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Premise: Spectroscopy is a powerful remote sensing tool for monitoring plant biodiversity over broad geographic areas. Increasing evidence suggests that foliar spectral reflectance can be used to identify trees at the species level. However, most studies have focused on only a limited number of species at a time, and few studies have explored the underlying phylogenetic structure of leaf spectra. Accurate species identifications are important for reliable estimations of biodiversity from spectral data. Methods: Using over 3500 leaf‐level spectral measurements, we evaluated whether foliar reflectance spectra (400–2400 nm) can accurately differentiate most tree species from a regional species pool in eastern North America. We explored relationships between spectral, phylogenetic, and leaf functional trait variation as well as their influence on species classification using a hurdle regression model. Results: Spectral reflectance accurately differentiated tree species (κ = 0.736, ±0.005). Foliar spectra showed strong phylogenetic signal, and classification errors from foliar spectra, although present at higher taxonomic levels, were found predominantly between closely related species, often of the same genus. In addition, we find functional and phylogenetic distance broadly control the occurrence and frequency of spectral classification mistakes among species. Conclusions: Our results further support the link between leaf spectral diversity, taxonomic hierarchy, and phylogenetic and functional diversity, and highlight the potential of spectroscopy to remotely sense plant biodiversity and vegetation response to global change. [ABSTRACT FROM AUTHOR]

Geckos are a speciose and globally distributed clade of Squamata (lizards, including snakes and amphisbaenians) that are characterized by a host of modifications for nocturnal, scansorial and insectivorous ecologies. They are among the oldest divergences in the lizard crown, so understanding the origin of geckoes (Gekkota) is essential to understanding the origin of Squamata, the most species-rich extant tetrapod clade. However, the poor fossil record of gekkotans has obscured the sequence and timing of the assembly of their distinctive morphology. Here, we describe the first North American stem gekkotan based on a three-dimensionally preserved skull from the Morrison Formation of western North America. Despite its Late Jurassic age, the new species already possesses several key characteristics of the gekkotan skull along with retained ancestral features. We show that this new stem gekkotan, and several previously named species of uncertain phylogenetic relationships, comprise a widespread clade of early crown lizards, substantiating faunal homogeneity in Laurasia during the Late Jurassic that extended across disparate ecological, body-size and physiological classes. [ABSTRACT FROM AUTHOR]

Bryoria (Parmeliaceae, Ascomycota) is one of the dominant genera of hair lichens in western North America and is characteristic of high-elevation conifer forest ecosystems. In areas where Bryoria is abundant, it is common to find thalli in which the thalline filaments become conglutinated, forming brittle dead zones. After sampling Bryoria thalli across western Canada and the northwestern United States at different times of the year, we found that this dieback phenomenon is associated with the winter growth of a mold-forming basidiomycete. We report that this fungus belongs to Athelia (Atheliaceae, Basidiomycota), a genus known to contain lichen pathogens, most notably A. arachnoidea. By sequencing a combination of genetic markers—nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS), partial nuc 28S rDNA (28S), and partial translation elongation factor 1-α (TEF1)—paired with morphometric analyses, we reveal the involvement of at least three additional lineages of lichen-associated Athelia and describe one as a new species, A. abscondita. Athelia abscondita is morphologically distinguished from other Athelia species by its basidia and basidiospores, was found to frequently infect members of Bryoria sect. Implexae, and was occasionally on other foliose and fruticose species within Parmeliaceae. [ABSTRACT FROM AUTHOR]

Lampreys are an ancient lineage of jawless fish for which the relationships among some lineages are uncertain. We addressed these information gaps for Lampetra species with a focus on western North America. Phylogenetic analysis using all publicly available sequences of two mitochondrial genes—cyt b and COI—supported designation of western North American Lampetra as a distinct genus from Lampetra in Europe, Asia, and eastern North America. Species delimitation analysis of cyt b sequences identified seven species, only three of which are currently recognized. Lampetra ayresii and L. richardsoni, regarded as separate under the "paired species concept," were not genetically distinct; we recommend synonymizing L. richardsoni with L. ayresii because the latter has precedence, yet continuing to recognize each ecotype using its current common name. Other than the widespread L. ayresii clade, all other species exhibited limited ranges often restricted to one or two locations. Within headwaters of the Willamette River, L. ayresii demonstrated strong genetic structure and lack of gene flow among subbasins, indicating that the subbasin scale may represent an appropriate management unit. However, the appropriate management scale in other areas may differ based on evolutionary histories and gene flow. Subsequent work is needed across western North America to better delineate the ranges of the aforementioned species and to evaluate whether other unrecognized taxa in this lineage may be present. [ABSTRACT FROM AUTHOR]

Premise: The true blueberries (Vaccinium sect. Cyanococcus; Ericaceae), endemic to North America, have been intensively studied for over a century. However, with species estimates ranging from nine to 24 and much confusion regarding species boundaries, this ecologically and economically valuable group remains inadequately understood at a basic evolutionary and taxonomic level. As a first step toward understanding the evolutionary history and taxonomy of this species complex, we present the first phylogenomic hypothesis of the known diploid blueberries. Methods: We used flow cytometry to verify the ploidy of putative diploid taxa and a target‐enrichment approach to obtain a genomic data set for phylogenetic analyses. Results: Despite evidence of gene flow, we found that a primary phylogenetic signal is present. Monophyly for all morphospecies was recovered, with two notable exceptions: one sample of V. boreale was consistently nested in the V. myrtilloides clade and V. caesariense was nested in the V. fuscatum clade. One diploid taxon, Vaccinium pallidum, is implicated as having a homoploid hybrid origin. Conclusions: This foundational study represents the first attempt to elucidate evolutionary relationships of the true blueberries of North America with a phylogenomic approach and sets the stage for multiple avenues of future study such as a taxonomic revision of the group, the verification of a homoploid hybrid taxon, and the study of polyploid lineages within the context of a diploid phylogeny. [ABSTRACT FROM AUTHOR]

Generic delimitation in Caryophyllaceae has been challenging and has been informed most recently by use of molecular phylogenetic data. In this study, analysis of 29 samples from the small segregate Mononeuria using nuclear ITS and plastid rps16 data revealed it to be polyphyletic. The type species, (M. patula) and two other species (M. muscorum and M. paludicola) were shown to belong to the Sabulina clade. The remaining species formed a clade that also included the previously monotypic Geocarpon and was sister to a heterogeneous group that included the Hawaiian Schiedea and three other monotypic genera, Honckenya , Wilhelmsia and Triplateia. Although several nomenclatural options are available, we propose to place the species from this clade into a single genus, Geocarpon , which basically follows the most recent treatment after exclusion of Sabulina spp. but with the necessary new genus placements. New combinations are proposed: Sabulina muscorum ; Sabulina paludicola ; Geocarpon carolinianum ; Geocarpon cumberlandensis ; Geocarpon glabrum ; Geocarpon groendlandicum ; Geocarpon nuttallii and Geocarpon uniflorum. Analysis of the sequence data revealed remarkable variability among populations of Sabulina patula (formerly Mononeuria patula), Sabulina paludicola (formerly Mononeuria paludicola) and Geocarpon groenlandicum (formerly Mononeuria groenlandica), suggesting that cryptic species may be present. The data also suggested that broader sampling of Sabulina and Geocarpon could lead to increased understanding of the timing and origins of occupation of calcareous glades and rock outcrop habitats in eastern North America. [ABSTRACT FROM AUTHOR]

