An Integrated Ecological Niche Modelling Framework for Risk Mapping of Peste des Petits Ruminants Virus Exposure in African Buffalo (Syncerus caffer) in the Greater Serengeti-Mara Ecosystem.

Peste des petits ruminants (PPR) is a highly contagious viral disease of small ruminants that threatens livelihoods and food security in developing countries and, in some cases, wild ungulate species conservation. The Greater Serengeti-Mara Ecosystem (GSME) encompasses one of the major wildlife populations of PPR virus (PPRV)-susceptible species left on earth, although no clinical disease has been reported so far. This study aimed to gain further knowledge about PPRV circulation in the GSME by identifying which factors predict PPRV seropositivity in African buffalo (Syncerus caffer). Following an ecological niche modeling framework to map host-pathogen distribution, two models of PPRV exposure and buffalo habitat suitability were performed using serological data and buffalo censuses. Western Maasai Mara National Reserve and Western Serengeti National Park were identified as high-risk areas for PPRV exposure in buffalo. Variables related to wildlife-livestock interaction contributed to the higher risk of PPRV seropositivity in buffalo, providing supportive evidence that buffalo acquire the virus through contact with infected livestock. These findings can guide the design of cost-effective PPRV surveillance using buffalo as a sentinel species at the identified high-risk locations. As more intensive studies have been carried out in Eastern GSME, this study highlights the need for investigating PPRV dynamics in Western GSME.

Towards a scientific community consensus on designating Vulnerable Marine Ecosystems from imagery.

Management of deep-sea fisheries in areas beyond national jurisdiction by Regional Fisheries Management Organizations/Arrangements (RFMO/As) requires identification of areas with Vulnerable Marine Ecosystems (VMEs). Currently, fisheries data, including trawl and longline bycatch data, are used by many RFMO/As to inform the identification of VMEs. However, the collection of such data creates impacts and there is a need to collect non-invasive data for VME identification and monitoring purposes. Imagery data from scientific surveys satisfies this requirement, but there currently is no established framework for identifying VMEs from images. Thus, the goal of this study was to bring together a large international team to determine current VME assessment protocols and establish preliminary global consensus guidelines for identifying VMEs from images. An initial assessment showed a lack of consistency among RFMO/A regions regarding what is considered a VME indicator taxon, and hence variability in how VMEs might be defined. In certain cases, experts agreed that a VME could be identified from a single image, most often in areas of scleractinian reefs, dense octocoral gardens, multiple VME species' co-occurrence, and chemosynthetic ecosystems. A decision flow chart is presented that gives practical interpretation of the FAO criteria for single images. To further evaluate steps of the flow chart related to density, data were compiled to assess whether scientists perceived similar density thresholds across regions. The range of observed densities and the density values considered to be VMEs varied considerably by taxon, but in many cases, there was a statistical difference in what experts considered to be a VME compared to images not considered a VME. Further work is required to develop an areal extent index, to include a measure of confidence, and to increase our understanding of what levels of density and diversity correspond to key ecosystem functions for VME indicator taxa. Based on our results, the following recommendations are made: 1. There is a need to establish a global consensus on which taxa are VME indicators. 2. RFMO/As should consider adopting guidelines that use imagery surveys as an alternative (or complement) to using bycatch and trawl surveys for designating VMEs. 3. Imagery surveys should also be included in Impact Assessments. And 4. All industries that impact the seafloor, not just fisheries, should use imagery surveys to detect and identify VMEs.

100 million years of turtle paleoniche dynamics enable the prediction of latitudinal range shifts in a warming world.

Past responses to environmental change provide vital baseline data for estimating the potential resilience of extant taxa to future change. Here, we investigate the latitudinal range contraction that terrestrial and freshwater turtles (Testudinata) experienced from the Late Cretaceous to the Paleogene (100.5-23.03 mya) in response to major climatic changes. We apply ecological niche modeling (ENM) to reconstruct turtle niches, using ancient and modern distribution data, paleogeographic reconstructions, and the HadCM3L climate model to quantify their range shifts in the Cretaceous and late Eocene. We then use the insights provided by these models to infer their probable ecological responses to future climate scenarios at different representative concentration pathways (RCPs 4.5 and 8.5 for 2100), which project globally increased temperatures and spreading arid biomes at lower to mid-latitudes. We show that turtle ranges are predicted to expand poleward in the Northern Hemisphere, with decreased habitat suitability at lower latitudes, inverting a trend of latitudinal range contraction that has been prevalent since the Eocene. Trionychids and freshwater turtles can more easily track their niches than Testudinidae and other terrestrial groups. However, habitat destruction and fragmentation at higher latitudes will probably reduce the capability of turtles and tortoises to cope with future climate changes.

