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opencc-zeroDec 2016View details →

Data from: The origin and evolution of coral species richness in a marine biodiversity hotspot

The Coral Triangle region of the Indo-Pacific realm harbors an extraordinary number of species, with richness decreasing away from this biodiversity hotspot. Despite multiple competing hypotheses, the dynamics underlying this regional diversity pattern remain poorly understood. Here we use a time-calibrated evolutionary tree of living reef coral species, their current geographic ranges, and model-based estimates of regional rates of speciation, extinction, and geographic range shifts to show that origination rates within the Coral Triangle are lower than in surrounding regions, a result inconsistent with the long-standing center of origin hypothesis. Furthermore, endemism of coral species in the Coral Triangle is low, and the Coral Triangle endemics are older than relatives found outside this region. Overall, our model results suggest that the high diversity of reef corals in the Coral Triangle is largely due to range expansions into this region of species that evolved elsewhere. These findings strongly support the notion that geographic range shifts play a critical role in generating species diversity gradients. They also show that preserving the processes that gave rise to the striking diversity of corals in the Coral Triangle requires protecting not just reefs within the hotspot, but also those in the surrounding areas.

Data from: Shrubs as ecosystem engineers across an environmental gradient: effects on species richness and exotic plant invasion

Ecosystem-engineering plants modify the physical environment and can increase species diversity and exotic species invasion. At the individual level, the effects of ecosystem engineers on other plants often become more positive in stressful environments. In this study, we investigated whether the community-level effects of ecosystem engineers also become stronger in more stressful environments. Using comparative and experimental approaches, we assessed the ability of a native shrub (Ericameria ericoides) to act as an ecosystem engineer across a stress gradient in a coastal dune in northern California, USA. We found increased coarse organic matter and lower wind speeds within shrub patches. Growth of a dominant invasive grass (Bromus diandrus) was facilitated both by aboveground shrub biomass and by growing in soil taken from shrub patches. Experimental removal of shrubs negatively affected species most associated with shrubs and positively affected species most often found outside of shrubs. Counter to the stress-gradient hypothesis, the effects of shrubs on the physical environment and individual plant growth did not increase across the established stress gradient at this site. At the community level, shrub patches increased beta diversity, and contained greater rarified richness and exotic plant cover than shrub-free patches. Shrub effects on rarified richness increased with environmental stress, but effects on exotic cover and beta diversity did not. Our study provides evidence for the community-level effects of shrubs as ecosystem engineers in this system, but shows that these effects do not necessarily become stronger in more stressful environments.

opencc-zeroDec 2018View details →

Data from: Correlation of native and exotic species richness: a global meta-analysis finds no invasion paradox across scales

Support for the "biotic resistance hypothesis," that species-rich communities are more successful at resisting invasion by exotic species than are species-poor communities, has long been debated. It has been argued that native-exotic richness relationships (NERR) are negative at small spatial scales and positive at large scales, but evidence for the role of spatial scale on NERR has been contradictory. However, no formal quantitative synthesis has previously examined whether NERR is scale-dependent across multiple studies, and previous studies on NERR have not distinguished spatial grain and extent, which may drive very different ecological processes. We used a global systematic review and hierarchical mixed-effects meta-analysis to provide a comprehensive quantitative assessment of the patterns of NERR over a range of spatial grain sizes and spatial extents, based on 204 individual cases of observational (non-experimental) NERRs from 101 publications. We show that NERR was indeed highly scale-dependent across studies and increased with the log of grain size. However, mean NERR was not negative at any grain size, although there was high heterogeneity at small grain sizes. We found no clear patterns of NERR across different spatial extents, suggesting that extent plays a less important role in determining NERR than does grain, although there was a complex interaction between extent and grain size. Almost all studies on NERR were conducted in North America, western Europe, and a few other regions, with little information on tropical or Arctic regions. We did find that NERR increased northward in temperate regions and also varied with longitude. We discuss possible explanations for the patterns we found, and caution that our results do not show that invasive species are benign or have no negative consequences for biodiversity preservation. This study represents the first global quantitative analysis of scale-based NERR and casts doubt on the existence of an "invasion paradox" of negative NERR at small scales and positive correlations at large scales in non-experimental studies.

