Endogenous Avian Leukosis Virus subgroup E elements of the chicken reference genome

The chicken reference genome contains two endogenous Avian Leukosis Virus subgroup E (ALVE) insertions, but gaps and unresolved repetitive sequences in previous assemblies has hindered their precise characterisation. Detailed analysis of the most recent reference genome (GRCg6a) now shows both ALVEs within contiguous chromosome assemblies for the first time. ALVE6 (ALVE-JFevA) and ALVE-JFevB are both located on chromosome 1, with ALVE6 close to the p arm telomere. ALVE-JFevB is a structurally intact element containing the ALVE gag, pol and env genes, and is capable of forming replication competent viruses. In contrast, ALVE6 (ALVE-JFevA) contains a 3352 bp 5’ truncation and lacks the entire 5’ LTR and gag gene. Despite this, ALVE6 remains able to produce intact envelope protein, likely due to a mutation in the recognition site for a known inhibitory miRNA (miR-155). Whole genome resequencing datasets from layers, broilers and three independent sources of wild-caught red junglefowl were surveyed for the presence of each of these reference genome ALVEs. ALVE-JFevB was found in no other chicken or red junglefowl genomes, whereas ALVE6 was identified in some layers, broilers and native breeds, but not within any other red junglefowl genome. Improved assembly contiguity has facilitated better characterisation of the two ALVEs of the chicken reference genome. However, both the limited ALVE content and unique presence of ALVE-JFevB suggests that the reference individual is unrepresentative of ancestral Gallus gallus ALVE diversity

Karyotype, Sex Determination, and Meiotic Chromosome Behavior in Two Pholcid (Araneomorphae, Pholcidae) Spiders: Implications for Karyotype Evolution

There are 1,111 species of pholcid spiders, of which less than 2% have published karyotypes. Our aim in this study was to determine the karyotypes and sex determination mechanisms of two species of pholcids: Physocyclus mexicanus (Banks, 1898) and Holocnemus pluchei (Scopoli, 1763), and to observe sex chromosome behavior during meiosis. We constructed karyotypes for P. mexicanus and H. pluchei using information from both living and fixed cells. We found that P. mexicanus has a chromosome number of 2n = 15 in males and 2n = 16 in females with X0-XX sex determination, like other members of the genus Physocyclus. H. pluchei has a chromosome number of 2n = 28 in males and 2n = 28 in females with XY-XX sex determination, which is substantially different from its closest relatives. These data contribute to our knowledge of the evolution of this large and geographically ubiquitous family, and are the first evidence of XY-XX sex determination in pholcids

The discovery of endogenous retroviruses

When endogenous retroviruses (ERV) were discovered in the late 1960s, the Mendelian inheritance of retroviral genomes by their hosts was an entirely new concept. Indeed Howard M Temin's DNA provirus hypothesis enunciated in 1964 was not generally accepted, and reverse transcriptase was yet to be discovered. Nonetheless, the evidence that we accrued in the pre-molecular era has stood the test of time, and our hypothesis on ERV, which one reviewer described as 'impossible', proved to be correct. Here I recount some of the key observations in birds and mammals that led to the discovery of ERV, and comment on their evolution, cross-species dispersion, and what remains to be elucidated

DNA Barcoding for Community Ecology - How to Tackle a Hyperdiverse, Mostly Undescribed Melanesian Fauna

