus (ISAV) is a pathogen of marine-farmed Atlantic salmon (Salmo salar); a disease first diagnosed in Norway in 1984. This virus, which was first characterized following its isolation in cell culture in 1995, belongs to the family Orthomyxoviridae, genus, Isavirus. The Isavirus genome consists of eight single-stranded RNA segments of negative sense, each with one to three open reading frames flanked by 3' and 5' non-coding regions (NCRs). Although the terminal sequences of other members of the family Orthomyxoviridae such as Influenzavirus A have been extensively analyzed, those of Isavirus remain largely unknown, and the few reported are from different ISAV strains and on different ends of the different RNA segments. This paper describes a comprehensive analysis of the 3' and 5' end sequences of the eight RNA segments of ISAV of both European and North American genotypes, and evidence of quasispecies of ISAV based on sequence variation in the untranslated regions (UTRs) of transcripts., Results: Two different ISAV strains and two different RNA preparations were used in this study. ISAV strain ADL-PM 3205 ISAV-07 (ADL-ISAV-07) of European genotype was the source of total RNA extracted from ISAV-infected TO cells, which contained both viral mRNA and cRNA. ISAV strain NBISA01 of North American genotype was the source of vRNA extracted from purified virus. The NCRs of each segment were identified by sequencing cDNA prepared by three different methods, 5' RACE (Rapid amplification of cDNA ends), 3' RACE, and RNA ligation mediated PCR. Sequence analysis of five clones each derived from one RT-PCR product from each NCR of ISAV transcripts of segments 1 to 8 revealed significant heterogeneity among the clones of the same segment end, providing unequivocal evidence for presence of intra-segment ISAV quasispecies. Both RNA preparations (mRNA/cRNA and vRNA) yielded complementary sequence information, allowing the simultaneous identification and confirmation of the 3' and 5' NCR sequences of the 8 RNA genome segments of both genotypes of ISAV. The 3' sequences of the mRNA transcripts of ADL-ISAV-07 terminated 13-18 nucleotides from the full 3' terminus of cRNA, continuing as a poly(A) tail, which corresponded with the location of the polyadenylation signal. The lengths of the 3' and 5' NCRs of the vRNA were variable in the different genome segments, but the terminal 7 and 11 nucleotides of the 3' and 5' ends, respectively, were highly conserved among the eight genomic segments of ISAV. The first three nucleotides at the 3' end are GCU-3' (except in segment 5 with ACU-3'), whereas at the 5' end are 5'-AGU with the polyadenylation signal of 3-5 uridines 13-15 nucleotides downstream of the 5' end terminus of the vRNA. Exactly the same features were found in the respective complementary 5' and 3' end NCR sequences of the cRNA transcripts of ADL-ISAV-07, indicating that the terminal sequences of the 8 RNA genome segments are highly conserved among the two ISAV genotypes. The 5' NCR sequences of segments 1, 2, 3, 5, and 7, and the 3' NCR sequences of segments 3 and 4 cRNA were 100% identical in the two genotypes, and the 3' NCR sequences of segment 5 cRNA was the most divergent, with a sequence identity of 77.2%., Conclusions: We report for the first time, the presence of intra-segment ISAV quasispecies, based on sequence variation in the NCR sequences of transcripts. In addition, this is the first report of a comprehensive unambiguous analysis of the 3' and 5' NCR sequences of all 8 RNA genome segments from two strains of ISAV representing the two genotypes of ISAV. Because most ISAV sequences are of cDNA to mRNA, they do not contain the 3' end sequences, which are removed during polyadenylation of the mRNA transcripts. We report for the first time the ISAV consensus sequence CAT/ATTTTTACT-3' (in the message sense 5'-3') in all segments of both ISAV genotypes.

In this paper we provide a molecular phylogeny based on three mitochondrial and three nuclear markers for all long-tailed tit species of the genus Aegithalos including several doubtful subspecies (17 taxa) plus three close allies of SE Asian Leptopoecile and North American Psaltriparus. Genus Aegithalos is divided into three major clades, two of them showing only minor differentiation. Separation of two mitchondrial haploytpe clusters in the N Palearctic Long-tailed Tit, Ae. caudatus, was dated back to the Late Pleistocene, however, descendants from both lineages underwent a rapid post-Pleistocene range expansion and largely mixed over the entire distribution area. The Chinese populations of the glaucogularis subspecies group represent a slightly earlier Pleistocene split from the Ae. caudatus clade. Genetic differentiation among several doubtful SE Asian species taxa on the sister clade of the latter N Palearctic/Chinese clade matches the intraspecific differentiation within Ae. caudatus. Unexpectedly, cytochrome-b distances among Himalayan Ae. iouschistos (including the subspecies bonvaloti from China and sharpei from Myanmar) and the Chinese endemic Ae. fuliginosus range at approximately 0.5% and apparently all these extant populations separated only very recently during late Pleistocene times, too. W Himalayan Ae. niveogularis clearly appeared as the sister species of the latter taxon assemblage. Unlike the two latter major clades, Ae. concinnus shows strong intraspecific differentiation with cyt-b distances as high as 6% among two Himalayan populations of ssp. iredalei, ssp. manipurensis from Myanmar and a fourth lineage from SW and SC China including ssp. talifuensis and nominate concinnus. A sister-group relationship between all Ae. concinnus and Ae. leucogenys was strongly supported. N American bushtits of genus Psaltriparus represent the sister clade to Palearctic genus Aegithalos, including a clear split between the minimus and the plumbeus subspecies group which was again dated back to Pleistocene times. The two tit-warbler species of genus Leptopoecile are strongly differentiated from one another and represent an early split from the Aegithalidae tree., (2010 Elsevier Inc. All rights reserved.)

A growing number of molecular studies show that many fungi have phylogeographic structures and that their distinct lineages are usually limited to different continents. As a conservative test of the extent to which wind-dispersed mycorrhizal fungi may exhibit phylogeographic structure, we chose to study Amanita muscaria, a host-generalist, widespread, wind-dispersed fungus. In this paper, we document the existence of several distinct phylogenetic species within A. muscaria, based on multilocus DNA sequence data. According to our findings, A. muscaria has strong intercontinental genetic disjunctions, and, more surprisingly, has strong intracontinental phylogeographic structure, particularly within North America, often corresponding to certain habitats and/or biogeographic provinces. Our results indicate that the view of A. muscaria as a common, widespread, easily identifiable, ecologically plastic fungus with a wide niche does not correctly represent the ecological and biological realities. On the contrary, the strong associations between phylogenetic species and different habitats support the developing picture of ecoregional endemisms and relatively narrow to very narrow niches for some lineages.

