Phylogenetic signal,feeding behaviour and brain volume in Neotropical bats

Comparative correlational studies of brain size and ecological traits (e.g. feeding habits and habitat complexity) have increased our knowledge about the selective pressures on brain evolution. Studies conducted in bats as a model system assume that shared evolutionary history has a maximum effect on the traits. However, this effect has not been quantified. In addition, the effect of levels of diet specialization on brain size remains unclear. We examined the role of diet on the evolution of brain size in Mormoopidae and Phyllostomidae using two comparative methods. Body mass explained 89% of the variance in brain volume. The effect of feeding behaviour (either characterized as feeding habits, as levels of specialization on a type of item or as handling behaviour) on brain volume was also significant albeit not consistent after controlling for body mass and the strength of the phylogenetic signal (λ). Although the strength of the phylogenetic signal of brain volume and body mass was high when tested individually, λ values in phylogenetic generalized least squares models were significantly different from 1. This suggests that phylogenetic independent contrasts models are not always the best approach for the study of ecological correlates of brain size in New World bats.     

Morphology and Molecular Phylogeny of a New Marine Hypotrichous Ciliate,Hypotrichidium paraconicum n. sp. (Ciliophora,Hypotrichia)

A new saline hypotrich, Hypotrichidium paraconicum n. sp., found in coastal waters near Hong Kong, China, was investigated with emphasis on its living morphology, infraciliature, ontogenesis, and phylogenetic position. A body that is pyriform, with a posterior end that is twisted helically toward the left, a distinct tail and a dark colour, characterizes H. paraconicum n. sp. The buccal cavity is prominent and the cortical granules, which are scattered or sparsely distributed, are colourless, round, and about 1 μm in diam. The contractile vacuole is near the left middle of the cell and there are one or two frontal cirri, four meridional rows and five or six cirral rows which exhibit a left‐handed spiral and which are distributed in the posterior portion on both sides. Three dorsal kineties are distributed in the anterior portion of the dorsal side. In our molecular phylogenies, based on SSU rRNA gene sequences, the position of H. paraconicum n. sp. is rather poorly resolved, providing some indication of a relationship with Neokeronopsis aurea and Rubrioxytricha ferruginea, which fall into the assemblage of oxytrichids (s.l.).     

Modelling dendritic ecological networks in space: an integrated network perspective

Dendritic ecological networks (DENs) are a unique form of ecological networks that exhibit a dendritic network topology (e.g. stream and cave networks or plant architecture). DENs have a dual spatial representation; as points within the network and as points in geographical space. Consequently, some analytical methods used to quantify relationships in other types of ecological networks, or in 2‐D space, may be inadequate for studying the influence of structure and connectivity on ecological processes within DENs. We propose a conceptual taxonomy of network analysis methods that account for DEN characteristics to varying degrees and provide a synthesis of the different approaches within the context of stream ecology. Within this context, we summarise the key innovations of a new family of spatial statistical models that describe spatial relationships in DENs. Finally, we discuss how different network analyses may be combined to address more complex and novel research questions. While our main focus is streams, the taxonomy of network analyses is also relevant anywhere spatial patterns in both network and 2‐D space can be used to explore the influence of multi‐scale processes on biota and their habitat (e.g. plant morphology and pest infestation, or preferential migration along stream or road corridors).     

Morphological similarity and molecular divergence of Trochulus striolatus and T. montanus,and their relationship to sympatric congeners (Gastropoda: Pulmonata: Hygromiidae)

Shell morphology has played an important role in the differentiation of mollusc species. However, extensive morphological variation and the lack of readily available diagnostic characters often lead to confusion and controversy in taxonomy of closely related species, such as the genus Trochulus. Two nominal species Trochulus striolatus and T. montanus show only subtle differences in their reproductive systems and are indistinguishable on the basis of sole conchological traits. Therefore, we performed molecular and morphological analyses to establish robust species limits among the taxa. The canonical discriminant analysis (CDA) of shell characters confirmed strong similarity between the species. It also revealed high intraspecific variability of the shell morphology, which allowed the distinguishing of some populations as two extremely distinct forms, while simultaneously making it difficult to discriminate between the two species. Analysis of the genital morphology indicated that differences were continuous and practically negligible among the species. In contrast, phylogenetic analyses based on newly obtained 114 Trochulus sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene and 55 homologues retrieved from the GenBank database showed clear genetic divergence between T. striolatus and T. montanus. Moreover, they revealed a close relationship between some T. montanus, some T. caelatus and T. clandestinus samples, which formed a monophyletic group. Some of their haplotypes were even identical. It suggested that their recent common origin or recurrent gene flow occurred between these populations. However, T. sericeus sequences were split into independent diverged lineages, which were separated by many unidentified Trochulus species. It suggested that this taxon may represent a paraphyletic species complex.     

Coevolutionary and Phylogenetic Analysis of Mimiviral Replication Machinery Suggest the Cellular Origin of Mimiviruses

Mimivirus is one of the most complex and largest viruses known. The origin and evolution of Mimivirus and other giant viruses have been a subject of intense study in the last two decades. The two prevailing hypotheses on the origin of Mimivirus and other viruses are the reduction hypothesis, which posits that viruses emerged from modern unicellular organisms; whereas the virus-first hypothesis proposes viruses as relics of precellular forms of life. In this study, to gain insights into the origin of Mimivirus, we have carried out extensive phylogenetic, correlation, and multidimensional scaling analyses of the putative proteins involved in the replication of its 1.2-Mb large genome. Correlation analysis and multidimensional scaling methods were validated using bacteriophage, bacteria, archaea, and eukaryotic replication proteins before applying to Mimivirus. We show that a large fraction of mimiviral replication proteins, including polymerase B, clamp, and clamp loaders are of eukaryotic origin and are coevolving. Although phylogenetic analysis places some components along the lineages of phage and bacteria, we show that all the replication-related genes have been homogenized and are under purifying selection. Collectively our analysis supports the idea that Mimivirus originated from a complex cellular ancestor. We hypothesize that Mimivirus has largely retained complex replication machinery reminiscent of its progenitor while losing most of the other genes related to processes such as metabolism and translation.     

