Miracle-dz/UniFAR-FTUs huggingface dataset:
Widespread decreases in topsoil inorganic carbon stocks across China's grasslands during 1980s–2000s

Soil carbon (C) stocks consist of inorganic and organic components, ~1.7 times larger than the total of the C stored in vegetation and the atmosphere together. Significant soil C losses could thus offset any C sink in vegetation, creating a positive feedback to climate change. However, compared with the susceptible sensitivity of organic matter decay to climate warming, soil inorganic carbon (SIC) stocks are often assumed to be relatively stable. Here, we evaluated SIC changes across China's grasslands over the last two decades using data from a recent regional soil survey during 2001–2005 and historical national soil inventory during the 1980s. Our results showed that SIC stocks in the top 10 cm decreased significantly between the two sampling periods, with a mean rate of 26.8 (95% confidence interval: 15.8–41.7) g C m−2 yr−1. The larger decreases in SIC stocks were observed in those regions with stronger soil acidification and richer soil carbonates. The lost SIC could be released to the atmosphere as carbon dioxide, redistributed to the deeper soil layer, and transferred to the nearby regions. The fraction of soil carbonates entering into the atmosphere may diminish the strength of terrestrial C sequestration and amplify the positive C‐climate feedback.
‘Building a Future for Wildlife’? Evaluating the contribution of the world zoo and aquarium community to in situ conservation

In light of the United Nations declaring 2010 as the‘International Year of Biodiversity’, we carried out anaudit of in situ conservation projects supported by theworld zoo and aquarium community. The results of ourquestionnaire survey show that the 113 evaluated projectsare helping to improve the conservation status of high-proﬁle threatened species and habitats in biodiversity-richregions of the world. Our results show that thanks to theinvestment made by zoos and aquariums, particularlyﬁnancial, these projects reached overall impact scores of amagnitude suggestive of an appreciable contribution toglobal biodiversity conservation. The present ﬁrst globalappraisal of the contribution of the world zoo and aqua-rium community to in situ conservation from a supportedproject’s perspective thus suggests that zoos and aqua-riums are on track for ‘Building a Future for Wildlife’, asstipulated in the revised World Zoo and Aquarium Con-servation Strategy of 2005. However, zoosand aquariumscouldmakeanevenstrongercontributionbyallocatingmore resources to in situ conservation, which – as ourresults show – would signiﬁcantly increase the projects’conservation impact. Increased pooling of resourcesamongzoologicalinstitutionsthusappearstobeadvisable.Key-words: aquarium; biodiversity; evaluation; in situconservation; WAZA; zoo.
Exploiting genetic diversity to balance conservation and harvest of migratory salmon

Population-based management is central to the conservation of highly exploited species. Managing to sustain population diversity is especially challenging for migratory species. The aggregate of populations of sockeye salmon (Oncorhynchus nerka) that spawn in drainages of Bristol Bay, Alaska, is the most abundant in the world and supports the largest high-value salmon fishery in North America. We applied molecular tools (genetic data from 38 single nucleotide polymorphisms, assayed in 96 populations) to detect migratory trends in stock composition of sockeye salmon returning to Bristol Bay and to inform fisheries management in real time. We reliably and repeatedly detected abundances that were unanticipated based upon preseason forecasts, fishing effort was shifted accordingly, and the fleet and local economies benefited while the risk of overharvesting weaker stocks was minimized. This approach is being developed for other species and fisheries and provides a useful model for conservation wherever migrat.
Processes and Rates of Bacterial Evolution

