Background: Understanding biodiversity patterns is a central topic in biogeography and ecology, and it is essential for conservation planning and policy development. Diversity estimates that consider the evolutionary relationships among species, such as phylogenetic diversity and phylogenetic endemicity indices, provide valuable insights into the functional diversity and evolutionary uniqueness of biological communities. These estimates are crucial for informed decision-making and effective global biodiversity management.
View Article and Find Full Text PDFUNITE (https://unite.ut.ee) is a web-based database and sequence management environment for molecular identification of eukaryotes.
View Article and Find Full Text PDFEarly natural historians-Comte de Buffon, von Humboldt, and De Candolle-established environment and geography as two principal axes determining the distribution of groups of organisms, laying the foundations for biogeography over the subsequent 200 years, yet the relative importance of these two axes remains unresolved. Leveraging phylogenomic and global species distribution data for Mimosoid legumes, a pantropical plant clade of c. 3500 species, we show that the water availability gradient from deserts to rain forests dictates turnover of lineages within continents across the tropics.
View Article and Find Full Text PDFThe Legume Phylogeny Working Group's Taxonomy Working Group was tasked to create a community endorsed global legume checklist that will serve as a primary source of taxa for biodiversity data platforms and legume-related research. The checklist was published in June 2021, recognising 772 genera and 22,360 species. It is disseminated through the new Legume Data Portal as part of the Global Biodiversity Information Facility (GBIF) hosted portal initiative.
View Article and Find Full Text PDFThe early twenty-first century has witnessed massive expansions in availability and accessibility of digital data in virtually all domains of the biodiversity sciences. Led by an array of asynchronous digitization activities spanning ecological, environmental, climatological, and biological collections data, these initiatives have resulted in a plethora of mostly disconnected and siloed data, leaving to researchers the tedious and time-consuming manual task of finding and connecting them in usable ways, integrating them into coherent data sets, and making them interoperable. The focus to date has been on elevating analog and physical records to digital replicas in local databases prior to elevating them to ever-growing aggregations of essentially disconnected discipline-specific information.
View Article and Find Full Text PDFThe flora of China is well known for its high diversity and endemism. Identifying centers of endemism and designating conservation priorities are essential goals for biodiversity studies. However, there is no comprehensive study from a rigorous phylogenetic perspective to understand patterns of diversity and endemism and to guide biodiversity conservation in China.
View Article and Find Full Text PDFThe accessibility of global biodiversity information has surged in the past two decades, notably through widespread funding initiatives for museum specimen digitization and emergence of large-scale public participation in community science. Effective use of these data requires the integration of disconnected datasets, but the scientific impacts of consolidated biodiversity data networks have not yet been quantified. To determine whether data integration enables novel research, we carried out a quantitative text analysis and bibliographic synthesis of >4,000 studies published from 2003 to 2019 that use data mediated by the world's largest biodiversity data network, the Global Biodiversity Information Facility (GBIF).
View Article and Find Full Text PDFAustralia is an excellent setting to explore relationships between climate change and diversification dynamics. Aridification since the Eocene has resulted in spectacular radiations within one or more Australian biomes. Acacia is the largest plant genus on the Australian continent, with around 1000 species, and is present in all biomes.
View Article and Find Full Text PDFWe present the largest comparative biogeographical analysis that has complete coverage of Australia's geography (20 phytogeographical subregions), using the most complete published molecular phylogenies to date of large Australian plant clades (Acacia, Banksia and the eucalypts). Two distinct sets of areas within the Australian flora were recovered, using distributional data from the Australasian Virtual Herbarium (AVH) and the Atlas of Living Australia (ALA): younger Temperate, Eremaean and Monsoonal biomes, and older southwest + west, southeast and northern historical biogeographical regions. The analyses showed that by partitioning the data into two sets, using either a Majority or a Frequency method to select taxon distributions, two equally valid results were found.
View Article and Find Full Text PDFBiological invasions are on the rise globally. To reduce future invasions, it is imperative to determine the naturalization potential of species. Until now, screening approaches have relied largely on species-specific functional feature data.
View Article and Find Full Text PDFSummary: Phylolink is a research collaboration toolkit through which biodiversity can be explored from a phylogenetic perspective. It is an update of PhyloJiVE that has been integrated into the framework of the Atlas of Living Australia, including its spatial portal. Phylolink connects phylogenetic tree nodes with species occurrence records, environmental data, and species trait information.
View Article and Find Full Text PDFHigh species diversity may result from recent rapid speciation in a 'cradle' and/or the gradual accumulation and preservation of species over time in a 'museum'. China harbours nearly 10% of angiosperm species worldwide and has long been considered as both a museum, owing to the presence of many species with hypothesized ancient origins, and a cradle, as many lineages have originated as recent topographic changes and climatic shifts-such as the formation of the Qinghai-Tibetan Plateau and the development of the monsoon-provided new habitats that promoted remarkable radiation. However, no detailed phylogenetic study has addressed when and how the major components of the Chinese angiosperm flora assembled to form the present-day vegetation.
