A Reverse Taxonomic Approach to Assess Macrofaunal Distribution Patterns in Abyssal Pacific Polymetallic Nodule Fields

Heightened interest in the exploitation of deep seafloor minerals is raising questions on the consequences for the resident fauna. Assessing species ranges and determination of processes underlying current species distributions are prerequisites to conservation planning and predicting faunal responses to changing environmental conditions. The abyssal central Pacific nodule belt, located between the Clarion and Clipperton Fracture Zones (CCZ), is an area prospected for mining of polymetallic nodules. We examined variations in genetic diversity and broad-scale connectivity of isopods and polychaetes across the CCZ. Faunal assemblages were studied from two mining claims (the eastern German and French license areas) located 1300 km apart and influenced by different productivity regimes. Using a reverse taxonomy approach based on DNA barcoding, we tested to what extent distance and large-scale changes in environmental parameters lead to differentiation in two macrofaunal taxa exhibiting different functions and life-history patterns. A fragment of the mitochondrial gene Cytochrome Oxidase Subunit 1 (COI) was analyzed. At a 97% threshold the molecular operational taxonomic units (MOTUs) corresponded well to morphological species. Molecular analyses indicated high local and regional diversity mostly because of large numbers of singletons in the samples. Consequently, variation in composition of genotypic clusters between sites was exceedingly large partly due to paucity of deep-sea sampling and faunal patchiness. A higher proportion of wide-ranging species in polychaetes was contrasted with mostly restricted distributions in isopods. Remarkably, several cryptic lineages appeared to be sympatric and occurred in taxa with putatively good dispersal abilities, whereas some brooding lineages revealed broad distributions across the CCZ. Geographic distance could explain variation in faunal connectivity between regions and sites to some extent, while assumed dispersal capabilities were not as important.     

Xenophyophores (Rhizaria,Foraminifera), including four new species and two new genera,from the western Clarion-Clipperton Zone (abyssal equatorial Pacific)

The Clarion-Clipperton Zone (CCZ) occupies a vast swathe of the Pacific with extensive polymetallic nodule deposits. Eastern and central parts host diverse assemblages of xenophyophores (megafaunal agglutinated foraminifera). Here we describe xenophyophores obtained using a Remotely Operated Vehicle from the western CCZ. Eleven distinct forms include two known species, Stannophyllum zonarium Haeckel, 1888 and Aschemonella monile Gooday and Holzmann in Gooday et al., 2017b. Another four are described as new species based on morphological and genetic data. In Abyssalia foliformis gen. nov., sp. nov. and Abyssalia sphaerica sp. nov. the flattened or spherical test comprises a homogeneous framework of sponge spicules. Psammina tenuis sp. nov. has a delicate, thin, plate-like test. Moanammina semicircularis gen. nov., sp. nov. has a stalked, fan-shaped test and is genetically identical to ‘Galatheammina sp. 6’ of Gooday and co-workers from the eastern CCZ. Sequence data revealed a spherical ‘mudball’, which disintegrated and cannot be formally described, to be a novel xenophyophore. Finally, four morphospecies are represented by dead tests: Psammina spp., Reticulammina sp., and an unknown genus with a unique test structure. This collection enhances our knowledge of Pacific xenophyophore diversity and provides the first genetic confirmation of wide geographic ranges for abyssal species.     

A tri-oceanic perspective: DNA barcoding reveals geographic structure and cryptic diversity in Canadian polychaetes

Background

Although polychaetes are one of the dominant taxa in marine communities, their distributions and taxonomic diversity are poorly understood. Recent studies have shown that many species thought to have broad distributions are actually a complex of allied species. In Canada, 12% of polychaete species are thought to occur in Atlantic, Arctic, and Pacific Oceans, but the extent of gene flow among their populations has not been tested.

Methodology/Principal Findings

Sequence variation in a segment of the mitochondrial cytochrome c oxidase I (COI) gene was employed to compare morphological versus molecular diversity estimates, to examine gene flow among populations of widespread species, and to explore connectivity patterns among Canada''s three oceans. Analysis of 1876 specimens, representing 333 provisional species, revealed 40 times more sequence divergence between than within species (16.5% versus 0.38%). Genetic data suggest that one quarter of previously recognized species actually include two or more divergent lineages, indicating that richness in this region is currently underestimated. Few species with a tri-oceanic distribution showed genetic cohesion. Instead, large genetic breaks occur between Pacific and Atlantic-Arctic lineages, suggesting their long-term separation. High connectivity among Arctic and Atlantic regions and low connectivity with the Pacific further supports the conclusion that Canadian polychaetes are partitioned into two distinct faunas.

