Ecological traits influence the phylogenetic structure of bird species co‐occurrences worldwide

The extent to which species’ ecological and phylogenetic relatedness shape their co‐occurrence patterns at large spatial scales remains poorly understood. By quantifying phylogenetic assemblage structure within geographic ranges of >8000 bird species, we show that global co‐occurrence patterns are linked – after accounting for regional effects – to key ecological traits reflecting diet, mobility, body size and climatic preference. We found that co‐occurrences of carnivorous, migratory and cold‐climate species are phylogenetically clustered, whereas nectarivores, herbivores, frugivores and invertebrate eaters tend to be more phylogenetically overdispersed. Preference for open or forested habitats appeared to be independent from the level of phylogenetic clustering. Our results advocate for an extension of the tropical niche conservatism hypothesis to incorporate ecological and life‐history traits beyond the climatic niche. They further offer a novel species‐oriented perspective on how biogeographic and evolutionary legacies interact with ecological traits to shape global patterns of species coexistence in birds.     

Scale dependence in the phylogenetic relatedness of alien and native taxa

达尔文的归化假说提出,由于生态位的不同,成功建群的外来物种与本地物种的关系不太密切。先前的研究对这一假设有支持也有反对,其中一个原因是外来物种和本地物种在大的空间尺度上有系统发育聚类的倾向,而在细微尺度上存在过度分散的倾向。然而,对于外来物种的系统发育关系如何改变其入侵群落的系统发育结构,以及在何种空间尺度上可能表现出这种影响,人们知之甚少。在本研究中,我们调查被入侵的森林下层植物群落在系统发育上是聚集的还是或过度分散的,亲缘关系如何随空间尺度变化,以及外来物种如何影响下层群落的系统发育模式。在澳大利亚东南部干旱森林的下层群落进行了5个空间尺度(1, 20, 500, 1500和4500 m²)的实地调查。使用两个指标的标准化效应量[(i)平均成对距离和(ii)平均最近分类单元距离]来量化群落与其外来和本地亚群落之间的系统发育关系,并研究系统发育模 式如何随空间尺度变化。研究结果表明,外来物种之间的亲缘关系非常密切,而且这种亲缘关系会随着尺度的增加而增加。在中等空间尺 度下(20–500 m²), 整个群落呈随机分布趋势,而本地物种高度分散,外来亚群落高度聚集。这说明亲缘关系密切的外来物种入侵使群落系统发育结构由过度分散向随机分布转变。外来物种和本地物种在空间尺度上是远亲,这支持了达尔文的归化假说,但只是在系统发育距离被量化为平均最近分类单元距离时成立。外来物种和本地物种的系统发育差异随着空间尺度的增加而增加,这与预期的模式相反。我们的研究结果表明,外来物种强大的系统发育聚类是由人类干预的引入驱动的,牵涉能够成功建群和传播的密切相关的类群。系统发育相关性的尺度依赖模式可能是由火灾和散布等随机过程引起的,这表明竞争和生境过滤并不是分别在小和大尺度上控制系统发育关系的唯一因素。区分不同进化深度的指标很重要,因为不同的指标可以显示不同的尺度依赖模式。     

Waterbird assemblages and associated habitat characteristics of farm ponds in the Western Cape, South Africa

Natural freshwater wetlands are among the most threatened habitats on Earth. Effective wetland biodiversity conservation can not, however, be evaluated without fully understanding the roles of artificial waterbodies as refuges for water-dependent plants and animals. Waterbird assemblages were examined on 59 farm ponds in the Elgin and Caledon districts of the Western Cape, South Africa. This study examines the relationship between waterbird use and habitat characteristics of farm ponds. Patterns of temporal and spatial variation of waterbird species richness and abundance were quantified in relation to the habitat characteristics of each pond. Cluster analysis and multiple regression analyses identified surface area of the farm ponds as an important variable determining the presence and abundance of many waterbird species. Structural diversity in terms of vegetation in and around the ponds was especially important in determining their usage by waterbirds. These variables were evaluated in terms of creating a mosaic of habitat types (by varying vegetation structure and pond topography), which may be a useful way to enhance waterbird diversity at farm ponds. This study concludes that the high number of farm ponds in the transformed habitat matrix of the Western Cape plays an important role in conserving waterbirds.     

