Miracle-dz/UniFAR-FTUs huggingface dataset:
A multi-method hierarchical modeling approach to quantifying bias in occupancy from noninvasive genetic tagging studies

Detecting ecological change in mammalian communities requires large volumes of data collected across large landscapes. Noninvasive genetic tagging (NGT) can provide such data and is a common method of estimating species occupancy, distribution, and abundance. Methods to correct errors in genetic analysis exist, but estimating and accounting for detection error in NGT studies—specifically, detection error during hair trapping—has received less attention. If detectability varies with an ecological characteristic that is instead attributed to occupancy, detection error may lead to spurious conclusions. We demonstrate how multi-method occupancy models informed by camera-trapping data can quantify error, partition sources of variability, and estimate occupancy from NGT studies. We surveyed marten (Martes americana), fisher (Pekania pennanti), and wolverine (Gulo gulo) occurrence via hair trapping and camera trapping for 3 repeated monthly surveys at 66 sites in the Rocky Mountains of Alberta, Canada. Camera traps photographed the hair traps and surrounding sampling site. We used multi-method occupancy models to estimate site occupancy, probability of detection, and conditional occupancy at a hair trap. We tested the predictions that detection error in NGT studies could be induced by temporal variability and behavioral variability arising from the presence of heterospecifics. Models indicated that NGT via hair trapping consistently underestimated occupancy of marten, fisher, and wolverine compared to cameras. The magnitude of bias varied, but at worst underestimated occupancy by half. The presence of a heterospecific affected a species' detection at hair traps. Wolverine presence increased marten detection, whereas marten decreased fisher detection at NGT traps. For all species, detection error was reduced through successive monthly surveys, although heterogeneity induced by other mustelids remained. Detection error from multiple sources can bias NGT occupancy estimates, with implications for population estimation, ecological inference, species' legal status assessments, and conservation decisions. We recommend that NGT studies quantify and correct for detection error using independent survey methods and multi-method occupancy models, to improve the ability to answer ecological questions and make conservation decisions in the face of ecological change. © 2014 The Wildlife Society.
Petrosal and inner ear anatomy and allometry amongst specimens referred to Litopterna (Placentalia)

New isolated petrosals from the Itaborai beds of Brazil (late Palaeocene or early Eocene) are here described and referred to the early diverging litoptern Miguelsoria parayirunhor, based on phylogenetic, size, and abundance arguments. Both the external and internal anatomy of these specimens were investigated, which for the first time document many details of the auditory region of a Palaeogene litoptern. Our cladistic analysis, which included our new observations, failed to recover a monophyletic Litopterna but did not exclude it. A constrained analysis for the monophyly of this order showed that several features such as a (sub)quadrangular and anteroposteriorly elongated tensor tympani fossa and a large notch in the vicinity of the external opening of the cochlear canaliculus may constitute synapomorphies for Litopterna. The evolution of several other auditory characters amongst Litopterna is discussed and the relative dimensions of the inner ear and surrounding petrosal in the group were also investigated. This allowed detection of negative allometry of the bony labyrinth within the petrosal, which was confirmed by measurements and regression analysis across a larger sample of placental mammals. This scaling effect probably has an important influence on several characters of the bony labyrinth and petrosal, amongst which are the length of the vestibular aqueduct and cochlear canaliculus. It demonstrates that many aspects of the morphological variation of the bony labyrinth need to be thoroughly investigated before being incorporated into phylogenetic analyses. © 2015 The Linnean Society of London
Breeding Ecology and Distribution of White-rumped Vultures (Gyps bengalensis) in Himachal Pradesh, India