Conclusions/Significance

Results of this study confirm that COI sequences are an effective tool for species identification in polychaetes, and suggest that DNA barcoding will aid the recognition of species overlooked by the current taxonomic system. The consistent geographic structuring within presumed widespread species suggests that historical range fragmentation during the Pleistocene ultimately increased Canadian polychaete diversity and that the coastal British Columbia fauna played a minor role in Arctic recolonization following deglaciation. This study highlights the value of DNA barcoding for providing rapid insights into species distributions and biogeographic patterns in understudied groups.     

Deconstructing the dimensions of alpha diversity in squamate reptiles (Reptilia: Squamata) across the Americas

Aim

Our aim is to document the dimensions of current squamate reptile biodiversity in the Americas by integrating taxonomic, phylogenetic and functional data, and assessing how this may vary across phylogenetic scales. We also explore the potential underlying mechanisms that may be responsible for the observed geographical diversity patterns.

Location

The Americas.

Time period

Present.

Major taxa

Squamate reptiles.

Methods

We used published data on the distribution, phylogeny, and body size of squamate reptiles to document the current dimensions of their alpha diversity in the Americas. We overlapped species ranges to estimate taxonomic diversity (TD) and calculated phylogenetic diversity (PD) using mean pairwise phylogenetic distance (MPD), speciation rate (DivRate) and Faith's phylogenetic index (PD). We estimated functional diversity (FD) as trait dispersion in the multivariate space using body size and leg development data. We implemented a deconstructive macroecological approach to understand how spatial mismatches between the three facets of diversity vary across phylogenetic scales, and the potential eco-evolutionary mechanisms driving these patterns across space.

Results

We found a strong latitudinal gradient of TD with a large accumulation in tropical regions. PD and FD patterns were largely similar likely due to the high phylogenetic signal in the traits used, and higher values tended to be concentrated in harsh and/or heterogeneous environments. We found differences between major clades within Squamata that display contrasting geographical patterns. Several regions across the continent shared the same spatial mismatches between dimensions across clades, suggesting that similar eco-evolutionary processes are shaping these regional reptile assemblages. However, we also found evidence that non-mutually exclusive processes can operate differently across clades.

Main conclusions

The deconstructive approach implemented here is based on a solid macroecological framework. We can extend this to other taxonomic groups to establish whether there are particularities about how different eco-evolutionary mechanisms shape biodiversity facets in a spatially explicit context.     

A new genus and species of abyssal sponge commonly encrusting polymetallic nodules in the Clarion-Clipperton Zone,East Pacific Ocean

The Clarion-Clipperton Zone (CCZ) in the East Pacific is a vast region targeted for deep-sea mineral exploration, for which there are almost no published taxonomic data. Here we describe Plenaster craigi gen. nov. sp. nov. from depths of ～4000 m in the eastern CCZ polymetallic nodule province. Despite over 40 years of intense exploration in the area, we reveal that P. craigi sp. nov. is the most abundant sponge and the most common metazoan encrusting on nodules in our study area at the eastern CCZ. It has a mean abundance of 15.3 ± 8.9 individuals per m² across 11 stations in a 30 × 30 km study site nested within the Singapore exploration area. The white encrusting sponge is filled with spheroxyasters with occasional styles protruding the surface. Plenaster craigi sp. nov. is morphologically similar to genera from three different families in two orders: Timea (Timeidae; Tethyida); Hemiasterella and Leptosastra (Hemiasterellidae; Tethyida); and Paratimea (Stelligeridae; Axinellida). However, based on the molecular (COI and 28S) phylogenetic trees generated in this study, P. craigi sp. nov. was located in the Order Axinellida and appeared to be distant to Timea, Hemiasterella, Leptosastra, and Paratimea. We propose a new genus for our material to be placed provisionally in the family Stelligeridae, as it is the only family in the order Axinellida whose members possess euasters. This provisional placement may change when sequences of the type specimens of these genera and advanced phylogenetic reconstruction methods become available in the future. However, we have shown clearly that Plenaster gen. nov. is unique and distinct from all currently known taxa. Plenaster craigi sp. nov. being an abundant metazoan encrusting on nodule and easily identified filter-feeding animal is a potentially indicator species for future mining impacts in the eastern CCZ, and possibly across the entire CCZ.

