Miracle-dz/UniFAR-FTUs huggingface dataset:
Extensive Rangewide Mitochondrial Introgression Indicates Substantial Cryptic Hybridization in the Golden-winged Warbler ( Vermivora chrysoptera)

Widespread population declines of the Golden-winged Warbler (Vermivora chrysoptera) are thought to be due in part to hybridization with the expanding Blue-winged Warbler (V. pinus), which predictably replaces Golden-winged Warblers at breeding sites in which the two species come into contact. However, the mechanism by which this replacement occurs remains unresolved. Recent genetic work has indicated that, even in areas where the two species have been in contact for a short period, introgression of Blue-winged mitochondrial (mtDNA) and nuclear genes into Golden-winged individuals is common. To explore this process on a broader scale, we screened more than 750 individuals from nine U.S. states and three provinces to examine geographic patterns of mtDNA introgression. The only population in which all phenotypic Golden-winged Warblers had Golden-winged mtDNA haplotypes, and in which there are no breeding Blue-winged or hybrid individuals, was in the province of Manitoba, near the northwestern edge of the species’ breeding distribution. The near ubiquity of mitochondrial introgression suggests that there are far fewer genetically pure populations of Goldenwinged Warblers than previously believed, a finding with important implications for this threatened species. RÉSUMÉ. On pense que le déclin à grande échelle des populations de Paruline à ailes dorées (Vermivora chrysoptera) est en partie attribuable à son hybridation avec la Paruline à ailes bleues (V. pinus), laquelle est en expansion et remplace, comme on peut s’y attendre, la Paruline à ailes dorées aux sites de nidification où les deux espèces entrent en contact. Toutefois, le processus par lequel survient ce remplacement demeure inconnu. Des études génétiques récentes ont montré que, même aux endroits où les deux espèces n’ont été en contact que sur une courte période, l’introgression des gènes mitochondriaux (ADNmt) et nucléaires de la Paruline à ailes bleues chez les individus de Paruline à ailes dorées est commune. Pour explorer ce processus à plus grande échelle, nous avons procédé au criblage de plus de 750 individus provenant de neufs États des États-Unis et de trois provinces afin d’examiner les variations géographiques de l’introgression mitochondriale. La seule population dans laquelle toutes les Parulines à ailes dorées phénotypiques présentaient des haplotypes d’ADNmt de Paruline à ailes dorées, et dans laquelle il n’y avait pas d’individus nicheurs de Paruline à ailes bleues ni d’hybrides, se trouvait au Manitoba, près de la limite nord-ouest de l’aire de reproduction de l’espèce. La quasiomniprésence de l’introgression mitochondriale permet de croire qu’il y a beaucoup moins de populations génétiquement pures de Paruline à ailes dorées que ce qu’on pensait, une découverte significative pour cette espèce menacée.
Using playback of territorial calls to investigate mechanisms of kin discrimination in red squirrels

Lay Summary Red squirrels can recognize relatives, but only act favorably towards them under certain conditions. We measured how red squirrels behaved in response to recordings of calls from relatives and nonrelatives to test whether squirrels recognize relatives because of their previous experience with those individuals or because relatives exhibit cues of genetic relatedness. Contrary to previous experiments, squirrels did not respond differently to the calls of relatives and nonrelatives.Twitter: @JuliaShonfield
Effect of Temperature on Germination Characteristics of Glyphosate-Resistant and Glyphosate-Susceptible Kochia (Kochia scoparia)