The palm tribe Chamaedoreeae reaches its higher diversity in Central America, however, its distribution ranges from the north eastern part of Mexico to Bolivia with a disjunction to the Mascarene Islands in the Indian Ocean. The disjunct distribution of Chamaedoreeae is generally considered a result of Gondwana vicariance and extinction from Africa and/or Madagascar. However, latitudinal migrations and their role in shaping the distribution of this tribe in the Americas have been largely overlooked. In this study we used seven plastid and two nuclear DNA regions to investigate the phylogenetic relationships and biogeography of the Chamaedoreeae. The resulting phylogeny fully resolved the generic relationships within the tribe. The exact area of origin of the tribe remains uncertain, but dating analyses indicated an initial diversification of the Chamaedoreeae during the Early Eocene, followed by long distance dispersion to the Mascarene Islands in the late Miocene. The radiation of Hyophorbe could have taking place on islands in the Indian Ocean now submerged, but its former presence in Africa or Madagascar cannot be ruled out. At least two independent migrations between North and South America predating the rise of the Panama isthmus need to be postulated to explain the distribution of Chamaedoreeae, one during the Middle Eocene and a second during the Miocene. Whereas the traditional interpretation of distribution of Chamaedoreeae species assumes a west Gondwana origin of the group, the findings presented in this paper make it equally possible to interpret the group as a primarily boreotropical element.

Allelic variation within individuals holds information regarding the relationships of organisms, which is expected to be particularly important for reconstructing the evolutionary history of closely related taxa. However, little effort has been committed to incorporate such information for reconstructing the phylogeny of organisms. Haplotype trees represent a solution when one nonrecombinant marker is considered, but there is no satisfying method when multiple genes are to be combined. In this paper, we propose an algorithm that converts a distance matrix of alleles to a distance matrix among organisms. This algorithm allows the incorporation of allelic variation for reconstructing the phylogeny of organisms from one or more genes. The method is applied to reconstruct the phylogeny of the seven native diploid species of Rosa sect. Cinnamomeae in North America. The glyceralgehyde 3-phosphate dehydrogenase (GAPDH), the triose phosphate isomerase (TPI), and the malate synthase (MS) genes were sequenced for 40 individuals from these species. The three genes had little genetic variation, and most species showed incomplete lineage sorting, suggesting these species have a recent origin. Despite these difficulties, the networks (NeighborNet) of organisms reconstructed from the matrix obtained with the algorithm recovered groups that more closely match taxonomic boundaries than did the haplotype trees. The combined network of individuals shows that species west of the Rocky Mountains, Rosa gymnocarpa and R. pisocarpa, form exclusive groups and that together they are distinct from eastern species. In the east, three groups were found to be exclusive: R. nitida-R. palustris, R. foliolosa, and R. blanda-R. woodsii. These groups are congruent with the morphology and the ecology of species. The method is also useful for representing hybrid individuals when the relationships are reconstructed using a phylogenetic network.

This paper focuses on the phylogenetic relationships of eight North American caenophidian snake species (Carphophis amoena, Contia tenuis, Diadophis punctatus, Farancia abacura, Farancia erytrogramma, Heterodon nasicus, Heterodon platyrhinos, and Heterodon simus) whose phylogenetic relationships remain controversial. Past studies have referred to these "relict" North American snakes either as colubrid, or as Neotropical dipsadids and/or xenodontids. Based on mitochondrial DNA ribosomal gene sequences and a likelihood-based Bayesian analysis, our study suggests that these North American snakes are not monophyletic and are nested within a group (Dipsadoidea) that contains the Dipsadidae, Xenodontidae, and Natricidae. In addition, we use the relationships proposed here to highlight putative examples of parallel evolution of hemipenial morphology among snake clades.

The Family Neokoninckophyllidae and its type genus Neokoninckophyllum Fomichev, 1939 (type species: N. tanaicum Fomichev, 1939) are discussed and emended. In addition, the genera Orygmophyllum Fomichev, 1953 and Yuanophylloides Fomichev, 1953, originally included in the Families Campophyllidae Wedekind, 1922 and Lophophyllidae Grabau, 1928, respectively, are emended as well and transferred to the Neokoninckophyllidae. Two early Bashkirian species, viz. Yuanophylloides rectus (Vassilyuk in Aizenverg et al., 1983) and Y. inauditus (Moore and Jeffords, 1945), and the Moscovian Neokoninckophyllum sp. nov. are described on the basis of new collections from the Donets Basin. Neokoninckophyllum tanaicum, Yuanophylloides gorskyi Fomichev, 1953 (both Moscovian in age) and Y. cruciformis Fomichev, 1953 (latest Bashkirian), are redescribed on the basis of peels taken from Fomichev's (1953) type specimens. Derivation of the Family Neokoninckophyllidae from the Subfamily Dibunophyllinae Wang, 1950 is postulated and phylogenetic links within the former are hinted at. The occurrence of Yuanophylloides inauditus in both the Donets Basin and the Western Interior Province of North America points to marine communication between those areas during the Bashkirian. The slightly earlier appearance of the oldest neokoninckophyllids in the Donets Basin, in comparison to North America (i.e., R1 vs R2 ammonoid biozones), documents the common roots and monophyletic development of the Neokoninckophyllidae in both areas. [ABSTRACT FROM AUTHOR]

This contribution to the genus Cantharellus in North America deals with the smaller, reddish pink species from the Gulf of Mexico states and eastern United States. C. texensis sp. nov. is presented as a new southern lookalike of C. cinnabarinus. The morphological species concepts are supported by newly generated molecular sequence data from the protein coding gene tef1. Similarities to C. persicinus, a third pinkish taxon, are discussed. The very different microscopic features for the three taxa are illustrated in detail. C. cinnabarinus is neotypified. C. minor forma intensissima is considered to be possibly unrelated not only to the discussed taxa in this paper but also to typical C. minor. [ABSTRACT FROM AUTHOR]

Amplified Fragment Length Polymorphism (AFLP) markers are formed by selective amplification of DNA fragments from digested total genomic DNA. The technique is popular because it is a relatively inexpensive way to produce large numbers of reproducible genetic markers. In this paper, we describe a Bayesian approach to modeling AFLP marker evolution by nucleotide substitution and an MCMC approach to estimate phylogeny from AFLP marker data. We demonstrate the method on species in Carex section Ovales, a group of sedges common in North America. We compare the results of our analysis with a clustering method based on Nei and Li's restriction-site distance and a two-state Bayesian analysis using MrBay. [ABSTRACT FROM AUTHOR]