LSID: urn:lsid:zoobank.org:act:99D2DDBA-4643-4752-8C8A-AFF314E6B6E3     

Phylogenetic community patterns suggest Central Indian tropical dry forests are structured by montane climate refuges

Aim

We used an eco-phylogenetic approach to investigate the diversity and assembly patterns of tropical dry forests (TDFs) in Central India. We aimed at informing conservation and restoration practices in these anthropogenically disturbed forests by identifying potential habitats of conservation significance and elements of regional biodiversity most vulnerable to human impact and climate change.

Location

Tropical dry forests of Madhya Pradesh, Central India.

Methods

We analysed the species richness, stem density, basal area and phylogenetic structure (standardized effect size of MNTD, MPD, PD and community evolutionary distinctiveness cED) of 117 tree species assemblages distributed across a ~230 to ~940 m elevational gradient. We examined how these community measures and taxonomic (Sørensen) and phylogenetic (UniFrac) beta diversity varied with elevation, precipitation, temperature and climatic stress.

Results

Species richness, phylogenetic diversity, stem density and basal area were positively correlated with elevation, with high-elevation plots exhibiting cooler temperatures, higher precipitation and lower stress. High-elevation assemblages also trended towards greater phylogenetic dispersion, which diminished at lower elevations and in drier, more stressful plots. Phylogenetic turnover was observed across the elevation gradient, and species evolutionary distinctiveness increased at lower elevations and under harsher abiotic conditions.

Main Conclusions

Harsher abiotic conditions at low elevations may act as a selective filter on plant lineages, leading to phylogenetically clustered low-diversity assemblages. These assemblages contained more evolutionarily distinct species that may contribute disproportionately to biodiversity. Conversely, milder abiotic conditions at high elevations may serve as refuges for drought-sensitive species, resulting in more diverse assemblages. Conservation practices that prioritize both high- and low-elevation habitats could promote the persistence of evolutionarily distinct species and areas of high biodiversity within the Central Indian landscape. Establishing connectivity between these habitats may provide a range of climatic conditions for species to retreat to or persist within as climates change.     

Differential extinction and the contrasting structure of polar marine faunas

Background

The low taxonomic diversity of polar marine faunas today reflects both the failure of clades to colonize or diversify in high latitudes and regional extinctions of once-present clades. However, simple models of polar evolution are made difficult by the strikingly different faunal compositions and community structures of the two poles.

Methodology/Principal Findings

A comparison of early Cenozoic Arctic and Antarctic bivalve faunas with modern ones, within the framework of a molecular phylogeny, shows that while Arctic losses were randomly distributed across the tree, Antarctic losses were significantly concentrated in more derived families, resulting in communities dominated by basal lineages. Potential mechanisms for the phylogenetic structure to Antarctic extinctions include continental isolation, changes in primary productivity leading to turnover of both predators and prey, and the effect of glaciation on shelf habitats.

Conclusions/Significance

These results show that phylogenetic consequences of past extinctions can vary substantially among regions and thus shape regional faunal structures, even when due to similar drivers, here global cooling, and provide the first phylogenetic support for the “retrograde” hypothesis of Antarctic faunal evolution.     

Biodiversity of the deep-sea continental margin bordering the Gulf of Maine (NW Atlantic): relationships among sub-regions and to shelf systems

Background

In contrast to the well-studied continental shelf region of the Gulf of Maine, fundamental questions regarding the diversity, distribution, and abundance of species living in deep-sea habitats along the adjacent continental margin remain unanswered. Lack of such knowledge precludes a greater understanding of the Gulf of Maine ecosystem and limits development of alternatives for conservation and management.

