Network analysis of host–virus communities in bats and rodents reveals determinants of cross‐species transmission

Bats are natural reservoirs of several important emerging viruses. Cross‐species transmission appears to be quite common among bats, which may contribute to their unique reservoir potential. Therefore, understanding the importance of bats as reservoirs requires examining them in a community context rather than concentrating on individual species. Here, we use a network approach to identify ecological and biological correlates of cross‐species virus transmission in bats and rodents, another important host group. We show that given our current knowledge the bat viral sharing network is more connected than the rodent network, suggesting viruses may pass more easily between bat species. We identify host traits associated with important reservoir species: gregarious bats are more likely to share more viruses and bats which migrate regionally are important for spreading viruses through the network. We identify multiple communities of viral sharing within bats and rodents and highlight potential species traits that can help guide studies of novel pathogen emergence.     

Identifying conservation priorities when data are scanty: A case study with small mammals in Italy

Species prioritisation is an important component of conservation strategies. However, identifying species that are threatened is not easy for many taxa that lack detailed information on distribution and population trends. We propose a ranking system for small mammals, based on their degree of vulnerability and their conservation value. Scores were derived from data on life history traits and ecological requirements of individual species, with respect to their sensitivity to changes in landscape and the composition and qualities of ecosystems. Twelve variables were considered, related to the distribution, demography, ecological adaptability, and their endemism and taxonomic diversification. Rodents with the highest score values were either characteristic of mountain habitats (Apodemus alpicola, Chionomys nivalis and Marmota marmota), typical of lowlands (Micromys minutus) or forest species (dormice), and they were also short living, with few reproduction events. Top ranking Soricomorpha were endemic (Crocidura sicula, C. pachyura), range restricted (Sorex alpinus, Talpa caeca) and habitat specialists (Neomys fodiens, N. anomalus), and were further characterised by low reproduction, low dispersal ability, and restricted elevation range. The factors used in the score system were able to emphasise localised endemisms that could be recognised in the future whenever subspecies should be promoted to the rank of species. Soricomorpha, highlighted in the IUCN national red list as nearly threatened or for the absence of information, ranked at the top of our list. The methodological framework proposed here could be used when a pool of species needs to be evaluated for further investigation or conservation actions, helping by focusing on species that are more sensitive to habitat changes or have an intrinsic conservation value.     

贵州洋溪省级自然保护区翼手类物种多样性调查

2018年7月至2021年2月,采用栖息地调查法和网捕法对贵州洋溪省级自然保护区翼手目动物物种多样性及保护现状进行了调查。共记录到翼手目动物3科6属13种,包括蝙蝠科5种,菊头蝠科5种,蹄蝠科3种。按照中国动物地理区划,以东洋界种类为主,共有11种,另有2种为广布种。列入《中国生物多样性红色名录:哺乳动物》近危级(NT)7种、无危级(LC)物种6种;列入IUCN物种红色名录近危(NT)级1种,无危级(LC)12种。此次在洋溪自然保护区共调查了27个洞穴,其中20个洞穴有蝙蝠栖息。大蹄蝠(Hipposideros armiger)分布最广,在10个洞穴有分布;其次是皮氏菊头蝠(Rhinolophus pearsonii),在8个洞穴发现;小菊头蝠(R.pusillus)在7个洞穴有分布。对蝙蝠栖息洞穴的干扰情况进行调查发现,超过一半(55%,n=20)的洞穴存在人类干扰活动,如村民进洞游玩、在洞内饲养家畜、驱赶蝙蝠、进行祭祀活动以及破坏洞口等。建议对村民在洞内养殖家畜、游玩、驱赶蝙蝠等行为加以限制,并通过引导村民文明祭祀、对被封洞口进行疏通、对古老建筑进行修缮等方式,加强对该地区蝙蝠的保护。同时还建议对该保护区的蝙蝠及其栖息地进行长期监测。     

DNA barcoding in surveys of small mammal communities: a field study in Suriname

The performance of DNA barcoding as a tool for fast taxonomic verification in ecological assessment projects of small mammals was evaluated during a collecting trip to a lowland tropical rainforest site in Suriname. We also compared the performance of tissue sampling onto FTA CloneSaver cards vs. liquid nitrogen preservation. DNA barcodes from CloneSaver cards were recovered from 85% of specimens, but DNA degradation was apparent, because only 36% of sequence reads were long (over 600 bp). In contrast, cryopreserved tissue delivered 99% barcode recovery (97% > 600 bp). High humidity, oversampling or tissue type may explain the poor performance of CloneSaver cards. Comparison of taxonomic assignments made in the field and from barcode results revealed inconsistencies in just 3.4% of cases and most of the discrepancies were due to field misidentifications (3%) rather than sampling/analytical error (0.5%). This result reinforces the utility of DNA barcoding as a tool for verification of taxonomic identifications in ecological surveys, which is especially important when the collection of voucher specimens is not possible.     

