Adaptation and Cryptic Pseudogenization in Penguin Toll-Like Receptors

Penguins (Sphenisciformes) are an iconic order of flightless, diving seabirds distributed across a large latitudinal range in the Southern Hemisphere. The extensive area over which penguins are endemic is likely to have fostered variation in pathogen pressure, which in turn will have imposed differential selective pressures on the penguin immune system. At the front line of pathogen detection and response, the Toll-like receptors (TLRs) provide insight into host evolution in the face of microbial challenge. TLRs respond to conserved pathogen-associated molecular patterns and are frequently found to be under positive selection, despite retaining specificity for defined agonist classes. We undertook a comparative immunogenetics analysis of TLRs for all penguin species and found evidence of adaptive evolution that was largely restricted to the cell surface-expressed TLRs, with evidence of positive selection at, or near, key agonist-binding sites in TLR1B, TLR4, and TLR5. Intriguingly, TLR15, which is activated by fungal products, appeared to have been pseudogenized multiple times in the Eudyptes spp., but a full-length form was present as a rare haplotype at the population level. However, in vitro analysis revealed that even the full-length form of Eudyptes TLR15 was nonfunctional, indicating an ancestral cryptic pseudogenization prior to its eventual disruption multiple times in the Eudyptes lineage. This unusual pseudogenization event could provide an insight into immune adaptation to fungal pathogens such as Aspergillus, which is responsible for significant mortality in wild and captive bird populations.     

Causes,temporal trends,and the effects of urbanization on admissions of wild raptors to rehabilitation centers in England and Wales

Data from wildlife rehabilitation centers (WRCs) can provide on‐the‐ground records of causes of raptor morbidity and mortality, allowing threat patterns to be explored throughout time and space. We provide an overview of native raptor admissions to four WRCs in England and Wales, quantifying the main causes of morbidity and mortality, trends over time, and associations between threats and urbanization between 2001 and 2019. Throughout the study period, 14 raptor species were admitted totalling 3305 admission records. The Common Buzzard (Buteo buteo; 31%) and Tawny Owl (Strix aluco; 29%) were most numerous. Relative to the proportion of breeding individuals in Britain and Ireland, Peregrine Falcons (Falco peregrinus), Little Owls (Athene noctua), and Western Barn Owls (Tyto alba) were over‐represented in the admissions data by 103%, 73%, and 69%, respectively. Contrastingly Northern Long‐eared Owls (Asio otus), Western Marsh Harriers (Circus aeruginosus), and Merlin (Falco columbarius) were under‐represented by 187%, 163%, and 126%, respectively. Across all species, vehicle collisions were the most frequent anthropogenic admission cause (22%), and orphaned young birds (10%) were most frequent natural cause. Mortality rate was highest for infection/parasite admissions (90%), whereas orphaned birds experienced lowest mortality rates (16%). For one WRC, there was a decline in admissions over the study period. Red Kite (Milvus milvus) admissions increased over time, whereas Common Buzzard and Common Kestrel admissions declined. There were significant declines in the relative proportion of persecution and metabolic admissions and an increase in orphaned birds. Urban areas were positively associated with persecution, building collisions, and unknown trauma admissions, whereas vehicle collisions were associated with more rural areas. Many threats persist for raptors in England and Wales, however, have not changed substantially over the past two decades. Threats associated with urban areas, such as building collisions, may increase over time in line with human population growth and subsequent urban expansion.     

The ecology of the banded civet (Hemigalus derbyanus) in Southeast Asia with implications for mesopredator release,zoonotic diseases,and conservation

Habitat loss and degradation threaten forest specialist wildlife species, but some generalist mesopredators exploit disturbed areas and human‐derived food, which brings them into closer contact with humans. Mesopredator release is also important for human health for known zoonotic disease reservoirs, such as Asian civets (Viverridae family), since this group includes the intermediator species for the SARS‐CoV‐1 outbreak. Here we use camera trapping to evaluate the habitat associations of the widespread banded civet (Hemigalus derbyanus) across its range in Southeast Asia. At the regional scale, banded civet detections among published studies were positively associated with forest cover and negatively associated with human population. At the local scale (within a landscape), hierarchical modeling of new camera trapping showed that abundance was negatively associated with forest loss and positively associated with distance to rivers. These results do not support mesopredator release and suggest a low likelihood overlap with humans in degraded habitats and, therefore, a low risk of zoonotic disease transmission from this species in the wild. We also estimate that banded civet distribution has contracted to under 21% of its currently recognized IUCN Red List range, only 12% of which falls within protected areas, and a precipitous recent decline in population size. Accordingly, we suggest the banded civet''s Red List status should be re‐evaluated in light of our findings.     

