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Abstract

Resolving trade-offs between economic development and biodiversity conservation needs is crucial in currently developing countries and in particularly sensitive systems harboring high biodiversity. Yet, such a task is challenging because human activities have complex effects on biodiversity. We assessed the effects of intense economic development on Hainan Island (southern China) on different components of biodiversity. This highly biodiverse tropical island has undergone extensive economic development and conversion of forest to agriculture and urban area. We identified 3 main transformation areas (low, medium, and high transformation) based on land-use, local-climate, and economic changes across 145 grids (10 × 10 km), and estimated changes in avian biodive6rsity from 1998 to 2013. We recorded ongoing taxonomic biotic homogenization throughout the island. Differences between traditional and directional alpha diversity decreased by 5%. Phylogenetically clustering increased by 0.5 points (W = 7928, p < 0.01), and functional overdispersion increased by 1 point (W = 16,411, p < 0.01). Initial taxonomic, phylogenetic, and functional scores correlated negatively with changes in these scores across all transformation areas (all ps < 0.01). At the local scale, economic and environmental indicators showed complex and divergent effects across transformation areas and biodiversity components. These effects were only partially ameliorated in an ecological function conservation area in the mountainous central part of the island. We found complex effects of economic development on different biodiversity dimensions in different areas with different land uses and protection regimes and between local and regional spatial scales. Profound ecosystem damage associated with economic development was partially averted, probably due to enhanced biodiversity conservation policies and law enforcement, but not without regional-scale biotic homogenization and local-scale biodiversity loss.

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... Finally, it should be noted that although harboring lower species richness, sites within buffer area of the natural reserve still had higher phylogenetic heterogeneity than sites outside the natural reserve. A recent study on a tropical island suggests that economic development and changes in land use may cause increased phylogenetic clustering (Pganani-Nunez et al., 2022). Our results support this idea, as sites with less economic development (i.e., sites within the natural reserve) were associated with less phylogenetic clustering. ...
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Background A principal function of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) is to “perform regular and timely assessments of knowledge on biodiversity.” In December 2013, its second plenary session approved a program to begin a global assessment in 2015. The Convention on Biological Diversity (CBD) and five other biodiversity-related conventions have adopted IPBES as their science-policy interface, so these assessments will be important in evaluating progress toward the CBD’s Aichi Targets of the Strategic Plan for Biodiversity 2011–2020. As a contribution toward such assessment, we review the biodiversity of eukaryote species and their extinction rates, distributions, and protection. We document what we know, how it likely differs from what we do not, and how these differences affect biodiversity statistics. Interestingly, several targets explicitly mention “known species”—a strong, if implicit, statement of incomplete knowledge. We start by asking how many species are known and how many remain undescribed. We then consider by how much human actions inflate extinction rates. Much depends on where species are, because different biomes contain different numbers of species of different susceptibilities. Biomes also suffer different levels of damage and have unequal levels of protection. How extinction rates will change depends on how and where threats expand and whether greater protection counters them. Advances Recent studies have clarified where the most vulnerable species live, where and how humanity changes the planet, and how this drives extinctions. These data are increasingly accessible, bringing greater transparency to science and governance. Taxonomic catalogs of plants, terrestrial vertebrates, freshwater fish, and some marine taxa are sufficient to assess their status and the limitations of our knowledge. Most species are undescribed, however. The species we know best have large geographical ranges and are often common within them. Most known species have small ranges, however, and such species are typically newer discoveries. The numbers of known species with very small ranges are increasing quickly, even in well-known taxa. They are geographically concentrated and are disproportionately likely to be threatened or already extinct. We expect unknown species to share these characteristics. Current rates of extinction are about 1000 times the background rate of extinction. These are higher than previously estimated and likely still underestimated. Future rates will depend on many factors and are poised to increase. Finally, although there has been rapid progress in developing protected areas, such efforts are not ecologically representative, nor do they optimally protect biodiversity. Outlook Progress on assessing biodiversity will emerge from continued expansion of the many recently created online databases, combining them with new global data sources on changing land and ocean use and with increasingly crowdsourced data on species’ distributions. Examples of practical conservation that follow from using combined data in Colombia and Brazil can be found at www.savingspecies.org and www.youtube.com/watch?v=R3zjeJW2NVk .