Herbivory versus corallivory: are parrotfish good or bad for Caribbean coral reefs?

With coral cover in decline on many Caribbean reefs, any process of coral mortality is of potential concern. While sparisomid parrotfishes are major grazers of Caribbean reefs and help control algal blooms, the fact that they also undertake corallivory has prompted some to question the rationale for their conservation. Here the weight of evidence for beneficial effects of parrotfishes, in terms of reducing algal cover and facilitating demographic processes in corals, and the deleterious effects of parrotfishes in terms of causing coral mortality and chronic stress, are reviewed. While elevated parrotfish density will likely increase the predation rate upon juvenile corals, the net effect appears to be positive in enhancing coral recruitment through removal of macroalgal competitors. Parrotfish corallivory can cause modest partial colony mortality in the most intensively grazed species of Montastraea but the generation and healing of bite scars appear to be in near equilibrium, even when coral cover is low. Whole colony mortality in adult corals can lead to complete exclusion of some delicate, lagoonal species of Porites from forereef environments but is only reported for one reef species (Porites astreoides), for one habitat (backreef), and with uncertain incidence (though likely <<10%). No deleterious effects of predation on coral growth or fecundity have been reported, though recovery of zooxanthellae after bleaching events may be retarded. The balance of evidence to date finds strong support for the herbivory role of parrotfishes in facilitating coral recruitment, growth, and fecundity. In contrast, no net deleterious effects of corallivory have been reported for reef corals. Corallivory is unlikely to constrain overall coral cover but contraints upon dwindling populations of the Montastraea annularis species complex are feasible and the role of parrotfishes as a vector of coral disease requires evaluation. However, any assertion that conservation practices should guard against protecting corallivorous parrotfishes appears to be unwarranted at this stage.     

澳门翼手目物种多样性补充调查及其保护现状

<正>翼手目为哺乳动物中的第二大目,中国的翼手目多样性也在不断更新,Smith和解焱(2009)统计中国翼手目118种,蒋志刚等(2015)则认为中国翼手目有7科34属134种。广东省翼手目有6科24属55种(邹发生和叶冠锋,2016),此后也仍陆续有新纪录,如长指鼠耳蝠(Myotis longipes)(张琴等,2017)、卡氏伏翼(Hypsugo cadornae)(Xie et al., 2021);我们前期对澳门翼手目的调查,发现5科8属10种(黄继展等,2013)。     

Vertebrate metacommunity structure along an extensive elevational gradient in the tropics: a comparison of bats,rodents and birds

Aim We evaluated the structure of metacommunities for each of three vertebrate orders (Chiroptera, Rodentia and Passeriformes) along an extensive elevational gradient. Using elevation as a proxy for variation in abiotic characteristics and the known elevational distributions of habitat types, we assessed the extent to which variation in those factors may structure each metacommunity based on taxon‐specific characteristics. Location Manu Biosphere Reserve in the Peruvian Andes. Methods Metacommunity structure is an emergent property of a set of species distributions across geographic or environmental gradients. We analysed elements of metacommunity structure (coherence, range turnover and range boundary clumping) to determine the best‐fit structure for each metacommunity along an elevational gradient comprising 13 250‐m elevational intervals and 58 species of rodent, 92 species of bat or 586 species of passerine. Results For each taxon, the environmental gradient along which the metacommunity was structured was highly correlated with elevation. Clementsian structure (i.e. groups of species replacing other such groups along the gradient) characterized rodents, with a group of species that was characteristic of rain forests and a group of species that was characteristic of higher elevation habitats (i.e. above 1500 m). Distributions of bats were strongly nested, with more montane communities comprising subsets of species at lower elevations. The structure of the passerine metacommunity was complex and most consistent with a quasi‐Clementsian structure. Main conclusions Each metacommunity exhibited a different structure along the same elevational gradient, and each structure can be accounted for by taxon‐specific responses to local environmental factors that vary predictably with elevation. The structures of rodent and bird metacommunities suggest species sorting associated with habitat specializations, whereas structure of the bat metacommunity is probably moulded by a combination of species‐specific tolerances to increasingly cold, low‐productivity environs of higher elevations and the diversity and abundance of food resources associated with particular habitat types.     