The unexpected discovery of extensive intraindividual variation of the 18S rRNA gene in nine North American species of sturgeon (and its absence in the North American paddlefish) was described in a previous paper by Krieger and Fuerst (2002b). As part of the study, genomic 18S rRNA genes from a lake sturgeon (Acipenser fulvescens) individual were amplified by polymerase chain reaction (PCR), cloned and sequenced, resulting in the identification of at least 17 different sequence variants. Because of the number of variants detected and the improbability that such a large number of different alleles are required for survival, these sequence variants were subjected to further analyses (sequence comparison, phylogenetic and relative rate) to examine the possibility that some variants may be pseudogenes. The cDNA produced by reverse transcriptase (RT)-PCR amplification of 18S rRNA isolated from lake sturgeon liver tissue was also sequenced. The topology of the phylogenetic tree produced suggests a split of the sequence variants into two groups: paddlefish-like (PL) alleles and non-paddlefish-like (NPL) alleles. Relative rate comparisons of these two groups indicate that the alleles within the NPL allele group are evolving more quickly than those in the paddlefish-like (PL) group, and so are likely under relaxed functional constraints. Less than one-third of nucleotide changes in the non-paddlefish-like (NPL) alleles occur at positions that are considered to be highly conserved in a universal eukaryotic model of rRNA structure. No substitutions at eukaryotic universally conserved sites occur in the PL alleles. Analysis of the sequence of the RT-PCR product shows that a single lake sturgeon 18S rDNA sequence variant is expressed in major quantities in the liver, and that this single product is identical to the allele most similar in sequence to the paddlefish. These results provide support for the idea that many variants are unimportant for proper cellular function or are pseudogenes. Although concerted evolution has apparently failed to homogenize the many rDNA sequence variants found within sturgeon, the detection of a single major expressed sequence variant in lake sturgeon indicates that the expression of the variants is in fact under the control of selective factors. [ABSTRACT FROM AUTHOR]

Reconstructing a robust species phylogeny and disentangling the evolutionary and biogeographic history of the gymnosperm genus Ephedra, which has a large genome and rich polyploids, remain a big challenge. Here we reconstructed a transcriptome‐based phylogeny of 19 diploid Ephedra species, and explored evolutionary reticulations in this genus represented by 50 diploid and polyploid species, using four low‐copy nuclear and nine plastid genes. The diploid species phylogeny indicates that the Mediterranean species diverged first, and the remaining species split into three clades, including the American species (Clade A), E. rhytidosperma, and all other Asian species (Clade B). The single‐gene trees placed E. rhytidosperma sister to Clade A, Clade B, or Clades A + B in similar proportions, suggesting that radiation and gene flow likely occurred in the early evolution of Ephedra. In addition, reticulate evolution occurred not only among the deep nodes, but also in the recently evolved South American species, which further caused difficulty in phylogenetic reconstruction. Moreover, we found that allopolyploid speciation was pervasive in Ephedra. Our study also suggests that Ephedra very likely originated in the Tethys coast during the late Cretaceous, and the South American Ephedra species have a single origin by dispersal from Mexico or North America. [ABSTRACT FROM AUTHOR]

The family Acipenseridae consists of 25 extant sturgeon species (19 species of Acipenserinae and 6 species of Scaphirhynchinae). Together with two extant paddlefish species, Polyodon spathula and Psephurus gladius (Polyodontidae), it composes the order Acipenseriformes, the most numerous of all living "fossil" fishes. This paper presents results of sequencing of three regions of the cytochrome b gene (650 bp), and fragments of 12S (150 bp) and 16S (350 bp) rRNA genes, from all extant species of Acipenserinae (species of Acipenser and Huso) and Scaphirhynchus albus (Scaphirhynchinae). The phylogenetic tree obtained for combined data is the first comprehensive treatment of phylogeny within the Acipenserinae. Three general conclusions are inferred from the tree: (1) The pallid sturgeon, S. albus, is the sister-species of all species of Acipenser and Huso. (2) The two species of Huso are embedded within the genus Acipenser. It also appears that Huso is not a separate taxonomic unit. (3) There are at least three main clades within Acipenser: A. sturio-A. oxyrinchus, A. schrenckii-A. transmontanus, and all Ponto-Caspian species plus A. dabryanus and A. brevirostrum. There is congruence between ploidy and the branching patterns of the sturgeon species. A hypothetical evolutionary history of the Acipenseriformes based on the paleontological, geological, and molecular data is discussed.

Sidera, belonging to the Rickenella clade of Hymenochaetales, is a worldwide genus with mostly poroid hymenophore of wood-inhabiting fungi. Two new species in the genus, Sidera americana and S. borealis, are described and illustrated from China and North America based on morphological and molecular evidence. They were mainly found growing on rotten wood of Abies, Picea and Pinus. S. americana is characterized by annual, resupinate basidiomata with silk sheen when dry, round pores (9-11 per mm), a dimitic hyphal system, and allantoid basidiospores measuring 3.5-4.2 × 1 µm. S. borealis is characterized by annual, resupinate basidiomata with cream to pinkish buff dry pore surface, angular pores (6-7 per mm), a dimitic hyphal system, and allantoid basidiospores measuring 3.9-4.1 × 1-1.1 µm. Phylogenetic analysis based on a combined 2-locus dataset [ITS1-5.8S-ITS2 (ITS) + nuclear large subunit RNA (nLSU)] shows that the two species are members of Sidera, and they are compared with morphologically similar and phylogenetically related species, respectively. An identification key to 18 accepted species of Sidera in worldwide is provided. [ABSTRACT FROM AUTHOR]

We describe nearly complete skeletons of basal Anseriformes from the Latest Paleocene to the early Eocene of North America and Europe. Collectively, these birds appear to be representative of anseriforms near the divergence of Anhimae and Anseres, but their exact positions relative to these clades remains uncertain. A new family, Anachronornithidae nov. fam., is erected on the basis of one of these, Anachronornis anhimops nov. gen., nov. gen. et sp., to which the others cannot be confidently assigned. The new fossils augment a growing collection of early Pan-Anseriformes, which in their diversity do not paint an unambiguous picture of phylogeny or character state evolution on the path to or within crown-Anseriformes. Anachronornis nov. gen. is similar in some aspects of both cranial and postcranial anatomy to other well-represented early Paleogene Anseriformes and members of Anseres, such as Presbyornis Wetmore, 1926. However, it exhibits a more landfowl-like bill, like that of Anhimae and unlike the spatulate bill of Anseres. Additional specimens of similar basal Anseriformes of uncertain affinities from the early Eocene of North America and Europe further complicate interpretation of character state polarity due to the mosaicism of primitive and derived characters they exhibit. [ABSTRACT FROM AUTHOR]

