Daniel Faith

Daniel Faith

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Introduction
For latest research on biodiversity by Daniel P Faith see https://danielpfaith.wordpress.com/

Publications

Publications (184)
Preprint
Full-text available
The global biodiversity crisis threatens the natural world and its capacity to provide benefits to humans into the future. The conservation of evolutionary history, captured by the measure phylogenetic diversity (PD), is linked to the maintenance of these benefits and future options. The Evolutionarily Distinct and Globally Endangered (EDGE) metric...
Article
Full-text available
The term “biodiversity” generally refers to living variation. Biodiversity has recognized anthropocentric values of insurance and investment. Values of “nature” include those of biodiversity and also many other aspects reflecting the scope of human-nature relationships. Systematic conservation planning methods can integrate this range of local to g...
Article
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Various prioritisation strategies have been developed to cope with accelerating biodiversity loss and limited conservation resources. These strategies could become more engaging for decision-makers if they reflected the positive effects conservation can have on future projected biodiversity, by targeting net positive outcomes in future projected bi...
Article
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“Nature’s contributions to people” (NCP) is an important expansion beyond the standard ecosystem services framework, particularly as a pathway to better address global/regional biodiversity values. NCP18, “maintenance of options,” refers broadly to the capacity of ecosystems, habitats, species, or genotypes to keep options open to support a good qu...
Preprint
Full-text available
Following our failure to fully achieve any of the 20 Aichi biodiversity targets, the future of biodiversity rests in the balance. The Convention on Biological Diversity's Post-2020 Global Biodiversity Framework (GBF) presents us with the opportunity to preserve Nature's Contributions to People (NCPs) for current and future generations through conse...
Conference Paper
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The concepts ‘Ecological Integrity’ (EI) and ‘Biodiversity’ (living variation) are founding principles of ecologicallysustainable development under NSW environmental legislation, including NSW’s Biodiversity Conservation Act (2016). Ecological Integrity is a high-level goal for biodiversity conservation requiring integration of habitat repair and m...
Article
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Changes in species concepts and the rapid advances in DNA-based taxonomy and phylogeny of the past decades have led to increasing splits of single species into several new species. The consequences of such splits include the delineation of post-split species that may have restricted ranges and potentially increased extinction risks. Species splitti...
Chapter
PD or “phylogenetic diversity” was proposed by Faith (Biol Conserv 61:1–10, 1992) as a measure of biodiversity “option value”, justifying its importance as a target of biodiversity conservation. The threats to phylogenetic diversity can be quantified by integrating PD with IUCN Red List categories and corresponding inferred extinction probabilities...
Chapter
“Phylogenetic diversity” and its abbreviation “PD” have now become popular terms describing a fundamental aspect of biodiversity based on phylogeny. After more than 25 years of work on PD (following the 1992 paper in Biological Conservation), methods and applications have explored a wide range of taxonomic groups and geographic scales. PD provides...
Chapter
Phylogenetic diversity (PD) is a valuable component of biodiversity, reflecting variation produced by past evolutionary processes and providing options for future generations. A challenge is to design and implement effective conservation actions for the preservation of PD for multiple taxonomic groups. We here proposed a region-level approach to th...
Book
“Biodiversity” refers to the variety of life. It is now agreed that there is a “biodiversity crisis”, corresponding to extinction rates of species that may be 1000 times what is thought to be “normal”. Biodiversity science has a higher profile than ever, with the new Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services i...
Article
Full-text available
D P Faith research on biodiversity, including phylogenetic diversity - from philosophy to policy
Chapter
DNA is the most elemental level of biodiversity, drives the process of speciation, and underpins other levels of biodiversity, including functional traits, species and ecosystems. Until recently biodiversity indicators have largely overlooked data from the molecular tools that are available for measuring variation at the DNA level. More direct anal...
Article
Premise of research. Rain forest ecosystems globally are synonymous with biodiversity, yet these vegetation communities vary widely in structure and composition. Historical biogeography and environment are thought to have significantly impacted Australian rain forest diversity and composition. Rain forest in Australia is extensively fragmented, and...
Article
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Intraspecific variation is a major component of biodiversity, yet it has received relatively little attention from governmental and non-governmental organizations, especially with regard to conservation plans and the management of wild species. This omission is ill-advised because phenotypic and genetic variation within and among populations can ha...
