Miracle-dz/UniFAR-FTUs huggingface dataset:
Male Song Variation and Female Mate Choice in the Golden-Winged Warbler

Abstract. We investigated the distinctiveness of males' song and the relationship between song variables and females' mate choice in the Golden-winged Warbler (Vermivora chrysoptera). We recorded the songs of 23 males and quantified them to examine performance-related traits and specific song content. We carried out discriminant function analysis to compare variation within and among males for characteristics of both song types I and II. We used microsatellite DNA to identify the parents of 62 nestlings from 17 nests. By assigning paternity to males in our population we could examine relationships between females' choice and variation in males' song by comparing characteristics of within- and extra-pair sires. While we were able to discriminate statistically between individual males' songs, we found no significant differences in song variables between the within- and extra-pair males at a given nest. Therefore, female Golden-winged Warblers do not appear to be using these differences in song in choosing a mate. Further research on the Golden-winged Warbler is needed to understand song function and to gain insight into this species' reproductive biology, both of which could have important conservation implications for this declining species.
DPMAS: pipeline for 450K top table replication with MiSeq amplicons

DNA methylation is one of the most important epigenetic modifications in gene expression regulation and it plays a crucial role in multiple biological processes. Therefore, DNA methylation profiling is important to reveal regions of the genome that are altered during development or that are perturbed by disease. Methylation signals at CpG sites can be assessed using bisulfite conversion method and massive sequencing technologies. Here we present the implementation of a bioinformatics pipeline for replication with MiSeq sequencing amplicons of the top hits obtained from Infinium 450K differential methylation experiments. CONCLUSIONS We have implemented a bioinformatics pipeline for replication of the top hits obtained from Infinium 450K experiments using MiSeq sequencing amplicons. For this purpose we have used well-established software for genome analysis as well as applications developed in our lab, all of them open source. The proposed workflow has proved to be useful for methylation level assessment while maintaining a good data quality control. Source code will be available at: https://github.com/pamag/DPMAS PIPELINE REPORT 450K results The assessment of methylation level at CpG sites from raw genetic sequences involves quality control and several processing steps. The main building blocks of the pipeline include SNP selection from 450K experiments, sequencing of the regions containing those SNPs with directional primers, mapping of the reads to the reference amplicon sequences and variant calling at cytosines in CpG sites. Finally, a dashboard report is produced as an analysis summary. Other SNP selection Directional amplification primers design MiSeq sequencing Adaptor removal and quality trimming Mapping
Monitoring sugarcane moth borers in Indonesia: towards better preparedness for exotic incursions.

SUGARCANE moth borers were surveyed on 931 farms across Java, Indonesia in 2008–09. Five moth borer species caused varying levels of damage to sugarcane plantations: Chilo auricilius, C. sacchariphagus, Scirpophaga excerptalis, Sesamia inferens and Tetramoera schistaceana. The first three were the most abundant. All five species caused ‘dead hearts’ in sugarcane, with S. excerptalis (top borer) being responsible for the majority of dead heart symptoms in both young and mature cane. Chilo species (stalk borers) cause dead hearts only in young cane and later tunnel inside cane stalks and damage the internodes. Farms managed by sugar factories suffered more S. excerptalis dead hearts than those managed by individual growers. This may be the result of crop diversification and shorter crop cycles practiced by individual farmers. In addition, S. excerptalis dead heart symptoms were more common in older ratoons, indicating progressive build up of infestation in older crops. C. sacchariphagus was more widespread in Java than C. auricilius, with the former species preferring irrigated areas while C. auricilius was more abundant in drier areas. S. excerptalis was equally abundant in both irrigated and rainfall areas. Parasitoid species recovered were Cotesia flavipes from C. sacchariphagus, Diatraeophaga striatalis from both Chilo species, and Rhaconotus roslinensis, R. scirpophagae, Stenobracon sp. , Elasmus sp. and Isotima sp from S. excerptalis. All moth borers have a high potential of colonising sugarcane in Australia, especially in central and north Queensland where climatic conditions are similar to conditions in their area of origin. Knowledge of the distribution and dynamics of these pests is essential to the development of sound Incursion Management Plans to ensure better preparedness for any incursion into Australia.
Characterization and Plasmid Profiling of Salmonella Enteritidis Isolated from Broiler Chickens

