phyloregion: R package for biogeographical regionalization and macroecology

Daru, Barnabas H.; Karunarathne, Piyal; Schliep, Klaus

doi:10.1111/2041-210x.13478

Cited by 98 publications

(107 citation statements)

References 44 publications

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“…The optimal number of units was defined using the ‘elbow’ method, setting the maximum number of clusters to k = 30 (Daru et al , 2020). The ‘elbow’ method identifies the optimal number of units based on the range of explained variances (Daru et al , 2020). We additionally evaluated the sensitivity of the resulting regionalisation scheme by setting the number of units to match the number of previosly recognized floristic kingdoms: k = 3, 4, 5, 6.…”

Section: Methodsmentioning

confidence: 99%

A global phylogenetic regionalisation of vascular plants reveals a deep split between Gondwanan and Laurasian biotas

Carta

Peruzzi

Ramírez‐Barahona

2021

Preprint

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Existing global regionalisation schemes for plants consider the compositional affinities among biotas, but these have not considered phylogenetic information explicitly. Incorporating phylogenetic information may substantially advance our understanding of the relationships among regions and the synopsis of biogeographical schemes, because phylogeny captures information on the evolutionary history of taxa. Here, we present the first phytogeographical delineation of the global vascular flora based on the evolutionary relationships of species. We analysed 8,738,520 geographical occurrence records for vascular plant species together with a time-calibrated phylogenetic tree including 67,420 species. We estimated species composition within 200x200 km grid cells across the world, and used a metric of phylogenetic beta diversity to generate a phylogenetic delineation of floristic regions. We contrasted these results with a regionalisation generated using a taxonomic beta diversity metric. We identified 16 phylogenetically distinct phytogeographical units, deeply split into two main clusters that broadly correspond to the Laurasia-Gondwana separation. Our regionalisation broadly matches currently recognized phytogeographical classifications, but also highlights that the Gondwanan area is split into a large Holotropical cluster and an Australian-NeoZelandic-Patagonian cluster. In turn, we found that the northernmost and southernmost units have the most evolutionarily distinct vascular plant assemblages. In contrast, taxonomic dissimilarity returned a regionalisation composed of 23 units with a high degree of shared taxa between Laurasian and Gondwanan areas, with no clear split among their biotas. The integration of phylogenetic information provided new insights into the historical relationships among phytogeographical units, enabling the identification of three large, clearly differentiated biotas, here referred to as kingdoms: Holarctic, Holotropical, and Austral. Our regionalization scheme provides further evidence for delineating transition zones between the Holarctic and Holotropical kingdoms. The latitudinal patterns of evolutionary distinctiveness of vascular plant assemblages are consistent with recent evidence of higher and more recent diversification of flowering plants outside tropical regions.

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Section: Methodsmentioning

confidence: 99%

A global phylogenetic regionalisation of vascular plants reveals a deep split between Gondwanan and Laurasian biotas

Carta

Peruzzi

Ramírez‐Barahona

2021

Preprint

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“…For instance, the US National Science Foundation-funded software BiotaPhy facilitates integration, data collection and analysis by connecting to existing data repositories such as the Open Tree of Life, iDigBio, and Lifemapper (BiotaPhy, 2020), whereas the open-source package sampbias allows quantification of geographic sampling biases in species distribution data (Zizka et al, 2020). The R software package phyloregion -designed for biogeographic regionalization and macroecology -can overcome some computational challenges (Daru et al, 2020b). It contains tools for biogeographical regionalization, macroecology, conservation, and visualizing biodiversity patterns, and has potential application in diverse fields including evolution, microbial diversity, systematics, ecology, phylogenetics, and many others (Daru et al, 2020b).…”

Section: Overcoming the Impedimentsmentioning

confidence: 99%

“…The R software package phyloregion -designed for biogeographic regionalization and macroecology -can overcome some computational challenges (Daru et al, 2020b). It contains tools for biogeographical regionalization, macroecology, conservation, and visualizing biodiversity patterns, and has potential application in diverse fields including evolution, microbial diversity, systematics, ecology, phylogenetics, and many others (Daru et al, 2020b). We expect that the proliferation of more open-source analytical tools to greatly facilitate comprehensive understanding of seagrass sensitivity to ecological change driven by anthropogenic causes.…”

Section: Overcoming the Impedimentsmentioning

confidence: 99%

Impediments to Understanding Seagrasses’ Response to Global Change

Rock

Daru

2021

Front. Mar. Sci.

