Sex-linked transcriptional divergence in the hermaphrodite fungus Neurospora tetrasperma

In the filamentous ascomycete Neurospora tetrasperma, a large (approx. 7 Mbp) region of suppressed recombination surrounds the mating-type (mat) locus. While the remainder of the genome is largely homoallelic, this region of recombinational suppression, extending over 1500 genes, is associated with sequence divergence. Here, we used microarrays to examine how the molecular phenotype of gene expression level is linked to this divergent region, and thus to the mating type. Culturing N. tetrasperma on agar media that induce sexual/female or vegetative/male tissue, we found 196 genes significantly differentially expressed between mat A and mat a mating types. Our data show that the genes exhibiting mat-linked expression are enriched in the region genetically linked to mating type, and sequence and expression divergence are positively correlated. Our results indicate that the phenotype of mat A strains is optimized for traits promoting sexual/female development and the phenotype of mat a strains for vegetative/male development. This discovery of differentially expressed genes associated with mating type provides a link between genotypic and phenotypic divergence in this taxon and illustrates a fungal analogue to sexual dimorphism found among animals and plants.     

Phylogenetic fields through time: temporal dynamics of geographical co-occurrence and phylogenetic structure within species ranges

Species co-occur with different sets of other species across their geographical distribution, which can be either closely or distantly related. Such co-occurrence patterns and their phylogenetic structure within individual species ranges represent what we call the species phylogenetic fields (PFs). These PFs allow investigation of the role of historical processes—speciation, extinction and dispersal—in shaping species co-occurrence patterns, in both extinct and extant species. Here, we investigate PFs of large mammalian species during the last 3 Myr, and how these correlate with trends in diversification rates. Using the fossil record, we evaluate species'' distributional and co-occurrence patterns along with their phylogenetic structure. We apply a novel Bayesian framework on fossil occurrences to estimate diversification rates through time. Our findings highlight the effect of evolutionary processes and past climatic changes on species'' distributions and co-occurrences. From the Late Pliocene to the Recent, mammal species seem to have responded in an individualistic manner to climate changes and diversification dynamics, co-occurring with different sets of species from different lineages across their geographical ranges. These findings stress the difficulty of forecasting potential effects of future climate changes on biodiversity.     

水淹干扰下水库水滨带植物群落谱系结构与物种多样性格局

群落谱系结构将物种系统发育信息整合到群落中,给生物多样性研究提供了全新视角。为探讨水淹干扰下水库水滨带植物群落物种多样性维持机制,以丹江口水库水滨带为研究区域,以南水北调中线一期工程运行前的原有水滨带植被为研究对象,分析不同水淹干扰强度下群落谱系结构和物种多样性及其与环境因素的关系。结果表明：(1)随着水淹干扰强度增加,群落物种丰富度、物种多样性和谱系多样性显著降低。谱系结构指数虽无显著差异,但随着水淹干扰强度增加呈现由发散到聚集的变化趋势。表明水滨带植物群落物种多样性维持机制是生境过滤和生态位分化共同驱动的结果,并且随着水淹干扰强度增加呈现生境过滤作用增加、物种间竞争排斥作用减弱的生态过程影响规律。(2)坡度、土壤质地、速效氮和全氮含量对整个水滨带植物群落物种丰富度、物种多样性和谱系多样性影响显著。此外,土层厚度和速效磷对物种丰富度和土层厚度对谱系多样性也影响显著。而仅有速效氮含量对谱系结构指数影响显著;轻度水淹干扰下坡向、速效磷含量与多样性指数显著相关;中度水淹干扰下坡度、土层厚度、土壤质地、土壤总氮含量与多样性指数显著相关,土壤pH、全氮和全磷含量与谱系结构指数显著相关;重度水淹...     

