Miracle-dz/UniFAR-FTUs huggingface dataset:
New measurements of distribution of homoplasy and reliability of parsimonious cladograms

Levels of homoplasy, measured by consistency index (CI) or retention index (RI), have been commonly used as indicators of reliability of parsimonious cladograms. Less attention has been paid to distribution of homoplasy which, however, may be another important parameter for estimating the reliability of cladograms. Average unit character consistency (AUCC), measuring distribution of homoplasy among the characters on parsimonious cladograms, is defined as the average of total unit character consistencies. When cladograms with the same CI are compared, the one with the largest AUCC also has the most asymmetric distribution of homoplasy, i.e., it is compatible with the largest portion of the characters, and homoplasy is concentrated in the smallest portion of cladistically unreliable or fast evolved characters of this cladogram. Homoplasy distribution index (HDI) is defined as the difference between the AUCC and CI, and can be used to compare distribution of homoplasy among cladograms with similar levels of homoplasy. A new measurement of the reliability of parsimonious cladograms, homoplasy distribution ratio (HDR), is defined as the ratio of the HDI to the homoplasy index (HI).
Relationship of Basal to Summit Metabolic Rate in Passerine Birds and the Aerobic Capacity Model for the Evolution of Endothermy

The aerobic capacity modelfor the evolution of endothermy contends that endothermy arose as a result of selection for enhanced aerobic capacity rather than for thermoregulatory considerations. An implicit assumption of this model is that basal metabolism (BMR) increases with an increase in sustainable activity (i.e., aerobic capacity). We tested this assumption for passerine birds using individuals of 10 diferent species to determine whether basal and summit (maximum coldinduced) metabolic rates were correlated. Metabolic rates were measured as oxygen consumption by open-circuit respirometry. Regressions of basal and summit metabolism against body mass (log10-log10 transformations) indicated that both BMR and summit metabolism were positively and significantly related to mass. Slopes of the two regression lines were not significantly diferent, which indicates similar scaling properties for BMR and summit metabolism. Residuals of log10-log10 transformations of summit metabolism and BMR against body mass demonstrated that summit metabolism was correlated with BMR independently of mass (r = 0.869). In addition, analyses generating phylogenetically independent contrasts indicated that contrasts of log10 BMR and log10 summit metabolism were both positively and significantly correlated with contrasts of log10 body mass. Residuals from these regression lines demonstrated that the significant positive correlation between BMR and summit metabolism (r = 0.861) remained when effects of both mass and phylogeny were removed. Thus, metabolic rates of the passerines in this study are consistent with the aerobic capacity model for the evolution of endothermy.
Does Solar Energy Control Organic Diversity? Butterflies, Moths and the British Climate

In Britain, the diversity of butterflies, measured as the number of species present in an area of 900 km2, is highly correlated with sunshine and temperature during the summer months May to September. These two variables explain nearly eighty percent of the variance in diversity, and also explain it to some extent independently of latitude. Diversity shows a negative correlation with the average temperature for the three winter months December to February. Diversity (species number) therefore appears to be strongly influenced by the amount of energy available during the favourable season. The simplest explanation for this relationship is the extreme ectothermic behaviour of adult butterflies, which depend on both warm air and direct sunshine to maintain normal activity. Heavy bodied, endothermic, nocturnal moths however show a very similar correlation with the climatic variables, suggesting that larvae as well as adults benefit from sunshine and warmth. Butterfly and moth diversity is shown also to be influenced by habitat diversity. It is suggested that these findings support the "species-energy hypothesis" of D. H. Wright, which explains global latidudinal gradients in diversity by the gradient of direct and atmospherically transported solar energy. They appear also to explain some temporal fluctuations in butterfly diversity.
Biological activities and metabolic fate of olive oil phenols

