Gauging the effects of sampling failure in biogeographical analysis

Aim Various methods are employed to recover patterns of area relationships in extinct and extant clades. The fidelity of these patterns can be adversely affected by sampling error in the form of missing data. Here we use simulation studies to evaluate the sensitivity of an analytical biogeographical method, namely tree reconciliation analysis (TRA), to this form of sampling failure. Location Simulation study. Methods To approximate varying degrees of taxonomic sampling failure within phylogenies varying in size and in redundancy of biogeographical signal, we applied sequential pruning protocols to artificial taxon–area cladograms displaying congruent patterns of area relationships. Initial trials assumed equal probability of sampling failure among all areas. Additional trials assigned weighted probabilities to each of the areas in order to explore the effects of uneven geographical sampling. Pruned taxon–area cladograms were then analysed with TRA to determine if the optimal area cladograms recovered match the original biogeographical signal, or if they represent false, ambiguous or uninformative signals. Results The results indicate a period of consistently accurate recovery of the true biogeographical signal, followed by a nonlinear decrease in signal recovery as more taxa are pruned. At high levels of sampling failure, false biogeographical signals are more likely to be recovered than the true signal. However, randomization testing for statistical significance greatly decreases the chance of accepting false signals. The primary inflection of the signal recovery curve, and its steepness and slope depend upon taxon–area cladogram size and area redundancy, as well as on the evenness of sampling. Uneven sampling across geographical areas is found to have serious deleterious effects on TRA, with the accuracy of recovery of biogeographical signal varying by an order of magnitude or more across different sampling regimes. Main conclusions These simulations reiterate the importance of taxon sampling in biogeographical analysis, and attest to the importance of considering geographical, as well as overall, sampling failure when interpreting the robustness of biogeographical signals. In addition to randomization testing for significance, we suggest the use of randomized sequential taxon deletions and the construction of signal decay curves as a means to assess the robustness of biogeographical signals for empirical data sets.     

Species richness and distortion in reciprocal averaging and detrended correspondence analysis

Gradients in beta diversity and species richness cause different forms of distortion in reciprocal averaging ordinations. Detrended correspondence analysis largely removes the beta diversity effect and reduces, but does not eliminate, the influence of species richness.     

A note on the occasional instability of detrending in correspondence analysis

When the two first eigenvalues of correspondence analysis are close to each other, their order can be reversed due to random variation in the data. The first axis can actually be in any direction in the plane defined by the two axes. However, the configuration of the points in the plane can remain unchanged but their projections onto any line in the plane can be very variable. The ordering in the first axis is preserved in detrending. The second axis is detrended with respect to the first one and therefore very variable configurations result when the orientation of the first axis in the plane is changed. This can lead to a situation where the detrended solutions are very unstable under random variation and therefore they can be only casually interpretable.     

A numerical phytoclimatic classification of China

The relationship is examined between vegetation and climate using climatic variables collected from 644 meteorological stations located throughout China. Multivariate methods are applied directly to the raw climatic data in order to define climatic clusters and to examine the relationship between the clusters and vegetation types. This approach is based on the concept of multidimensional climatic space defined by the combination of climatic variables. Phytoclimatic classes are defined on the basis of the distribution of vegetation types in climatic clusters and a new phytoclimatic classification of China is proposed. Patterns of climatic changes between neighbouring phytoclimatic classes are described. Two indexes of the influence of climate on vegetation are proposed based on discriminant analysis.     

