A hidden Markov movement model for rapidly identifying behavioral states from animal tracks

Electronic telemetry is frequently used to document animal movement through time. Methods that can identify underlying behaviors driving specific movement patterns can help us understand how and why animals use available space, thereby aiding conservation and management efforts. For aquatic animal tracking data with significant measurement error, a Bayesian state‐space model called the first‐Difference Correlated Random Walk with Switching (DCRWS) has often been used for this purpose. However, for aquatic animals, highly accurate tracking data are now becoming more common. We developed a new hidden Markov model (HMM) for identifying behavioral states from animal tracks with negligible error, called the hidden Markov movement model (HMMM). We implemented as the basis for the HMMM the process equation of the DCRWS, but we used the method of maximum likelihood and the R package TMB for rapid model fitting. The HMMM was compared to a modified version of the DCRWS for highly accurate tracks, the DCRWS, and to a common HMM for animal tracks fitted with the R package moveHMM. We show that the HMMM is both accurate and suitable for multiple species by fitting it to real tracks from a grey seal, lake trout, and blue shark, as well as to simulated data. The HMMM is a fast and reliable tool for making meaningful inference from animal movement data that is ideally suited for ecologists who want to use the popular DCRWS implementation and have highly accurate tracking data. It additionally provides a groundwork for development of more complex modeling of animal movement with TMB. To facilitate its uptake, we make it available through the R package swim.     

Temperature niche conservatism and strong genetic structure are involved in the trans-Panamanian colonization of Matudaea (Hamamelidaceae) to Andean forests

Matudaea is the only genus of the Hamamelidaceae found in South America. The genus is composed by two extant species, M. trinervia, from Mexico and Costa Rica, and Matudaea colombiana, from the Colombian Andes; additional fossil records are present in Central Europe. Population genetics, molecular phylogenetics and niche modelling approaches were applied to explain processes related with the trans-Panamanian M. trinervia/M. colombiana split and the putative colonization of the latter to the northern Andes. The split between the two Matudaea species was estimated during Middle Miocene. The colonization of Matudaea into South America could have been facilitated by the closure of the Isthmus of Panama and the global decreasing of temperature during Miocene. Five haplotypes of M. colombiana were identified, which show an eastwards decline of genetic diversity and suggest a founder effect in the colonization of Eastern cordillera of the Colombian Andes. We detected a niche conservatism signal between the two Matudaea species related with Temperature of Coldest Month and Mean Temperature of Driest Quarter bioclimatic variables; this signal might be related to the narrow altitudinal range occupied by the two species.     

Epidemiology of skeletal eroding band on the Great Barrier Reef and the role of injury in the initiation of this widespread coral disease

Skeletal eroding band (SEB), which manifests as dense aggregations of the ciliate Halofolliculina corallasia, was the first coral disease described from the Indo-Pacific. Little is known about its etiology or impact. This study describes the distribution, prevalence and host range of SEB on a 500 km extent of the Great Barrier Reef (GBR), together with in situ rates of progression and infection following experimental injury. SEB occurred on 90–100% of reefs surveyed (n=18) in each of 3 years, demonstrating that SEB is widely distributed and persistent. SEB had the highest prevalence of any disease, affecting approximately 2% of 283,486 scleractinians and hydrocorals surveyed. Its host range was large, affecting 12 families and at least 82 scleractinian species, as well as the hydrocoral, Millepora. Corals in the families Pocilloporidae and Acroporidae were most susceptible, the former being up to five times more susceptible than other families. Progressive tissue loss was recorded on 95% of Acropora muricata colonies monitored (n = 18), with rates of SEB progression averaging ∼2 mm/day. Injury experiments demonstrated that H. corallasia, the putative pathogen of SEB, readily colonised recently exposed coral skeleton in the absence of a vector, but did not colonise intact coral tissue. Invading ciliates failed to form band-like aggregations associated with progressive tissue loss on any of three coral species tested experimentally, suggesting that, while H. corallasia readily colonises recently exposed coral skeleton, it may not be sufficient in itself to cause tissue mortality. Interactions with additional agents or factors, increasing ciliate virulence or lowering disease resistance of coral hosts may be required before halofolliculinid infections become associated with tissue loss.     

