Nest survival in year‐round breeding tropical red‐capped larks Calandrella cinerea increases with higher nest abundance but decreases with higher invertebrate availability and rainfall

Nest survival is critical to breeding in birds and plays an important role in life‐history evolution and population dynamics. Studies evaluating the proximate factors involved in explaining nest survival and the resulting temporal patterns are biased in favor of temperate regions. Yet, such studies are especially pertinent to the tropics, where nest predation rates are typically high and environmental conditions often allow for year‐round breeding. To tease apart the effects of calendar month and year, population‐level breeding activity and environmental conditions, we studied nest survival over a 64‐month period in equatorial, year‐round breeding red‐capped larks Calandrella cinerea in Kenya. We show that daily nest survival rates varied with time, but not in a predictable seasonal fashion among months or consistently among years. We found negative influences of flying invertebrate biomass and rain on nest survival and higher survival of nests when nests were more abundant, which suggests that nest predation resulted from incidental predation. Although an increase in nest predation is often attributed to an increase in nest predators, we suggest that in our study, it may be caused by altered predator activity resulting from increased activity of the primary prey, invertebrates, rather than activity of the red‐capped larks. Our results emphasize the need to conduct more studies in Afro‐tropical regions because proximate mechanisms explaining nest predation can be different in the unpredictable and highly variable environments of the tropics compared with the relatively predictable seasonal changes found in temperate regions. Such studies will aid in better understanding of the environmental influences on life‐history variation and population dynamics in birds.     

Lifelong foraging and individual specialisation are influenced by temporal changes of resource availability

Resource availability largely determines the distribution and behaviour of organisms. In plant–pollinator communities, availability of floral resources may change so rapidly that pollinator individuals can benefit from switching between multiple resources, i.e. different flowering plant species. Insect pollinator individuals of a given generation often occur in different time windows during the reproductive season. This temporal variation in individual occurrences, together with the rapidly changing resource availability, may lead individuals of the same population to encounter and use different resources, resulting in an apparent individual specialisation. We hypothesized, that 1) individual pollinators change their resource use (flower visitation) during their lifetime according to the changing availability of floral resources, and that 2) temporal variation in individual occurrences of pollinators and in resource availability will partly explain individual specialisation. To test these hypotheses, we observed flower visitations of individually marked clouded Apollo butterflies Parnassius mnemosyne during one reproductive season. We found temporal changes in lifetime individual resource use that followed the changes in resource availability, indicating that butterflies can adjust foraging to varying resource availability. Individuals differed considerably in their resource use. This variation was partly explained by temporal variation in both floral resource availability and temporal occurrence of individual butterflies. We suggest the butterfly as a sequential specialist, i.e. short‐term specialist and long‐term generalist. This foraging plasticity can be essential for short‐living insect pollinators in rapidly changing environments. Although flowering dynamics do not fully explain the variability in foraging, our results highlight the importance of temporal dimension in resource use studies. Ultimately, the relative pace of environmental change compared to individual lifespan may be a key factor in resource use plasticity.     

Growth of the tropical Pinus kesiya as influenced by climate and nutrient availability along an elevational gradient

与温带地区相比,人们对在热带山脉中,尤其是热带针叶林中,沿海拔梯度的个体树种生长减少的原因知之甚少。我们的研究目的是检验气候或土壤条件是否会导致在高海拔分布的卡西亚松(Pinus kesiya,一种在南亚和东南亚广泛分布的松树)的生长减少。我们对越南中南部山脉中沿海拔梯度约在900~2000米之间的卡西亚松的树干直径增量和其年轮中13C(△13C)的同位素判别进行分析。同时确定其生长与△13C、气候和土壤变量的关系。研究发现,树木的断面积生长量(BAI)与温度或降水之间没有一致的相关关系。相反,沿海拔梯度,我们发现BAI与△13C以及与上层矿质土壤的C/N比和δ15N特征呈显著负相关。BAI与土壤中有效磷(Pa)和“碱性”阳离子(钙、镁、钾)的浓度呈正相关。我们的结论是,较高海拔下的较低温度会对树木生长产生间接影响,主要通过产生较高的C/N比并降低氮(N)和P矿化率而产生作用,而这些影响因其他负面反馈而进一步受到阻碍。主要包括：降水增加的淋溶作用而导致较低浓度的“碱性”阳离子以及较高海拔土壤矿化的N和P的有效性降低。本研究结果可以进一步解释卡西亚松的最高生长极限以及该物种在其他山区出现的情况     

