Molecular phylogenetics of slit‐faced bats (Chiroptera: Nycteridae) reveal deeply divergent African lineages

The bat family Nycteridae contains only the genus Nycteris, which comprises 13 currently recognized species from Africa and the Arabian Peninsula, one species from Madagascar, and two species restricted to Malaysia and Indonesia in South‐East Asia. We investigated genetic variation, clade membership, and phylogenetic relationships in Nycteridae with broad sampling across Africa for most clades. We sequenced mitochondrial cytochrome b (cytb) and four independent nuclear introns (2,166 bp) from 253 individuals. Although our samples did not include all recognized species, we recovered at least 16 deeply divergent monophyletic lineages using independent mitochondrial and multilocus nuclear datasets in both gene tree and species tree analyses. Mean pairwise uncorrected genetic distances among species‐ranked Nycteris clades (17% for cytb and 4% for concatenated introns) suggest high levels of phylogenetic diversity in Nycteridae. We found a large number of designated clades whose members are distributed wholly or partly in East Africa (10 of 16 clades), indicating that Nycteris diversity has been historically underestimated and raising the possibility that additional unsampled and/or undescribed Nycteris species occur in more poorly sampled Central and West Africa. Well‐resolved mitochondrial, concatenated nuclear, and species trees strongly supported African ancestry for SE Asian species. Species tree analyses strongly support two deeply diverged subclades that have not previously been recognized, and these clades may warrant recognition as subgenera. Our analyses also strongly support four traditionally recognized species groups of Nycteris. Mitonuclear discordance regarding geographic population structure in Nycteris thebaica appears to result from male‐biased dispersal in this species. Our analyses, almost wholly based on museum voucher specimens, serve to identify species‐rank clades that can be tested with independent datasets, such as morphology, vocalizations, distributions, and ectoparasites. Our analyses highlight the need for a comprehensive revision of Nycteridae.     

Genomic analyses and the origin of the eukaryotes

The availability of whole-genome data has created the extraordinary opportunity to reconstruct in fine details the 'tree of life'. The application of such comprehensive effort promises to unravel the enigmatic evolutionary relationships between prokaryotes and eukaryotes. Traditionally, biologists have represented the evolutionary relationships of all organisms by a bifurcating phylogenetic tree. But recent analyses of completely sequenced genomes using conditioned reconstruction (CR), a newly developed gene-content algorithm, suggest that a cycle graph or 'ring' rather than a 'tree' is a better representation of the evolutionary relationships between prokaryotes and eukaryotes. CR is the first phylogenetic-reconstruction method to provide precise evidence about the origin of the eukaryotes. This review summarizes how the CR analyses of complete genomes provide evidence for a fusion origin of the eukaryotes.     

Ascotricha bosei—分离自牛皮杜鹃的中国新记录种(英文)

自吉林省长白山植物牛皮杜鹃(Rhododendron aureum)叶片上分离到1株内生真菌,经鉴定为鲍氏刺囊壳(Ascotricha bosei)。该菌的典型特征是子囊壳外壁着生曲膝状附属丝和产生碟形子囊孢子。该菌为我国首次报道。     

UPGMA树的不惟一性问题及其解决方法

对于一组给定的DNA或蛋白质序列,UPGMA算法构建的二叉进化树可能是不惟一的,其具体拓扑结构与序列输入顺序相关,这一现象通常被称为"tied trees"。提出了UPGMA的一种改进算法——不加权算术平均组群方法(UMGMA),用以解决UPGMA树的不惟一问题。在UPGMA树惟一时,该方法产生的进化树与UPGMA树相同;而在UPGMA树不惟一时,该方法可以产生一棵惟一的、与序列输入顺序无关的多叉进化树,而且该算法还具有一个可调的容差参数,来控制生成进化树的主要分枝结构,这对于突出大规模进化树的总体脉络具有重要意义。     

Bioassay and Identification of Root Exudates of Three Fruit Tree Species

A laboratory bioassay was designed to determine the aileiopathic potential of root exudates of three fruit tree species on apple germination. The results showed that root exudates of apple （Malus pumila L.） and peach （Prunus persica L.）, each at concentrations of 0.02 and 0.2 mg/L, inhibited germination and radicle growth of apple seeds by 56.7%, 60.7%, 51.5%, and 59.3%, respectively. The corresponding shoot growth inhibition rate was 49.5%, 46.7%, 36. 4%, and 44%, respectively. Root exudates of jujube （Ziziphus jujuba Mill.） had no significant effect on apple seeds. Qualitative determination of root exudates of apple, peach, and jujube tree was developed with gas chromatography-mass spectrometry. The root exudates of apple seedlings mainly contain organic acids, glycol, esters, and benzenphenol derivatives. Peach root exudates contained phenolic acids and benzenphenoi derivatives in addition to two unidentified compounds. The root exudates of jujube did not contain any phenolic acids.     

Scale‐dependent effects of forest restoration on Neotropical fruit bats

Neotropical fruit bats (family Phyllostomidae) facilitate forest regeneration on degraded lands by dispersing shrub and tree seeds. Accordingly, if fruit bats can be attracted to restoration sites, seed dispersal could be enhanced. We surveyed bat communities at 10 sites in southern Costa Rica to evaluate whether restoration treatments attracted more fruit bats if trees were planted on degraded farmlands in plantations or island configurations versus natural regeneration. We also compared the relative influence of tree cover at local and landscape spatial scales on bat abundances. We captured 68% more fruit bat individuals in tree plantations as in controls, whereas tree island plots were intermediate. Bat activity also responded to landscape tree cover within a 200‐m radius of restoration plots, with greater abundance but lower species richness in deforested landscapes. Fruit bat captures in controls and tree island plots declined with increasing landscape tree cover, but captures in plantations were relatively constant. Individual species responded differentially to tree cover measured at different spatial scales. We attribute restoration effects primarily to habitat structure rather than food resources because no planted trees produced fruits regularly eaten by bats. The magnitude of tree planting effects on fruit bats was less than previous studies have found for frugivorous birds, suggesting that bats may play a particularly important role in dispersing seeds in heavily deforested and naturally regenerating areas. Nonetheless, our results show that larger tree plantations in more intact landscapes are more likely to attract diverse fruit bats, potentially enhancing seed dispersal.