Miracle-dz/UniFAR-FTUs huggingface dataset:
Statistical Inference and Decision Making in Conservation Biology

Since the formulation of hypothesis testing by Neyman and Pearson in 1933, the approach has been subject to continuous criticism. Yet, until recently this criticism, for the most part, has gone unheeded. The negative appraisal focuses mainly on the fact that P-values provide no evidential support for either the null hypothesis (H0 ) or the alternative hypothesis (Ha ). Although hypothesis testing done under tightly controlled conditions can provide some insight regarding the alternative hypothesis based on the uncertainty of H0 , strictly speaking, this does not constitute evidence. More importantly, well controlled research environments rarely exist in field-centered sciences such as ecology. These problems are manifestly more acute in applied field sciences, such as conservation biology, that are expected to support decision making, often under crisis conditions. In conservation biology, the consequences of a Type II error are often far worse than a Type I error. The "advantage" afforded to H0 by settin.
Influence of Temperature, Water Hardness, and Stocking Density on MS-222 Response in Three Species of Fish

Abstract Three responses of rainbow trout (Salmo gairdneri), common carp (Cyprinus carpio), and fathead minnows (Pimephales promelas) to the anesthetic MS-222 (tricaine methanesulfonate) were identified: induction times to total loss of equilibrium decreased with increasing temperatures; resistance to MS-222 increased with increasing water hardness; and resistance to the drug increased when the density of test fish was increased from 0.3 to 0.9 g/L in rainbow trout, 0.4 to 1.2 g/L in carp, and 0.3 to 0.8 g/L in fathead minnows. Our results and others from the literature suggest that temperature, water hardness, and density of test fish, as well as pH and dissolved oxygen, may have significant interacting effects on the anesthetic properties of MS-222.
The sister group relation of Parmeliaceae (Lecanorales, Ascomycota)

The family Parmeliaceae (Lecanorales, Ascomycota) is possibly the largest, best known and most thoroughly studied lichen family within its order. Despite this fact the relationship between Parmeliaceae and other groups in Lecanorales is still poorly known. The aim of the present study is to contribute to finding the sister group of Parmeliaceae as an aid in future studies on the phylogeny and character evolution of the group. We do this by sampling all potential relatives to the Parmeliaceae that we have identified, i.e. Gypsoplaca, Japewia, Mycoblastus, Protoparmelia, and Tephromela, a good representation of the major groups within the Parmeliaceae s. lat. and a good representation of other taxa in the core Lecanorales. We use molecular data from two genes, the large subunit of the nuclear ribosomal RNA gene (nrLSU) and the small subunit of the mitochondrial ribosomal RNA gene (mrSSU), and a Bayesian analysis of the combined data. The results show that the closest relatives to Parmeliaceae are the two genera Protoparmelia and Gypsoplaca, which are crustose lichens. Parmeliaceae in our sense is a well supported group, including also the family segregates Alectoriaceae, Hypogymniaceae, Usneaceae and Anziaceae.
Summertime herbivory and egg production by Acartia tonsaat the Montevideo Coast - Rio De La Plata

Abstract We present the first data on copepod feeding and production in the Río de 1a Plata, and discuss their correlation to the physical and biological environment. Sampling was performed at a protected area on the Montevideo coast where temperature, salinity and size fractionated chlorophyll aand phaeopigments were monitored weekly from January through February 2003, plus two additional observations in March and April. Acartia tonsaingestion was measured by gut fluorescence, and gut evacuation rates, egg production and egg hatching success were estimated using standard methods. Food availability was moderate/high, but quality appeared low as reflected by chlorophyll a:phaeopig-ment ratios <1. Ingestion correlated with both chl-a and pha, suggesting that A. tonsafed also on detrital matter. Egg production rates were low (1.4-7.5 eggs female1 d-1) — except for one exceptional record of ca. 88 eggs female-1 d-1 — indicating low productivity rates. Egg hatching success ranged from 30-94% and tended to increase during the study period. Overall results suggest that at the study site A. tonsafed on both phytoplankton and detritus, and that its production was limited by food quality.
From controversy to consensus: making the case for recent climate change in the Arctic using lake sediments

