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Coro G, Magliozzi C, Vanden Berghe E, Bailly N, Ellenbroek A, Pagano P (2016)
Ecological Modelling 323 61-76.
Estimating absence locations of a species is important in conservation biology and conservation planning. For instance, using reliable absence as much as presence information, species distribution models can enhance their performance and produce more accurate predictions of the distribution of a species. Unfortunately, estimating reliable absence locations is difficult and often requires a deep knowledge of the species’ distribution and of its abiotic and biotic environmental preferences and tolerance. In this paper, we propose a methodology to reconstruct reliable absence information from presence-only information, and the conditions that those presence-only data have to meet to make this possible. Large species occurrence data collections (otherwise called occurrence datasets) contain high quality and expert-reviewed species observation records from scientific surveys. These surveys can be used to retrieve species presence locations, but they also record places where the species in their target list were not observed. Although these absences could be simply due to sampling variation, it is possible to intersect many of these reports to estimate true absence locations, i.e. those due to habitat unsuitability or geographical hindrances. In this paper, we present a method to generate reliable absence locations of this type for marine species, using scientific surveys reports contained in the Ocean Biogeographic Information System (OBIS), an authoritative species occurrence dataset. Our method spatially aggregates information from surveys focussing on the same target species. It detects absence locations for a given species as those locations in which repeated surveys (that included the species of interest in their target list) reported information only on other species. We qualitatively demonstrate the reliability of our method using distribution records of the Atlantic cod as a case study. Additionally, we quantitatively estimate its performance using another authoritative large species occurrence dataset, the Global Biodiversity Information Facility (GBIF). We also demonstrate that our approach has higher accuracy and presents complementary behaviour with respect to another method using environmental envelopes. Our process can support species distribution models (as well as other types of models, e.g. climate change models) by providing reliable data to presence/absence approaches. It can manage regional as well as global scale scenarios and runs within a collaborative e-Infrastructure (D4Science) that publishes it as-a-Service, allowing biologists to reproduce, repeat and share experimental results.
Keywords: Absence locations, Ecological niche modelling, Marine biodiversity, Occurrence data, Scientific surveys, Species distribution maps
Huang D, Hoeksema B, Affendi Y, Ang P, Chen C, Huang H et al. (2016)
Biodiversity and Conservation.
The South China Sea in the Central Indo-Pacific is a large semi-enclosed marine region that supports an extraordinary diversity of coral reef organisms (including stony corals), which varies spatially across the region. While one-third of the world’s reef corals are known to face heightened extinction risk from global climate and local impacts, prospects for the coral fauna in the South China Sea region amidst these threats remain poorly understood. In this study, we analyse coral species richness, rarity, and phylogenetic diversity among 16 reef areas in the region to estimate changes in species and evolutionary diversity during projected anthropogenic extinctions. Our results show that richness, rarity, and phylogenetic diversity differ considerably among reef areas in the region, and that their outcomes following projected extinctions cannot be predicted by species diversity alone. Although relative rarity and threat levels are high in species-rich areas such as West Malaysia and the Philippines, areas with fewer species such as northern Vietnam and Paracel Islands stand to lose disproportionately large amounts of phylogenetic diversity. Our study quantifies various biodiversity components of each reef area to inform conservation planners and better direct sparse resources to areas where they are needed most. It also provides a critical biological foundation for targeting reefs that should be included in a regional network of marine protected areas in the South China Sea
Keywords: IUCN Red List, Marine biodiversity, Phylogenetic diversity, Rarity, Scleractinia, Species richness
Diesmos AC, Watters JL, Huron NA, Davis DR, Alcala AC, Crombie RI, Afuang LE, Gee-Das G, Sison RV, Sanguila MB, Penrod ML, Labonte MJ, Davey CS, Leone EA, Diesmos ML, Sy EY, Welton LJ B (2015)
Proceedings of the California Academy of Sciences 62(20) 457-539.
The herpetological fauna of the Philippines Islands is high in diversity and endemism, yet faces threats suc as habitat modification and loss, natural catastrophes, invasive speciesm hunting for food or the pet trade, and the spread of chytrid fungus. New species descriptions have been steadily rising since the early 1990s due to the increased sampling, an aareness of species boundaries based on phylogenetic studies, and changes in our understanding of what definesa species. Developing a complete species list for amphibians is essential for conservation planning and informed management decisions. Previous lists were derived in part from working compendiums, developed and distributed separately by RIC and ACD; these simpe lists focused on taxonomic and conservation status of the included species, respectively, but were of limited us for other purposes.
Keywords: IUCN Red List, Marine biodiversity, Phylogenetic diversity, Rarity, Scleractinia, Species richness
Chao Y, Rouhan G, Amoroso V, Chiou W (2014)
Annals of Botany 109-124.