Specific alleles at immune genes,rather than genome‐wide heterozygosity,are related to immunity and survival in the critically endangered Attwater's prairie‐chicken

The negative effects of inbreeding on fitness are serious concerns for populations of endangered species. Reduced fitness has been associated with lower genome‐wide heterozygosity and immune gene diversity in the wild; however, it is rare that both types of genetic measures are included in the same study. Thus, it is often unclear whether the variation in fitness is due to the general effects of inbreeding, immunity‐related genes or both. Here, we tested whether genome‐wide heterozygosity (20 990 SNPs) and diversity at nine immune genes were better predictors of two measures of fitness (immune response and survival) in the endangered Attwater's prairie‐chicken (Tympanuchus cupido attwateri). We found that postrelease survival of captive‐bred birds was related to alleles of the innate (Toll‐like receptors, TLRs) and adaptive (major histocompatibility complex, MHC) immune systems, but not to genome‐wide heterozygosity. Likewise, we found that the immune response at the time of release was related to TLR and MHC alleles, and not to genome‐wide heterozygosity. Overall, this study demonstrates that immune genes may serve as important genetic markers when monitoring fitness in inbred populations and that in some populations specific functional genes may be better predictors of fitness than genome‐wide heterozygosity.     

Plant sexual systems and a review of the breeding system studies in the Caatinga, a Brazilian tropical dry forest

BACKGROUNDS AND AIMS: The reproductive biology of a community can provide answers to questions related to the maintenance of the intraspecific pollen flow and reproductive success of populations, sharing and competition for pollinators and also questions on conservation of natural habitats affected by fragmentation processes. This work presents, for the first time, data on the occurrence and frequency of plant sexual systems for Caatinga communities, and a review of the breeding system studies of Caatinga species. METHODS: The sexual systems of 147 species from 34 families and 91 genera occurring in three Caatinga areas in north-eastern Brazil were analysed and compared with worldwide studies focusing on reproductive biology of different tropical communities. KEY RESULTS: The frequency of hermaphrodite species was 83.0 % (122 species), seven of these (or 4.8 % of the total) being heterostylous. Monoecy occurred in 9.5 % (14) of the species, and andromonoecy in 4.8 % (seven). Only 2.7 % (four) of the species were dioecious. A high percentage of hermaphrodite species was expected and has been reported for other tropical ecosystems. With respect to the breeding system studies with species of the Caatinga, the authors' data for 21 species and an additional 18 species studied by others (n = 39) revealed a high percentage (61.5 %) of obligatory self-incompatibility. Agamospermy was not recorded among the Caatinga studied species. CONCLUSIONS: The plant sexual systems in the Caatinga, despite the semi-arid climate, are similar to other tropical dry and wet forest communities, including those with high rainfall levels, except for the much lower percentage of dioecious species. The high frequency of self-incompatible species is similar to that reported for Savanna areas in Brazil, and also for dry (deciduous and semideciduous) and humid tropical forest communities.     

Long‐term mammal and nocturnal bird trends are influenced by vegetation type,weather and climate in temperate woodlands

Many studies have documented the individual effects of variables such as vegetation, long‐term climate and short‐term weather on biodiversity. Few, however, have explicitly explored how interactions among these major drivers can influence species abundance. We used data from a 15‐year study (2002–2017) in the endangered temperate woodlands of south‐eastern Australia to test hypotheses associated with the effects of vegetation type, long‐term climate and short‐term weather on population trajectories of seven species of (largely) nocturnal mammals and birds. Despite prolonged drought conditions, there was a significant increase in the abundance of some species over time (e.g. the Eastern Grey Kangaroo). It is possible that destocking of domestic livestock may have reduced competition with Kangaroos, thereby facilitating increases in abundance. The Common Brushtail Possum and Common Ringtail Possum were significantly less likely to occur in replanted woodlands, possibly because of the paucity of nesting sites. We found no evidence that replanted woodlands are refuges for exotic pest species like the European Rabbit and Red Fox. Short‐ and long‐term rainfall and vegetation type had important independent and combined effects on animal abundance. That is, responses to periods of high short‐term rainfall were dependent on vegetation type and whether sites occurred in long‐term climatically wet versus climatically dry locations. For example, the Red Fox responded positively to high levels of short‐term rainfall, but only at climatically dry sites. Our results highlight the complementary value of different vegetation types across the landscape and the context‐specific responses of animals to short‐term fluctuations in moisture availability. They also underscore the value of long‐term monitoring at a landscape scale for examining how multiple interacting factors influence trends in animal abundance.     

