The role of habitat diversity in generating the small-island effect

The small-island effect (SIE) has become a widespread pattern in island biogeography and biodiversity research. However, in most previous studies only area is used for the detection of the SIE, while other causal factors such as habitat diversity is rarely considered. Therefore, the role of habitat diversity in generating SIEs is poorly known. Here, we compiled 86 global datasets that included the variables of habitat diversity, area and species richness to systematically investigate the prevalence and underlying factors determining the role of habitat diversity in generating SIEs. For each dataset, we used both path analysis and breakpoint regressions to identify the existence of an SIE. We collected a number of system characteristics and employed logistic regression models and an information–theoretic approach to determine which combination of variables was important in determining the role of habitat diversity in generating SIEs. Among the 61 datasets with adequate fits, habitat diversity was found to influence the detection of SIEs in 32 cases (52.5%) when using path analysis. By contrast, SIEs were detected in 26 of 61 cases (42.6%) using breakpoint regressions. Model selection and model-averaged parameter estimates showed that Number of sites, Habitat range and Species range were three key variables that determined the role of habitat diversity in generating SIEs. However, Area range, Taxon group and Site type received considerably less support. Our study demonstrates that the effect of habitat diversity on generating SIEs is quite prevalent. The inclusion of habitat diversity is important because it provides a causal factor for the detection of SIEs. We conclude that for a better understanding of the causes of SIEs, habitat diversity should be included in future studies.     

生态学的多样性指数:功能与系统发育

生物多样性是生态学的核心问题。传统的多样性指数仅包含物种数和相对多度的信息,这类基于分类学的多样性指数并不能很好地帮助理解群落构建和生态系统功能。不同物种对群落构建和生态系统功能所起到的作用类型和贡献也不完全相同,且物种在生态过程中的作用和贡献往往与性状密切相关,因此功能多样性已经成为反映物种群落构建、干扰以及环境因素对群落影响的重要指标。同时,由于亲缘关系相近的物种往往具有相似的性状,系统发育多样性也可以作为功能多样性的一个替代。功能多样性和系统发育多样性各自具有优缺点,但二者均比分类多样性更能揭示群落和生态系统的构建、维持与功能。     

Contrasting patterns of phylogenetic diversity across climatic zones of Western Ghats: A biodiversity hotspot in peninsular India

This study attempts to understand the biogeographic history of the Western Ghats forests by investigating decoupling between phylogenetic and taxonomic diversity. We specifically test whether the deciduous forests have been recently established, whether the southern region was a refuge, and whether the deciduous and evergreen forest species have disparate evolutionary histories. We used species composition data from 23 forest types along the Western Ghats for all woody angiosperms above 10‐cm diameter at breast height. Forests were broadly grouped as either evergreen or deciduous. Mean phylogenetic distances corrected for species richness and mean phylogenetic beta diversity corrected for shared species were assessed using z‐scores from null distributions. Null distributions were generated by randomizing the species relationships on the phylogeny. We found that all evergreen forests showed a greater phylogenetic diversity as compared with null expectations. Deciduous forests showed the inverse pattern. Within the evergreen belt, there was a decreasing phylogenetic diversity from south to north, as predicted by the southern refuge hypothesis. The phylogenetic beta diversity across evergreen–deciduous forests was lesser than the null expectation, whereas it was much higher across forests within the evergreen belt. This study provides the first phylogenetic evidence for the antiquity of evergreen forests as well as the southern refuge hypothesis in the Western Ghats. The deciduous forests species have shared evolutionary histories with the evergreen forest species, suggesting multiple shifts between evergreen and deciduous states through the lineages. Conversely, the evergreen species exhibited a disparate evolutionary history across these forests, possibly owing to sharper ecological or climatic gradients.     