Glyphosate-resistant (GR) kochia is an increasing concern for growers across the U.S. Great Plains and Canadian prairies. Integrated strategies to mitigate resistance will require an improved understanding of the seed germination dynamics of GR kochia populations. Experiments were conducted to characterize the germination of GR vs. glyphosate-susceptible (GS) kochia populations under different constant (5 to 35 C) and alternating (5/10 to 30/35 C) temperatures. Seven GR and two GS populations were collected from wheat—fallow fields in northern Montana. Selected lines of GR and GS were obtained after three generations of recurrent group selection in the greenhouse. The GR-selected lines had 4.1 to 10.8 average EPSPS copies compared with a single EPSPS gene copy for the GS selected lines. Four out of seven GR selected lines had lower final germination (d parameter) and took more time to complete 50% cumulative germination (I50 values) under all constant and alternating temperatures, compared with the GS selected lines. Those GR selected lines also had a delayed germination initiation (I10 values), particularly at lower temperatures (5 to 10 C constant or 5/10 C alternating). In contrast, the final germination (d) of the other three GR selected lines did not differ from GS lines at a majority of temperatures tested. The I50 values of those GR lines were also comparable to GS lines under a majority of the temperatures. There was no significant correlation of observed percent cumulative germination and EPSPS gene copy number of selected kochia lines. The temperature-dependent dormancy and altered germination characteristics of the four GR kochia lines reflect the common selection of resistance and avoidance (glyphosate or other preseeding treatments) mechanisms. This is most likely attributed to long-term, intensive cropping practices and less diverse weed control methods, rather than a fitness cost or pleiotropic effect of multiple copies of the EPSPS gene. Nomenclature: Glyphosate, kochia; Kochia scoparia (L.) Schrad.
Differences in growth responses between Cryptomeria japonica and Chamaecyparis obtusa planted in group selection openings in Kyushu, southern Japan

ABSTRACT We quantified the differences in growth responses between Cryptomeria japonica and Chamaecyparis obtusa trees in approximately 0.1-ha group selection openings in southern Japan. We measured the position, height (H), and diameter at ground level (D) of 6- and 13-year-old C. japonica and C. obtusa trees that were planted in two respective openings. The annual H and D growth of C. japonica increased until trees were 10 and 8 m, respectively, distant from the nearest edge of the opening. For C. obtusa, the annual H and D growth increased slightly until the trees were 6 m distant from the nearest edge, but they did not significantly differ between 6 and 18 m distant from the nearest edge. While the shortest distance from the edge explained 63% and 50% of the variationsal H and D growth, respectively, of C. obtusa. Our result demonstrates that C. obtusa is less sensitive to edge effects than C. japonica. We conclude that C. obtusa is likely to be more suitable than C. japonica for planting within 0.1-ha group openings, as it will result in faster early stage growth, with less variation, within the openings.
Antitumoral cell-based therapies Review Article

Summary Cell therapies are based on biological agents involving cells to be administered to patients with diverse diseases. Examples of cell-based therapies include implantation of cells as an in vivo source of an enzyme, cytokine or factor; infusion of immune cells such as lymphocytes, or transplant of cell populations such as hematopoietic cells, hepatocytes or pancreatic islet cells to perform a complex biological function. A similar concept can be applied to cancer in a new antitumor approach. In this case, carrier cells are usually modified ex vivo by vectors or by preloading with bioactive materials such as toxins or viruses. Several cell types target naturally to the tumor mass, or are engineered to improve this preferential homing.
Pollination Success among Standard Hybrids and Indonesian Species of Phalaenopsis

One of the constrains limitting the succes of Phalaenopsis breeding is incompatibility between the parents. The objective of this study was to evaluate pollination compatibilities among Indonesian Phalaenopsis species and the standard hybrid group. The species used were Phal. Violaceae âSumateraâ, Phal. cornu-cervi âKalimantanâ, Phal. amboinensis, Phal. Tetraspis and Phal. modesta and Phal. Amabilis. The Phalaenopsis standard hybrids used were eight commercially available hybrid accessions in the Indonesian flower market. The pollination schemes evaluated include: self- and cross-pollination among standard hybrids (intra-hybrids) and reciprocal crosses among standard hybrids and the Indonesian species of Phalaenopsis (inter-hybrids). Prior to pollination, the following parental characters were noted: inflorescence length, flower number at anthesis, flower sizes, leaf stomatal size and stomatal density, respectively. After pollination, the following characters were recorded: pod set number, pod size, and seed set, respectively. Samples of mature pods of intra-hybrid crosses were harvested, the seeds were germinated aseptically, and the protocorm growth from the seeds were evaluated. Results of the evaluation indicated Indonesian Phalaenopsis species in general showed smaller inflorescence length, flower number at anthesis, and flower sizes than the standard hybrid accessions. The species also exhibited smaller stomatal cell size and higher stomatal cell densities than the hybrid ones. Standard Phalaenopsis hybrids commercially available in Indonesia might have different ploidy level than the Indonesian Phalaenopsis species. Such hypothesis was supported by the the contrasting morphological characters, stomatal cell sizes and stomatal density. Furthermore, it was supported by the failure to obtain either pod set or seed set in the majority of reciprocal cross pollination among Phalaenopsis standard hybrids and the species. Growth and multiplication of protocom derived from two intra-hybrid populations into protocorm like bodies (PLBs) was not affected by the medium composition but by the genetic background of the parents. Protocorm originated from cross pollination of White A Pink standard hybrid accessions gave higher multiplication rate than that of Pink A White standard hybrids.
Argentine ant control around homes: efficacy of treatments and urban runoff