Evolution of mitochondrial and nuclear genomes in Pennatulacea.

We examine the phylogeny of sea pens using sequences of whole mitochondrial genomes and the nuclear ribosomal cluster generated through low coverage Illumina sequencing. Taxon sampling includes 30 species in 19 genera representing 13 families. Ancestral state reconstruction shows that most sea pen mitochondrial genomes have the ancestral gene order, and that Pennatulacea with diverse gene orders are found in a single clade. The monophyly of Pennatulidae and Protoptilidae are rejected by both the mitochondrial and nuclear dataset, while the mitochondrial dataset further rejects monophyly of Virgulariidae, and the nuclear dataset rejects monophyly of Kophobelemnidae. We show discordance between nuclear ribosomal gene cluster phylogenies and whole mitochondrial genome phylogenies and highlight key Pennatulacea taxa that could be included in cnidarian genome-wide studies to better resolve the sea pen tree of life. We further illustrate how well frequently sequenced markers capture the overall diversity of the mitochondrial genome and the nuclear ribosomal genes in sea pens.

What's left in the tank? Identification of non-ascribed aquarium's coral collections with DNA barcodes as part of an integrated diagnostic approach.

The unprecedented threats to coral reef ecosystems from global climate change require an urgent response from the aquarium community, which is becoming an increasingly vital coral conservation resource. Unfortunately, many hermatypic corals in aquaria are not identified to species level, which hinders assessment of their conservation significance. Traditional methods of species identification using morphology can be challenging, especially to non-taxonomists. DNA barcoding is an option for species identification of Scleractinian corals, especially when used in concert with morphology-based assessment. This study uses DNA barcodes to try to identify aquarium specimens of the diverse reef-forming genus Acropora from 127 samples. We identified to our best current knowledge, to species name 44% of the analysed samples and provided provisional identification for 80% of them (101/127, in the form of a list of species names with associate confidence values). We highlighted a sampling bias in public nucleotide sequences repertories (e.g. GenBank) towards more charismatic and more studied species, even inside a well-studied genus like Acropora. In addition, we showed a potential "single observer" effect with over a quarter of the reference sequences used for these identifications coming from the same study. We propose the use of barcoding and query matching as an additional tool for taxonomic experts and general aquarists, as an additional tool to increase their chances of making high confidence species-level identifications. We produce a standardised and easily repeatable methodology to increase the capacity of aquariums and other facilities to assess non-ascribed species, emphasising the value of integrating this approach with morphological identification optimising usage of authoritative identification guides and expert opinion. Supplementary Information: The online version contains supplementary material available at 10.1007/s12686-021-01250-3.

Complete mitochondrial genomes of three reef forming Acropora corals (Acroporidae, Scleractinia) from Chagos Archipelago, Indian Ocean.

We present the first mitochondrial genomes from Chagos Archipelago, Indian Ocean, of three putative species of reef forming Acropora (Acropora aff. tenuis, Acropora aff.cytherea and Acropora aff. orbicularis). The circular genome consists respectively of 18,334 bp, 18,353 bp and 18,584 bp. All mitochondrial genomes recovered comprise 13 protein-coding genes, two transfer RNA genes and two ribosomal RNA genes, with an overall GC content ranging from 37.9% to 38.0%. These new genomic data contribute to our increased understanding of genus Acropora and its species boundaries, ultimately aiding species monitoring and conservation efforts.

Moving conferences online: lessons learned from an international virtual meeting.

We consider the opportunities and challenges associated with organizing a conference online, using a case study of a medium-sized (approx. 400 participants) international conference held virtually in August 2020. In addition, we present quantifiable evidence of the participants' experience using the results from an online post-conference questionnaire. Although the virtual meeting was not able to replicate the in-person experience in some aspects (e.g. less engagement between participants) the overwhelming majority of respondents found the meeting an enjoyable experience and would join similar events again. Notably, there was a strong desire for future in-person meetings to have at least some online component. Online attendance by lower-income researchers was higher compared with a past, similar-themed in-person meeting held in a high-income nation, but comparable to one held in an upper-middle-income nation. This indicates that online conferences are not a panacea for diversity and inclusivity, and that holding in-person meetings in developing economies can be at least as effective. Given that it is now relatively easy to stream contents of meetings online using low-cost methods, there are clear benefits in making all presented content accessible online, as well as organizing online networking events for those unable to attend in person.