Salmonella Enteritidis is considered one of the main causes of economic losses among poultry industry and production. The present study was aimed to characterize Salmonella Enteritidis isolated from broiler chickens and provide an insight toward plasmid profile of these isolates. A total of 125 samples were collected from broiler chickens; and bacteriological isolation was carried out using tetrathionate broth and MacConkey agar medium. Five isolates of S. Enteritidis were obtained by serotyping using O and H antisera and confirmed by Polymerase Chain Reaction (PCR). Plasmid profile which was carried out on these isolates indicated that this five isolates having three different plasmid profiles concluding that phenotypically similar strains of SE may be genotypically different and plasmid profile is a simple method that could detect this genotypic variation.
MOLECULAR CHARACTERIZATION AND PROKARYOTIC EXPRESSION OF ORF507 STERILITY-ASSOCIATED GENE IN CHILLI PEPPER (CAPSICUM ANNUM L.) CYTOPLASMIC MALE STERILITY

A is a cytoplasmic male sterility (CMS) of chilli pepper (Capsicum annuum L) that has been commercially used in chilli pepper hybrid production in China. However, little is known about the CMS-associated gene in chilli pepper 9704A.In this study, according to the sequence of relative references, a fragment of 593 bp including a 507-bp single-coding exon, Orf507 (GenBank accession No. GU357841) was cloned from leaves of chilli pepper CMS-9704A. Results revealed that the orf456-2 had one nucleotide deleted in codon 150 (nt450delC) and consists of a 507-bp single-coding exon which encodes 168 amino acid compared with the original sequence data of orf456. RT-PCR results showed that the Orf507 was transcribed in buds and leaves at all developmental stages of CMS-9704A and a hybrid F1, while no band was detected in the maintainer line. The nuclear restorer gene may restore fertility by post-transcriptional processing or translational/post- translational modification, but did not interfere with transcription of Orf507 directly. The entire coding region of the Orf507 was inserted into an expression vector pET32α(+) and transformed into Escherichia coli Rosetta. Expression of the fusion protein was successfully induced by isopropyl-β-D-thiogalactopyranoside. This study could establish a basis for understanding the molecular mechanism of chilli pepper CMS.
Phenotypic selection and population differentiation in Platanthera bifolia

The present study explored whether differentiation in phenology and morphology between a woodland and an alvar population of the hawkmoth-pollinated orchid Platanthera bifolia could be related to differences in patterns of phenotypic selection. Supplemental hand-pollination experiments were performed to quantify pollen limitation and to determine whether selection on floral traits could be attributed to interaction with pollinators. Fitness was estimated as pollinia removal (male function) and seed production (female function). Patterns of selection were generally the same in the large-flowered, early-flowering woodland population and in the small-flowered, late-flowering alvar population, although the strength of selection differed. Both phenology and flower number were under selection through female function, while only flower number was subject to selection through male function. Flower size and spur length were not under direct selection. The supplemental hand-pollination experiments showed that seed production was pollen limited in both populations, and that pollinators exerted selection on flower number through female function in the alvar population. Differences in selection did not correspond to population differences in phenology and morphology, which might be due to variation in selection among years. Introduction The evolution of floral traits is believed to be driven largely by pollinator-mediated selection (Darwin 1862; Fenster et al. 2004). Geographic variation in habitat conditions and the composition of the pollinator community may lead to divergent selection on floral traits, and genetic differentiation among populations. At present it is commonly agreed that floral displays in hermaphrodite plants evolve in response to both female function (seed production) and male function (pollen export), but the relative importance of selection through male and female functions is unknown (Ashman and Morgan 2004). Generally, it is difficult to estimate components of male fitness, such as pollen donation and siring success. However, in orchids, pollinia removal can be estimated easily by scoring the number of pollinia removed per plant, as pollen grains are held together in the pollinium. In this study, I investigated phenotypic selection through both male and female functions in two morphologically and phenologically differentiated populations of the moth-pollinated orchid Platanthera bifolia on the island of Oland, southeast of Sweden. The woodland population started and ended flowering earlier, and the plants were taller with larger flowers and longer spurs compared to the alvar population. The aim was to determine whether population differentiation was related to differences in selection in the two habitats. The main questions examined were: 1. Do patterns of selection on flowering phenology and morphology differ between populations? If so, do patterns of selection correspond to differences observed in floral traits? 2. Can selection on flowering phenology and floral morphology be attributed to selection mediated by pollinators?
WKY Fatty Rat as a Model of Obesity and Non-insulin-dependent Diabetes Mellitus