Article
Predicting the consequences of climate change for biodiversity is critical to conservation efforts. Extensive range losses have been predicted for thousands of individual species, but less is known about how climate change might impact whole clades and landscape-scale patterns of biodiversity. Here, we show that climate change scenarios imply signi...
Article
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Australia's Great Sandy Region is of international significance containing two World Heritage areas and patches of rainforest growing on white sand. Previous broad-scale analysis found the Great Sandy biogeographic subregion contained a significantly more phylogenetically even subset of species than expected by chance contrasting with rainforest on...
Data
Summary of nine Orders, dates used and the reference pertaining to each (Shapcott et al., 2015) used to date the SEQ rainforest phylogenetic tree in the PATHd8 program. Where MRCA is the most recent common ancestor of the two taxa that span the clade being dated on the tree. (DOCX)
Data
Summary Table of details for all new additions to the SEQld rainforest barcode phylogeny. The species name, Genbank accession codes for each of the three DNA barcode markers used as well as the Queensland Herbarium (BRI) collector name or number which is used by BRI as specimen identifier as well as the BRI accession number where available at time...
Chapter
Full-text available
Phylogenetic diversity has become invaluable for conservation biology in the last decades, refl ecting its link to option values and to evolutionary potential. We argue that its use will continue to grow rapidly in the next decades because of the transformation of systematics with new molecular techniques and especially metagenomics. In a near futu...
Chapter
Full-text available
The PD phylogenetic diversity measure provides a measure of biodiversity that reflects variety at the level of features, among species or other taxa. PD is based on a simple model which assumes that shared ancestry explains shared features. PD provides a family of calculations that operate as if we were directly counting up features of taxa. PD-dis...
Chapter
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Feature diversity refers to the relative number of different features represented among species or other taxa. As a storehouse of possible future benefits to people, it is an important focus for biodiversity conservation. The PD phylogenetic diversity measure provides a way to measure biodiversity at the level of features. PD assumes an evolutionar...
Article
Phylodiversity measures summarise the phylogenetic diversity patterns of groups of organisms. By using branches of the tree of life, rather than its tips (e.g., species), phylodiversity measures provide important additional information about biodiversity that can improve conservation policy and outcomes. As a biodiverse nation with a strong legisla...
Article
Functional diversity indices typically focus on a small number of recognised important traits. The phylogenetic diversity measure (PD) has provided one way to make inferences about a broader array of traits. However, PD’s assumption that shared ancestry explains shared features cannot account for all shared traits. An alternative functional diversi...
Article
Because conservation planners typically lack data on where species occur, environmental surrogates-including geophysical settings and climate types-have been used to prioritize sites within a planning area. We reviewed 622 evaluations of the effectiveness of abiotic surrogates in representing species in 19 study areas. Sites selected using abiotic...
Article
Full-text available
In a rapidly changing climate, conservation practitioners could better use geodiversity in a broad range of conservation decisions. We explored selected avenues through which this integration might improve decision making and organized them within the adaptive management cycle of assessment, planning, implementation, and monitoring. Geodiversity is...
Article
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Geodiversity has been used as a surrogate for biodiversity when species locations are unknown, and this utility can be extended to situations where species locations are in flux. Recently, scientists have designed conservation networks that aim to explicitly represent the range of geophysical environments, identifying a network of physical stages t...
Article
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Australian rainforests have been fragmented due to past climatic changes and more recently landscape change as a result of clearing for agriculture and urban spread. The subtropical rainforests of South Eastern Queensland are significantly more fragmented than the tropical World Heritage listed northern rainforests and are subject to much greater h...
Article
The phylogenetic diversity measure, ('PD'), measures the relative feature diversity of different subsets of taxa from a phylogeny. At the level of feature diversity, PD supports the broad goal of biodiversity conservation to maintain living variation and option values. PD calculations at the level of lineages and features include those integrating...
Article
‘Key biodiversity areas' are defined as sites contributing significantly to the global persistence of biodiversity. The identification of these sites builds from existing approaches based on measures of species and ecosystem diversity and process. Here, we therefore build from the work of Sgró et al. (2011 Evol. Appl. 4, 326–337. (doi:10.1111/j.175...
Article
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Evolutionary studies have played a fundamental role in our understanding of life, but until recently, they had only a relatively modest involvement in addressing conservation issues. The main goal of the present discussion meeting issue is to offer a platform to present the available methods allowing the integration of phylogenetic and extinction r...