Molecular breeding of genes, pathways and genomes by DNA shuffling

Existing methods for optimization of sequences by random mutagenesis generate libraries with a small number of mostly deleterious mutations, resulting in libraries containing a large fraction of non-functional clones that explore only a small part of squence space. Large numbers of clones need to be screened to find the rare mutants with improvements. Library display formats are useful to screen very large libraries but impose screening limitations that limit the value of this approach for most commercial applications. By contrast, in both classical breeding and in DNA shuffling, natural diversity is permutated by homologous recombination, generating libraries of very high quality, from which improved clones can be identified with a small number of complex screens. Given that this small number of screens can be performed under the conditions of actual use of the product, commercially relevant improvements can be reliably obtained.     

Variation in food availability mediate the impact of density on cannibalism,growth, and survival in larval yellow spotted mountain newts (Neurergus microspilotus): Implications for captive breeding programs

In this study, we examined cannibalistic behavior, growth, metamorphosis, and survival in larval and post‐metamorph endangered yellow spotted mountain newts Neurergus microspilotus hatched and reared in a captive breeding facility. We designed a 2 × 2 factorial experiment, crossing two levels of food with two levels of density including high food/high density, high food/low density, low food/high density, and low food/low density. The level of cannibalistic behavior (including the loss of fore and hind limbs, missing toes, tail, gills, body damage, and whole body consumption) changed as the larvae grew, from a low level during the first 4 weeks, peaking from weeks 7 to 12, and then dropped during weeks 14–52. Both food level and density had a significant effect on cannibalism. The highest frequency of cannibalism was recorded for larvae reared in the low food/high density and lowest in high food/low density treatments. Growth, percent of larval metamorphosed, and survival were all highest in the high food/low density and lowest in low food/high density treatment. Food level had a significant effect on growth, metamorphosis, and survival. However, the two levels of density did not influence growth and metamorphosis but showed a significant effect on survival. Similarly, combined effects of food level and density showed significant effects on growth, metamorphosis, and survival over time. Information obtained from current experiment could improve productivity of captive breeding facilities to ensure the release of adequate numbers of individuals for reintroduction programs. Zoo Biol. 35:513–521, 2016. © 2016 The Authors. Zoo Biology published by Wiley Periodicals, Inc.     

Fine‐scale habitat use in Indo‐Pacific humpback dolphins,Sousa chinensis,may be more influenced by fish rather than vessels in the Pearl River Estuary,China

Shifts in habitat use and distribution patterns in dolphins are often concerns that can result from habitat degradation. We investigated how potential changes to a habitat from human activity may alter dolphin distributions within Lingding Bay in the Pearl River Estuary, China, by studying the relationship between fish choruses, vessel presence and Indo‐Pacific humpback dolphin (Sousa chinensis) detection rates. Analyses revealed temporal and spatial variation within fish choruses, vessel presence and dolphin detection rates. After accounting for any temporal autocorrelation, correlations between fish choruses and dolphin detection rates were also found; however, no relationship between fish choruses and vessel presence or dolphin detection rates and vessel presence were observed. Furthermore, fewer dolphins were detected at sites where fish activity was less intense. Thus fish activity, rather than vessels, may be a key factor influencing the distribution of the dolphins within the estuary. These findings emphasize the risk of potential shifts in habitat use for Indo‐Pacific humpback dolphins due to detrimental changes to prey availability and dolphin feeding grounds from human activity, such as overfishing and coastal developments, within the estuary. This is a critical conservation issue for this dolphin population that is facing intense anthropogenic pressure.     

In adult onset myositis, the presence of interstitial lung disease and myositis specific/associated antibodies are governed by HLA class II haplotype, rather than by myositis subtype

