Urbanisation tolerance and the loss of avian diversity

Urbanisation is considered an important driver of current biodiversity loss, but the underlying causes are not fully understood. It is generally assumed that this loss reflects the fact that most organisms do not tolerate well the environmental alterations associated with urbanisation. Nevertheless, current evidence is inconclusive and the alternative that the biodiversity loss is the result of random mechanisms has never been evaluated. Analysing changes in abundance between urbanised environments and their non‐urbanised surroundings of > 800 avian species from five continents, we show here that although random processes account for part of the species loss associated with urbanisation, much of the loss is associated with a lack of appropriate adaptations of most species for exploiting resources and avoiding risks of the urban environments. These findings have important conservation implications because the extinction of species with particular features should have higher impact on biodiversity and ecosystem function than a random loss.     

The worldwide impact of urbanisation on avian functional diversity

Urbanisation is driving rapid declines in species richness and abundance worldwide, but the general implications for ecosystem function and services remain poorly understood. Here, we integrate global data on bird communities with comprehensive information on traits associated with ecological processes to show that assemblages in highly urbanised environments have substantially different functional composition and 20% less functional diversity on average than surrounding natural habitats. These changes occur without significant decreases in functional dissimilarity between species; instead, they are caused by a decrease in species richness and abundance evenness, leading to declines in functional redundancy. The reconfiguration and decline of native functional diversity in cities are not compensated by the presence of exotic species but are less severe under moderate levels of urbanisation. Thus, urbanisation has substantial negative impacts on functional diversity, potentially resulting in impaired provision of ecosystem services, but these impacts can be reduced by less intensive urbanisation practices.     

Successful city dwellers: a comparative study of the ecological characteristics of urban birds in the Western Palearctic

Numerous species have adapted to the proximity of humans, and this feature is no clearer than among species that have invaded towns and cities. The characteristics of species that have successfully managed to expand their range into urban areas remain largely unexplored, although they are of general interest in a world that is increasingly urbanised. I hypothesised that widely distributed species with high dispersal abilities, species with a high rate of innovation, a high level of risk-taking, and a fast life history would have a selective advantage in habitats influenced by humans. Consistent with this hypothesis, in a comparative analysis of 39 independent evolutionary events of urbanisation of birds in the Western Palearctic (thus taking the fact that closely related species that have become urbanised are caused by common phylogenetic descent rather than convergent evolution), bird species that adapted to urban habitats were characterised by large breeding ranges, high propensity for dispersal, high rates of feeding innovation (novel ways of acquiring food), short flight distances when approached by a human, and a life history characterised by high annual fecundity and high adult survival rate. Urban species may be disproportionately resistant to parasitism and predation because they had disproportionately strong immune responses, as reflected by the size of the bursa of Fabricius, and a history of weak predation-mediated natural selection, as reflected by the force required to remove feathers from the rump. Urban species had high overall ecological success as indicated by large range size and population size and high population density. This suggests that a suite of ecological features providing them with general ecological success characterises species of birds that have successfully invaded urban environments. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Selective extinction and rapid loss of evolutionary history in the bird fauna

The extinction of species results in a permanent loss of evolutionary history. Recent theoretical studies show that this loss may be proportionally much smaller than the loss of species, but under some conditions can exceed it. Such conditions occur when the phylogenetic tree that describes the evolutionary relationships among species is highly imbalanced due to differences between lineages in past speciation and/or extinction rates. I used the taxonomy by C. G. Sibley and B. L. Monroe Jr to estimate the global loss of bird evolutionary history from historical and predicted extinctions, and to quantify the ensuing changes in balance of the bird phylogenetic tree. In the global bird fauna, evolutionary history is being lost at a high rate, similar to the rate of species extinction. The bird phylogenetic tree is highly imbalanced, and the imbalance is increased significantly by anthropogenic extinction. Historically, the elevated loss of bird evolutionary history has been fuelled mostly by phylogenetic non-randomness in the extinction of species, but the direct effect of tree imbalance is substantial and could dominate in the future.     