陆地生境岛屿藓类植物小岛屿效应驱动因素分析——以太行山脉中段山顶为例

小岛屿效应描述了种-面积关系的一种特殊现象,是当前生物地理学和生物多样性研究理论框架的重要组成部分。随着气候变暖,山顶物种的生存受到威胁,然而以山顶生境岛屿为载体对小岛屿效应的研究还十分缺乏。该研究以太行山脉中段19个面积0.06–801.58km²的山顶生境岛屿为研究区,在2019–2021年的夏秋季对藓类进行调查。共记录到藓类131种,隶属于23科68属。采用6种种-面积关系回归模型,分别检测了所有藓和6个常见藓科是否存在小岛屿效应。根据小岛屿效应形成机制的生境多样性假说、灭亡假说和营养补给假说,选择了岛屿高度、温度年变化范围和单位面积净初级生产力作为变量,对小岛屿效应的驱动因素进行分析。在各类群组中,使用多元线性回归和变差分解分别评估上述3个变量对物种丰富度变化的线性影响。首先使用5个面积最小的岛屿进行分析,计算出3个变量对物种丰富度变化的贡献,然后以迭代的方式逐次加入面积更大的1个岛屿,并再次进行变差分解分析。最后使用广义线性回归分析了3个变量对物种丰富度变化的贡献在迭代过程中的变化趋势。结果显示,所有藓和6个常见藓科均存在小岛屿效应,其面积阈值分布在0....     

A guide to phylogenetic metrics for conservation,community ecology and macroecology

The use of phylogenies in ecology is increasingly common and has broadened our understanding of biological diversity. Ecological sub‐disciplines, particularly conservation, community ecology and macroecology, all recognize the value of evolutionary relationships but the resulting development of phylogenetic approaches has led to a proliferation of phylogenetic diversity metrics. The use of many metrics across the sub‐disciplines hampers potential meta‐analyses, syntheses, and generalizations of existing results. Further, there is no guide for selecting the appropriate metric for a given question, and different metrics are frequently used to address similar questions. To improve the choice, application, and interpretation of phylo‐diversity metrics, we organize existing metrics by expanding on a unifying framework for phylogenetic information. Generally, questions about phylogenetic relationships within or between assemblages tend to ask three types of question: how much; how different; or how regular? We show that these questions reflect three dimensions of a phylogenetic tree: richness, divergence, and regularity. We classify 70 existing phylo‐diversity metrics based on their mathematical form within these three dimensions and identify ‘anchor’ representatives: for α‐diversity metrics these are PD (Faith's phylogenetic diversity), MPD (mean pairwise distance), and VPD (variation of pairwise distances). By analysing mathematical formulae and using simulations, we use this framework to identify metrics that mix dimensions, and we provide a guide to choosing and using the most appropriate metrics. We show that metric choice requires connecting the research question with the correct dimension of the framework and that there are logical approaches to selecting and interpreting metrics. The guide outlined herein will help researchers navigate the current jungle of indices.     

Re‐approaching the small island effect

Aim To propose a new approach to the small island effect (SIE) and a simple mathematical procedure for the estimation of its upper limit. The main feature of the SIE is that below an upper size threshold an increase of species number with increase of area in small islands is not observed. Location Species richness patterns from different taxa and insular systems are analysed. Methods Sixteen different data sets from 12 studies are analysed. Path analysis was used for the estimation of the upper limit of the SIE. We studied each data set in order to detect whether there was a certain island size under which the direct effects of area were eliminated. This detection was carried out through the sequential exclusion of islands from the largest to the smallest. For the cases where an SIE was detected, a log‐log plot of species number against area is presented. The relationships between habitat diversity, species number and area are studied within the limits of the SIE. In previous studies only area was used for the detection of the SIE, whereas we also encompass habitat diversity, a parameter with well documented influence on species richness, especially at small scales. Results An SIE was detected in six out of the 16 studied cases. The upper limit of the SIE varies, depending on the characteristics of the taxon and the archipelago under study. In general, the values of the upper limit of the SIE calculated according to the approach undertaken in our study differ from the values calculated in previous studies. Main conclusions Although the classical species–area models have been used to estimate the upper limit of the SIE, we propose that the detection of this phenomenon should be undertaken independently from the species–area relationship, so that the net effects of area are calculated excluding the surrogate action of area on other variables, such as environmental heterogeneity. The SIE appears when and where area ceases to influence species richness directly. There are two distinct SIE patterns: (1) the classical SIE where both the direct and indirect effects of area are eliminated and (2) the cryptic SIE where area affects species richness indirectly. Our approach offers the opportunity of studying the different factors influencing biodiversity on small scales more accurately. The SIE cannot be considered a general pattern with fixed behaviour that can be described by the same model for different island groups and taxa. The SIE should be recognized as a genuine but idiosyncratic phenomenon.     