A long-standing question in evolutionary biology is whether adaptation will typically proceed through a few mutations with large selective effects or many mutations with small effects. Many studies have implicated few loci of major effect, but it has been predicted that small-effect mutations should exist and contribute to adaptation. However, such mutations have not been found in many studies, either because they do not exist or because the experimental design limited their detection. To determine the effects and types of mutations contributing to adaptation, I studied laboratory and wild populations of bacteria. I characterized the distribution of the effect sizes in laboratory populations of an aerobic bacterium, Methylobacterium extorquens, and studied the types of genetic changes associated with adaptation to a novel host in wild populations of Mycoplasma gallisepticum. Chapters 1, 2 and 3 describe tools and strains that I developed to perform extensively replicated evolution experiments in Methylobacterium extorquens. I created a robotic system to assay bacterial cultures under high-throughput conditions, designed a medium that allowed for stable growth of M. extorquens and genetically manipulated Methylobacterium to remove genes preventing reproducible assays in batch culture. In chapter 4, I applied these tools to infer the distribution of selective effects for beneficial mutations and the rate at which they occur in M. extorquens. I evolved 192 populations at two different sizes: a large population size treatment to screen for rare beneficial mutations with large selective effects and a small population size treatment to screen for mutations with smaller iv effects. In contrast to expectations, I found a high beneficial mutation rate and a distribution skewed towards large effects. In chapter 5, I used genome re-sequencing to examine the genetic changes that occurred in a population of pathogenic Mycoplasma gallisepticum over a 13-year period following a host shift to house finches (Carpodacus mexicanus). In addition to many genomic changes, I observed a surprising loss of the immunity (CRISPR) genes. I recorded the highest rate of nucleotide variation introduced per year measured in a bacterium, demonstrating that one can study the kinetics of genetic change occurring in this population on tractable time-scales.
The Early Evolution of Archosaurs: Relationships and the Origin of Major Clades

Abstract Archosaurs have a nearly 250 million year record that originated shortly after the Permian-Triassic extinction event and is continued today by two extant clades, the crocodylians and the avians. The two extant lineages exemplify two bauplan extremes among a diverse and complex evolutionary history, but little is known about the common ancestor of these lineages. Renewed interest in early archosaurs has led to nearly a doubling of the known taxa in the last 20 years. This study presents a thorough phylogenetic analysis of 80 species-level taxa ranging from the latest Permian to the early part of the Jurassic using a dataset of 412 characters. Each terminal taxon is explicitly described and all specimens used in the analysis are clearly stated. Additionally, each character is discussed in detail and nearly all of the character states are illustrated in either a drawing or highlighted on a specimen photograph. A combination of novel characters and comprehensive character sampling has bridged previously published analyses that focus on particular archosauriform subclades. A well-resolved, robustly supported consensus tree (MPTs = 360) found a monophyletic Archosauria consisting of two major branches, the crocodylian-line and avian-line lineages. The monophyly of clades such as Ornithosuchidae, Phytosauria, Aetosauria, Crocodylomorpha, and Dinosauria is supported in this analysis. However, phytosaurs are recovered as the closest sister taxon to Archosauria, rather than basal crocodylian-line archosaurs, for the first time. Among taxa classically termed as “rauisuchians,” a monophyletic poposauroid clade was found as the sister taxon to a group of paraphyletic “rauisuchians” and monophyletic crocodylomorphs. Hence, crocodylomorphs are well nested within a clade of “rauisuchians,” and are not more closely related to aetosaurs than to taxa such as Postosuchus. Basal crocodylomorphs such as Hesperosuchus and similar forms (“Sphenosuchia”) were found as a paraphyletic grade leading to the clade Crocodyliformes. Among avian-line archosaurs, Dinosauria is well supported. A monophyletic clade containing Silesaurus and similar forms is well supported as the sister taxon to Dinosauria. Pterosaurs are robustly supported at the base of the avian line. A time-calibrated phylogeny of Archosauriformes indicates that the origin and initial diversification of Archosauria occurred during the Early Triassic following the Permian-Triassic extinction. Furthermore, all major basal archosaur lineages except Crocodylomorpha were established by the end of the Anisian. Early archosaur evolution is characterized by high rates of homoplasy, long ghost lineages, and high rates of character evolution. These data imply that much of the early history of Archosauria has not been recovered from the fossil record. Not only were archosaurs diverse by the Middle Triassic, but they had nearly a cosmopolitan biogeographic distribution by the end of the Anisian.
Influence of Glufosinate on Seed Weight, Seed Germination, and Seedling Vigor of Glufosinate-Resistant Rice1