Multicontinental community phylogenetics of avian mixed‐species flocks reveal the role of the stability of associations and of kleptoparasitism

If understood as a way to forage socially without incurring intra‐specific competition for mates or other resources, mixed‐species foraging flocks are predicted to be composed of functionally similar species. In the most intensively studied mixed‐species foraging system, understory forest birds, relevant functional traits are however extremely difficult to measure and best replaced by phylogenetic relatedness. A multicontinental analysis of flock phylogenetic structure revealed departures from the expected phylogenetic clustering. Long‐lasting associations (> one day) were phylogenetically overdispersed, indicating that these associations are affected by competitive exclusion or by mutualistic interactions. However, where kleptoparasites occurred, this effect disappeared completely, as expected if the dilution of kleptoparasitism risk compensated competition between related species. Mixed‐species flocks should not be analyzed as a homogeneous phenomenon.     

The effects of phylogenetic relatedness on invasion success and impact: deconstructing Darwin's naturalisation conundrum

Darwin's naturalisation conundrum describes the paradox that the relatedness of exotic species to native residents could either promote or hinder their success through opposing mechanisms: niche pre‐adaptation or competitive interactions. Previous studies focusing on single snapshots of invasion patterns have provided support to both sides of the conundrum. Here, by examining invasion dynamics of 480 plots over 40 years, we show that exotic species more closely related to native species were more likely to enter, establish and dominate the resident communities, and that native residents more closely related to these successful exotics were more likely to go locally extinct. Therefore, non‐random displacement of natives during invasion could weaken or even reverse the negative effects of exotic–native phylogenetic distances on invasion success. The scenario that exotics more closely related to native residents are more successful, but tend to eliminate their closely related natives, may help to reconcile the 150‐year‐old conundrum.     

Longitudinal gradients in the phylogenetic community structure of European Tenebrionidae (Coleoptera) do not coincide with the major routes of postglacial colonization

Species specific colonization abilities and biotic and abiotic filters influence the local and regional faunal composition along colonization trajectories. Using a recent compilation of the occurrences of 1373 darkling beetle (Tenebrionidae) species and subspecies in 49 European countries and major islands, we reconstructed the tenebrionid postglacial colonization of middle and northern Europe from southern European glacial refuges and linked species composition to latitudinal and longitudinal gradients in phylogenetic relatedness across Europe. The majority of European islands and mainland countries appeared to be phylogenetically clustered. We did not find significant latitudinal trends in average phylogenetic relatedness of regional faunas along the supposed postglacial colonization routes but detected a strong positive correlation between mean relatedness and longitude of mainland faunas and an opposite negative correlation for island faunas. The strength of phylogenetic relatedness in the regional tenebrionid faunas decreased significantly with latitude and to a lesser degree with longitude. These findings are in accordance with two trajectories of postglacial colonization from centres in Spain and middle Asia that caused a strong longitudinal trend in the phylogenetic relatedness. Subsequent pair‐wise analyses of species co‐occurrences showed that species of similar distributional ranges tend to be phylogenetically clustered and species of different spatial distribution to be phylogenetically segregated. Both findings are in accordance with the concept of ‘range size heritability’. Our study demonstrates that taxonomic data are sufficiently powerful to infer continental wide patterns in phylogenetic relatedness that can be linked to colonization history and geographic information.     

Effect of landscape configuration and habitat quality on the community structure of waterbirds using a man-made habitat

Species occurrence and community structure are strongly influenced by multiple factors like habitat selection, species movement capabilities, competition, or conspecific and heterospecific attractions. More specifically, in waterbird communities, previous studies have identified the importance of environmental and structural characteristics of wetlands for their occupation and use. However, the effect of the surrounding landscape configuration remains unknown. In this article, we use a large network of artificial irrigation ponds to evaluate the importance of pond features in comparison to the effect of landscape and spatial configuration on the community at three different spatial scales. Our results show that landscape configuration has relatively little influence on structure of the waterbird community. Pond features were by far the most important variables to describe waterbird abundance and richness. At the species level, we detected differences in habitat preferences relating to species-specific ecological requirements. Our results highlight the importance of using a multiscale approach to understand and predict richness and abundance in waterbird communities. Our findings emphasize the need to maintain high-quality ponds to enhance their suitability for use as breeding and foraging sites.     