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For this article, I reviewed empirical studies finding significant ecological responses to habitat fragmentation per se—in other words, significant responses to fragmentation independent of the effects of habitat amount (hereafter referred to as habitat fragmentation). I asked these two questions: Are most significant responses to habitat fragmentation negative or positive? And do particular attributes of species or landscapes lead to a predominance of negative or positive significant responses? I found 118 studies reporting 381 significant responses to habitat fragmentation independent of habitat amount. Of these responses, 76% were positive. Most significant fragmentation effects were positive, irrespective of how the authors controlled for habitat amount, the measure of fragmentation, the taxonomic group, the type of response variable, or the degree of specialization or conservation status of the species or species group. No support was found for predictions that most significant responses to fragmentation should be negative in the tropics, for species with larger movement ranges, or when habitat amount is low; most significant fragmentation effects were positive in all of these cases. Thus, although 24% of significant responses to habitat fragmentation were negative, I found no conditions in which most responses were negative. Authors suggest a wide range of possible explanations for significant positive responses to habitat fragmentation: increased functional connectivity, habitat diversity, positive edge effects, stability of predator–prey/host–parasitoid systems, reduced competition, spreading of risk, and landscape complementation. A consistent preponderance of positive significant responses to fragmentation implies that there is no justification for assigning lower conservation value to a small patch than to an equivalent area within a large patch—instead, it implies just the opposite. This finding also suggests that land sharing will usually provide higher ecological value than land sparing. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics Volume 48 is November 2, 2017. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Despite the recognised conservation value of phylogenetic diversity, little is known about how it is affected by the urbanisation process. Combining a complete avian phylogeny with surveys along urbanisation gradients from five continents, we show that highly urbanised environments supported on average 450 million fewer years of evolutionary history than the surrounding natural environments. This loss was primarily caused by species loss and could have been higher had not been partially compensated by the addition of urban exploiters and some exotic species. Highly urbanised environments also supported fewer evolutionary distinctive species, implying a disproportionate loss of evolutionary history. Compared with highly urbanised environments, changes in phylogenetic richness and evolutionary distinctiveness were less substantial in moderately urbanised environments. Protecting pristine environments is therefore essential for maintaining phylogenetic diversity, but moderate levels of urbanisation still preserve much of the original diversity.
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Urbanization is increasing faster than ever, contributing to a global extinction crisis. Recently, scientists have debated whether species richness on local and regional scales is mostly declining, but long-term changes in phylogenetic richness and divergence were largely disregarded. Space-for-time approaches revealed that plant phylogenetic divergence is lower in urban than in non-urban areas. However, such approaches cannot fully disentangle the relative importance of the biotic processes that drive temporal changes in diversity. Using a unique European urban flora covering 320 years in seven time steps, combined with a comprehensive plant phylogeny, we examined (i) how species richness changed with urbanization over time; (ii) whether trends in phylogenetic richness and divergence parallel trends in species richness; and (iii) whether species extirpation or immigration is driving these changes. We found that over time urban species richness increased, but phylogenetic richness and divergence decreased. Extirpations of phylogenetically distinct native species and immigrations of phylogenetically common native and non-native species caused a non-random loss of phylogenetic diversity. Our analyses suggest that if future extirpations and immigrations continue to follow the patterns observed over history, this loss will continue. Synthesis and applications. Measures to protect phylogenetic diversity should combine the protection of threatened habitats and their species with the maintenance of habitats that mitigate heat and safeguard evolutionary history. Urban planners should consider a phylogenetically diverse set of species when designing green spaces.
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1. Here, I present a new, multifunctional phylogenetics package, phytools, for the R statistical computing environment. 2. The focus of the package is on methods for phylogenetic comparative biology; however, it also includes tools for tree inference, phylogeny input/output, plotting, manipulation and several other tasks. 3. I describe and tabulate the major methods implemented in phytools, and in addition provide some demonstration of its use in the form of two illustrative examples. 4. Finally, I conclude by briefly describing an active web-log that I use to document present and future developments for phytools. I also note other web resources for phylogenetics in the R computational environment.
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