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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. [Allelic variation; gene tree–species tree; haplotype trees; hybridization; incomplete lineage sorting; phylogenetic networks; Rosa ; total evidence.] [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 phylogeny of thamnophiine snakes has not been fully resolved, largely because previous phylogenetic estimates have been based on incomplete taxon sampling or relied solely on mitochondrial sequence data. To address this deficiency, we collected data from multiple autosomal loci collected from 50 taxa before estimating the most robust phylogeny of Thamnophiini to date. Our findings clarify the relationships of taxa not previously included in molecular analyses and also lend evidence to previously recommended taxonomic revisions. Differences in topological estimates between competing models of evolution were minimal and not strongly supported; however, a multispecies coalescent model of evolution was highly favoured over a concatenated model based on marginal likelihood estimates. Additionally, we estimated the timing of divergence among the three major lineages to have occurred during the Miocene period (approximately 11-14 Mya), followed by a decline in speciation rates in all major lineages. [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]

The Mylagaulidae are a family of burrowing rodents abundant in Miocene faunas from western North America. Recent taxonomic revisions of mylagaulids from the Great Plains suggest that their systematics may be best understood on a regional basis. Previous studies addressed the taxonomy and evolutionary history of mylagaulids from the Great Basin, but recent discoveries of specimens, new phylogenetic data, and more detailed stratigraphical information necessitate a thorough reanalysis of their relationships and occurrences. We present a revision of the systematics of the mylagaulids from the Great Basin. In addition to rare large mylagaulids of uncertain taxonomic affinity, we recognize four species of mylagaulids distributed throughout Oregon and Nevada from the late Hemingfordian through to the early late Hemphillian: Alphagaulus vetus, Hesperogaulus gazini, Hesperogaulus wilsoni, and a new species from the genus Hesperogaulus. All species are known from large sample sizes of isolated premolars, allowing consideration of ontogenetic variation in determining the key morphological differences that allow recognition of different species. Although the number of enamel lakes varies within a given taxon, the presence of some of these lakes is taxonomically significant. This result emphasizes the importance of understanding ontogeny in describing species of fossil hypsodont mammals. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 164, 427-450. [ABSTRACT FROM AUTHOR]

Coliiformes (mousebirds) are represented by just six extant species. These species, restricted to sub-Saharan Africa, are all primarily frugivorous and are among the most sedentary of living birds. Previously described fossil Coliiformes preserving feather traces share the short, rounded wing shape of extant mousebirds. Along with osteological evidence, these observations have been proposed to support poor sustained flight capabilities across the stem mousebird lineage. We report a new species of Coliiformes from the early Eocene (51.66 ± 0.09 Ma) Fossil Butte Member of the Green River Formation, represented by one of the comparatively few fossils from these deposits preserving carbonized traces of the wing and tail feathering. Feather traces indicate an elongate, tapering wing shape similar to that of some extant aerial insectivores, and suggestive of a capacity for sustained and agile open-air flight. Traces of the rectrices reveal the tail accounted for approximately two-thirds of the total length of the bird, a proportion similar to that in living mousebirds. Phylogenetic analysis places the new species as a stem representative of Coliiformes, demonstrating for the first time that the two major clades of Coliiformes - Sandcoleidae and Colii - co-occurred at Fossil Lake. Based on the recovered phylogeny, as well as the osteology and feathering of extant and fossil Coliiformes, the wing shape of the new species is interpreted as apomorphic. In addition to documenting unexpected morphological specialization within stem-lineage Coliiformes, the new species adds yet another taxon to the emerging reconstruction of the diverse Paleogene avifauna from the tightly dated and nearly synchronous fossiliferous deposits of the Fossil Butte Member. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, , 685-706. [ABSTRACT FROM AUTHOR]