We describe cranial and mandibular remains of three undescribed individuals of the giant mustelid Megalictis ferox Matthew, 1907 from the latest Arikareean (Ar4), Early Miocene mammal fauna of Nebraska, and Wyoming (USA) housed at the American Museum of Natural History (New York, USA). Our phylogenetic hypothesis indicates that Ar4 specimens assigned to M. ferox constitute a monophyletic group. We assign three additional species previously referred to Paroligobunis to Megalictis: M. simplicidens, M. frazieri, and “M.” petersoni. The node containing these four species of Megalictis and Oligobunis forms the Oligobuninae. We test the hypothesis that Oligobuninae (Megalictis and Oligobunis) is a stem mustelid taxon. Our results indicate that the Oligobuninae form the sister clade to the crown extant mustelids. Based on the cranium, M. ferox is a jaguar-size mustelid and the largest terrestrial mustelid known to have existed. This new material also sheds light on a new ecomorphological interpretation of M. ferox as a bone-crushing durophage (similar to hyenas), rather than a cat-like hypercarnivore, as had been previously described. The relative large size of M. ferox, together with a stout rostrum and mandible made it one of the more powerful predators of the Early Miocene of the Great Plains of North America. [ABSTRACT FROM AUTHOR]

Two new species belonging to the lichen genus Anaptychia are described from western North America. Anaptychia nevadensis is superficially similar to the Eurasian A. desertorum but is distinguished by having longer ascospores, in producing scant pruina only near the lobe tips, and in regularly producing variolaric acid. Anaptychia roemerioides is described to accommodate North American material which has previously been called A. ulotrichoides. It is macro-morphologically identical to the Asian species A. roemeri but differs in having longer ascospores and conidia. Both new species are strongly supported by phylogenetic analysis of ITS sequences. We also call attention to the existence of a further undescribed but possibly cryptic species within A. elbursiana. Variolaric acid is newly reported to occur occasionally in A. desertorum and A. elbursiana. A global key to the desert species of Anaptychia is provided. [ABSTRACT FROM AUTHOR]

Restriction site‐associated DNA sequencing (RAD‐seq) enables obtaining thousands of genetic markers for phylogenomic studies. However, RAD‐seq data are subject to allele dropout (ADO) due to polymorphisms at enzyme cutting sites. We developed a new pipeline, RAD‐seq Allele Dropout Remedy in our study of the gymnosperm genus, Torreya, to mitigate ADO in outgroups by recovering missing loci from previously published transcriptomes. By using RADADOR to supplement Rad‐seq data in combination with plastome and mitochondrial gene sequences, morphology, and fossil records, we reconstructed the phylogenetic and biogeographic histories of the genus and tested hypotheses on anomalies of biodiversity of the eastern Asian‐North American floristic disjunction. Our results showed that our pipeline recovered many loci missing from the outgroup, and the improved data yielded a more robust phylogeny for Torreya. Using the fossilized birth–death model and divergence–extinction–cladogenesis method, we resolved a detailed biogeographic history of Torreya that suggested a Jurassic origin spanning Laurasia and differential speciation and extinction among continents accounting for modern diversity, which is biased toward eastern Asia (EA). The biogeographic results also supported a vicariance origin of modern Torreya from a widespread ancestor in EA and North America (NA) in the mid‐Eocene, and cross Beringian exchange in the early Paleogene before the vicariant isolation, in contrast to the "out of NA" pattern common to gymnosperms and to the "out of EA" hypothesis previously proposed for the genus. Furthermore, we observed phylogenetic discordance between the nuclear and plastid phylogenies for Torreya jackii, suggesting differential lineage sorting of plastid genomes among species of Torreya or plastid genome capture in T. jackii. [ABSTRACT FROM AUTHOR]

Powdery mildews are a monophyletic group of obligate plant pathogenic fungi in the family Erysiphaceae. Powdery mildews are economically important in that they cause damage to many agriculturally significant crops and plants in ecologically important habitats. In this contribution, we introduce a new series of publications focusing on the phylogeny and taxonomy of this group, with an emphasis on specimens collected from North America. The first part of the series focuses on the genus Golovinomyces and includes a section detailing the powdery mildew species concept. We conducted analyses of Golovinomyces spp. with available rDNA sequence data from GenBank and supplemented the data set with rDNA (ITS, 28S, IGS) as well as protein-coding (GAPDH) data from 94 North American collections. Many of the species evaluated are included in phylogenetic and morphological analyses for the first time, including the American species G. americanus, G. brunneopunctatus, G. californicus, G. greeneanus, G. hydrophyllacearum, and G. sparsus. A special emphasis was placed on acquiring ex-type or ex-epitype sequences or presenting reference sequences for phylogenetic-taxonomic purposes. Three new species, G. eurybiarum, G. galiorum, and G. malvacearum, are described, and the new combinations G. fuegianus, G. mutisiae, and G. reginae are introduced. Ex-holotype sequences of Erysiphe sparsa (≡ G. sparsus) reveal that it should be reduced to synonymy with G. ambrosiae, and ex-epitype sequences of G. valerianae reveal that it should be reduced to synonymy with G. orontii. Multiple epitypes are designated with ex-epitype sequences. [ABSTRACT FROM AUTHOR]

Metoposaurids are a clade of large-bodied temnospondyls commonly found in non-marine Late Triassic deposits across northern Pangea. Three taxa are known from North America: Anaschisma browni, Apachesaurus gregorii, and "Metoposaurus" bakeri. While the osteology of most metoposaurids has been recently revised, that of a few taxa, including "Metoposaurus" bakeri remains poorly characterized. This taxon was formally described in 1931 as "Buettneria bakeri," and its taxonomy has remained in flux ever since then. "Metoposaurus" bakeri is the earliest appearing metoposaurid in North America (Carnian of Texas), and Metoposaurus has frequently been utilized as an index taxon of the Otischalkian estimated holochron ('land vertebrate faunachron') and for biostratigraphic correlations with other geographic regions. The taxonomy of this species is therefore relevant for both taxonomic experts and biostratigraphers. Here we redescribe all material from the type locality of "M." bakeri, the Elkins Place bone bed, and perform a phylogenetic analysis using a revised matrix assembled from several previous studies. Anatomical comparisons and phylogenetic analyses do not support placement in either Metoposaurus, a taxon otherwise only found in Europe, or Anaschisma, the only other large-bodied taxon from North America. Therefore, we erect a new genus, Buettnererpeton gen. nov., to accommodate this species. Metoposaurus is consequently absent from North America, and this genus cannot be used in global biostratigraphy. Phylogenetic analyses provide evidence that the phylogeny of the Metoposauridae remains extremely labile, with drastic differences in topological resolution and structure being linked to just a handful of characters and scores. Metoposaurids' morphological conservatism and the increased recognition of intraspecific variation thus continue to be major confounds to elucidating the evolutionary history of this clade. [ABSTRACT FROM AUTHOR]