The future of evolutionary diversity in reef corals

One-third of the world''s reef-building corals are facing heightened extinction risk from climate change and other anthropogenic impacts. Previous studies have shown that such threats are not distributed randomly across the coral tree of life, and future extinctions have the potential to disproportionately reduce the phylogenetic diversity of this group on a global scale. However, the impact of such losses on a regional scale remains poorly known. In this study, we use phylogenetic metrics in conjunction with geographical distributions of living reef coral species to model how extinctions are likely to affect evolutionary diversity across different ecoregions. Based on two measures—phylogenetic diversity and phylogenetic species variability—we highlight regions with the largest losses of evolutionary diversity and hence of potential conservation interest. Notably, the projected loss of evolutionary diversity is relatively low in the most species-rich areas such as the Coral Triangle, while many regions with fewer species stand to lose much larger shares of their diversity. We also suggest that for complex ecosystems like coral reefs it is important to consider changes in phylogenetic species variability; areas with disproportionate declines in this measure should be of concern even if phylogenetic diversity is not as impacted. These findings underscore the importance of integrating evolutionary history into conservation planning for safeguarding the future diversity of coral reefs.     

Diversity of plant evolutionary lineages promotes arthropod diversity

Large‐scale habitat destruction and climate change result in the non‐random loss of evolutionary lineages, reducing the amount of evolutionary history represented in ecological communities. Yet, we have limited understanding of the consequences of evolutionary history on the structure of food webs and the services provided by biological communities. Drawing on 11 years of data from a long‐term plant diversity experiment, we show that evolutionary history of plant communities – measured as phylogenetic diversity – strongly predicts diversity and abundance of herbivorous and predatory arthropods. Effects of plant species richness on arthropods become stronger when phylogenetic diversity is high. Plant phylogenetic diversity explains predator and parasitoid richness as strongly as it does herbivore richness. Our findings indicate that accounting for evolutionary relationships is critical to understanding the severity of species loss for food webs and ecosystems, and for developing conservation and restoration policies.     

Are Flying-Foxes Coming to Town? Urbanisation of the Spectacled Flying-Fox (Pteropus conspicillatus) in Australia

Urbanisation of wildlife populations is a process with significant conservation and management implications. While urban areas can provide habitat for wildlife, some urbanised species eventually come into conflict with humans. Understanding the process and drivers of wildlife urbanisation is fundamental to developing effective management responses to this phenomenon. In Australia, flying-foxes (Pteropodidae) are a common feature of urban environments, sometimes roosting in groups of tens of thousands of individuals. Flying-foxes appear to be becoming increasingly urbanised and are coming into increased contact and conflict with humans. Flying-fox management is now a highly contentious issue. In this study we used monitoring data collected over a 15 year period (1998–2012) to examine the spatial and temporal patterns of association of spectacled flying-fox (Pteropus conspicillatus) roost sites (camps) with urban areas. We asked whether spectacled flying-foxes are becoming more urbanised and test the hypothesis that such changes are associated with anthropogenic changes to landscape structure. Our results indicate that spectacled flying-foxes were more likely to roost near humans than might be expected by chance, that over the period of the study the proportion of the flying-foxes in urban-associated camps increased, as did the number of urban camps. Increased urbanisation of spectacled flying-foxes was not related to changes in landscape structure or to the encroachment of urban areas on camps. Overall, camps tended to be found in areas that were more fragmented, closer to human habitation and with more urban land cover than the surrounding landscape. This suggests that urbanisation is a behavioural response rather than driven by habitat loss.     

Predicting loss of evolutionary history: Where are we?