Improved bathymetry leads to >4000 new seamount predictions in the global ocean - but beware of phantom seamounts!

Seamounts are important marine habitats that are hotspots of species diversity. Relatively shallow peaks, increased productivity and offshore locations make seamounts vulnerable to human impact and difficult to protect. Present estimates of seamount numbers vary from anywhere between 10,000 to more than 60,000. Seamount locations can be estimated by extracting large, cone-like features from bathymetry grids (based on criteria of size and shape). These predicted seamounts are a useful reference for marine researchers and can help direct exploratory surveys. However, these predictions are dependent on the quality of the surveys underpinning the bathymetry. Historically, quality has been patchy, but is improving as mapping efforts step up towards the target of complete seabed coverage by 2030. This study presents an update of seamount predictions based on SRTM30 PLUS global bathymetry version 11 and examines a potential source of error in these predictions. This update was prompted by a seamount survey in the British Indian Ocean Territory in 2016, where locations of two putative seamounts were visited. These 'seamounts' were targeted based on previous predictions, but these features were not detected during echosounder surveys. An examination of UK hydrographic office navigational (Admiralty) charts for the area showed that the summits of these putative features had soundings reporting 'no bottom detected at this depth' where 'this depth' was similar to the seabed reported from the bathymetry grids: we suspect that these features likely resulted from an initial misreading of the charts. We show that 15 'phantom seamount' features, derived from a misinterpretation of no bottom sounding data, persist in current global bathymetry grids and updated seamount predictions. Overall, we predict 37,889 seamounts, an increase of 4437 from the previous predictions derived from an older global bathymetry grid (SRTM30 PLUS v6). This increase is due to greater detail in newer bathymetry grids as acoustic mapping of the seabed expands. The new seamount predictions are available at https://doi.pangaea.de/10.1594/PANGAEA.921688.

Novel diversity in mitochondrial genomes of deep-sea Pennatulacea (Cnidaria: Anthozoa: Octocorallia).

We present the first documented complete mitogenomes of deep-sea Pennatulacea, representing nine genera and eight families. These include one species each of the deep-sea genera Funiculina, Halipteris, Protoptilum and Distichoptilum, four species each of Umbellula and Pennatula, three species of Kophobelemnon and two species of Anthoptilum, as well as one species of the epi- and mesobenthic genus Virgularia. Seventeen circular genomes ranged from 18,513 bp (Halipteris cf. finmarchica) to 19,171 bp (Distichoptilum gracile) and contained all genes standard to octocoral mitochondrial genomes (14 protein-coding genes, two ribosomal RNA genes and one transfer RNA). We found at least three different gene orders in Pennatulacea: the ancestral gene order, the gene order found in bamboo corals (Family Isididae), and a novel gene order. The mitogenome of one species of Umbellula has a bipartite genome (∼13 kbp and ∼5 kbp), with good evidence that both parts are circular.

Climate change and the oceans--what does the future hold?

The ocean has been shielding the earth from the worst effects of rapid climate change by absorbing excess carbon dioxide from the atmosphere. This absorption of CO2 is driving the ocean along the pH gradient towards more acidic conditions. At the same time ocean warming is having pronounced impacts on the composition, structure and functions of marine ecosystems. Warming, freshening (in some areas) and associated stratification are driving a trend in ocean deoxygenation, which is being enhanced in parts of the coastal zone by upwelling of hypoxic deep water. The combined impact of warming, acidification and deoxygenation are already having a dramatic effect on the flora and fauna of the oceans with significant changes in distribution of populations, and decline of sensitive species. In many cases, the impacts of warming, acidification and deoxygenation are increased by the effects of other human impacts, such as pollution, eutrophication and overfishing. The interactive effects of this deadly trio mirrors similar events in the Earth's past, which were often coupled with extinctions of major species' groups. Here we review the observed impacts and, using past episodes in the Earth's history, set out what the future may hold if carbon emissions and climate change are not significantly reduced with more or less immediate effect.

Phylogeny and systematics of deep-sea sea pens (Anthozoa: Octocorallia: Pennatulacea).