Predicting biodiversity loss in island and countryside ecosystems through the lens of taxonomic and functional biogeography

We investigate how variation in patch area and forest cover quantified for three different spatial scales (buffer size of 500, 1500 and 3000 m radius) affects species richness and functional diversity of bat assemblages in two ecosystems differing in fragment–matrix contrast: a landbridge island system in Panama and a countryside ecosystem in the Brazilian Amazon. Bats were sampled on 11 islands and the adjacent mainland in Panama, and in eight forest fragments and nearby continuous forest in Brazil. Species–area relationships (SAR) were assessed based on Chao1 species richness estimates, and functional diversity–area relationships (FAR) were quantified using Chao1 functional diversity estimates measured as the total branch length of a trait dendrogram. FARs were calculated using three trait sets: considering five species functional traits (FAR_ALL), and trait subsets reflecting ‘diet breadth’ (FAR_DIET) and ‘dispersal ability’ (FAR_DISPERSAL). We found that in both study systems, FAR_ALL was less sensitive to habitat loss than SAR, in the sense that an equal reduction in habitat loss led to a disproportionately smaller loss of functional diversity compared to species richness. However, the inhospitable and static aquatic matrix in the island ecosystem resulted in more pronounced species loss with increasing loss of habitat compared to the countryside ecosystem. Moreover, while we found a significant FAR_DISPERSAL for the island ecosystem in relation to forest cover within 500 m landscape buffers, FAR_DIET and FAR_DISPERSAL were not significant for the countryside ecosystem. Our findings highlight that species richness and functional diversity in island and countryside ecosystems scale fundamentally differently with habitat loss, and suggest that key bat ecological functions, such as pollination, seed dispersal and arthropod suppression, may be maintained in fragments despite a reduction in species richness. Our study reinforces the importance of increasing habitat availability for decreasing the chances of losing species richness in smaller fragments.     

The merging of community ecology and phylogenetic biology

The increasing availability of phylogenetic data, computing power and informatics tools has facilitated a rapid expansion of studies that apply phylogenetic data and methods to community ecology. Several key areas are reviewed in which phylogenetic information helps to resolve long-standing controversies in community ecology, challenges previous assumptions, and opens new areas of investigation. In particular, studies in phylogenetic community ecology have helped to reveal the multitude of processes driving community assembly and have demonstrated the importance of evolution in the assembly process. Phylogenetic approaches have also increased understanding of the consequences of community interactions for speciation, adaptation and extinction. Finally, phylogenetic community structure and composition holds promise for predicting ecosystem processes and impacts of global change. Major challenges to advancing these areas remain. In particular, determining the extent to which ecologically relevant traits are phylogenetically conserved or convergent, and over what temporal scale, is critical to understanding the causes of community phylogenetic structure and its evolutionary and ecosystem consequences. Harnessing phylogenetic information to understand and forecast changes in diversity and dynamics of communities is a critical step in managing and restoring the Earth's biota in a time of rapid global change.     

Small area and low connectivity constrain the diversity of plant life strategies in temporary ponds

Aim

(i) To determine whether area and connectivity of temporary ponds can predict plant species diversity, and the diversity and abundance of different plant life histories; (ii) To explore whether pond connectivity with the river prior to river regulation predicts better plant diversity patterns than current pond connectivity, suggestive of possible effects of connectivity loss.