Phylogenetic diversity,trait diversity and niches: species assembly of ferns along a tropical elevational gradient

Aim To analyse the structure of pteridophyte assemblages, based on phylogenetic relatedness and trait properties, along an elevational gradient. Ecological theory predicts that co‐occurring species may be: randomly selected from a regional pool; ecologically sorted so that they are functionally different hence resulting in reduced competition (overdispersion); or functionally similar as an adaptation to specific ecological conditions (clustering). Location Braulio Carrillo National Park and Cerro de la Muerte, Costa Rica, Central America. Methods We used an empirical dataset of the quantitative pattern of species occurrences and individual numbers of ferns within 156 plots along a tropical elevational gradient to test whether directed ecological sorting might cause deviations in patterns of trait and phylogenetic diversity. Mean pairwise distances of species based on phylogenetic and trait properties were compared with two different sets of null assemblages, one maintaining species frequency distributions (constrained) and one not (unconstrained). Results Applying different null models resulted in varying degrees of overdispersion and clustering, but overall patterns of deviation from random expectations remained the same. Contrary to theoretical predictions, phylogenetic and trait diversity were relatively independent from one another. Phylogenetic diversity showed no patterns along the elevational gradient, whereas trait diversity showed significant trends for epiphytes. Main conclusions Under stressful environmental conditions (drought at low elevations and frost at high elevations), epiphytic fern assemblages tended to be clustered with respect to trait characteristics, which suggests environmental filtering. Conversely, under less extreme environmental conditions (middle of the transect), the sorting was biased towards high differentiation (overdispersion), presumably because of interspecific competition and trait shifts among closely related species (character displacement).     

A multilocus genealogical approach to phylogenetic species recognition in the model eukaryote Neurospora

To critically examine the relationship between species recognized by phylogenetic and reproductive compatibility criteria, we applied phylogenetic species recognition (PSR) to the fungus in which biological species recognition (BSR) has been most comprehensively applied, the well-studied genus Neurospora. Four independent anonymous nuclear loci were characterized and sequenced from 147 individuals that were representative of all described outbreeding species of Neurospora. We developed a consensus-tree approach that identified monophyletic genealogical groups that were concordantly supported by the majority of the loci, or were well supported by at least one locus but not contradicted by any other locus. We recognized a total of eight phylogenetic species, five of which corresponded with the five traditional biological species, and three of which were newly discovered. Not only were phylogenetic criteria superior to traditional reproductive compatibility criteria in revealing the full species diversity of Neurospora, but also significant phylogenetic subdivisions were detected within some species. Despite previous suggestions of hybridization between N. crassa and N. intermedia in nature, and the fact that several putative hybrid individuals were included in this study, no molecular evidence in support of recent interspecific gene flow or the existence of true hybrids was observed. The sequence data from the four loci were combined and used to clarify how the species discovered by PSR were related. Although species-level clades were strongly supported, the phylogenetic relationships among species remained difficult to resolve, perhaps due to conflicting signals resulting from differential lineage sorting.     

Phylogenetic skew: an index of community diversity

The distribution of divergence times between member species of a community reflects the pattern of species composition. In this study, we contrast the species composition of a community against the meta‐community, which we define as the species composition of a set of target communities. We regard the collection of species that comprise a community as a sample from the set of member species of the meta‐community, and interpret the pattern of the community species composition in terms of the type of species sampled from the meta‐community. A newly defined effective species sampling proportion explains the amount of the difference between the divergence time distributions of the community and that of the meta‐community, assuming random sampling. We propose a new index of phylogenetic skew (PS), as the ratio of the maximum‐likelihood estimate of the effective species sampling proportion to the observed sampling proportion. A PS value of 1 is interpreted as random sampling. If the value is >1, the sampling is suspected to be phylogenetically skewed. If it is <1, systematic thinning of species is likely. Unlike other indices, the PS does not depend on species richness as long as the community has more than a few members of a species. Because it is possible to compare partially observed communities, the index may be effectively used in exploratory analysis to detect candidate communities with unique species compositions from a large number of communities.     

Phylogenetic diversity and the functioning of ecosystems

Phylogenetic diversity (PD) describes the total amount of phylogenetic distance among species in a community. Although there has been substantial research on the factors that determine community PD, exploration of the consequences of PD for ecosystem functioning is just beginning. We argue that PD may be useful in predicting ecosystem functions in a range of communities, from single-trophic to complex networks. Many traits show a phylogenetic signal, suggesting that PD can estimate the functional trait space of a community, and thus ecosystem functioning. Phylogeny also determines interactions among species, and so could help predict how extinctions cascade through ecological networks and thus impact ecosystem functions. Although the initial evidence available suggests patterns consistent with these predictions, we caution that the utility of PD depends critically on the strength of phylogenetic signals to both traits and interactions. We advocate for a synthetic approach that incorporates a deeper understanding of how traits and interactions are shaped by evolution, and outline key areas for future research. If these complexities can be incorporated into future studies, relationships between PD and ecosystem function bear promise in conceptually unifying evolutionary biology with ecosystem ecology.     