Clematis subgenus Viorna of North America currently consists of 21 species with most of the diversity found in the southeastern United States. Past taxonomic treatments of Clematis subg. Viorna have varied greatly, which has led to unclear species limits across multiple species complexes. Often recognized as a single, polymorphic species with a high degree of ecological amplitude, variation in the Clematis reticulata species complex has previously been attributed to phenotypic plasticity. A combination of herbarium specimen examination and extensive fieldwork led to the formation of seven a priori morphological groups, or hypothesized taxa, in the C. reticulata species complex based on previously used and novel morphological characters. We employ an integrative approach to species delimitation with data from morphometric studies of herbarium and common garden datasets, as well as a phylogeny inferred from ddRADseq. Of the seven hypothesized taxa, six were supported by evidence from morphology and phylogeny with corroborating biogeography and ecology. Recognition of Clematis terminalis sp. nov. renders C. subreticulata comb. nov. paraphyletic. Because of its morphological, ecological, and phenological distinctiveness, it may represent a case of peripheral speciation by isolation. Four new species are recognized: C. arenicola sp. nov., C. cumberlandensis sp. nov., C. ouachitensis sp. nov., and C. terminalis sp. nov. Viorna subreticulata is given a new combination in Clematis and the newly defined C. reticulata s.s. is re-circumscribed. An updated dichotomous key, species descriptions, ecological notes, and distribution maps are provided. [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]

Orthopoxviruses (OPXVs) not only infect their natural hosts, but some OPXVs can also cause disease in humans. Previously, we partially characterized an OPXV isolated from an 18-year-old male living in Northern Norway. Restriction enzyme analysis and partial genome sequencing characterized this virus as an atypical cowpox virus (CPXV), which we named CPXV-No-H2. In this study, we determined the complete genome sequence of CPXV-No-H2 using Illumina and Nanopore sequencing. Our results showed that the whole CPXV-No-H2 genome is 220,276 base pairs (bp) in length, with inverted terminal repeat regions of approximately 7 kbp, containing 217 predicted genes. Seventeen predicted CPXV-No-H2 proteins were most similar to OPXV proteins from the Old World, including Ectromelia virus (ECTV) and Vaccinia virus , and North America, Alaskapox virus (AKPV). CPXV-No-H2 has a mosaic genome with genes most similar to other OPXV genes, and seven potential recombination events were identified. The phylogenetic analysis showed that CPXV-No-H2 formed a separate clade with the German CPXV isolates CPXV_GerMygEK938_17 and CPXV_Ger2010_MKY, sharing 96.4 and 96.3% nucleotide identity, respectively, and this clade clustered closely with the ECTV-OPXV Abatino clade. CPXV-No-H2 is a mosaic virus that may have arisen out of several recombination events between OPXVs, and its phylogenetic clustering suggests that ECTV-Abatino-like cowpox viruses form a distinct, new clade of cowpox viruses. [ABSTRACT FROM AUTHOR]

Haustoriid amphipods have received little recent attention and their systematics and phylogenetics are largely unresolved. Some efforts have been made at classifying the family within the broader Amphipoda, but there is persistent incongruence in its placement among different authors and techniques. Furthermore, there exists no phylogenetic hypothesis of intrafamilial relationships. In this work, we evaluate the competing hypotheses on the phylogenetic position of the Haustoriidae within Amphipoda by examining new and previously published sequences of nearly 100 species across 38 families. We find strong support for the Haustoriidae as basal gammarids, and that other families placed within the parvorder 'Haustoriidira' are spread across Amphipoda. The radiation began during the Eocene and may have been driven in North America by the rapid filling of a coastal niche opened by the Chesapeake Bay impact crater. Unlike previous work, we find that the Pacific-endemic genus Eohaustorius is the most basal haustoriid, and that it separated from the rest of the family ~31 Mya. Finally, we provide taxonomic recommendations for relationships within Haustoriidae, including the elevation of a new genus, Cryptohaustorius gen. nov.. We conclude by recommending that the 'Haustoriidira' be abandoned. [ABSTRACT FROM AUTHOR]

Aim: Dispersal and subsequent adaptation to local environmental and climatic conditions play major roles in the evolution and current‐day distribution of plants and animals, but their relative importance is not always easy to disentangle. The aim of this study was to provide a comprehensive phylogenetic analysis of the terrestrial orchid genus Cypripedium to better understand the role of niche evolution and historical dispersal events in driving the radiation of the genus in North America and Eurasia. Location: Northern Hemisphere. Taxon: Cypripedium (Orchidaceae). Methods: We used a relaxed molecular clock analysis to infer phylogenetic relationships among 45 Cypripedium species and to estimate divergence times. Niche modelling was used to assess the potential distribution of each species in both continents, whereas ancestral area reconstructions using BioGeoBEARS were used to estimate changes in historical biogeography. Subsequently, the ancestral state of niche conditions was assessed for each species using maximum likelihood methods and we tested for phylogenetic signal in the evolution of niche conditions using Blomberg's K and Pagel's λ. A mantel test was used to test for a correlation between phylogenetic distances and niche overlap in Cypripedium. Results: We found that Cypripedium originated in Central America and underwent multiple dispersal events between North America and Eurasia after long‐distance seed dispersal or dispersal via the Bering land bridge. The mountainous area of Southwest China provided refuge areas for Cypripedium orchids during episodes of increased glaciation. Our results further showed that Cypripedium has gradually increased its tolerance to seasonal temperature changes, providing evidence for significant niche evolution through time. No significant correlation between current niches and phylogenetic relatedness was observed. Main conclusions: Our study provides clear evidence that repeated dispersal and adaptation to increased cooling after the Eocene−Oligocene Transition has contributed to the radiation of Cypripedium in the Northern Hemisphere. [ABSTRACT FROM AUTHOR]

The North American tiger salamander species complex, including its best-known species, theMexican axolotl, has long been a source of biological fascination. The complex exhibits a wide range of variation in developmental life history strategies, including populations and individuals that undergo metamorphosis; those able to forego metamorphosis and retain a larval, aquatic lifestyle (i.e., paedomorphosis); and those that do both. The evolution of a paedomorphic life history state is thought to lead to increased population genetic differentiation and ultimately reproductive isolation and speciation, but the degree to which it has shaped population- and species-level divergence is poorly understood. Using a large multilocus dataset from hundreds of samples across North America, we identified genetic clusters across the geographic range of the tiger salamander complex. These clusters often contain a mixture of paedomorphic and metamorphic taxa, indicating that geographic isolation has played a larger role in lineage divergence than paedomorphosis in this system. This conclusion is bolstered by geography-informed analyses indicating no effect of life history strategy on population genetic differentiation and by modelbased population genetic analyses demonstrating gene flow between adjacent metamorphic and paedomorphic populations. This fine-scale genetic perspective on life history variation establishes a framework for understanding how plasticity, local adaptation, and gene flow contribute to lineage divergence. Many members of the tiger salamander complex are endangered, and theMexican axolotl is an important model system in regenerative and biomedical research. Our results chart a course for more informed use of these taxa in experimental, ecological, and conservation research. [ABSTRACT FROM AUTHOR]

Range contraction and expansion from glaciation have led to genetic divergence that may be particularly pronounced in fossorial species with low dispersal. The plains pocket gopher (Geomys bursarius) is a fossorial species that ranges widely across North America but has a poorly understood phylogeny. We used mitogenomes (14,996 base pairs) from 56 individuals across seven subspecies, plus two outgroup species, to assess genetic divergence from minimum spanning trees, measure genetic distances, and infer phylogenetic trees using BEAST. We found G. b. wisconsinensis was monophyletic with recent divergence. Further assessment is needed for G. b. major because it was paraphyletic and exhibited inconsistent groupings with other clades. Importantly, we identified G. b. illinoensis as being genetically distinct and monophyletic likely due to a unique colonization event eastward across the Mississippi River. Because G. b. illinoensis faces continued pressures from niche reduction and habitat loss, we recommend that G. b. illinoensis be considered an evolutionary significant unit warranting conservation actions to promote connectivity and restore suitable habitat. Such conservation efforts should benefit other grassland species including those originating from clades west of the Mississippi River that may also be evolutionary significant units., (© The American Genetic Association. 2024.)