A study on the vegetation in the east side of Helan Mountain

This paper analyzed the vegetation data obtained from a field survey conducted in the East Side of Helan Mountain, China, to reveal the features of mountainous vegetation growing in a transitional zone between the steppe and desert regions. Detrended correspondence analysis (DCA) was applied to the process of analysis, to clarify the spatial variation of floristic composition of the vegetation in the lower mountain range.The preliminary results obtained from the analysis are: (1) There are 53 vegetation formations existing in the area, following the China's criteria of vegetation classification system. (2) Those vegetation types compose a vertical vegetation spectrum in the East Side of Helan Mountain due to the climatic gradient caused by elevation variation. The spectrum consists of 4 zones. They are, from the foot up to the peak in turn, mountain steppe zone, mountain open forest and steppe zone, mountain coniferous forest zone, and alpine bush and meadow zone. The mountain coniferous forest zone can be further divided into two subzones: Pine forest subzone and Spruce forest subzone. (3) Most of the vegetation types show clear xeromorphic features due to the base zone of the vertical vegetation spectrum lying in the arid region of China. (4) The distribution of vegetation types and flora is sensitive and susceptible to the moisture condition that the vertical vegetation spectrum has quite different expressions between northern and southern exposures. (5) Floristic composition of the vegetation shows a northern temperate feature. The families that are rich in species in the area include Gramineae, Compositae, Leguminosae, Chenopodiaceae, Rosaceae and others, most of which are abundant in herbaceous species. (6) The variation of the ecological conditions from the north to the south also leads to the differentiation of vegetation and its floristic composition in the area. (7) The broad-leaved forest can not form a forest zone in the vertical vegetation spectrum. This may be a special characteristic of the spectrum sitting on a transitional zone between the steppe and desert regions.     

A study on relations of vegetation,climate and soils in Shanxi province,China

Relationships of vegetation, climate and soils in Shanxi plateau wereanalyzed by use of Canonical Correspondence Analysis (CCA). Shanxi province,located at 34°35–40°43 N, 110°15–114°33 E, was divided into a series of rectangular districts of30 latitude by 20 longitude. Areas of vegetation formations and soil types ineach district were measured carefully using fine grain on the vegetation andsoil maps of Shanxi. Climatic data were mean values of 25 years records in eachdistrict. Three data matrices of climate, vegetation and soil were combined byCCA. The results showed that the distribution of vegetation is closely relatedto the variety of climates and to soils distribution.     

荒漠啮齿动物群落与植物群落的对应分析

动物与其生存环境变量之间的关系一直是生态学家们广泛关注的问题.啮齿动物作为荒漠生态系统中重要的功能群,其数量大小和生态功能对生态系统的平衡和稳定具有重要意义.生境中的植被为啮齿动物提供赖以生存的食物资源和栖息地,了解啮齿动物群落与植被特征之间的关系对于理解动物群落变动规律具有重要意义.不同植被条件下啮齿动物群落的结构不同,Hernández等(2005)研究发现北美Chihuahuan荒漠的灌木生境中啮齿动物密度高于草地生境.     

Woodlands at the edge: A European perspective on the Atlantic Oakwood Plant Communities

Summary

The Atlantic Oakwoods can be seen as ‘at the edge’ in two ways. First, they lie at the extreme oceanic end of a series of Quercus robur and Q. petraea woodlands which stretches eastwards from the North Atlantic coast to the continental heartland of Europe. Second, they are at the northern limit of a range of oceanic oakwoods which extends southwards to Iberia where Q. pyrenaica is an important canopy companion. This paper outlines the main variations in trees, shrubs, herbs and cryptogams that can be seen along these two climatic gradients, so as to highlight what is truly distinctive about the Atlantic Oakwoods and how we might rightly value them.     

The biogeographical division of the Arctic and North Atlantic by the mysid (Crustacea: Mysidacea) fauna

The biogeographical analysis of Arctic and North Atlantic waters north of 30°N is based upon the distribution of 150 Mysidacea (Crustacea) species. The reasons for biogeographical divisions conducted independently by faunae of pelagic and benthopelagic mysids are adduced. The original schemes of the Arctic and North Atlantic division are proposed. Using the fauna of pelagic mysids, one biogeographical realm, one province and one transitional zone are designated in cold and temperate waters. Using the fauna of benthopelagic mysids, one biogeographical realm and four provinces are designated in those waters.     