View Article and Find Full Text PDFMany studies quantify total phenolics or total tannins, but understanding the ecological role of polyphenolic secondary metabolites requires at least an understanding of the diversity of phenolic groups present. We used UPLC-MS/MS to measure concentrations of different polyphenol groups - including the four most common tannin groups, the three most common flavonoid groups, and quinic acid derivatives - in foliage from 628 eucalypts from the genera Eucalyptus, Angophora and Corymbia. We also tested for phylogenetic signal in each of the phenolic groups.
View Article and Find Full Text PDFFor a plant species to become invasive it has to progress along the introduction-naturalization-invasion (INI) continuum which reflects the joint direction of niche breadth. Identification of traits that correlate with and drive species invasiveness along the continuum is a major focus of invasion biology. If invasiveness is underlain by heritable traits, and if such traits are phylogenetically conserved, then we would expect non-native species with different introduction status (i.
View Article and Find Full Text PDFThe ecological and evolutionary factors that drive the emergence and maintenance of variation in mutualistic benefit (i.e., the benefits provided by one partner to another) in mutualistic symbioses are not well understood.
View Article and Find Full Text PDFCombining whole genome data with previously obtained amplicon sequences has the potential to increase the resolution of phylogenetic analyses, particularly at low taxonomic levels or where recent divergence, rapid speciation or slow genome evolution has resulted in limited sequence variation. However, the integration of these types of data for large scale phylogenetic studies has rarely been investigated. Here we conduct a phylogenetic analysis of the whole chloroplast genome and two nuclear ribosomal loci for 65 Acacia species from across the most recent Acacia phylogeny.
View Article and Find Full Text PDFIdentifying geographical areas with the greatest representation of the tree of life is an important goal for the management and conservation of biodiversity. While there are methods available for using a single phylogenetic tree to assess spatial patterns of biodiversity, there has been limited exploration of how separate phylogenies from multiple taxonomic groups can be used jointly to map diversity and endemism. Here, we demonstrate how to apply different phylogenetic approaches to assess biodiversity across multiple taxonomic groups.
View Article and Find Full Text PDFPhylodiversity measures summarise the phylogenetic diversity patterns of groups of organisms. By using branches of the tree of life, rather than its tips (e.g.
View Article and Find Full Text PDFBecause ferns have a wide range of habitat preferences and are widely distributed, they are an ideal group for understanding how diversity is distributed. Here we examine fern diversity on a broad-scale using standard and corrected richness measures as well as phylogenetic indices; in addition we determine the environmental predictors of each diversity metric. Using the combined records of Australian herbaria, a dataset of over 60,000 records was obtained for 89 genera to infer richness.
View Article and Find Full Text PDFPremise Of The Study: The classification of the primarily Australasian group of orchids Caladenia and allied genera (Caladeniinae: Diurideae) containing 71 federally listed threatened species has proven controversial. Analyzing these species using genetic material will provide a sound basis for their classification and the capacity to ensure accurate conservation measures can be implemented.
Methods: We present a multigene analysis based on nuclear ribosomal ITS and five plastid regions from 54 species representing all major taxonomic groups within Caladeniinae.
Philos Trans R Soc Lond B Biol Sci
February 2015
Evolutionary and genetic knowledge is increasingly being valued in conservation theory, but is rarely considered in conservation planning and policy. Here, we integrate phylogenetic diversity (PD) with spatial reserve prioritization to evaluate how well the existing reserve system in Victoria, Australia captures the evolutionary lineages of eucalypts, which dominate forest canopies across the state. Forty-three per cent of remaining native woody vegetation in Victoria is located in protected areas (mostly national parks) representing 48% of the extant PD found in the state.
View Article and Find Full Text PDFSaline or alkaline soils present a strong stress on plants that together may be even more deleterious than alone. Australia's soils are old and contain large, sometimes overlapping, areas of high salt and alkalinity. Acacia and other Australian plant lineages have evolved in this stressful soil environment and present an opportunity to understand the evolution of salt and alkalinity tolerance.
View Article and Find Full Text PDFUnderstanding spatial patterns of biodiversity is critical for conservation planning, particularly given rapid habitat loss and human-induced climatic change. Diversity and endemism are typically assessed by comparing species ranges across regions. However, investigation of patterns of species diversity alone misses out on the full richness of patterns that can be inferred using a phylogenetic approach.
View Article and Find Full Text PDFRich collections of biodiversity data are now synthesized in publically available databases and phylogenetic knowledge now provides a sound understanding of the origin of organisms and their place in the tree of life. However, these knowledge bases are poorly linked, leading to underutilization or worse, an incorrect understanding of biodiversity because there is poor evolutionary context. We address this problem by integrating biodiversity information aggregated from many sources onto phylogenetic trees.
View Article and Find Full Text PDFThe largest digitized dataset of land plant distributions in Australia assembled to date (750,741 georeferenced herbarium records; 6,043 species) was used to partition the Australian continent into phytogeographical regions. We used a set of six widely distributed vascular plant groups and three non-vascular plant groups which together occur in a variety of landscapes/habitats across Australia. Phytogeographical regions were identified using quantitative analyses of species turnover, the rate of change in species composition between sites, calculated as Simpson's beta.
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