Gene duplication followed by nucleotide differentiation is one of the simplest mechanisms to develop new functions for genes. However, the evolutionary processes underlying the divergence of multigene families remain controversial. We used multigene families found within the diversity of toxic proteins in centipede venom to test two hypotheses related to venom evolution: the two-speed mode of venom evolution and the rapid accumulation of variation in exposed residues (RAVER) model. The two-speed mode of venom evolution proposes that different types of selection impact ancient and younger venomous lineages with negative selection being the predominant form in ancient lineages and positive selection being the dominant form in younger lineages. The RAVER hypothesis proposes that, instead of different types of selection acting on different ages of venomous lineages, the different types of selection will selectively contribute to amino acid variation based on whether the residue is exposed to the solvent where it can potentially interact directly with toxin targets. This hypothesis parallels the longstanding understanding of protein evolution that suggests that residues found within the structural or active regions of the protein will be under negative or purifying selection, and residues that do not form part of these areas will be more prone to positive selection. To test these two hypotheses, we compared the venom of 26 centipedes from the order Scolopendromorpha from six currently recognized species from across North America using both transcriptomics and proteomics. We first estimated their phylogenetic relationships and uncovered paraphyly among the genus Scolopendra and evidence for cryptic diversity among currently recognized species. Using our phylogeny, we then characterized the diverse venom components from across the identified clades using a combination of transcriptomics and proteomics. We conducted selection-based analyses in the context of predicted three-dimensional properties of the venom proteins and found support for both hypotheses. Consistent with the two-speed hypothesis, we found a prevalence of negative selection across all proteins. Consistent with the RAVER hypothesis, we found evidence of positive selection on solvent-exposed residues, with structural and less-exposed residues showing stronger signal for negative selection. Through the use of phylogenetics, transcriptomics, proteomics, and selection-based analyses, we were able to describe the evolution of venom from an ancient venomous lineage and support principles of protein evolution that directly relate to multigene family evolution., (© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Vibrio parahaemolyticus is the most common cause of seafood-borne illness reported in the United States. The draft genomes of 132 North American clinical and oyster V. parahaemolyticus isolates were sequenced to investigate their phylogenetic and biogeographic relationships. The majority of oyster isolate sequence types (STs) were from a single harvest location; however, four were identified from multiple locations. There was population structure along the Gulf and Atlantic Coasts of North America, with what seemed to be a hub of genetic variability along the Gulf Coast, with some of the same STs occurring along the Atlantic Coast and one shared between the coastal waters of the Gulf and those of Washington State. Phylogenetic analyses found nine well-supported clades. Two clades were composed of isolates from both clinical and oyster sources. Four were composed of isolates entirely from clinical sources, and three were entirely from oyster sources. Each single-source clade consisted of one ST. Some human isolates lack tdh, trh, and some type III secretion system (T3SS) genes, which are established virulence genes of V. parahaemolyticus. Thus, these genes are not essential for pathogenicity. However, isolates in the monophyletic groups from clinical sources were enriched in several categories of genes compared to those from monophyletic groups of oyster isolates. These functional categories include cell signaling, transport, and metabolism. The identification of genes in these functional categories provides a basis for future in-depth pathogenicity investigations of V. parahaemolyticus. [ABSTRACT FROM AUTHOR]

The red turpentine beetle (RTB; Dendroctonus valens) is a bark beetle that is native to Central and North America. This insect is well-known to live in association with a large number of Ophiostomatalean fungi. The beetle is considered a minor pest in its native range, but has killed millions of indigenous pine trees in China after its appearance in that country in the late 1990s. In order to increase the base of knowledge regarding the RTB and its symbionts, surveys of the beetle's fungal associates were initially undertaken in China, and in a subsequent study in its native range in North America. A total of 30 Ophiostomatalean species that included several undescribed taxa, were identified in these surveys. In the present study, seven of the undescribed taxa collected during the surveys were further characterised based on their morphological characteristics and multi-gene phylogenies. We proceeded to describe five of these as novel Leptographium spp. and two as new species of Ophiostoma. Four of the Leptographium spp. resided in the G. galeiformis-species complex, while one formed part of the L. olivaceumspecies complex. One Ophiostoma sp. was a member of the O. ips-species complex, while the only new species from China was closely related to O. floccosum. Two of the previously undescribed taxa from North America were shown to be congeneric with L. terebrantis, implying that this species was most often isolated in association with the RTB in North America. The undescribed taxon from North America was identified as O. ips, and like L. terebrantis, this species was also not recognized during the initial North American survey. Resolving the identities of these taxa provides essential baseline information to better understand the movement of fungal pathogens with this beetle. This then enhances our ability to accurately assess and predict the risks of invasions by these and related fungi. [ABSTRACT FROM AUTHOR]

While among the most common Holarctic land snails, species of the Euconulus fulvus group have been subject to considerable recent taxonomic controversy. Based on 76 Euconulus populations collected across Eurasia and North America, we empirically evaluated these competing taxonomic hypotheses through an integration of nDNA and mtDNA phylogenetics, shell morphometrics and various qualitative traits. Our results support the existence of five taxa: Euconulus alderi (Atlantic Europe to western North America), E. fresti sp. nov. (North America), E. fulvus fulvus (Europe), E. fulvus egenus (central Asia to Atlantic North America), and E. polygyratus (north-eastern North America). Each species-level entity possessed a unique suite of observable shell features allowing for accurate identification without need of DNA sequence information. Our data did not support the recent erection of E. callopisticus, E. praticola, and E. trochiformis to species-level status. This work also helps illustrate the importance of using consensus across DNA and shell/soft body features in assessing species-level taxonomy and in determining those features which allow for accurate identification. It furthermore documents the importance of basing taxonomic work on samples drawn from across the entire geographic and ecological range of the study group. [ABSTRACT FROM AUTHOR]

Lichens are widely acknowledged to be a key component of high latitude ecosystems. However, the time investment needed for full inventories and the lack of taxonomic identification resources for crustose lichen and lichenicolous fungal diversity have hampered efforts to fully gauge the depth of species richness in these ecosystems. Using a combination of classical field inventory and extensive deployment of chemical and molecular analysis, we assessed the diversity of lichens and associated fungi in Glacier Bay National Park, Alaska (USA), a mixed landscape of coastal boreal rainforest and early successional low elevation habitats deglaciated after the Little Ice Age. We collected nearly 5000 specimens and found a total of 947 taxa, including 831 taxa of lichen-forming and 96 taxa of lichenicolous fungi together with 20 taxa of saprotrophic fungi typically included in lichen studies. A total of 98 species (10.3% of those detected) could not be assigned to known species and of those, two genera and 27 species are described here as new to science: Atrophysma cyanomelanos gen. et sp. nov., Bacidina circumpulla, Biatora marmorea, Carneothele sphagnicola gen. et sp. nov., Cirrenalia lichenicola, Corticifraga nephromatis, Fuscidea muskeg, Fuscopannaria dillmaniae, Halecania athallina, Hydropunctaria alaskana, Lambiella aliphatica, Lecania hydrophobica, Lecanora viridipruinosa, Lecidea griseomarginata, L. streveleri, Miriquidica gyrizans, Niesslia peltigerae, Ochrolechia cooperi, Placynthium glaciale, Porpidia seakensis, Rhizocarpon haidense, Sagiolechia phaeospora, Sclerococcum fissurinae, Spilonema maritimum, Thelocarpon immersum, Toensbergia blastidiata and Xenonectriella nephromatis. An additional 71 'known unknown' species are cursorily described. Four new combinations are made: Lepra subvelata (G. K. Merr.) T. Sprib., Ochrolechia minuta (Degel.) T. Sprib., Steineropsis laceratula (Hue) T. Sprib. & Ekman and Toensbergia geminipara (Th. Fr.) T. Sprib. & Resl. Thirty-eight taxa are new to North America and 93 additional taxa new to Alaska. We use four to eight DNA loci to validate the placement of ten of the new species in the orders Baeomycetales, Ostropales, Lecanorales, Peltigerales, Pertusariales and the broader class Lecanoromycetes with maximum likelihood analyses. We present a total of 280 new fungal DNA sequences. The lichen inventory from Glacier Bay National Park represents the second largest number of lichens and associated fungi documented from an area of comparable size and the largest to date in North America. Coming from almost 60°N, these results again underline the potential for high lichen diversity in high latitude ecosystems. [ABSTRACT FROM AUTHOR]

