Regression and Time Series Model Selection in Small Samples

Hurvich, Clifford M.; Tsai, Chih‐Ling

doi:10.2307/2336663

Cited by 1,588 publications

(1,813 citation statements)

References 7 publications

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“…ProtTest version 3 (refs 78,79) was employed to select the best-fit model of aminoacid replacement from 120 models (15 matrices: +G, +I or + G+I; +F) with a starting topology based on maximum likelihood. As the Bayesian information criterion (BIC; also known as the Schwarz criterion, or SC) 80 , the corrected Akaike information criterion (AICc) 81,82 and the decision theory framework (DT) 83 favoured LG+I+G, the phylogeny was then inferred using RAxML version 8.2.4 (ref. 84) with the LG amino acid matrix 85 , a gamma model of rate heterogeneity and an estimate of proportion of invariable sites.…”

Section: Phylogenetic Analysismentioning

confidence: 99%

Nitrogen fixation in a chemoautotrophic lucinid symbiosis

et al. 2016

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The shallow water bivalve Codakia orbicularis lives in symbiotic association with a sulfur-oxidizing bacterium in its gills. The endosymbiont fixes CO 2 and thus generates organic carbon compounds, which support the host's growth. To investigate the uncultured symbiont's metabolism and symbiont-host interactions in detail we conducted a proteogenomic analysis of purified bacteria. Unexpectedly, our results reveal a hitherto completely unrecognized feature of the C. orbicularis symbiont's physiology: the symbiont's genome encodes all proteins necessary for biological nitrogen fixation (diazotrophy). Expression of the respective genes under standard ambient conditions was confirmed by proteomics. Nitrogenase activity in the symbiont was also verified by enzyme activity assays. Phylogenetic analysis of the bacterial nitrogenase reductase NifH revealed the symbiont's close relationship to free-living nitrogen-fixing Proteobacteria from the seagrass sediment. The C. orbicularis symbiont, here tentatively named 'Candidatus Thiodiazotropha endolucinida', may thus not only sustain the bivalve's carbon demands. C. orbicularis may also benefit from a steady supply of fixed nitrogen from its symbiont-a scenario that is unprecedented in comparable chemoautotrophic symbioses. Mutualistic associations between marine invertebrates and sulfur-oxidizing (thiotrophic) bacteria are a well-documented and widespread phenomenon in a variety of sulfidic habitats ranging from hydrothermal vents to shallow-water coastal ecosystems 1-3 . Thioautotrophic symbionts generate energy through sulfide oxidation and provide their hosts with organic carbon. In the Lucinidae, a diverse family of marine bivalves, all members are obligatorily dependent on their bacterial gill endosymbionts after larval development and metamorphosis 4 . The shallowwater lucinid Codakia orbicularis, which lives in the sediment beneath the tropical seagrass Thalassia testudinum along the Caribbean and Western Atlantic coast 5 , harbours a single species of endosymbionts in its gills 6 . The symbiont has been shown to be newly acquired by each clam generation 7,8 from a pool of freeliving symbiosis-competent bacteria in the environment 9 , rather than being inherited from clam parents. C. orbicularis appears not to release its endosymbionts, even under adverse conditions, but can digest them as a source of nutrition [10][11][12] . Moreover, bacterial cell division seems to be inhibited inside the host tissue. The majority of the symbiont population was shown to be polyploid (that is, containing multiple genome copies), while dividing symbiont cell stages are very rarely observed in host bacteriocytes 13 . The host undoubtedly benefits from the symbiont both by way of detoxification of its sulfidic environment and by supply of organic compounds through the bacterial Calvin-Benson cycle. It remains questionable, however, whether the symbiont gains any advantage from this association in evolutionary terms 11 .Biological nitrogen fixation (diazotrophy) is the conversion of ...

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Section: Phylogenetic Analysismentioning

confidence: 99%

Nitrogen fixation in a chemoautotrophic lucinid symbiosis

et al. 2016

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“…Both the BIC and the small-sample corrected AIC of Hurvich and Tsai (1989) indicate that a model with a single lag is the most favored model. Thus, although our conceptual model suggests that a second lag may be relevant, including the second lag reduces precision and does not improve fit significantly.…”