The Earth's evolutionary history is threatened by species loss in the current sixth mass extinction event in Earth's history. Such extinction events not only eliminate species but also their unique evolutionary histories. Here we review the expected loss of Earth's evolutionary history quantified by phylogenetic diversity (PD) and evolutionary distinctiveness (ED) at risk. Due to the general paucity of data, global evolutionary history losses have been predicted for only a few groups, such as mammals, birds, amphibians, plants, corals and fishes. Among these groups, there is now empirical support that extinction threats are clustered on the phylogeny; however this is not always a sufficient condition to cause higher loss of phylogenetic diversity in comparison to a scenario of random extinctions. Extinctions of the most evolutionarily distinct species and the shape of phylogenetic trees are additional factors that can elevate losses of evolutionary history. Consequently, impacts of species extinctions differ among groups and regions, and even if global losses are low within large groups, losses can be high among subgroups or within some regions. Further, we show that PD and ED are poorly protected by current conservation practices. While evolutionary history can be indirectly protected by current conservation schemes, optimizing its preservation requires integrating phylogenetic indices with those that capture rarity and extinction risk. Measures based on PD and ED could bring solutions to conservation issues, however they are still rarely used in practice, probably because the reasons to protect evolutionary history are not clear for practitioners or due to a lack of data. However, important advances have been made in the availability of phylogenetic trees and methods for their construction, as well as assessments of extinction risk. Some challenges remain, and looking forward, research should prioritize the assessment of expected PD and ED loss for more taxonomic groups and test the assumption that preserving ED and PD also protects rare species and ecosystem services. Such research will be useful to inform and guide the conservation of Earth's biodiversity and the services it provides.     

Micro‐evolutionary diversification among Indian Ocean parrots: temporal and spatial changes in phylogenetic diversity as a consequence of extinction and invasion

Almost 90% of global bird extinctions have occurred on islands. The loss of endemic species from island systems can dramatically alter evolutionary trajectories of insular species biodiversity, resulting in a loss of evolutionary diversity important for species adaptation to changing environments. The Western Indian Ocean islands have been the scene of evolution for a large number of endemic parrots. Since their discovery in the 16th century, many of these parrots have become extinct or have declined in numbers. Alongside the extinction of species, a number of the Indian Ocean islands have experienced colonization by highly invasive parrots, such as the Ring‐necked Parakeet Psittacula krameri. Such extinctions and invasions can, on an evolutionary timescale, drive changes in species composition, genetic diversity and turnover in phylogenetic diversity, all of which can have important impacts on species potential for adaptation to changing environmental and climatic conditions. Using mtDNA cytochrome b data, we resolve the taxonomic placement of three extinct Indian Ocean parrots: the Rodrigues Psittacula exsul, Seychelles Psittacula wardi and Reunion Parakeets Psittacula eques. This case study quantifies how the extinction of these species has resulted in lost historical endemic phylogenetic diversity and reduced levels of species richness, and illustrates how it is being replaced by non‐endemic invasive forms such as the Ring‐necked Parakeet. Finally, we use our phylogenetic framework to identify and recommend a number of phylogenetically appropriate ecological replacements for the extinct parrots. Such replacements may be introduced once invasive forms have been cleared, to rejuvenate ecosystem function and restore lost phylogenetic diversity.     

The evolution of sexual and parthenogenetic Warramaba: a window onto Plio–Pleistocene diversification processes in an arid biome

Environmental changes over the Plio‐Pleistocene have been key drivers of speciation patterns and genetic diversification in high‐latitude and mesic environments, yet comparatively little is known about the evolutionary history of species in arid environments. We applied phylogenetic and phylogeographic analyses to understand the evolutionary history of Warramaba grasshoppers from the Australian arid zone, a group including sexual and parthenogenetic lineages. Sequence data (mitochondrial COI) showed that the four major sexual lineages within Warramaba most likely diverged in the Pliocene, around 2–7 million years ago. All sexual lineages exhibited considerable phylogenetic structure. Detailed analyses of the hybrid parthenogenetic species W. virgo and its sexual progenitors showed a pattern of high phylogenetic diversity and phylogeographic structure in northern lineages, and low diversity and evidence for recent expansion in southern lineages. Northern sexual lineages persisted in localized refugia over the Pleistocene, with sustained barriers promoting divergence over this period. Southern parts of the present range became periodically unsuitable during the Pleistocene, and it is into this region that parthenogenetic lineages have expanded. Our results strongly parallel those for sexual and parthenogenetic lineages of the gecko Heteronotia from the same region, indicating a highly general effect of Plio‐Pleistocene environmental change on diversification processes in arid Australia.     