We have been studying the biological activities of olive oil phenols in vitro and in vivo including the bioavailability of phenols and their effects in animals and humans. In vitro, ortho-diphenolic (catecholic) compounds such as oleuropein and hydroxytyrosol exert potent antioxidant activities, such as inhibition of low density lipoproteins oxidation and free radical scavenging. They modify pathophysiological processes at cellular level favorably, e.g. by inhibiting not only the production of superoxide anions and the respiratory burst of neutrophils, but also platelet aggregation and the production of thromboxane and leukotriene B 4 by neutrophils. Finally, oleuropein stimulates the release of nitric oxide by macrophages. Most important, recent data demonstrate that oleuropein and hydroxytyrosol, active at concentrations in the low μM range, are dose-dependently absorbed by humans and rats and, at very low doses, maintain their antioxidant activities in vivo. This is indicated by the increase in plasma antioxidant capacity and the reduced excretion of isoprostanes in humans and in sidestream smoke-exposed rats. To this end, our studies demonstrated that high quality, phenol-rich olive oil provides bioactive compounds that exert salubrious effects in humans and thus may contribute to the beneficial properties of the Mediterranean diet.
Influences of phase delay shifts of light and food restriction on blood pressure and heart rate in telemetry monitored rats†

Effects of phase delay shifts (PDS) of light in combination with moderately increased salt intake (SL) (2%) or time restriction of food (FR) during the light-time (passive phase) on heart rate (HR), blood pressure (BP) and locomotor activity (LA) in radiotelemetry-measured rats were evaluated. PDS decreased amplitude and spectral power of circadian oscillations of HR, BP and LA. Moderately increased SL did not interfere with the circadian rhythmicity of HR, BP or LA. A prominent decrease in amplitude and spectral power of circadian oscillations was observed if food was available during the lighttime. Combination of PDS with FR split cardiovascular and behavioural parameters. In conclusion, food availability during the light-time in combination with PDS decreased amplitude and spectral power of circadian oscillations of BP, HR and LA more than PDS only. Different response of cardiovascular and behavioural parameters to photic and non-photic stimuli can have consequences for shift workers.
Sox2 co-occupies distal enhancer elements with cell-type-specific POU factors to specify cell identity in embryonic stem cells and neural precursor cells

Sox2 is a master regulator of two distinct cellular states, that of pluripotent embryonic stem cells (ESCs) and multipotent neural progenitor cells (NPCs), but what common or distinct roles Sox2 may play in these cell types not fully understood. Further, the molecular mechanisms by which Sox2 can specify two distinct cell identities are as of yet unclear. This thesis is aimed at answering these fundamental questions. In ESCs, Sox2 was associated with a subset of poised regulators of nervous system development, and upon differentiation into NPCs Sox2 selectively activates those which are important for progenitor cell state, while keeping others poised to become activated in later neural development. These data suggested that Sox2 might act as a pioneer factor for neural development throughout embryogenesis. While Sox2 is known to co-occupy target loci in ESCs with the POU factor Oct4, in NPCs Sox2 interacts with the central-nervous-system-expressed POU factors Brn1 and Brn2. By utilizing distinct composite Sox:Octamer motifs in each cell type, Sox2:POU modules control the expression of thousands of genes involved in the development of the neural lineage in a cell-type-specific manner. These data advance our understanding of the mechanism by which transcription factors control cell fate transitions, and indicate that combinatorial interactions between transcription factors may be a pervasive mechanism of transcriptional control in development. Thesis Supervisor: Rudolf Jaenisch Title: Professor of Biology
Faculty Opinions recommendation of Involvement of the vacuoles of the endodermis in the early process of shoot gravitropism in Arabidopsis.

The endodermal cells of the shoot are thought to be the gravity-sensing cells in Arabidopsis. The amyloplasts in the endodermis that sediment in the direction of gravity may act as statoliths. Endodermis-specific expression of SGR2 and ZIG using the SCR promoter could complement the abnormal shoot gravitropism of the sgr2 and zig mutants, respec-tively. The abnormalities in amyloplast sedimentation observed in both mutants recovered simultaneously. These results indicate that both genes in the endodermal cell layer are crucial for shoot gravitropism. ZIG encodes AtVTI11, which is a SNARE involved in vesicle transport to the vacuole. The fusion protein of SGR2 and green fluorescent protein localized to the vacuole and small organelles. These observations indicate that ZIG and SGR2 are involved in the formation and function of the vacuole, a notion supported by the results of subcellular analysis of the sgr2 and zig mutants with electron microscopy. These results strongly suggest that the vacuole participates in the early events of gravitropism and that SGR2 and ZIG
A new species and a new combination of Phalaenopsis (Orchidaceae: Epidendroideae: Aeridinae): evidence from morphological and DNA analysis

