In search of relevant predictors for marine species distribution modelling using the MarineSPEED benchmark dataset

Aim

Ideally, datasets for species distribution modelling (SDM) contain evenly sampled records covering the entire distribution of the species, confirmed absences and auxiliary ecophysiological data allowing informed decisions on relevant predictors. Unfortunately, these criteria are rarely met for marine organisms for which distributions are too often only scantly characterized and absences generally not recorded. Here, we investigate predictor relevance as a function of modelling algorithms and settings for a global dataset of marine species.

Location

Global marine.

Methods

We selected well‐studied and identifiable species from all major marine taxonomic groups. Distribution records were compiled from public sources (e.g., OBIS, GBIF, Reef Life Survey) and linked to environmental data from Bio‐ORACLE and MARSPEC. Using this dataset, predictor relevance was analysed under different variations of modelling algorithms, numbers of predictor variables, cross‐validation strategies, sampling bias mitigation methods, evaluation methods and ranking methods. SDMs for all combinations of predictors from eight correlation groups were fitted and ranked, from which the top five predictors were selected as the most relevant.

Results

We collected two million distribution records from 514 species across 18 phyla. Mean sea surface temperature and calcite are, respectively, the most relevant and irrelevant predictors. A less clear pattern was derived from the other predictors. The biggest differences in predictor relevance were induced by varying the number of predictors, the modelling algorithm and the sample selection bias correction. The distribution data and associated environmental data are made available through the R package marinespeed and at http://marinespeed.org .

Main conclusions

While temperature is a relevant predictor of global marine species distributions, considerable variation in predictor relevance is linked to the SDM set‐up. We promote the usage of a standardized benchmark dataset (MarineSPEED) for methodological SDM studies.

     

Mismatch of morphological and molecular identifications in native and invasive subspecies of Codium fragile (Bryopsidophyceae,Chlorophyta)

Several subspecies are defined within Codium fragile, including the invasive C. fragile ssp. fragile, first reported in New Zealand in 1973. An endemic subspecies, C. fragile ssp. novae‐zelandiae, is also found throughout New Zealand. The two subspecies exhibit morphological and molecular variation, although these have never been evaluated together. We compared variation between subspecies at locations in Auckland, identifying subspecies using rps3‐rpl16 DNA sequence data, and assessing gross morphological differences, anatomical utricle characters and morphometrics. The taxonomic utility of the morphometric data sets was assessed by linear discriminant analysis. Utricle characters and measurements varied within individual thalli and between different preservation methods. The phenotypes of both subspecies were highly variable and influenced by environment. Accurate subspecies delimitation using morphological data was not possible; the discriminant analyses performed no better than chance for all combinations of the morphological data. Specimens from New Zealand, Canada, Australia and Ireland were sequenced using both the rps3‐rpl16 and tufA plastid markers. The tufA elongation factor was shown to be a good candidate for differentiating subspecies of C. fragile. This marker is twice the length of the rps3‐rpl16 spacer, shows greater variation between ssp. fragile and novae‐zelandiae, and is less prone to sequencing error. A simple restriction enzyme digest of the tufA amplicon can distinguish ssp. fragile and ssp. novae‐zelandiae. Our study expands the known range of the ssp. fragile in New Zealand, including the first record of this subspecies from the west coast of Auckland, and points to a need to re‐evaluate morphological and molecular criteria for subspecies currently defined within C. fragile.     

Introduced Macroalgae – a Growing Concern

Introductions of non-indigenous species to new ecosystems are one of the major threats to biodiversity, ecosystem functions and services. Globally, species introductions may lead to biotic homogenisation, in synergy with other anthropogenic disturbances such as climate change and coastal pollution. Successful marine introductions depend on (1) presence of a transport vector, uptake of propagules and journey survival of the species; (2) suitable environmental conditions in the receiving habitat; and (3) biological traits of the invader to facilitate establishment. Knowledge has improved of the distribution, biology and ecology of high profile seaweed invaders, e.g. Caulerpa taxifolia, Codium fragile ssp. tomentosoides, Sargassum muticum, and Undaria pinnatifida. Limited, regional information is available for less conspicuous species. The mechanisms of seaweed introductions are little understood as research on introduced seaweeds has been mostly reactive, following discoveries of introductions. Sources of introductions mostly cannot be determined with certainty apart from those directly associated with aquaculture activities and few studies have addressed the sometimes serious ecological and economic impacts of seaweed introductions. Future research needs to elucidate the invasion process, interactions between invaders, and impacts of introductions to support prevention and management of seaweed introductions.     