The genus Rhododendron comprises over 1000 evergreen and deciduous species. In the Pacific Northwest Coast region of North America (PNWC), powdery mildews infecting deciduous Rhododendron spp. are well documented but less so on evergreen Rhododendron spp. Infections of both groups of hosts historically have been attributed to Erysiphe azaleae or E. vaccinii. No formal characterizations of powdery mildew fungi infecting either deciduous or evergreen Rhododendron spp. in the PNWC have been completed. The objectives of this study were to identify the powdery mildew pathogens infecting evergreen Rhododendron spp. in the PNWC and to assess the phylogenetic position of these fungi within the Erysiphaceae. To ascertain valid taxonomic conclusions, and to determine whether potential introductions of exotic Rhododendron powdery mildews in North America have occurred, it was necessary to put the new North American phylogenetic data into a worldwide context. Therefore, available phylogenetic data from all Erysiphe spp. on Rhododendron have been included in our analyses. Based on analyses of numerous new internal transcribed spacer (ITS) and 28S rDNA sequences and already available sequences deposited in GenBank retrieved from evergreen and deciduous Rhododendron spp., the following Erysiphe spp. could be phylogenetically confirmed (all belonging to Erysiphe sect. Microsphaera): Erysiphe azaleae nom. cons. (Oidium ericinum could be verified as a synonym), E. digitata (holotype sequenced), E. izuensis, and E. vaccinii. Erysiphe azaleae and E. vaccinii are epitypified with sequenced specimens, and an ex-neotype sequence has been obtained for Oidium ericinum. Erysiphe rhododendri (Erysiphe sect. Erysiphe), only known from two collections in India (Himalayan region), was not available for phylogentic analyses. [ABSTRACT FROM AUTHOR]

Angelica is a taxonomically complex genus widespread throughout the North Temperate Zone. Previous phylogenetic studies of the genus have focused primarily on its East Asian species. The relationships among its North American members, the monophyly of these species, and the value of fruit morphology in circumscribing its taxa have yet to be examined. This study represents the most comprehensive sampling of Angelica to date (100 species) and includes all 26 species in North America. Relationships are inferred using Bayesian inference, maximum likelihood, and maximum parsimony analyses of ITS sequences and, for multiple accessions of each North American species, cpDNA ndhF‐rpl32, rpl32‐trnL, and psbM‐psbD sequences. The fruit morphological characters examined were those considered phylogenetically important in East Asian Angelica. The results revealed that the North American species fell into three major clades: North American Angelica clade, Archangelica clade, and the Eurasian Angelica clade. Angelica dawsonii has affinities with Lomatium brandegeei. Fourteen species within the North American Angelica clade were strongly supported as monophyletic. Two paraphyletic species resulted in new combinations in A. lineariloba and A. venenosa. Conflict between the ITS‐derived and cpDNA‐derived phylogenies and the lack of resolution in portions of the trees may be due to chloroplast capture and rapid species radiation. Fruit morphology supported some interspecific relationships based on molecular data, and relationships revealed by ITS and cpDNA data were roughly in accordance with fruit classification type and geographic distribution region, respectively. A diagnostic key based on fruit morphology is provided for the identification of the North American Angelica taxa. [ABSTRACT FROM AUTHOR]

Fagus L. is a key component in temperate deciduous broadleaf forests of the Northern Hemisphere. However, its biogeographic history has not been examined under the framework of a fully resolved and reasonably time‐calibrated phylogeny. In this study, we sequenced 28 nuclear single/low‐copy loci (18 555 bp in total) of 11 Fagus species/segregates and seven outgroups. Phylogenetic trees were reconstructed using both concatenation‐based (maximum parsimony, maximum likelihood, and Bayesian inference) and coalescent‐based methods (StarBEAST2, ASTRAL). The monophyly of two subgenera (Fagus and Engleriana) and most sections was well supported, except for sect. Lucida, which was paraphyletic with respect to sect. Longipetiolata. We also found a major phylogenetic conflict among North American, East Asian, and West Eurasian lineages of subgen. Fagus. Three segregates that have isolated distribution (F. mexicana, F. multinervis, and F. orientalis) were independent evolutionary units. Biogeographic analysis with fossils suggested that Fagus could have originated in the North Pacific region in late early Eocene. Major diversifications coincided with a climate aberration at the Eocene/Oligocene boundary and the global cooling since mid‐Miocene. The late Miocene accelerated global cooling and the Pleistocene glaciations would have driven beeches into East Asia, North America, and West Eurasia. Meanwhile, range reduction and extinction in high latitudes, central Asia, and western North America converged to form the beech modern distribution pattern. This study provides a first attempt to disentangle the biogeographic history of beeches in the context of a nearly resolved and time‐calibrated phylogeny, which could shed new insights into the formation of the temperate biome in the Northern Hemisphere. [ABSTRACT FROM AUTHOR]

Theromyzon Philippi, 1867 is a genus of sanguivorous, freshwater leeches in the family Glossiphoniidae. The genus is broadly distributed across the globe, possibly due to the frequent feeding in the nasopharyngeal cavities of migratory waterfowl that may allow for long distance dispersal. The genus has a history of taxonomic confusion resulting from mischaracterisations of key morphological features of type specimens that have produced several re-descriptions and synonyms. Here, we bring partial order to this confusion through robust morphological investigations of newly collected North American (and a single South American) specimens, representing most of the known species diversity from this continent. We also produce the first species-level phylogeny for Theromyzon and attempt to understand species boundaries regarding both morphology and genetics. Our results demonstrate that there are at least five species of Theromyzon present in North America (T. bifarium, T. tessulatum, T. rude, T. trizonare, and a clade that needs further investigation), and a hitherto undescribed taxon that does not conform to any previously published description, and represents a unique lineage in the phylogeny; we describe this new species under the name Theromyzon tigris sp. nov. This study sheds light on the discriminatory power of select morphological characters and the distribution of phenotypes within the genus. We also provide a comprehensive classification framework for the known species within the genus designed to facilitate identification and minimise future taxonomic confusion. [ABSTRACT FROM AUTHOR]

