Cavity-nesting birds are limited by nesting habitat in Neotropical agricultural landscapes

Most studies comparing biodiversity between natural and human-modified landscapes focus on patterns in species occurrence or abundance, but do not consider how different habitat types meet species' breeding requirements. Organisms that use or nest in tree cavities may be especially threatened by habitat conversion due to the loss of their nesting sites. Although cavity-nesting bird diversity is highest in the tropics, little is known about how tropical birds use cavities, how agriculture affects their reproductive biology, and how effective nest boxes could be as a conservation strategy in tropical agriculture. Here, we explored how habitat conversion from tropical forests to pasture affects the abundance, nesting habitat availability, and nest success of cavity-nesting birds in Northwest Ecuador. We conducted bird surveys and measured natural cavity availability and use in forest and agriculture. We also added artificial nest boxes to forest and agriculture to see whether cavity limitation in agriculture would elicit higher use of artificial nest boxes. We found evidence of cavity limitation in agriculture—there were many more natural cavities in forest than in agriculture, as well as more avian use of nest boxes placed in agriculture as compared to forest. Our results suggest that it is important to retain remnant trees in tropical agriculture to provide critical nesting habitat for birds. In addition, adding nest boxes to tropical agricultural systems could be a good conservation strategy for certain species, including insectivores that could provide pest-control services to farmers. Abstract in Spanish is available with online material.     

Soil nutrient dissimilarity and litter nutrient limitation as major drivers of home field advantage in riparian tropical forests

Decomposition is a key process driving carbon and nutrient cycling in ecosystems worldwide. The home field advantage effect (HFA) has been found to accelerate decomposition rates when litter originates from “home” when compared to other (“away”) sites. It is still poorly known how HFA plays out in tropical, riparian forests, particularly in forests under restoration. We carried out three independent reciprocal litter transplant experiments to test how litter quality, soil nutrient concentrations, and successional stage (age) influenced HFA in tropical riparian forests. These experimental areas formed a wide gradient of soil and litter nutrients, which we used to evaluate the more general hypothesis that HFA varies with dissimilarity in soil nutrients and litter quality. We found that HFA increased with soil nutrient dissimilarity, suggesting that litter translocation uncouples relationships between decomposers and litter characteristics; and with litter N:P, indicating P limitation in this system. We also found negative HFA effects at a site under restoration that presented low decomposer ability, suggesting that forest restoration does not necessarily recover decomposer communities and nutrient cycling. Within each of the independent experiments, the occurrence of HFA effects was limited and their magnitude was not related to forest age, nor soil and litter quality. Our results imply that HFA effects in tropical ecosystems are influenced by litter nutrient limitation and soil nutrient dissimilarity between home and away sites, but to further disentangle major HFA drivers in tropical areas, a gradient of dissimilarity between litter and soil properties must be implemented in future experimental designs.     

Forest development during 6,300–3,000 yBP (Early to Late Jomon Periods) at the Akayama Site,central Japan

Fossil wood assemblages deposited during 6.300–3.000 yBP, are studied at the Akayama Site, central Japan. Layer III containing fossil woods was divided into three subunits according to intercalating tephras, and total 3618 fossil woods were studied. In the composition, deciduous broad-leaved trees dominated, accompanied by some evergreen conifers. In the diameter distribution, nine taxa accounted for nearly 90% of individuals exceeding 10 cm in diameter. Spatial distribution of nine major and three minor taxa and that of thick individuals clarified the following points: 1)Fraxinus established a lowland forest during 5,000–4,500 yBP, accompanied byAlnus sect.Gymnothyrsus, Acer andAesculus turbinata; 2) small trees ofAlnus sect.Gymnothyrsus extensively intermingled in the lowlandFraxinus forest during 4,500–3,000 yBP; 3)Quercus sect.Prinus and Castanea crenata constituted escarpment forests during 6,300–3,000 yBP; 4)Carpinus sect.Eucarpinus became a major component during 5,000–4,500 yBP, andOstrya japonica replacedCastanea crenata during 4,500–3,000 yBP. Comparison with the other five contemporaneous fossil wood assemblages shows prevalence ofFraxinus-dominant forests during the Late to Latest Jomon Periods in the southern part of the Kanto Plain.     