Desiccation tolerance of the introduced marine green alga <Emphasis Type="Italic">Codium fragile</Emphasis> ssp. <Emphasis Type="Italic">tomentosoides</Emphasis> – clues for likely transport vectors?

The invasive marine green macroalga Codium fragile ssp. tomentosoides is now considered to be an introduced marine pest along the northwest Atlantic and southern Australian coasts. International or domestic translocation of C. fragile ssp. tomentosoides is usually attributed to the fouling of ship hulls or shellfish, particularly oysters. A likely domestic vector is shipboard transport, involving the translocation of whole thalli or fragments entangled in fishing nets, ropes, etc. that are then released in a previously unaffected area. Here we investigated the survival of C. fragile ssp. tomentosoides under emersed conditions, simulating shipboard transport. C. fragile ssp. tomentosoides was able to survive periods of emersion of up to 90 days in high relative air humidity. Net photosynthesis remained positive at about 50% of the rates of submersed control thalli. After 2 days of emersion and 4 days of rehydration under submersed conditions thalli recover to their initial net photosynthesis rates. Hence, C. fragile ssp. tomentosoides is likely to survive long shipboard journeys entrapped in fishing nets, anchor wells or other protected, high-humidity areas of a vessel. Furthermore, C. fragile ssp. tomentosoides may survive emersion on an exposed deck during short trips, especially in cooler conditions such as at night. The incursion sites of C. fragile ssp. tomentosoides in Australia are generally in modified environments, often associated with shipping-related infrastructure such as wharves, jetties, rip rap, and moorings.     

CELL‐WALL POLYMER MAPPING IN THE COENOCYTIC MACROALGA CODIUM VERMILARA (BRYOPSIDALES,CHLOROPHYTA)1

Cell walls in the coenocytic green seaweed Codium vermilara (Olivi) Chiaje (Bryopsidales, Chlorophyta) are composed of ～32% (w/w) β‐(1→4)‐d‐mannans, ～12% sulfated polysaccharides (SPs), and small amounts of hydroxyproline‐rich glycoprotein‐like (HRGP‐L) compounds of the arabinogalactan proteins (AGPs) and arabinosides (extensins). Similar quantities of mannans and SPs were reported previously in the related seaweed C. fragile (Suringar) Hariot. Overall, both seaweed cell walls comprise ～40%–44% of their dry weights. Within the SP group, a variety of polysaccharide structures from pyruvylated arabinogalactan sulfate and pyruvylated galactan sulfate to pyranosic arabinan sulfate are present in Codium cell walls. In this paper, the in situ distribution of the main cell‐wall polymers in the green seaweed C. vermilara was studied, comparing their arrangements with those observed in cell walls from C. fragile. The utricle cell wall in C. vermilara showed by TEM a sandwich structure of two fibrillar‐like layers of similar width delimiting a middle amorphous‐like zone. By immuno‐ and chemical imaging, the in situ distribution of β‐(1→4)‐d‐mannans and HRGP‐like epitopes was shown to consist of two distinct cell‐wall layers, whereas SPs are distributed in the middle area of the wall. The overall cell‐wall polymer arrangement of the SPs, HRGP‐like epitopes, and mannans in the utricles of C. vermilara is different from the ubiquitous green algae C. fragile, in spite of both being phylogenetically very close. In addition, a preliminary cell‐wall model of the utricle moiety is proposed for both seaweeds, C. fragile and C. vermilara.     