To investigate the evolutionary relationships and biogeographical history among the species of Calamagrostis and other members of subtribes Agrostidinae, Calothecinae, Echinopogoninae, and Paramochloinae, we generated a phylogeny based on DNA sequences from one nuclear ribosomal (ITS) and three plastid regions (rpl32‐trnL spacer, rps16‐trnK spacer, and rps16 intron). Based on our phylogeny, we identified seven species groups (clades) within Calamagrostis: the Meridionalis group comprises two species from Central and South America, the Americana group comprises species from North America, the Deyeuxia and Epigeios groups comprise species from Eurasia, the Orientalis group comprises species from East Asia, the Purpurea group comprises species from Eurasia and North America, and the Calamagrostis group comprises species from Eurasia and North America. We hypothesize that Calamagrostis originated in North America with the primary split of the Meridionalis group, followed by split between the autochthonous Americana group and two future Eurasian branches encompassing all the remaining groups, which possibly dispersed into Eurasia independently. The molecular data suggest that hybridization and genomic introgression played a prominent role in the evolutionary history of Calamagrostis. We propose a new genus, Condilorachia, segregated from Trisetum s.l., with three species from South America for which we propose new combinations: Condilorachia bulbosa, Condilorachia brasiliensis, and Condilorachia juergensii; a new combination in Greeneochloa, Greeneochloa expansa; and the subsumption of Dichelachne into Pentapogon with 20 new combinations: Pentapogon avenoides, Pentapogon brassii, Pentapogon chaseianus, Pentapogon crinita, Pentapogon densus, Pentapogon frigidus, Pentapogon gunnianus, Pentapogon hirtella, Pentapogon inaequiglumis, Pentapogon lautumia, Pentapogon micrantha, Pentapogon parva, Pentapogon quadrisetus, Pentapogon rara, Pentapogon robusta, Pentapogon scaberulus, Pentapogon sclerophyllus, Pentapogon suizanensis, Pentapogon sieberiana, and Pentapogon validus. We provide a diagnosis, description, and a key to the species of Condilorachia. [ABSTRACT FROM AUTHOR]

Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships. In this study, 785 single‐copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus Malus sensu lato, an economically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy events. The nuclear phylogeny recovered the monophyly of Malus s.l. (including Docynia); however, the genus was supported to be biphyletic in the plastid phylogeny. An ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear discordance. Our conflict analysis demonstrated that ILS, hybridization, and allopolyploidy could explain the widespread nuclear gene tree discordance. One deep hybridization event (Malus doumeri) and one recent event (Malus coronaria) were detected in Malus s.l. Furthermore, our historical biogeographic analysis integrating living and fossil data supported a widespread East Asian‐western North American origin of Malus s.l. in the Eocene, followed by several extinction and dispersal events in the Northern Hemisphere. We also propose a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming data sets. [ABSTRACT FROM AUTHOR]

With 30 species and a natural distribution in North America, 28 confined to Mexico, Physocyclus Simon 1893 is the most diverse genus within the pholcid spider subfamily Arteminae. This paper provides the first phylogenetic test of the genus's monophyly through a cladistic analysis of 54 morphological characters using equal and implied weighting. The equally weighted analysis found 12 most parsimonious trees, whereas the analysis with implied weights varying the concavity values (K = 6-10) found five or six most parsimonious trees. The monophyly of the genus Physocyclus is supported by three synaphomorphies: 1) the paired ventral apophysis on the anterior part of the epigynum; 2) the lateral constraints in the middle part of the epigynum; and 3) the arc of the uterus, with a single sclerotized projection on the anterior part. The genus Physocyclus contains two clades treated as species groups: the globosus group, with 11 species, and the dugesi group with 19 species. The species relationships within the globosus group were better resolved than those in the dugesi group. The globosus group has a biogeographical distribution pattern in the Mesoamerican and Mexican Mountain biotic components, whereas the dugesi group has a distribution pattern in the Mesoamerican and Continental Nearctic biotic components. Given the complex biogeography in Mexico, apparently a large-scale vicariant event separated the two major clades within the genus Physocyclus. [ABSTRACT FROM AUTHOR]

Abstract: Sauropod dinosaurs reached their acme in abundance and diversity in North America during the Late Jurassic. Persisting in lesser numbers into the Early Cretaceous, sauropods disappeared from the North American fossil record from the Cenomanian until the Campanian or Maastrichtian stage of the Late Cretaceous. This ca. 25–30million-year long sauropod hiatus has been attributed to either a true extinction, perhaps due to competition with ornithischian dinosaurs, or a false extinction, due to non-preservation of sediments bearing sauropods. The duration of the sauropod hiatus remains in question due to uncertainty in the ages and affinities of the specimens bounding the observed gap. In this paper, we re-examine the phylogenetic affinity of materials from Campanian-aged sediments of Adobe Canyon, Arizona that currently mark the end of the sauropod hiatus. Based on the original description of those remains and new specimens from the same formation, we conclude that the Adobe Canyon vertebrae do not pertain to titanosaurs, but to hadrosaurid dinosaurs. Other reports of Campanian North American titanosaurs are imprecisely or erroneously dated and/or identified. Based on this reassessment, the sauropod hiatus extended until the last 5millionyears of the Cretaceous. Reintroduction of sauropods into North America in the Maastrichtian is first registered ca. 30millionyears after the first recorded dispersals of dinosaur taxa between the continent and Asia (e.g., ceratopsians, pachycephalosaurids, theropods), but is nearly coincident with the dispersal of derived hadrosaurids to South America. [ABSTRACT FROM AUTHOR]

In this paper, we test the phylogenetic utility of the nuclear gene beta-actin for the sunfish genus Lepomis using maximum parsimony and maximum likelihood analyses. Using only the beta-actin sequence all major species-clades were recovered in both analyses. However, more basal nodes were only weakly supported. Results indicate that beta-actin performs moderately well as a phylogenetic marker and should be subjected to further use. Secondly, we explore the utility of the beta-actin gene to develop a rapid, non-lethal polymerase chain reaction (PCR)-based species identification method. We developed taxon-specific primers to identify Lepomis species based on polymorphisms in the introns of the beta-actin nuclear gene. Products were diagnostic for all species except for the L. cyanellus/L. symmetricus and L. minatus/L. punctatus species pairs. [ABSTRACT FROM AUTHOR]