Macro‐ and microenvironmental factors affecting tyre‐breeding flies (Insecta: Diptera) in urbanised areas

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Integrating data‐deficient species in analyses of evolutionary history loss

There is an increasing interest in measuring loss of phylogenetic diversity and evolutionary distinctiveness which together depict the evolutionary history of conservation interest. Those losses are assessed through the evolutionary relationships between species and species threat status or extinction probabilities. Yet, available information is not always sufficient to quantify the threat status of species that are then classified as data deficient. Data‐deficient species are a crucial issue as they cause incomplete assessments of the loss of phylogenetic diversity and evolutionary distinctiveness. We aimed to explore the potential bias caused by data‐deficient species in estimating four widely used indices: HEDGE, EDGE, PDloss, and Expected PDloss. Second, we tested four different widely applicable and multitaxa imputation methods and their potential to minimize the bias for those four indices. Two methods are based on a best‐ vs. worst‐case extinction scenarios, one is based on the frequency distribution of threat status within a taxonomic group and one is based on correlates of extinction risks. We showed that data‐deficient species led to important bias in predictions of evolutionary history loss (especially high underestimation when they were removed). This issue was particularly important when data‐deficient species tended to be clustered in the tree of life. The imputation method based on correlates of extinction risks, especially geographic range size, had the best performance and enabled us to improve risk assessments. Solving threat status of DD species can fundamentally change our understanding of loss of phylogenetic diversity. We found that this loss could be substantially higher than previously found in amphibians, squamate reptiles, and carnivores. We also identified species that are of high priority for the conservation of evolutionary distinctiveness.     

Landscape transformation alters functional diversity in coastal seascapes

The ecological impacts of landscape modification and urbanisation have transformed the composition of plant and animal assemblages, and altered the condition of ecosystems globally. Landscape transformation influences the spatial distribution of species and ecological functions by selecting for generalist species with wide ecological niches, which can adapt to opportunities in highly-modified environments. These effects of landscape modification can shape functional diversity on land, but it is not clear whether they have similar functional consequences in the sea. We used estuaries as a model system to test how landscape transformation alters functional diversity in coastal seascapes, and measured how variation in level of urbanisation, catchment modification and habitat loss influenced fish diversity across thirty-nine estuaries in eastern Australia. Fish were surveyed with baited remote underwater video stations and functional diversity was indexed with three metrics that describe variation in the functional traits and niche space of assemblages. The extent of landscape transformation in the catchment of each estuary was associated with variation in the functional diversity of estuarine fish assemblages. These effects were, however, not what we expected as functional diversity was highest in modified estuaries that supported a large area of both urban and grazing land in their catchments, were bordered by a small area of natural terrestrial vegetation and that contained a moderate area of mangroves. Zoobenthivores and omnivores dominated assemblages in highly-modified estuaries, and piscivorous fishes were common in natural waterways. Our results demonstrate, that the modification and urbanisation of ecosystems on land can alter functional diversity in the sea. Intense landscape transformation appears to select for abundant generalists with wide trophic niches, and against species with specialised diets, and we suggest that these changes might have fundamental consequences for ecosystem functioning in estuaries, and other highly modified seascapes.     