The eastern fox squirrel (Sciurus niger) occurs naturally over most of eastern North America. The striking patterns of geographic variation in size and coat color displayed by this species are consistent with a hypothesis of southward range contraction and isolation in 2 refugia (in Texas and Florida) during the Last Glacial Maximum, followed by northward range expansion after the glaciers receded. Similar hypotheses have been proposed to explain the patterns in phylogeographic structure exhibited by many plants and animals in eastern North America. We analyzed DNA sequence variation in a 402--base-pair segment of the mitochondrial cytochrome-b gene in populations throughout the species' range. Despite our broad geographic sampling, we failed to detect any phylogeographic structure. Unique haplotypes differed from high-frequency haplotypes by only 1 or 2 base pairs, producing a starlike phylogeny of haplotypes. Genetic variation within populations and the species as a whole was characterized by high haplotype diversity and low nucleotide diversity. Taken together, our data indicate that the eastern fox squirrel underwent a rapid range expansion and rapid morphological divergence within the past 14,000 years. [ABSTRACT FROM AUTHOR]

We report a nearly complete skeleton of a new species of stem roller (Aves, Coracii) from the early Eocene Green River Formation of North America. The new species is most closely related to two species-depauperate lineages, Coraciidae (rollers) and Brachypteraciidae (ground rollers), that form a monophyletic crown clade (Coracioidea) with an exclusively Old World extant distribution. Phylogenetic analysis utilizing a matrix of 133 morphological characters and sequence data from three genes ( RAG-1, c-myc, and ND2) identifies the new species as a stem member of the Coracii more closely related to the crown clade than the only previously identified New World taxon, Primobucco mcgrewi. The phylogenetic placement of the new species and Primobucco mcgrewiindicates a widespread northern hemisphere distribution in the Eocene with subsequent restriction to Africa, Madagascar, Australia, and temperate to tropical parts of Europe and Asia. It provides evidence of further ecological diversity in early stem Coracii and convergence on crown morphologies. The new species contributes to mounting evidence that extant distributions for major avian subclades may be of comparatively recent origin. Further late Palaeogene sampling is needed to elucidate potential drivers for shifting avian distributions and disappearance of Coracii from North America. [ABSTRACT FROM AUTHOR]

Eastern North America is the location of the world's most species-rich temperate freshwater fish fauna. Hypotheses regarding the geographic and temporal scale of teleost diversification in this region have not been broadly investigated using absolute divergence time estimates among the constituent lineages. This study used time-calibrated molecular phylogenies estimated from mitochondrial and nuclear genes to investigate the temporal and geographic signatures of diversification within barcheek darters, a clade of allopatrically distributed species endemic to the Eastern Highlands. Results from divergence time estimates using an uncorrelated lognormal model suggest that the barcheek darters are an ancient group with a crown node estimate of 16.3 mya, 95% highest posterior density (HPD): [12.4, 20.5], and the clade is characterized by substantial intraspecific divergence times within several species. In particular, the Caney Fork endemic Etheostoma basilare comprises five strongly supported and deeply divergent clades with a most recent common ancestor estimated at 8.0 mya, 95% HPD: [5.6, 10.7]. These results are concordant with the hypothesis that geologically stable areas of eastern North America have facilitated both the generation and preservation of lineages across a substantial breadth of evolutionary time, and that allopatric speciation in darters has occurred at much smaller spatial scales than previously realized. [ABSTRACT FROM AUTHOR]

Peromyscine mice of the cricetid subfamily Neotominae comprise the most common and speciose assemblage of North American rodents. The composition and phylogenetic relationships within this group have been addressed using multiple character systems but remain unresolved, particularly the branching pattern of deeply rooted lineages. The relationships and status of several taxa formerly included within Peromyscus also are controversial. We present a new phylogenetic hypothesis based on combined mitochondrial and nuclear sequences using cytochrome b, interphotoreceptor retinoid-binding protein, and growth hormone receptor gene sequences, and include all major peromyscine lineages. Bayesian and parsimony approaches recover a congruent, well-resolved phylogeny, wherein Peromyscus forms a monophyletic assemblage only if a number of putative genera are included within it. Onychomys rather than Reithrodontomys is the sister taxon to Peromyscus (within which are included Habromys, Osgoodomys, Megadontomys, Podomys, and Neotomodon). Reithrodontomys in turn is the sister taxon to Isthmomys, and these 2 genera are the nearest outlier to Onychomys plus an expanded concept of Peromyscus, consistent with the recent recognition of this entire group as the tribe Reithrodontomyini. The Baiomyini, Ochrotomyini, and Neotoma (Neotomini) appear as successive outgroups to this clade. Based on these results, we present a systematic review of higher-level relationships among peromyscine rodents. [ABSTRACT FROM AUTHOR]