Environmental controls on the global distribution of shallow‐water coral reefs

Aim Elucidating the environmental limits of coral reefs is central to projecting future impacts of climate change on these ecosystems and their global distribution. Recent developments in species distribution modelling (SDM) and the availability of comprehensive global environmental datasets have provided an opportunity to reassess the environmental factors that control the distribution of coral reefs at the global scale as well as to compare the performance of different SDM techniques. Location Shallow waters world‐wide. Methods The SDM methods used were maximum entropy (Maxent) and two presence/absence methods: classification and regression trees (CART) and boosted regression trees (BRT). The predictive variables considered included sea surface temperature (SST), salinity, aragonite saturation state (Ω_Arag), nutrients, irradiance, water transparency, dust, current speed and intensity of cyclone activity. For many variables both mean and SD were considered, and at weekly, monthly and annually averaged time‐scales. All were transformed to a global 1° × 1° grid to generate coral reef probability maps for comparison with known locations. Model performance was compared in terms of receiver operating characteristic (ROC) curves and area under the curve (AUC) scores. Potential geographical bias was explored via misclassification maps of false positive and negative errors on test data. Results Boosted regression trees consistently outperformed other methods, although Maxent also performed acceptably. The dominant environmental predictors were the temperature variables (annual mean SST, and monthly and weekly minimum SST), followed by, and with their relative importance differing between regions, nutrients, light availability and Ω_Arag. No systematic bias in SDM performance was found between major coral provinces, but false negatives were more likely for cells containing ‘marginal’ non‐reef‐forming coral communities, e.g. Bermuda. Main conclusions Agreement between BRT and Maxent models gives predictive confidence for exploring the environmental limits of coral reef ecosystems at a spatial scale relevant to global climate models (c. 1° × 1°). Although SST‐related variables dominate the coral reef distribution models, contributions from nutrients, Ω_Arag and light availability were critical in developing models of reef presence in regions such as the Bahamas, South Pacific and Coral Triangle. The steep response in SST‐driven probabilities at low temperatures indicates that latitudinal expansion of coral reef habitat is very sensitive to global warming.     

Detecting the impacts of notorious invaders: experiments versus observations in the invasion of eelgrass meadows by the green seaweed <Emphasis Type="Italic">Codium fragile</Emphasis>

Biological invasions can vary in the extent of their effects on indigenous communities but predicting impacts for particular systems remains difficult. In coastal marine ecosystems, the green seaweed Codium fragile ssp. fragile is a notorious invader with its reputation based on studies conducted largely on rocky shores. The green seaweed has recently invaded soft-bottom eelgrass communities by attaching epiphytically to eelgrass (Zostera marina) rhizomes, thereby creating the potential for disruption of these coastal habitats through competition or disturbance. We investigated the effect of this invader on various aspects of eelgrass performance (shoot density and length, shoot growth, above- and below-ground biomass, carbohydrate storage) using both small-scale manipulative and large-scale observational experiments. Manipulative experiments that varied Codium abundance demonstrated clear negative effects over a 4-month period on shoot density and carbohydrate reserves, but only for high, but realistic, Codium biomass levels. Light levels were much lower under canopies for high and medium density Codium treatments relative to low and control Codium cover treatments, suggesting that shading may influence eelgrass growing under the algal cover. In contrast, these effects were either not detectable or very weak when examined correlatively with field surveys conducted at larger spatial scales, even for sites that had been invaded for over 4 years. It is premature to extend generalizations of Codium’s impact derived from studies in other systems to eelgrass communities; further efforts are required to assess the long-term threats that the alga poses to this ecosystem. This study demonstrates the need to investigate impacts of invasions over multiple scales, especially those that incorporate the temporal and spatial heterogeneity of the invader’s abundance.     

Combining physiological threshold knowledge to species distribution models is key to improving forecasts of the future niche for macroalgae

Species distribution models (SDM) are a useful tool for predicting species range shifts in response to global warming. However, they do not explore the mechanisms underlying biological processes, making it difficult to predict shifts outside the environmental gradient where the model was trained. In this study, we combine correlative SDMs and knowledge on physiological limits to provide more robust predictions. The thermal thresholds obtained in growth and survival experiments were used as proxies of the fundamental niches of two foundational marine macrophytes. The geographic projections of these species’ distributions obtained using these thresholds and existing SDMs were similar in areas where the species are either absent‐rare or frequent and where their potential and realized niches match, reaching consensus predictions. The cold‐temperate foundational seaweed Himanthalia elongata was predicted to become extinct at its southern limit in northern Spain in response to global warming, whereas the occupancy of southern‐lusitanic Bifurcaria bifurcata was expected to increase. Combined approaches such as this one may also highlight geographic areas where models disagree potentially due to biotic factors. Physiological thresholds alone tended to over‐predict species prevalence, as they cannot identify absences in climatic conditions within the species’ range of physiological tolerance or at the optima. Although SDMs tended to have higher sensitivity than threshold models, they may include regressions that do not reflect causal mechanisms, constraining their predictive power. We present a simple example of how combining correlative and mechanistic knowledge provides a rapid way to gain insight into a species’ niche resulting in consistent predictions and highlighting potential sources of uncertainty in forecasted responses to climate change.     