We live in a constantly changing environment, yet tracking ecological change is often very difficult. Long-term monitoring data are frequently lacking and are especially sparse from Arctic ecosystems, where logistical difficulties limit most monitoring programs. Fortunately, lake and pond sediments contain important archives of past limnological communities that can be used to reconstruct environmental change. Here, we summarize some of the paleolimnological studies that have documented recent climate warming in Arctic lakes and ponds. Several hypotheses have been evaluated to determine if warming, resulting in changes in ice cover and related variables (eg increased habitat availability), was the factor most strongly influencing recent diatom and other biotic changes. Striking and often unprecedented community changes were evident in post-1850 sediments, and could be linked to ecological shifts consistent with warming. Because future temperature increases are predicted to be greatly amplified in polar re.
Chemical Quality Indexes of Mullet ( Mugilplatanus ) Stored on Ice

The present study was conducted aiming at establishing chemical quality parameters to assess ice stored mullet (0℃ ± 1℃) through the evaluation of nucleotide (adenosine monophosphate [AMP], inosine [HxR] and hypoxanthine [Hx]) degradation, biogenic amine (histamine [HI], putrescine [PU], cadaverine [CA] and tyramine [TI]) quantification and mesophilic and psychrotrophic bacteria count monitoring. The microbial load of 7 log CFU·g–1 established as maximum acceptable limit was attained after the 20th day of ice storage. IMP concentration declined during the storage period to levels below the detection limit. HxR content increased only up to time T3 and then declined. Hx level increased during all the storage period. CA and HI content increase was not observed, on the other hand, PU and TI contents significantly increased (p ℃ ± 1℃ can be consumed up to the 20th storage day.
The transcripts of several components of the protein synthesis machinery are cold-regulated in a chloroplast-dependent manner in barley and wheat

Summary Nine clones coding different components of the protein synthesis machinery were selected from an EST barley library prepared from cold exposed plants and tested for their expression at low temperature. Northern analysis revealed that expression of elongation factor (EF) 1Bβ and two ribosomal protein (RP) genes S7 and L7A was enhanced following exposure to 3 °C, but not during dehydration or exogenous ABA treatment. The mRNA levels of EF1Bβ, RPS7, and RPL7A did not vary between cultivars with different frost tolerance, but differences in expression were found between different species. Experiments with an albino mutant and etiolated plants revealed that the cold-dependent regulation of EF1Bβ, RPS7, and RPL7A transcripts is controlled by a chloroplast-related pathway impaired in the mutant.
MOLECULAR SYSTEMATICS OF A HOLARCTIC RODENT (MICROTUS: MURIDAE)

Abstract The Bering Land Bridge was the intermittent connection that allowed exchange of mammals between Asia and North America. Because some mammalian genera are widely distributed on both continents, recovery of phylogenetic histories of species within these genera may help reconstruct the sequence of intercontinental exchanges. We tested phylogenetic and biogeographic hypotheses in the widespread genus Microtus through parsimony and likelihood analysis of mtDNA-sequence data. The extant species of Microtus in North America are thought to be derived from multiple invasions from Asia or, alternatively, as a single invasion followed by autochthonous speciation. Mitochondrial cytochrome-b gene sequences were obtained for 78 individuals representing 24 species of Microtus. Data supported 1 clade of taiga voles (M. pennsylvanicus, M. montanus, M. townsendii, and M. canicaudus), a clade of Asian species (M. kikuchii, M. fortis, M. montebelli, and M. middendorffi), plus the Holarctic M. oeconomus and several other previously identified clades. M. gregalis also was found to be distant from M. abbreviatus and M. miurus, thus contradicting monophyly of the subgenus Stenocranius. Monophyly of North American species was supported, albeit weakly. Basal relationships were not robust, reflecting a single pulse of diversification about 1.3 × 106 years ago. This pulse mirrors the fossil record and may be partially responsible for the unstable taxonomic history.
Inheritance of Cancer in Mice