Towards unification of national vegetation classifications: A comparison of two methods for analysis of large data sets

Abstract. In European phytosociology, national classifications of corresponding vegetation types show considerable differences even between neighbouring countries. Therefore, the European Vegetation Survey project urgently needs numerical classification methods for large data sets that are able to produce compatible classifications using data sets from different countries. We tested the ability of two methods, TWINSPAN and COCKTAIL, to produce similar classifications of wet meadows (Calthion, incl. Filipendulenion) for Germany (7909 relevés) and the Czech Republic (1287 relevés) in this respect. In TWINSPAN, the indicator ordination option was used for classification of two national data sets, and the extracted assignment criteria (indicator species) were applied crosswise from one to the other national data set. Although the data sets presumably contained similar community types, TWINSPAN revealed almost no correspondence between the groups derived from the proper classification of the national data set and the groups defined by the assignment criteria taken from the other national data set. The reason is probably the difference in structure between the national data sets, which is a typical, but hardly avoidable, feature of any pair of phytosociological data sets. As a result, the first axis of the correspondence analysis, and consequently the first TWINSPAN division, are associated with different environmental gradients; the difference in the first division is transferred and multiplied further down the hierarchy. COCKTAIL is a method which produces relevé groups on the basis of statistically formed species groups. The user determines the starting points for the formation of species groups, and groups already found in one data set can be tested for existence in the other data set. The correspondence between the national classifications produced by COCKTAIL was fairly good. For some relevé groups, the lack of correspondence to groups in the other national data set could be explained by the absence of the corresponding vegetation types in one of the countries, rather than by methodological problems.     

对应分析和去趋势分析在有蹄类取食模式研究中的应用

本研究将2009年1月和2010年1月小兴安岭大沾河湿地自然保护区二可河林场内驼鹿冬季食性作为原始数据,分别以对应分析（CA）、去趋势分析（DCA）,并将数据以样本为单位进行标准化后,再进行去趋势分析（DCA_std）3种排序方法,对驼鹿冬季取食模式进行了研究,后通过普鲁克分析,比较了不同排序方法对大型有蹄类取食模式研究的效果。结果表明,3种排序法的1轴和2轴均能涵盖绝大多数信息量,CA涵盖79.27%,DCA涵盖66.65%,DCA_std涵盖68.22%;3种方法均能够在1轴上区分针叶树和落叶乔木类食物,在2轴上,3种方法主要能够达到针叶树种与除落叶乔木外的其他植物类别的区分。虽三者均能够展现有蹄类取食模式,但在图形可视化后,仅DCA_std无明显的弓形效应。普鲁克分析结果表明,DCA_std样本位移平方和与CA和DCA均有很大差异,即将数据先进行标准化再进行DCA分析能够有效去除弓形效应。因此,在由多度组成的食性数据在进行标准DCA分析前,应对数据进行前期处理会得到更好的效果。同时,以样本为单位的标准化将使排序分析结果生态学意义更明确。     

A biogeographical analysis of terrestrial isopods (Isopoda, Oniscidea) from the central Aegean islands (Greece)

Abstract. Terrestrial isopods (Isopoda, Oniscidea) of forty-three central Aegean islands and islets are analysed from a biogeographical point of view. The oniscid fauna consists of sixty-nine species, thirty-two genera and fourteen families and is characterized by Aegean elements that have an eastern Mediterranean origin. Endemism is at the level of 20%, similar to that of oniscids from other Mediterranean archipelagoes. Analysis of species distribution through both idiographic and quantitative approaches (faunal similarity among islands using Jaccard's index, simple matching indices and the UPGMA clustering technique) resulted in the recognition of a major disjunction between Kykladesplus-Ikaria and eastern islands-plus-Astypalea and four noteworthy island groups: the eastern islands, Naxos-Ikaria, Amorgos, and all other Kyklades. Island similarities are generally consistent with the known palaeogeography of the area with the exception of Ikaria's placement with Naxos among the Kyklades. Also, the 'eastern' character of Astypalea is in conflict with evidence from other known taxa.     

A biogeographical analysis of Muhlenbergia (Poaceae: Chloridoideae: Cynodonteae: Muhlenbergiinae)