TRACING SPECIES INVASION IN CODIUM,A SIPHONOUS GREEN ALGA,USING MOLECULAR TOOLS

The siphonous green alga Codium fragile occurs in many temperate marine regions and is composed of a number of distinct subspecies. Included in this taxon is the common open coast C. fragile subsp. fragile of the northeast Pacific and the weedy C. fragile subsp. tomentosoides which has invaded temperate marine communities in the Atlantic and Pacific oceans. The center of origin of this weedy subspecies is not known, although it is thought to have dispersed from the northwest Pacific. To examine the relationship of the weedy subspecies to the indigenous northeast Pacific form, chloroplast DNA was compared. Each of these subspecies has a restriction map that is uniform throughout its geographic distribution, and the patterns are distinct from each other and from other Codium species examined. However, the two share an almost identical genome size and arrangement of genes. A population in San Francisco Bay was found to be indistinguishable from the weed C. fragile subsp. tomentosoides from the Atlantic. The potential for using molecular data in solving systematic problems in Codium has been clearly demonstrated.     

Climate‐driven range shifts explain the distribution of extant gene pools and predict future loss of unique lineages in a marine brown alga

The climate‐driven dynamics of species ranges is a critical research question in evolutionary ecology. We ask whether present intraspecific diversity is determined by the imprint of past climate. This is an ongoing debate requiring interdisciplinary examination of population genetic pools and persistence patterns across global ranges. Previously, contrasting inferences and predictions have resulted from distinct genomic coverage and/or geographical information. We aim to describe and explain the causes of geographical contrasts in genetic diversity and their consequences for the future baseline of the global genetic pool, by comparing present geographical distribution of genetic diversity and differentiation with predictive species distribution modelling (SDM) during past extremes, present time and future climate scenarios for a brown alga, Fucus vesiculosus. SDM showed that both atmospheric and oceanic variables shape the global distribution of intertidal species, revealing regions of persistence, extinction and expansion during glacial and postglacial periods. These explained the distribution and structure of present genetic diversity, consisting of differentiated genetic pools with maximal diversity in areas of long‐term persistence. Most of the present species range comprises postglacial expansion zones and, in contrast to highly dispersive marine organisms, expansions involved only local fronts, leaving distinct genetic pools at rear edges. Besides unravelling a complex phylogeographical history and showing congruence between genetic diversity and persistent distribution zones, supporting the hypothesis of niche conservatism, range shifts and loss of unique genetic diversity at the rear edge were predicted for future climate scenarios, impoverishing the global gene pool.     

Tackling intraspecific genetic structure in distribution models better reflects species geographical range

Genetic diversity provides insight into heterogeneous demographic and adaptive history across organisms’ distribution ranges. For this reason, decomposing single species into genetic units may represent a powerful tool to better understand biogeographical patterns as well as improve predictions of the effects of GCC (global climate change) on biodiversity loss. Using 279 georeferenced Iberian accessions, we used classes of three intraspecific genetic units of the annual plant Arabidopsis thaliana obtained from the genetic analyses of nuclear SNPs (single nucleotide polymorphisms), chloroplast SNPs, and the vernalization requirement for flowering. We used SDM (species distribution models), including climate, vegetation, and soil data, at the whole‐species and genetic‐unit levels. We compared model outputs for present environmental conditions and with a particularly severe GCC scenario. SDM accuracy was high for genetic units with smaller distribution ranges. Kernel density plots identified the environmental variables underpinning potential distribution ranges of genetic units. Combinations of environmental variables accounted for potential distribution ranges of genetic units, which shrank dramatically with GCC at almost all levels. Only two genetic clusters increased their potential distribution ranges with GCC. The application of SDM to intraspecific genetic units provides a detailed picture on the biogeographical patterns of distinct genetic groups based on different genetic criteria. Our approach also allowed us to pinpoint the genetic changes, in terms of genetic background and physiological requirements for flowering, that Iberian A. thaliana may experience with a GCC scenario applying SDM to intraspecific genetic units.     

Potential of marine lactic acid bacteria to ferment Sargassum sp. for enhanced anticoagulant and antioxidant properties

Aim

To evaluate the suitability of marine lactic acid bacteria (LAB) as starter cultures for Sargassum sp. fermentation to enhance its antioxidant and anticoagulation activity.