帕金森病模型研究进展

帕金森病（Parkinson’s disease，PD）是一种常见于中老年的神经退行性疾病，其特征性的病理改变为黑质纹状体多巴胺能神经元选择性缺失以及胞浆内涵物Lewy小体的形成。PD的发病机制目前尚不清楚，但已经明确环境因素和遗传因素在PD的发病中起重要作用。为阐明PD的病理生理机制，进一步探索新的治疗手段，迫切需要与PD密切相似的模型。本文将就目前发展的各种PD模型做一综述。     

Piping Plover Chick Foraging,Growth, and Survival in the Great Plains

Abstract: We tested the hypothesis that piping plover (Charadrius melodus) habitat quality and chick survival on the Missouri River, USA, were lower on a cold-water reservoir and downstream from a hypolimnetic (cold-water) release dam with diel water fluctuations (Garrison Dam) than downstream from an epilimnetic dam (Gavins Point Dam). Plovers in adjacent alkali wetlands provided an index to the maximum reproductive potential in the region. Chicks gained weight more rapidly in the alkali wetlands than on epilimnetic and hypolimnetic river reaches. Invertebrate numbers and biomass were higher in the wetlands and epilimnetic reach, but chick survival was lower on the epilimnetic reach. Thus, piping plovers adapted to a variety of prey densities, and other factors, likely predation, reduced survival rates in the epilimnetic reach. Temporal and spatial variability in site quality indices suggests the need for a regional management strategy with different strategies at each site. Managers can minimize effects of local fluctuations in resource abundance and predators by ensuring protection of or creating geographically dispersed habitat. (JOURNAL OF WILDLIFE MANAGEMENT 72(3):682–687; 2008)     

The life-history strategy of deepwater sculpin, Myoxocephalus thompsoni (Girard), in Lake Michigan: dispersal and settlement patterns during the first year of life

Deepwater sculpin, Myoxocephalus thompsoni (Girard), were sampled from six stations from the 15–100 m depth contours in Lake Michigan between April 1983 and July 1984. In south-eastern Lake Michigan M. thompsoni lay benthic eggs in offshore waters, which hatch between November and August, with peak hatching in March. Abundance of larvae in pelagic samples was higher offshore than inshore, but larval size was greater and development more advanced at inshore stations, indicating an inshore movement after hatching. Larvae reached metamorphosis at 20 mm and settled to the bottom beginning in July. Pelagic larvae 20–40 mm were found in the lower water column at all stations, but newly settled individuals were only captured with bottom trawls at inshore locations (≤60 m depth). Data from ichthyoplankton and bottom trawl samples in 1983 and 1984 indicated that locations for successful settlement of larvae to the bottom extended only as deep as the shallowest fringe of the adult population (> 50 m in 1983). In 1983, maximum density of larvae reached 0.4 individuals m⁻³ by June. Survival from the pelagic larval stage to the demersal young-of-year stage in 1983/1984 was c . 0.1–0.4%. The specific mechanism of mortality at the time of transition to a demersal habit has not been determined.     

Latitudinal variation in blue tit and great tit nest characteristics indicates environmental adjustment

Aim The laying of eggs and the building of a nest structure to accommodate them are two of the defining characteristics of members of the class Aves. Nest structures vary considerably across avian taxa and for many species the structure of the completed nest can have important consequences both for parents and their offspring. While nest characteristics are expected to vary adaptively in response to environmental conditions, large‐scale spatial variation in nest characteristics has been largely overlooked. Here, we examine the effects of latitudinal variation in spring temperatures on nest characteristics, including insulatory properties, and reproductive success of blue tits, Cyanistes caeruleus, and great tits, Parus major. Location Great Britain. Methods Nests and reproductive data were collected from seven study sites, spread over 5° of latitude. The nest insulatory properties were then determined before the nests were separated into nest base material and cup lining material. Results As spring temperatures increased with decreasing latitude, the mass of the nest base material did not vary in either species, while the mass of the cup lining material and nest insulatory properties decreased in both species. This suggests that in response to increasing temperatures the breeding female reduces the mass of the cup lining material, thereby maintaining an appropriate microclimate for incubating and brooding. The mean first egg date of both species advanced with decreasing latitude and increasing spring temperatures, although clutch size and brood size at hatching and fledging did not vary. Main conclusions This is the first study to demonstrate that the nest‐construction behaviour of birds varies in response to large‐scale spatial variation in ambient temperatures. Therefore, nest composition reliably indicates environmental conditions and we suggest that studies of nest structure may be sentinels for the early signs of rapid climate change.     

