Defining appropriate null expectations for species distribution hypotheses is important because sampling bias and spatial autocorrelation can produce realistic, but ecologically meaningless, geographic patterns. Generating null species occurrences with similar spatial structure to observed data can help overcome these problems, but existing methods focus on single or pairs of species and do not incorporate between-species spatial structure that may occlude comparative biogeographic analyses. Here, we describe an algorithm for generating randomised species occurrence points that mimic the within-and between-species spatial structure of real datasets and implement it in a new R package -fauxcurrence. The algorithm can be implemented on any geographic domain for any number of species, limited only by computing power. To demonstrate its utility, we apply the algorithm to two common analysis-types: testing the fit of species distribution models (SDMs) and evaluating niche-overlap. The method works well on all tested datasets within reasonable timescales. We found that many SDMs, despite a good fit to the data, were not significantly better than null expectations and identified only two cases (out of a possible 32) of significantly higher niche divergence than expected by chance. The package is user-friendly, flexible and has many potential applications beyond those tested here, such as joint SDM evaluation and species co-occurrence analysis, spanning the areas of ecology, evolutionary biology and biogeography.
Defining appropriate null expectations for species distribution hypotheses is important because sampling bias and spatial autocorrelation can produce realistic, but ecologically meaningless, geographic patterns. Generating null species occurrences with similar spatial structure to observed data can help overcome these problems, but existing methods focus on single or pairs of species and do not incorporate between-species spatial structure that may occlude comparative biogeographic analyses. Here, we describe an algorithm for generating randomised species occurrence points that mimic the within- and between-species spatial structure of real datasets and implement it in a new R package - fauxcurrence. The algorithm can be implemented on any geographic domain for any number of species, limited only by computing power. To demonstrate its utility, we apply the algorithm to two common analysis-types: testing the fit of species distribution models (SDMs) and evaluating niche-overlap. The method works well on all tested datasets within reasonable timescales. We found that many SDMs, despite a good fit to the data, were not significantly better than null expectations and identified only two cases (out of a possible 32) of significantly higher niche divergence than expected by chance. The package is user-friendly, flexible and has many potential applications beyond those tested here, such as joint SDM evaluation and species co-occurrence analysis, spanning the areas of ecology, evolutionary biology and biogeography.
Aim:In the most widely used family of methods for ancestral range estimation (ARE), dispersal, speciation and extirpation events are estimated from information on extant lineages. However, this approach fails to consider the geographic distribution of extinct species and their position on the phylogenetic tree, an omission that could compromise reconstruction. Here, we present a method that models the geographic distribution of extinct species and we quantify the potential inaccuracy in ancestral range estimation when extinction rates are above zero.Location: Global applications, with an example from the Americas.Taxon: All taxa, with an example from hummingbirds (Amazilia).Methods: Methods capable of explicitly modelling extinct branches along with their reconstructed geographic information (GeoSSE) have been overlooked in ARE analysis, perhaps due to the inherent complexity of implementation. We develop a userfriendly platform, which we term LEMAD (Lineage Extinction Model of Ancestral Distribution) that generalizes the likelihood described in GeoSSE for any number of areas and under several sets of geographic assumptions. We compare LEMAD and extinction-free approaches using extensive simulations under different macroevolutionary scenarios. We apply our method to revisit the historical biogeography of Amazilia hummingbirds. Results:We find that accounting for the lineages removed from a tree by extinction improves reconstructions of ancestral distributions, especially when rates of vicariant speciation are higher than rates of in situ speciation, and when rates of extinction and range evolution are high. Rates of in situ and vicariant speciation are accurately estimated by LEMAD in all scenarios. North America as the most likely region for the common ancestor of hummingbirds.Main conclusions: Methods that neglect lineage extinction are less likely to accurately reconstruct true biogeographic histories of extant clades. Our findings on an
The taxonomy and biogeography of potter wasps with a petiolate metasoma occurring in the Indonesian Archipelago are reviewed. Literature review and specimens examination were carried out for the present study. Within the Eumeninae, the wasps with a petiolate metasoma distributed in the region have been more or less well studied compared with those with a non-petiolate metasoma, but their generic affinities and the concepts of some species yet remain unestablished. A total of 80 species belonging to 16 genera of the “petiolate metasoma” are known to occur from the region. Sumatra, Java, Bali and Borneo have mainly Oriental eumenine fauna, including several area- specific species of the Oriental genera. New Guinean fauna is comprised of Papua-Australian species of the widely distributed genera, together with widely distributed species and species endemic to New Guinea. The Wallacean fauna is constituted mainly with the area-specific species in the rather widely distributed genera; in the western part of Wallacea, they are represented mainly by widely distributed genera, together with Oriental genera; in the eastern part of Wallacea, they are constituted mainly by area endemic species of widely distributed Oriental genera. Widely distributed species generally show a wide range of variation in the marking patterns, and occurs sympatrically in some areas, even the peripheral populations usually characterized by the island(s)-specific marking patterns. Sympatric occurrences of forms with quite different color patterns in widely distributed species need further study to establish their taxonomic status, namely whether they are variations within a given area or different species.
Up to present, Indonesia has 900 described species of dragonflies with around 70% are endemic; among them, the most diverse is in Papua. This data is collected based on 356 publications from scientific journals, bulletins, magazines, books, theses, and proceedings from 1773 to 2019. There is still a lack of information about what is the most and least popular topics and where is the most explored regions in Indonesia for Odonata research. I categorized the topics into biodiversity, taxonomy and systematics, biogeography, conservation, ecology, education, ethnozoology, history, and molecular. The result shows that the most popular topic is biodiversity by 139 publications and the least are history and molecular by only one publication. Most popular group to be observed is dragonflies in general (both suborders) by 200 publications and the least observed is Anisoptera by only 71 publications. Java is the most explored island for about 160 publications in 250 years.
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