Methodology/Principal Findings

We use data from the published literature, unpublished studies, museum records and online sources, to: (1) assess the current state of knowledge of species diversity in the deep-sea habitats adjacent to the Gulf of Maine (39–43°N, 63–71°W, 150–3000 m depth); (2) compare patterns of taxonomic diversity and distribution of megafaunal and macrofaunal species among six distinct sub-regions and to the continental shelf; and (3) estimate the amount of unknown diversity in the region. Known diversity for the deep-sea region is 1,671 species; most are narrowly distributed and known to occur within only one sub-region. The number of species varies by sub-region and is directly related to sampling effort occurring within each. Fishes, corals, decapod crustaceans, molluscs, and echinoderms are relatively well known, while most other taxonomic groups are poorly known. Taxonomic diversity decreases with increasing distance from the continental shelf and with changes in benthic topography. Low similarity in faunal composition suggests the deep-sea region harbours faunal communities distinct from those of the continental shelf. Non-parametric estimators of species richness suggest a minimum of 50% of the deep-sea species inventory remains to be discovered.

Conclusions/Significance

The current state of knowledge of biodiversity in this deep-sea region is rudimentary. Our ability to answer questions is hampered by a lack of sufficient data for many taxonomic groups, which is constrained by sampling biases, life-history characteristics of target species, and the lack of trained taxonomists.     

Patterns,biases and prospects in the distribution and diversity of Neotropical snakes

Motivation

We generated a novel database of Neotropical snakes (one of the world's richest herpetofauna) combining the most comprehensive, manually compiled distribution dataset with publicly available data. We assess, for the first time, the diversity patterns for all Neotropical snakes as well as sampling density and sampling biases.

Main types of variables contained

We compiled three databases of species occurrences: a dataset downloaded from the Global Biodiversity Information Facility (GBIF), a verified dataset built through taxonomic work and specialized literature, and a combined dataset comprising a cleaned version of the GBIF dataset merged with the verified dataset.

Spatial location and grain

Neotropics, Behrmann projection equivalent to 1° × 1°.

Time period

Specimens housed in museums during the last 150 years.

Major taxa studied

Squamata: Serpentes.

Software format

Geographical information system (GIS).

Results

The combined dataset provides the most comprehensive distribution database for Neotropical snakes to date. It contains 147,515 records for 886 species across 12 families, representing 74% of all species of snakes, spanning 27 countries in the Americas. Species richness and phylogenetic diversity show overall similar patterns. Amazonia is the least sampled Neotropical region, whereas most well‐sampled sites are located near large universities and scientific collections. We provide a list and updated maps of geographical distribution of all snake species surveyed.

Main conclusions

The biodiversity metrics of Neotropical snakes reflect patterns previously documented for other vertebrates, suggesting that similar factors may determine the diversity of both ectothermic and endothermic animals. We suggest conservation strategies for high‐diversity areas and sampling efforts be directed towards Amazonia and poorly known species.     

Do Rapoport's rule,the mid‐domain effect or the source–sink hypotheses predict bathymetric patterns of polychaete richness on the Pacific coast of South America?

Aim We evaluated the bathymetric gradient of benthic polychaete species richness from the Chilean coast, as well as its possible underlying causes. We tested three possible hypotheses to explain the richness gradient: (1) Rapoport's effect; (2) the mid‐domain effect (MDE); and (c) the source–sink hypothesis. Location South‐eastern Pacific coast of Chile. Methods The bathymetric gradient in richness was evaluated using the reported ranges of bathymetric distribution of 498 polychaete species, from the intertidal to abyssal zone (c. 4700 m). Rapoport's effect was evaluated by examining the relationship between bathymetric mid‐point and bathymetric range extent, and species richness and depth. The MDE was tested using the Monte Carlo simulation program. The source–sink hypothesis was tested through nestedness analysis. Results Species richness shows significant exponential decay across the bathymetric gradient. The pattern is characterized by a high presence of short‐ranged species on the continental shelf area; while only a few species reach abyssal depths, and they tend to show extremely wide bathymetric ranges. Our simulation analyses showed that, in general, the pattern is robust to sampling artefacts. This pattern cannot be reproduced by the MDE, which predicts a parabolic richness gradient. Rather, results agree with the predictions of Rapoport's effect. Additionally, the data set is significantly nested at species, genus and family levels, supporting the source–sink hypothesis. Main conclusions The sharp exponential decay in benthic polychaete richness across the bathymetric gradient supports the general idea that abyssal environments should harbour fewer species than shallower zones. This pattern may be the result of colonization–extinction dynamics, characterized by abyssal assemblages acting as ‘sinks’ maintained mainly by shallower ‘sources’. The source–sink hypothesis provides a conceptual and methodological framework that may shed light on the search for general patterns of diversity across large spatial scales.     

