Partitioning the turnover and nestedness components of beta diversity

Aim  Beta diversity (variation of the species composition of assemblages) may reflect two different phenomena, spatial species turnover and nestedness of assemblages, which result from two antithetic processes, namely species replacement and species loss, respectively. The aim of this paper is to provide a unified framework for the assessment of beta diversity, disentangling the contribution of spatial turnover and nestedness to beta-diversity patterns.
Innovation  I derive an additive partitioning of beta diversity that provides the two separate components of spatial turnover and nestedness underlying the total amount of beta diversity. I propose two families of measures of beta diversity for pairwise and multiple-site situations. Each family comprises one measure accounting for all aspects of beta diversity, which is additively decomposed into two measures accounting for the pure spatial turnover and nestedness components, respectively. Finally, I provide a case study using European longhorn beetles to exemplify the relevance of disentangling spatial turnover and nestedness patterns.
Main conclusion  Assigning the different beta-diversity patterns to their respective biological phenomena is essential for analysing the causality of the processes underlying biodiversity. Thus, the differentiation of the spatial turnover and nestedness components of beta diversity is crucial for our understanding of central biogeographic, ecological and conservation issues.     

Partitioning multiple-site tree-like beta diversity into turnover and nestedness components without pairwise comparisons

In this letter, I extend a species-level partitioning framework for a multiple-site dissimilarity index established by Ricotta and Pavoine (2015) to account for tree-like information (i.e., evolutionary history, taxonomic classification or functional divergence of species). This novel framework can be applied to evaluate the relative contribution of turnover versus nestedness to total multiple-site tree-like beta diversity in empirical settings. The feature of the framework is to account for expectedly and unexpectedly absence of species in the sites without pairwise comparisons between sites. Simple examples with step-by-step calculation details and corresponding R computing code are provided to better understand and apply the proposed framework.     

Climatic history and dispersal ability explain the relative importance of turnover and nestedness components of beta diversity

Aim We tested whether the geographic variation in the proportion of beta diversity attributed to nestedness or turnover components was explained by the effect of past glaciation events. Specifically, we tested the hypothesis that most of the beta diversity in regions retaining ice until recent periods was due to nestedness. Additionally, we tested whether the variation was influenced by thermal tolerance and the dispersal ability of species. Location This study analysed data from the New World. Methods We used presence/absence data for amphibians, birds and mammals of the New World. We calculated beta diversity among each 1°× 1° cell and the adjacent cells using the Sorensen dissimilarity index that expresses the total beta diversity. Furthermore, we partitioned it into turnover and nestedness components. The relative importance of the two latter components was expressed as the proportion of total beta diversity explained by nestedness (β_ratio). We calculated the correlation between β_ratio and the time each cell was free of ice since the last glaciation (cell age). To control the effects of spatial autocorrelation, we calculated geographically effective degrees of freedom. Results The proportion of beta diversity attributed to nestedness was negatively correlated with cell age. Moreover, this effect was stronger for amphibians than mammals, and stronger for mammals than birds. Main conclusions Our results are in accordance with the hypothesis that the nestedness component of beta diversity is more important in areas affected by glaciations until recent time. The beta diversity in high latitudes is the result of past extinctions and recent recolonization, which result in higher levels of nestedness. This process is more evident for vertebrates with lower dispersal ability and lower temperature tolerance.     

A meta‐analysis of nestedness and turnover components of beta diversity across organisms and ecosystems

Aim

The number of studies investigating the nestedness and turnover components of beta diversity has increased substantially, but our general understanding of the drivers of turnover and nestedness remains elusive. Here, we examined the effects of species traits, spatial extent, latitude and ecosystem type on the nestedness and turnover components of beta diversity.

Location

Global.

Time period

1968–2017.

Major taxa studied

From bacteria to mammals.

Methods

From the 99 studies that partition total beta diversity into its turnover and nestedness components, we assembled 269 and 259 data points for the pairwise and multiple site beta‐diversity metrics, respectively. Our data covered a broad variation in species dispersal type, body size and trophic position. The data were from freshwater, marine and terrestrial realms, and encompassed geographical areas from the tropics to near polar regions. We used linear modelling as a meta‐regression tool to analyse the data.

Results

Pairwise turnover, multiple site turnover and total beta diversity all decreased significantly with latitude. In contrast, multiple site nestedness showed a positive relationship with latitude. Beta‐diversity components did not generally differ among the realms. The turnover component and total beta diversity increased with spatial extent, whereas nestedness was scale invariant for pairwise metrics. Multiple site beta‐diversity components did not vary with spatial extent. Surprisingly, passively dispersed organisms had lower turnover and total beta diversity than flying organisms. Body size showed a relatively weak relationship with beta diversity but had important interactions with trophic position, thus also affecting beta diversity via interactive effects. Producers had significantly higher average pairwise turnover and total beta diversity than carnivores.