ABSTRACT Pest management professionals in California receive more customer complaints about Argentine ants than for any other urban ant pest. Fipronil, applied as a 30 × 30 cm band around the house foundation, has become the preferred treatment used to control these ants. Unfortunately, fipronil is now showing up in urban waterways at levels that are toxic to aquatic invertebrates. Our recent studies are aimed at mitigating insecticide runoff while still controlling the ant infestations. A high priority is preventing fipronil runoff from the driveway to the street, where it can flow into drains and from there to urban waterways. In this paper, two related studies address these issues. Not treating driveways with fipronil reduced by two to three orders of magnitude its runoff when compared with earlier studies. However, not treating the driveway can reduce efficacy of treatments. Granular bifenthrin, indoxacarb, botanicals, and a thiamethoxam ant bait were tested as supplemental treatments. The gel bait showed the best result as a supplement, but only after 8 weeks. We have reduced fipronil runoff while maintaining efficacy of the ant treatments.
Organic and inorganic P forms in soil as affected by cover crops and nitrogen fertilization

The objective of this work was to evaluate the effects on organic and inorganic forms of soil phosphorus of the cultivation of cover crops and the use of nitrogen levels in soil under notillage system. The experiment was carried out in a randomized complete block design, in split plot, on a Rhodic Hapludox. The main treatments were cover crops: four legumes, one grass, and fallow (spontaneous vegetation); the secondary treatments were N fertilization in top dressing (0 and 120 kg ha -1 ) applied on corn. Soil samples were collected 12 years after the beginning of the experiment, and organic and inorganic P forms were measured in them. The P forms were extracted with: resin; solutions of NaHCO 3 , NaOH, and HCl; and a mixture of H 2 SO 4 +H 2 O 2 +HF. The obtained forms were classified as labile P (resin-P + NaHCO 3 -P), moderately labile P (NaOH-P) and non-labile P. The cultivation of sunn hemp, lablab, and velvet bean in corn pre-cropping increases the moderately labile organic P (Po NaOHI ) in the topsoil in comparison with the fallow area. Nitrogen fertilization favors organic P mineralization in soil and redistributes forms of inorganic and organic P between the labile and moderately labile compartments, without impacting available P.
Peruvian Tenebrionidae: A Review of Present Knowledge and Biodiversity

Abstract. A review of several aspects dealing with Tenebrionidae in Peru is presented. The study includes a taxonomic history, depositories of type specimens, taxonomic diversity, endemicity, ecological studies, and other research involving Peruvian tenebrionids in medicine, agriculture, food protection and production. Analyses of the geographic distribution, habitats and estimation of the species richness are performed. A final recommendation suggesting the development of four main lines of research on Peruvian tenebrionids is presented, including: 1) systematics and biogeography, 2) spatial and temporal patterns of epigaeic assemblages, 3) morphological adaptations to aridity, and 4) preserving material of some representatives of Peruvian taxa for molecular studies.
Movement patterns and rheoreaction of larvae of a fluvial specialist (nase, Chondrostoma nasus): the role of active versus passive components of behaviour in dispersal