Australian Sphingidae – DNA Barcodes Challenge Current Species Boundaries and Distributions

Main Objective

We examine the extent of taxonomic and biogeographical uncertainty in a well-studied group of Australian Lepidoptera, the hawkmoths (Sphingidae).

Methods

We analysed the diversity of Australian sphingids through the comparative analysis of their DNA barcodes, supplemented by morphological re-examinations and sequence information from a nuclear marker in selected cases. The results from the analysis of Australian sphingids were placed in a broader context by including conspecifics and closely related taxa from outside Australia to test taxonomic boundaries.

Results

Our results led to the discovery of six new species in Australia, one case of erroneously synonymized species, and three cases of synonymy. As a result, we establish the occurrence of 75 species of hawkmoths on the continent. The analysis of records from outside Australia also challenges the validity of current taxonomic boundaries in as many as 18 species, including Agrius convolvuli (Linnaeus, 1758), a common species that has gained adoption as a model system. Our work has revealed a higher level of endemism than previously recognized. Most (90%) Australian sphingids are endemic to the continent (45%) or to Australia, the Pacific Islands and the Papuan and Wallacean regions (45%). Only seven species (10%) have ranges that extend beyond this major biogeographical boundary toward SE Asia and other regions of the Old World.

Main Conclusions

This study has established that overlooked cryptic diversity and inaccurate species delineation produced significant misconceptions concerning diversity and distribution patterns in a group of insects that is considered well known taxonomically. Because DNA barcoding represents a straightforward way to test taxonomic boundaries, its implementation can improve the accuracy of primary diversity data in biogeography and conservation studies.     

Environmental filters shaping angiosperm tree assembly along climatic and geographic gradients

Question

Global‐scale forest censuses provide an opportunity to understand diversification processes in woody plant communities. Based on the climatic or geographic filtering hypotheses associated with tropical niche conservatism and dispersal limitation, we analysed phylogenetic community structures across a wide range of biomes and evaluated to what extent region‐specific processes have influenced large‐scale diversity patterns of tree species communities across latitude or continent.

Location

Global.

Methods

We generated a data set of species abundances for 21,379 angiosperm woody plants in 843 plots worldwide. We calculated net relatedness index (NRI) for each plot, based on a single global species pool and regional species pools, and phylogenetic β‐diversity (PBD) between plots. Then, we explored the correlations of NRI with climatic and geographic variables, and clarified phylogenetic dissimilarity along geographic and climatic differences. We also compared these patterns for South America, Africa, the Indo‐Pacific, Australia, the Nearctic, Western Palearctic and Eastern Palearctic.

Results

NRI based on a global‐scale species pool was negatively associated with precipitation and positively associated with Quaternary temperature change. PBD was positively associated with geographic distance and precipitation difference between plots across tropical and extratropical biomes. Moreover, phylogenetic dissimilarity was smaller in extratropical regions than in regions including the tropics, although temperate forests of the Eastern Palearctic showed a greater dissimilarity within extratropical regions.

Conclusions

Our findings support predictions of the climatic and geographic filtering hypotheses. Climatic filtering (climatic harshness and paleoclimatic change) relative to tropical niche conservatism played a role in sorting species from the global species pool and shaped the large‐scale diversity patterns, such as the latitudinal gradient observed across continents. Geographic filtering associated with dispersal limitation substantially contributed to regional divergence of tropical/extratropical biomes among continents. Old, long‐standing geographic barriers and recent climatic events differently influenced evolutionary diversification of angiosperm tree communities in tropical and extratropical biomes.     

Phylogenomic and morphological data reveal hidden patterns of diversity in the national tree of Brazil,Paubrasilia echinata

Premise

Paubrasilia echinata (common names, pau brasil, brazilwood) is the national tree of Brazil and an endangered species endemic to the Brazilian Atlantic Forest. Over its wide distribution of 2000 km, its leaflets morphology exhibits extensive plasticity. Three morphotypes are commonly identified based on leaf size, but it is unclear if they represent distinct taxa or a single polymorphic species. This study aims to clarify the taxonomic position of the three morphotypes to inform conservation decisions.