Location

Eastern Carpathian Mountains, Romania, Europe.

Methods

We fitted linear and generalized linear models (LM and GLM) to examine whether pond area and current distance from the Olt River predict plant species richness, Shannon diversity and relative cover of different social behaviour types and overall plant species richness and Shannon diversity. Using historical maps, we measured pond distance from the river ca. 60 years before the Olt River was regulated, and we refitted the LM and GLM models using pond area and past distance from the river as independent variables.

Results

Total plant species richness increased with pond area, and it decreased with the distance from the river, but total plant Shannon diversity index was affected, positively, only by pond area. The strength of responses to pond area and connectivity of species richness, Shannon diversity and relative cover varied across the different social behaviour types. Past and current distances between ponds and riverbeds had similar effects on plant diversity, with some evidence for stronger effect of the present connectivity on specialist species Shannon diversity and a weaker effect on disturbance tolerants, generalists and competitors.

Main Conclusions

Pond area and connectivity with the landscape are important predictors of the diversity of plant life history strategies, and therefore, useful tools in pond conservation. Consistent species richness and Shannon diversity responses of wetland specialists to pond area and connectivity make this life history type well suited for monitoring pond condition.     

Orchids of the West Indies: predictability of diversity and endemism

Aim We examined phytogeographical patterns of West Indian orchids, and related island area and maximum elevation with orchid species richness and endemism. We expected strong species–area relationships, but that these would differ between low and montane island groups. In so far as maximum island elevation is a surrogate for habitat diversity, we anticipated a strong relationship with maximum elevation and both species richness and endemism for montane islands. Location The West Indies. Methods Our data included 49 islands and 728 species. Islands were classified as either montane (≥ 300 m elevation) or low (< 300 m). Linear and multivariate regression analyses were run to detect relationships between either area or maximum island elevation and species richness or the number of island endemic species. Results For all 49 islands, the species–area relationship was strong, producing a z‐value of 0.47 (slope of the regression line) and explaining 46% of the variation. For 18 relatively homogeneous, low islands we found a non‐significant slope of z = −0.01 that explained only 0.1% of the variation. The 31 montane islands had a highly significant species–area relationship, with z = 0.49 and accounting for 65% of the variation. Species numbers were also strongly related to maximum island elevation. For all islands < 750 km², we found a small‐island effect, which reduced the species–area relationship to a non‐significant z = 0.16, with only 5% of the variation explained by the model. Species–area relationships for montane islands of at least 750 km² were strong and significant, but maximum elevation was the best predictor of species richness and accounted for 79% of the variation. The frequency of single‐island endemics was high (42%) but nearly all occurred on just nine montane islands (300 species). The taxonomic distribution of endemics was also skewed, suggesting that seed dispersability, while remarkable in some taxa, is very limited in others. Montane island endemics showed strong species–area and species–elevation relationships. Main conclusions Area and elevation are good predictors of orchid species diversity and endemism in the West Indies, but these associations are driven by the extraordinarily strong relationships of large, montane islands. The species richness of low islands showed no significant relationship with either variable. A small‐island effect exists, but the montane islands had a significant relationship between species diversity and maximum elevation. Thus, patterns of Caribbean orchid diversity are dependent on an interplay between area and topographic diversity.     

Spatial patterns of phylogenetic diversity

Ecologists and conservation biologists have historically used species-area and distance-decay relationships as tools to predict the spatial distribution of biodiversity and the impact of habitat loss on biodiversity. These tools treat each species as evolutionarily equivalent, yet the importance of species' evolutionary history in their ecology and conservation is becoming increasingly evident. Here, we provide theoretical predictions for phylogenetic analogues of the species-area and distance-decay relationships. We use a random model of community assembly and a spatially explicit flora dataset collected in four Mediterranean-type regions to provide theoretical predictions for the increase in phylogenetic diversity - the total phylogenetic branch-length separating a set of species - with increasing area and the decay in phylogenetic similarity with geographic separation. These developments may ultimately provide insights into the evolution and assembly of biological communities, and guide the selection of protected areas.     