The World Health Organization declared mpox a public health emergency of international concern in July 2022. To investigate global mpox transmission and population-level changes associated with controlling spread, we built phylogeographic and phylodynamic models to analyze MPXV genomes from five global regions together with air traffic and epidemiological data. Our models reveal community transmission prior to detection, changes in case reporting throughout the epidemic, and a large degree of transmission heterogeneity. We find that viral introductions played a limited role in prolonging spread after initial dissemination, suggesting that travel bans would have had only a minor impact. We find that mpox transmission in North America began declining before more than 10% of high-risk individuals in the USA had vaccine-induced immunity. Our findings highlight the importance of broader routine specimen screening surveillance for emerging infectious diseases and of joint integration of genomic and epidemiological information for early outbreak control. [Display omitted] • Phylodynamic models reveal swift early mpox spread between five global regions • Extensive, underdetected dissemination promoted rapid local transmission • Later mpox introductions played a negligible role in prolonging regional epidemics • N. America epidemic declined before 10% of high-risk group had vaccine-induced immunity Joint analysis of genomic, mobility, and epidemiological data reveals that the 2022 mpox epidemic was characterized by rapid, underdetected local spread among high-risk groups following initial regional viral seeding events. Local behavioral changes played a larger role in curbing transmission than did travel restrictions and vaccination campaigns. [ABSTRACT FROM AUTHOR]

The carnivorous mammalian fauna from the Uintan (late middle Eocene) of North America remains relatively poorly documented. This is unfortunate, as this is a critical interval in the transition from 'creodont' to carnivoran dominated carnivore guilds. This study reports a new species from the Uinta Formation of the Uinta Basin, Utah, the first North American species of the otherwise Asian hyaenodont genus Propterodon. The new species, Propterodon witteri, represented by a dentary with M2-3 from the late Uintan Leota Quarry, is larger than the well-known P. morrisi and P. tongi and has a larger M3 talonid, but is otherwise very similar. A phylogenetic analysis of hyaenodont interrelationships recovers P. witteri as a hyaenodontine but is generally poorly resolved. A relationship between Hyaenodontinae and Oxyaenoides, recovered by many recent analyses, is not supported. Among the Asian species of Propterodon, P. pishigouensis is reidentified as a machaeroidine oxyaenid and recombined as Apataelurus pishigouensis new combination. Isphanatherium ferganensis may also represent an Asian machaeroidine. Identification of a North American species of Propterodon and an Asian Apataelurus increases the similarity of North American Uintan and Asian Irdinmanhan faunas and suggests that there was substantial exchange of carnivorous fauna during the late middle Eocene. [ABSTRACT FROM AUTHOR]

This study integrates biogeographical and phylogenetic data to determine the evolutionary history of the New World Dermacentor , and the origin of D. variabilis. The phylogenetic reconstructions presented here strongly support the hypothesis of an Afrotropical origin for Dermacentor , with later dispersal to Eurasia and the Nearctic. Phylogenetic and biogeographical data suggest that the genus reached the New World through the Beringia land bridge, from south-east Asia. The monophyly of the genus is supported, and most of the New World Dermacentor species appear as monophyletic. Dermacentor occidentals constitutes the sister lineage of D. variabilis , and the latter is subdivided into two well-supported clades: an eastern and a western clade. The western clade is genetically more variable than the eastern. The genus Dermacentor probably originated in Africa, and dispersed to the Palearctic and then to the New World through the Beringian route. Dermacentor variabilis appears to have originated in western North America, and then dispersed to eastern North America, probably in a single migration event. [ABSTRACT FROM AUTHOR]

Canine circovirus (CanineCV) was detected, together with canine parvovirus (CPV), in samples from an outbreak of fatal gastroenteritis in dogs in Argentina. We obtained the full-length genome of this recently discovered virus by overlapping PCR, designated strain UBA-Baires. Sequence analysis revealed a highly conserved genome but also showed several unique mutations in amino acids from the capsid protein that have not been previously reported. Phylogenetic analysis shows that this strain is more closely related to European strains than to viruses detected in North America or Asia. Although the pathogenic role of CanineCV in dogs is still unclear, this study highlights the importance of CanineCV as a coinfecting virus in disease development. To our knowledge, this is the first report of the involvement of CanineCV in severe clinical disease in dogs in South America. Our results expand our information on the geographical extent of this virus and contribute to the understanding of its role in disease. [ABSTRACT FROM AUTHOR]

Galphimia glauca is a plant that is endemic to Mexico and has been commonly used since pre-Hispanic times to treat various illnesses, including central nervous system disorders and inflammation. The first studies investigating a natural population of G. glauca in Mexico showed that the plant has anxiolytic and sedative activities in mice and humans. The plant’s bioactive compounds were isolated and identified, and they belong to a family of nor-secofriedelanes called galphimines. The integration of DNA barcoding and thin-layer chromatography analysis was performed to clarify whether the botanical classification of the populations in the study, which were collected in different regions of Mexico, as G. glauca was correct or if the populations consist of more than one species of the genus Galphimia. We employed six DNA barcodes (matK, rbcL, rpoC1, psbA-trnH, ITS1 and ITS2) that were analyzed individually and in combination and then compared each other, to indicate differences among the studied populations. In the phylogenetic analysis, ITS1 and ITS2 markers as well as the combination of all DNA regions were the most efficient for discriminating the population studied. The thin-layer chromatography analysis exhibited four principal chemical profiles, one of which corresponded to the populations that produced galphimines. DNA barcoding was consistent and enabled us to differentiate the populations that produce galphimines from those that do not. The results of this investigation suggest that the studied populations belong to at least four different species of the genus Galphimia. The phylogenetic analysis and the thin-layer chromatography chemical profiles were convenient tools for establishing a strong relationship between the genotype and phenotype of the studied populations and could be used for quality control purposes to prepare herbal medicines from plants of the genus Galphimia. [ABSTRACT FROM AUTHOR]

The American mink (Neovison vison), native to North America, is a controversial invasive species in many European countries, including Poland. Mitochondrial DNA data (concatenated MT-CYTB and MT-COI sequences) were used to investigate the genetic diversity of native, introduced, and farm populations of this species. Phylogenetic analysis revealed two major clades including individuals from the farm, feral, and wild populations. This supports the origin of Polish minks from the two native lineages existing in North America. The genetic structure in the invasive range may result from the diverse origins of the released founder individuals and the rapid expansion and contact zones of the introduced populations. Spatial mixing of both North American lineages in Polish feral populations may lead to higher levels of genetic diversity in introduced populations, despite some evidence of a founder effect as one of the main factors influencing their diversity. [ABSTRACT FROM AUTHOR]