The aim of this study was to investigate HLA class II associations in polymyositis (PM) and dermatomyositis (DM), and to determine how these associations influence clinical and serological differences. DNA samples were obtained from 225 UK Caucasian idiopathic inflammatory myopathy patients (PM = 117, DM = 108) and compared with 537 randomly selected UK Caucasian controls. All cases had also been assessed for the presence of related malignancy and interstitial lung disease (ILD), and a number of myositis-specific/myositis-associated antibodies (MSAs/MAAs). Subjects were genotyped for HLA-DRB1, DQA1 and DQB1. HLA-DRB1*03, DQA1*05 and DQB1*02 were associated with an increased risk for both PM and DM. The HLA-DRB1*03-DQA1*05-DQB1*02 haplotype demonstrated strong association with ILD, irrespective of myositis subtype or presence of anti-aminoacyl-transfer RNA synthetase antibodies. The HLA-DRB1*07-DQA1*02-DQB1*02 haplotype was associated with risk for anti-Mi-2 antibodies, and discriminated PM from DM (odds ratio 0.3, 95% confidence interval 0.1-0.6), even in anti-Mi-2 negative patients. Other MSA/MAAs showed specific associations with other HLA class II haplotypes, irrespective of myositis subtype. There were no genotype, haplotype or serological associations with malignancy. The HLA-DRB1*03-DQA1*05-DQB1*02 haplotype associations appear to not only govern disease susceptibility in Caucasian PM/DM patients, but also phenotypic features common to PM/DM. Though strongly associated with anti-Mi-2 antibodies, the HLA-DRB1*07-DQA1*02-DQB1*02 haplotype shows differential associations with PM/DM disease susceptibility. In conclusion, these findings support the notion that myositis patients with differing myositis serology have different immunogenetic profiles, and that these profiles may define specific myositis subtypes.     

In adult onset myositis, the presence of interstitial lung disease and myositis specific/associated antibodies are governed by HLA class II haplotype, rather than by myositis subtype

The Fcγ receptors play important roles in the initiation and regulation of many immunological and inflammatory processes, and genetic variants (FCGR) have been associated with numerous autoimmune and infectious diseases. The data in rheumatoid arthritis (RA) are conflicting and we previously demonstrated an association between FCGR3A and RA. In view of the close molecular proximity with FCGR2A, FCGR2B and FCGR3B, additional polymorphisms within these genes and FCGR haplotypes were examined to refine the extent of association with RA. Biallelic polymorphisms in FCGR2A, FCGR2B and FCGR3B were examined for association with RA in two well characterized UK Caucasian and North Indian/Pakistani cohorts, in which FCGR3A genotyping had previously been undertaken. Haplotype frequencies and linkage disequilibrium were estimated across the FCGR locus and a model-free analysis was performed to determine association with RA. This was followed by regression analysis, allowing for phase uncertainty, to identify the particular haplotype(s) that influences disease risk. Our results reveal that FCGR2A, FCGR2B and FCGR3B were not associated with RA. The haplotype with the strongest association with RA susceptibility was the FCGR3A–FCGR3B 158V-NA2 haplotype (odds ratio 3.18, 95% confidence interval 1.13–8.92 [P = 0.03] for homozygotes compared with all genotypes). The association was stronger in the presence of nodules (odds ratio 5.03, 95% confidence interval 1.44–17.56; P = 0.01). This haplotype was also more common in North Indian/Pakistani RA patients than in control individuals, but not significantly so. Logistic regression analyses suggested that FCGR3A remained the most significant gene at this locus. The increased association with an FCGR3A–FCGR3B haplotype suggests that other polymorphic variants within FCGR3A or FCGR3B, or in linkage disequilibrium with this haplotype, may additionally contribute to disease pathogenesis.     

The adult body size variation of Dryas iulia (Lepidoptera,Nymphalidae, Heliconiinae) in different populations is more influenced by temperature variation than by host‐plant availability during the seasons

The body size of insects is affected by environmental conditions during development and can present considerable intraspecific variations, which can be seen as an ultimate consequence/adaptation to environmental conditions. This paper evaluated whether the body size of the butterfly Dryas iulia from subtropical populations was influenced by changing climate conditions and food source availability during the seasons. The likely reasons behind body size variation were also investigated. First, field data on body size variation, host‐plant availability and climate fluctuation throughout the seasons were recorded. Then, the effects of host‐plant species and temperature on body size were analyzed by controlled experiments. Field data revealed that body size and host‐plant availability varied significantly through the seasons. Populations had the smallest body size during the spring and the biggest size during summer, whereas host‐plant availability was lower during winter and higher during spring. The controlled experiments revealed that both temperature and host‐plant had significant effect on the plasticity of body size. Larvae subjected to winter temperature treatment led to smaller butterflies when compared to immatures reared under summer temperature treatment, and larvae fed with Passiflora misera produced bigger adults when compared to larvae reared on Passiflora suberosa. The combination of data gathered in the field and in the laboratory suggests that seasonal body size variation in D. iulia is related mainly to differences in the temperatures to which larvae are subjected during development, while host‐plant shifts caused by differential availability of food through the seasons had slightly effects on the variation observed.