Methods and Results

LAB isolated from marine source were characterized for their ability to utilize seaweed as a sole carbon source and applied to Sargassum fermentation. Fermentation period was optimized by monitoring the fermented sample at regular interval for a period of 18 days. Results revealed that a fermentation period of 12 days was effective with maximum culture viability and other desirable characteristics such as pH, total titratable acidity, total and reducing sugars. Under optimum fermentation period, the sample fermented with P1‐2CB‐w1 (Enterococcus faecium) exhibited maximum anticoagulation activity and antioxidant activity.

Conclusions

The study reveals a novel well‐defined starter culture from marine origin intended for seaweed fermentation for recovery of bioactive molecules.

Significance and Impact of the study

The study provides information for the enhancement of bioactive molecules in an eco‐friendly manner and also paves a way towards the development of wide range of seaweed functional foods.     

Macroecology meets macroevolution: evolutionary niche dynamics in the seaweed Halimeda

Aim Because of their broad distribution in geographical and ecological dimensions, seaweeds (marine macroalgae) offer great potential as models for marine biogeographical inquiry and exploration of the interface between macroecology and macroevolution. This study aims to characterize evolutionary niche dynamics in the common green seaweed genus Halimeda, use the observed insights to gain understanding of the biogeographical history of the genus and predict habitats that can be targeted for the discovery of species of special biogeographical interest. Location Tropical and subtropical coastal waters. Methods The evolutionary history of the genus is characterized using molecular phylogenetics and relaxed molecular clock analysis. Niche modelling is carried out with maximum entropy techniques and uses macroecological data derived from global satellite imagery. Evolutionary niche dynamics are inferred through application of ancestral character state estimation. Results A nearly comprehensive molecular phylogeny of the genus was inferred from a six‐locus dataset. Macroecological niche models showed that species distribution ranges are considerably smaller than their potential ranges. We show strong phylogenetic signal in various macroecological niche features. Main conclusions The evolution of Halimeda is characterized by conservatism for tropical, nutrient‐depleted habitats, yet one section of the genus managed to invade colder habitats multiple times independently. Niche models indicate that the restricted geographical ranges of Halimeda species are not due to habitat unsuitability, strengthening the case for dispersal limitation. Niche models identified hotspots of habitat suitability of Caribbean species in the eastern Pacific Ocean. We propose that these hotspots be targeted for discovery of new species separated from their Caribbean siblings since the Pliocene rise of the Central American Isthmus.     

Influence of device accuracy and choice of algorithm for species distribution modelling of seabirds: a case study using black‐browed albatrosses

Species distribution models (SDM) based on tracking data from different devices are used increasingly to explain and predict seabird distributions. However, different tracking methods provide different data resolutions, ranging from < 10 m to > 100 km. To better understand the implications of this variation, we modeled the potential distribution of black‐browed albatrosses Thalassarche melanophris from South Georgia that were simultaneously equipped with a platform terminal transmitter (PTT) (high resolution) and a global location sensor (GLS) logger (coarse resolution), and measured the overlap of the respective potential distribution for a total of nine different SDM algorithms. We found slightly better model fits for the PTT than for GLS data (AUC values 0.958 ± 0.048 vs 0.95 ± 0.05) across all algorithms. The overlaps of the predicted distributions were higher between device types for the same algorithm, than among algorithms for either device type. Uncertainty arising from coarse‐resolution location data is therefore lower than that associated with the modeling technique. Consequently, the choice of an appropriate algorithm appears to be more important than device type when applying SDMs to seabird tracking data. Despite their low accuracy, GLS data appear to be effective for analyzing the habitat preferences and distribution patterns of pelagic species.     

<Emphasis Type="Italic">Codium fragile</Emphasis>: rhizomatous growth in the<Emphasis Type="Italic"> Zostera</Emphasis> thief of eastern Canada

