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"Gardner, A"
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The future of hyperdiverse tropical ecosystems
The tropics contain the overwhelming majority of Earth’s biodiversity: their terrestrial, freshwater and marine ecosystems hold more than three-quarters of all species, including almost all shallow-water corals and over 90% of terrestrial birds. However, tropical ecosystems are also subject to pervasive and interacting stressors, such as deforestation, overfishing and climate change, and they are set within a socio-economic context that includes growing pressure from an increasingly globalized world, larger and more affluent tropical populations, and weak governance and response capacities. Concerted local, national and international actions are urgently required to prevent a collapse of tropical biodiversity.
The immense biodiversity of tropical ecosystems is threatened by multiple interacting local and global stressors that can only be addressed by the concerted efforts of grassroots organizations, researchers, national governments and the international community.
Journal Article
A radically different method of moments
The four primary moment-based probability density estimation and associated moment-based parameter estimation methods used in classical statistical inference when the probability density functions for the observed data are unknown or are intractable are briefly described as background for the introduction of an entirely new method. This new method is radically different in approach yet provides a solution that requires essentially the same information as the existing methods: (1) model moments with known dependence on unknown parameters and (2) associated sample moments. However, the new method, unlike the classical method of moments and its generalized counterparts, requires only the solution of simultaneous linear equations. A theoretical comparison between the new and old methods is made, and reference is made to the Author’s earlier work on analytical comparisons with Bayesian parameter estimation and decision for cyclostationary processes. The next step required for finding this new method’s place in practice among present methods of moments is an extensive comparison of the performance of these methods applied to a diverse variety of multivariate data sets. This next step is beyond the scope of this theoretical paper, the purpose of which is to demonstrate for the first time that the method from engineering work on inference for cyclostationary processes in communications systems in the 1970s is a genuine method of moments for multivariate data though this non-obvious equivalence was not originally recognized even by the Author or, apparently, anyone else for half a century.
Journal Article
genetic architecture of maize height
Height is one of the most heritable and easily measured traits in maize (Zea mays L.). Given a pedigree or estimates of the genomic identity-by-state (IBS) among related plants, height is also accurately predictable. But, mapping alleles explaining natural variation in maize height remains a formidable challenge. To address this challenge, we measured the plant height, ear height, flowering time, and node counts of plants grown in >64,500 plots across 13 environments. These plots contained >7,300 inbreds representing most publically available maize inbreds in the U.S.A. as well as families of the maize Nested Association Mapping (NAM) panel. Joint-linkage mapping of quantitative trait loci (QTL), fine mapping in near isogenic lines (NILs), genome wide association studies (GWAS), and genomic best linear unbiased prediction (GBLUP) were performed. The heritability of plant height was estimated to be over 90%. Mapping of NAM family-nested QTL revealed the largest explained about 2.1 ± 0.9% of height variation. The effects of two tropical alleles at this QTL were independently validated by fine mapping. Several significant associations found by GWAS co-localized with established height loci including brassinosteroid-deficient dwarf1, dwarf plant1, and semi-dwarf2. GBLUP explained >80% of plant height variation in the observed panels and outperformed bootstrap aggregation of family-nested QTL models in evaluations of prediction accuracy. These results revealed maize height was under strong genetic control and had a highly polygenic genetic architecture. They also showed that multiple models of genetic architecture differing in polygenicity and effect sizes can plausibly explain a population’s variation in maize height, but they may vary in predictive efficacy.
Journal Article
A large-scale pedigree resource of wheat reveals evidence for adaptation and selection by breeders
Information on crop pedigrees can be used to help maximise genetic gain in crop breeding and allow efficient management of genetic resources. We present a pedigree resource of 2,657 wheat (Triticum aestivum L.) genotypes originating from 38 countries, representing more than a century of breeding and variety development. Visualisation of the pedigree enables illustration of the key developments in United Kingdom wheat breeding, highlights the wide genetic background of the UK wheat gene pool, and facilitates tracing the origin of beneficial alleles. A relatively high correlation between pedigree- and marker-based kinship coefficients was found, which validated the pedigree and enabled identification of errors in the pedigree or marker data. Using simulations with a combination of pedigree and genotype data, we found evidence for significant effects of selection by breeders. Within crosses, genotypes are often more closely related than expected by simulations to one of the parents, which indicates selection for favourable alleles during the breeding process. Selection across the pedigree was demonstrated on a subset of the pedigree in which 110 genotyped varieties released before the year 2000 were used to simulate the distribution of marker alleles of 45 genotyped varieties released after the year 2000, in the absence of selection. Allelic diversity in the 45 varieties was found to deviate significantly from the simulated distributions at a number of loci, indicating regions under selection over this period. The identification of one of these regions as coinciding with a strong yield component quantitative trait locus (QTL) highlights both the potential of the remaining loci as wheat breeding targets for further investigation, as well as the utility of this pedigree-based methodology to identify important breeding targets in other crops. Further evidence for selection was found as greater linkage disequilibrium (LD) for observed versus simulated genotypes within all chromosomes. This difference was greater at shorter genetic distances, indicating that breeder selections have conserved beneficial linkage blocks. Collectively, this work highlights the benefits of generating detailed pedigree resources for crop species. The wheat pedigree database developed here represents a valuable community resource and will be updated as new varieties are released at https://www.niab.com/pages/id/501/UK_Wheat_varieties_Pedigree.