Abstract: Although the deserts of North America are of very recent origin, their characteristic arid-adapted endemic plant lineages have been suggested to be much older. Earlier researchers have hypothesized that the ancestors of many of these modern desert lineages first adapted to aridity in highly localized arid or semi-arid sites as early as the late Cretaceous or early Tertiary, and that these lineages subsequently spread and diversified as global climate became increasingly arid during the Cenozoic. No study has explicitly examined these hypotheses for any North American arid-adapted plant group. The current paper tests these hypotheses using the genus Tiquilia (Boraginaceae), a diverse North American desert plant group. A strongly supported phylogeny of the genus is estimated using combined sequence data from three chloroplast markers (matK, ndhF, and rps16) and two nuclear markers (ITS and waxy). Ages of divergence events within the genus are estimated using penalized likelihood and a molecular clock approach on the ndhF tree for Tiquilia and representative outgroups, including most of the major lineages of Boraginales. The dating analysis suggests that the stem lineage of Tiquilia split from its nearest extant relative in the Paleocene or Eocene (∼59–48Ma). This was followed by a relatively long period before the first divergence in the crown group near the Eocene/Oligocene boundary (∼33–29Ma), shortly after the greatest Cenozoic episode of rapid aridification. Divergence of seven major lineages of Tiquilia is dated to the early-to-mid Miocene (∼23–13Ma). Several major lineages show a marked increase in diversification concomitant with the onset of more widespread semi-arid and then arid conditions beginning in the late Miocene (∼7Ma). This sequence of divergence events in Tiquilia agrees well with earlier researchers’ ideas concerning North American desert flora assembly. [Copyright &y& Elsevier]

As currently delineated, Hygrophorus sect. Olivaceoumbrini is a polyphyletic assembly within subg. Colorati, encompassing glutinous and pigmented taxa. According to available literature, between a dozen and twenty species may belong in the section, mostly represented in continental and boreal forests of Europe and North America. However, the limited phylogenetic and biogeographic coverage of the genus does not presently allow for a reliable assessment of its taxonomic boundaries, nor does it provide a complete picture of species diversity within sect. Olivaceoumbrini. In an ongoing effort to confer an evolutionary backbone to Hygrophorus systematics, we assembled and analysed a dataset comprising 268 intercontinental sequences, including holotypes of 7 taxa previously not positioned phylogenetically, and enriched with collections from largely unexplored Mediterranean and Anatolian ecosystems. Overall, 30 clades are identified within 5 distinct lineages, including 11 species putatively new to science. Seven of these are formally described here as H. agathosmoides, H. albofloccosus, H. canadensis, H. limosus, H. marcocontui, H. pinophilus and H. pustulatoides spp. nov. This enriched coverage of section Olivaceoumbrini s.lat. calls for a re-evaluation of its natural boundaries into a core monophyletic clade, including H. olivaceoalbus and five closely related lookalikes, as well as the assignment of the section rank to the four remaining lineages: sect. Fuscocinerei sect. nov., sect. Limacini sect. nov., sect. Nudolidi sect. nov. and sect. Tephroleuci, respectively. We also stabilize the usage of six historical names, H. glutinifer, H. hyacinthinus, H. mesotephrus, H. olivaceoalbus, H. pustulatus and H. tephroleucus, through designation of two neotypes, three lectotypes and four epitypes. [ABSTRACT FROM AUTHOR]

Evolutionary history, systematics and taxonomy of charrs of the genus Salvelinus and especially of the representatives of the S. alpinus–S. malma species complex remain confused that is connected with a substantial ecological and morphological flexibility of this group and with supposed ancient hybridization between some taxa. For the analysis of phylogenetic relationships and introgressive hybridization between the species of the genus Salvelinus including three endemic species from Lake El'gygytgyn and all main representatives of the S. alpinus–S. malma species complex, nucleotide sequences of the mtDNA control region and two nuclear genes (ITS1 and RAG1) were analyzed. The differences in the topologies of individual gene trees, among other reasons, were connected with incomplete lineage sorting and historical introgressive hybridization between certain taxa. Several cases of mtDNA capture by different taxa and phylogenetic groups were proposed. Main phylogenetic groups of the S. alpinus–S. malma species complex were revised. The origin and phylogenetic relationships of southern Dolly Varden from North America were not unambiguously defined. We proposed that introgressive hybridization had an important role in the evolutionary history of charrs, in particular, in the appearance of a high level of morphological, ecological and taxonomical diversity. [ABSTRACT FROM AUTHOR]

Heterobasidion species are amongst the most intensively studied polypores because several species are aggressive white rot pathogens of managed coniferous forests mainly in Europe and North America. In the present study, both morphological and multilocus phylogenetic analyses were carried out on Heterobasidion samples from Asia, Oceania, Europe and North America. Three new taxa were found, i.e., H. armandii , H. subinsulare , and H. subparviporum are from Asia and are described as new species. H. ecrustosum is treated as a synonym of H. insulare. So far, six taxa in the H. annosum species complex are recognized. Heterobasidion abietinum , H. annosum , and H. parviporum occur in Europe, H. irregulare , and H. occidentale in North America, and H. subparviporum in East Asia. The North American H. irregulare was introduced to Italy during the Second World War. Species in the H. annosum complex are pathogens of coniferous trees, except H. subparviporum that seems to be a saprotroph. Ten species are found in the H. insulare species complex, all of them are saprotrophs. The pathogenic species are distributed in Europe and North America; the Asian countries should consider the European and North American species as entry plant quarantine fungi. Parallelly, European countries should consider the American H. occidentale and H. irregulare as entry plant quarantine fungi although the latter species is already in Italy, while North America should treat H. abietinum , H. annosum s.s., and H. parviporum as entry plant quarantine fungi. Eight Heterobasidion species found in the Himalayas suggest that the ancestral Heterobasidion species may have occurred in Asia. [ABSTRACT FROM AUTHOR]