Main conclusions

The present results provide evidence that species turnover, being consistently the larger component of total beta diversity, and nestedness are related to the latitude of the study area and intrinsic organismal features. We showed that two beta‐diversity components had generally opposing patterns with regard to latitude. We highlight that beta‐diversity partition may give additional insights into the underlying causes of spatial variability in biotic communities compared with total beta diversity alone.     

Distinguishing between turnover and nestedness in the quantification of biotic homogenization

Compositional changes through local extinction and colonization are inherent to natural communities, but human activities are increasingly influencing the rate and nature of the species being lost and gained. Biotic homogenization refers to the process by which the compositional similarity of communities increases over time through a non-random reshuffling of species. Despite the extensive conceptual development of the homogenization framework, approaches to quantify patterns of homogenization are scarcely developed. Most studies have used classical dissimilarity indices that actually quantify two components of compositional variation: turnover and nestedness. Here we demonstrate that a method that partitions those two components reveals patterns of homogenization that are otherwise obscured using traditional techniques. The forest understorey vegetation of an unmanaged reserve was recorded in permanent plots in 1979 and 2009. In only thirty years, the local species richness significantly decreased and the variation in the species composition from site to site shifted towards a structure with reduced true species turnover and increased dissimilarity due to nestedness. A classic analysis masked those patterns. In summary, we illustrated the need to move beyond the simple quantification of homogenization using classical indices and advocate integration of the multitude of ways to quantify community similarity into the homogenization framework.     

Historical legacies in the geographical diversity patterns of New World palm (Arecaceae) subfamilies

The extent to which species richness patterns of the major palm subfamilies in the Americas are controlled by lineage history was studied. Based on the fossil record, we suggest that the subfamily Coryphoideae has followed a boreotropical dispersal route into Central and South America, whereas Calamoideae (tribe Lepidocaryeae), Ceroxyloideae and Arecoideae have Gondwana/South America-biased histories. However, Arecoideae has been present and diverse in both South and Central America at least since the early Tertiary. We used regression analyses to evaluate the relative importance of environmental factors and spatial variables (as substitutes for historical or other non-environmental factors) as determinants of geographical variation in species richness for each subfamily. Given the different lineage histories, we hypothesized that: (1) coryphoid richness should be least strongly controlled by the modern environment and exhibit a strong non-environmental bias towards Central and North America, reflecting its boreotropical invasion route, (2) calamoid species richness should exhibit a non-environmental bias towards South America, reflecting its long African–South American history, and (3) arecoid species richness should be most strongly environmentally determined, reflecting the long arecoid residency in both Central and South America. The regression analyses confirmed the hypothesized effects of lineage history on the geographical patterns in species richness. Hence, modern species richness patterns in the New World palm subfamilies strongly reflect their divergent biogeographical histories.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 151 , 113–125.     

Habitat complexity drives the turnover and nestedness patterns in a periphytic algae community

Limnology - Habitat complexity drives aquatic community attributes, including the beta diversity components. We tested the hypothesis that community diversity, richness and density are higher on...     

Geographical patterns of turnover and nestedness-resultant components of allelic diversity among populations

The analysis of geographical patterns in population divergence has always been a powerful way to infer microevolutionary processes involved in population differentiation, and several approaches have been used to investigate such patterns. Most frequently, multivariate spatial patterns of population differentiation are analyzed by computing pairwise genetic distances or F_ST (or related statistics, such as ?_ST from AMOVA), which are then correlated with geographical distances or landscape features. However, when calculating distances, especially based on presence-absence of alleles in local populations, there would be a confounding effect of allelic richness differences in the population differentiation. Moreover, the relative magnitude of these components and their spatial patterns can help identifying microevolutionary processes driving population differentiation. Here we show how recent methodological advances in ecological community analyses that allows partitioning dissimilarity into turnover (turnover) and richness differences, or nestedness-resultant dissimilarity, can be applied to allelic variation data, using an endemic Cerrado tree (Dipteryx alata) as a case study. Individuals from 15 local populations were genotyped for eight microsatellite loci, and pairwise dissimilarities were computed based on presence-absence of alleles. The turnover of alleles among populations represented 69?% of variation in dissimilarity, but only the richness difference component shows a clear spatial structure, appearing as a westward decrease of allelic richness. We show that decoupling richness difference and turnover components of allelic variation reveals more clearly how similarity among populations reflects geographical patterns in allelic diversity that can be interpreted in respect to historical range expansion in the species.     