Pleistocene glaciations had significant effects on the distribution and evolution of species inhabiting the Holarctic region. Phylogeographic studies concerning the entire region are still rare. Here, we compared global phylogeographic patterns of one boreo-montane and one boreo-temperate butterflies with largely overlapping distribution ranges across the Northern Hemisphere, but with different levels of range fragmentation and food specialization. We reconstructed the global phylogeographic history of the boreo-montane specialist Boloria eunomia (n = 223) and of the boreo-temperate generalist Boloria selene (n = 106) based on mitochondrial and nuclear DNA markers, and with species distribution modelling (SDM). According to the genetic structures obtained, both species show a Siberian origin and considerable split among populations from Nearctic and Palaearctic regions. According to SDMs and molecular data, both butterflies could inhabit vast areas during the moderate glacials. In the case of B. selene, high haplotype diversity and low geographic structure suggest long-lasting interconnected gene flow among populations. A stronger geographic structuring between populations was identified in the specialist B. eunomia, presumably due to the less widespread, heterogeneously distributed food resources, associated with cooler and more humid climatic conditions. Populations of both species show opposite patterns across major parts of North America and in the case of B. eunomia also across Asia. Our data underline the relevance to cover entire distribution ranges to reconstruct the correct phylogeographic history of species. [ABSTRACT FROM AUTHOR]

Accurate species delimitation and description are necessary to guide effective conservation of imperiled species, and this synergy is maximized when multiple data sources are used to delimit species. We illustrate this point by examining Drymarchon couperi (Eastern Indigo Snake), a large, federally-protected species in North America that was recently divided into two species based on gene sequence data from three loci and heuristic morphological assessment. Here, we re-evaluate the two-species hypothesis for D. couperi by evaluating both population genetic and gene sequence data. Our analyses of 14 microsatellite markers revealed 6–8 genetic population clusters with significant admixture, particularly across the contact zone between the two hypothesized species. Phylogenetic analyses of gene sequence data with maximum-likelihood methods suggested discordance between mitochondrial and nuclear markers and provided phylogenetic support for one species rather than two. For these reasons, we place Drymarchon kolpobasileus into synonymy with D. couperi. We suggest inconsistent patterns between mitochondrial and nuclear DNA are driven by high dispersal of males relative to females. We advocate for species delimitation exercises that evaluate admixture and gene flow in addition to phylogenetic analyses, particularly when the latter reveal monophyletic lineages. This is particularly important for taxa, such as squamates, that exhibit strong sex-biased dispersal. Problems associated with over-delimitation of species richness can become particularly acute for threatened and endangered species, because of high costs to conservation when taxonomy demands protection of more individual species than are supported by accumulating data. [ABSTRACT FROM AUTHOR]

Herpes simplex virus 2 (HSV-2) is a large double-stranded DNA virus that causes genital sores when spread by sexual contact and is a principal cause of viral encephalitis in newborns and infants. Viral glycoproteins enable virion entry into and spread between cells, making glycoproteins a prime target for vaccine development. A truncated glycoprotein D2 (gD2) vaccine candidate, recently tested in the phase 3 Herpevac Trial for Women, did not prevent HSV-2 infection in initially seronegative women. Some women who became infected experienced multiple recurrences during the trial. The HSV US7, US8, and US9 genes encode glycoprotein I (gI), glycoprotein E (gE), and the US9 type II membrane protein, respectively. These proteins participate in viral spread across cell junctions and facilitate anterograde transport of virion components in neurons, prompting us to investigate whether sequence variants in these genes could be associated with frequent recurrence. The nucleotide sequences and dN/dS ratios of the US7-US9 region from viral isolates of individuals who experienced multiple recurrences were compared with those who had had a single episode of disease. No consistent polymorphism(s) distinguished the recurrent isolates. In frequently recurring isolates, the dN/dS ratio of US7 was low while greater variation (higher dN/dS ratio) occurred in US8, suggesting conserved function of the former during reactivation. Phylogenetic reconstruction of the US7-US9 region revealed eight strongly supported clusters within the 55 U.S. HSV-2 strains sampled, which were preserved in a second global phylogeny. Thus, although we have demonstrated evolutionary diversity in the US7-US9 complex, we found no molecular evidence of sequence variation in US7-US9 that distinguishes isolates from subjects with frequently recurrent episodes of disease. [ABSTRACT FROM AUTHOR]

The salamander family Sirenidae is represented by four extant species that are restricted to North America. Sirens are abundant throughout the southern United States and are among the world’s largest amphibians, yet the biology, ecology, and phylogeography of this group is poorly-known. In this study we use morphological and genetic evidence to describe a previously unrecognized species from southern Alabama and the Florida panhandle. We name this species the Reticulated Siren, Siren reticulata. Future studies will enable more precise phylogenetic information about S. reticulata and will almost surely reveal additional undescribed species within the family. [ABSTRACT FROM AUTHOR]

Horses were a dominant component of North American Pleistocene land mammal communities and their remains are well represented in the fossil record. Despite the abundant material available for study, there is still considerable disagreement over the number of species of Equus that inhabited the different regions of the continent and on their taxonomic nomenclature. In this study, we investigated cheek tooth morphology and ancient mtDNA of late Pleistocene Equus specimens from the Western Interior of North America, with the objective of clarifying the species that lived in this region prior to the end-Pleistocene extinction. Based on the morphological and molecular data analyzed, a caballine (Equus ferus) and a non-caballine (E. conversidens) species were identified from different localities across most of the Western Interior. A second non-caballine species (E. cedralensis) was recognized from southern localities based exclusively on the morphological analyses of the cheek teeth. Notably the separation into caballine and non-caballine species was observed in the Bayesian phylogenetic analysis of ancient mtDNA as well as in the geometric morphometric analyses of the upper and lower premolars. Teeth morphologically identified as E. conversidens that yielded ancient mtDNA fall within the New World stilt-legged clade recognized in previous studies and this is the name we apply to this group. Geographic variation in morphology in the caballine species is indicated by statistically different occlusal enamel patterns in the specimens from Bluefish Caves, Yukon Territory, relative to the specimens from the other geographic regions. Whether this represents ecomorphological variation and/or a certain degree of geographic and genetic isolation of these Arctic populations requires further study. [ABSTRACT FROM AUTHOR]

We described newly discovered baenid specimens from the Uintan North American Land Mammal Age (NALMA), in the Uinta Formation, Uinta Basin, Utah. These specimens include a partial skull and several previously undescribed postcranial elements of Baena arenosa, and numerous well-preserved shells of B. arenosa and Chisternon undatum. Baenids from the Uintan NALMA (46.5–40 Ma) are critical in that they provide valuable insight into the morphology and evolution of the diverse and speciose baenid family near the end of its extensive radiation, just prior to the disappearance of this clade from the fossil record. These Uintan specimens greatly increase the known variation in these late-surviving taxa and indicate that several characters thought to define these species should be reassessed. The partial cranium of B. arenosa, including portions of the basicranium, neurocranium, face, and lower jaw, was recently recovered from Uinta B sediments. While its morphology is consistent with known specimens of B. arenosa, we observed several distinct differences: a crescent-shaped condylus occipitalis that is concave dorsally, tuberculum basioccipitale that flare out laterally, and a distinct frontal-nasal suture. The current sample of plastral and carapacial morphology considerably expands the documented variation in the hypodigms of B. arenosa and C. undatum. Novel shell characters observed include sigmoidal extragular-humeral sulci, and small, subtriangular gular scutes. Subadult specimens reveal ontogenetic processes in both taxa, and demonstrate that diagnostic morphological differences between them were present from an early developmental age. [ABSTRACT FROM AUTHOR]