IN the following we shall give a summary of our investigations into the part heredity plays in the origin of cancer. Our interest in this problem dates back a considerable number of years. In 1S99, in conjunction with Dr. Jobson, we made our first observations on the endemic occurrence of cancer at the Stockvards in Chicago. At that time we found cattle coming from a certain ranch in Wyoming especially prone to have cancer at the inner canthus of the eve (1). A few years later we observed an endemic occurrence of sarcoma of the thyroid in a family of rats. In this case we pointed out that the circumstances under which these sarcomata originated pointed to a hereditary condition rather than to an infection. At that time (1904)1 we referred to the desirability of investigating experimentally this endemic occurrence of cancer (2) and we had particularly in mind an analysis of the etiological factor in breeding establishments of mice or rats. Such an opportunity presented itself a few years later in the breeding establishment of Miss Lathrop in Granby, Mass. A preliminary investigation here revealed the fact that cancer occurred with much greater frequency in certain inbred strains than in others, and that no indications whatever could be found of cage infection or direct infection from animal to animal. We concluded in 1907 on the basis of these observations that there existed a hereditary predisposition which was responsible for the endemic occurrence of cancer (3). At that time we planned further much more extensive experiments on the mode of hereditary transmission of cancer in following isolated families and strains of mice through several generations and in study-
Origins And Evolution Of Pathways Of Anaerobic Metabolism In The Animal Kingdom

Energetic characteristics and functional roles define two main types of anaerobicpathways in the animal kingdom: high efficiency/low rates of energy production pathways geared to anoxia survival (aspartate-succinate and glucose-succinate pathways), and low efficiency? /high rates of energy production pathways geared to maintaining or increasing metabolic activity (multiple opine pathways and lactate pathway). The aspartate-succinate and opine pathways require both amino acids and carbohydrate as substrates, whereas the glucose-succinate and lactate pathways are dependent on carbohydrate only. Phylogenetic, functional and chemical considerations indicate an evolutionary progression from amino acid-linked to carbohydrate-based anaerobic pathways. The tauropine and strombine pathwaysare possibly the most ancient opine pathways so far discovered, and the octopine pathway the most advanced. The roles of the aspartate-succinate and opine pathways may originally have been not too dissimilar. A hierarchy of “rates of energy production pathways” of phosphagen > lactate > octopine > other opine pathways is proposed, which defines much of their phylogenetic selection and how they are used. The different properties of phosphocreatine compared to other phosphagens is indicated to have been a key factor in the emergence of vertebrates
Oviposition behavior of Zabrotes subfasciatus females (Coleoptera, Bruchidae) under conditions of host deprivation

Oviposition of Zabrotes subfasciatus (Boheman, 1833) on Phaseolus vulgaris (Linnaeus, 1753) was studied immediately after emergence of the adults throughout the females life and in situations of host deprivation lasting for 1 to 10 days. The number of eggs laid daily, longevity, duration of oviposition and distribution of eggs per grain were studied. The number of eggs laid per day varied significantly, with the oviposition peak in the presence of the host (control group) occurring between day 2 and day 5 of oviposition. In the absence of the host, a shift in the oviposition peak to the first day after deprivation was observed, except for the group deprived for one day which showed a peak between days 1 and 4 after introduction of the host. The distribution of the eggs per grain in the control group and in the groups deprived of the host for 2, 5, 8 and 10 days, a larger egg aggregation was observed for all deprived groups compared to the control group.
Breeding System, Insect Flower Visitation, and Floral Traits of Two Alpine Cerastium Species in Norway

Abstract Many alpine/arctic flowering plant species have presumably evolved the ability to self-pollinate as a reproductive assurance mechanism under harsh abiotic environmental conditions that restrict insect flower visitation. We compared self-pollination, pollen limitation, insect flower visitation, and dichogamy of low- and high-elevation populations of Cerastium alpinum, a species in established alpine communities, and Cerastium cerastoides, a pioneer species in disturbed habitats. Cerastium alpinum has large showy flowers, while C. cerastoides has smaller and paler flowers. The temporal separation of pollen release and stigma receptivity within a flower (dichogamy) was smallest in C. cerastoides, which was also more highly self-compatible. No pollen limitation on seed set occurred in any species, possibly due to their high selfing ability. Despite a substantially higher pollinator visitation to C. alpinum compared to C. cerastoides, the latter had the higher seed set. Pollen limitation, autogamy, and pollinator visitation did not differ between altitudes for either species. Differences in habitat and flower size, color, and development between the species are consistent with their different selfing ability.
Mainstem Leaf Development and Tiller Formation in Wheat Cultivars