The timing of non-avian dinosaur decline is one of the most debated subjects in dinosaur palaeontology. Dinosaur faunas from the last few million years of the Mesozoic appear far less diverse than those from earlier in the Cretaceous, a trend that could suggest non-avian dinosaur extinction occurred gradually. However, the limited nature of the latest Cretaceous dinosaur record outside western North America has obscured patterns in dinosaur diversity just before the extinction. Here, I describe two associated skeletons and several isolated fossils recovered from the New Egypt Formation of New Jersey, a latest Maastrichtian unit that underlies the K–Pg boundary. The larger skeleton appears to be a small-bodied adult from a lineage outside Hadrosauridae, the dominant group of these animals during the Maastrichtian, that persisted along the eastern coast of North America. Smaller specimens are identifiable as juvenile hadrosauromorphs. These results substantiate an important assemblage of herbivorous dinosaurs from the poorly-known Cretaceous of eastern North America. The marine depositional setting for these skeletons demonstrates that proposed ecosystem preferences among hadrosauromorphs may be biased by post-mortem transportation, and the adult skeleton has implications for assessing the proposed relictual nature of Late Cretaceous eastern North American vertebrates. [ABSTRACT FROM AUTHOR]

The shape of the tree of life is the result of shifting diversification rates, and identifying the factors driving these shifts is one of the main aims in evolutionary biology. Various biotic and abiotic factors have been proposed to have an impact on mammal diversification, such as climatic and tectonic changes, the acquisition of new traits, and expansion into new ecosystems or landmasses.We used phylogenetic comparative methods to quantify the influence of potential drivers on diversification patterns in extant squirrels (Sciuridae, Rodentia). We conducted a multilayer approach, comparing diversification rates among squirrel lineages depending on their degree of biome specialisation, biogeographic realm occupancy, locomotion adaptations, and presence in mountainous regions.We generated the most complete phylogeny of squirrels to date, encompassing almost 80% of the extant species, and applied multiple and binary state‐dependent diversification models. All the traits examined showed an influence on diversification rates.The biome specialist lineages showed the highest speciation rates, suggesting a major role of bioclimatic specialisation on macroevolutionary patterns. A single major event, the Miocene–Pleistocene radiation of terrestrial‐adapted lineages in North America, left a signal that was recovered in two of our analyses. Both the Nearctic lineages and the terrestrial‐adapted lineages showed high speciation rates, highlighting the fact that that major evolutionary episodes may produce confounding effects in state‐dependent diversification models.Ancestral reconstructions showed that cold and warm intervals in Earth's history had different effects on squirrels' diversification, depending on their climatic affinities. Tropical and arboreal squirrels evolved predominantly in the warm intervals, while terrestrial and cold‐adapted squirrels radiated in the cold intervals.Our findings suggest that, while global climatic shifts are key for the speciation processes in mammalian lineages, lineage‐specific ecological adaptations are critical modulators of the responses of lineages to such environmental shifts, in an interplay that ultimately affects their diversification patterns. [ABSTRACT FROM AUTHOR]

This contribution presents a complete revision of the extinct geoemydid Echmatemys from North America, based on new information and a re-evaluation of previously published specimens. Echmatemys is the most diverse and widely distributed geoemydid turtle in the fossil record of North America, known from numerous shells. The different morphotypes are assigned to the currently accepted valid species and their evolutionary history is evaluated in a cladistic context. Their function is further evaluated with an anatomical network analysis. This re-appraisal is based mainly on 'Gilmore's slab', a slab containing several turtle shells collected from the Bridgerian of Levett Creek (Wyoming, USA). The fossils from this slab are described in detail for the first time and are completely re-identified. As this slab represents a snapshot of the turtle community in past Wyoming during the Bridgerian it offers a unique opportunity to discuss the evolution and diversity of Echmatemys. The morphological variability in the shells of Echmatemys challenges its recovery as a monophyletic group under parsimony analysis. Also, most Echmatemys spp. are recovered in a derived position within Geoemydidae, a result that poses new problems in the interpretation of the origin and the palaeobiogeographical evolution of this clade in North America. [ABSTRACT FROM AUTHOR]

Investigating the biogeographical disjunction of East Asian and North American flora is key to understanding the formation and dynamics of biodiversity in the Northern Hemisphere. The small Cupressaceae genus Thuja, comprising five species, exhibits a typical disjunct distribution in East Asia and North America. Owing to obscure relationships, the biogeographical history of the genus remains controversial. Here, complete plastomes were employed to investigate the plastome evolution, phylogenetic relationships, and biogeographic history of Thuja. All plastomes of Thuja share the same gene content arranged in the same order. The loss of an IR was evident in all Thuja plastomes, and the B-arrangement as previously recognized was detected. Phylogenomic analyses resolved two sister pairs, T. standishii-T. koraiensis and T. occidentalis-T. sutchuenensis, with T. plicata sister to T. occidentalis-T. sutchuenensis. Molecular dating and biogeographic results suggest the diversification of Thuja occurred in the Middle Miocene, and the ancestral area of extant species was located in northern East Asia. Incorporating the fossil record, we inferred that Thuja likely originated from the high-latitude areas of North America in the Paleocene with a second diversification center in northern East Asia. The current geographical distribution of Thuja was likely shaped by dispersal events attributed to the Bering Land Bridge in the Miocene and subsequent vicariance events accompanying climate cooling. The potential effect of extinction may have profound influence on the biogeographical history of Thuja. [ABSTRACT FROM AUTHOR]

Background: The plant-parasitic nematode Hoplolaimus columbus is a pathogen that uses a wide range of hosts and causes substantial yield loss in agricultural fields in North America. This study describes, for the first time, the complete mitochondrial genome of H. columbus from South Carolina, USA. Methods: The mitogenome of H. columbus was assembled from Illumina 300 bp pair-end reads. It was annotated and compared to other published mitogenomes of plant-parasitic nematodes in the superfamily Tylenchoidea. The phylogenetic relationships between H. columbus and other 6 genera of plant-parasitic nematodes were examined using protein-coding genes (PCGs). Results: The mitogenome of H. columbus is a circular AT-rich DNA molecule 25,228 bp in length. The annotation result comprises 12 PCGs, 2 ribosomal RNA genes, and 19 transfer RNA genes. No atp8 gene was found in the mitogenome of H. columbus but long non-coding regions were observed in agreement to that reported for other plant-parasitic nematodes. The mitogenomic phylogeny of plant-parasitic nematodes in the superfamily Tylenchoidea agreed with previous molecular phylogenies. Mitochondrial gene synteny in H. columbus was unique but similar to that reported for other closely related species. Conclusions: The mitogenome of H. columbus is unique within the superfamily Tylenchoidea but exhibits similarities in both gene content and synteny to other closely related nematodes. Among others, this new resource will facilitate population genomic studies in lance nematodes from North America and beyond. [ABSTRACT FROM AUTHOR]