Global patterns of phylogenetic relatedness of invasive flowering plants

Aim

The ability of predicting which naturalized non-native species are likely to become invasive can help manage and prevent species invasions. The goal of this study is to test whether invasive angiosperm (flowering plant) species are a phylogenetically clustered subset of naturalized species at global, continental and regional scales, and to assess the relationships of phylogenetic relatedness of invasive species with climate condition (temperature and precipitation).

Location

Global.

Time period

Current.

Taxon

Angiosperms (flowering plants).

Methods

The globe is divided into 290 regions, which are grouped into seven biogeographic (continental) regions. Two phylogenetic metrics (net relatedness index and nearest taxon index), which represent different evolutionary depths, are used to quantify phylogenetic relatedness of invasive angiosperms, with respect to different tailor-made species pools. Phylogenetic relatedness of invasive angiosperms is related to climatic variables.

Results

The global assemblage of invasive angiosperm species is a strongly phylogenetically clustered subset of the species of the entire global angiosperm flora. Most invasive angiosperm assemblages are a phylogenetically clustered subset of their respective naturalized species pools, and phylogenetic clustering reflecting shallow evolutionary history is greater than that reflecting deep evolutionary history. In general, the phylogenetic relatedness of invasive species is greater in regions with lower temperature and precipitation across the world.

Main conclusions

The finding that invasive angiosperm assemblages across the globe are, in general, phylogenetically clustered subsets of their respective naturalized species pools has significant implications in biological conservation, particularly in predicting and controlling invasive species based on phylogenetic relatedness among naturalized species.     

Fire modifies the phylogenetic structure of soil bacterial co‐occurrence networks

Fire alters ecosystems by changing the composition and community structure of soil microbes. The phylogenetic structure of a community provides clues about its main assembling mechanisms. While environmental filtering tends to reduce the community phylogenetic diversity by selecting for functionally (and hence phylogenetically) similar species, processes like competitive exclusion by limiting similarity tend to increase it by preventing the coexistence of functionally (and phylogenetically) similar species. We used co‐occurrence networks to detect co‐presence (bacteria that co‐occur) or exclusion (bacteria that do not co‐occur) links indicative of the ecological interactions structuring the community. We propose that inspecting the phylogenetic structure of co‐presence or exclusion links allows to detect the main processes simultaneously assembling the community. We monitored a soil bacterial community after an experimental fire and found that fire altered its composition, richness and phylogenetic diversity. Both co‐presence and exclusion links were more phylogenetically related than expected by chance. We interpret such a phylogenetic clustering in co‐presence links as a result of environmental filtering, while that in exclusion links reflects competitive exclusion by limiting similarity. This suggests that environmental filtering and limiting similarity operate simultaneously to assemble soil bacterial communities, widening the traditional view that only environmental filtering structures bacterial communities.     

Agricultural ponds as alternative habitat for waterbirds: spatial and temporal patterns of abundance and management strategies

The progressive lost of natural wetlands as a consequence of human activities has lead to the use of new habitats by the species linked to water presence. In Southeast Spain, thousands of irrigation ponds have been lately constructed to store water for agriculture and are used by waterbirds as an alternative habitat. For this study, breeding and wintering waterbirds were counted in a subset of irrigation ponds between 2002 and 2007. Breeding communities were more abundant than wintering communities, but they presented a similar richness and diversity. The ponds were selected by waterbirds according to their characteristics, and breeding communities were more selective than wintering communities. Our results enhance the importance of pond size (area), connectivity (distance to the nearest wetland) and habitat quality (resource offer and construction material) in the pond selection process. The presence and design of these impoundments could be playing a crucial role for some waterbirds species. Therefore, the long-term information provided here can be useful for establishing management strategies for these artificial wetlands.     