opencc-zeroDec 2011View details →

Data from: Opposing mechanisms drive richness patterns of core and transient bird species

Studies of biodiversity typically assume that all species are equivalent. However, some species in a community maintain viable populations in the study area, while others occur only occasionally as transient individuals. Here we show that North American bird communities can reliably be divided into core and transient species groups, and that the richness of each group is driven by different processes. The richness of core species is influenced primarily by local environmental conditions, while the richness of transient species is influenced primarily by the heterogeneity of the surrounding landscape. This demonstrates that the well-known effects of the local environment and landscape heterogeneity on overall species richness are the result of two sets of processes operating differentially on core and transient species. Models of species richness should focus on explaining two distinct patterns, those of core and transient species, rather than a single pattern for the community as a whole.

Data from: Age and area predict patterns of species richness in pumice rafts contingent on oceanic climatic zone encountered

The Theory of Island Biogeography predicts that area and age explain species richness patterns (or alpha diversity) in insular habitats. Using a unique natural phenomenon, pumice rafting, we measured the influence of area, age and oceanic climate on patterns of species richness. Pumice rafts are formed simultaneously when submarine volcanoes erupt, the pumice clasts break-up irregularly, forming irregularly shaped pumice stones which while floating through the ocean are colonised by marine biota. We analyse two eruption events and more than 5000 pumice clasts collected from 29 sites and three climatic zones. Overall the older and larger pumice clasts held more species. Pumice clasts arriving in tropical and subtropical climates showed this same trend, where in temperate locations species richness (alpha diversity) increased with area but decreased with age. Beta diversity analysis of the communities forming on pumice clasts that arrived in different climatic zones showed that tropical and subtropical clasts transported similar communities while species composition on temperate clasts differed significantly from both tropical and subtropical arrivals. Using these thousands of insular habitats, we find strong evidence that area and age but also climatic conditions predict the fundamental dynamics of species richness colonising pumice clasts.

Data from: Conservation action based on threatened species capture taxonomic and phylogenetic richness in breeding and wintering populations of Central Asian birds

Although phylogenetic diversity has been suggested to be relevant from a conservation point of view, its role is still limited in applied nature conservation. Recently, the practice of investing conservation resources based on threatened species was identified as a reason for the slow integration of phylogenetic diversity in nature conservation planning. One of the main arguments is based on the observation that threatened species are not evenly distributed over the phylogenetic tree. However this argument seems to dismiss the fact that conservation action is a spatially explicit process, and even if threatened species are not evenly distributed over the phylogenetic tree, the occurrence of threatened species could still indicate areas with above average phylogenetic diversity and consequently could protect phylogenetic diversity. Here we aim to study the selection of important bird areas in Central Asia, which were nominated largely based on the presence of threatened bird species. We show that although threatened species occurring in Central Asia do not capture phylogenetically more distinct species than expected by chance, the current spatially explicit conservation approach of selecting important bird areas covers above average taxonomic and phylogenetic diversity of breeding and wintering birds. We conclude that the spatially explicit processes of conservation actions need to be considered in the current discussion of whether new prioritization methods are needed to complement conservation action based on threatened species.

opencc-zeroDec 2016View details →

Data from: Resource stoichiometry and availability modulate species richness and biomass of tropical litter macro-invertebrates