Canopy photosynthetic production in a Japanese larch forest. II. Estimation of the canopy photosynthetic production

Seasonal changes and yearly gross canopy photosynthetic production were estimated for an 18 year old Japanese larch (Larix leptolepis) forest between 1982 and 1984. A canopy photosynthesis model was applied for the estimation, which took into account the effect of light interception by the non-photosynthetic organs. Seasonal changes in photosynthetic ability, amount of canopy leaf area and light environment within the canopy were also taken into account. Amount of leaf area was estimated by the leaf area growth of a single leaf. The change of light environment within the canopy during the growing season was estimated with a light penetration model and the leaf increment within the canopy. Canopy respiration and surplus production were calculated as seasonal and yearly values for the three years studied. Mean yearly estimates of canopy photosynthesis, canopy respiration and surplus production were 37, 13 and 23 tCO₂ ha⁻¹ year⁻¹, respectively. Vertical trend, seasonal changes and yearly values of the estimates were analyzed in relation to environmental and stand factors.     

Individual risk prediction: Comparing random forests with Cox proportional-hazards model by a simulation study

With big data becoming widely available in healthcare, machine learning algorithms such as random forest (RF) that ignores time-to-event information and random survival forest (RSF) that handles right-censored data are used for individual risk prediction alternatively to the Cox proportional hazards (Cox-PH) model. We aimed to systematically compare RF and RSF with Cox-PH. RSF with three split criteria [log-rank (RSF-LR), log-rank score (RSF-LRS), maximally selected rank statistics (RSF-MSR)]; RF, Cox-PH, and Cox-PH with splines (Cox-S) were evaluated through a simulation study based on real data. One hundred eighty scenarios were investigated assuming different associations between the predictors and the outcome (linear/linear and interactions/nonlinear/nonlinear and interactions), training sample sizes (500/1000/5000), censoring rates (50%/75%/93%), hazard functions (increasing/decreasing/constant), and number of predictors (seven, 15 including noise variables). Methods' performance was evaluated with time-dependent area under curve and integrated Brier score. In all scenarios, RF had the worst performance. In scenarios with a low number of events (⩽70), Cox-PH was at least noninferior to RSF, whereas under linearity assumption it outperformed RSF. Under the presence of interactions, RSF performed better than Cox-PH as the number of events increased whereas Cox-S reached at least similar performance with RSF under nonlinear effects. RSF-LRS performed slightly worse than RSF-LR and RSF-MSR when including noise variables and interaction effects. When applied to real data, models incorporating survival time performed better. Although RSF algorithms are a promising alternative to conventional Cox-PH as data complexity increases, they require a higher number of events for training. In time-to-event analysis, algorithms that consider survival time should be used.     

The mycorrhizal status of vascular epiphytes in Bale Mountains National Park,Ethiopia

Roots of 28 species of epiphytic vascular plants were collected on tree trunks and branches at six afromontane forest sites between 1700 and 3300 m above sea level in Bale Mountains National Park, Ethiopia. Seven of the 28 epiphyte species were colonized by vesicular-arbuscular mycorrhizal fungi (VAM). Mycorrhizal colonization only occurred at two of the six sites examined, at 2900 m and 3300 m, but more than one type of VAM endophyte was present in each case. Three facultative epiphytic species were all highly colonized by VAM on the forest floor, whereas roots from epiphytic habitats were weakly colonized. No correlations were found between VAM colonization, fine root diameter and root hair length, but VAM colonization and root hair abundance were negatively correlated. The lack of VAM colonization of potential, epiphytic host species at the majority of the sites examined points to the dispersal of VAM propagules as the factor limiting mycorrhizal colonization of epiphytic habitats. It is suggested that root systems of hemiepiphytic tree species serve as corridors between forest floor and tree trunks through which VAM may spread via hyphal growth.     