Random placement models predict species–area relationships in duck communities despite species aggregation

Species–area relationships are the product of many ecological processes and their interactions. Explanations for the species–area relationship (SAR) have focused on separating putative niche‐based mechanisms that correlate with area from sampling effects caused by patches with more individuals containing more species than patches with fewer individuals. We tested the hypothesis that SARs in breeding waterfowl communities are caused by sampling effects (i.e. random placement from the regional species pool). First, we described observed SARs and patterns of species associations for fourteen species of ducks on ponds in prairie Canada. Second, we used null models, which randomly allocated ducks to ponds, to test if observed SARs and patterns of species associations differed from those expected by chance. Consistent with the sampling effects hypothesis, observed SARs were accurately predicted by null models in three different years and for diving and dabbling duck guilds. This is the first demonstration that null models can predict SARs in waterbirds or any other aquatic organisms. Observed patterns of species association, however, were not well predicted by null models as in all years there was less observed segregation among species (i.e. more aggregation) than under the random expectation, suggesting that intraspecific competition could play a role in structuring duck communities. Taken together, our results indicate that when emergent properties of ecological communities such as the SAR appear to be caused by random processes, analyses of species associations can be critical in revealing the importance of niche‐based processes (e.g. competition) in structuring ecological communities.     

Co‐occurrence and phylogenetic distance in communities of mammalian ectoparasites: limiting similarity versus environmental filtering

Similarity between species plays a key role in the processes governing community assembly. The co‐occurrence of highly similar species may be unlikely if their similar needs lead to intense competition (limiting similarity). On the other hand, persistence in a particular habitat may require certain traits, such that communities end up consisting of species sharing the same traits (environmental filtering). Relatively little information exists on the relative importance of these processes in structuring parasite communities. Assuming that phylogenetic relatedness reflects ecological similarity, we tested whether the co‐occurrence of pairs of flea species (Siphonaptera) on the same host individuals was explained by the phylogenetic distance between them, among 40 different samples of mammalian hosts (rodents and shrews) from different species, areas or seasons. Our results indicate that frequency of co‐occurrence between flea species increased with decreasing phylogenetic distance between them in 37 out of 40 community samples, with 14 of these correlations being statistically significant. A meta‐analysis across all samples confirmed the overall trend for closely related species to co‐occur more frequently on the same individual hosts than expected by chance, independently of the identity of the host species or of environmental conditions. These findings suggest that competition between closely related, and therefore presumably ecologically similar, species is not important in shaping flea communities. Instead, if only fleas with certain behavioural, ecological and physiological properties can encounter and exploit a given host, and if phylogenetic relationships determine trait similarity among flea species, then a process akin to environmental filtering, or host filtering, could favour the co‐occurrence of related species on the same host.     

冬季水鸟对崇明东滩水产养殖塘的利用

自然湿地的丧失和退化给依赖湿地生存的水鸟带来了严重威胁,人工湿地作为水鸟栖息地的功能日益受到关注.水产养殖塘是人工湿地的重要类型之一.通过研究崇明东滩水产养殖塘冬季水鸟群落组成及其栖息地特征,发现大面积养殖塘比小面积养殖塘吸引更多种类和更高密度的水鸟.养殖塘在放水前水位较高时吸引更多游禽栖息,而在放水后水位较低时吸引更多涉禽;在放水过程中,养殖塘中水鸟的种类最多,密度最大.另外,在放水的不同时期,不同的环境因子对水鸟群落的影响不同:放水之前,养殖塘水面面积和平均水深是水鸟种类和数量的主要影响因子,其中游禽种类和数量受水面面积影响较大,涉禽种类和数量受平均水深影响较大;放水过程中,裸地面积、芦苇面积、干扰程度、平均水深和水深变异对水鸟、游禽和涉禽的种类和数量起主要作用;放水之后,水深变异对水鸟种类和数量的影响较大,而影响游禽种类和数量的主要因子是水面面积,影响涉禽种类和数量的主要因子是水深变异.研究表明,通过对影响水鸟栖息地利用的主要因子的有效管理,养殖塘在提供经济效益的同时也能为水鸟提供适宜的栖息地.     