Methods

A morphometric study of leaf characters of herbarium specimens was coupled with genetic analyses using genotype-by-sequencing data. We used maximum-likelihood and coalescent methods to evaluate the phylogenetic and population structure of the species. We compared these with a morphological dendrogram built from hierarchical clustering.

Results

Two of the three morphotypes formed separately evolving lineages, the third morphotype formed two geographically separate lineages, and northern trees with intermediate leaf morphology formed a separate fifth lineage. Leaflet size varied by over 35-fold, and although morphological clustering generally matched the genetic patterns, there were some overlaps, highlighting the cryptic diversity within this group.

Conclusions

Our genetic and morphological results provide some evidence that cultivated trees from different states in Brazil seem to have a limited genetic origin and do not reflect the broader genetic and geographical diversity of the species. As a result, more care is likely needed to preserve the overall genomic diversity of this endangered and iconic species.     

Fish taxonomic,functional, and phylogenetic diversity and their vulnerabilities in the largest river in southeastern China

1. Freshwater biodiversity is currently under multiple threats. Conservation of freshwater fish biodiversity needs to be prioritized because natural conservation resources are always limited.
2. Samples were collected at 24 sites in the Min River, the largest basin in southeastern China. Taxonomic, functional, and phylogenetic diversity were analyzed. Biodiversity vulnerability was measured by removing one species each time out of the community with replacement.
3. Results suggested that hotspots for taxonomic and phylogenetic diversity were located at two impounded sites, while for functional diversity were those sites with no upstream dams. Little congruence was observed between taxonomic, functional, and phylogenetic diversity. Fragmentation of river network connectivity caused by dams was a significant factor affecting the biodiversity patterns. Beta turnover was the driving component for beta diversity, indicating that biodiversity dissimilarity along the river was mostly explained by environmental sorting. Fifteen out of 16 species that contributed the most to different facets of biodiversity were mostly endemic, either they had distinctive functional traits or they were the most prevalent species. Sites with the highest diversity vulnerability were characterized by these distinctive species. Functional diversity was more vulnerable to species loss comparing with the other two biodiversity facets.
4. Prioritizing those biodiversity hotspots, sites with extreme functional vulnerability, and those distinctive endemic species which contributed the most to biodiversity vulnerability is suggested in the Min River. The study found evidence that congruence among different facets of biodiversity is hard to achieve, and functional diversity is the most vulnerable in a freshwater system fragmented by intensive dam constructions. This work will help to develop systematic conservation planning from the perspective of different biodiversity facets.

     

The role of dominant prairie species ecotypes on plant diversity patterns of restored grasslands across a rainfall gradient in the US Great Plains

Questions

A robust ecosystem requires a functionally heterogeneous community of organisms with ecological traits that permit broad resource partitioning. Understanding community diversity patterns can help investigate drivers of community assembly and assess restoration success. Do biodiversity patterns differ among grassland communities sown with different ecotypes of dominant species during restoration along a rainfall gradient in the tallgrass prairie of the central US Great Plains?

Location

Four field sites across a rainfall gradient within the North American Great Plains: Colby, Kansas (39°23′17.8″N, 101°04′57.4″W), Hays, Kansas (38°51′13.2″N, 99°19′08.6″W), Manhattan, Kansas (39°08′22.3″N, 96°38′23.3″W), and Carbondale, Illinois (IL, 37°41′47.0″N, 89°14′19.2″W).

Methods

We applied linear mixed models to assess the effect of dominant species ecotype, year, and location on grassland taxonomic, phylogenetic, and functional diversity.

Results

The non-local grass ecotype (compared to the local ecotype) promoted species richness. In contrast, the effect of the dominant species ecotype on phylogenetic or functional diversity was site-specific over the 10-year restoration. Richness decreased across the rainfall gradient from dry to moist sites, and the wettest site had the highest phylogenetic and functional diversity.

Conclusions

Our results suggest that abiotic filtering by rainfall is a key assembly mechanism that could predict grassland changes in biodiversity in the early restoration phases. Given the community response across the tallgrass prairie, restoration practitioners should consider the impact of regional sources of dominant species used in restoration when biodiversity is a restoration goal. It is recommended for future grassland restoration to detect gaps and limitations in evolutionary and trait structure that will reveal which diversity components to evaluate.     