A phylogeny based on the analysis of six DNA sequence markers (ITS, ndhA intron, rpl32-trnL, rps3, rps16 intron, and rps16-trnK) is used to infer ancestral areas and divergence times, and reconstruct the biogeographical history and evolution of 150 of the 183 (82%) species of Muhlenbergia. Our results suggest that the genus originated 9.3 mya in the Sierra Madre (Occidental and Oriental) in Mexico, splitting into six lineages: M. ramulosa diverging 8.2 mya, M. subg. Muhlenbergia at 5.9 mya, M. subg. Pseudosporobolus at 5.9 mya, M. subg. Clomena at 5.4 mya, M. subg. Bealia at 4.3 mya, and M. subg. Trichochloa at 1 mya, each of these with a high probability of Sierra Madrean origin. Our results further suggest that founder-event speciation from Sierra Madre to South America occurred independently multiple times in all five subgenera during the Pleistocene and late Pliocene. One long-distance dispersal event most likely originating from Central or Eastern North America to East and Central Asia occurred 1.6–1 mya in M. subg. Muhlenbergia. In our cladogram, members of M. subg. Trichochloa show little genetic resolution, suggesting very low levels of divergence among the species, and this may be a consequence of rapid radiation.     

Effects of detrending and rescaling on correspondence analysis: solution stability and accuracy

Detrending and non-linear axis rescaling potentially improve the accuracy of gradient recovery in correspondence analyses but also reduce the stability or consistency of solutions. Variation among bootstrapped ordination solutions was compared across methods in analyses of both field and simulated data. Solution accuracy, measured with mean squared errors from Procrustes analysis, was compared using simulated data with known structure.Standard detrending-by-segments combined with non-linear rescaling entailed some cost in solution stability, but could improve the accuracy of solutions for long gradients. Without non-linear rescaling these solutions were usually less stable and less accurate. Although detrending-by-polynomials might be preferable on other grounds, it did not produce more accurate or stable solutions than detrending-by-segments.Abbreviations CA = correspondence analysis - DCA = detrended correspondence analysis - MSE = Procrustes mean squared error statistic - SD = standard deviation units of species turnover - SRV = scaled variance in species ranks     

以林相图为基础的不同取样方式对植被排序分析结果的影响

以6种不同方式对林相图中同一样带取样,采用CA、DCA和CCA 3种排序方法,研究了取样方式对排序轴的解释效果、物种与环境因子、环境因子之间、环境因子与坐标轴之间关系的影响.结果表明,样方大小和形状的变化在不同程度上改变了排序结果.大样方和长方形样方都增强了排序轴的解释效果,并对双序图中稀有种、独特种的位置有较大的影响;环境因子中土壤因子对样方的大小和形状都很敏感,坡度、经纬度只对样方大小敏感,坡位、海拔、温度和降水则对样方形状敏感;随着样方面积的增加,海拔、温度和降水的作用降低,而坡向的作用增加.     

Problems of joint display of species and site scores in correspondence analysis

Joint plots of species and site scores in correspondence analysis can be interpreted so that points which are in the same direction from the origin are closely associated. Species and site scores can thus be compared. Within each set of scores the location of points is also meaningful. Owing to the unimodal species response model which can be recovered by the correspondence analysis, the location of the species points in respect to the site points indicates the location of the optimum when direct weighted averages are used. However, when the eigenvalue of the solution is low, very different joint plots are derived when the set which is used for computing the weighted averages for the other set is changed. This makes the interpretation of the between-set proximities in the joint plot vague. Generally, it is not possible to deduce the species composition of a site or sites where a species occurs from the joint plot, although for some pairs of species and sites this is justified. Although the proximity interpretation is not possible in every case, a joint plot display can greatly enhance the interpretation of results.     

Build-up of the Himalayan avifauna through immigration: a biogeographical analysis of the Phylloscopus and Seicercus warblers

The Himalayan mountain range is one of the most species-rich areas in the world, harboring about 8% of the world's bird species. In this study, we compare the relative importance of immigration versus in situ speciation to the build-up of the Himalayan avifauna, by evaluating the biogeographic history of the Phylloscopus/Seicercus warblers, a speciose clade that is well represented in Himalayan forests. We use a comprehensive, multigene phylogeny in conjunction with dispersal-vicariance analysis to discern patterns of speciation and dispersal within this clade. The results indicate that virtually no speciation has occurred within the Himalayas. Instead, several speciation events are attributed to dispersal into the Himalayas followed by vicariance between the Himalayas and China/Southeast Asia. Most, perhaps all, of these events appear to be pre-Pleistocene. The apparent lack of speciation within the Himalayas stands in contrast to the mountain-driven Pleistocene speciation suggested for the Andes and the East African mountains.