Taxonomic Resolution and Quantification of Freshwater Macroinvertebrate Samples from an Australian Dryland River: The Benefits and Costs of Using Species Abundance Data

In studies using macroinvertebrates as indicators for monitoring rivers and streams, species level identifications in comparison with lower resolution identifications can have greater information content and result in more reliable site classifications and better capacity to discriminate between sites, yet many such programmes identify specimens to the resolution of family rather than species. This is often because it is cheaper to obtain family level data than species level data. Choice of appropriate taxonomic resolution is a compromise between the cost of obtaining data at high taxonomic resolutions and the loss of information at lower resolutions. Optimum taxonomic resolution should be determined by the information required to address programme objectives. Costs saved in identifying macroinvertebrates to family level may not be justified if family level data can not give the answers required and expending the extra cost to obtain species level data may not be warranted if cheaper family level data retains sufficient information to meet objectives. We investigated the influence of taxonomic resolution and sample quantification (abundance vs. presence/absence) on the representation of aquatic macroinvertebrate species assemblage patterns and species richness estimates. The study was conducted in a physically harsh dryland river system (Condamine-Balonne River system, located in south-western Queensland, Australia), characterised by low macroinvertebrate diversity. Our 29 study sites covered a wide geographic range and a diversity of lotic conditions and this was reflected by differences between sites in macroinvertebrate assemblage composition and richness. The usefulness of expending the extra cost necessary to identify macroinvertebrates to species was quantified via the benefits this higher resolution data offered in its capacity to discriminate between sites and give accurate estimates of site species richness. We found that very little information (<6%) was lost by identifying taxa to family (or genus), as opposed to species, and that quantifying the abundance of taxa provided greater resolution for pattern interpretation than simply noting their presence/absence. Species richness was very well represented by genus, family and order richness, so that each of these could be used as surrogates of species richness if, for example, surveying to identify diversity hot-spots. It is suggested that sharing of common ecological responses among species within higher taxonomic units is the most plausible mechanism for the results. Based on a cost/benefit analysis, family level abundance data is recommended as the best resolution for resolving patterns in macroinvertebrate assemblages in this system. The relevance of these findings are discussed in the context of other low diversity, harsh, dryland river systems.     

Comparison of different methods for diversity ordering

Abstract. The measurement of diversity, one of the most important concepts in present-day ecology, can be improved by methods of diversity ordering which have recently been developed. This ordering is achieved by a D(α) diversity index family. Indices of this family show varying sensitivities to the rare and abundant species as the scale parameter, α, changes. The aim of this paper is to review and assess 12 methods of diversity ordering and discuss their relationships in detail. Two of the methods are new to the ecological literature. The diversity ordering methods are compared as to their effectiveness in graphically displaying the differences of community structure and demonstrating the (non-)comparability of communities. Small, medium and large data sets were used to evaluate the methods. A small artificial data set (five to seven species) and a large semi-artificial data set (31 — 141 species) are used in this paper. The results suggest that Rényi's diversity index family and Logarithmic dominance ordering are the most useful methods for diversity ordering of communities of all sizes. Right-tailsum diversity ordering performs well for small communities.     

CALIBRATED DIVERSITY,TREE TOPOLOGY AND THE MOTHER OF MASS EXTINCTIONS: THE LESSON OF TEMNOSPONDYLS

Abstract: Three family‐level cladistic analyses of temnospondyl amphibians are used to evaluate the impact of taxonomic rank, tree topology, and sample size on diversity profiles, origination and extinction rates, and faunal turnover. Temnospondyls are used as a case study for investigating replacement of families across the Permo‐Triassic boundary and modality of recovery in the aftermath of the end‐Permian mass extinction. Both observed and inferred (i.e. tree topology‐dependent) values of family diversity have a negligible effect on the shape of the diversity curve. However, inferred values produce both a flattening of the curve throughout the Cisuralian and a less pronounced increase in family diversity from Tatarian through to Induan than do observed values. Diversity curves based upon counts of genera and species display a clearer distinction between peaks and troughs. We use rarefaction techniques (specifically, rarefaction of the number of genera and species within families) to evaluate the effect of sampling size on the curve of estimated family‐level diversity during five time bins (Carboniferous; Cisuralian; Guadalupian–Lopingian; Early Triassic; Middle Triassic–Cretaceous). After applying rarefaction, we note that Cisuralian and Early Triassic diversity values are closer to one another than they are when the observed number of families is used; both values are also slightly higher than the Carboniferous estimated diversity. The Guadalupian–Lopingian value is lower than raw data indicate, reflecting in part the depauperate land vertebrate diversity from the late Cisuralian to the middle Guadalupian (Olson’s gap). The time‐calibrated origination and extinction rate trajectories plot out close to one another and show a peak in the Induan, regardless of the tree used to construct them. Origination and extinction trajectories are disjunct in at least some Palaeozoic intervals, and background extinctions exert a significant role in shaping temnospondyl diversity in the lowermost Triassic. Finally, species‐, genus‐, and family trajectories consistently reveal a rapid increase in temnospondyl diversity from latest Permian to earliest Triassic as well as a decline near the end of the Cisuralian. However, during the rest of the Cisuralian family diversity increases slightly and there is no evidence for a steady decline, contrary to previous reports.     

