Hoehn, Kenneth B. · Hoehn, Kenneth B.

Scripts used to calculate average pairwise differences between all 6 pairwise combinations along the XR chromosome between Drosophila pseudoobscura, Drosophila persimilis, Sex-Ratio Drosophila persimilis, and Drosophila miranda. These output file can then be used to calculate RND between D pseudoobscura, D persimilis, and SR D persimilis in another program such as Microsoft Excel. All scripts are written in Perl. Author: Kenneth Hoehn. Date: May-5-2011. Sections: 1. Constructing the combined, raw input file from PILEUP outputs (skip if combined input file is provided); 2. Necessary input files for final analysis; 3. Editing combined input file and calculating average pairwise differences; 4. Calculating RND; 5. Double checking output; 6. Simple window writing script. See README.txt for more details.

Hoehn, Kenneth B.

This document contains the multiple genome alignment file associated with this publication. A total of four XR chromosome sequences were used for this study – one D. miranda, one D. pseudoobscura, and two D. persimilis.

Hekkala, Evon · Shirley, Matthew H. · Amato, George · et al.

The Nile crocodile (Crocodylus niloticus) is an ancient icon of both cultural and scientific interest. The species is emblematic of the great civilizations of the Nile River valley and serves as a model for international wildlife conservation. Despite its familiarity, a centuries-long dispute over the taxonomic status of the Nile crocodile remains unresolved. This dispute not only confounds our understanding of the origins and biogeography of the “true crocodiles” of the crown genus Crocodylus, but also complicates conservation and management of this commercially valuable species. We have taken a total evidence approach involving phylogenetic analysis of mitochondrial and nuclear markers as well as karyotype analysis of chromosome number and structure to assess the monophyletic status of the Nile crocodile. Samples were collected from throughout Africa, covering all major bioregions. We also utilized specimens from museum collections, including mummified crocodiles from the ancient Egyptian temples at Thebes and the Grottes de Samoun, to reconstruct the genetic profiles of extirpated populations. Our analyses reveal a cryptic evolutionary lineage within the Nile crocodile that elucidates the biogeographic history of the genus and clarifies long-standing arguments over the species’ taxonomic identity and conservation status. An examination of crocodile mummy haplotypes indicates that the cryptic lineage corresponds to an earlier description of C. suchus and suggests that both African Crocodylus lineages historically inhabited the Nile River. Recent survey efforts indicate that C. suchus is declining or extirpated throughout much of its distribution. Without proper recognition of this cryptic species, current sustainable use-based management policies for the Nile crocodile may do more harm than good.

Hekkala, Evon · Shirley, Matthew H. · Amato, George · et al.

Nexus file containing sequence data for the 12S rRNA mitochondrial gene region. Please refer to Table 2 of the associated manuscript, as well as the Methods section, for specimen information.

Hekkala, Evon · Shirley, Matthew H. · Amato, George · et al.

Nexus file containing sequence data for the 16S rRNA mitochondrial gene region. Please refer to Table 2 of the associated manuscript, as well as the Methods section, for specimen information.

Hekkala, Evon · Shirley, Matthew H. · Amato, George · et al.

Nexus file containing sequence data for the control region/dloop mitochondrial gene region. Please refer to Table 2 of the associated manuscript, as well as the Methods section, for specimen information.

Hekkala, Evon · Shirley, Matthew H. · Amato, George · et al.

Nexus file containing sequence data for the NADH dehydrogenase subunit 4 mitochondrial gene region. Please refer to Table 2 of the associated manuscript, as well as the Methods section, for specimen information.

Hekkala, Evon · Shirley, Matthew H. · Amato, George · et al.

Nexus file containing sequence data for the WANCY tRNA cluster from the ND2-flanking region including tRNA_Trp, tRNA_Ala, tRNA_Asn, tRNA_Cys, and part of tRNA_Tyr mitochondrial gene region. Please refer to Table 2 of the associated manuscript, as well as the Methods section, for specimen information.

Hekkala, Evon · Shirley, Matthew H. · Amato, George · et al.

Nexus file containing sequence data for the rag-1 recombination activating gene-1 nuclear gene region. Please refer to Table 2 of the associated manuscript, as well as the Methods section, for specimen information.

Hekkala, Evon · Shirley, Matthew H. · Amato, George · et al.

Nexus file containing sequence data for the ribosomal protein S6 nuclear gene region. Please refer to Table 2 of the associated manuscript, as well as the Methods section, for specimen information.

Hekkala, Evon · Shirley, Matthew H. · Amato, George · et al.