新的蜜环菌生物种

对湖北、西藏等地区的蜜环菌进行调查,发现了1个新蜜环菌生物种CBS P和2个互交不育子实体标本,均为四极性异宗配合。扩大了部分生物种的分布范围,试验结果显示西南地区为CBS J的分布中心。     

新的蜜环菌生物种

对湖北、西藏等地区的蜜环菌进行调查,发现了1个新蜜环菌生物种CBSP和2个互交不育子实体标本,均为四极性异宗配合。扩大了部分生物种的分布范围,试验结果显示西南地区为CBSJ的分布中心。     

Phylogenetic species delimitation in ectomycorrhizal fungi and implications for barcoding: the case of the Tricholoma scalpturatum complex (Basidiomycota)

Population studies have revealed that the fungal ectomycorrhizal morphospecies Tricholoma scalpturatum consists of at least two genetically distinct groups that occur sympatrically in several geographical areas. This discovery prompted us to examine species boundaries and relationships between members formerly assigned to T. scalpturatum and allied taxa using phylogenetic analyses. Sequence data were obtained from three nuclear DNA regions [internal transcribed spacer (ITS), gpd and tef], from 101 carpophores collected over a large geographical range in Western Europe, and some reference sequences from public databases. The ITS was also tested for its applicability as DNA barcode for species delimitation. Four highly supported phylogenetic clades were detected. The two previously detected genetic groups of T. scalpturatum were assigned to the phylospecies Tricholoma argyraceum and T. scalpturatum. The two remaining clades were referred to as Tricholoma cingulatum and Tricholoma inocybeoides. Unexpectedly, T. cingulatum showed an accelerated rate of evolution that we attributed to narrow host specialization. This study also reveals recombinant ITS sequences in T. inocybeoides, suggesting a hybrid origin. The ITS was a useful tool for the determination of species boundaries: the mean value of intraspecific genetic distances in the entire ITS region (including 5.8S rDNA) was <0.2%, whereas interspecific divergence estimates ranged from 1.78% to 4.22%. Apart from giving insights into the evolution of the T. scalpturatum complex, this study contributes to the establishment of a library of taxonomically verified voucher specimens, an a posteriori correlation between phenotype and genotype, and DNA barcoding of ectomycorrhizal fungi.     

戴云山物种多样性与系统发育多样性海拔梯度分布格局及驱动因子

生物多样性的海拔分布格局是生态学研究的热点。海拔作为综合性因子驱动着植物群落的物种、系统发育与功能多样性的空间分布。以戴云山南坡900-1600 m森林植物群落为研究对象,探讨物种多样性、系统发育指数与环境驱动因子的相互关系以及环境因子在群落构建与多样性维持中的重要意义。结果表明：（1）森林植物群落的系统发育多样性与物种多样性沿海拔均呈现中间高度膨胀格局。（2）物种多样性Margalef指数、Shannon-Wiener指数与系统发育多样性指数呈显著正相关,表明物种多样性越高,系统发育多样性也越高。Shannon-Wiener指数与物种多样性指数（Margalef、Pielou、Simpson指数）、系统发育多样性及系统发育结构都存在显著相关性,一定程度上Shannon-Wiener指数可以代替其他指数。Pielou指数、Simpson指数、Shannon-Wiener指数与系统发育结构NRI （Net relatedness index）指数、NTI （Net nearest taxa index）指数存在显著正相关,表明群落优势度、均匀度与系统发育结构相关性较强。（3）土壤全磷含量是影响系统发育多样性和物种多样性的主要驱动因子,土壤含水量是影响Shannon-Wiener、Pielou、Simpson指数的最显著因子,海拔是影响群落系统发育结构的主要因素。海拔是影响系统发育结构变化的主要环境因子,而土壤因子是影响物种多样性与系统发育多样性的主要因素,进一步验证了物种多样性与系统发育多样性的高度相关,结果旨在揭示物种群落空间分布规律。     

Detecting cryptic species in sympatry and allopatry: analysis of hidden diversity in Polyommatus (Agrodiaetus) butterflies (Lepidoptera: Lycaenidae)