The bacterial phylogenetic structure of soils from four distinctly different sites in South and North America was analyzed. One hundred and thirty-nine thousand sequences of the V9 region of the small subunit of the bacterial ribosomal RNA gene generated for a previous study were used for this work. Whereas the previous work estimated levels of species richness, this study details the degree of bacterial community overlap between the four soils. Sequences from the four soils were classified and grouped into different phyla and then assigned to operational taxonomic units (OTUs) as defined by 97 or 100% sequence similarity. Pairwise Jaccard and θ similarity indices averaged over all phyla equalled 6 and 12% respectively at the 97% similarity level, and 15% for both at the 100% similarity level. At 100 and 97% sequence similarity, 1.5 and 4.1% of OTUs were found in all four soils respectively, and 87.9 and 74.4%, respectively were a unique particular soil. These analyses, based on the largest soil bacterial sequence retrieval to date, establish the high degree of community structure difference for randomly sampled dissimilar soils and support the idea that wide sampling is important for bioprospecting. The 10 most abundant cultured genera were determined in each soil. These 10 genera comprised a significant proportion of the reads obtained from each soil (31.3–37.4%). Chitinophaga was the most abundant or the second most abundant genus in all four soils with 7.5–13.8% of the total bacterial sequences in these soils. The striking result is that several culturable genera, whose roles in soil are virtually unknown, were found among these dominant sequences.The ISME Journal (2008) 2, 901–910; doi:10.1038/ismej.2008.55; published online 5 June 2008 [ABSTRACT FROM AUTHOR]

The spider genus Nanoa gen. nov. (Araneae, Pimoidae) is described to place Nanoa enana, a new species of pimoids from Western North America. Parsimony analysis of morphological characters provides support for the monophyly of Pimoa plus Nanoa and corroborates the monophyly of Pimoidae and of the clade Linyphiidae plus Pimoidae. © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society, 2005, 145, 249–262. [ABSTRACT FROM AUTHOR]

Brooding characters have figured prominently in the classification of North American freshwater pearly mussels (Bivalvia: Unionoidea). The purpose of our study was to evaluate phylogenetic hypotheses of brooding character evolution in order to test homology statements suggested by earlier taxonomic systems of the Unionoidea. Parsimony analysis of partial COI sequences from 29 species of freshwater mussels and 13 outgroups were used to derive a phylogeny. Thirteen brooding characters (e.g., brooding period, marsupium arrangement, structure of interlamellar septa, etc.) were traced onto this phylogeny. Results indicate that long-term brooding (bradytictia) is the derived state among North American freshwater mussels; short-term brooding (tachytictia) is plesiomorphic. Bradytictia evolved independently in the Anodontinae and Lampsilini, with unique morphological modifications derived in those clades to facilitate long-term brooding. [ABSTRACT FROM PUBLISHER]

The article presents information on armored scale genus Quernaspis separated into two genera of the North American and the East Asian species. Since there is consistent morphological separation between these groups in the first instars, second stage males, and adult females, a new genus for the East Asian species is erected. The genus is referable to the Diaspididae and is morphologically similar to Quernaspis, but significant morphological differences occur in the first instars, second stage males, and adult females. It informs that it can be believed that these genera are very closely related phylogenetically, and may have arisen from common ancestral stock.