1. The high biodiversity and biomass of soil communities is crucial for litter decomposition in terrestrial ecosystems such as tropical forests. However, the leaf litter that these communities consume is of particularly poor quality as indicated by elemental stoichiometry. The impact of resource quantity, quality, and other habitat parameters on species richness and biomass of consumer communities is often studied in isolation, although much can be learned from simultaneously studying both community characteristics. 2. Using a data set of 780 macro-invertebrate consumer species across 32 sites in tropical lowland rainforest and agricultural systems on Sumatra, Indonesia, we investigated the effects of basal resource stoichiometry (C:X ratios of N, P, K, Ca, Mg, Na, S in local leaf litter), litter mass (basal resource quantity and habitat space), plant species richness (surrogate for litter habitat heterogeneity), and soil pH (acidity) on consumer species richness and biomass across different consumer groups (i.e., three feeding guilds and ten selected taxonomic groups). 3. In order to distinguish the most important predictors of consumer species richness and biomass, we applied a standardised model averaging approach investigating the effects of basal resource stoichiometry, litter mass, plant species richness, and soil pH on both consumer community characteristics. This standardised approach enabled us to identify differences and similarities in the magnitude and importance of such effects on consumer species richness and biomass. 4. Across consumer groups, we found litter mass to be the most important predictor of both species richness and biomass. Resource stoichiometry had a more pronounced impact on consumer species richness than on their biomass. As expected, taxonomic groups differed in which resource and habitat parameters (basal resource stoichiometry, litter mass, plant species richness, and pH) were most important for modulating their community characteristics. 5. The importance of litter mass for both species richness and biomass indicates that these tropical consumers strongly depend on habitat space and resource availability. Our study supports previous theoretical work indicating that consumer species richness is jointly influenced by resource availability and the balanced supply of multiple chemical elements in their resources.

Data from: Tree species richness increases ecosystem carbon storage in subtropical forests

Forest ecosystems are an integral component of the global carbon cycle as they take up and release large amounts of C in short time (C flux) or accumulate it over longer time (C stock). However, there remains uncertainty about whether and in which direction C fluxes and in particular C stocks may differ between forests of high vs. low species richness. Based on a comprehensive dataset derived from field-based measurements, we tested the effect of species richness (3–20 tree species) and stand age (22–116 years) on six compartments of above- and belowground C stocks and four components of C fluxes in subtropical forests in south-east China. Across forest stands, total C stock was 149 ± 12 Mg ha-1 with richness explaining 28.5% and age explaining 29.4% of variation in this measure. Species-rich stands had higher C stocks and fluxes than stands with low richness; and, in addition, old stands had higher C stocks than young ones. Overall, for each additional tree species the total C stock increased by 6.4%. Our results provide comprehensive evidence for diversity-mediated above- and belowground C sequestration in species-rich subtropical forests in south-east China. Therefore, afforestation policies in this region and elsewhere should consider a change from the current focus on monocultures to multi-species plantations to increase C fixation and thus slow increasing atmospheric CO2 concentrations and global warming.

opencc-zeroDec 2015View details →

Data from: Ectomycorrhizal fungal richness declines towards the host species' range edge

Plant range boundaries are generally considered to reflect abiotic conditions; however, a rise in negative or decline in positive species interactions at range margins may contribute to these stable boundaries. While evidence suggests that pollinator mutualisms may decline near range boundaries, little is known about other important plant mutualisms, including microbial root symbionts. Here, we used molecular methods to characterize root-associated fungal communities in populations of two related temperate tree species from across the species' range in the eastern United States. We found that ectomycorrhizal fungal richness on plant roots declined with distance from the centre of the host species range. These patterns were not evident in nonmycorrhizal fungal communities on roots nor in fungal communities in bulk soil. Climatic and soil chemical variables could not explain these biogeographic patterns, although these abiotic gradients affected other components of the bulk soil and rhizosphere fungal community. Depauperate ectomycorrhizal fungal communities may represent an underappreciated challenge to marginal tree populations, especially as rapid climate change pushes these populations outside their current climate niche.

opencc-zeroDec 2018View details →

Data from: A pre-Miocene Irano-Turanian cradle: origin and diversification of the species-rich monocot genus Gagea (Liliaceae)