Article
Ecosystem services programs are rapidly increasing and are seen as a pathway for biodiversity conservation based on the attractive idea that quantified values of the ecosystem services of intact land may exceed any gains from conversion to intensive logging or other non-conservation uses. However, I show that, even when all local biodiversity is pr...
Article
Full-text available
Traditional species diversity measures do not make distinctions among species. Faith's phylogenetic diversity (PD), which is defined as the sum of the branch lengths of a phylogenetic tree connecting all species, takes into account phylogenetic differences among species and has found many applications in various research fields. In this paper, we e...
Article
Full-text available
Biodiversity is a key to human well-being. However universally acknowledged, this reality is not appre-ciated as much as one might imagine or hope. Having achieved a high standing in the Convention on Biological Diversity (CBD) in 1992, biodiversity appears to have gradually fallen from that position in the 20 years since. This is evidenced by the...
Article
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The co-authors of this paper hereby state their intention to work together to launch the Genomic Observatories Network (GOs Network) for which this document will serve as its Founding Charter. We define a Genomic Observatory as an ecosystem and/or site subject to long-term scientific research, including (but not limited to) the sustained study of g...
Chapter
Sustainable use of biodiversity requires the use of biodiversity in a way that does not foreclose benefits for future generations. Biodiversity option values reflect this capacity to provide future benefits that are often unanticipated. The phylogenetic diversity measure, PD, quantifies the option values represented by different sets of species. PD...
Article
Full-text available
A Content Needs Assessment (CNA) survey has been conducted in order to determine what GBIF-mediated data users may be using, what they would be using if available, and what they need in terms of primary biodiversity data records. The survey was launched in 2009 in six languages, and collected more than 700 individual responses. Analysis of the resp...
Article
Full-text available
A strong case has been made for freely available, high quality data on species occurrence, in order to track changes in biodiversity. However, one of the main issues surrounding the provision of such data is that sources vary in quality, scope, and accuracy. Therefore publishers of such data must face the challenge of maximizing quality, utility an...
Article
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This viewpoint paper explores the potential of genomics technology to provide accurate, rapid, and cost efficient observations of the marine environment. The use of such approaches in next generation marine monitoring programs will help achieve the goals of marine legislation implemented world-wide. Genomic methods can yield faster results from mon...
Article
Evolutionary biology is a core discipline in biodiversity science. Evolutionary history or phylogeny provides one natural measure of biodiversity through the popular phylogenetic diversity (PD) measure. The evolutionary model underlying PD means that it can be interpreted as quantifying the relative feature diversity of sets of species. Quantifying...
Article
Full-text available
While many plant species are considered threatened under anthropogenic pressure, it remains uncertain how rapidly we are losing plant species diversity. To fill this gap, we propose a Global Legume Diversity Assessment (GLDA) as the first step of a global plant diversity assessment. Here we describe the concept of GLDA and its feasibility by review...
Article
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Reducing the rate of biodiversity loss and averting dangerous biodiversity change are international goals, reasserted by the Aichi Targets for 2020 by Parties to the United Nations (UN) Convention on Biological Diversity (CBD) after failure to meet the 2010 target ( 1, 2). However, there is no global, harmonized observation system for delivering re...
Article
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The possible loss of whole branches from the tree of life is a dramatic, but under-studied, biological implication of climate change. The tree of life represents an evolutionary heritage providing both present and future benefits to humanity, often in unanticipated ways. Losses in this evolutionary (evo) life-support system represent losses in "evo...
Article
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New global initiatives require clarity about similarities and differences between biodiversity and ecosystem services. One argument is that ecosystem services capture utilitarian values, while biodiversity captures intrinsic values. However, the concept of biodiversity equally emerges from anthropogenic use values. Measures of biodiversity indicate...
Article
24 DIVERSITAS, the international programme on biodiversity science, is releasing a strategic vision presenting scientific challenges for the next decade of research on biodiversity and ecosystem services: ''Biodiversity and Ecosystem Services Science for a Sustainable Planet''. This new vision is a response of the biodiversity and ecosystem service...
Article
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As part of the Zootaxa special issue on molecules and morphology in systematics, Faith et al. (2011) discussed how corroboration assessment can support integrative systematics. They argued that integrative systematics should be open to a wide variety of potential supporting evidence for phylogenetic (or species) hypotheses, with the condition that...
Article
Full-text available
The Group on Earth Observations Biodiversity Observation Network (GEO BON) has been in formal existence for three years, following several years of design and discussion. It is the realisation of the biodiversity societal benefit area envisaged in the GEO System of Systems (GEOSS). GEO BON links together existing networks, each covering particular...