Modern multilocus molecular techniques are a powerful tool in the detection and analysis of cryptic taxa. However, its shortcoming is that with allopatric populations it reveals phylogenetic lineages, not biological species. The increasing power of coalescent multilocus analysis leads to the situation in which nearly every geographically isolated or semi‐isolated population can be identified as a lineage and therefore raised to species rank. It leads to artificial taxonomic inflation and as a consequence creates an unnecessary burden on the conservation of biodiversity. To solve this problem, we suggest combining modern lineage delimitation techniques with the biological species concept. We discuss several explicit principles on how genetic markers can be used to detect cryptic entities that have properties of biological species (i.e. of actually or potentially reproductively isolated taxa). Using these principles we rearranged the taxonomy of the butterfly species close to Polyommatus (Agrodiaetus) ripartii. The subgenus Agrodiaetus is a model system in evolutionary research, but its taxonomy is poorly elaborated because, as a rule, most of its species are morphologically poorly differentiated. The taxon P. (A.) valiabadi has been supposed to be one of the few exceptions from this rule due to its accurately distinguishable wing pattern. We discovered that in fact traditionally recognized P. valiabadi is a triplet of cryptic species, strongly differentiated by their karyotypes and mitochondrial haplotypes.     

Phylogenetic beta diversity of native and alien species in European urban floras

Aim Human activities have weakened biogeographical barriers to dispersal, increasing the rate of introduction of alien plants. However, their impact on beta diversity and floristic homogenization is poorly understood. Our goal is to compare the phylogenetic beta diversity of native species with that of two groups of alien species, archaeophytes and neophytes (introduced before and after ad 1500, respectively), across European urban floras to explore how biological invasions affect phylogenetic turnover at a continental scale. Location Twenty European cities located in six countries between 49 and 53° N latitude in continental Europe and the British Isles. Methods To compare the phylogenetic beta diversity of native and alien species we use the average phylogenetic dissimilarity of individual floras from their group centroid in multivariate space. Differences in phylogenetic beta diversity among different species groups are then assessed using a randomization test for homogeneity of multivariate dispersions. Results Across European urban floras, and when contrasted with natives, archaeophytes are usually associated with lower levels of phylogenetic beta diversity while neophytes tend to increase phylogenetic differentiation. Main conclusions While archaeophytes tend to promote limited homogenization in phylogenetic beta diversity, because of their diverse geographical origin together with short residence times in the invaded regions, neophytes are not promoting biotic homogenization of urban floras across Europe. Therefore, in spite of the increasing rate of alien invasion, an intense phylogenetic homogenization of urban cities is not to be expected soon.     

Reproductive isolation and phylogenetic divergence in Neurospora: comparing methods of species recognition in a model eukaryote

We critically examined methods for recognizing species in the model filamentous fungal genus Neurospora by comparing traditional biological species recognition (BSR) with more comprehensive applications of both BSR and phylogenetic species recognition (PSR). Comprehensive BSR was applied to a set of 73 individuals by performing extensive crossing experiments and delineating biological species based on patterns of reproductive success. Within what were originally considered two species, N. crassa and N. intermedia, we recognized four reproductively isolated biological species. In a concurrent study (Dettman et al. 2003), we used genealogical concordance of four independent nuclear loci to recognize phylogenetic species in Neurospora. Overall, the groups of individuals identified as species were similar whether recognized by reproductive success or by phylogenetic criteria, and increased genetic distance between parents was associated with decreased reproductive success of crosses, suggesting that PSR using genealogical concordance can be used to reliably recognize species in organisms that are not candidates for BSR. In one case, two phylogenetic species were recognized as a single biological species, indicating that significant phylogenetic divergence preceded the development of reproductive isolation. However, multiple biological species were never recognized as a single phylogenetic species. Each of the putative N. crassa x N. intermedia hybrids included in this study was confidently assigned to a single species, using both PSR and BSR. As such, no evidence for a history of hybridization in nature among Neurospora species was observed. By performing reciprocal mating tests, we found that mating type, parental role, and species identity of parental individuals could all influence the reproductive success of matings. We also observed sympatry-associated sexual dysfunction in interspecific crosses, which was consistent with the existence of reinforcement mechanisms.     