BACKGROUND AND AIMS: Pteris (Pteridaceae), comprising over 250 species, had been thought to be a monophyletic genus until the three monotypic genera Neurocallis, Ochropteris and Platyzoma were included. However, the relationships between the type species of the genus Pteris, P. longifolia, and other species are still unknown. Furthermore, several infrageneric morphological classifications have been proposed, but are debated. To date, no worldwide phylogenetic hypothesis has been proposed for the genus, and no comprehensive biogeographical history of Pteris, crucial to understanding its cosmopolitan distribution, has been presented. METHODS: A molecular phylogeny of Pteris is presented for 135 species, based on cpDNA rbcL and matK and using maximum parsimony, maximum likelihood and Bayesian inference approaches. The inferred phylogeny was used to assess the biogeographical history of Pteris and to reconstruct the evolution of one ecological and four morphological characters commonly used for infrageneric classifications. KEY RESULTS: The monophyly of Pteris remains uncertain, especially regarding the relationship of Pteris with Actiniopteris + Onychium and Platyzoma. Pteris comprises 11 clades supported by combinations of ecological and morphological character states, but none of the characters used in previous classifications were found to be exclusive synapomorphies. The results indicate that Pteris diversified around 47 million years ago, and when species colonized new geographical areas they generated new lineages, which are associated with morphological character transitions. CONCLUSIONS: This first phylogeny of Pteris on a global scale and including more than half of the diversity of the genus should contribute to a new, more reliable infrageneric classification of Pteris, based not only on a few morphological characters but also on ecological traits and geographical distribution. The inferred biogeographical history highlights long-distance dispersal as a major process shaping the worldwide distribution of the species. Colonization of different niches was followed by subsequent morphological diversification. Dispersal events followed by allopatric and parapatric speciation contribute to the species diversity of Pteris.
Keywords: actiniopteris, allopatric speciation, biogeography, brake ferns, long-distance dispersal, mat k, morphological character evolution, onychium, parapatric speciation, phylogeny, platyzoma, pteridaceae, pteris, rbc l
Hosner P, Boggess N, Alviola P, Sánchez-González L, Oliveros C, Urriza R et al. (2013)
Phylogeography of the Robsonius Ground-Warblers (Passeriformes: Locustellidae) Reveals an Undescribed Species from Northeastern Luzon, Philippines
The Condor 115(3) 630-639.
The Robsonius ground-warblers are forest birds endemic to the Luzon Island complex in the Philippine archipelago. Their systematic relationships have long remained ambiguous; until recently they were included in the timaliid genus Napothera. Two Robsonius species are currently recognized on the basis of plumage differences: R. rabori from northern Luzon in the Cordillera Central and the northern Sierra Madre, and R. sorsogonensis from southern Luzon and Catanduanes Island. Recent specimen collections, including the first adult specimen from the Cordillera Central, establish plumage differences between populations of R. rabori in the Cordillera Central and Sierra Madre and reveal a third diagnosable population within Luzon. These differences have gone unnoticed because R. rabori (sensu stricto) had been known only from the juvenile holotype. Molecular phylogenetic data further support the hypothesis that three highly divergent taxa occur across the Luzon Island complex: Robsonius rabori is known only from the northern Cordillera Central in Ilocos Norte; an undescribed taxon (formerly included in R. rabori) occurs in the northern Sierra Madre in Cagayan, Isabela, Aurora, and Nueva Vizcaya provinces; and R. sorsogonensis occurs in southern Luzon (Bulacan and Laguna provinces), the Bicol Peninsula, and on Catanduanes Island. The existence of three putatively allopatric species within the Luzon island complex highlights the role of in situ diversification in island systems, and brings attention to the need for forest conservation to protect geographically restricted populations throughout the Luzon Island complex.
Keywords: diversification, endemism, napothera, philippines, phylogeography
Last P, Gaudiano J (2011)
Gollum suluensis sp. nov. (Carcharhiniformes: Pseudotriakidae), a new gollumshark from the southern Philippines
Zootaxa 3002 17-30.
A second nominal species of the pseudotriakid genus Gollum, otherwise known as false catsharks or gollumsharks, is de- scribed on the basis of seven specimens collected from the Sulu Sea. Gollum suluensis sp. nov., was discovered at the Puer- to Princesa fish market in Palawan during a project initiated by the World Wildlife Fund during the 1990s to investigate elasmobranch biodiversity in the Philippines. The genus Gollum is presently represented by a single nominal species G. attenuatus (Garrick), known from the outer continental shelf and upper slope adjacent New Zealand. Gollum suluensis differs from its congener in having a darker, plainer and less contrasted coloration, softer body, shorter and broader snout, smaller spiracle, larger pectoral fin, wider head, as well as larger proportions of the nostril, mouth and interorbital space. Based on their narrow and widely separated distributions, these sharks are probably relict species.
Keywords: CSIRO, Gollum suluensis, Philippines, Pseudotriakidae, Sulu Sea, WWF-Philippines, false catshark, new species
Ready J, Kaschner K, South A, Eastwood P, Rees T, Rius J et al. (2010)
Ecological Modelling 221(3) 467-478.
We present and evaluate AquaMaps, a presence-only species distribution modelling system that allows the incorporation of expert knowledge about habitat usage and was designed for maximum output of standardized species range maps at the global scale. In the marine environment there is a significant challenge to the production of range maps due to large biases in the amount and location of occurrence data for most species. AquaMaps is compared with traditional presence-only species distribution modelling methods to determine the quality of outputs under equivalently automated conditions. The effect of the inclusion of expert knowledge to AquaMaps is also investigated. Model outputs were tested internally, through data partitioning, and externally against independent survey data to determine the ability of models to predict presence versus absence. Models were also tested externally by assessing correlation with independent survey estimates of relative species abundance. AquaMaps outputs compare well to the existing methods tested, and inclusion of expert knowledge results in a general improvement in model outputs. The transparency, speed and adaptability of the AquaMaps system, as well as the existing online framework which allows expert review to compensate for sampling biases and thus improve model predictions are proposed as additional benefits for public and research use alike.
Keywords: Expert review, Global marine biodiversity, Model comparison, Range maps, Species distribution modelling, Trawl surveys