The dispersal of fish larvae in rivers might result from water movement but also from larval behaviour. Although potentially crucial for dispersion, knowledge of the role of behaviour is still fragmentary. This study intends to contribute to the question of how riverine fish larvae drift or move. All dispersal-relevant movement patterns of larvae of a characteristic rheophilic species were analyzed based on the parameters (i) swimming activity, (ii) direction of movement, and (iii) the orientation towards the current vector. Experiments were conducted in a novel flume mesocosm at three different flow scenarios covering the current velocity range of natural habitats. Mean current velocities in these scenarios were under, near, and over the “critical current velocity”, above which fish larvae are not able to constantly hold their position in the water column. Three consecutive larval stages were tested to account for possible ontogenetic shifts in movement behaviour, both during the day and at night. Our re.
Inferring trends and linkages between shark abundance and shark bites on humans for shark-hazard mitigation

The present study aims at inferring linkages between the abundance of potentially dangerous sharks (PDSs) and shark hazard, so as to derive information about the underlying processes of shark peril off Recife, Brazil. Fishery-independent longline and drumline data collected from May 2004 through December 2014 for Carcharhinus leucas and Galeocerdo cuvier measuring ≥109cm were considered for analysis. Generalised additive models showed that the frequency of shark bites was directly proportional to and followed the same seasonal trends as PDS abundance, meeting the hypothesis that higher shark abundance may result in an increased chance of a shark bite. However, the species-specific seasonality of bull and tiger sharks seemed to follow distinct patterns. This method was helpful in comparing the abundance dynamics of the PDSs caught by the local shark hazard-mitigation program with the distribution of shark bites, so as to infer whether the species involved in the incidents were being effectively captured. Also, it provided some information about each species’ contribution to the overall dynamics in local shark hazard. However, despite being a potentially useful risk-management tool, its predictive efficacy for shark-peril mitigation may depend on the availability of abundant data spanning across wide temporal ranges.
Envelope-tACS modulates intelligibility of speech in noise

Cortical entrainment of the auditory cortex to the broad-band temporal envelope of a speech signal is crucial for speech comprehension. This entrainment results in phases of high and low neural excitability which structure and decode the incoming speech signal. Entrainment to speech is strongest in the theta frequency range (4–8 Hz), the average frequency of the speech envelope. If a speech signal is degraded, for example masked by irrelevant information such as noise, entrainment to the speech envelope is weaker and speech intelligibility declines. Besides perceptually evoked cortical entrainment, transcranial alternating current stimulation (tACS) can entrain neural oscillations by applying an electric signal to the brain. Accordingly, tACS-induced entrainment in auditory cortex has been shown to improve auditory perception. The aim of the current study was to externally modulate speech intelligibility by means of tACS such that the electric current corresponds to the envelope of the presented speech stream. Participants performed the Oldenburg sentence test with sentences presented in noise in combination with tACS. Critically, the time lag between sentence presentation and tACS was manipulated from 0 to 250 ms in 50-ms steps (auditory stimuli were simultaneous to or preceded tACS). First, we were able to show that envelope-tACS modulated sentence comprehension such that on average sentence comprehension at the time lag of the best performance was significantly better than sentence comprehension of the worst performance. Second, sentence comprehension across time lags was modulated sinusoidally. In sum, envelope tACS modulates intelligibility of speech in noise presumably by enhancing (time lag with in-phase stimulation) and disrupting (time lag with out-of-phase stimulation) cortical entrainment to the speech envelope in auditory cortex.
Genetics of social interactions in laying hens : improving survival and productivity