A new species of Phalaenopsis , P. pingxiangensis, from Guangxi, China, is described and illustrated. Detailed morphological comparison between the newly discovered orchid and other members of Phalaenopsis s.l. indicate that P. pingxiangensis is similar to P. marriottiana . The new species differs from the latter in its small stature, short inflorescence with two flowers, smaller and pink flower with pale yellow sepals abaxially, orbicular petals, purple-red, flabellate lip and terete column without wings. The molecular analyses of Phalaenopsis indicate that P. pingxiangensis is a distinct species nested in P. subgenus Hygrochilus. In addition, Hygrochilus tsii is transferred to Phalaenopsis .
The genetic and phenotypic consequences of translocations of deer (genus Cervus) in Scotland

Asian sika deer (Cervus nippon Teniminick, 1836) were introduced across Scotland at the turn of the last century and have since established several large feral populations. Their potential to cause economic damage to forestry and hybridise with native red deer (C. elaphus L. 1758) has provoked widespread concern and highlighted a lack of basic ecological and genetic data relevant to their management. A preliminary genetic investigation of two Scottish populations (Great Glen & Argyll) revealed introgression at both sites. The aim of this thesis is to expand and develop this work by investigating the genetic and phenotypic causes and consequences of hybndisation across Scotland. Tissue samples and cull data were collected from 670 red deer, 266 sika and 8 phenotypic hybrids originating from 9 areas around Scotland with documented sika introductions. The samples were genotyped for 10 microsatellite and one mitochondrial DNA (mtDNA) marker loci. Skeletal material and genetic samples were collected from a further 339 red and 307 sika from Argyll in an intensive study involving an additional 15 microsatellite markers. All markers used were putatively diagnostic, though the interpretation of some rare alleles was problematic. Samples with several introgressed alleles at different loci provided strong evidence for hybridisation since introduction in Argyll, Galloway and Sutherland and Ross-shire, but different patterns of introgression emerged. In Argyll, hybridisation is rare but followed by repeated backcrossing to give substantial introgression, with 62% of sika-like deer and 33% of red-like deer containing opposite-taxon alleles. Evidence of recent hybridisation was restricted to sample sites at the leading edge of sika colomsation. In Galloway a number of earlygeneration hybrids were identified. In Sutherland and Ross-shire, introgression was common (>75% of individuals) in sika-like deer at 5 of the 10 microsatellite loci but almost absent at the other loci, suggesting a hybridisation event(s) several generations ago followed by backcrossing and strong assortative mating. Introgression was uncommon in the remaining sika-like populations (<20% of individuals) and rare in red-like populations (<5%), but most red-like populations contained rare alleles whose origins were difficult to interpret. These alleles may represent polymorphism, introgression from unreported sika introductions or introgression from introduced wapiti (C. canadensis L. 1758). Across all samples, mtDNA introgression was rare and restricted to Argyll sika-like deer having red mtDNA. Furthermore, all recently generated hybrids contained red mtDNA, suggesting hybndisation events usually involve sika males covering red females.
Functional diversity enhances silver fir growth resilience to an extreme drought