Abstract I studied breeding ecology of White-rumped Vultures (Gyps bengalensis) in Himachal Pradesh, northern India, 2009–2012. Twenty-four breeding colonies of White-rumped Vultures were found, mainly in the Shahpur, Nurpur, and Kangra regions of Kangra District. In 2011–2012, the colonies contained a total of 102 nests, at which 81 pairs bred successfully. Nest success increased slightly from 56.1% in 2009–2010 to 79.4% in 2011–2012. All the nests of White-rumped Vultures were built in pine trees (Pinus roxburghii), at an average height of 15.4 m. In 2011–2012, approximately 65% of the nests were newly built, possibly indicating a high percentage of intra-colony movements. The number of adult and immature birds counted at the nesting colonies during the breeding season ranged from 13.3–27.3 individuals/colony; the ratio of immatures/adults varied from 0.44–0.97. Disturbance due to human activity and roads is a cause of concern for most of the breeding sites of White-rumped Vultures in Himachal Pradesh.
Baleen whale acoustic activity in the North Pacific: historical analysis and current occurrence

Abstract : Unclassified historic acoustic data were used to examine long time scale changes in the seasonal and geographic occurrence of large whales in the Pacific and to correlate these changes with oceanographic variables such as sea surface temperature, chlorophyll alpha, etc. Distribution of northeastern Pacific blue whales (as indicated by the numbers of their calls), while insignificantly related to SST, did show a clear seasonal pattern both to chl alpha concentration (negative) and to the mixed layer depth (positive). It was speculated that the negative correlation with chl a might be due to a lag from primary to secondary productivity: as phytoplankton are eaten by zooplankton (which in turn become available to whales), the overall amount of chl alpha decreases. It is recommended that in collaboration with other agencies hydrophones be deployed in the northeastern Gulf of Alaska to provide current information on the occurrence of vocally active whale species, including low-requency baleen whales and higher frequency odontocetes. A likely time might be during the Northern Edge 2008 exercise in Prince William Sound. Meanwhile, a new efficient, low-power, low-cost recorder that can be easily deployed, in an array with other instruments or independently, from a mid-size vessel is being developed.
Genetic Diversity Patterns among Phytophthora Resistant Soybean Plant Introductions Based on SSR Markers

Genetic diversity is low among elite Northern American soybean [Glycine max (L.) Merr. ] breeding populations. Fewer than 20 soybean cultivars are responsible for 80% of the genes in public soybean cultivars released in recent years. Diversifying the soybean germplasm base could introduce new genes for agronomic diversity as well. Recently, soybean plant introductions (PIs) have been identified as additional sources of both partial and specific resistance to Phytophthora sojae MJ. Kaufmann & J.W. Gerdemann (syn. P. megasperma Drechs. f. sp. glycinea T. Kuan & D.C. Erwin). The objective of this study was to compare the genetic diversity present among soybean PIs resistant to P. sojae in relation to cultivars and breeding lines that represent U.S. breeding germplasm, and to develop guidelines for the genetic study and practical use of these resistant resources in applied breeding. Ninety-three accessions from South Korea, China, and Japan and 15 genotypes from the USA were evaluated for 52 simple sequence repeat (SSR) primer pairs. The South Korean material included 32 P. sojae resistant, 49 partially resistant, and 7 susceptible accessions. The SSR data were used to compute Nei's distance estimates. Clustering and multivariate analysis of Nei's distance estimates demonstrated that accessions from South Korea are genetically different from U.S. germplasm. These results indicate that the South Korean germplasm may contain alleles not present in U.S. cultivars, such as new alleles for P. sojae resistance. Additionally, this study identifies SSR markers that can be used to begin mapping P. sojae resistance alleles in South Korean germplasm.
Developmental and Reproductive Toxicity of Progestagens in the Xenopus ( Silurana ) tropicalis Test System