Seeds were collected from field-grown glufosinate-resistant rice treated at various growth stages from the one-leaf through the boot stage with glufosinate at 0.84 kg ai/ha. The collected seeds were evaluated for 100-count seed weights, germination, and seedling vigor. Germination of the long-grain transformant CPRS PB-13 at five temperatures was unaffected by glufosinate treatment or temperature. At 14 d after initiation, germination of the medium-grain transformant BNGL HC-11/62 was reduced at 22 C when treated at the preboot timing. One hundred–count seed weights and seedling vigor were not affected for either glufosinate-resistant line. Nomenclature: Glufosinate; rice, Oryza sativa L. , ‘BNGL HC-11/62’, ‘CPRS PB-13’. Additional index word: Liberty-Link rice. Abbreviations: AOSA, Association of Official Seed Analysts; DAI, days after initiation; POST, postemergence.
Use of herbivore‐induced plant volatiles as search cues by Tiphia vernalis and Tiphia popilliavora to locate their below‐ground scarabaeid hosts

Japanese beetle, Popillia japonica Newman, and oriental beetle, Anomala orientalis (Waterhouse) (both Coleoptera: Scarabaeidae) are considered invasive species and have been reported as key pests of urban landscapes in the Northeastern USA. Tiphia vernalis Rohwer and Tiphia popilliavora Rohwer (Hymenoptera: Tiphiidae) were introduced as biocontrol agents against these beetles. These parasitic wasps burrow into the soil and search for grubs. When a host is found, the wasp attaches an egg in a location that is specific for the wasp species. It is unknown if these wasps can detect patches of concealed hosts from a distance above ground and what role, if any, herbivore‐induced plant volatiles play in their host location. This study evaluated the responses of female T. vernalis and T. popilliavora to grub‐infested and healthy plants in Y‐tube olfactometer bioassays. Also the effect of root herbivory on the composition of turfgrass (Poaceae) volatile profiles was investigated by collecting volatiles from healthy and grub‐infested grasses. Tiphia wasps were highly attracted to volatiles emitted by grub‐infested tall fescue (Festuca arundinacea Schreb.) and Kentucky bluegrass (Poa pratensis L.) over healthy grasses. In contrast, wasps did not exhibit a significant preference for grub‐infested perennial ryegrass (Lolium perenne L.) as compared with the control plants. The terpene levels emitted by grub‐infested Kentucky bluegrass and tall fescue were greater than that of control plants. Low levels of terpenes were observed for both test and control perennial ryegrass. The elevated levels of terpenes emitted by grub‐infested Kentucky bluegrass and tall fescue coincided with the attractiveness to the tiphiid wasps. Here, we provide evidence that plant exposure to root‐feeding insects P. japonica and A. orientalis resulted in an increase in terpenoid levels in turfgrasses, which strongly attracts their above‐ground parasitoids.
Biological effects of the growth hormone gene polymorphism in the American mink (Neovison vison Schreb., 1777) - does synonymous always mean silent?

Most often, genetic variation causing phenotypical changes is calculated exclusively upon the occurrence of nonsynonymous variation. However, it has been increasingly more common to state that synonymous mutations and polymorphisms, as well as nucleotide variation present in introns, can have very serious biological effects. In the following work, the potential biological effect (including molecular phenotype) of nucleotide variation within the growth hormone gene in American mink (Neovison vison Schreb., 1777) was evaluated, based on multilocus genotypes of 389 individuals (wild mink from Canada, six colour types of ranch mink, mink acquired from the natural environment in Poland and Iceland), identified by direct sequencing. The focus is on the possible occurrence of changes in a splicing regulatory sequences and sequence motifs, different reading of codons and on an influence on the mRNA secondary structure. The results obtained confirm the hypothesis that synonymity of single-nucleotide variation does not always signify its neutrality.
Reproductive seasonality and maturity of male Neophocaena phocaenoides asiaeorientalis in captivity: A case study based on the hormone evidence