Evolutionary history of larval skeletal morphology in sea urchin Echinometridae (Echinoidea: Echinodermata) as deduced from mitochondrial DNA molecular phylogeny

The larval skeletons of sea urchins show considerable morphological diversity, even between closely related species, although the evolutionary history and functional significance of this diversity are poorly understood. To infer the evolutionary history of the skeletal morphology, we focused on echinometrid species for which the morphological variation in larval skeletons had been investigated qualitatively and quantitatively. We reconstructed the phylogenetic relationships among 14 echinometrid species based on mitochondrial ND1 and ND2 genes and mapped the morphological characters onto the resultant trees. The monophyly of each genus in the Echinometridae was well supported by our results, as was the close affinity between Colobocentrotus, Heterocentrotus, and Echinometra. The mapping of the morphological characters of the larval skeletons indicated that the length, direction, and density of spines on the postoral rods was well conserved in each group of Echinometridae and that the abundance of spines and the size and shape of the body skeleton changed relatively frequently and hence were less conserved. In Echinometrid species, morphological variation in relatively unconserved features tends to be associated with latitudinal distributions, rather than phylogenetic relationships, indicating that the morphological diversity of larval skeletons could have been caused by adaptation to the habitat environment. Some morphological differences, however, seem to be nonfunctional and generated by the constraints on larval skeletogenesis. Thus, echinometrid species can be a good model with which to study the evolutionary history from both ecological and developmental standpoints.     

Investing in evolutionary history: implementing a phylogenetic approach for mammal conservation

Under the impact of human activity, global extinction rates have risen a thousand times higher than shown in the fossil record. The resources available for conservation are insufficient to prevent the loss of much of the world's threatened biodiversity during this crisis. Conservation planners have been forced to prioritize their protective activities, in the context of great uncertainty. This has become known as 'the agony of choice'. A range of methods have been proposed for prioritizing species for conservation attention; one of the most strongly supported is prioritizing those species that maximize phylogenetic distinctiveness (PD). We evaluate how a composite measure of extinction risk and phylogenetic isolation (EDGE) has been used to prioritize species according to their degree of unique evolutionary history (evolutionary distinctiveness, ED) weighted by conservation urgency (global endangerment, GE). We review PD-based approaches and provide an updated list of EDGE mammals using the 2010 IUCN Red List. We evaluate how robust this method is to changes in phylogenetic uncertainty, knowledge of taxonomy and extinction risk, and examine how mammalian species that rank highly in EDGE score are representative of the collective from which they are drawn.     

A phylogenetic perspective on the evolutionary processes of floristic assemblages within a biodiversity hotspot in eastern Asia

Abstract How to maximize the conservation of biodiversity is critical for conservation planning, particularly given rapid habitat loss and global climatic change. The importance of preserving phylogenetic diversity has gained recognition due to its ability to identify some influences of evolutionary history on contemporary patterns of species assemblages that traditional taxonomic richness measures cannot identify. In this study, we evaluate the relationship between taxonomic richness and phylogenetic diversity of angiosperms at genus and species levels and explore the spatial pattern of the residuals of this relationship. We then incorporate data on historical biogeography to understand the process that shaped contemporary floristic assemblages in a global biodiversity hotspot, Yunnan Province, located in southwestern China. We identified a strong correlation between phylogenetic diversity residuals and the biogeographic affinity of the lineages in the extant Yunnan angiosperm flora. Phylogenetic diversity is well correlated with taxonomic richness at both genus and species levels between floras in Yunnan, where two diversity centers of phylogenetic diversity were identified (the northwestern center and the southern center). The northwestern center, with lower phylogenetic diversity than expected based on taxonomic richness, is rich in temperate‐affinity lineages and signifies an area of rapid speciation. The southern center, with higher phylogenetic diversity than predicted by taxonomic richness, contains a higher proportion of lineages with tropical affinity and seems to have experienced high immigration rates. Our results highlight that maximizing phylogenetic diversity with historical interpretation can provide valuable insights into the floristic assemblage of a region and better‐informed decisions can be made to ensure different stages of a region's evolutionary history are preserved.     