Säfholm, M. 2014. Developmental and Reproductive Toxicity of Progestagens in the Xenopus (Silurana) tropicalis Test System. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 1099. 51 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-554-8812-3. Progestagenic compounds are emerging contaminants found in surface and ground water around the world. Information on the effects and potency of progestagens is needed in order to understand the environmental risks posed by these compounds. Using the Xenopus (Silurana) tropicalis test system, developmental and reproductive toxicity after exposure to selected progestagens were determined. Larval exposure to levonorgestrel (LNG) severely impaired oviduct and ovary development causing sterility. No effects on testicular development, spermcount or male fertility were observed. Hepatic mRNA expression of the androgen receptor was increased in the females indicating that the receptor is involved in LNGinduced developmental reproductive toxicity. Exposure of adult females to LNG, norethindrone (NET) or progesterone (P) increased the proportions of previtellogenic oocytes and reduced the proportions of vitellogenic oocytes compared with the controls, indicating an inhibited vitellogenesis. The effects on oocyte development were ascertained at environmentally relevant concentrations of LNG, NET and P (1.3, 1 and 10 ng/L respectively). Since unintentional coexposure of progestagens and ethinylestradiol (EE2) occurs in wildlife and also in human infants, data on mixture effects of combined exposures to these hormones during development are needed. Co-exposure during development showed antagonistic effects of EE2 and LNG. EE2 caused a female biased sex ratio which showed a tendency to be antagonized by LNG. Moreover, the hepatic AR induction by LNG was counteracted by co-exposure to EE2. In conclusion, the results show that female amphibians are susceptible to reproductive toxicity of progestagens after developmental exposure as well as after adult exposure during the breeding period. The differentiating Müllerianduct and ovary, and the egg development are sensitive targets for progestagens. Finally, the findings reported in this thesis show that environmental progestagens impairs reproductive function in amphibians and may present a threat to reproduction in wild populations.
EFFECTS OF FASTING AND WATER RESTRICTION ON CARCASS SHRINK AND PORK QUALITY

One hundred and twenty market weight (90 kg) pigs were allocated at random to one of three treatments: immediate slaughter and 24 h or 48 h without feed or water after arrival at an abattoir. All pigs were removed from feed 17 h before arrival at the abattoir. Weights of body organs and the digestive tract full and emptied of digesta were recorded along with warm carcass weight. After chilling for 24 h a pork chop 25 mm thick was removed along with the commercial ham and belly from the left carcass side and frozen for later quality determinations. Live weight shrink over 48 h amounted to 6.8 kg with 75% (5.1 kg) of this loss being attributed to loss in carcass weight. The 24-h holding period also resulted in a significant loss in carcass weight (3 kg). Approximately 20% of the total shrink over 48 h was due to a reduction in digestive tract contents. Body organs showed little change in weight over the 48-h holding period apart from the liver which was reduced in weight by 14.6%. Final longissimus muscle p.
Selección de leguminosas herbáceas para el fomento de cobertura en plantaciones de naranja Valencia late

El establecimiento de leguminosas herbaceas dentro de las areas de frutales precisa de estudios que demuestren la compatibilidad de estas asociaciones, con vista a mejorar la produccion en estos agroecosistemas. El objetivo del presente trabajo fue seleccionar la especie leguminosa mas adecuada para emplearla como cobertura viva en plantaciones de naranja Valencia late , sobre la base de su caracterizacion morfoagronomica. El estudio se realizo en areas de la Empresa de Citricos Ciego de Avila. Para ello se establecieron parcelas de 3 m2, sobre un suelo Ferralitico Rojo compactado, donde no se habia aplicado fertilizantes ni herbicidas. Se utilizaron 14 tratamientos y se midieron los siguientes indicadores: emergencia (a los 7, 14, 21, 28 y 35 dias despues de la siembra en cada parcela), altura (cm), cobertura foliar (%) y produccion de semillas (t ha-1). De acuerdo con los resultados, Teramnus labialis fue la especie mas adecuada para usarla como cobertura viva en plantaciones citricolas, en correspondencia con el porcentaje de emergencia, el area cubierta, la altura estacional y la produccion de semilla alcanzada durante el proceso de evaluacion, por lo que se recomienda su utilizacion en los ecosistemas citricolas de naranja V. late de Ciego de Avila.
Postmortem examination and causes of death of northern elephant seal (Mirounga angustirostris) pups of the San Benito Islands, Baja California, Mexico