Historical legacies and ecological determinants of grass naturalizations worldwide

The global distribution of exotic species is the result of abiotic, biotic and dispersal filtering processes that shape the movement and success of species outside their native range. In this study we aim to understand how these filtering processes drive the fluxes of grass species among regions, the factors that influence which species establish outside of their native range, and where they do so. We used national and subnational checklists of native and introduced grass species to determine the extent to which each region was a source or recipient of exotic grass species. We asked how species traits may distinguish those grass species that have naturalized outside their native range from those that have not, and how environmental conditions are related to the distribution of exotic grass species. We found that exotic grass establishment is shaped by an array of factors including characteristics of regions, traits of species and their interactions. Regions with a longer history of human occupation and larger numbers of native grass species were generally the most important sources of exotic species. Global flows of species were mostly driven by a climate match between the native and exotic ranges, but were also highly asymmetric, with regions with recent human arrival being the major hosts of exotic grass species. Tall, annual and C4 grass species exhibited particularly high probabilities of establishment outside their native range. Despite the idiosyncrasy and stochasticity characteristic of exotic species establishment, this biogeographical analysis revealed important generalities across this large plant group. Our results suggest that grass species that have co-occurred with humans for a longer time may be better adapted to living in anthropogenic landscapes, explaining the global asymmetry in species introductions.     

Ancestral organization of the MHC revealed in the amphibian Xenopus

With the advent of the Xenopus tropicalis genome project, we analyzed scaffolds containing MHC genes. On eight scaffolds encompassing 3.65 Mbp, 122 MHC genes were found of which 110 genes were annotated. Expressed sequence tag database screening showed that most of these genes are expressed. In the extended class II and class III regions the genomic organization, excluding several block inversions, is remarkably similar to that of the human MHC. Genes in the human extended class I region are also well conserved in Xenopus, excluding the class I genes themselves. As expected from previous work on the Xenopus MHC, the single classical class I gene is tightly linked to immunoproteasome and transporter genes, defining the true class I region, present in all nonmammalian jawed vertebrates studied to date. Surprisingly, the immunoproteasome gene PSMB10 is found in the class III region rather than in the class I region, likely reflecting the ancestral condition. Xenopus DMalpha, DMbeta, and C2 genes were identified, which are not present or not clearly identifiable in the genomes of any teleosts. Of great interest are novel V-type Ig superfamily (Igsf) genes in the class III region, some of which have inhibitory motifs (ITIM) in their cytoplasmic domains. Our analysis indicates that the vertebrate MHC experienced a vigorous rearrangement in the bony fish and bird lineages, and a translocation and expansion of the class I genes in the mammalian lineage. Thus, the amphibian MHC is the most evolutionary conserved MHC so far analyzed.     

The amphibian globin gene repertoire as revealed by the Xenopus genome

The draft genome sequence of the Western clawed frog Xenopus (Silurana) tropicalis facilitates the identification, expression analysis and phylogenetic classification of the amphibian globin gene repertoire. Frog and mammalian neuroglobin display about 67% protein sequence identity, with the expected predominant expression in frog brain and eye. Frog and mammalian cytoglobins share about 69% of their amino acids, but the frog protein lacks the mammalian-type extension at the C-terminus. Like in mammals, X. tropicalis cytoglobin is expressed in many organs including neural tissue. Neuroglobin and cytoglobin genomic regions are syntenically conserved in all vertebrate classes. Frog and fish globin X show only 57% amino acid identity, but gene synteny analysis confirms orthology. The expression pattern of X. laevis globin X differs from that in fish, with a prominent expression in the eye and weak expression in most other examined tissues. Globin X is possibly present as two paralogous copies in X. tropicalis, with one copy showing transition stages of non-functionalization. The amphibian genome contains a previously unknown globin type (tentatively named 'globin Y') which is expressed in a broad range of tissues and is distantly related to the cytoglobin lineage. The globin Y gene is linked to a cluster of larval and adult hemoglobin alpha and beta genes which contains substantially more paralogous hemoglobin gene copies than previously published. Database and gene synteny analyses confirm the absence of a myoglobin gene in X. tropicalis.     

Lower genetic diversity and hatchability in amphibian populations isolated by urbanization

Many amphibian populations worldwide have declined rapidly and been threatened with extinction in the past few decades because of human impacts on the environment. It is well known that urbanization reduces the genetic diversity of isolated populations. The concept that a reduction in genetic diversity leads to lower reproductive fitness has been predominantly supported by studies involving laboratory organisms, but has rarely been tested in wild populations. Here we examined whether genetic diversity affected hatchability, a population parameter related to reproductive success, in the populations of two pond-breeding amphibian species (Hynobius tokyoensis and Rana ornativentris) affected by urbanization. We surveyed 81 populations in the southwestern Kanto region of Japan. Mean hatchability of the populations was determined and genetic diversities were estimated via mitochondrial or microsatellite DNA analyses. Firstly, Random Forests (an ensemble machine learning method) models were applied to clarify the effects of environmental factors on both hatchability and genetic diversity. Subsequently, the relationships among environmental factors, genetic diversity, and mean hatchability were evaluated using path analysis. Mean hatchability was significantly affected by both urbanization and genetic diversity. This result shows that loss of genetic diversity may decrease a population’s reproductive success in the field.     