Browsing herbivores improve the state and functioning of savannas: A model assessment of alternative land‐use strategies

Changing climatic conditions and unsustainable land use are major threats to savannas worldwide. Historically, many African savannas were used intensively for livestock grazing, which contributed to widespread patterns of bush encroachment across savanna systems. To reverse bush encroachment, it has been proposed to change the cattle‐dominated land use to one dominated by comparatively specialized browsers and usually native herbivores. However, the consequences for ecosystem properties and processes remain largely unclear. We used the ecohydrological, spatially explicit model EcoHyD to assess the impacts of two contrasting, herbivore land‐use strategies on a Namibian savanna: grazer‐ versus browser‐dominated herbivore communities. We varied the densities of grazers and browsers and determined the resulting composition and diversity of the plant community, total vegetation cover, soil moisture, and water use by plants. Our results showed that plant types that are less palatable to herbivores were best adapted to grazing or browsing animals in all simulated densities. Also, plant types that had a competitive advantage under limited water availability were among the dominant ones irrespective of land‐use scenario. Overall, the results were in line with our expectations: under high grazer densities, we found heavy bush encroachment and the loss of the perennial grass matrix. Importantly, regardless of the density of browsers, grass cover and plant functional diversity were significantly higher in browsing scenarios. Browsing herbivores increased grass cover, and the higher total cover in turn improved water uptake by plants overall. We concluded that, in contrast to grazing‐dominated land‐use strategies, land‐use strategies dominated by browsing herbivores, even at high herbivore densities, sustain diverse vegetation communities with high cover of perennial grasses, resulting in lower erosion risk and bolstering ecosystem services.     

Habitat occupancy of sloth bear Melursus ursinus in Chitwan National Park,Nepal

Mammals have experienced a massive decline in their populations and geographic ranges worldwide. The sloth bear, Melursus ursinus (Shaw, 1791), is one of many species facing conservation threats. Despite being endangered in Nepal, decades of inattention to the situation have hindered their conservation and management. We assessed the distribution and patterns of habitat use by sloth bears in Chitwan National Park (CNP), Nepal. We conducted sign surveys from March to June, 2020, in 4 × 4 km grids (n = 45). We collected detection/non‐detection data along a 4‐km trail that was divided into 20 continuous segments of 200 m each. We obtained environmental, ecological, and anthropogenic covariates to understand determinants of sloth bear habitat occupancy. The data were analyzed using the single‐species single‐season occupancy method, with a spatially correlated detection. Using repeated observations, these models accounted for the imperfect detectability of the species to provide robust estimates of habitat occupancy. The model‐averaged occupancy estimate for the sloth bear was 69% and the detection probability was 0.25. The probability of habitat occupancy by sloth bears increased with the presence of termites and fruits and in rugged, dry, open, undisturbed habitats. Our results indicate that the sloth bear is elusive, functionally unique, and widespread in CNP. Future conservation interventions and action plans aimed at sloth bear management must adequately consider their habitat requirements.     

Maternal and sibling factors induce dormancy in dimorphic seed pairs of Aegilops triuncialis

Germination and emergence are stimulated by environmental cues, but strongly influenced by maternal controls. However, traits related to seed dispersal may have important influences on germination as well. For example, the sibling rivalry hypothesis suggests that germination may be inhibited when sibling seeds remain within a single dispersal unit. These two influences on germination suggest different, and possibly conflicting, evolutionary strategies for optimizing individual fitness. Using an invasive annual grass that produces dispersal units with dimorphic seeds, I found significant reductions in seedling emergence that suggested the presence of both strong maternal and sibling influences on the germination of the smaller seed of dimorphic pairs. Both influences were capable of nearly complete germination suppression of the small seed, but there was no strong evidence for a hierarchy among the two factors. The maternal effect is consistent with a bet-hedging strategy for survival in variable environments where resource availability can be unpredictable, but the sibling effect likely represents a mechanism for reducing competition between closely related individuals, particularly under conditions of resource limitation.     