Trigonopterus weevils are widely distributed throughout Melanesia and hyperdiverse in New Guinea. They are a dominant feature in natural forests, with narrow altitudinal zonation. Their use in community ecology has been precluded by the "taxonomic impediment". We sampled >6,500 specimens from seven areas across New Guinea; 1,002 specimens assigned to 270 morphospecies were DNA sequenced. Objective clustering of a refined dataset (excluding nine cryptic species) at 3% threshold revealed 324 genetic clusters (DNA group count relative to number of morphospecies = 20.0% overestimation of species diversity, or 120.0% agreement) and 85.6% taxonomic accuracy (the proportion of DNA groups that "perfectly" agree with morphology-based species hypotheses). Agreement and accuracy were best at an 8% threshold. GMYC analysis revealed 328 entities (21.5% overestimation) with 227 perfect GMYC entities (84.1% taxonomic accuracy). Both methods outperform the parataxonomist (19% underestimation; 31.6% taxonomic accuracy). The number of species found in more than one sampling area was highest in the Eastern Highlands and Huon (Sørensen similarity index 0.07, 4 shared species); ⅓ of all areas had no species overlap. Success rates of DNA barcoding methods were lowest when species showed a pronounced geographical structure. In general, Trigonopterus show high α and β-diversity across New Guinea. DNA barcoding is an excellent tool for biodiversity surveys but success rates might drop when closer localities are included. Hyperdiverse Trigonopterus are a useful taxon for evaluating forest remnants in Melanesia, allowing finer-grained analyses than would be possible with vertebrate taxa commonly used to date. Our protocol should help establish other groups of hyperdiverse fauna as target taxa for community ecology. Sequencing delivers objective data on taxa of incredible diversity but mostly without a solid taxonomic foundation and should help pave the road for the eventual formal naming of new species

Molecular approaches to trematode systematics: 'best practice' and implications for future study

To date, morphological analysis has been the cornerstone to trematode systematics. However, since the late-1980s we have seen an increased integration of genetic data to overcome problems encountered when morphological data are considered in isolation. Here, we provide advice regarding the ‘best molecular practice’ for trematode taxonomy and systematic studies, in an attempt to help unify the field and provide a solid foundation to underpin future work. Emphasis is placed on defining the study goals and recommendations are made regarding sample preservation, extraction methods, and the submission of molecular vouchers. We advocate generating sequence data from all parasite species/host species/geographic location combinations and stress the importance of selecting two independently evolving loci (one ribosomal and one mitochondrial marker). We recommend that loci should be chosen to provide genetic variation suitable to address the question at hand and for which sufficient ‘useful’ comparative sequence data already exist. Quality control of the molecular data via using proof-reading Taq polymerase, sequencing PCR amplicons using both forward and reverse primers, ensuring that a minimum of 85% overlap exists when constructing consensus sequences, and checking electropherograms by eye is stressed. We advise that all genetic results are best interpreted using a holistic biological approach, which considers morphology, host identity, collection locality, and ecology. Finally, we consider what advances next-generation sequencing holds for trematode taxonomy and systematics

Phylogeny and Classification of the Trapdoor Spider Genus Myrmekiaphila: An Integrative Approach to Evaluating Taxonomic Hypotheses

Background: Revised by Bond and Platnick in 2007, the trapdoor spider genus Myrmekiaphila comprises 11 species. Species delimitation and placement within one of three species groups was based on modifications of the male copulatory device. Because a phylogeny of the group was not available these species groups might not represent monophyletic lineages; species definitions likewise were untested hypotheses. The purpose of this study is to reconstruct the phylogeny of Myrmekiaphila species using molecular data to formally test the delimitation of species and species-groups. We seek to refine a set of established systematic hypotheses by integrating across molecular and morphological data sets. Methods and Findings: Phylogenetic analyses comprising Bayesian searches were conducted for a mtDNA matrix composed of contiguous 12S rRNA, tRNA-val, and 16S rRNA genes and a nuclear DNA matrix comprising the glutamyl and prolyl tRNA synthetase gene each consisting of 1348 and 481 bp, respectively. Separate analyses of the mitochondrial and nuclear genome data and a concatenated data set yield M. torreya and M. millerae paraphyletic with respect to M. coreyi and M. howelli and polyphyletic fluviatilis and foliata species groups. Conclusions: Despite the perception that molecular data present a solution to a crisis in taxonomy, studies like this demonstrate the efficacy of an approach that considers data from multiple sources. A DNA barcoding approach during the species discovery process would fail to recognize at least two species (M. coreyi and M. howelli) whereas a combine

PENGARUH PENGETAHUAN, KETERAMPILAN, KONSEP DIRI DAN KARAKTERISTIK PRIBADI TERHADAP KINERJA STAF PADA SMK N SE KOTA PEKALONGAN