The Irano‐Turanian (IT) floristic region is considered an important centre of origin for many taxa. However, there is a lack of studies dealing with typical IT genera that also occur in neighbouring areas. The species-rich monocot genus Gagea Salisb. shows a centre of diversity in IT region and a distribution in adjacent regions, therefore representing a good study object to investigate spatial and temporal relationships among IT region and its neighbouring areas (East-Asia, Euro-Siberia, Himalaya, and Mediterranean). We aimed at (i) testing the origin of the genus and of its major lineages in the IT region, (ii) reconstructing divergence times and (iii) reconstructing colonisation events. To address these problems, sequences of the ribosomal DNA internal transcribed spacer (ITS) region of 418 individuals and chloroplast intergenic spacers sequences (psbA-trnH, trnL-trnF) of 497 individuals, representing 116 species from all sections of the genus and nearly its entire distribution area were analysed. Divergence times were estimated under a random molecular clock based on nrITS phylogeny, which was the most complete data set regarding the representation of species and distribution areas. Ancestral distribution ranges were estimated for the nrITS data set as well as for a combined data set, revealing that Gagea most likely originated in southwestern Asia. This genus first diversified there starting in the Early Miocene. In the Middle Miocene, Gagea migrated to the Mediterranean and to East Asia, while migration into Euro-Siberia took place in the Late Miocene. During the Pleistocene, the Arctic was colonised and Gagea serotina, the most widespread species, reached North America. The Mediterranean basin was colonised multiple times from southwestern Asia or Euro-Siberia. Most of the currently existing species originated during the last 3 Ma.

opencc-zeroMar 2020View details →

Population asynchrony alone does not explain stability in species rich soil animal assemblages: the stabilising role of forest age on oribatid mite communities

1. The importance of microbial and plant communities in the control of the diversity and structure of soil animal communities has been clarified over the last decade. Previous research focused on abiotic factors, niche separation and spatial patterns. Significant gaps still exist in our knowledge of the factors that control the stability of these communities over time. 2. We analysed a nine-year data set form the national Long-term Ecological Research Network of Latvia. We focused on 117 oribatid species from three Scots pine forests of different age (<40 yrs, 65 yrs, and >150 yrs) and structure. For each forest type, 100 samples were collected each year, providing very high replication and long of time series for a soil community. We assessed different aspects of stability: we used a dynamic null model, parametrised on observed growth rates, to test the hypothesis that asynchrony in species populations stabilises total community size; we also analysed alpha and beta diversity over time to test the hypothesis that temporal variation in species composition and relative abundances is controlled by forest attributes. 3. Real communities can be more stable than their stochastic counterparts if species are asynchronous, confirming for the first time the role of asynchrony in stabilising soil communities. Yet, while some real communities were more stable and had higher abundance and growth rates than others, they were not necessarily more asynchronous than the less stable communities. Species composition and relative abundances were also less variable in the more stable communities. 4. Species asynchrony generally stabilises species rich communities but is not sufficient to explain different levels of stability between forests. Forest age is a key factor explaining different levels of overyielding and so stability. Data suggests that both asynchrony and high diversity of microhabitat structure of Scots pine forests promote stability of soil animal communities.

Data from: Phytoplankton species richness along coastal and estuarine salinity continua

High number of freshwater species at low salinity, and a corresponding high number of marine species at high salinity, enveloping a conspicuous richness minimum at intermediate salinities, has shaped our basic understanding of biodiversity along a coastal salinity gradient for almost 80 years. Visualized as the 'Remane curve', this iconic concept was originally based on sedentary macroinvertebrates in the Baltic Sea. To what extent the concept can be generalized, particularly to free-drifting organisms, is currently debated. Here we use ca 16 000 phytoplankton samples from 2 large coastal ecosystems, the Baltic Sea and the Chesapeake Bay, to analyze the relationship between salinity and phytoplankton species richness. Alpha diversity showed a consistent variation along the salinity gradient, with a minimum at mesohaline salinities at around 7 – 9. Rarefied species pools at narrow salinity intervals also showed reduced diversity at intermediate salinities, surrounded by high richness towards both ends of the gradient. The cumulative likelihood of species presence validated the minimum at intermediate salinities. Community composition changed abruptly at the α diversity minimum in the Baltic Sea, while it changed gradually along the salinity gradient in the Chesapeake Bay. We conclude that the Remane concept is in every respect valid for phytoplankton.

opencc-zeroDec 2016View details →

Data from: Breaking down the lithification bias: the effect of preferential sampling of larger specimens on the estimate of species richness, evenness, and average specimen size