A rhizomatous growth form of Codium fragile is described for the first time. Plants were collected in the Gulf of St. Lawrence in estuaries dominated by Zostera marina. Rhizomatous plants developed from propagules of whole plants that settled horizontally. Horizontal axes of C. fragile were up to 1 m long in plants collected in situ. Plants developed several to dozens of erect axes at right angle to the base. Horizontal growth of up to 0.2 m was found in field experiments where fragments were tied to plastic mesh and left in situ for 4 months. The unconsolidated filaments at the base of C. fragile often wrapped around the rhizomes of Z. marina and up to five separate attachment sites to eelgrass were found in single plants of C. fragile. In four estuaries, 57–100% of Codium plants with identifiable substratum were attached to shoots and rhizomes of Z. marina. The rhizomatous growth form was found in plants identified as C. fragile ssp. tomentosoides (Nova Scotia and Prince Edward Island) and C. fragile ssp. atlanticum (Prince Edward Island), suggesting that this is a phenotypic response to growth in soft bottom environments.Communicated by K Lüning     

Detecting outliers in species distribution data

Aim

Species distribution data play a pivotal role in the study of ecology, evolution, biogeography and biodiversity conservation. Although large amounts of location data are available and accessible from public databases, data quality remains problematic. Of the potential sources of error, positional errors are critical for spatial applications, particularly where these errors place observations beyond the environmental or geographical range of species. These outliers need to be identified, checked and removed to improve data quality and minimize the impact on subsequent analyses. Manually checking all species records within large multispecies datasets is prohibitively costly. This work investigates algorithms that may assist in the efficient vetting of outliers in such large datasets.

Location

We used real, spatially explicit environmental data derived from the western part of Victoria, Australia, and simulated species distributions within this same region.

Methods

By adapting species distribution modelling (SDM), we developed a pseudo‐SDM approach for detecting outliers in species distribution data, which was implemented with random forest (RF) and support vector machine (SVM) resulting in two new methods: RF_pdSDM and SVM_pdSDM. Using virtual species, we compared eight existing multivariate outlier detection methods with these two new methods under various conditions.

Results

The two new methods based on the pseudo‐SDM approach had higher true skill statistic (TSS) values than other approaches, with TSS values always exceeding 0. More than 70% of the true outliers in datasets for species with a low and intermediate prevalence can be identified by checking 10% of the data points with the highest outlier scores.

Main conclusions

Pseudo‐SDM‐based methods were more effective than other outlier detection methods. However, this outlier detection procedure can only be considered as a screening tool, and putative outliers must be examined by experts to determine whether they are actual errors or important records within an inherently biased set of data.     

Disregarding the edaphic dimension in species distribution models leads to the omission of crucial spatial information under climate change: the case of Quercus pubescens in France

Species distribution modelling is an easy, persuasive and useful tool for anticipating species distribution shifts under global change. Numerous studies have used only climate variables to predict future potential species range shifts and have omitted environmental factors important for determining species distribution. Here, we assessed the importance of the edaphic dimension in the niche‐space definition of Quercus pubescens and in future spatial projections under global change over the metropolitan French forest territory. We fitted two species distribution models (SDM) based on presence/absence data (111 013 plots), one calibrated from climate variables only (mean temperature of January and climatic water balance of July) and the other one from both climate and edaphic (soil pH inferred from plants) variables. Future predictions were conducted under two climate scenarios (PCM B2 and HadCM3 A2) and based on 100 simulations using a cellular automaton that accounted for seed dispersal distance, landscape barriers preventing migration and unsuitable land cover. Adding the edaphic dimension to the climate‐only SDM substantially improved the niche‐space definition of Q. pubescens, highlighting an increase in species tolerance in confronting climate constraints as the soil pH increased. Future predictions over the 21st century showed that disregarding the edaphic dimension in SDM led to an overestimation of the potential distribution area, an underestimation of the spatial fragmentation of this area, and prevented the identification of local refugia, leading to an underestimation of the northward shift capacity of Q. pubescens and its persistence in its current distribution area. Spatial discrepancies between climate‐only and climate‐plus‐edaphic models are strengthened when seed dispersal and forest fragmentation are accounted for in predicting a future species distribution area. These discrepancies highlight some imprecision in spatial predictions of potential distribution area of species under climate change scenarios and possibly wrong conclusions for conservation and management perspectives when climate‐only models are used.     