Health. Peterson, R. G. , A. K. Sharma, L. A. Little, M. Neel, C. G. Potter, and J. Eichberg. 1988b. Peripheral nerve abnormalities in Wistar fatty diabetic rats. Pp. 488-491 in Frontiers in Diabetes Research. Lessons from Animal Diabetes II, E. Shafrir and A. E. Renold, eds. London: John Libbey. Seino, Y. , S. Seino, M. Usami, K. Tsuda, J. Takemura, S. Nishi, H. Ishida, and H. Imura. 1984. Somatostatin, glucagon, and insulin secretion from isolated perfused pancreas of new genetically obese hyperglycemic rats. Metabolism 33(5):429-431. Sugiyama, Y. , Y. Shimura, and H. Ikeda. 1989a. Pathogenesis of hyperglycemia in genetically obese-hyperglycemic rats, Wistar fatty: Presence of hepatic insulin resistance. Endocrinol. Japon. 36(1):6573. Sugiyama, Y. , Y. Shimura, and H. Ikeda. 1989b. Derangement in hepatic enzymes caused by sucrose-drinking and its implication for the development of hyperglycemia in female Wistar fatty rats. Endocrinol. Japon. 36(2):245-251. Sussman, K. 1985. Spectrum of defects in non-insulin-dependent diabetes mellitus. Am. J. Med. 79 (suppl. 79): 1-5. Terrettaz, J., and B. Jeanrenaud. 1983. In vivo hepatic and peripheral insulin resistance in genetically obese (fa/fa) rats. Endocrinology 112:1346-1351. West, D. B. , R. Rohlfing, R. Kava, and M. R. C. Greenwood. In press. Hepatic glucose production (HGP) is elevated in obese diabetic Wistar fatty (Wf) rats. Int. J. Obesity (abstr.). Zucker, L. M. , and T. F. Zucker. 1961. Fatty, a new mutation in the rat. J. Hered. 52:275-278.
Systematic revision and phylogeny of the plant bug tribe Monaloniini (Insecta: Heteroptera: Miridae: Bryocorinae) of the world

A systematic revision, redescription and a first generic conspectus on a worldwide basis of the scarcely studied plant bug tribe Monaloniini (Insecta: Heteroptera: Miridae: Bryocorinae) is given. This reclassification is of great significance to agriculture as some monaloniines are major pests of cocoa, cashew, tea and other foodplants. A key to genera is given, as well as generic diagnoses and descriptions, photographs, scanning electron micrographs, illustration of male and female genitalia, host plant information and distributional maps. This reclassification is based on a phylogenetic analysis of external and genitalic characters, with 118 species and 32 genera codified. The phylogenetic analysis resulted in the recognition of a monophyletic Monaloniini, and strongly supported non-monophyly of the previously recognized subtribes Monaloniina and Odoniellina, resulting in the rejection of a formal subtribal classification for the tribe. The following new synonymy is recognized: Boxia (= Boxiopsis syn. nov.), Chamus (= Chamopsis syn. nov., Parachamus syn. nov.), Volkeliopsis (= Mircarvalhoia syn. nov.), Platyngomiris (= Platyngomiriodes syn. nov.), Platyngomiris coreoides (= Platyngomiriodes apliformis syn. nov.), Lycidocoris (= Pantilioforma syn. nov.). Afropeltis is raised to full generic status. Onconotellus and Pachypeltopsis are transferred to the Orthotylinae and Deraeocorinae, respectively. Volkeliopsis mindanao sp. nov. is described as new to science. © 2015 The Linnean Society of London
Equine Color Genetics