Journal Article
Actor-specific contributions to the deforestation slowdown in the Brazilian Amazon
Annual deforestation rates in the Brazilian Amazon fell by 77% between 2004 and 2011, yet have stabilized since 2009 at 5,000–7,000 km ². We provide the first submunicipality assessment, to our knowledge, of actor-specific contributions to the deforestation slowdown by linking agricultural census and remote-sensing data on deforestation and forest degradation. Almost half (36,158 km ²) of the deforestation between 2004 and 2011 occurred in areas dominated by larger properties (>500 ha), whereas only 12% (9,720 km ²) occurred in areas dominated by smallholder properties (<100 ha). In addition, forests in areas dominated by smallholders tend to be less fragmented and less degraded. However, although annual deforestation rates fell during this period by 68–85% for all actors, the contribution of the largest landholders (>2,500 ha) to annual deforestation decreased over time (63% decrease between 2005 and 2011), whereas that of smallholders went up by a similar amount (69%) during the same period. In addition, the deforestation share attributable to remote areas increased by 88% between 2009 and 2011. These observations are consistent across the Brazilian Amazon, regardless of geographical differences in actor dominance or socioenvironmental context. Our findings suggest that deforestation policies to date, which have been particularly focused on command and control measures on larger properties in deforestation hotspots, may be increasingly limited in their effectiveness and fail to address all actors equally. Further reductions in deforestation are likely to be increasingly costly and require actor-tailored approaches, including better monitoring to detect small-scale deforestation and a shift toward more incentive-based conservation policies.
Significance The Brazilian Amazon is at a critical juncture after the recent stabilization of deforestation rates. Identifying opportunities for continued deforestation reductions requires an understanding of the contribution of different actors to overall deforestation. We provide the first such assessment, to our knowledge, that reports on two headline findings. First, between 2004 and 2011, areas dominated by properties larger than 500 ha accounted for 48% of the deforestation compared with only 12% for smallholders (<100 ha). Second, the deforestation share attributed to the largest properties (≥2,500 ha) declined by 63% from a peak in 2005, whereas that of smallholders increased by 69%. Further reductions in deforestation are likely to require a shift toward more incentive-based policies that are tailored toward different actors.
Journal Article
Diel niche variation in mammals associated with expanded trait space
Mammalian life shows huge diversity, but most groups remain nocturnal in their activity pattern. A key unresolved question is whether mammal species that have diversified into different diel niches occupy unique regions of functional trait space. For 5,104 extant mammals we show here that daytime-active species (cathemeral or diurnal) evolved trait combinations along different gradients from those of nocturnal and crepuscular species. Hypervolumes of five major functional traits (body mass, litter size, diet, foraging strata, habitat breadth) reveal that 30% of diurnal trait space is unique, compared to 55% of nocturnal trait space. Almost half of trait space (44%) of species with apparently obligate diel niches is shared with those that can switch, suggesting that more species than currently realised may be somewhat flexible in their activity patterns. Increasingly, conservation measures have focused on protecting functionally unique species; for mammals, protecting functional distinctiveness requires a focus across diel niches.
Most mammals are nocturnal, but a new analysis suggests that although most groups of species active at a particular time of day or night occupy different ecological niches, a surprisingly large proportion of species are more flexible in the timing of their activity than previously thought.
Journal Article
An automated framework for exploring and learning potential-energy surfaces
Machine learning has become ubiquitous in materials modelling and now routinely enables large-scale atomistic simulations with quantum-mechanical accuracy. However, developing machine-learned interatomic potentials requires high-quality training data, and the manual generation and curation of such data can be a major bottleneck. Here, we introduce an automated framework for the exploration and fitting of potential-energy surfaces, implemented in an openly available software package that we call
autoplex
(‘automatic potential-landscape explorer’). We discuss design choices, particularly the interoperability with existing software architectures, and the ability for the end user to easily use the computational workflows provided. We show wide-ranging capability demonstrations: for the titanium–oxygen system, SiO
2
, crystalline and liquid water, as well as phase-change memory materials. More generally, our study illustrates how automation can speed up atomistic machine learning in computational materials science.
Machine learning is revolutionising materials modelling but requires high-quality training data. Here, the authors introduce autoplex, an open framework automating exploration and fitting of potential-energy surfaces across diverse materials.
Journal Article
Discovering and modeling hidden periodicities in science data
Hidden periodicities in science data have long been a popular topic of investigation. The popularity stems from the fact that detecting and characterizing periodicities can provide a means for extracting information from science data—information that might not otherwise be accessible. In other words, periodicities in data can be exploited for the purposes of statistical inference and decision making. The long history of this topic is briefly reviewed with heavy reference to a historical essay on the topic by H.O.A. Wold, written more than half a century ago, following which the treatise focuses on a paradigm shifting advance in theory and methodology for characterizing hidden periodicities that was initiated by the second author in the mid-1980s and further advanced by both authors since then, including a plethora of algorithms for performing the needed computations in applications. The data models this theory is based on are generally called cyclostationary but include variations that are labeled with modifiers like wide-sense, strict sense, n-th order for n = 1, 2, 3,..., almost, poly, and irregular . The theory is probabilistic, but is intentionally not based on stochastic processes which, it is argued, are inappropriate for many, if not most, applications. The basis used is Fraction-of-Time (FOT) Probability . The concept, theory, and methodology of FOT Probability is itself a major paradigm shift, also initiated by the second Author more than half a century ago, and it is an integral part of the (preferred) non-stochastic theory of cyclostationarity. Since the birth of this topic, both authors have continued to advance these paradigm shifts, including further development of theory, associated methodology, and computational algorithms. The most advanced of the concepts described (viz., irregular poly-cyclostationarity) is illustrated with an application of the associated algorithms to science data consisting of time series of Sunspot numbers containing approximately 75,000 daily measurements representing a period of about 200 years. The results include the first methodical characterization of the irregularity of the poly-periodicity hidden in the data.
Journal Article