ELENA SALOGNI, Elephant Seal Research Group, Via Buonarroti 35, 20145 Milan, Italy and Dipartimento di Bioscienze, Universit a degli Studi di Milano, Via Festa del Perdono 7, 20122 Milan, Italy; SIMONA SANVITO, Elephant Seal Research Group, Via Buonarroti 35, 20145 Milan, Italy and Facultad de Ciencias Marinas, Universidad Aut onoma de Baja California, Km 103 Carretera Tijuana-Ensenada, Ensenada 22860, Baja California, Mexico; FILIPPO GALIMBERTI, Elephant Seal Research Group, Via Buonarroti 35, 20145 Milan, Italy.
Relative taxonomic and ecologic stability in Devonian marine faunas of New York State: a test of coordinated stasis

Abstract The concept of coordinated stasis, manifest as a pattern of long intervals of concurrent taxonomic and ecologic persistence separated by comparatively abrupt periods of biotic change, has been challenged in recent studies that claim a lack of prolonged persistence of taxa and associations. A key problem has been the difficulty of distinguishing faunal change owing to localized, short-term environmental fluctuation or patchiness from that indicating regionally pervasive, long-term evolutionary or ecological change. Here, we use an extensive database from the Middle Devonian Hamilton Group of the Appalachian Basin to test for taxonomic and ecologic persistence within this ecological-evolutionary subunit, a succession of purported relative stability. Replicate samples collected from many localities and stratigraphic horizons over a wide geographic area allow us to address the effects of small-scale environmental variation and localized faunal patchiness while exploring basin-scale variation in faunal composition within and between the formations of the Hamilton Group. Observed stratigraphic distributions of fossils are consistent with a scenario in which all taxa are present from bottom to top of the Hamilton Group, and absences result only from sampling failure. Although small-scale variation in faunal composition indeed does occur, there is no more variation among formations than occurs within them. Assemblages from different formations, whether they are defined by taxonomic or ecologic composition, are statistically indistinguishable according to several independent metrics, including ANOSIM and a maximum likelihood estimation that evaluates stratigraphic turnover using Bayesian “Information Criterion. ” Simulated data sets indicate that test results are most consistent with species-level extinction of 2.6% per Myr within the Hamilton Group, far lower than the Givetian rate of 11.5% per Myr generic extinction derived from a global database. Such faunal persistence over the ∼5.5 Myr encompassed by this unit is consistent with the pattern of coordinated stasis. Earlier studies showing greater amounts of temporal turnover in Hamilton Group faunas are likely influenced by their smaller geographic scale of analysis, suggesting that regional studies done elsewhere may yield similar results.
Some Yield Characteristics of Genotype Groups Obtained by Crossbreeding Kıvırcık with Imported Mutton Sheep Breeds (Hampshire Down, Lincoln and Blackhead German)

This research was conducted to determine growth and survival characteristics of F1 and F2 genotype groups of lambs and reproduction characteristics of F1 genotype groups obtained from crossbreeding Kivircik to Hampshire Down, Lincoln and Blackhead German mutton sheep breeds raised at Bandirma Sheep Research Institute. Differences between reproductive characteristics of Hampshire Down x Kivircik and Blackhead German x Kivircik F1 crossbred sheep were not significant. Effects of birth type and sex on weights at birth, 60. , 120. and 180 days in all genotype groups were statistically significant (P
The parasitoid complex of Aphis fabae cirsiiacanthoidis Scop. (Homoptera: Aphididae) and its changes along a geographical gradient in the Rhone valley

13 Especes de parasitoides primaires d'Aphis fabae c. ont ete trouvees sur le chardon Cirsium arvense dans la vallee du Rhone entre Lyon et la Camargue.Etude des variations geographiques du complexe parasitaire le long d'un gradient latitudinal et repartition actuelle d'une espece importee Lysiphlebus testaceipes
Influence of stocking rate and mixed grazing of Angora goats and Merino sheep on animal and pasture production in southern Australia. 1. Botanical composition, sward characteristics and availability of components of annual temperate pastures