Historical climate‐change influences modularity and nestedness of pollination networks

The structure of species interaction networks is important for species coexistence, community stability and exposure of species to extinctions. Two widespread structures in ecological networks are modularity, i.e. weakly connected subgroups of species that are internally highly interlinked, and nestedness, i.e. specialist species that interact with a subset of those species with which generalist species also interact. Modularity and nestedness are often interpreted as evolutionary ecological structures that may have relevance for community persistence and resilience against perturbations, such as climate‐change. Therefore, historical climatic fluctuations could influence modularity and nestedness, but this possibility remains untested. This lack of research is in sharp contrast to the considerable efforts to disentangle the role of historical climate‐change and contemporary climate on species distributions, richness and community composition patterns. Here, we use a global database of pollination networks to show that historical climate‐change is at least as important as contemporary climate in shaping modularity and nestedness of pollination networks. Specifically, on the mainland we found a relatively strong negative association between Quaternary climate‐change and modularity, whereas nestedness was most prominent in areas having experienced high Quaternary climate‐change. On islands, Quaternary climate‐change had weak effects on modularity and no effects on nestedness. Hence, for both modularity and nestedness, historical climate‐change has left imprints on the network structure of mainland communities, but had comparably little effect on island communities. Our findings highlight a need to integrate historical climate fluctuations into eco‐evolutionary hypotheses of network structures, such as modularity and nestedness, and then test these against empirical data. We propose that historical climate‐change may have left imprints in the structural organisation of species interactions in an array of systems important for maintaining biological diversity.     

福建省两栖类物种多样性评估

地区性物种多样性评价是当前全球生物多样性研究的重要组成部分。本文采用G-F指数对福建省两栖类物种多样性进行评估,同时利用弦距离类间平均连锁的方法对福建省22个县（市）和5个两栖动物地理省进行聚类分析。结果表时：福建省各县（市）的两栖类物种多样性差异较大,其中武夷山市两栖类物种多样性的G指数,F指数和G-F指数分别为2.978,4.863和0.388。处于华中区的3个地理省（闽北、闽东和闽西地理省）首先聚类,而后与处于华南区的闽中地理省聚类,最后与闽南地理省合并。聚类结果与福建省两栖动物地理区划大体一致,但个别县（市）不太相符,作者建议将大田县划归在华中区的闽西地理省。     

海口和三亚两城市破碎化林地中鸟类群落多样性与嵌套分布格局

城市化是生物多样性快速丧失的主要原因之一。鸟类作为城市生态系统的重要组成部分, 其生物多样性格局和物种保护已成为城市生态学研究的热点。为揭示城市化过程中城区和郊区破碎化林地中鸟类群落的多样性差异和嵌套格局, 本研究于2021年春、夏季鸟类繁殖期采用样线法对海口和三亚市的城区、郊区共13个林地斑块中的鸟类群落进行调查。使用NODF (nestedness metric based on overlap and decreasing fill)和WNODF (weighted nestedness metric based on overlap and decreasing fill)方法进行嵌套格局分析。研究发现: (1)共记录到林鸟100种, 隶属于11目39科, 其中三亚郊区的鸟类丰富度最高, 共8目29科68种。记录到国家重点保护鸟类共18种, 其中两城市郊区的国家重点保护鸟类物种数均多于城区, 海口郊区还记录到国家I级重点保护鸟类黄胸鹀(Emberiza aureola)。(2)鸟类群落多度、物种丰富度、Pielou均匀度指数和Shannon-Wiener多样性指数在不同区域中均存在差异。海口城区的鸟类群落多度显著高于海口郊区(P < 0.05), 三亚郊区的鸟类群落物种丰富度、Pielou均匀度指数和Shannon-Wiener多样性指数均显著高于三亚城区和海口郊区(P < 0.05)。(3)嵌套分析结果表明, 海口和三亚市的城区、郊区林地鸟类群落均呈现反嵌套分布格局。线性回归分析显示, 三亚市城区和郊区的斑块面积与鸟类物种丰富度呈显著正相关, 而物种丰富度与斑块距最近大面积林地的距离之间无显著相关性。研究表明, 两城市鸟类群落多样性都表现出郊区高于城区的特点, 少数优势种(如白头鹎 Pycnonotus sinensis)占据了城市中的主要生态位。受城市化的影响, 海口郊区与城区鸟类群落有同质化的趋势。鸟类在城区和郊区斑块间的高流动性、种间竞争和斑块中资源的可利用性等因素可能导致斑块间鸟类群落的反嵌套分布格局。我们建议应加强城区和郊区鸟类的保护, 减少对林地的破坏, 提高城市鸟类多样性。