A taxonomic and phylogenetic perspective on plant community assembly along an elevational gradient in subtropical forests

亚热带森林植物群落沿海拔梯度的分类与系统发育研究 生物多样性沿海拔梯度的分布格局已受到广泛关注。然而,生物多样性格局沿海拔梯度的变异及其潜在机制尚不清楚。整合生物多样性的多维度信息为理解群落构建机制提供了新思路。本研究在我国东部亚热带森林沿海拔270–1470 m的梯度上设置了17个木本植物固定样地,分析了沿海拔梯度植物群落 构建的生态和进化驱动力。基于样地内物种出现(0–1数据)和多度信息,计算群落内被子植物的物种和系统发育alpha和beta多样性、系统发育结构等,并量化多样性指标与微气候和地形之间的关系。研究发现,不论多度加权与否,物种alpha多样性均沿海拔升高而增加,物种和系统发育的相似性随海拔距离的增加而呈衰减趋势。然而,多度加权与否会形成不同的系统发育alpha多样性格局。对于系统发育结构而言,沿海拔增加并无明显趋势。地形和微气候是多样性格局和系统发育结构的主要驱动力。与未考虑物种多度的多样性指标相比,多度加权的指标与坡度和胸高断面积相关性更高。这些结果表明,由局域物种多度介导的确定性过程对沿海拔梯度的植物群落构建具有一定影响。     

A global analysis of avian island diversity–area relationships in the Anthropocene

Research on island species–area relationships (ISAR) has expanded to incorporate functional (IFDAR) and phylogenetic (IPDAR) diversity. However, relative to the ISAR, we know little about IFDARs and IPDARs, and lack synthetic global analyses of variation in form of these three categories of island diversity–area relationship (IDAR). Here, we undertake the first comparative evaluation of IDARs at the global scale using 51 avian archipelagic data sets representing true and habitat islands. Using null models, we explore how richness-corrected functional and phylogenetic diversity scale with island area. We also provide the largest global assessment of the impacts of species introductions and extinctions on the IDAR. Results show that increasing richness with area is the primary driver of the (non-richness corrected) IPDAR and IFDAR for many data sets. However, for several archipelagos, richness-corrected functional and phylogenetic diversity changes linearly with island area, suggesting that the dominant community assembly processes shift along the island area gradient. We also find that archipelagos with the steepest ISARs exhibit the biggest differences in slope between IDARs, indicating increased functional and phylogenetic redundancy on larger islands in these archipelagos. In several cases introduced species seem to have ‘re-calibrated’ the IDARs such that they resemble the historic period prior to recent extinctions.     

The influence of biogeographic history on the functional and phylogenetic diversity of passerine birds in savannas and forests of the Brazilian Amazon

Passeriformes is the largest and most diverse avian order in the world and comprises the Passeri and Tyranni suborders. These suborders constitute a monophyletic group, but differ in their ecology and history of occupation of South America. We investigated the influence of biogeographic history on functional and phylogenetic diversities of Passeri and Tyranni in forest and savanna habitats in the Brazilian Amazon. We compiled species composition data for 34 Passeriformes assemblages, 12 in savannas and 22 in forests. We calculated the functional (Rao's quadratic entropy, FD_Q) and phylogenetic diversities (mean pairwise distance, MPD, and mean nearest taxon distance, MNTD), and the functional beta diversity to investigate the potential role of biogeographic history in shaping ecological traits and species lineages of both suborders. The functional diversity of Passeri was higher than for Tyranni in both habitats. The MPD for Tyranni was higher than for Passeri in forests; however, there was no difference between the suborders in savannas. In savannas, Passeri presented higher MNTD than Tyranni, while in forest areas, Tyranni assemblages showed higher MNTD than Passeri. We found a high functional turnover (~75%) between Passeri and Tyranni in both habitats. The high functional diversity of Passeri in both habitats is due to the high diversity of ecological traits exhibited by species of this group, which enables the exploitation of a wide variety of resources and foraging strategies. The higher Tyranni MPD and MNTD in forests is likely due to Tyranni being older settlers in this habitat, resulting in the emergence and persistence of more lineages. The higher Passeri MNTD in savannas can be explained by the existence of a larger number of different Passeri lineages adapted to this severe habitat. The high functional turnover between the suborders in both habitats suggests an ecological strategy to avoid niche overlap.     