Triplophysa ferganaensis,a new loach species from Fergana Valley in Central Asia (Teleostei: Nemacheilidae)

Triplophysa ferganaensis sp. nov. is described from the Shakhimardan stream, a small tributary of the Syr Darya, which does not reach the river in Fergana Valley. It can be distinguished from other valid Triplophysa loaches based on the following combination of characters: body smooth and scaleless, lateral line complete, posterior chamber of air bladder degenerated, inner gill rakers 10–11 on the first-gill arch, outer gill rakers absent, vertebrae 4 + 35–36, 8 + 8 branched caudal-fin rays, caudal peduncle depth 2.1–2.7 times its length, two supratemporal pores, dorsal-fin origin closer to the caudal-fin base than to the snout tip, caudal fin emarginated and pelvic-fin tip reaching the anus. The new species can also be distinguished from its congeners based on the molecular analyses of mitochondrial cytochrome oxidase subunit I (coI) gene sequences. The phylogenetic position of this new species indicates that it is a sister taxon of Triplophysa tenuis.     

基于功能和谱系视角分析繁殖留鸟对风机的响应

风电作为清洁可再生绿色能源越来越受到世界各国的重视,其建设规模也在不断扩大,导致风电建设与鸟类保护的矛盾进一步凸显,如何协调风电发展与物种保护已成为生态学家和保护生物学家关注的热点主题。为了探究风机对鸟类物种、功能和谱系的影响,本研究于2019年1、3、4、5月,采用样线法对连山风电场的鸟类多样性进行了4次调查。根据样线离风机距离的远近设置4个梯度: 100～300 m有6条样线,300～500 m 有13条样线,500～700 m 有8条样线,>700 m 有5条样线。结果表明: 本次调查中记录了繁殖留鸟76种,隶属于11目31科,目、科中数量最多是雀形目(53种)和画眉科(12种)。鸟类物种丰富度、功能丰富度(FRic)和谱系多样性(Faith PD)随着离风机距离的增加呈增加趋势: 在500 m以内未显著增加,500 m外呈显著增加趋势;鸟类群落水平的扩散能力呈现出增加趋势。鸟类群落的平均成对功能和谱系距离的标准化效应值(SES.MFD和SES.MPD)均小于0,其中显著低于随机值的样线占比约为50%(P<0.05)。风力发电机对鸟类物种、功能和谱系的影响主要在前500 m的距离;本研究的4个梯度中,鸟类群落的功能和谱系结构均表现为聚集特征。研究证实,风机对鸟类的影响是多维度的,在评估风机对鸟类群落的影响时仅考虑物种多样性可能难以提供全面的信息。     

极小种群濒危植物广西火桐、丹霞梧桐的叶绿体基因组特征

广西火桐(Firmiana kwangsiensis)和丹霞梧桐(F. danxiaensis)是我国南方特有物种, 其分布范围狭窄, 种群数量少。为了解其叶绿体基因组结构及系统发生关系, 本文通过高通量测序方法获得广西火桐和丹霞梧桐的浅层基因组数据, 通过生物信息学方法对叶绿体全基因组进行组装, 并对其结构特征进行分析。结果表明: 广西火桐和丹霞梧桐的叶绿体基因组大小分别为160,836 bp和161,253 bp, 具有典型被子植物叶绿体基因组环状四分体结构, 包含长度分别为89,700 bp、90,142 bp的大单拷贝区(large single copy, LSC), 长度分别为19,970 bp、20,067 bp的小单拷贝区(small single copy, SSC)及长度分别为25,583 bp、25,522 bp的2个反向重复序列区(inverted repeat sequence, IR)。两个物种的叶绿体基因组共注释得到131个基因, 包括86个蛋白编码基因、37个tRNA基因和8个rRNA基因。广西火桐的叶绿体基因组中共检测出26个正向重复序列、2个反向重复序列、21个回文重复序列、21个串联重复序列和98个简单重复序列; 丹霞梧桐叶绿体基因组中共检测出23个正向重复序列、5个反向重复序列、21个回文重复序列、30个串联重复序列和107个简单重复序列。系统发生分析结果表明5种梧桐属(Firmiana)植物构成两个强烈支持的分支(支持率100%), 一个分支为广西火桐、美丽火桐(F. pulcherrima)和火桐(F. colorata), 其中广西火桐与美丽火桐构成姐妹群; 另一分支是互为姐妹群的丹霞梧桐和云南梧桐(F. major)。综上所述, 广西火桐和丹霞梧桐的叶绿体基因组结构、基因排列及重复序列具有较高的相似性, 系统进化树将5种梧桐属物种分为两个分支, 其中广西火桐和美丽火桐最近; 而丹霞梧桐与云南梧桐关系最近。本研究鉴定的SSR位点可为梧桐属物种系统发生、进化关系的研究提供遗传信息。