Measuring biodiversity to explain community assembly: a unified approach

One of the oldest challenges in ecology is to understand the processes that underpin the composition of communities. Historically, an obvious way in which to describe community compositions has been diversity in terms of the number and abundances of species. However, the failure to reject contradictory models has led to communities now being characterized by trait and phylogenetic diversities. Our objective here is to demonstrate how species, trait and phylogenetic diversity can be combined together from large to local spatial scales to reveal the historical, deterministic and stochastic processes that impact the compositions of local communities. Research in this area has recently been advanced by the development of mathematical measures that incorporate trait dissimilarities and phylogenetic relatedness between species. However, measures of trait diversity have been developed independently of phylogenetic measures and conversely most of the phylogenetic diversity measures have been developed independently of trait diversity measures. This has led to semantic confusions particularly when classical ecological and evolutionary approaches are integrated so closely together. Consequently, we propose a unified semantic framework and demonstrate the importance of the links among species, phylogenetic and trait diversity indices. Furthermore, species, trait and phylogenetic diversity indices differ in the ways they can be used across different spatial scales. The connections between large‐scale, regional and local processes allow the consideration of historical factors in addition to local ecological deterministic or stochastic processes. Phylogenetic and trait diversity have been used in large‐scale analyses to determine how historical and/or environmental factors affect both the formation of species assemblages and patterns in species richness across latitude or elevation gradients. Both phylogenetic and trait diversity have been used at different spatial scales to identify the relative impacts of ecological deterministic processes such as environmental filtering and limiting similarity from alternative processes such as random speciation and extinction, random dispersal and ecological drift. Measures of phylogenetic diversity combine phenotypic and genetic diversity and have the potential to reveal both the ecological and historical factors that impact local communities. Consequently, we demonstrate that, when used in a comparative way, species, trait and phylogenetic structures have the potential to reveal essential details that might act simultaneously in the assembly of species communities. We highlight potential directions for future research. These might include how variation in trait and phylogenetic diversity alters with spatial distances, the role of trait and phylogenetic diversity in global‐scale gradients, the connections between traits and phylogeny, the importance of trait rarity and independent evolutionary history in community assembly, the loss of trait and phylogenetic diversity due to human impacts, and the mathematical developments of biodiversity indices including within‐species variations.     

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.     

Slimes in the city: The diversity of myxomycetes from inner-city and semi-urban parks in Sydney,Australia

Natural and agricultural areas are rapidly becoming urbanised, causing changes in habitat structure and diversity. Although the effect of urbanisation on the diversity of terrestrial plants and animals has been well studied, there is a significant gap in our understanding of how urbanisation impacts diversity in protists. Here, we measure the diversity of plasmodial slime moulds (a group of large, macroscopic protists also known as myxomycetes) in inner-city and semi-urban parks. We studied the impact of a range of environmental characteristics (pH, temperature, canopy cover, area of green space and substrate type) on species richness and composition of myxomycetes. We also examined the influence of different degrees of urban development surrounding these parks. Species composition was significantly different between substrate types but not between inner-city and semi-urban parks. Temperature was the only environmental characteristic that affected diversity, having a negative effect on myxomycete presence. Our findings suggest that myxomycete diversity in urban parks is driven by factors at the substrate level, and not by the park's location within the city (inner city or semi-urban).     

Plant-Pollinator Coextinctions and the Loss of Plant Functional and Phylogenetic Diversity

Plant-pollinator coextinctions are likely to become more frequent as habitat alteration and climate change continue to threaten pollinators. The consequences of the resulting collapse of plant communities will depend partly on how quickly plant functional and phylogenetic diversity decline following pollinator extinctions. We investigated the functional and phylogenetic consequences of pollinator extinctions by simulating coextinctions in seven plant-pollinator networks coupled with independent data on plant phylogeny and functional traits. Declines in plant functional diversity were slower than expected under a scenario of random extinctions, while phylogenetic diversity often decreased faster than expected by chance. Our results show that plant functional diversity was relatively robust to plant-pollinator coextinctions, despite the underlying rapid loss of evolutionary history. Thus, our study suggests the possibility of uncoupled responses of functional and phylogenetic diversity to species coextinctions, highlighting the importance of considering both dimensions of biodiversity explicitly in ecological studies and when planning for the conservation of species and interactions.