丙型肝炎病毒基因组结构及功能

丙型肝炎病毒（hepatitis C virus, HCV）是单股正链的RNA 病毒，全长为9.6 kb，包括1个大的开放阅读框（ORF）和两侧的5′，3′非编码区（UTRs）.核糖体通过进入HCV 5′UTR 端的内部核糖体进入位点（IRES）,将HCV基因组翻译成1个聚蛋白前体.前体聚蛋白被宿主和病毒的蛋白酶共同切割成为若干个具有独立功能的HCV蛋白，根据功能的不同分别命名为C、E1、E2、p7、NS2、NS3、NS4A、NS4B、NS5A 和NS5B，它们不但在HCV的生活史中发挥着重要的作用，也影响着宿主细胞的信号传导、凋亡及物质代谢等一系列生化过程.近年来，随着HCV体外细胞摸型的不断发展，其病毒分子生物学方面的研究取得了很大的进展.本文从基因组结构及其编码的蛋白功能等方面阐述了HCV病毒的研究进展，为致病机理的研究及抗HCV药物的开发和疫苗研制等提供理论基础.     

川芎嗪对慢性压迫性损伤大鼠神经病理痛行为学的影响

目的探讨川芎嗪对慢性压迫性损伤（CCI）大鼠行为学的影响。方法建立大鼠坐骨神经CCI神经病理痛模型,取40只雄性大鼠随机分成4组,Ⅰ组为空白对照组,Ⅱ组为假手术组,Ⅲ组为CCI＋川芎嗪治疗组,Ⅲ组在术后第1天开始腹腔注射100 mg/kg川芎嗪注射液,Ⅳ组为CCI手术组。分别于术前（0 d）及术后1、3、5、7、91、1、14 d以von Frey细丝法和热辐射法测定机械缩足反射阈值（mechanical withdrawal threshold,MWT）和热缩足反射潜伏期（thermal withdrawal latency,TWL）,观察CCI大鼠神经病理痛的行为学变化。结果术后14 d,Ⅳ组和I、Ⅱ、Ⅲ组相比较,大鼠后爪的机械和热痛敏阈值明显降低（P〈0.01）;I、Ⅱ、Ⅲ组之间相比,大鼠后爪的机械和热痛敏阈值差异没有显著性（P〉0.05）。结论川芎嗪可以缓解CCI大鼠的慢性神经病理痛行为学表现。     

5′-磷酸腺苷对小鼠脾细胞氧化应激损伤的保护作用

目的研究5′-磷酸腺苷（5′-AMP）体外抗氧化和对体外氧化损伤脾细胞的损伤修复能力。方法用化学比色法测定5′-AMP体外清除二苯代苦味酰基自由基（DPPH自由基）的能力;建立过氧化氢（H2O2）氧化损伤体外培养小鼠脾细胞模型,用MTT法检测5′-AMP修复受损伤脾细胞的作用,并分析其对细胞抗氧化体系及抗氧化能力的影响。结果5′-AMP具有剂量依赖性的体外抗氧化和清除活性氧能力,添加0.5mmol/L、1mmol/L、5mmol/L和10mmol/L5′-AMP均能显著修复H2O2诱导的脾细胞氧化损伤（P〈0.05）,总抗氧化能力和抗氧化酶类活力（P〈0.01）,5′-AMP添加量大于1mmol/L时,可显著降低丙二醛（MDA）含量（P〈0.01）。其细胞培养液的氧自由基（ROS）水平逐渐降低,5′-AMP添加量为10mmol/L时,ROS水平接近对照组水平。结论5′-磷酸腺苷能显著修复氧化损伤,具有显著的抗氧化作用。