Article
Highlights ► Human well-being depends on multiple ecosystem services, many of them being underpinned by biodiversity. ► Biodiversity continues to be lost at an unprecedented rate. ► Decision-makers and policy-makers require sound scientific foundation to secure the planet's biodiversity and ecosystem services, while contributing to human well-being...
Article
Enzymatic amplification of homologous regions of DNA using 'universal' polymerase chain reaction primers has provided insight into insect systematics, phylogeography, molecular evolution and species identification. One of the more commonly amplified and sequenced regions is a short region of the cytochrome c oxidase subunit I gene (COI), commonly c...
Article
Full-text available
The Convention on Biological Diversity has adopted 20 targets as part of its new Strategic Plan. Perrings et al. have proposed that such targets should focus solely on critical ecosystem services. Such a strategy may neglect the need to conserve overall biodiversity and corresponding option values. It also may neglect the important role of ecosyste...
Article
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Mooi & Gill (2010) argued that careful character study and well-understood synapomorphies do not have the strong role that they deserve as the basis for evidence in phylogenetics. We agree, but suggest that the problem is even greater. Not only character synapomorphies, but also other forms of phylogenetic evidence, typically do not receive the cri...
Article
A recent paper in this journal (Hortal et al., 2009) claimed to have evaluated the ED biodiversity surrogates methods of [10] and [11], and to have provided evidence for poor performance of the continuous ED method. In fact, their study neither used nor evaluated the continuous ED method. Here, I document their misrepresentation. I then discuss so...
Article
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The ability to extrapolate from the known to the unknown is essential if we are to use the turnover of overall biodiversity, as opposed to a few well-known groups, to inform conservation planning. We investigated the usefulness of using evolutionary relationships of plants as a surrogate for the turnover of their associated beetle assemblages. If p...
Article
In their Policy Forum “Ecosystem services for 2020” (15 October, p. [323][1]), C. Perrings et al. discuss possible missing elements in the Convention on Biological Diversity's proposed new targets. They suggest that targets for biodiversity be based directly on ecosystem services because people
Article
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Questions: How can a resemblance (similarity or dissimilarity) measure be formulated to include information on both the evolutionary relationships and abundances of organisms, and how does it compare to measures lacking such information? Methods: We extend the family of Phylogenetic Diversity (PD) measures to include a generalized method for calcul...
Conference Paper
Background/Question/Methods Loss of evolutionary history is a major concern within the broader biodiversity crisis. We now have a useful calculus for measuring various aspects of loss of evolutionary history, based on the PD (phylogenetic diversity) measure. Essentially, any conventional species-level index may have its counter-part at the level...
Article
A framework for exploring regional-scale trade-offs among ecosystem services and biodiversity protection has been established for some time, and it is clear that optimizing these trade-offs provides a strategy to address targets for a reduced rate of biodiversity loss. Recent trade-off studies have highlighted the need for better biodiversity measu...
Article
Genetic elements determine phenotypes of organisms by interacting with environments. Despite genetic diversity within and between species being the fundamental basis of biological diversity, its contribution has been long neglected in biodiversity studies. This situation is rapidly changing as quantification of genetic diversity, from intraspecific...
Article
The bold commitment made by the world's governments to reduce the rate of biodiversity loss by 2010 will soon be tested. On the basis of the continuing declines measured by most indicators, it now seems inevitable that the outcome will be that it has not been achieved. Here, in order to build on the momentum created by the 2010 target, we propose a...
Article
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Evolutionary biologists have long endeavored to document how many species exist on Earth, to understand the processes by which biodiversity waxes and wanes, to document and interpret spatial patterns of biodiversity, and to infer evolutionary relationships. Despite the great potential of this knowledge to improve biodiversity science, conservation,...
Article
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It is rarely cost-effective to survey invertebrates for use in systematic conservation planning activities. The efficiency of sampling methods needs to be improved, and this is especially important at landscape and regional scales. We investigated two methods that could be used to improve regional scale sampling efficiency using a case study of ant...
Article
Full-text available
The PD measure of phylogenetic diversity interprets branch lengths cladistically to make inferences about feature diversity. PD calculations extend conventional species-level ecological indices to the features level. The "phylogenetic beta diversity" framework developed by microbial ecologists calculates PD-dissimilarities between community localit...