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Uncertainties from sampling biases present challenges to ecologists and evolutionary biologists in understanding species sensitivity to anthropogenic climate change. Here, we synthesize possible impediments that can constrain research to assess present and future seagrass response from climate change. First, our knowledge of seagrass occurrence information is prevalent with biases, gaps and uncertainties that can influence inferences on species response to global change. Second, research on seagrass diversity has been focused on species-level metrics that can be measured with data from the present – but rarely accounting for the shared phylogenetic relationships and evolutionary distinctiveness of species despite species evolved and diversified from shared ancestors. Third, compared to the mass production of species occurrence records, computational tools that can analyze these datasets in a reasonable amount of time are almost non-existent or do not scale well in terms of computer time and memory. These impediments mean that scientists must work with incomplete information and often unrepresentative data to predict how seagrass diversity might change in the future. We discuss these shortfalls and provide a framework for overcoming the impediments and diminishing the knowledge gaps they generate.

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“…The relative contribution of a species to PD can also be used to represent evolutionary distinctiveness (ED), which reflects the degree of phylogenetic isolation/uniqueness for a particular species (Pavoine et al 2005;Redding & Mooers 2006;Isaac et al 2007). When ED is combined with extinction risk derived from the International Union for Conservation of Nature (IUCN) Red List, the Evolutionary Distinctiveness and Global Endangerment (EDGE) index can be used to prioritize species for conservation not only based on their likelihood of extinction, but also on their irreplaceability (Redding & Mooers 2006;Isaac et al 2007;Daru et al 2017Daru et al , 2020. Each of these metrics is informative for a specific facet of biodiversity and when integrated within a unified framework across multiple taxonomic groups, can provide a more robust and comprehensive characterization of evolutionary history and biodiversity patterns that can be used to prioritize conservation initiatives (Posadas et al 2001;González-Orozco et al 2015).…”

Section: Introductionmentioning

confidence: 99%

Integrating spatial, phylogenetic, and threat assessment data from frogs and lizards to identify areas for conservation priorities in Peninsular Malaysia

Onn¹,

Grismer

2021

Preprint

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Malaysia is recognized as a megadiverse country and biodiversity hotspot, which necessitates sufficient levels of habitat protection and effective conservation management. However, conservation planning in Malaysia has hitherto relied largely on species distribution data without taking into account the rich evolutionary history of taxa. This represents the first study that integrates spatial and evolutionary approaches to identify important centers of diversity, endemism, and bioregionalization that can be earmarked for conservation priorities in Peninsular Malaysia. Using georeferenced species occurrences, comprehensive phylogenies, and threat assessments of frogs and lizards, we employed a spatial phylogenetics framework that incorporates various diversity metrics including weighted endemism, phylogenetic diversity, phylogenetic endemism, and evolutionary distinctiveness and global endangerment. Ten areas of high conservation value were identified via the intersection of these metrics, i.e., northern Perlis, Langkawi Geopark, southern Bintang range, Cameron Highlands, Frasers Hill, Benom-Krau complex, Selangor-Genting complex, Endau-Rompin National Park, Seribuat Archipelago (Tioman and Pemanggil Islands), and southern Johor. Of these, Cameron Highlands requires the highest conservation priority based on severe environmental degradation, inadequately protected areas, and high numbers of endangered and evolutionary distinct species. Other areas, especially in the northwestern (states of Kedah and Penang) and northeastern regions (states of Kelantan) were not only identified as areas of high conservation value but also areas of biogeographic importance. Taken together, frogs and lizards demonstrate distinct east-west and north-south patterns of bioregionalization that are largely modulated by mountain ranges.

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phyloregion: R package for biogeographical regionalization and macroecology

Cited by 98 publications

References 44 publications

A global phylogenetic regionalisation of vascular plants reveals a deep split between Gondwanan and Laurasian biotas

A global phylogenetic regionalisation of vascular plants reveals a deep split between Gondwanan and Laurasian biotas

Impediments to Understanding Seagrasses’ Response to Global Change

Integrating spatial, phylogenetic, and threat assessment data from frogs and lizards to identify areas for conservation priorities in Peninsular Malaysia

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