Nexus file containing sequence data for the tropomyosin intron nuclear gene region. Please refer to Table 2 of the associated manuscript, as well as the Methods section, for specimen information.

Hekkala, Evon · Shirley, Matthew H. · Amato, George · et al.

Nexus file containing sequence data for the ornithine decarboxylase intron nuclear gene region. Please refer to Table 2 of the associated manuscript, as well as the Methods section, for specimen information.

Hekkala, Evon · Shirley, Matthew H. · Amato, George · et al.

Nexus file containing sequence data for the 12s rRNA mitochondrial gene region. Sequences listed here are the "short 12s" sequences for the museum and mummy specimens only. Please refer to the associated manuscript Table 2, and Methods, for further specimen information.

Hekkala, Evon · Shirley, Matthew H. · Amato, George · et al.

Nexus file containing sequence data for the control region/dloop mitochondrial gene region. Sequences listed here are the "short dloop" sequences for the museum and mummy specimens only. Please refer to the associated manuscript Table 2, and Methods, for further specimen information.

Ketchum, Hilary F. · Benson, Roger B. J.

A partial skeleton from the Sigiloceras enodatum ammonite Subzone (early Callovian, Middle Jurassic) of the Oxford Clay Formation of Quest Pit, near Stewartby, Bedfordshire, UK respresents one of the basalmost Middle Jurassic pliosaurids. Marmornectes candrewi gen. et sp. nov. possesses seven autapomorphies and a longirostrine snout. Reassessment of pliosauroid relationships demonstrates that Thalassiodracon hawkinsii, Hauffiosaurus spp. and Attenborosaurus conybeari are successively more derived basal representatives of Pliosauridae. This indicates that a longirostrine snout was acquired among Early Jurassic pliosaurids (such as Hauffiosaurus), but that these early taxa had a small body size, long neck, and gracile skull and limb bones relative to the contemporaneous rhomaleosaurids, which were robust, large-bodied macropredators. The pliosaurid lineage only acquired its ‘characteristic’ large size, robust skull and short neck in the late Middle Jurassic after the extinction of Rhomaleosauridae.

Henk, Daniel A. · Eagle, Carly E. · Brown, Kevin · et al.

Eighty years ago, Alexander Fleming described the antibiotic effects of a fungus that had contaminated his bacterial culture, kick starting the antimicrobial revolution. The fungus was later ascribed to a putatively globally distributed asexual species, Penicillium chrysogenum. Recently, the species has been shown to be genetically diverse, and possess mating-type genes. Here, phylogenetic and population genetic analyses show that this apparently ubiquitous fungus is actually composed of at least two genetically distinct species with only slight differences detected in physiology. We found each species in air and dust samples collected in and around St Mary’s Hospital where Fleming worked. Genotyping of 30 markers across the genome showed that preserved fungal material from Fleming’s laboratory was nearly identical to derived strains currently in culture collections and in the same distinct species as a wild progenitor strain of current penicillin producing industrial strains rather than the type species P. chrysogenum. Global samples of the two most common species were found to possess mating-type genes in a near 1:1 ratio, and show evidence of recombination with little geographic population subdivision evident. However, no hybridization was detected between the species despite an estimated time of divergence of less than 1 MYA. Growth studies showed significant interspecific inhibition by P. chrysogenum of the other common species, suggesting that competition may facilitate species maintenance despite globally overlapping distributions. Results highlight under-recognized diversity even among the best-known fungal groups and the potential for speciation despite overlapping distribution.

Henk, Daniel A. · Eagle, Carly E. · Brown, Kevin · et al.

Location, allelic profiles, and species assignment in a single datasheet. A second datasheet contains allelic size information.

Duellman, William E. · Catenazzi, Alessandro · Blackburn, David C.

Gastrotheca nebulanastes sp. nov. from cloud forests in the upper Kosñipata Valley, Manu National Park, in the Andes of southern Peru is similar to G. excubitor, which inhabits grasslands in higher elevations than the cloud forests. The two species differ in relative lengths of the fingers, skin texture, coloration, and advertisement call. Although the new species has an elevational range of 2000–3300 m, it is most abundant at 2400–2800 m. A phylogenetic analysis of a previously defined clade of Gastrotheca based on a fragment of 16S mitochondrial gene provides strong support that the sister taxon to the new species is G. atympana, a species from farther north in the Cordillera Oriental in Peru.

Blackburn, David C.

Multiple sequence alignment of DNA sequence data for mitochondrial 16S ribosomal RNA gene.