Shrews of the Sorex genus are an evolutionarily successful group that includes more than 77 species widely distributed in Eurasia and North America. The genus is one of the rare cases where karyotypic changes reflect well the evolutionary relationships among its species. The taxa showing the greatest variation in karyotype are usually classified into the Sorex araneus group. Its evolution was associated with chromosomal rearrangements, which could have promoted fast diversification of this group into many chromosomal races and species. These processes were additionally complicated by introgressions of mitochondrial DNA, which made the evolutionary history of this group quite complex and difficult to infer. To tackle the problem, we performed multi-method phylogenetic analyses based on mitochondrial cytochrome b that is considered a good molecular marker available for many representatives of Sorex. The results were compared with phylogenies based on chromosomal rearrangement data and put into temporal and spatial context using molecular dating and historical biogeography methods. We complemented the study with the estimation of diversification rates within the S. araneus group as well as comparing the results with paleontological records and climatic oscillations within the last 4 million years. Based on the gathered data, we proposed a hypothetical scenario for the evolution and geographic dispersion of species belonging to the S. araneus group. The shrews began to diversify about 2.7 million years ago in Eurasia and then migrated at least twice to North America. The evolution of shrews was driven by Pleistocene glacial and interglacial cycles, which increased their speciation rate and the emergence of new lineages. The migrations of populations were accompanied by introgressions of mitochondrial DNA into native shrews and occurred at least twice. [ABSTRACT FROM AUTHOR]

This study reports the assembly of a DNA barcode reference library for species in the lepidopteran superfamily Noctuoidea from Canada and the USA. Based on the analysis of 69,378 specimens, the library provides coverage for 97.3% of the noctuoid fauna (3565 of 3664 species). In addition to verifying the strong performance of DNA barcodes in the discrimination of these species, the results indicate close congruence between the number of species analyzed (3565) and the number of sequence clusters (3816) recognized by the Barcode Index Number (BIN) system. Distributional patterns across 12 North American ecoregions are examined for the 3251 species that have GPS data while BIN analysis is used to quantify overlap between the noctuoid faunas of North America and other zoogeographic regions. This analysis reveals that 90% of North American noctuoids are endemic and that just 7.5% and 1.8% of BINs are shared with the Neotropics and with the Palearctic, respectively. One third (29) of the latter species are recent introductions and, as expected, they possess low intraspecific divergences. [ABSTRACT FROM AUTHOR]

The extent to which evolution is deterministic (predictable), or random, is a fundamental question in evolution. This case study attempts to determine the extent to which interspecific divergence can be predicted from intraspecific trends related species. The mountainous Lesser Antilles are occupied by one or two anole species with very substantial intraspecific differences in the quantitative traits between xeric and rainforest habitats. These ecologically determined differences tend to be in parallel in each island species. A related species (Anolis bonairensis) lives on the far more xeric island of Bonaire, and this study tests the extent to which its interspecific divergence in hue and pattern traits can be predicted from the parallel intraspecific variation exhibited in Lesser Antillean anoles. Regression against a multivariate climate variable suggests that the hue and pattern of the Bonaire anole are consistently predicted from the ecologically determined intraspecific variation of its Lesser Antillean relatives. However, this predictability may be less consistent with other character systems, for example, scalation. [ABSTRACT FROM AUTHOR]

Mylagaulid fossorial rodents are a common component of North American Miocene fossil faunas. However outside of North America, only three species are known from Asia. Here we report two new mylagaulids, Irtyshogaulus minor gen. et sp. nov. and Irtyshogaulus major gen. et sp. nov., recovered from early Miocene sediments in the Junggar Basin in northwestern China. The two new taxa are small-sized, high-crowned promylagauline rodents. Their lower molars possess high metastylid crests, small mesostylids, broad and posterolingually expanded labial inflections, and transversely extending metalophid IIs. The mesoconid is absent in both species. The anterior and posterior fossettids are large and equally developed. Their upper M1-2s possess a square occlusal surface with five deep fossettes. The two new taxa are distinguished from each other mainly by their size, the morphology of fossettes and fossettids, development of mesial and distal lophs, posterior reduction of M3, and the orientation of m2 hypolophid. Our phylogenetic analysis indicates that Irtyshogaulus and Lamugaulus (another early Miocene Asian mylagaulid) are sister taxa. The two genera are nested among the North American promylagaulines, and share a common ancestor from North America, indicating early Miocene intercontinental dispersal within this clade of rodents. [ABSTRACT FROM AUTHOR]

The species of Necremnus attacking two invasive pests of tomato and canola in Europe and North America, respectively, Tuta absoluta ( Meyrick) ( Lepidoptera: Gelechiidae) and Ceutorhynchus obstrictus ( Marsham) ( Coleoptera: Curculionidae), have been revised using an integrative taxonomy approach. Molecular data from the mitochondrial cytochrome oxidase c subunit I and the nuclear D2 expansion region of the 28S ribosomal subunit and internal transcribed spacer 2, the discovery of new morphological features, and study of type material resulted in the delineation of three species groups, the Necremnus artynes, Necremnus cosconius, and Necremnus tidius groups, the discovery of four new species, and the resurrection of three taxa from synonymy. Lectotypes have been designated for 13 species originally described in Eulophus by Walker. Although Necremnus has not been revised, an illustrated key is given to differentiate 23 recognized European species. The key, type images, and treatments of the three species groups will enable more accurate identification of the valid species of Necremnus in the future. They will also benefit biological control practitioners of pest species. The ecological consequences of the new taxonomic concepts are discussed. © 2015 The Authors. Zoological Journal of the Linnean Society published by John Wiley & Sons Ltd on behalf of The Linnean Society of London [ABSTRACT FROM AUTHOR]

The Richards Spur Locality of Oklahoma, USA, long known for its highly diverse Early Permian terrestrial tetrapod assemblage, is particularly interesting for the presence of many endemic taxa. The parareptilian component of the assemblage, rare members of other Early Permian communities, is especially diverse at Richards Spur, consisting of six species. The newest parareptile, A byssomedon williamsi gen. et sp. nov., consists of an articulated left jaw and various disarticulated cranial and postcranial elements. A new phylogenetic analysis of parareptiles, based on an updated modified data matrix revealed that Ab . williamsi is a member of the small clade Nyctiphruretidae. This makes Ab . williamsi the first and oldest nyctiphruretid, a clade of parareptiles otherwise known from the Middle and Late Permian of Russia, extending the age of the clade back into the Early Permian. This discovery also raises the possibility that nyctiphruretids may have dispersed from western Laurasia to eastern Laurasia. The characteristic jugal morphology of Ab . williamsi shows that it would have possessed a slender, deep, temporal emargination. The current topology of Parareptilia indicates that there was considerable variability in the patterns of lateral temporal openings amongst the various members of this clade, suggesting that there may have been multiple, independent modifications of this region of the skull. © 2014 The Linnean Society of London [ABSTRACT FROM AUTHOR]

A new ankylosaurid (Ankylosauria: Dinosauria), Ziapelta sanjuanensis, gen. et sp. nov., is based on a complete skull, an incomplete first cervical half ring, a possible fragment of the second cervical half ring, and additional fragmentary osteoderms. The holotype specimen is from the Upper Cretaceous (Upper Campanian, Kirtlandian Land-Vertebrate Age) Kirtland Formation (De-na-zin Member) at Hunter Wash, San Juan Basin, in northwestern New Mexico, USA. Diagnostic characters of Ziapelta include: a large, prominent triangular median nasal caputegulum; a mixture of flat and bulbous frontonasal caputegulae; ventrolaterally oriented squamosal horns with a sharp, prominent dorsal keel; and the ventral surface of basicranium with three prominent anteroposteriorly oriented fossae. A phylogenetic analysis suggests that Ziapelta is not closely related to the other ankylosaurid from the De-na-zin Member, Nodocephalosaurus, but allies it to the northern North American ankylosaurids Ankylosaurus, Anodontosaurus, Euoplocephalus, Dyoplosaurus, and Scolosaurus. [ABSTRACT FROM AUTHOR]