To provide hormone evidence on reproductive seasonality and maturity of the Yangtze finless porpoise, the authors monitored the monthly variations of serum reproductive hormones of a male Yangtze finless porpoise in captivity via radioimmunoassay from 1997 to 2003. It was demonstrated that the immature animal had a serum T level of 28–101 ng dL−1 (65 ± 52 ng dL−1), reached puberty with the serum T concentration ranging between 250 and 590 ng dL−1 (390 ± 130 ng dL−1), and attained reproductive maturity when the serum T level went beyond 1120 ± 180 ng dL−1 in the breeding season. The body length growth of the animal showed a pattern similar to the serum T variations during its adolescent period from the age of 4 to 6 years. Moreover, the serum T concentration of the male porpoise exhibited significant seasonal variations, indicating that its breeding season may start as early as March and end as late as September.
Nivalenol and 15-acetyldeoxynivalenol Chemotypes of Fusarium graminearum Clade Species are Prevalent on Maize throughout China

Fusarium graminearum clade species are among the main causative agents of Gibberella ear rot (GER) in maize and responsible for the various trichothecene mycotoxins accumulated in contaminated maize grains. In this study, a total of 620 isolates from diseased maize ears collected from 59 districts in 19 provinces throughout China, previously identified morphologically as Fusarium graminearum clade, was genetically characterized at the species level based on SCAR (Sequence Characterized Amplified Region) and for their potential capability of mycotoxin production using the genetic chemotyping assay. The results showed that 359 isolates were F. asiaticum (SCAR 5), which consisted of 97% nivalenol (NIV)-chemotypes, 0.8% 3-acetyldeoxynivalenol (3-ADON)-producing isolates and 2.2% 15-acetyldeoxynivalenol (15-ADON) producers, whereas the remaining 261 isolates were identified as F. graminearum sensu stricto (SCAR 1), all of which produced 15-ADON mycotoxins. This high proportion of NIV producers present in F. asiaticum is different from the chemotype patterns in F. asiaticum populations isolated from wheat and barley, where DON and its acetylated chemotypes were the predominant mycotoxins. Moreover, the majority of NIV producers (59.1%) and all the 3-ADON-producing strains were derived from the warmer regions in southern China, whereas most of the 15-ADON-producing strains (78.4%) were isolated from the colder regions in northern China. Our study is the first report of NIV chemotypes of F. asiaticum and 15-ADON chemotypes of F. graminearum sensu stricto that were associated with the GER of maize in China.
Ecology of the ringed seal, Phoca hispida, in its fast ice breeding habitat

Studies of the behavioral ecology of seals hauled out on the sea ice at Popham Bay (64°17′ N, 65°30′ W) southeastern Baffin Island were conducted from 8 May to 6 June 1978 and 1 May to 20 June 1979. Similar densities and seasonal changes in numbers of hauled out seals were seen in both years. Seal numbers were positively correlated with date and negatively correlated with wind speed. While lying on the ice seals were vigilant and aggressive towards other seals, and females suckled their pups. Individuals were recognized by their different pelage marks. Both males and females showed site tenacity. One male, seen in 1978, was resighted in the study area in 1979. Our observations indicate that ringed seals are territorial and similar to the polygynous Weddell seal of the antarctic in their social organization. Population regulation appears to be affected by availability of suitable fast ice in which to maintain feeding and breeding habitat, with some adjustment of annual recruitment possibly in response to d.
Host and environmental correlates of body size in ticks (Acari: Argasidae and Ixodidae)

To evaluate the influence of host mass and environmental temperature on the evolution of body size in ticks, a comparative analysis was performed using data from 193 species. Using the 20 possible phylogenetically independent contrasts among tick species, no relationship was found between body size of female ticks and either host mass or temperature. The statistical power of these analyses was low. Within the two most speciose genera of soft ticks, however, separate cross-species analyses revealed a positive and highly significant relationship between female tick size and host mass. Also, within the two most speciose genera of hard ticks, cross-species analyses showed a positive and highly significant relationship between scutum size of female ticks and host mass. The latter correlation is based on measurements of tick body size that are independent of the level of blood engorgement. No effect of temperature was observed in the within-genera analyses. These within-genera trends may be artefacts of unknown.
Does global warming threat the existence of Arctic charr, Salvelinus alpinus (Salmonidae), in northern Finland?