Multiple facets of biodiversity are threatened by mining-induced land-use change in the Brazilian Amazon

Aim

Mining is increasingly pressuring areas of critical importance for biodiversity conservation, such as the Brazilian Amazon. Biodiversity data are limited in the tropics, restricting the scope for risks to be appropriately estimated before mineral licensing decisions are made. As the distributions and range sizes of other taxa differ markedly from those of vertebrates—the common proxy for analysis of risk to biodiversity from mining—whether mining threatens lesser-studied taxonomic groups differentially at a regional scale is unclear.

Location

Brazilian Amazon.

Methods

We assess risks to several facets of biodiversity from industrial mining by comparing mining areas (within 70 km of an active mining lease) and areas unaffected by mining, employing species richness, species endemism, phylogenetic diversity and phylogenetic endemism metrics calculated for angiosperms, arthropods and vertebrates.

Results

Mining areas contained higher densities of species occurrence records than the unaffected landscape, and we accounted for this sampling bias in our analyses. None of the four biodiversity metrics differed between mining and nonmining areas for vertebrates. For arthropods, species endemism was greater in mined areas. Mined areas also had greater angiosperm species richness, phylogenetic diversity and phylogenetic endemism, although less species endemism than unmined areas.

Main Conclusions

Unlike for vertebrates, facets of angiosperm and arthropod diversity are relatively higher in areas of mining activity, underscoring the need to consider multiple taxonomic groups and biodiversity facets when assessing risk and evaluating management options for mining threats. Particularly concerning is the proximity of mining to areas supporting deep evolutionary history, which may be impossible to recover or replace. As pressures to expand mining in the Amazon grow, impact assessments with broader taxonomic reach and metric focus will be vital to conserving biodiversity in mining regions.     

Unravelling the evolutionary origins of biogeographic assemblages

Aim

Floristic and faunal diversity fall within species assemblages that can be grouped into distinct biomes or ecoregions. Understanding the origins of such biogeographic assemblages helps illuminate the processes shaping present‐day diversity patterns and identifies regions with unique or distinct histories. While the fossil record is often sparse, dated phylogenies can provide a window into the evolutionary past of these regions. Here, we present a novel phylogenetic approach to investigate the evolutionary origins of present‐day biogeographic assemblages and highlight their conservation value.

Location

Southern Africa.

Methods

We evaluate the evolutionary turnover separating species clusters in space at different time slices to determine the phylogenetic depth at which the signal for their present‐day structure emerges. We suggest present‐day assemblages with distinct evolutionary histories might represent important units for conservation. We apply our method to the vegetation of southern Africa using a dated phylogeny of the woody flora of the region and explore how the evolutionary history of vegetation types compares to common conservation currencies, including species richness, endemism and threat.

Results

We show the differentiation of most present‐day vegetation types can be traced back to evolutionary splits in the Miocene. The woody flora of the Fynbos is the most evolutionarily distinct, and thus has deeper evolutionary roots, whereas the Savanna and Miombo Woodland show close phylogenetic affinities and likely represent a more recent separation. However, evolutionarily distinct phyloregions do not necessarily capture the most unique phylogenetic diversity, nor are they the most species‐rich or threatened.

Main conclusions

Our approach complements analyses of the fossil record and serves as a link to the history of diversification, migration and extinction of lineages within biogeographic assemblages that is separate from patterns of species richness and endemism. Our analysis reveals how phyloregions capture conservation value not represented by traditional biodiversity metrics.

     

Fine-Scale Bacterial Beta Diversity within a Complex Ecosystem (Zodletone Spring,OK, USA): The Role of the Rare Biosphere

Background

The adaptation of pyrosequencing technologies for use in culture-independent diversity surveys allowed for deeper sampling of ecosystems of interest. One extremely well suited area of interest for pyrosequencing-based diversity surveys that has received surprisingly little attention so far, is examining fine scale (e.g. micrometer to millimeter) beta diversity in complex microbial ecosystems.