Highlights: [•] Amplified 27 anonymous nuclear loci across all Pseudacris chorus frog species. [•] Cost-effectively sequenced 30 loci for 44 individuals on an Illumina MiSeq. [•] Species tree analyses resolve relationships among four major clades of Pseudacris. [•] Found evidence of mitochondrial introgression and possible selective sweep. [Copyright &y& Elsevier]

Abstract: Gulls are important hosts of avian influenza A viruses (AIVs) and gull AIVs often contain gene segments of mixed geographic and host lineage origins. In this study, the prevalence of AIV in gulls of Newfoundland, Canada from 2008 to 2011 was analyzed. Overall prevalence was low (30/1645, 1.8%) but there was a distinct peak of infection in the fall. AIV seroprevalence was high in Newfoundland gulls, with 50% of sampled gulls showing evidence of previous infection. Sequences of 16 gull AIVs were determined and analyzed to shed light on the transmission, reassortment and persistence dynamics of gull AIVs in Atlantic North America. Intercontinental and waterfowl lineage reassortment was prevalent. Of particular note were a wholly Eurasian AIV and another with an intercontinental reassortant waterfowl lineage virus. These patterns of geographic and inter-host group transmission highlight the importance of characterization of gull AIVs as part of attempts to understand global AIV dynamics. [Copyright &y& Elsevier]

Over the last decades the phylogeography and genetic structure of a multitude of species inhabiting Europe and North America have been described. The flora and fauna of the vast landmasses of north-eastern Eurasia are still largely unexplored in this respect. The Eurasian lynx is a large felid that is relatively abundant over much of the Russian sub-continent and the adjoining countries. Analyzing 148 museum specimens collected throughout its range over the last 150 years we have described the large-scale genetic structuring in this highly mobile species. We have investigated the spatial genetic patterns using mitochondrial DNA sequences (D-loop and cytochrome b) and 11 microsatellite loci, and describe three phylogenetic clades and a clear structuring along an east-west gradient. The most likely scenario is that the contemporary Eurasian lynx populations originated in central Asia and that parts of Europe were inhabited by lynx during the Pleistocene. After the Last Glacial Maximum (LGM) range expansions lead to colonization of north-western Siberia and Scandinavia from the Caucasus and north-eastern Siberia from a refugium further east. No evidence of a Berinigan refugium could be detected in our data. We observed restricted gene flow and suggest that future studies of the Eurasian lynx explore to what extent the contemporary population structure may be explained by ecological variables. [ABSTRACT FROM AUTHOR]

Over the last decades the phylogeography and genetic structure of a multitude of species inhabiting Europe and North America have been described. The flora and fauna of the vast landmasses of north-eastern Eurasia are still largely unexplored in this respect. The Eurasian lynx is a large felid that is relatively abundant over much of the Russian sub-continent and the adjoining countries. Analyzing 148 museum specimens collected throughout its range over the last 150 years we have described the large-scale genetic structuring in this highly mobile species. We have investigated the spatial genetic patterns using mitochondrial DNA sequences (D-loop and cytochrome b) and 11 microsatellite loci, and describe three phylogenetic clades and a clear structuring along an east-west gradient. The most likely scenario is that the contemporary Eurasian lynx populations originated in central Asia and that parts of Europe were inhabited by lynx during the Pleistocene. After the Last Glacial Maximum (LGM) range expansions lead to colonization of north-western Siberia and Scandinavia from the Caucasus and north-eastern Siberia from a refugium further east. No evidence of a Berinigan refugium could be detected in our data. We observed restricted gene flow and suggest that future studies of the Eurasian lynx explore to what extent the contemporary population structure may be explained by ecological variables. [ABSTRACT FROM AUTHOR]

Recent arguments connecting Na-Dene languages of North America with Yeniseian languages of Siberia have been used to assert proof for the origin of Native Americans in central or western Asia. We apply phylogenetic methods to test support for this hypothesis against an alternative hypothesis that Yeniseian represents a back-migration to Asia from a Beringian ancestral population. We coded a linguistic dataset of typological features and used neighbor-joining network algorithms and Bayesian model comparison based on Bayes factors to test the fit between the data and the linguistic phylogenies modeling two dispersal hypotheses. Our results support that a Dene-Yeniseian connection more likely represents radiation out of Beringia with back-migration into central Asia than a migration from central or western Asia to North America. [ABSTRACT FROM AUTHOR]

Intense geological activity caused major topographic changes in Western North America over the past 15 million years. Major rivers here are composites of different ancient rivers, resulting in isolation and mixing episodes between river basins over time. This history influenced the diversification of most of the aquatic fauna. The genus Pantosteus is one of several clades centered in this tectonically active region. The eight recognized Pantosteus species are widespread and common across southwestern Canada, western USA and into northern Mexico. They are typically found in medium gradient, middle-elevation reaches of rivers over rocky substrates. This study (1) compares molecular data with morphological and paleontological data for proposed species of Pantosteus, (2) tests hypotheses of their monophyly, (3) uses these data for phylogenetic inferences of sister-group relationships, and (4) estimates timing of divergence events of identified lineages. Using 8055 base pairs from mitochondrial DNA protein coding genes, Pantosteus and Catostomus are reciprocally monophyletic, in contrast with morphological data. The only exception to a monophyletic Pantosteus is P. columbianus whose mtDNA is closely aligned with C. tahoensis because of introgression. Within Pantosteus, several species have deep genetic divergences among allopatric sister lineages, several of which are diagnosed and elevated to species, bringing the total diversity in the group to 11 species. Conflicting molecular and morphological data may be resolved when patterns of divergence are shown to be correlated with sympatry and evidence of introgression. [ABSTRACT FROM AUTHOR]

[Display omitted] • Multiple dating approaches help discern credible divergence timeframes. • Deeper nodes have greater age uncertainties in multispecies coalescent analysis. • Concatenation provides narrow age ranges but oversimplifies gene tree space. • Age ranges rather than median estimates lead to more stable evolutionary hypotheses. • First population-level sampling of genome-wide data for the Papilio glaucus group. Divergence times underpin diverse evolutionary hypotheses, but conflicting age estimates across studies diminish the validity of such hypotheses. These conflicts have continued to grow as large genomics datasets become commonplace and analytical approaches proliferate. To provide more stable temporal intervals, age estimations should be interpreted in the context of both the type of data and analysis being used. Here, we use multispecies coalescent (MSC), concatenation-based, and categorical data transformation approaches on genome-wide SNP data to infer divergence ages within the Papilio glaucus group of tiger swallowtail butterflies in North America. While the SNP data supported previously recognized relationships within the group (P. multicaudata , ((P. eurymedon , P. rutulus), (P. appalachiensis , P. canadensis , P. glaucus))), estimated ages of divergence between the major lineages varied substantially among analyses. MSC produced wide credibility intervals particularly for deeper nodes, reflecting uncertainty in the coalescence times as a possible result of conflicting signal across gene trees. Concatenation, in contrast, gave narrower and more well-defined posterior distributions for the node ages; however, the higher precision of these time estimates is a likely artefact due to more simplistic underlying assumptions of this approach that do not account for conflict among gene trees. Transformed categorical data analysis gave the least precise and the most variable results, with its simple substitution model coupled with a relaxed clock tending to produce spurious results from large genome-wide datasets. While median node ages differed considerably between analyses (∼2 Mya between MSC and concatenation-based results), their corresponding credibility intervals nonetheless highlight common temporal patterns for deeper divergences in the group as well as finer-scale phylogeography. Age distributions across analyses support an origin of the group during the warm period of the early to mid-Pliocene. Late Pliocene climate aridification and cooling drove divergence between eastern and western groups that further diversified during the period of repeated Pleistocene glaciations. Our results provide a structured comparative assessment of divergence time estimates and evolutionary relationships in a well-studied group of butterflies, and support better understanding of analytical biases in divergence time estimation. [ABSTRACT FROM AUTHOR]