Peningkatan para pelaku usaha makanan di Kota Semarang, pada tahun 2011 sebanyak 80 pelaku usaha, tahun 2012 bertambah 85 pelaku usaha, pada tahun 2013 bertambah 92 pelaku usaha, dan pada tahun 2014 bertambah menjadi 108 pelaku usaha makanan yang ada di Kota Semarang. Dengan peningkatan para pelaku usaha makanan tersebut ternyata tidak berdampak baik pada pendapatan yang diperoleh. Dari jumlah seluruh pendapatan UMKM makanan yang berada di Kota Semarang, pada tahun 2011 pendapatan mereka mencapai Rp. 13.13.000.000, pada tahun 2012-2013 mengalami penurunan 28,90% yaitu menjadi Rp. 9.323.000.000, pada tahun 2013 mengalami penurunan mencapai 53,33% yaitu menjadi Rp. 4.351.000.000, dan pada tahun 2014 juga mengalami penurunan sebesar 32,58% yaitu menjadi Rp.2.933.657.000. Penelitian ini merupakan penelitian kuantitatif dengan metode penelitian regrresi linier berganda. Subjek penelitian adalah para pelaku usaha makanan yang berada di Kecamatan Tembalang Kota Semarang, data awal yang diterima dari Dinas Koperasi dan UMKM Kota Semarang, jumlah pelaku usaha makanan yang terdaftar sebanyak 38 pelaku usaha. Setelah peneliti melakukan penelitian secara langsung hanya tersisa 36 pelaku usaha yang masih aktif menjalankan usahanya. Metode pengumpulan data adalah observasi, dan kuisioner (angket). Hasil penelitian diperoleh (Uji F) untuk varibael (X1) manajemen, (X2) lokasi usaha, (X3) pemasaran, diperoleh sebesar 0,992 dengan probabilitas 0,000. Karena 0,000<0,05 maka X1, X2, X3, ada pengaruh terhadap perolehan pendapatan usaha. Untuk (Uji t) variabel X1 di peroleh t hitung sebesar 1,030 dengan probabilitas 0,001. Untuk X2 diperoleh t hitung sebesar 2,510 dengan probabilitas 0,020. Untuk X3 di peroleh t hitung sebesar 2,596 dengan probabilitas 0,000. Untuk (Uji R2) variabel XI, X2, X3 diperoleh sebesar 0,791(79,1%). Dan untuk (Uji r2) untuk X1 diperoleh r hitung sebesar (0,305)2 atau 0,093 (9,3%), X2 diperoleh r hitung sebesar (0,490)2 atau 0,240 (24%), dan X3 diperoleh r hitung sebesar (0,567)2 atau 0,321 (32,1%). The increase in the food business operators in the city, in 2011 as many as 80 businesses, in 2012 increased 85 businesses, in 2013 increased 92 businesses, and in 2014 increased to 108 food business operators in the city of Semarang. With the increase in the food business operators did not have an impact both on the revenue earned. Of the total revenue of SMEs foods are in the city, in 2011 their income reached Rp. 13.13.000.000, in 2012-2013 decreased to Rp 28.90 ie. 9.323 billion, in 2013 decreased 53.33 which reached Rp. 4.351 billion, and in 2014 also decreased by 32.58 which is becoming Rp.2.933.657.000. This research is a quantitative research methods regrresi linear regression. The research subject is the food business operators in Sub Tembalang Semarang, the initial data received from the Department of Cooperatives and SMEs Semarang, the number of registered food business operators as many as 38 businesses. Once the researchers conducted research directly only the remaining 36 businesses are still active in business. Data collection method was observation and questionnaire (questionnaire). The results were obtained (Test F) for varibael (X1) management, (X2) the location of the business, (X3) marketing, obtained by 0.992 with a probability of 0.000. Because 0.000 &lt;0.05, X1, X2, X3, no effect on the acquisition of operating revenues. To (t test) X1 variable obtained t count equal to 1,030 with probability 0,001. For X2 obtained t count equal to 2,510 with probability 0,020. For X3 obtained t count equal to 2,596 with probability 0,000. For (Test R2) variable XI, X2, X3 obtained for 0.791 (79.1). And for (Test r2) for the X1 is obtained by calculating r (0,305) 2 or 0.093 (9.3), X2 is obtained by calculating r (0.490) 2 or 0.240 (24), and X3 obtained by calculating r (0.567) 2 or 0.321 (32.1)