It is expected that extreme climate events such as droughts will increase in both severity and intensity as a consequence of forecasted climate change. Complementarity among tree species in resource acquisition strategy may reduce interspecific competition and increase the occurrence of facilitative interactions, resulting in an improved tree growth and resilience to extreme climatic events. However, the response of individual trees growing in more functionally diverse stands to extreme events is still under debate. We investigate the growth response of silver fir (Abies alba) to an extreme drought event which occurred in 1985–1986 in the Central Spanish Pyrenees and how the growth and resilience of trees relate to their neighbourhood functional diversity, stand heterogeneity and intraspecific and interspecific competition. Dendroecological methods were used to reconstruct radial growth. We recorded all tree species living around each sampled tree and calculated indices of intra‐ and interspecific competition among coexisting trees. Functional diversity around each focal tree was calculated by using the Rao's quadratic entropy. Silver fir growth decreased significantly in response to the drought in the vast majority of trees, but most of them showed a growth recovery 3 years later. Despite most trees showed negative growth trends following the drought event (70%), those trees growing in more functionally diverse stands were more resilient, recovered more quickly and displayed greater growth and growth trends. Synthesis. The presented findings support the growing body of evidence that shows a positive impact of diversity on forest function. In addition, we provide a direct linkage between tree growth response to climate at the individual tree scale and a direct quantification of neighbourhood functional diversity and competition. An enhanced functional diversity facilitating a more efficient use of resources at the interspecific level and potentially increasing facilitative interactions contributes to lessening the negative impacts of extreme events as droughts on forest growth.
THERMOREGULATION AND MICROHABITAT CHOICE IN ERYTHRODIPLAX LATIMACULATA RIS MALES

L.B. CALVÃO1, M.V. C. VITAL2, L. JUEN3, G.F. LIMA FILhO4, J.M. B. OLIVEIRA-JUNIOR5, N.S. PINTO6 and P. DE MARCO Jr7* 1 Programa de Pós Graduação em Ecologia e Conservação, Universidade do Estado do Mato Grosso, Nova Xavantina, Mato Grosso, Brazil; 1 lenizecalvao@hotmail.com 2 Setor de Biodiversidade e Ecologia, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, BR-57.010-020, Maceió, Alagoas, Brazil; 1 marcosvital@gmail.com 3 Instituto de Ciências Biológicas, Universidade Federal do Pará, Rua Augusto Correia, no 1 Bairro Guama, BR-66.075-110, Belém, PA, Brazil; 1 leandrojuen@ufpa.br 4 Universidade Estadual de Goiás (UEG), Av. Rio Araguaia esq. Av. Paranaíba, Itapuranga, Go, BR-76680-000 Goiás, Brazil; 1 ecoufg@yahoo.com. br 5 Programa de Pós Graduação em Ecologia e Conservação, Universidade do Estado do Mato Grosso, Nova Xavantina, Mato Grosso, Brazil; 1 maxbio@hotmail.com 6 Programa de Pós Graduação em Ecologia e Evolução, Universidade Federal de Goiás, Goiânia, Goiás, Brazil; 1 nelsonsilvapinto@gmail.com 7 Laboratório de Ecologia Teórica e Síntese, Departamento de Ecologia, Universidade Federal de Goiás, BR-74.001-970 Goiânia, Goiás, Brazil; 1 pdemarco@icb.ufg. br
Comparison of Genome Size in Reed Canarygrass (Phalaris arundinacea L.) Exotic and Putative Native Japanese Genotypes by Flow Cytometry

Reed canarygrass (Phalaris arundinacea L.) is a cool-season perennial grass widely distributed throughout North America, Europe and Asia. P. arundinacea is currently considered a major invasive plant species in the USA. Despite recent concerns that P. arundinacea has become an invasive plant species in Japan, differences between invasive and native Japanese genotypes remain unclear. We used flow cytometry to clarify genome size differences among 14 populations of putative native Japanese P. arundinacea genotypes and three exotic cultivars. The average genome size of the 14 Japanese populations and the three exotic P. arundinacea differed significantly (P < 0.05) and ranged from 4963.90 to 5166.69 Mbp/C. These results implied that the sampled populations included native Japanese genotypes. These populations may be useful in discriminating between invasive and native Japanese P. arundinacea genotypes. Discipline: Genetic resources Additional key words: invasive plant *Corresponding author: Yukio Akiyama e-mail: akky@affrc.go. jp Received 27 February 2015; accepted 25 March 2015. Introduction Reed canarygrass (Phalaris arundinacea L.) is a coolseason perennial grass widely distributed throughout North America, Europe and Asia (Bews 1929, Hitchcock 1935). Two ploidy levels, tetraploid (2n = 4x = 28) and hexaploid (2n = 6x = 42), have been reported in P. arundinacea (McWilliam and Neal-Smith 1962). The creeping rhizomes of P. arundinacea exhibit vigorous growth, and the species exhibits a marked tolerance to changes in humidity, snow, cold and heat. In addition, because P. arundinacea can be propagated in various ways (seeds, tillers and rhizomes), the species has been an important source of forage in the USA since the nineteenth century, when the European cultivar was introduced, and is also expected to be a promising source of biomass material in the future (Lewandowski et al. 2003, Casler et al. 2009). However, the high propagation of P. arundinacea is also a potential ecological problem, and it is perceived as a major invasive species in the USA (Merigliano & Lesica 1998, Lavergne & Molofsky 2007). It is also thought that the introgression of germplasm from European cultivars into native North American genotypes could account for the increased invasiveness of the species (Merigliano & Lesica 1998). In Japan, P. arundinacea has been used extensively as forage since the latter half of the twentieth century, and, as in America, is currently considered an invasive plant species (Hokkaido Government 2004, 2010). The differences between native and invasive P. arundinacea populations have not yet been investigated, and it is unclear whether genotypes of native Japanese P. arundinacea still exist in the wild, or whether these have been contaminated
THE YELLOW-RUMPED CACIQUE AND ITS ASSOCIATED NEST PIRATES