Section: Parameter Estimates and Impulse Responsesmentioning

confidence: 99%

Commodity Storage and the Market Effects of Biofuel Policies

Carter

Rausser

Smith

2016

American J Agri Economics

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US legislation passed in 2007 (RFS2) increased by about 1.3 billion bushels the net amount of corn required to be processed annually into ethanol for motor-fuel use. Using modern time-series methods, we estimate that corn prices were about 30 percent higher between 2006 and 2014 than they would have been but for RFS2 and if pre-2006 trends had continued. We estimate a permanent corn demand increase of 1.3 billion bushels increased the long-run price by 31% (90% confidence interval is [5%,95%]). Our identification strategy is unique in the literature because it enables estimation of the effects of transitory shocks, such as weather, separately from the effects of persistent shocks, such as the ethanol mandate. Keywords:Ethanol; agriculture; energy policy; VAR; partial identification The difference between the RFS2 and RFS mandates is approximately 5.5 billion gallons (bgal) of ethanol annually in the years 2010-2012, which corresponds to about 1.3 billion bushels of corn after accounting for feed by-products. We take these 1.3 billion bushels as the permanent increase in corn demand in the RFS2, and we estimate that it caused a 31 percent long-run increase in corn prices.Interpreting our estimates correctly requires a precise statement about counterfactual ethanol production. In our counterfactual, ethanol production would have increased from its actual 2005 value of 3.9bgal to 8.8bgal in 2014. This path represents a continuation of the trend observed between 2002 and 2005 and is slightly below the path predicted by the USDA in early 2006. We argue it is a reasonable counterfactual path in the absence of the RFS2. We also point that our long-run estimate is scalable. To estimate the effect of increasing corn demand permanently by any multiple of 1.3 billion bushels, a reader could multiply our estimate by that multiple.Previous studies have also found that the increase in corn-ethanol production affected corn We focus our analysis on commodity inventory dynamics, which distinguishes our work from the extant literature. This approach enables us to estimate the price effects of persistent shocks to supply or demand separately from the effects of transitory shocks in a market for a storable commodity. This distinction is important in our context because persistent shocks have larger price effects than transitory shocks. The market can respond to a transitory shock, such as poor growing season weather, by drawing down inventory. This action mitigates the price effect. A persistent shock, such as an increase in current and expected future demand, cannot be mitigated by drawing down inventory.To identify these two types of shocks, we exploit their differential effects on inventory levels and on the term structure of futures prices. For example, all else equal, a sudden increase in this year's consumption demand reduces available inventories and raises spot prices relative to futures prices. This is a transitory shock. In contrast, a predicted increase in next year's consumption demand generates an increase in i...

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“…The gene genealogy was reconstructed using maximum parsimony (MP), maximum likelihood (ML), and Bayesian inference (BI), as implemented in PAUP v4.0b10 (Swofford 2002), PhyML v3 (Guindon and Gascuel 2003), and MrBayes v3.0b4 (Ronquist and Huelsenbeck 2003), respectively. Both the Corrected Akaike Information Criterion (AICc; Hurvich and Tsai 1989) and the Bayesian information criterion (BIC; Schwarz 1978) selected the TrN?G model as the best-fit model, using jModeltest v0.1.1 (Posada 2008;Guindon and Gascuel 2003). Under this model, the proportion of invariant sites (I) and the shape of the Gamma distribution (G) were set as 0 and 0.191, respectively.…”

Section: Phylogenetic Analysesmentioning

confidence: 99%

Phylogeographic Patterns of mtDNA Variation Revealed Multiple Glacial Refugia for the Frog Species Feirana taihangnica Endemic to the Qinling Mountains

et al. 2013

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Diversification patterns and demography of montane species are affected by Pleistocene climate fluctuations. Empirical cases from the Qinling Mountains (QM) region, which is a major biogeographic divider of East Asia, are few. We used DNA sequence data of the complete mitochondrial ND2 gene to detect effects of the Pleistocene glaciations on phylogeographic profiles of a frog species, Feirana taihangnica, which is endemic to the QM. Four distinct lineages consisting of seven sublineages were revealed. The strongest signal of biogeographical structure (F ct = 0.971, P \ 0.01) was found when populations were grouped according to these seven sublineages. One narrow secondary contact zone was detected in the middle QM between the lineage from middle QM and the lineage from eastern QM. Coalescent simulations indicated that this species colonized the QM region by a stepping-stone model. Divergences among lineages had likely been influenced by the uplift of the Tibetan Plateau during the late Miocene-tolate Pleistocene, as well as by the Pleistocene climatic cycles. Coalescent simulations also suggested that F. taihangnica populations have persisted through the Pleistocene glacial periods in multiple refugia across the QM region. Demographic analyses indicated that all lineages, except the lineage in the Funiu Mountains, have been experienced postglacial expansion of population size and distribution range. In conclusion, Pleistocene climate fluctuations and tectonic changes during the late Miocene-late Pleistocene have profoundly influenced the phylogeography and historical demography of F. taihangnica.

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Regression and Time Series Model Selection in Small Samples

Cited by 1,588 publications

References 7 publications

Nitrogen fixation in a chemoautotrophic lucinid symbiosis

Nitrogen fixation in a chemoautotrophic lucinid symbiosis

Commodity Storage and the Market Effects of Biofuel Policies

Phylogeographic Patterns of mtDNA Variation Revealed Multiple Glacial Refugia for the Frog Species Feirana taihangnica Endemic to the Qinling Mountains

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