Chapter 1. Introduction. Basic Considerations of Horse Color Identification. Basic Principles of Genetics. Pigments in Horses. Pigment Cell Function. Chapter 2. Basic Dark Horse Colors: Bay, Chestnut, Black, and Brown. Bay, Chestnut, and Black: Definition and Classification. Bay, Chestnut, and Black: Genetic Control. Dominant Black. Two Subtypes of Bay: Wild Bay and Bay. Seal Brown. General Factors Modifying Bay, Chestnut, and Black. Sorrel: Def. Mane and Tail Color on Chestnut and Sorrel: Gen. Bend Or Spots. Dapples. Chapter 3. Colors Built from the Basic Colors. Linebacked Dun: Definition and Classification. Linebacked Dun: Genetic Control. Cream-related Colors: Definition and Classification. Cream-related Colors: Genetic Control. Champagne: Definition and Classification. Champagne: Genetic Control. Pearl: Definition, Classification, and Genetic Control. Silver Dapple: Definition and Classification. Silver Dapple: Genetic Control. Mushroom: Definition, Classification, and Genetic Control. Other Dilutions. Compound Dilute Colors. Brindle. Eye Color. Foal Color. Summary of the Genetic Control of Horse Color. Chapter 4. Patterns of White. General Considerations. Patterns with Individual White Hairs: Grey and Roan. Patterns with Nonsymmetric Patches of White: White Mar. White. Patterns of White with Symmetric White Patches: The Leop. Leopard Complex: Definition and Classification. Leopard Complex: Genetic Control. Patterns of White Summary. Chapter 5. Horse Color and Horse Breeding . Chapter 6. Peculiarities of Hair Growth . Chapter 7. Donkey Color. Patterns of White. Genetics of Donkey Color. Summary of Donkey Color. Hair Growth in Donkeys. Chapter 8. Color Photographs . Appendix 1: Color Names by Category. Appendix 2: Loci, Alleles, and Effects. Appendix 3: UsualGenotypes of Major Colors. Appendix 4: Alleles Present in Representative Breeds in the USA. Appendix 5: Expected Results of Crossing Various Colors. Appendix 6: Unpublished Data Supporting Conclusions
Linkages between restriction fragment length, isozyme and morphological markers in rice

A genetic linkage map of rice comprising 130 centimorgans (cM) was constructed from ten restriction fragment length, six isozyme and one morphological markers in F2 population of a rice cross (IR 36 X Ma Hae). The DNA probes were labelled through nonradioactive dUTP. The relative distance between two markers varied from 5.7 cM to 24.1 cM. The morphological marker (Xa-4A: bacterial leaf blight resistance) could be placed between restriction fragment length polymorphic (RFLP) probes RG 303 and and RZ 536 at the distance of 18.9 cM and 16.1 cM, respectively. The RFLP marker RG 167 and isozyme marker Pgd-1 were located at the same position, i.e. 5.7 map units away from RG 1094. None of the isozyme marker could be detected to be closely linked to morphological marker under study.
Feeding responses of an oligophagous bean aphid, Megoura crassicauda, to primary and secondary substances in Vicia angustifolia

The feeding behaviour of the aphid Megoura crassicauda Mordivilko (Homoptera: Aphididae), which feeds selectively on plants in the genus Vicia (Fabaceae), was studied. The aphids deposited proteinaceous stylet sheaths intercellularly towards the phloem tissues of host plants. Similar stylet sheaths were formed on a Parafilm membrane when host‐specific acylated flavonoid glycosides [two 2″‐O‐(E)‐p‐coumaroyl esters of quercetin 3‐O‐diglycosides] present in the extracts of the narrow vetch, Vicia angustifolia L. , were supplied in the solution covered by the membrane. In contrast, their corresponding deacyl analogues, present more abundantly in the host plant tissues, were not stimulatory, which suggested specificity in the structural requirements of the probing stimulants. While the aphids imbibed an artificial diet composed of primary nutrients (e.g., sucrose and amino acids) and produced a large quantity of honeydew, acylated flavonoids alone and non‐acylated flavonoids supplied with the nutrients more or less suppressed honeydew production. These findings implied that the acylated flavonoids serve as a cue to navigate the stylet sheath towards the phloem prior to sap‐sucking, whereas non‐acylated flavonoids may serve as a negative stimulus to refrain from sucking during tissue penetration before tapping the phloem, although the distribution of these compounds in the plant tissues remains unknown. Thus, the feeding behaviour of M. crassicauda appears to be controlled by multiple chemical stimuli in the process of the settling on its host plant.
Genetic variation and correlation among yield and quality traits in cocksfoot (Dactylis glomerata L.)