Mainstem leaf stage and percent tiller formation are measurements utilized to evaluate the development of wheat (Triticum aestivum L.). This study was conducted to determine whether there are differences for these measurements among 11 winter wheat cultivars. Ten hard red winter wheat and one soft white winter wheat cultivars were grown in a controlled environment chamber to determine their rate of mainstem leaf stage and tiller formation percentage for coleoptile (T0), first (T1), second (T2), and third tillers (T3) when plants are grown in the absence of stress. Growth conditions were 12-h photophase at 24 o C and 12-h dark at 15 o C (.)
Primordia initiation of mushroom (Agaricus bisporus) strains on axenic casing materials

The mushroom (Agaricus bisporus) has a requirement for a “casing layer” that has specific physical, chemical and microbiological properties which stimulate and promote the initiation of primordia. Some of these primordia then may develop further into sporophores, involving differentiation of tissue. Wild and commercial strains of A. bisporus were cultured in axenic and nonaxenic microcosms, using a rye grain substrate covered by a range of organic and inorganic casing materials. In axenic culture, A. bisporus (commercial strain A15) was capable of producing primordia and mature sporophores on charcoal (wood and activated), anthracite coal, lignite and zeolite, but not on bark, coir, peat, rockwool, silica or vermiculite. Of six strains tested, only the developmental variant mutant, B430, produced rudimentary primordia on axenic peat-based casing material. However, none of these rudimentary primordia developed differentiated tissues or beyond 4 mm diameter, either on axenic casing material in the microcosms or in larger-scale culture. In larger-scale, nonaxenic culture, strain B430 produced severely malformed but mature sporophores in similar numbers to those of other strains. Typically, 3–6% of primordia developed into mature sporophores, but significant differences in this proportion, as well as in the numbers of primordia produced, were recorded between 12 A. bisporus strains.
Problematic Biases in the Availability of Molecular Markers in Protists: The Example of the Dinoflagellates

Dinoflagellates (Alveolata, Dinophyceae) are protists with a truly remarkable diversity in lifestyles (free-living, parasites and mutualistic symbionts), habitats (marine, freshwater, plankton, benthos), and trophic modes (heterotrophic, plastid-containing). Here dino- flagellates are used to evaluate biases in the availability of molecular markers in relation to the variety of functional and ecological charac - teristics of protists. A large number of dinoflagellate sequences are available in GenBank, at least one for 56% of the 264 described genera. The most common marker is the small ribosomal subunit ribosomal DNA (49%). At the species level, SSU rDNA or the large subunit rDNA are available for 15% of the 2,386 described species. Availability of sequences of the internal transcribed spacers (ITS) and cytochrome oxidase I (COI) show a strong bias towards cultivable species. Relative to trophic mode, while about half of the known dinoflagellates are heterotrophic, only 12% of them have been sequenced compared to 29% of the plastid-containing species. For the COI marker availability is 10 times greater for plastid-containing compared to heterotrophic species. Freshwater species are underrepresented (13%) relative to the marine forms (22%). A high proportion of benthic species have been sequenced (46%) reflecting interest in Symbiodinium and harmful epi- phytic taxa. Most of the relatively few described mutualistic species have been sequenced (> 80%). In contrast, only 17% of the described parasitic species have been sequenced, and most of the available sequences were not identified at the species level. In recent years, new species have been described mostly from coastal blooms or cultures. These studies are favored by the availability of abundant material for detailed studies of ultrastructure and multi-gene molecular phylogenies. Many methods are difficult to apply for the scarce specimens avail - able from the open ocean. The requirement of these protocols, easy to apply with cultured species, is an obstacle in our knowledge of the open ocean diversity because it discourages studies based on sparse material. Consequently, in recent years descriptions of new species from the open ocean have declined considerably.
Phellinus coronadensis: a new species from southern Arizona, USA