Copulation reduces male but not female longevity in Saltella sphondylli (Diptera: Sepsidae)

Mating more than once is extremely costly for females in many species, making the near ubiquity of polyandry difficult to understand. However, evidence of mating costs for males is much rarer. We investigated the effects of copulation on longevity of male and female flies (Saltella sphondylli). We also scrutinized potential fecundity and fertility benefits to females with differing mating history. Copulation per se was found to decrease the longevity of males but not that of females. However, when females were allowed to lay eggs, females that mated died earlier than virgin females, indicating costs of egg production and/or oviposition. Thus, although longevity costs of copulation are higher for males, reproduction is nevertheless costly for females. We also found no differences in fecundity or fertility relative to female mating history. Results suggest that polyandry may be driven by minor costs rather than by major benefits in this species.     

Hybridization and regional sex ratios in Nemophila menziesii

I tested whether a region of high female frequencies in the gynodioecious plant, Nemophila menziesii, may be due to hybridization between regionally distributed populations with different corolla colours. I crossed plants in the greenhouse from populations with different corolla colours and found that hybrid crosses yielded higher frequencies of females than within-colour crosses. In the field, I found that populations with high female frequencies had intermediate mean corolla colours and higher variance in corolla colour, two traits suggesting hybridization. Nemophila menziesii has nuclear-cytoplasmic sex inheritance, thus if populations with different corolla colours are fixed for different male-sterile cytoplasms and matching nuclear restorer alleles, hybridization between populations with different corolla colour should yield high frequencies of females. Two populations that are all hermaphroditic in the field segregated females in hybrid crosses suggesting that field populations may contain sex ratio distorters but appear undistorted, a prediction of genomic conflict theory.     

关于物种濒危等级标准之探讨--对IUCN物种濒危等级的思考

为了保存地球上的生物多样性,我们需要根据物种的种群数量与分布、种群数量波动与分布区下降速率来评定濒危物种的濒危等级,并针对物种的濒危等级提出具体的保护措施。1994年11月,IUCN第40次理事会会议正式通过了经过修订的Mace-Lande物种濒危等级标准作为IUCN物种濒危等级标准。IUCN濒危物种红色名录虽然不是国际法和国家法律,但是对于政府间组织、非政府组织的保护决策以及各国的自然法律法规的制定有着深远的影响,在保护生物学理论研究中也发挥了一定作用。我们在研究制定中国水生野生生物濒危等级标准时发现,如果直接应用IUCN物种濒危等级标准评定水生野生生物濒危等级将存在一些问题。如：(1)如何区别对待那些本来就数量稀少、分布区狭窄的物种和那些由于人类活动而导致其种群数量与生境面积急剧下降的物种?(2)不同的动物类群能否应用同一濒危标准尺度?(3)如何区别对待物种边缘分布区和核心分布区的种群数量与密度的差异?(4)如何处理种群的局部灭绝、局部濒危?(5)一些濒危物种在野生环境中濒危,但是这些物种可以人工繁殖,如何处理可以人工繁殖的濒危物种?(6)如果没有种群与栖息地的精确历史资料和统计数据,怎样应用物种的濒危标准评估其濒危等级?在实践中,我们针对这些问题提出了解决方案。考虑与国际流行的IUCN物种濒危等级标准接轨,我们提出来一个由“无危”、“值得关注”、“受胁”、“濒危”和“灭绝”等5个级构成的濒危等级系统,其中“值得关注”、“受胁”、“濒危”又分为“一般”与“高度”两个亚等级。我们提出应区分“生态濒危物种”、“进化濒危物种”;对于不同生物类群,应区分物种的生活史对策,制定不同生活史物种的濒危标准。对于r-对策物种,引入“经济灭绝”这一等级,将这一等级对应于“受胁”等级,以解决缺少物种数量的统计数据和历史数据这一难题;区别对待特有物种,将其濒危等级提升一等;引进集合种群(metapopulation)概念,将集合种群的局域种群(local population)作为“个体”对待。     

Costs and benefits of evolving under experimentally enforced polyandry or monogamy

Reproduction has classically been viewed as a predominantly cooperative process. However, over the last 20 years this concept has steadily yielded ground to one of continual conflict in which the interests of the sexes are typically discordant. Within this framework, males and females are seen to be locked into a perpetual arms race, each adaptation by one sex promoting the evolution of countermeasures in the other sex. However, under strict genetic monogamy, the interests of the sexes become congruent, and hence antagonistic coevolution does not occur. We subjected the fly Sepsis cynipsea, a species with conspicuous sexual conflict, to experimentally enforced monogamy or polyandry for 29 generations and evaluated the microevolutionary consequences. We found that there were longevity costs to females consistent with sexually antagonistic coevolution. However, our measure of female fitness, offspring emergence, did not differ between treatments, even though life-history characters such as fertility and fecundity did. Results are discussed in terms of costs and benefits of sexual selection and sexual conflict.