Methodology/Principal Findings

We examined the patterns of fine scale Beta diversity in four adjacent sediment samples (1mm apart) from the source of an anaerobic sulfide and sulfur rich spring (Zodletone spring) in southwestern Oklahoma, USA. Using pyrosequencing, a total of 292,130 16S rRNA gene sequences were obtained. The beta diversity patterns within the four datasets were examined using various qualitative and quantitative similarity indices. Low levels of Beta diversity (high similarity indices) were observed between the four samples at the phylum-level. However, at a putative species (OTU_0.03) level, higher levels of beta diversity (lower similarity indices) were observed. Further examination of beta diversity patterns within dominant and rare members of the community indicated that at the putative species level, beta diversity is much higher within rare members of the community. Finally, sub-classification of rare members of Zodletone spring community based on patterns of novelty and uniqueness, and further examination of fine scale beta diversity of each of these subgroups indicated that members of the community that are unique, but non novel showed the highest beta diversity within these subgroups of the rare biosphere.

Conclusions/Significance

The results demonstrate the occurrence of high inter-sample diversity within seemingly identical samples from a complex habitat. We reason that such unexpected diversity should be taken into consideration when exploring gamma diversity of various ecosystems, as well as planning for sequencing-intensive metagenomic surveys of highly complex ecosystems.     

Deep reefs are not refugium for shallow‐water fish communities in the southwestern Atlantic

1. The deep reef refugia hypothesis (DRRH) predicts that deep reef ecosystems may act as refugium for the biota of disturbed shallow waters. Because deep reefs are among the most understudied habitats on Earth, formal tests of the DRRH remain scarce. If the DRRH is valid at the community level, the diversity of species, functions, and lineages of fish communities of shallow reefs should be encapsulated in deep reefs.
2. We tested the DRRH by assessing the taxonomic, functional, and phylogenetic diversity of 22 Brazilian fish communities between 2 and 62 m depth. We partitioned the gamma diversity of shallow (<30 m) and deep reefs (>30 m) into independent alpha and beta components, accounted for species’ abundance, and assessed whether beta patterns were mostly driven by spatial turnover or nestedness.
3. We recorded 3,821 fishes belonging to 85 species and 36 families. Contrary to DRRH expectations, only 48% of the species occurred in both shallow and deep reefs. Alpha diversity of rare species was higher in deep reefs as expected, but alpha diversity of typical and dominant species did not vary with depth. Alpha functional diversity was higher in deep reefs only for rare and typical species, but not for dominant species. Alpha phylogenetic diversity was consistently higher in deep reefs, supporting DRRH expectations.
4. Profiles of taxonomic, functional, and phylogenetic beta diversity indicated that deep reefs were not more heterogeneous than shallow reefs, contradicting expectations of biotic homogenization near sea surface. Furthermore, pairwise beta‐diversity analyses revealed that the patterns were mostly driven by spatial turnover rather than nestedness at any depth.
5. Conclusions. Although some results support the DRRH, most indicate that the shallow‐water reef fish diversity is not fully encapsulated in deep reefs. Every reef contributes significantly to the regional diversity and must be managed and protected accordingly.

     

Using Phylogenetic,Functional and Trait Diversity to Understand Patterns of Plant Community Productivity

Background

Two decades of research showing that increasing plant diversity results in greater community productivity has been predicated on greater functional diversity allowing access to more of the total available resources. Thus, understanding phenotypic attributes that allow species to partition resources is fundamentally important to explaining diversity-productivity relationships.

Methodology/Principal Findings

Here we use data from a long-term experiment (Cedar Creek, MN) and compare the extent to which productivity is explained by seven types of community metrics of functional variation: 1) species richness, 2) variation in 10 individual traits, 3) functional group richness, 4) a distance-based measure of functional diversity, 5) a hierarchical multivariate clustering method, 6) a nonmetric multidimensional scaling approach, and 7) a phylogenetic diversity measure, summing phylogenetic branch lengths connecting community members together and may be a surrogate for ecological differences. Although most of these diversity measures provided significant explanations of variation in productivity, the presence of a nitrogen fixer and phylogenetic diversity were the two best explanatory variables. Further, a statistical model that included the presence of a nitrogen fixer, seed weight and phylogenetic diversity was a better explanation of community productivity than other models.

Conclusions

Evolutionary relationships among species appear to explain patterns of grassland productivity. Further, these results reveal that functional differences among species involve a complex suite of traits and that perhaps phylogenetic relationships provide a better measure of the diversity among species that contributes to productivity than individual or small groups of traits.