深圳小南山与应人石山地植物多样性比较研究

该文对深圳市小南山处在封育状态下的3个植物群落和应人石山地荒弃果林处于半自然恢复状态群落以及果林周边半自然状态发育的群落进行了调查,比较分析两区域植物群落的组成及多样性特征。结果表明：在群落科、属、种的数量组成上,两者的差异虽不很明显,但小南山的科和种类的数量稍多于后者;在群落各层次的种类组成上,则小南山乔木层种类较明显地多于应人石的群落,前者的灌木层及草本层的发育也较好,种类也较多;虽然应人石的灌木层及草本层的种类数也较多,而且灌木层种类数高于前者,但乔木层种类则明显少,草本层种类的数量也略低于小南山的2个群落。在物种的生物多样性Simpson指数、Shannon-Wiener指数和丰富度指数方面,小南山的3个群落各层次的大多指标及所有的整体指标值均高于后者。这说明小南山在较长期受到人为保护的状态下,植被的结构发育较好,各层次的种类数均较为丰富。而后者虽然是处于半自然状态发育的群落,但由于受到人为干扰和影响的印迹依然还没有消除,仍处在恢复初期或中间状态。这为目前争论较多的究竟是自然林生物多样性高,还是人工林高？或者是人为较多干扰的次生林高的理论问题提供了一个较好的证据和理论参考。在各群落的相似性系数方面,各层次的系数值均处在相对较低状态,表明同区域不同地点及不同区域相互间各群落在种类组成上差异较大,说明深圳这两个区域在大区域范围的植物多样性水平是较高的。     

Evolution of the cycloidea gene family in Antirrhinum and Misopates.

Studies at the nucleotide level on the nuclear flower development gene cycloidea (cyc) in seven Antirrhinum, two Misopates, one Linaria, one Cymbalaria, and one Digitalis species revealed that cyc is a member of a gene family composed of at least five apparently functional genes. The estimated ages of the duplication events that created this gene family are from 7.5 Myr to more than 75 Myr. We also report the first estimates of DNA sequence diversity for species of Antirrhinum and Misopates. Low between-species variability suggests that this group of species may have diverged recently.     

Robust estimation of microbial diversity in theory and in practice

Quantifying diversity is of central importance for the study of structure, function and evolution of microbial communities. The estimation of microbial diversity has received renewed attention with the advent of large-scale metagenomic studies. Here, we consider what the diversity observed in a sample tells us about the diversity of the community being sampled. First, we argue that one cannot reliably estimate the absolute and relative number of microbial species present in a community without making unsupported assumptions about species abundance distributions. The reason for this is that sample data do not contain information about the number of rare species in the tail of species abundance distributions. We illustrate the difficulty in comparing species richness estimates by applying Chao''s estimator of species richness to a set of in silico communities: they are ranked incorrectly in the presence of large numbers of rare species. Next, we extend our analysis to a general family of diversity metrics (‘Hill diversities''), and construct lower and upper estimates of diversity values consistent with the sample data. The theory generalizes Chao''s estimator, which we retrieve as the lower estimate of species richness. We show that Shannon and Simpson diversity can be robustly estimated for the in silico communities. We analyze nine metagenomic data sets from a wide range of environments, and show that our findings are relevant for empirically-sampled communities. Hence, we recommend the use of Shannon and Simpson diversity rather than species richness in efforts to quantify and compare microbial diversity.     

A proposal for the conservation of the family Cucurbitaceae in Mexico

The pantropical Cucurbitaceae is one of the most important families ofvascular plants. The family includes 118 genera and 825 species, and Mexicois one of its most important centers of diversity, with 34 genera and 141species and subspecific taxa, including 13 cultivated ones. Five genera and 70taxa are endemic to the country. Some Mexican and Latin American wild speciesare close relatives of important crops, and others are employed as food ormedicine. Accordingly, in countries like Mexico the conservation of members ofthis family should be a priority. In this paper a list of members ofCucurbitaceae occurring in Mexico and their distribution patterns at state levelare discussed. Using cluster strategies, the states were classified according totheir floristic similarities. Hotspots of total diversity and endemismsat state level are identified, in order to discuss their role in futureconservation strategies. Iterative methods applied by conservation biology todetermine the best places for conservation are used to identify hierarchicallythe most important states that merit to be considered in this goal. Resultsindicate that implementing conservation strategies in half of the states wouldallow the protection of all the diversity found in the country, especially theendemisms. The combination of the results provided by the different methods isalso discussed as a possibly more efficient way to propose conservationstrategies for important species of the family.     