Lithification, the transition of unconsolidated sediments to fully indurated rocks, can potentially bias estimates of species richness, evenness, and body size distribution derived from fossil assemblages. Fossil collections made from well-indurated rocks consistently exhibit lower species richness, lower evenness, and a specimen size distribution skewed towards larger specimens relative to collections made from unconsolidated sediments, even when collections are drawn from the same assemblage. This phenomenon is known as the lithification bias. While the bias itself has been demonstrated empirically, much less attention has been paid to its causes. Proposed causes include taphonomic processes (e.g., destruction of small specimens during early diagenesis) or methodological differences (e.g., sieving vs. counting specimens on outcrops, bedding surfaces, or mechanically split surfaces). Here we investigate the potential effects of preferential intersection that could also result in a methodologically related bias: the preferential sampling of larger specimens relative to smaller ones when fossils are counted on rock surfaces. We used an analog model to simulate preferential intersection (fossil collection via splitting fossiliferous rock) and compare the results to a random draw model that approximates the effects of sieving. The model was parameterized using nine different combinations of species abundance and species size distributions. The results show that, with rare exceptions, species richness is 5–23% lower, evenness 5-25% lower, and average specimen size 24–150% higher in preferential intersection than in random draw simulations. We conclude that preferential intersection can impose a significant bias independent of other mechanisms (e.g., preferential destruction of smaller specimens during diagenetic or sampling processes), that the magnitude of this bias is partially dependent on the species abundance and size distributions, and that this bias alone does not fully account for empirically observed lithification bias on species richness (i.e., other sources of bias are also at work).

Data from: Persistence at the final stage of volcanic island ontogeny: abiotic predictors explain native plant species richness on 111 remote Pacific atolls

Aim: The final island ontogeny of the General Dynamic Model (GDM) (i.e. before island submergence) in tropical oceans corresponds to the coral atoll stage. Here, we examined whether the species richness of native vascular plants (indigenous and endemic species) on atolls is controlled by spatial and/or physical processes. We also predicted that atolls strongly affected by anthropogenic disturbance would have lower native species richness than predicted by spatial and physical processes. Location: Marshall Islands, Kiribati Islands, Nauru, Niue, Johnston, Cook Islands, French Polynesia and Pitcairn Islands (Pacific Ocean). Taxon: Native vascular plants Methods: We used stepwise regression to test the relative influence of five biogeographic variables on native species richness. Relationships were assessed for the full set of 111 Pacific coral atolls, as well as for atoll subsets ranging from 9 to 45 atolls. An index of human impact was then estimated, and residuals in the regression model predicting species richness from biogeographic variables were compared with the level of human impact. Results: A regression model including atoll area, highest atoll elevation, the stepping stone distances from the nearest raised atoll and volcanic island explained native species richness on the 111 Pacific coral atolls. Regression models for different archipelagos and atoll subsets were also significant. Endemic species richness was significantly linked with highest atoll elevation and the stepping stone distances from the nearest raised atoll. Residuals in the biogeographic regression model were barely related to human impact across the 111 atolls but were significantly related to human impact in the Kiribati atolls. Main conclusions: Native species richness on atolls is mainly controlled by physical and spatial characteristics. However, anthropogenic disturbances have altered the predicted pattern of native species richness leading to a lower model fit in some atoll subsets.

opencc-zeroMar 2020View details →

Regional assemblages shaped by historical and contemporary factors: evidence from a species-rich insect group

Understanding the complex diversity patterns is one of the main aims of community ecology. It is important to take both historical and contemporary factors into account in investigating the potential roles in assembling diversity patterns. Here, We compared diversity patterns of two moth assemblages sampled from Taihang and Yanshan mountains in Northern China and performed ancestral range reconstructions using the Multi-State-Speciation and Extinction model to track the origins of these patterns. We subsequently estimate diversification rates of the two moth assemblages. Finally, we explored the effects of contemporary ecological factors on diversity patterns. From 7788 specimens we identified to 835 species belonging to 23 families, using both DNA barcode analysis and morphology. Overall, moths in YS mountains showed higher species diversity and phylogenetic diversity than in TH mountains. Ancestral range analysis indicated YS as the origin. Significant historical dispersals from YS to TH mountains were detected. Asymmetrical diversification, population expansion, along with frequent and considerable gene flow, were detected between communities. Moreover, dispersal limitation or the joint effect of environment filtering and dispersal limitation were inferred as main driving forces shaping current diversity patterns. In summary, we showed that a combined analysis of diversity patterns at multiples scales, including community, population and species levels, incorporating both historical and contemporary factors, are very informative for understanding factors of shaping diversity patterns.