Habitat Use by Waterbirds in Relation to Pond Size,Water Depth,and Isolation: Lessons from a Restoration in Southern Spain

Wetland restoration is increasingly important to reverse habitat degradation, recover ecosystem services, and maintain biodiversity. To aid project design, more information is required on the influence of wetland size, depth of water, and isolation on the waterbird communities that become established. During a restoration project in Doñana, one of the Europe's most important wetland complexes, an experimental network of 96 temporary ponds with standard shape but variable size, water depth, and isolation was created. We surveyed the waterbird community in spring from 2006 to 2008 and related species abundance and richness to abiotic pond characteristics. We also performed analyses pooling species by foraging guilds or body size. Waterbird abundance and species richness were highest in 2007, the wettest year when the ponds had longer hydroperiods. Larger ponds had consistently higher abundance and species richness for the entire community and for different guilds and body sizes. Moreover, the density of birds per hectare was higher in large ponds than in the smaller ones. Pond isolation and excavated depth did not affect overall abundance and richness, although opposing effects of depth were observed on some size classes, and ducks and large birds preferred isolated ponds. Some bird groups preferred ponds at a particular location. This is the first waterbird study to address the importance of pond size, depth, and isolation independently of confounding variables such as pond shape. It illustrates the varied responses from different bird groups and demonstrates the importance of varying depth, location, and isolation to enhance community abundance and diversity .     

Breeding waterbirds in relation to artificial pond attributes: implications for the design of irrigation facilities

The growth of inter-basin water transfers and the development of new irrigation facilities in southeastern Spain are responsible for a variety of ecological impacts. In spite of this, the construction of artificial ponds to keep water for intensive agriculture may also provide new habitats for breeding waterbirds. We counted waterbirds during the breeding season in artificial ponds that had been built up using different materials and measured their abiotic and biotic attributes. We found that ponds were used as breeding and foraging habitat by 22 different waterbird species and breeding numbers of a few of them seemed to be larger in these artificial facilities than in nearby natural and semi-natural wetlands. Abundance and richness of breeding waterbirds was influenced by construction materials. Ponds constructed with low density polyethylene and covered with sand and stones held more species and their numbers were higher than those constructed with other plastic materials. The presence of emergent and submerged vegetation as well as abiotic attributes, such as pond size, accounted for most of the deviance when modelling richness and species abundance.     

Darwin's naturalization hypothesis: scale matters in coastal plant communities

Darwin proposed two seemingly contradictory hypotheses for a better understanding of biological invasions. Strong relatedness of invaders to native communities as an indication of niche overlap could promote naturalization because of appropriate niche adaptation, but could also hamper naturalization because of negative interactions with native species (‘Darwin's naturalization hypothesis’). Although these hypotheses provide clear and opposing predictions for expected patterns of species relatedness in invaded communities, so far no study has been able to clearly disentangle the underlying mechanisms. We hypothesize that conflicting past results are mainly due to the neglected role of spatial resolution of the community sampling. In this study, we corroborate both of Darwin's expectations by using phylogenetic relatedness as a measure of niche overlap and by testing the effects of sampling resolution in highly invaded coastal plant communities. At spatial resolutions fine enough to detect signatures of biotic interactions, we find that most invaders are less related to their nearest relative in invaded plant communities than expected by chance (phylogenetic overdispersion). Yet at coarser spatial resolutions, native assemblages become more invasible for closely‐related species as a consequence of habitat filtering (phylogenetic clustering). Recognition of the importance of the spatial resolution at which communities are studied allows apparently contrasting theoretical and empirical results to be reconciled. Our study opens new perspectives on how to better detect, differentiate and understand the impact of negative biotic interactions and habitat filtering on the ability of invaders to establish in native communities.     

Macroevolution and climate change influence phylogenetic community assembly of North American hoofed mammals

Animal richness, community composition, and phylogenetic community structure (PCS) vary across the modern landscape. Animal communities vary from phylogenetically clustered (i.e. higher relatedness amongst co‐occurring species than is expected by chance) to phylogenetically even (i.e. co‐occurring taxa are more distantly related than expected by chance), which is explained by abiotic or climatic filtering and competitive exclusion, respectively. Under this model, the contribution of historical origination and extinction events to modern animal PCS remains relatively unknown. Because origination and extinction determine the make‐up of the terrestrial community, the study of historical changes in animal PCS is tantamount to understanding formation of modern communities. In the present study, we test the effects of macroevolution and climate changes on ‘hoofed mammals’ (i.e. perissodactyl and artiodactyl) PCS from the late Cenozoic of North America because they experience large, phylogenetically dispersed extinctions of browsing species and phylogenetically dispersed originations of grazing species associated with the evolution of grassland ecosystems during the late Miocene. We show that the loss of numerically dominant nonhypsodont (putatively browsing and mixed feeding) clades and phylogenetically dispersed origination of less speciose clades following the mid Miocene climatic optimum led to an increase in phylogenetic evenness at the regional scale that is well explained by global climate changes. Phylogenetic evenness and a reduced richness during the late Cenozoic may have facilitated reduced niche overlap among co‐occurring hoofed mammal species as global climates cooled. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 485–494.     