Phellinus coronadensis is characterized and described morphologically as a new species from southern Arizona, USA. This fungus was previously reported as P. torulosus based on morphological similarities of the basidiomes and type of wood decay. However, P. coronadensis is restricted to two mountain ranges in southern Arizona and found almost exclusively on living southwestern white pine (Pinus strobiformis). Phellinus torulosus is found primarily in Europe and parts of Asia and is primarily associated with hardwood hosts. Based on sequence analysis of small subunit mitochondrial ribosomal DNA (mt-SSU), we determined that P. coronadensis is in a different lineage from P. torulosus and apparently more closely related to the P. pini complex. The taxon associated with southwestern white pine, being distinct and not yet having been validly named, is proposed as a new species here.
Localization of 3β-Hydroxysteroid DehydrogenaseΔ5-Δ4-Isomerase in Rat Gonads and Adrenal Glands by Immunocytochemistry and in Situ Hybridization

The enzyme complex Δ5-3β-hydroxysteroid dehydrogenase/Δ5-Δ4 isomerase (3βHSD) is involved in the biosynthesis of all classes of steroids, namely glucocorticoids, mineralocorticoids, progesterone, and sex steroids. To obtain information on the precise localization of 3βHSD in rat gonads and adrenal glands, two complementary cytochemical techniques were used; immunocytochemical localization was achieved with antibodies developed against purified human placental 3βHSD, while 3βHSD mRNA localization was achieved by in situ hybridization performed with a recently cloned rat 3βHSD cDNA. In the testis, specific immunostaining was restricted to the cytoplasm of the interstitial cells, while by in situ hybridization, specific silver grains were also seen over the interstitial cells. In the ovary, immunostaining was found in the cytoplasm of cells of the corpus luteum and theca interna, while the granulosa cells of the follicles showed no positive reaction. By in situ hybridization, a specific hybridization signal .
Spruce budworm (Choristoneura spp.) biotype reactions to forest and climate characteristics

The spruce budworm (Choristoneura fumiferana) is the most destructive insect defoliator of forests in North America. Climatic influences on this species' life history are considered a major factor in restricting the extent and intensity of outbreaks. We examine the life history traits of the spruce budworm and related Choristoneura populations with respect to forecasting the conifer‐feeding responses of these insects in changing environments. Analysis of the evolutionary relationships between Choristoneura entities, including their hybridization, genetic distances, and their degree of sympatry leads us to distinguish 15 possible Choristoneura‘biotypes’.
Intersterility, morphology and taxonomy of Ceratocystis fimbriata on sweet potato, cacao and sycamore

Ceratocystis fimbriata is a large, diverse complex of species that cause wilt-type diseases of many economically important plants. Previous studies have shown that isolates in three monophyletic lineages within the Latin American clade of C. fimbriata are host-specialized to cacao (Theobroma cacao), sweet potato (Ipomoea batatas) and sycamore (Platanus spp.), respectively. We paired testers of opposite mating type from isolates of these lineages to find intersterility groups. Two intersterility groups corresponded to the sweet potato and sycamore lineages, respectively. The cacao lineage contained two intersterility groups, corresponding to two genetic sublineages centered in western Ecuador and Brazil/Costa Rica/Colombia. Six isolates from cacao that were not members of the cacao lineage and were not pathogenic to cacao in an earlier study also were intersterile with members of the two cacao intersterility groups. Some pairings between testers from different lineages or sublineages yielded perithecia from which a few abnormal progeny could be recovered, typical of interspecific hybrids. These progeny showed abnormal segregation of the MAT-2 gene and mycelial morphology, showing that they were indeed the result of crosses. Isolates of the sweet potato, cacao, and sycamore lineages were indistinguishable morphologically except for the presence or absence of a doliform (barrel-shaped) conidial state and minor differences in size of perithecial bases and necks and ascospores. C. fimbriata originally was described from sweet potato. We describe the cacao pathogen as a new species, Ceratocystis cacaofunesta and we raise the sycamore pathogen from a form to species Ceratocystis platani.