Molecular methods have been used for the first time to determine the phylogeny of families, genera and species within the Pennatulacea (sea pens). Variation in ND2 and mtMutS mitochondrial protein-coding genes proved adequate to resolve phylogenetic relationships among pennatulacean families. The gene mtMutS is more variable than ND2 and differentiates all genera, and many pennatulacean species. A molecular phylogeny based on a Bayesian analysis reveals that suborder Sessiliflorae is paraphyletic and Subselliflorae is polyphyletic. Many families of pennatulaceans do not represent monophyletic groups including Umbellulidae, Pteroeididae, and Kophobelemnidae. The high frequency of morphological homoplasy in pennatulaceans has led to many misinterpretations in the systematics of the group. The traditional classification scheme for pennatulaceans requires revision.

Past climate change and plant evolution in Western North America: a case study in Rosaceae.

Species in the ivesioid clade of Potentilla (Rosaceae) are endemic to western North America, an area that underwent widespread aridification during the global temperature decrease following the Mid-Miocene Climatic Optimum. Several morphological features interpreted as adaptations to drought are found in the clade, and many species occupy extremely dry habitats. Recent phylogenetic analyses have shown that the sister group of this clade is Potentilla section Rivales, a group with distinct moist habitat preferences. This has led to the hypothesis that the ivesioids (genera Ivesia, Horkelia and Horkeliella) diversified in response to the late Tertiary aridification of western North America. We used phyloclimatic modeling and a fossil-calibrated dated phylogeny of the family Rosaceae to investigate the evolution of the ivesioid clade. We have combined occurrence- and climate data from extant species, and used ancestral state reconstruction to model past climate preferences. These models have been projected into paleo-climatic scenarios in order to identify areas where the ivesioids may have occurred. Our analysis suggests a split between the ivesioids and Potentilla sect. Rivales around Late Oligocene/Early Miocene (∼23 million years ago, Ma), and that the ivesioids then diversified at a time when summer drought started to appear in the region. The clade is inferred to have originated on the western slopes of the Rocky Mountains from where a westward range expansion to the Sierra Nevada and the coast of California took place between ∼12-2 Ma. Our results support the idea that climatic changes in southwestern North America have played an important role in the evolution of the local flora, by means of in situ adaptation followed by diversification.

DNA barcodes for Mexican Cactaceae, plants under pressure from wild collecting.

DNA barcodes could be a useful tool for plant conservation. Of particular importance is the ability to identify unknown plant material, such as from customs seizures of illegally collected specimens. Mexican cacti are an example of a threatened group, under pressure because of wild collection for the xeriscaping trade and private collectors. Mexican cacti also provide a taxonomically and geographically coherent group with which to test DNA barcodes. Here, we sample the matK barcode for 528 species of Cactaceae including approximately 75% of Mexican species and test the utility of the matK region for species-level identification. We find that the matK DNA barcode can be used to identify uniquely 77% of species sampled, and 79-87% of species of particular conservation importance. However, this is far below the desired rate of 95% and there are significant issues for PCR amplification because of the variability of primer sites. Additionally, we test the nuclear ITS regions for the cactus subfamily Opuntioideae and for the genus Ariocarpus (subfamily Cactoideae). We observed higher rates of variation for ITS (86% unique for Opuntioideae sampled) but a much lower PCR success, encountering significant intra-individual polymorphism in Ariocarpus precluding the use of this marker in this taxon. We conclude that the matK region should provide useful information as a DNA barcode for Cactaceae if the problems with primers can be addressed, but matK alone is not sufficiently variable to achieve species-level identification. Additional complementary regions should be investigated as ITS is shown to be unsuitable.

Molecular systematics of the Cactaceae.

Bayesian, maximum-likelihood, and maximum-parsimony phylogenies, constructed using nucleotide sequences from the plastid gene region trnK-matK, are employed to investigate relationships within the Cactaceae. These phylogenies sample 666 plants representing 532 of the 1438 species recognized in the family. All four subfamilies, all nine tribes, and 69% of currently recognized genera of Cactaceae are sampled. We found strong support for three of the four currently recognized subfamilies, although relationships between subfamilies were not well defined. Major clades recovered within the largest subfamilies, Opuntioideae and Cactoideae, are reviewed; only three of the nine currently accepted tribes delimited within these subfamilies, the Cacteae, Rhipsalideae, and Opuntieae, are monophyletic, although the Opuntieae were recovered in only the Bayesian and maximum-likelihood analyses, not in the maximum-parsimony analysis, and more data are needed to reveal the status of the Cylindropuntieae, which may yet be monophyletic. Of the 42 genera with more than one exemplar in our study, only 17 were monophyletic; 14 of these genera were from subfamily Cactoideae and three from subfamily Opuntioideae. We present a synopsis of the status of the currently recognized genera. © The Willi Hennig Society 2011.