I describe the interactions between Yellow-rumped Caciques (Ca- cicus cela) in southeastern Peru and three species that often pirate their nests or destroy their eggs and kill nestlings. Individuals of one of these species, the Piratic Flycatcher (Legatus leucophaius\ harass caciques until they abandon their nests, which the flycatchers then use for their own eggs and young. The second species, the Russet-backed Oropendola (Psarocolius angustifrons), sometimes destroys the eggs or kills the young in cacique nests near its own in mixed colonies. The third species, the Troupial (Icterus icterus), exhibits both forms of behavior, it takes over a nest for its own use and then destroys the eggs and kills the young in adjacent cacique nests. The driving force behind nest destruction is unlikely to be interspecific com- petition for food because caciques, oropendolas, and Troupials forage in very different microhabitats. Instead, I hypothesize that the adaptive value of the destruction of neighboring nests is the creation of a maze of empty nests which makes it difficult for predators to find the occupied active nest. Direct observations of predator attacks on colonies indicate that such mazes are effective defenses against several frequent nest predators. Because nest pirates are very rare compared with the cacique host, their impact on the distribution of host nests appears to be negligible. Rarity of the piratic species relative to the host may be a necessary condition for the evolution of nest piracy, as in mimicry.
Effects of large-scale climate on avian population dynamics across species' North American breeding distributions

Global temperature increases of 0.6 C over the past century and predicted increases of 2 to 6 C over the next century have prompted many studies on effects of global warming on the population dynamics of plants and animals. Studies of landbirds in Europe and North America have shown effects of climatic variation on productivity and survival. However, such effects have been seen to translate to changes in population densities in only a few studies of European landbirds. Thus, the extent to which global warming has the potential to cause population declines in North American landbirds has remained unclear. In the research presented here, I model 39 years of climatic data, including indices of the North Atlantic Oscillation and El Niño Southern Oscillation, and distribution-wide Breeding Bird Survey data on 21 North American landbird species, to examine potential relationships between large-scale climate change and changes in avian population densities. Results of these analyses indicate geographic variation in strength of the effect of climate on population densities, with stronger effects in regions in which climate has stronger effects on local temperatures. Results also indicate that for species exhibiting long-term declines, there is a relationship between strength of the effect of local temperatures on population densities and magnitude of population decline. Additional analyses indicate that Neotropical-Nearctic migratory species are more negatively affected by warm winter temperatures than are closely-related North American residents. These results support the hypothesis that differences in climatic effects on migrants and residents may follow from greater trophic mismatch for species that are unable to time migration in response to earlier peaks in food availability. Finally, results of this work show that species are more highly affected by densities of sympatric congeners in areas in which they are also affected by climate, indicating that increased effects of climate on food resources may increase the effects of competition between congeners. Overall, results of this research indicate that North American landbird densities are affected by annual changes in large-scale climate, such that continued increases in global temperatures have the potential to affect long-term changes in landbird population densities across the continent.