The roles of geological history and colonization abilities in genetic differentiation between mammalian populations in the Philippine archipelago

Aim To test hypotheses that: (1) late Pleistocene low sea‐level shorelines (rather than current shorelines) define patterns of genetic variation among mammals on oceanic Philippine islands; (2) species‐specific ecological attributes, especially forest fidelity and vagility, determine the extent to which common genetic patterns are exhibited among a set of species; (3) populations show reduced within‐population variation on small, isolated oceanic islands; (4) populations tend to be most highly differentiated on small, isolated islands; and (5) to assess the extent to which patterns of genetic differentiation among multiple species are determined by interactions of ecological traits and geological/geographic conditions. Location The Philippine Islands, a large group of oceanic islands in Southeast (SE) Asia with unusually high levels of endemism among mammals. Methods Starch‐gel electrophoresis of protein allozymes of six species of small fruit bats (Chiroptera, Pteropodidae) and one rodent (Rodentia, Muridae). Results Genetic distances between populations within all species are not correlated with distances between present‐day shorelines, but are positively correlated with distances between shorelines during the last Pleistocene period of low sea level; relatively little intraspecific variation was found within these ‘Pleistocene islands’. Island area and isolation of oceanic populations have only slight effects on standing genetic variation within populations, but populations on some isolated islands have heightened levels of genetic differentiation, and reduced levels of gene flow, relative to other islands. Species associated with disturbed habitat (all of which fly readily across open habitats) show more genetic variation within populations than species associated with primary rain forest (all of which avoid flying out from beneath forest canopy). Species associated with disturbed habitats, which tend to be widely distributed in SE Asia, also show higher rates of gene flow and less differentiation between populations than species associated with rain forest, which tend to be Philippine endemic species. One rain forest bat has levels of gene flow and heterozygosity similar to the forest‐living rodent in our study. Main conclusions The maximum limits of Philippine islands that were reached during Pleistocene periods of low sea level define areas of relative genetic homogeneity, whereas even narrow sea channels between adjacent but permanently isolated oceanic islands are associated with most genetic variation within the species. Moreover, the distance between ‘Pleistocene islands’ is correlated with the extent of genetic distances within species. The structure of genetic variation is strongly influenced by the ecology of the species, predominantly as a result of their varying levels of vagility and ability to tolerate open (non‐forested) habitat. Readily available information on ecology (habitat association and vagility) and geological circumstances (presence or absence of Pleistocene land‐bridges between islands, and distance between oceanic islands during periods of low sea level) are combined to produce a simple predictive model of likely patterns of genetic differentiation (and hence speciation) among these mammals, and probably among other organisms, in oceanic archipelagos.     

Phylogenetic signals in host–parasite associations for Neotropical bats and Nearctic desert rodents

Hosts and their parasites have strong ecological and evolutionary relationships, with hosts representing habitats and resources for parasites. In the present study, we use approaches developed to evaluate the statistical dependence of species trait values on phylogenetic relationships to determine whether host–parasite relationships (i.e. parasite infections) are contingent on host phylogeny. If host–parasite relationships are contingent on the ability of hosts to provide habitat or resources to parasites, and if host phylogeny is an effective surrogate for among‐host variation in habitat and resource quality, host–parasite relationships should evince phylogenetic signals (i.e. be contingent on host phylogeny). Because the strength of ecological relationships between parasites and their hosts may affect the likelihood of phylogenetic signals occurring in host–parasite relationships, we hypothesized that (1) host specificity would be positively correlated with the strength of phylogenetic signals and (2) the strength of phylogenetic signals will be greater for parasites that rely more on their host throughout their life cycle. Analyses were conducted for ectoparasites from tropical bats and for ectoparasites, helminths, and coccidians from desert rodents. Phylogenetic signals were evaluated for parasite presence and for parasite prevalence. The frequency of phylogenetic signal occurrence was similar for parasite presence and prevalence, with a signal detected in 24–27% of cases at the species level and in 67% and 15% of cases at the genus level for parasites of bats and rodents, respectively. No differences in signal strength or the likelihood of detecting a signal existed between groups of parasites. Phylogenetic signal strength was correlated with host specificity, suggesting that mechanisms increasing host specificity also increase the likelihood of a phylogenetic signal in host use by parasites. Differences in the transmission mode did not affect signal strength or the likelihood of detecting a signal, indicating that variation in host switching opportunities associated with the transmission mode does not affect signal strength.     

Combining environmental suitability and habitat connectivity to map rare or Data Deficient species in the Tropics

The IUCN Red List is a widely accepted system for classifying species’ risk of extinction, based on quantitative criteria. Although IUCN discourages the liberal use of the category “Data Deficient” (DD), most assessed groups have a large number of their species assigned to this category, especially in the Tropics. Therefore, DD species can introduce considerable uncertainty into estimates of proportions of threatened species, and research focused on elucidating the true status of those species should be a priority. Here we propose a simple method to gather information on geographic distribution and guide the search for new populations of rare, small-ranged, forest species, using the literature, online data, and standard GIS procedures. The method involves: (i) creating a geographic distribution model; (ii) selecting the environmentally suitable sites from that model; (iii) removing sites that have lost natural vegetation; and (iv) removing habitat networks that are too small and/or isolated, based on thresholds established from known occurrence records and the literature for ecologically similar species. As a case study, we use Lonchophylla peracchii, a recently described forest-dependent bat endemic to southeastern Brazil. We found that environmentally suitable sites for L. peracchii are already heavily deforested, confirming habitat loss as a major threat. Importantly, we identified five priority sites to search for the species outside of its currently known distribution. From that, we discuss its likely status based on IUCN's Criterion B2 (Extent of Occurrence). This method could be useful for other poorly known forest species, especially in the Tropics where most of these species are, and funding for research and fieldwork is scarcest. Currently there are 1910 terrestrial vertebrates in tropical forest worldwide classified as DD that could be evaluated using this method, provided that they have at least 5–10 occurrence records.     