Potential effects of climate change on the distribution range of the main silicate sinker of the Southern Ocean

Fragilariopsis kerguelensis, a dominant diatom species throughout the Antarctic Circumpolar Current, is coined to be one of the main drivers of the biological silicate pump. Here, we study the distribution of this important species and expected consequences of climate change upon it, using correlative species distribution modeling and publicly available presence‐only data. As experience with SDM is scarce for marine phytoplankton, this also serves as a pilot study for this organism group. We used the maximum entropy method to calculate distribution models for the diatom F. kerguelensis based on yearly and monthly environmental data (sea surface temperature, salinity, nitrate and silicate concentrations). Observation data were harvested from GBIF and the Global Diatom Database, and for further analyses also from the Hustedt Diatom Collection (BRM). The models were projected on current yearly and seasonal environmental data to study current distribution and its seasonality. Furthermore, we projected the seasonal model on future environmental data obtained from climate models for the year 2100. Projected on current yearly averaged environmental data, all models showed similar distribution patterns for F. kerguelensis. The monthly model showed seasonality, for example, a shift of the southern distribution boundary toward the north in the winter. Projections on future scenarios resulted in a moderately to negligibly shrinking distribution area and a change in seasonality. We found a substantial bias in the publicly available observation datasets, which could be reduced by additional observation records we obtained from the Hustedt Diatom Collection. Present‐day distribution patterns inferred from the models coincided well with background knowledge and previous reports about F. kerguelensis distribution, showing that maximum entropy‐based distribution models are suitable to map distribution patterns for oceanic planktonic organisms. Our scenario projections indicate moderate effects of climate change upon the biogeography of F. kerguelensis.     

Integrating a comprehensive DNA barcode reference library with a global map of yews (Taxus L.) for forensic identification

Rapid and accurate identification of endangered species is a critical component of biosurveillance and conservation management, and potentially policing illegal trades. However, this is often not possible using traditional taxonomy, especially where only small or preprocessed parts of plants are available. Reliable identification can be achieved via a comprehensive DNA barcode reference library, accompanied by precise distribution data. However, these require extensive sampling at spatial and taxonomic scales, which has rarely been achieved for cosmopolitan taxa. Here, we construct a comprehensive DNA barcode reference library and generate distribution maps using species distribution modelling (SDM), for all 15 Taxus species worldwide. We find that trnL‐trnF is the ideal barcode for Taxus: It can distinguish all Taxus species and in combination with ITS identify hybrids. Among five analysis methods tested, NJ was the most effective. Among 4,151 individuals screened for trnL‐trnF, 73 haplotypes were detected, all species‐specific and some population private. Taxonomical, geographical and genetic dimensions of sampling strategy were all found to affect the comprehensiveness of the resulting DNA barcode library. Maps from SDM showed that most species had allopatric distributions, except T. mairei in the Sino‐Himalayan region. Using the barcode library and distribution map data, two unknown forensic samples were identified to species (and in one case, population) level and another was determined as a putative interspecific hybrid. This integrated species identification system for Taxus can be used for biosurveillance, conservation management and to monitor and prosecute illegal trade. Similar identification systems are recommended for other IUCN‐ and CITES‐listed taxa.     

Testing the utility of species distribution modelling using Random Forests for a species in decline

Habitat suitability estimates derived from species distribution models (SDMs) are increasingly used to guide management of threatened species. Poorly estimating species’ ranges can lead to underestimation of threatened status, undervaluing of remaining habitat and misdirection of conservation funding. We aimed to evaluate the utility of a SDM, similar to the models used to inform government regulation of habitat in our study region, in estimating the contemporary distribution of a threatened and declining species. We developed a presence‐only SDM for the endangered New Holland Mouse (Pseudomys novaehollandiae) across Victoria, Australia. We conducted extensive camera trap surveys across model‐predicted and expert‐selected areas to generate an independent data set for use in evaluating the model, determining confidence in absence data from non‐detection sites with occupancy and detectability modelling. We assessed the predictive capacity of the model at thresholds based on (1) sum of sensitivity and specificity (SSS), and (2) the lowest presence threshold (LPT; i.e. the lowest non‐zero model‐predicted habitat suitability value at which we detected the species). We detected P. novaehollandiae at 40 of 472 surveyed sites, with strong support for the species’ probable absence from non‐detection sites. Based on our post hoc optimised SSS threshold of the SDM, 25% of our detection sites were falsely predicted as non‐suitable habitat and 75% of sites predicted as suitable habitat did not contain the species at the time of our survey. One occupied site had a model‐predicted suitability value of zero, and at the LPT, 88% of sites predicted as suitable habitat did not contain the species at the time of our survey. Our findings demonstrate that application of generic SDMs in both regulatory and investment contexts should be tempered by considering their limitations and currency. Further, we recommend engaging species experts in the extrapolation and application of SDM outputs.