Separating the determinants of phylogenetic community structure

The role of competition in forbidding similar species from co-occurring has long been debated. A difficulty in identifying this repulsion of similar species is that similar species share similar environmental requirements and hence show an attraction to communities where these requirements are met. To disentangle these opposing patterns, we use phylogenetic relatedness as an objective metric of species similarities. Studying 11 sunfishes (Centrarchidae) from 890 lakes, we first show no phylogenetic pattern in the raw community data. We then regressed sunfish presence/absence against seven environmental variables and show that lakes with similar water clarity and latitude likely contain closely related species. After statistically removing the environmental effects, phylogenetic repulsion was apparent, with closely related sunfishes less likely to co-occur. Thus, both phylogenetic attraction, driven by environmental filtering, and phylogenetic repulsion, possibly caused by competition, simultaneously occur and obscure one another in the overall phylogenetic structure of sunfish communities.     

Unravelling virus community ecology in bats through the integration of metagenomics and community ecology

The spillover of viruses from wildlife into agricultural animals or humans has profound socioeconomic and public health impact. Vampire bats, found throughout South America, feed directly on humans and other animals and are an important reservoir for zoonotic viruses, including rabies virus. This has resulted in considerable effort in understanding both the ecology of bat‐borne viruses and the composition and associated correlates of the structure of entire virus communities in wildlife, particularly in the context of disease control interventions. In a From the Cover article in this issue of Molecular Ecology, Bergner et al. (2019) set out to reveal virus community dynamics in vampire bats by interrogating factors that affect the structure, diversity and richness of these communities. Due to the linkage of metagenomic sequence data with community ecology, this study represents an important advance in the field of virus ecology.     

Unravelling the evolutionary origins of biogeographic assemblages

Aim

Floristic and faunal diversity fall within species assemblages that can be grouped into distinct biomes or ecoregions. Understanding the origins of such biogeographic assemblages helps illuminate the processes shaping present‐day diversity patterns and identifies regions with unique or distinct histories. While the fossil record is often sparse, dated phylogenies can provide a window into the evolutionary past of these regions. Here, we present a novel phylogenetic approach to investigate the evolutionary origins of present‐day biogeographic assemblages and highlight their conservation value.

Location

Southern Africa.

Methods

We evaluate the evolutionary turnover separating species clusters in space at different time slices to determine the phylogenetic depth at which the signal for their present‐day structure emerges. We suggest present‐day assemblages with distinct evolutionary histories might represent important units for conservation. We apply our method to the vegetation of southern Africa using a dated phylogeny of the woody flora of the region and explore how the evolutionary history of vegetation types compares to common conservation currencies, including species richness, endemism and threat.

Results

We show the differentiation of most present‐day vegetation types can be traced back to evolutionary splits in the Miocene. The woody flora of the Fynbos is the most evolutionarily distinct, and thus has deeper evolutionary roots, whereas the Savanna and Miombo Woodland show close phylogenetic affinities and likely represent a more recent separation. However, evolutionarily distinct phyloregions do not necessarily capture the most unique phylogenetic diversity, nor are they the most species‐rich or threatened.

Main conclusions

Our approach complements analyses of the fossil record and serves as a link to the history of diversification, migration and extinction of lineages within biogeographic assemblages that is separate from patterns of species richness and endemism. Our analysis reveals how phyloregions capture conservation value not represented by traditional biodiversity metrics.