Don’t let me down: West Indian manatee,Trichechus manatus,is still critically endangered in Brazil

Sirenians have a unique ecological function in coastal ecosystems, deserving special conservation attention. The West Indian manatee (Trichechus manatus) is globally classified as Vulnerable by the IUCN. In Brazil, where the species was intensively hunted in the past and currently faces several threats, it was classified as Endangered during the last national assessment published in 2014. Here, we generated information based on available data to assess the species extinction risk in Brazil using IUCN regional guidelines, applying all criteria, and choosing the highest category of risk. Abundance at the national level was projected considering the density estimated in Ceará and Rio Grande do Norte states and the Criterion B EOO (Extent of Occurrence) estimated in this study (34,899 km²) and resulted in 1,047 individuals (95% CI: 538–2,038). Six scenarios of annual mortality were inferred and suspected based on evidence. We adopted a simple discrete logistic growth model to project population reduction in the past and future (three generations − 69 years) in 18 scenarios. Among the 18 projected scenarios, four resulted in extinction, six in decline and eight in population growth. Considering the low abundance bound, all scenarios indicate a reduction larger than 80% in population size, classifying the species as ‘Critically Endangered’ based on A4de. Reduction in EOO and abundance in the past classify the species as ‘Endangered’ based on A2c. The suspected number of mature animals (607;95% CI: 312–1,182) and the projected decline higher than 20% in two generations also classify the species as ‘Endangered’ based on C1 and ‘Vulnerable’ under D1. Our results indicate that information can be generated to produce more accurate assessments based on available data. The species national extinction risk needs to be reassessed, and the National Action Plan effectiveness evaluated.     

Extended flowering intervals of bamboos evolved by discrete multiplication

Numerous bamboo species collectively flower and seed at dramatically extended, regular intervals – some as long as 120 years. These collective seed releases, termed ‘masts’, are thought to be a strategy to overwhelm seed predators or to maximise pollination rates. But why are the intervals so long, and how did they evolve? We propose a simple mathematical model that supports their evolution as a two‐step process: First, an initial phase in which a mostly annually flowering population synchronises onto a small multi‐year interval. Second, a phase of successive small multiplications of the initial synchronisation interval, resulting in the extraordinary intervals seen today. A prediction of the hypothesis is that mast intervals observed today should factorise into small prime numbers. Using a historical data set of bamboo flowering observations, we find strong evidence in favour of this prediction. Our hypothesis provides the first theoretical explanation for the mechanism underlying this remarkable phenomenon.     

蒙古栎群落蒸腾特性的研究

本文用ZHT型数字式蒸腾仪对蒙古栎群落及其种群,进行了连续的时间及空间梯度测定与分析,得出了蒙古栎群落乔木、灌木及草本植物蒸腾强度的日变化规律,并从蒸腾生理角度提出了各种群在群落中的地位,说明了蒸腾强度是反映种群空间分布格局的一个生理指标。     

Two novel mitogenomes of Dipodidae species and phylogeny of Rodentia inferred from the complete mitogenomes

Two novel mitogenomes of Eozapus setchuanus (KJ648495) and Sicista concolor (KJ648496) were reported and their total lengths were 16,630 bp and 16,493 bp, respectively. Both mitogenomes which were analogous to other rodent mitogenomes, contained 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and a control region. Specifically, the ND2 gene of S. concolor has three amino acids lesser than that of two other Dipodidae species (E. setchuanus and Jaculus jaculus) due to a premature termination codon in the 3′ end. We detected a tandem repeat cluster of 221 bp and 274 bp in the control region of S. concolor and E. setchuanus, respectively. Along with phylogenetic relationship analysis, we speculated that the tandem repeats in control regions might be common in Dipodinae species. Our phylogenetic analysis using concatenated mitochondrial gene datasets suggested five suborder and 16 family monophyletic groups in 54 rodent taxa sampled and strongly supported a basal position of the squirrel-related clade (PP = 1; BP = 100). Dipodidae had a sister-group relationship with Muroidea, and Sicistinae was in the base of Dipodidae clade. The complete mitochondrial genomes showed high resolution in deep-level phylogenetic relationship reconstructions of Rodentia.