The effects of animal species (AS; Angora goats, Merino sheep or goats and sheep mixed grazed together at ratio 1 : 1) and stocking rate (SR; 7.5, 10 and 12.5 animals/ha) on the availability, botanical composition and sward characteristics of annual temperate pastures under continuous grazing were determined in a replicated experiment from 1981 to 1984. AS and SR had significant effects on pasture availability and composition and many AS × SR interactions were detected. The pastures grazed by sheep had significantly reduced content and proportion of subterranean clover and more undesirable grasses compared with those grazed by goats. There were no differences in dry matter availabilities between goat- and sheep-grazed pastures at 7.5/ha, but at 10 and 12.5/ha goat pastures had significantly increased availabilities of green grass, dead and green clover and less weeds compared with sheep pastures. There was a significant AS × SR interaction for the density of seedlings in May following pasture germination. Between July and January, the height of pastures was greater under goats than sheep but from January to March pasture height declined more on goat-grazed than on sheep-grazed pastures. There was an AS × SR interaction for incidence of bare ground. Increasing the SR increased bare ground in pastures grazed by sheep but no change occurred on pastures grazed by goats. Changes in pasture characteristics due to increased SR were minimised on pastures grazed by goats but the grazing of sheep caused larger and faster changes and the pastures were damaged at the highest SR. Goats did not always select the same herbage material as sheep, changed their selection between seasons and were not less selective than sheep. Angora goats were flexible grazers and continually adapted their grazing behaviour to changing herbage conditions. Goat grazing led to an increase in subterranean clover, an accumulation of dead herbage at the base of the sward, reduced bare ground, taller pastures in spring and a more stable botanical composition. Mixed-grazed pasture characteristics were altered with SR. With careful management Angora goats on sheep farms may be used to manipulate pasture composition, to speed up establishment of subterranean clover, to decrease soil erosion and to reduce weed invasion.
A General Model of Comparative Fecundity for Semelparous and Iteroparous Life Histories

Previous models of semelparity and iteroparity are critically reviewed. A general model is produced which incorporates population growth rate, juvenile and adult survivorship, prereproductive development time (PDT), time between reproductive episodes (TBR), and senescence. Increasing values of population growth rate and juvenile survivorship favor semelparity. Increasing values of adult survivorship, age of senescence, and the ratio of PDT to TBR favor iteroparity. Ambiguities arise when analyzing the effect of PDT or TBR depending on whether an absolute or a relative difference in fecundity is considered. The biological implications of this and other aspects of the model are discussed.
Progenitor cells in the postnatal central nervous system, characterization and genetic manipulation

New neurons are only generated in two places of the postnatal brain; the subventricular zone (SVZ) and hippocampus. The SVZ-derived cells specifically migrate to the olfactory bulb where they give rise to new interneurons. We have genetically manipulated the postnatal SVZ progenitor cells with the aim to direct them to a neuronal fate in the striatum. Our result showed that ectopic expression of the transcription factors Islet1 and Neurogenin2 directed the SVZ cells progeny to a new fate in the striatum and external capsule. Once removed to the culture dish they expressed the neuronal marker ? -III-tubulin. Thus, showing that ectopic expression of Islet1 and Neurogenin2 in the postnatal SVZ progenitor cells promote striatal recruitment for their progeny, which have potential to differentiate into neurons. (Less)
Stereochemistry of the reduction of nicotinic acid when it serves as a precursor of anatabine

Anatabine derived from [5,6-14C, 13C, 6-3H]-nicotinic acid (which is a precursor of both rings of the alkaloid) was almost devoid of tritium in its pyridine nucleus, but retained 100% at C-6′; this tritium was in a pro-S position, indicating that nicotinic acid was reduced at C-6 by the introduction of a hydrogen in the pro-R position.
PREVALENCE OF PARAMPHISTOMUM CERVI IN RUMINANTS SLAUGHTERED IN DISTRICT MUZAFFAR GARH

Rumen of 100 slaughtered animals viz. sheep (n=14), goats (n=42), cattle (n=34) and buffalo (n=10) were examined to determine the prevalence of adult Paramphistomum cervi during January 2007 in Tehsil Jatoi, District Muzaffar Garh, Pakistan. Overall prevalence was found to be 22% (22/100) and species wise prevalence was 28.57% (4/14) in sheep, 23.80% (10/42) in goats, 17.64% (6/34) in cattle and 20% (2/10) in buffaloes, the difference between the species being non significant.