Phylogenetic and functional structures of succession in plant communities on mounds of Marmota himalayana in alpine regions on the northeast edge of the Qinghai–Tibet Plateau

Few studies have examined the succession of plant communities in the alpine zone. Studying the succession of plant communities is helpful to understand how species diversity is formed and maintained. In this study, we used species inventories, a molecular phylogeny, and trait data to detect patterns of phylogenetic and functional community structure in successional plant communities growing on the mounds of Himalayan marmots (Marmota himalayana) on the southeast edge of the Qinghai-Tibet Plateau. We found that phylogenetic and functional diversities of plant communities on marmot mounds tended to cluster during the early to medium stages of succession, then trended toward overdispersion from medium to late stages. Alpine species in early and late stages of succession were phylogenetically and functionally overdispersed, suggesting that such communities were assembled mainly through species interactions, especially competition. At the medium and late stages of succession, alpine communities growing on marmot mounds were phylogenetically and functionally clustered, implying that the communities were primarily structured by environmental filtering. During the medium and late stages of succession the phylogenetic and functional structures of plant communities on marmot mounds differed significantly from those on neighboring sites. Our results indicate that environmental filtering and species interactions can change plant community composition at different successional stages. Assembly of plant communities on marmot mounds was promoted by a combination of traits that may provide advantages for survival and adaptation during periods of environmental change.     

Phylogenetic relatedness and the determinants of competitive outcomes

Recent hypotheses argue that phylogenetic relatedness should predict both the niche differences that stabilise coexistence and the average fitness differences that drive competitive dominance. These still largely untested predictions complicate Darwin's hypothesis that more closely related species less easily coexist, and challenge the use of community phylogenetic patterns to infer competition. We field parameterised models of competitor dynamics with pairs of 18 California annual plant species, and then related species' niche and fitness differences to their phylogenetic distance. Stabilising niche differences were unrelated to phylogenetic distance, while species' average fitness showed phylogenetic structure. This meant that more distant relatives had greater competitive asymmetry, which should favour the coexistence of close relatives. Nonetheless, coexistence proved unrelated to phylogeny, due in part to increasing variance in fitness differences with phylogenetic distance, a previously overlooked property of such relationships. Together, these findings question the expectation that distant relatives should more readily coexist.     

Effects of flyway‐wide weather conditions and breeding habitat on the breeding abundance of migratory boreal waterbirds

Anthropogenic habitat loss and climate change are among the major threats to biodiversity. Bioclimatic zones such as the boreal and arctic regions are undergoing rapid environmental change, which will likely trigger changes in wildlife communities. Disentangling the effects of different drivers of environmental change on species is fundamental to better understand population dynamics under changing conditions. Therefore, in this study we investigate the synergistic effect of winter and summer weather conditions and habitat type on the abundance of 17 migratory boreal waterbird species breeding in Finland using three decades (1986–2015) of count data. We found that above‐average temperatures and precipitations across the western and northern range of the wintering grounds have a positive impact on breeding numbers in the following season, particularly for waterbirds breeding in eutrophic wetlands. Conversely, summer temperatures did not seem to affect waterbird abundance. Moreover, waterbird abundance was higher in eutrophic than in oligotrophic wetlands, but long term trends indicated that populations are decreasing faster in eutrophic than in oligotrophic wetlands. Our results suggest that global warming may apparently benefit waterbirds, e.g. by increased winter survival due to more favourable winter weather conditions. However, the observed population declines, particularly in eutrophic wetlands, may also indicate that the quality of breeding habitat is rapidly deteriorating through increased eutrophication in Finland which override the climatic effects. The findings of this study highlight the importance of embracing a holistic approach, from the level of a single catchment up to the whole flyway, in order to effectively address the threats that waterbirds face on their breeding as well as wintering grounds.