Variation in sexual reproduction in orchids and its evolutionary consequences: a spasmodic journey to diversification

The great taxonomic diversity of the Orchidaceae is often attributed to adaptive radiation for specific pollinators driven by selection for outcrossing. However, when one looks beyond the product to the process, the evidence for selection is less than overwhelming. We explore this problem by discussing relevant aspects of orchid biology and asking which aspects of reproduction explain the intricate pollination mechanisms and diversification of this family. We reaffirm that orchids are primarily pollination limited, the severity of which is affected by resource constraints. Fruit set is higher in temperate than in tropical species, and in species which offer pollinator rewards than those that do not. Reproductive success is skewed towards few individuals in a population and effective population sizes are often small. Population structure, reproductive success and gene flow among populations suggest that in many situations genetic drift may be as important as selection in fostering genetic and morphological variation in this family. Although there is some evidence for a gradualist model of evolutionary change, we believe that the great diversity in this family is largely a consequence of sequential and rapid interplay between drift and natural selection.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 84 , 1–54.     

Morphological innovation,ecological opportunity,and the radiation of a major vascular epiphyte lineage

The emergence of angiosperm‐dominated tropical forests in the Cretaceous led to major shifts in the composition of biodiversity on Earth. Among these was the rise to prominence of epiphytic plant lineages, which today comprise an estimated one‐quarter of tropical vascular plant diversity. Among the most successful epiphytic groups is the Polypodiaceae, which comprises an estimated 1500 species and displays a remarkable breadth of morphological and ecological diversity. Using a time‐calibrated phylogeny for 417 species, we characterized macroevolutionary patterns in the family, identified shifts in diversification rate, and identified traits that are potential drivers of diversification. We find high diversification rates throughout the family, evidence for a radiation in a large clade of Paleotropical species, and support for increased rates of diversification associated with traits including chlorophyllous spores and noncordiform gametophytes. Contrary to previous hypotheses, our results indicate epiphytic species and groups with humus‐collecting leaves diversify at lower rates than the family as a whole. We find that diversification rates in the Polypodiaceae are positively correlated with changes in elevation. Repeated successful exploration of novel habitat types, rather than morphological innovation, appears to be the primary driver of diversification in this group.     

太行山东北部哺乳动物区系及多样性

为研究太行山东北部的哺乳动物区系及多样性格局, 2019年7月1日至10月30日间, 作者采用样线调查和红外相机监测、访谈、文献查阅等多种方法, 对该区域的哺乳动物进行调查, 分析了区系构成, 并基于多样性指数比较了太行山片区和燕山片区哺乳动物多样性及动物分布型的差异。结果表明: 太行山东北部区域分布有哺乳动物7目22科68种, 其中啮齿目种类最多(24种), 灵长目最少, 仅猕猴(Macaca mulatta) 1种; 区域内分布有2种国家I级(金钱豹Panthera pardus、豺Cuon alpinus)和10种国家II级重点保护野生动物。太行山片区和燕山片区的哺乳动物区系的平均动物区系相似性(average faunal resemblance)系数为0.844, 相似性较大, 太行山片区的哺乳动物种数(66)高于燕山片区(50), 其科的多样性指数(D_F= 2.994 ± 0.251, n = 13)和属的多样性指数(D_G = 2.443 ± 0.161, n = 13)也略高于燕山片区(D_F = 2.458 ± 0.170, D_G = 2.259 ± 0.149, n = 10), 但无显著差异(P> 0.05)。太行山片区哺乳动物G-F指数(D_G-F= 0.145 ± 0.022, n = 13)显著高于燕山片区(0.078 ± 0.014, n = 10) (P< 0.05)。研究结果表明, 太行山片区和燕山片区的哺乳动物的科、属组成相同, 但太行山片区的物种多样性高于燕山片区; 太行山东北部区域分布的哺乳动物以古北界物种为主, 太行山片区和燕山片区均有10类动物分布型的哺乳动物; 因太行山片区的纬度相对较低, 其东洋界物种比例(19.11%)略高于燕山片区(17.64%)。