声学指数在城市森林鸟类多样性评估中的应用

鸣声是鸟类之间进行沟通和传递信息的重要方式,这为通过声学监测评估鸟类多样性提供了独特的机会。利用声学指数快速评估生物多样性是一种新兴的调查方法,但城市森林中的复杂声环境可能会导致声学指数的指示结果出现偏差。为了解声学指数在城市森林中应用的可行性,本研究在北京市东郊森林公园设置了50个矩阵式调查样点,于2021年4–6月每月进行1次鸟类传统观测和同步鸣声采集,通过比较两种方法的结果来探究声学监测的有效性。采用Spearman相关分析和广义线性混合模型评估6个常用声学指数与鸟类丰富度和多度的关系,并衡量了每个指数的性能。结果表明:(1)本研究共记录到鸟类10目23科35种,通过声学监听识别的总物种数与传统鸟类观测相等,但具体鸟种存在差异;(2)不同月份间声学指数与鸟类丰富度和多度的相关性有明显差别,声学复杂度指数(ACI)和标准化声景差异指数(NDSI)优于其他指数,是评估鸟类多样性的关键变量;(3)声学指数对鸟类多度的预测能力(R²m=0.32,R2c=0.80)要高于丰富度(R²m=0.12,R2c=0.18)。声学指数为快速评估生物多样性提...     

浙江古田山亚热带常绿阔叶林叶衰老物候影响因子研究

该文选取浙江省古田山亚热带常绿阔叶林72种木本植物,探究气候因素、系统发育关系和功能性状对亚热带常绿阔叶林叶衰老物候的影响。结果表明,叶变色期在9—12月,落叶期在10—12月。每月落叶物种数与月均温、月均降水量和月均日照时数没有显著相关性,每月叶变色物种数与月均温和月均日照时数呈弱相关;落叶性对叶变色期和落叶期具有显著影响;植物间系统发育关系对叶变色期和落叶期没有显著影响。因此,生物和非生物因子都会影响常绿阔叶树种的叶衰老,这对于提高秋季物候预测模型具有重要价值。     

Comparison of mechanistic and hybrid modeling approaches for characterization of a CHO cultivation process: Requirements,pitfalls and solution paths

Despite the advantages of mathematical bioprocess modeling, successful model implementation already starts with experimental planning and accordingly can fail at this early stage. For this study, two different modeling approaches (mechanistic and hybrid) based on a four-dimensional antibody-producing CHO fed-batch process are compared. Overall, 33 experiments are performed in the fractional factorial four-dimensional design space and separated into four different complex data partitions subsequently used for model comparison and evaluation. The mechanistic model demonstrates the advantage of prior knowledge (i.e., known equations) to get informative value relatively independently of the utilized data partition. The hybrid approach displayes a higher data dependency but simultaneously yielded a higher accuracy on all data partitions. Furthermore, our results demonstrate that independent of the chosen modeling framework, a smart selection of only four initial experiments can already yield a very good representation of a full design space independent of the chosen modeling structure. Academic and industry researchers are recommended to pay more attention to experimental planning to maximize the process understanding obtained from mathematical modeling.     

Genome-wide RAD sequencing data suggest predominant role of vicariance in Sino-Japanese disjunction of the monotypic genus Conandron (Gesneriaceae)

Disjunct distribution is a key issue in biogeography and ecology, but it is often difficult to determine the relative roles of dispersal vs. vicariance in disjunctions. We studied the phylogeographic pattern of the monotypic Conandron ramondioides (Gesneriaceae), which shows Sino-Japanese disjunctions, with ddRAD sequencing based on a comprehensive sampling of 11 populations from mainland China, Taiwan Island, and Japan. We found a very high degree of genetic differentiation among these three regions, with very limited gene flow and a clear Isolation by Distance pattern. Mainland China and Japan clades diverged first from a widespread ancestral population in the middle Miocene, followed by a later divergence between mainland China and Taiwan Island clades in the early Pliocene. Three current groups have survived in various glacial refugia during the Last Glacial Maximum, and experienced contraction and/or bottlenecks since their divergence during Quaternary glacial cycles, with strong niche divergence between mainland China + Japan and Taiwan Island ranges. Thus, we verified a predominant role of vicariance in the current disjunction of the monotypic genus Conandron. The sharp phylogenetic separation, ecological niche divergence among these three groups, and the great number of private alleles in all populations sampled indicated a considerable time of independent evolution, and suggests the need for a taxonomic survey to detect potentially overlooked taxa.