opencc-zeroMay 2019View details →

Data from: Habitat diversity associated with island size and environmental filtering control the species richness of rock-savanna plants in neotropical inselbergs

Disentangling the multiple factors controlling species diversity is a major challenge in ecology. Island biogeography and environmental filtering are two influential theories emphasizing respectively island size and isolation, and the abiotic environment, as key drivers of species richness. However, few attempts have been made to quantify their relative importance and investigate their mechanistic basis. Here, we applied structural equation modelling, a powerful method allowing test of complex hypotheses involving multiple and indirect effects, on an island-like system of 22 French Guianan neotropical inselbergs covered with rock-savanna. We separated the effects of size (rock-savanna area), isolation (density of surrounding inselbergs), environmental filtering (rainfall, altitude) and dispersal filtering (forest-matrix openness) on the species richness of all plants and of various ecological groups (terrestrial versus epiphytic, small-scale versus large-scale dispersal species). We showed that the species richness of all plants and terrestrial species was mainly explained by the size of rock-savanna vegetation patches, with increasing richness associated with higher rock-savanna area, while inselberg isolation and forest-matrix openness had no measurable effect. This size effect was mediated by an increase in terrestrial-habitat diversity, even after accounting for increased sampling effort. The richness of epiphytic species was mainly explained by environmental filtering, with a positive effect of rainfall and altitude, but also by a positive size effect mediated by enhanced woody-plant species richness. Inselberg size and environmental filtering both explained the richness of small-scale and large-scale dispersal species, but these ecological groups responded in opposite directions to altitude and rainfall, that is positively for large-scale and negatively for small-scale dispersal species. Our study revealed both habitat diversity associated with island size and environmental filtering as major drivers of neotropical inselberg plant diversity and showed the importance of plant species growth form and dispersal ability to explain the relative importance of each driver.

Data from: When should species richness be energy limited, and how would we know?

Energetic constraints are fundamental to ecology and evolution, and empirical relationships between species richness and estimates of available energy (i.e. resources) have led some to suggest that richness is energetically constrained. However, the mechanism linking energy with richness is rarely specified and predictions of secondary patterns consistent with energy-constrained richness are lacking. Here, we lay out the necessary and sufficient assumptions of a causal relationship linking energy gradients to richness gradients. We then describe an eco-evolutionary simulation model that combines spatially explicit diversification with trait evolution, resource availability and assemblage-level carrying capacities. Our model identified patterns in richness and phylogenetic structure expected when a spatial gradient in energy availability determines the number of individuals supported in a given area. A comparison to patterns under alternative scenarios, in which fundamental assumptions behind energetic explanations were violated, revealed patterns that are useful for evaluating the importance of energetic constraints in empirical systems. We use a data set on rockfish (genus Sebastes) from the northeastern Pacific to show how empirical data can be coupled with model predictions to evaluate the role of energetic constraints in generating observed richness gradients.

opencc-zeroFeb 2020View details →

Data from: Burning savanna for avian species richness and functional diversity

Prescribed fire is used throughout fire-prone landscapes to conserve biodiversity. Current best practice in managing savanna systems advocates methods based on the assumption that increased fire-mediated landscape heterogeneity (pyrodiversity) will promote biodiversity. However, considerable knowledge gaps remain in our understanding of how savanna wildlife responds to the composition and configuration of pyrodiverse landscapes. The effects of pyrodiversity on functional diversity has rarely been quantified and assessing this relationship at a landscape scale which is commensurate with fire management is important for understanding mechanisms underlying ecosystem resilience. Here, we assess the impact of spatiotemporal variation in a long-term fire regime on avian diversity in North West Province, South Africa. <a name="_Hlk12800642">We examined the relationship between (a) species richness, (b) three indices of functional diversity</a> (i.e., functional richness, functional evenness and functional dispersion) and four measures of pyrodiversity, the spatial extents of fire age-classes, and habitat type at the landscape-scale. We then used null models to assess differences between observed and expected functional diversity. <a name="_Hlk23757785">We found that the proportion of newly-burned (<1-year post-fire), old, unburned (≥10 years post-fire), and woodland habitat on the landscape predicted species and functional richness. </a><a name="_Hlk535845085">Species richness also increased with the degree of edge contrast between patches of varying fire age, while functional dispersion increased with the degree of patch shape complexity. Lower than expected levels of functional richness suggest that habitat filtering is occurring, resulting in functional redundancy across our study sites. </a>We demonstrate that evaluating functional diversity and redundancy is an important component of conservation planning as they may contribute to previously reported fire resilience. Our findings suggest that it is the type and configuration, rather than the diversity, of fire patches on the landscape that promote avian diversity and conserve ecological functions. A management approach is needed that includes significant coverage of adjacent newly-burned and older, unburned savanna habitat; the latter, in particular, is inadequately represented under current burning practices.

