TREEasy: An automated workflow to infer gene trees,species trees,and phylogenetic networks from multilocus data

Multilocus genomic data sets can be used to infer a rich set of information about the evolutionary history of a lineage, including gene trees, species trees, and phylogenetic networks. However, user‐friendly tools to run such integrated analyses are lacking, and workflows often require tedious reformatting and handling time to shepherd data through a series of individual programs. Here, we present a tool written in Python—TREEasy—that performs automated sequence alignment (with MAFFT), gene tree inference (with IQ‐Tree), species inference from concatenated data (with IQ‐Tree and RaxML‐NG), species tree inference from gene trees (with ASTRAL, MP‐EST, and STELLS2), and phylogenetic network inference (with SNaQ and PhyloNet). The tool only requires FASTA files and nine parameters as inputs. The tool can be run as command line or through a Graphical User Interface (GUI). As examples, we reproduced a recent analysis of staghorn coral evolution, and performed a new analysis on the evolution of the “WGD clade” of yeast. The latter revealed novel patterns that were not identified by previous analyses. TREEasy represents a reliable and simple tool to accelerate research in systematic biology ( https://github.com/MaoYafei/TREEasy ).     

Effect of woody plant expansion on decomposition of fine root mixtures in a grass-dominated temperate wetland

Wetlands Ecology and Management - Little is known about the effect of woody plant expansion on decomposition of root mixtures in grass-dominant temperate wetlands. Here, we collected fine roots...     

四川黑竹沟地区非飞行小型兽类物种多样性与群落组成

四川黑竹沟国家级自然保护区位于生物多样性丰富的凉山山系, 在保护和维持区域生物多样性方面具有极其重要的地位, 然而对该自然保护区兽类群落的研究却极为缺乏。为了了解该自然保护区及周边的小型兽类群落,本文作者在2018年4-10月调查了该区域的非飞行小型兽类物种多样性及其群落组成。在海拔1,537-3,830 m间共设置样方184个, 布设鼠夹9,016铗日, 捕获小型兽类536只, 隶属4目7科13属21种。包括滇攀鼠(Vernaya fulva)和等齿鼩鼹(Uropsilus aequodonenia)两个稀有物种在内的共计9个物种为该地区首次报道, 丰富了物种分布记录。结合历史资料, 黑竹沟地区共记录小型兽类43种, 隶属4目9科28属。在43种小型兽类中, 东洋界物种37种, 占绝对优势(86%), 分布型以喜马拉雅-横断山型占优, 为18种(占东洋界48.6%)。本次调查捕获的21种小型兽类中, 群落优势种为中华姬鼠(Apodemus draco, 33.2%)、北社鼠(Niviventer confucianus, 21.3%)和中华绒鼠(Eothenomys chinensis, 12.7%)。随着海拔上升, 群落优势种组成发生变化, 由北社鼠 + 中华姬鼠 + 针毛鼠(Niviventer fulvescens) + 短尾鼩(Anourosorex squamipes)群落, 转变为中华绒鼠 + 中华姬鼠 + 凉山沟牙田鼠(Proedromys liangshanensis) + 西南绒鼠(Eothenomys custos)群落。群落物种区系的分布型组成随着海拔升高而发生变化, 喜马拉雅-横断山型物种随海拔升高所占比例增大; 分布于喜马拉雅-横断山的特有种分布的下限、中点和上限平均海拔都高于非特有种, 且特有种和非特有种的中点和下限平均海拔差异显著(n = 21, df = 19, P = 0.013; n = 21, df = 19, P < 0.01), 说明该区域物种具有明显的东洋界特征, 中高海拔主要由特有种构成。本研究丰富了黑竹沟地区小型兽类及群落多样性的数据资料, 有利于该地区物种多样性的研究和保护。     

Allopatric divergence and hybridization within Cupressus chengiana (Cupressaceae), a threatened conifer in the northern Hengduan Mountains of western China

Having a comprehensive understanding of population structure, genetic differentiation and demographic history is important for the conservation and management of threatened species. High‐throughput sequencing (HTS) provides exciting opportunities to address a wide range of factors for conservation genetics. Here, we generated HTS data and identified 266,884 high‐quality single nucleotide polymorphisms from 82 individuals of Cupressus chengiana, to assess population genomics across the species' full range, comprising the Daduhe River (DDH), Minjiang River (MJR) and Bailongjiang River (BLJ) catchments in western China. admixture , principal components analysis and phylogenetic analyses indicated that each region contains a distinct lineage, with high levels of differentiation between them (DDH, MJR and BLJ lineages). MJR was newly distinguished compared to previous surveys, and evidence including coalescent simulations supported a hybrid origin of MJR during the Quaternary. Each of these three lineages should be recognized as an evolutionarily significant unit (ESU), due to isolation, differing genetic adaptations and different demographic history. Currently, each ESU faces distinct threats, and will require different conservation strategies. Our work shows that population genomic approaches using HTS can reconstruct the complex evolutionary history of threatened species in mountainous regions, and hence inform conservation efforts, and contribute to the understanding of high biodiversity in mountains.     

Differential responses of litter decomposition in the air and on the soil surface to shrub encroachment in a graminoid-dominated temperate wetland

Plant and Soil - Graminoid-dominated wetlands have been subjected to widespread shrub encroachment, yet the effect of this shift in species composition on litter decomposition remains unclear,...     

Different leaf carbon,nitrogen, and phosphorus stoichiometry and carbon and nitrogen isotopes among peatland plants in northeastern China

Plant and Soil - Plant carbon (C), nitrogen (N), phosphorus (P) levels and their stoichiometry and N uptake strategies are important aspects influencing vegetation composition and C dynamics in...