Through social interactions, individuals affect one another’s phenotype. The heritable effect of an animal on its own phenotype is referred to as a direct genetic effect (DGE), while the heritable effect of an animal on the phenotype of a conspecific is referred to as an indirect genetic effect (IGE). Both DGEs and IGEs determine a population’s potential to respond to selection, i.e. the total genetic variance. This thesis focusses on the genetic architecture of survival time in laying hens showing feather pecking and cannibalistic behaviour, a well-known social interaction trait. DGEs and IGEs for survival time were estimated in purebred and crossbred laying hens. Unrelated birds of the same line or cross were kept in groups of four. Beaks were kept intact. Results showed that IGEs contribute around half of the total genetic variance in purebreds and the majority of the total genetic variance in crossbreds (up to 87%). The direct-indirect genetic correlations were close to zero in purebreds and moderately to highly negative in crossbreds. Consequently, unlike purebreds, crossbreds would fail to respond positively to mass selection. To ensure positive response to selection, animals should be selected based on their total breeding value. Moreover, increased response to selection can be obtained when including genotypic information. With genomics, the accuracy of estimated breeding values increased with 20 up to 110%, showing the added value of genotypic information. In addition, the genetic correlation between survival time (individual data) and early egg production (pooled data) was calculated. Results showed that, unlike for individual data, pooled data cannot be used to estimate DGEs and IGEs. However, pooled data can be used to estimate total genetic effects. The default bivariate model did not allow all non-genetic correlations between both traits to be fitted and, therefore, resulted in biased genetic parameter estimates. When this issue was resolved, the genetic correlation between survival time and early egg production was slightly negative (-0.09), but not significantly different from zero. Finally, the interpretation of as a measure of inheritance for social interaction traits was discussed. expresses the total genetic variance relative to the phenotypic variance. Throughout this thesis it became clear that, for social interaction traits, the level of data collection (individual vs pooled data) and the within-group relatedness affects the phenotypic variance and, consequently, affects . Therefore, can differ between experimental set-ups, even though the underlying genetic parameters are the same. This is undesirable for the comparison of studies. For survival time, a 30 up to 40% decrease in was observed when using pooled data instead of individual data. This illustrates that , as a measure of inheritance, should be used with care.
Kinetoplastids biology, from the group phylogeny and evolution into the secrets of the mitochondrion of one representative: Trypanosoma brucei, the model organism in which new roles of the evolutionary conserved genes can be explored

This thesis is composed of two topics, for which trypanosomatids and evolution are common denominators. First part deals with phylogenetic relationships among monoxenous trypanosomatids, with emphasis on flagellates parasitizing dipteran hosts, analyzed mainly from biogeographical and evolutionary perspectives. Second part focuses on the trypanosomatid Trypanosoma brucei, causative agent of severe diseases, which serves as a model organism for functional studies of evolutionary conserved mitochondrial proteins, in particular those involved in replication, maintenance and expression of the mitochondrial genome, also termed the kinetoplast. This thesis identified the mtHsp70/mtHsp40 chaperone machinery as an essential component of replication and maintenance of the kinetoplast, and also identified numerous conditions under which mtHsp70 has a tendency to aggregate. Moreover, several conserved proteins, previously identified to be part of the mitochondrial ribosome, were shown to be important for translation of the mitochondrial transcripts.
Abiotic effects on the clear-winged grasshopper (Orthoptera: Acridae) and its fungal pathogen Entomophaga grylli (Entomophthorales: Entomophthoraceae) in an intermountain bunch-grass prairie

Abstract The grasshopper, Camnula pellucida Scudder (Orthoptera: Acridae), is a severe pest of small grains and rangeland forage in North America. In a field experiment using cages containing C. pellucida in northwestern Montana, United States of America, we manipulated exposure to the fungal entomopathogen, Entomophaga grylli Fresenius (Entomophthorales: Entomophthoraceae) pathotype 1, temperature using small greenhouses, and moisture for the pathogen with water pillows. Treatment effects on fungal infection (mycosis) rates and grasshopper survivorship were assessed. Water pillows provided additional moist habitat for E. grylli without having an impact on grasshopper performance or the plant biomass and nitrogen content. Number of fungal spores, pathogen-induced mortality rates, and treatment effects on grass biomass and nitrogen content were also measured. Water pillows benefited the pathogen by increasing fungal spore levels by eightfold, which in turn shortened pathogen-exposed grasshopper survival time by half. In contrast, warming reduced fungal spore levels by 50% and subsequently reduced mortality from E. grylli by 67%. However, warmed pathogen-exposed grasshoppers did not exhibit enhanced survival, which may be due, in part, to intraspecific competition among the surviving grasshoppers.