Four groups of equids, “Anchitheriinae,” Merychippine-grade Equinae, Hipparionini, and Equini, coexisted in the middle Miocene, but only the Equini remains after 16 Myr of evolution and extinction. Each group is distinct in its occlusal enamel pattern. These patterns have been compared qualitatively but rarely quantitatively. The processes influencing the evolution of these occlusal patterns have not been thoroughly investigated with respect to phylogeny, tooth position, and climate through geologic time. We investigated Occlusal Enamel Index, a quantitative method for the analysis of the complexity of occlusal patterns. We used analyses of variance and an analysis of co-variance to test whether equid teeth increase resistive cutting area for food processing during mastication, as expressed in occlusal enamel complexity, in response to increased abrasion in their diet. Results suggest that occlusal enamel complexity was influenced by climate, phylogeny, and tooth position through time. Occlusal enamel complexity in middle Miocene to Modern horses increased as the animals experienced increased tooth abrasion and a cooling climate. [ABSTRACT FROM AUTHOR]

Wild birds, including waterfowl such as ducks, are reservoir hosts of influenza A viruses. Despite the increased number of avian influenza virus (AIV) genome sequences available, our understanding of AIV genetic structure and transmission through space and time in waterfowl in North America is still limited. In particular, AIVs in ducks of the Atlantic flyway of North America have not been thoroughly investigated. To begin to address this gap, we analyzed 109 AIV genome sequences from ducks in the Atlantic flyway to determine their genetic structure and to document the extent of gene flow in the context of sequences from other locations and other avian and mammalian host groups. The analyses included 25 AIVs from ducks from Newfoundland, Canada, from 2008–2011 and 84 available reference duck AIVs from the Atlantic flyway from 2006–2011. A vast diversity of viral genes and genomes was identified in the 109 viruses. The genetic structure differed amongst the 8 viral segments with predominant single lineages found for the PB2, PB1 and M segments, increased diversity found for the PA, NP and NS segments (2, 3 and 3 lineages, respectively), and the highest diversity found for the HA and NA segments (12 and 9 lineages, respectively). Identification of inter-hemispheric transmissions was rare with only 2% of the genes of Eurasian origin. Virus transmission between ducks and other bird groups was investigated, with 57.3% of the genes having highly similar (≥99% nucleotide identity) genes detected in birds other than ducks. Transmission between North American flyways has been frequent and 75.8% of the genes were highly similar to genes found in other North American flyways. However, the duck AIV genes did display spatial distribution bias, which was demonstrated by the different population sizes of specific viral genes in one or two neighbouring flyways compared to more distant flyways. [ABSTRACT FROM AUTHOR]

The large dicynodont Eubrachiosaurus browni from the Upper Triassic Popo Agie Formation of Wyoming is redescribed. Eubrachiosaurus is a valid taxon that differs from Placerias hesternus, with which it was previously synonymized, by greater anteroposterior expansion of the scapula dorsally and a very large, nearly rectangular humeral ectepicondyle with a broad supinator process. Inclusion of Eubrachiosaurus in a revised phylogenetic analysis of anomodont therapsids indicates that it is a stahleckeriid closely related to the South American genera Ischigualastia and Jachaleria. The recognition of Eubrachiosaurus as a distinct lineage of North American dicynodonts, combined with other recent discoveries in the eastern USA and Europe, alters our perception of Late Triassic dicynodont diversity in the northern hemisphere. Rather than being isolated relicts in previously therapsid-dominated regions, Late Triassic stahleckeriid dicynodonts were continuing to disperse and diversify, even in areas like western North America that were otherwise uninhabited by coeval therapsids (i.e., cynodonts). [ABSTRACT FROM AUTHOR]

Aim Aridification of western North America from the Miocene to the Recent has spurred plant migrations, as species invaded and/or diversified into newly formed floristic regions. The 51 species of Mentzelia section Bartonia (Loasaceae) inhabit most of these regions, providing an opportunity to investigate lineage-specific diversification among the western floras. Lineage-specific formation of the modern western North American flora was investigated by applying statistical phylogenetic methods to molecular data. Location Western North America, including the intermountain region, south-western deserts, Rocky Mountains and North American Prairies Province. Methods Internal and external transcribed spacer region data for all taxa in section Bartonia and outgroups were analysed with maximum likelihood and Bayesian inference methods for phylogenetic relationships. Distribution and phylogenetic data were then analysed by Bayesian, maximum likelihood, parsimony, and stochastic mapping optimization methods for inference of biogeographical transitions among floristic regions. Model fitting was used to assess the symmetry of transitions from mesic to arid environments. Results Multiple transitions were inferred, especially those associated with the Colorado Plateau and the Rocky Mountains. The ancestral area for section Bartonia was estimated equivocally to be all regions except the Great Basin in parsimony reconstructions, but to be the Colorado Plateau with highest probability with the Bayesian approach. Throughout these regions, transitions between mesic to arid habitats were consistent with expectations under a null model, suggesting no directional bias in transitions. In section Bartonia, within-region diversification occurred in all areas except the Great Basin and Sonoran Desert, the diversity of which is explained as the result of movement into these regions. Main conclusions The floristic regions of western North America have exchanged numerous migrants throughout their history. Among them, the Colorado Plateau, Great Basin and Rocky Mountains were particularly important floristic sources and recipients of migrants. Although previous studies have revealed a strong association among the south-western deserts, these results suggest that the plant diversities in these deserts can be influenced more by adjacent provinces than by each other. [ABSTRACT FROM AUTHOR]

The Baltic Sea is one of the world's most intensive centres for maritime traffic. This sea has become an important recipient of alien species transported with ballast water from all over the world. Sibling species are a special group of invasive animals that are hardly distinguishable from relative but often ecologically different local species. In this study, a molecular genetic diagnosis was performed, based on the analysis of DNA nucleotide sequences (barcoding) in the populations of a dominant circumpolar speciesEurytemora affinis(Poppe, 1880) from the Gulf of Finland and the Atlantic coast of European estuaries and ofEurytemora carolleeaeAlekseev and Souissi, 2011, a new North American suspected invasive form. The results of the diagnosis were completed by morphological analyses. Considering the key role ofE. affinisin the Baltic Sea zooplankton community, the invasion ofE. carolleeaemight have consequences for biodiversity, biogeography, conservation and ecosystem management in this area. [ABSTRACT FROM AUTHOR]

Multiple species of troglomorphic, spring-associated Stygobromus amphipods, including the endangered, narrow-range endemic Stygobromus pecki, occupy sites in the Edwards Plateau region of North America. Given the prevalence of cryptic diversity observed in disparate subterranean, animal taxa, we evaluated geographical genetic variation and tested whether Stygobromus contained undetected biodiversity. Nominal Stygobromus taxa were treated as hypotheses and tested with mitochondrial sequence cytochrome oxidase C subunit 1, nuclear sequence (internal transcribed spacer region 1), and AFLP data. Stygobromus pecki population structure and diversity was characterized and compared with congeners. For several Stygobromus species, the nominal taxonomy conflicted with molecular genetic data and there was strong evidence of significant cryptic diversity. Whereas S. pecki genetic diversity was similar to that of congeners, mitochondrial data identified two significantly diverged but sympatric clades. AFLP data for S. pecki indicated relatively recent and ongoing gene flow in the nuclear genome. These data for S. pecki suggest either a substantial history of isolation followed by current sympatry and ongoing admixture, or a protracted period of extremely large effective population size. This study demonstrates that Edwards Plateau Stygobromus are a complex, genetically diverse group with substantially more diversity than currently recognized. © 2013 The Linnean Society of London [ABSTRACT FROM AUTHOR]