Are both agricultural intensification and farmland abandonment threats to biodiversity? A test with bird communities in paddy-dominated landscapes

Land-use changes, including agricultural intensification and farmland abandonment, influence biodiversity in agricultural landscapes. However, few studies have focused on how the two major land-use changes affect different types of species at landscape scales. This study examined the relationships between the richness and abundance of five bird groups (agricultural wetland species, agricultural land species, grassland species, edge species, and woodland species) as well as the total species richness and abundance, and intensification or abandonment in 28 square, 100-ha grid cells in paddy-dominated landscapes in the Tone River basin of central Japan. Rice-field intensification and abandonment were not completely segregated spatially: intensification occurred in both plain and hilly areas surrounded by forests, while abandonment tended to occur in hilly areas. The effects of intensification and abandonment differed among species groups and between seasons. The richness or abundance of agricultural wetland species in summer were negatively associated with both intensification and abandonment. While the abundance of agricultural land species in winter and grassland species in both seasons were positively associated with intensification and abandonment, respectively. The total species richness and abundance did not show clear association with intensification and abandonment due to a variety of responses of the five bird groups. Based on prefectural Red Data Books, agricultural wetland species, followed by grassland species, were more threatened than other three groups in both summer and winter. This study found that (1) the diversity of habitats (including consolidated and abandoned farmlands) provides buffer areas for the different bird groups on different times of the year and (2) agricultural wetland species that use flooded rice fields in summer, such as egrets and shorebirds, are particularly threatened by both intensification and abandonment.We thank Yoshinori Tokuoka, Susumu Yamada, Eun-Young Kim, and Shori Yamamoto for providing land-use data. We also appreciate two anonymous reviewers for their constructive comments and suggestions. This study was conducted as part of the research project “Developing management techniques for agricultural and aquatic ecosystems in river basins in pursuit of coexistence with nature,” funded by the Agriculture, Forestry and Fisheries Research Council of Japan. N.K. and T.O. were also financially supported by JSPS (Japan Society for the Promotion of Science) KAKENHI Grant Numbers 25830154 and 24710038, respectively. T.A. was supported by the European Commission’s Marie Curie International Incoming Fellowship Programme (PIIFGA-2011-303221).This is the author accepted manuscript. The final version is available from Elsevier via http://dx.doi.org/10.1016/j.agee.2015.08.01

Replication Study of Candidate Genes Associated With Type 2 Diabetes Based On Genome-Wide Screening

OBJECTIVE—The present study was conducted to confirm possible associations between candidate genes from genome-wide association studies and type 2 diabetes in Japanese diabetic patients and a community-based general population. A total of 11 previously reported single-nucleotide polymorphisms (SNPs) from the TCF7L2, CDKAL1, HHEX, IGF2BP2, CDKN2A/B, SLC30A8, and KCNJ11 genes were analyzed

The Mechanisms of Codon Reassignments in Mitochondrial Genetic Codes

Many cases of non-standard genetic codes are known in mitochondrial genomes. We carry out analysis of phylogeny and codon usage of organisms for which the complete mitochondrial genome is available, and we determine the most likely mechanism for codon reassignment in each case. Reassignment events can be classified according to the gain-loss framework. The gain represents the appearance of a new tRNA for the reassigned codon or the change of an existing tRNA such that it gains the ability to pair with the codon. The loss represents the deletion of a tRNA or the change in a tRNA so that it no longer translates the codon. One possible mechanism is Codon Disappearance, where the codon disappears from the genome prior to the gain and loss events. In the alternative mechanisms the codon does not disappear. In the Unassigned Codon mechanism, the loss occurs first, whereas in the Ambiguous Intermediate mechanism, the gain occurs first. Codon usage analysis gives clear evidence of cases where the codon disappeared at the point of the reassignment and also cases where it did not disappear. Codon disappearance is the probable explanation for stop to sense reassignments and a small number of reassignments of sense codons. However, the majority of sense to sense reassignments cannot be explained by codon disappearance. In the latter cases, by analysis of the presence or absence of tRNAs in the genome and of the changes in tRNA sequences, it is sometimes possible to distinguish between the Unassigned Codon and Ambiguous Intermediate mechanisms. We emphasize that not all reassignments follow the same scenario and that it is necessary to consider the details of each case carefully.Comment: 53 pages (45 pages, including 4 figures + 8 pages of supplementary information). To appear in J.Mol.Evo

Neural Advantages of Older Musicians Involve the Cerebellum: Implications for Healthy Aging Through Lifelong Musical Instrument Training

This study compared 30 older musicians and 30 age-matched non-musicians to investigate the association between lifelong musical instrument training and age-related cognitive decline and brain atrophy (musicians: mean age 70.8 years, musical experience 52.7 years; non-musicians: mean age 71.4 years, no or less than 3 years of musical experience). Although previous research has demonstrated that young musicians have larger gray matter volume (GMV) in the auditory-motor cortices and cerebellum than non-musicians, little is known about older musicians. Music imagery in young musicians is also known to share a neural underpinning [the supramarginal gyrus (SMG) and cerebellum] with music performance. Thus, we hypothesized that older musicians would show superiority to non-musicians in some of the abovementioned brain regions. Behavioral performance, GMV, and brain activity, including functional connectivity (FC) during melodic working memory (MWM) tasks, were evaluated in both groups. Behaviorally, musicians exhibited a much higher tapping speed than non-musicians, and tapping speed was correlated with executive function in musicians. Structural analyses revealed larger GMVs in both sides of the cerebellum of musicians, and importantly, this was maintained until very old age. Task-related FC analyses revealed that musicians possessed greater cerebellar-hippocampal FC, which was correlated with tapping speed. Furthermore, musicians showed higher activation in the SMG during MWM tasks; this was correlated with earlier commencement of instrumental training. These results indicate advantages or heightened coupling in brain regions associated with music performance and imagery in musicians. We suggest that lifelong instrumental training highly predicts the structural maintenance of the cerebellum and related cognitive maintenance in old age