Abstract Predicted global warming is expected to raise the water temperatures 2–6° C after doubling of atmospheric CO2. As an extreme coldwater fish species the Arctic charr appear to avoid water temperatures above 16–18° C. Arctic charr lives in Finland only in the mountain lakes of northernmost parts of the country and in some deep lakes of eastern Finland. Charr is most abundant at high altitudes. The global warming is expected to threaten first populations living in low altitude shallow lakes in which no thermal summer stratification occurs. Climatic warming will increase duration of high temperatures and thermal stratification in deep lakes. This indicates that Arctic charr will spend longer periods in minimum thermal habitats. Assuming that no factors other than temperature will change in future climates, reductions in summer habitat will probably lead to noticeable reductions in many charr populations. Populations living in deep lakes will survive better than those living in shallow lakes provided .
Genetic evaluation of crossbred lamb production. 3. Growth and carcass performance of second-cross lambs

This study evaluated the growth and carcass performance of second-cross lambs that were the progeny of common terminal sires and a range of first-cross ewes. The first-cross ewes were the progeny of 91 industry sires from several maternal breeds including the Border Leicester, East Friesian, Finnsheep, Coopworth, White Suffolk, Corriedale, and Booroola Leicester breeds. The first-cross ewes were generated at 3 sites over 3 years, and 3 common maternal sires were used at each site and each year to provide genetic links for combined analysis. The 2726 first-cross ewes were mated naturally to common terminal sires for 3 years at each site to quantify the variation in maternal genetics on the performance of 11 341 second-cross cross lambs. The birthweight, weaning weight (at an average age of 100 days) and post-weaning weight (at an average age of 200 days) of the second-cross lambs were analysed using mixed-model procedures. The lambs were slaughtered (n = 8878) at an average target carcass weight of 22 kg and dressing yield, carcass fat, muscle, meat colour, and meat pH were analysed. Crossbred ewe breed (the maternal grand sire breed) was significant for birthweight (range of 0.9 kg), weaning weight (range 4.4 kg) and post-weaning weight (range 4.6 kg). Type of birth and rearing, age of dam, and sex effects were significant for all liveweights. Ewe breed was significant for hot carcass weight, carcass fat levels, and muscle dimensions, but not for meat colour and ultimate meat pH. There was a significant difference between wether and ewe lamb carcasses for most traits, with other fixed effects generally being small when carcass weight was included as a covariate. Lamb carcasses from East Friesian-cross ewes were very lean compared with carcasses from all other ewe breeds (~2 mm lower fat depth at the GR site at 22 kg carcass weight). This comprehensive study of maternal sire breeds provides an opportunity to exploit between-breed variation for some maternal growth and carcass traits. There was, however, considerable overlap among breeds and opportunities exist for additional improvement by exploiting between-maternal sire genetic variance. The role of improved growth and carcass performance in profitability of prime lamb enterprises is discussed.
Movement and Habitat Use by Radio‐Tagged Paddlefish in the Upper Mississippi River and Tributaries

Abstract We used radio telemetry to evaluate the movement and habitat use of paddlefish Polyodon spathula in the upper Mississippi River and two tributary rivers. Radio transmitters were surgically implanted into 71 paddlefish in Navigation Pools 5A and 8 of the upper Mississippi River, the Chippewa River, and the Wisconsin River during fall 1994 through fall 1996. Radio-tagged paddlefish were located through summer 1997. The range of paddlefish movement was typically low during all seasons except spring, but some paddlefish moved throughout the 420-km extent of the study area. Paddlefish tagged in the Chippewa River were closely linked with the upper Mississippi River, as substantial portions of the population inhabited the adjacent Navigation Pool 4 each spring; paddlefish in the Wisconsin River, however, rarely ventured out of that tributary. The use of aquatic area types by paddlefish varied among the study reaches. A cartographic model of paddlefish habitat suitability was developed for Navigation Po.