叶蜂总科生物地理研究IV东亚区特有属的分布式样及迁移路线(膜翅目)

本文分析归纳了东亚叶蜂总科特有属的分布式样及迁移路线。东亚区分布的１７９个叶蜂总科特有属可归纳为１个主要特化中心：川滇缅高原;５个小型次级特化中心：喜马拉雅中段小中心、浙闽山地小中心、秦巴山地小中心、燕山山地小中心和长白山地小中心;４条主要迁移演化路线：从主要中心沿喜马拉雅山脉走廊向西发展的西线,从主要中心沿缅－马走廊向南发展的南线,从主要中心沿南岭走廊向东发展的东线,从主要中心向北沿第二阶梯东缘走廊（大娄山－伏牛山－太行山－燕山）及西部走廊（第一阶梯东缘走廊）发展的北线,其中北线因四川盆地隔离可分为东西两支,但东西两支从秦岭山脉始重新部分融合;一个中心区域类型和３８种分布式样。     

鸟兽物种多样性测度的G-F指数方法

评价物种多样性是目前生物多样性研究中的一项紧迫任务。我们提出一种基于信息测度的G-F指数公式,利用生物普查得到的鸟类和兽类名录计算一个地区的物种多样性。首先计算属间的多样性（G指数）和科间的多样性（F指数）,然后,再利用G指数和F指数的比值进行标准化,得出G-F指数。在这一指数体系中,F指数包括科中和科间的多样性。如果G-F指数趋近1,则代表科间多样性的F指数下降,或者代表属多样性的G指数上升;否则G-F指数趋近零或为负数。信息测度通常也用于生物群落的生态多样性。然而,G-F指数与生态多样性不同。G-F指数测定的一个地区一个生物类群中科属间的物种多样性,而生态多样性指数研究生物群落中物种组成及种间个体的多寡。利用G-F指数研究评估生物多样性保护有如下优点：（1）G-F指数提供了一种简捷有效的生物多样性保护评估方法,因为在许多地点已经进行过生物普查,编写了动物、植物名录;（2）G-F指数是一种标准化指数,可以进行不同地区间生物多样性比较。在动物界,特别是无脊椎动物中,尚未鉴定的物种占多数,而鸟类和兽类中尚未鉴定的物种很少。我们应用鸟类和兽类名录计算了G-F指数,选择了梵净山、大瑶山、伏牛山、凉水、北京—天津、海北、白音锡勒、青海湖和帕米尔高原等9个地区,进行了物种多样性的比较研究。结果表明：在上述地区,鸟类的G指数高于兽类的G指数,但差异并不显著（p=0.11）。鸟类的F指数显著地高于兽类的F指数（p<0.05）。鸟类G-F指数与兽类G-F指数相关(r=0.68, p<0.05)。     

太白山地区蜜环菌种类

对太白山地区的蜜环菌进行了调查,共发现4个互交不育群:Armillaria borealis、CBSJ、CBSN和CBS F,均为四极性异宗配合。扩大了部分种类的分布范围,该地区可能为CBSJ种群的最北分布界线。     

线粒体细胞色素氧化酶I (mt COI) 序列分析揭示扶桑绵粉蚧复合种存在隐存谱系

过去约20年间扶桑绵粉蚧Phenacoccus solenopsis Tinsley在许多国家造成严重危害。近年来该害虫传入我国, 对农业生产构成严峻威胁。外来入侵物种的快速准确鉴定是科学研究及其管理的基础。本研究对来自海南三亚和陵水地区的扶桑绵粉蚧的线粒体细胞色素氧化酶I （mt COI）测序并与美国佛罗里达州的扶桑绵粉蚧序列进行了比较。系统发育树表明该物种存在两个遗传支系, 即海南支系与佛罗里达支系; 这两个支系的遗传距离约3%。这是利用mt COI分子标记对我国扶桑绵粉蚧的首次分子鉴定. 这些结果提示：（1）扶桑绵粉蚧可能是至少含有两个隐存谱系或姊妹种的复合种; （2）新入侵我国海南三亚和陵水地区的扶桑绵粉蚧是该复合种内的一个隐存谱系或物种, 且海南三亚和陵水种群可能不是来自美国佛罗里达州。扶桑绵粉蚧隐存谱系的发现对于该物种的分子鉴定及其入侵生态学研究具有重要意义。