SUMMARY The objective of the present research was to study the genetic variability for total dry matter (DM) yield, tiller number, heading date and three quality traits, namely content of digestible dry matter (DDM), water-soluble carbohydrate (WSC) and crude protein (CP), in cocksfoot (Dactylis glomerata L.). Twenty-five parents were randomly chosen from a genetically broad-based population, and their respective half-sib (HS) families were generated. Clonally-propagated parents and their HS family seeds were grown as individual plants using a randomized complete block design with two replications in Alborz Research Center, Karaj, Iran, during 2002–04. The results of combined analyses over 2 years showed significant variances between clonal parents for all traits except CP. In the HS generation, between-family variances were only significant for tiller number, heading date and WSC. Clone×year (S2GY) and family×year (S2FY) interactions were significant for all traits except for WSC in HS families. The estimates of broad-sense heritability (h2b) were moderate to high for all traits (h2b=0·37–0·69), except CP. Narrow-sense heritability (h2n) estimates from analyses of progenies and from regression of HS progenies on parents (h2op) were moderate, relatively the same values as h2b for heading date, tiller number and WSC, which suggested that additive genetic variance was the main component controlling these traits. For DM yield and DDM, h2n and h2op estimates were low, whereas h2b estimates were moderate, which suggested that both additive and non-additive gene effects played an important role in the genetic regulation of these traits. Genetic correlations among CP with both WSC and DDM were generally negative, whereas WSC was positively correlated with DDM and tiller number. The genetic correlation among DM yield with DDM was weak and inconsistent and, in general, negative. DM yield had negative and positive correlation with heading date and tiller number, respectively. It was concluded that there was significant variation and moderate heritability for most traits in the cocksfoot populations evaluated to improve yield and quality traits. Selection for high WSC is a means to improve quality in general. The data also indicate that response to combined selection for both DDM and DM yield should be possible. Selection for DDM alone could result in reduction in yield.
Growth and reproduction of the deep-sea brittlestar

RESUME Disk-size frequencies of the brittlestar were measured from large samples obtained from a 3-year time series of Agassiz-trawl hauls from a fixed location in the Rockall Trough (N ortheast A dan tic). Parameters of Ga us sian mixtures frtted to the se da ta are in terpreted to show a pattern of annual recruitment and von Bertalanffy growth. Juveniles are thought to grow to about 11-12 mm in disk diameter in their fust year. Thereafter growth slows to about 7-8 mm in their second year, and to about 5 mm or Jess in their third wh en they attain reproductive maturity and breed. The year classes thereafter merge into a numerically dominant mode of slow growing adults. Mortality amongst postlarvae is sufftciently high to result in only a tin y proportion surviving to attain asymptotic size, L 00 • Egg-size (max. 460 J.lm), fecundity (up to 12 000 eggs per individual) and Jack ofbrooding indicate a lecithotrophic larval development. Contingency table analysis of oocyte-size frequencies supports the absence of annual periodicity, as found in previous investigations. The gonad apparent! y remains reproductively active throughout the year with a mean female fecundity of 9 500 eggs. The authors reconcile this with the inferred pattern of annual recruitment by postulating a seasonal cycle in survival of postlarvae. This is thought to occur as a response to annual fluctuation in downward flux of food particles from the surface, reflecting the seasonal cycle of primary production. A marked increase observed in the proportion of postlarvae in la te summer supports this hypothesis.
Swarming flights of the fungus-growing termite, Macrotermes natalensis (Haviland) (Isoptera: Macrotermitinae), and the environmental factors affecting their timing and duration

Dispersal flights of termites are the result of the sum of a number of complex and highly orchestrated behavioural responses by different castes to a variety of cues. Macrotermes natalensis (Haviland) produced a single brood of alates each year. These alates left their parent nests in dispersal flights early in the summer rainy season from late September to early December, with a peak during October. Rainfall was the primary stimulatory factor triggering flight; 5 mm was the threshold for initial flights. Large flights usually occurred later in the season and required more rain to trigger them. The initiation and duration of individual flights were regulated by factors such as temperature, light intensity, and wind. The threshold temperature for swarming flights lay between 17–19°C. If the air temperature dropped below this the flight was aborted. The species did not fly during rain and major flights took place between 39 % and 90 % relative humidity. Windless conditions were favoured for flight which ensured that alates were not distributed so widely that the chances of finding a mate were jeopardized and that the female sex pheromone was not so dispersed that males failed to locate mates. Flight times varied over the flight season as they were governed by light intensity and took place at dusk in low light intensities with alates leaving the nest from 1 to 30 lux. The majority of swarming flights occurred with a waxing moon.