Lost in space? Searching for directions in the spatial modelling of individuals, populations and species ranges.

The workshop 'Spatial models in animal ecology, management and conservation' held at Silwood Park (UK), 9-11 March 2010, aimed to synthesize recent progress in modelling the spatial dynamics of individuals, populations and species ranges and to provide directions for research. It brought together marine and terrestrial researchers working on spatial models at different levels of organization, using empirical as well as theory-driven approaches. Different approaches, temporal and spatial scales, and practical constraints predominate at different levels of organization and in different environments. However, there are theoretical concepts and specific methods that can fruitfully be transferred across levels and systems, including: habitat suitability characterization, movement rules, and ways of estimating uncertainty.

How global is the global biodiversity information facility?

There is a concerted global effort to digitize biodiversity occurrence data from herbarium and museum collections that together offer an unparalleled archive of life on Earth over the past few centuries. The Global Biodiversity Information Facility provides the largest single gateway to these data. Since 2004 it has provided a single point of access to specimen data from databases of biological surveys and collections. Biologists now have rapid access to more than 120 million observations, for use in many biological analyses. We investigate the quality and coverage of data digitally available, from the perspective of a biologist seeking distribution data for spatial analysis on a global scale. We present an example of automatic verification of geographic data using distributions from the International Legume Database and Information Service to test empirically, issues of geographic coverage and accuracy. There are over 1/2 million records covering 31% of all Legume species, and 84% of these records pass geographic validation. These data are not yet a global biodiversity resource for all species, or all countries. A user will encounter many biases and gaps in these data which should be understood before data are used or analyzed. The data are notably deficient in many of the world's biodiversity hotspots. The deficiencies in data coverage can be resolved by an increased application of resources to digitize and publish data throughout these most diverse regions. But in the push to provide ever more data online, we should not forget that consistent data quality is of paramount importance if the data are to be useful in capturing a meaningful picture of life on Earth.

A phyloclimatic study of Cyclamen.

BACKGROUND: The impact of global climate change on plant distribution, speciation and extinction is of current concern. Examining species climatic preferences via bioclimatic niche modelling is a key tool to study this impact. There is an established link between bioclimatic niche models and phylogenetic diversification. A next step is to examine future distribution predictions from a phylogenetic perspective. We present such a study using Cyclamen (Myrsinaceae), a group which demonstrates morphological and phenological adaptations to its seasonal Mediterranean-type climate. How will the predicted climate change affect future distribution of this popular genus of garden plants? RESULTS: We demonstrate phylogenetic structure for some climatic characteristics, and show that most Cyclamen have distinct climatic niches, with the exception of several wide-ranging, geographically expansive, species. We reconstruct climate preferences for hypothetical ancestral Cyclamen. The ancestral Cyclamen lineage has a preference for the seasonal Mediterranean climate characteristic of dry summers and wet winters. Future bioclimatic niches, based on BIOCLIM and Maxent models, are examined with reference to a future climate scenario for the 2050s. Over the next 50 years we predict a northward shift in the area of climatic suitability, with many areas of current distribution becoming climatically unsuitable. The area of climatic suitability for every Cyclamen species is predicted to decrease. For many species, there may be no areas with a suitable climate regardless of dispersal ability, these species are considered to be at high risk of extinction. This risk is examined from a phylogenetic perspective. CONCLUSION: Examining bioclimatic niches from a phylogenetic perspective permits novel interpretations of these models. In particular, reconstruction of ancestral niches can provide testable hypothesis about the historical development of lineages. In the future we can expect a northwards shift in climatic suitability for the genus Cyclamen. If this proves to be the case then dispersal is the best chance of survival, which seems highly unlikely for ant-dispersed Cyclamen. Human-assisted establishment of Cyclamen species well outside their native ranges offers hope and could provide the only means of dispersal to potentially suitable future environments. Even without human intervention the phylogenetic perspective demonstrates that major lineages could survive climate change even if many species are lost.