Data from: Information dropout patterns in restriction site associated DNA phylogenomics and a comparison with multilocus Sanger data in a species-rich moth genus

A rapid shift from traditional Sanger sequencing-based molecular methods to the phylogenomic approach with large numbers of loci is underway. Among phylogenomic methods, RAD (Restriction site Associated DNA) sequencing approaches have gained much attention as they enable rapid generation of up to thousands of loci randomly scattered across the genome and are suitable for non-model species. RAD data sets however suffer from large amounts of missing data and rapid locus dropout along with decreasing relatedness among taxa. The relationship between locus dropout and the amount of phylogenetic information retained in the data has remained largely un-investigated. Similarly, phylogenetic hypotheses based on RAD have rarely been compared with phylogenetic hypotheses based on multilocus Sanger sequencing, even less so using exactly the same species and specimens. We compared the Sanger-based phylogenetic hypothesis (8 loci; 6,172 bp) of 32 species of the diverse moth genus Eupithecia (Lepidoptera, Geometridae) to that based on double-digest RAD sequencing (3,256 loci; 726,658 bp). We observed that topologies were largely congruent, with some notable exceptions that we discuss. The locus dropout effect was strong. We demonstrate that number of loci is not a precise measure of phylogenetic information since the number of single-nucleotide polymorphisms (SNPs) may remain low at very shallow phylogenetic levels despite large numbers of loci. As we hypothesize, the number of SNPs and parsimony informative SNPs (PIS) is low at shallow phylogenetic levels, peaks at intermediate levels and, thereafter, declines again at the deepest levels as a result of decay of available loci. Similarly, we demonstrate with empirical data that the locus dropout affects the type of loci retained, the loci found in many species tending to show lower interspecific distances than those shared among fewer species. We also examine the effects of the numbers of loci, SNPs and PIS on nodal bootstrap support, but could not demonstrate with our data our expectation of a positive correlation between them. We conclude that RAD methods provide a powerful tool for phylogenomics at an intermediate phylogenetic level as indicated by its broad congruence with an eight-gene Sanger data set in a genus of moths. When assessing the quality of the data for phylogenetic inference, the focus should be on the distribution and number of SNPs and PIS rather than on loci.

Data from: Species richness-productivity relationships of tropical terrestrial ferns at regional and local scales

1. The species richness-productivity relationship (SRPR), by which the species richness of habitats or ecosystems is related to the productivity of the ecosystem or the taxon, has been documented both on regional and local scales, but its generality, biological meaning, and underlying mechanisms remain debated. 2. We evaluated the SRPR and 3 mechanistic hypotheses using terrestrial ferns in 18 study plots along an elevational gradient (500-4000 m) in Ecuador. We measured annual increases in above-ground biomass of 6175 fern individuals from 91 species over 2 years, and estimated plot-level tree productivity from increases in above-ground woody biomass of 560 trees. Analyses were conducted by (a) comparing plots along the elevational gradient (regional scale) and (b) comparing plots within each elevational belt (local scale). 3. Fern diversity was related to the productivity of the fern assemblages, but not to above-ground productivity of the trees. At the regional scale, we found a positive relationship of fern species richness to fern productivity that appeared to be determined by an increase in the number of fern individuals and niche availability. In contrast, at the local scale this relationship was negative and likely driven by interspecific competition. 4. Synthesis: Plot diversity of ferns appears to be limited by the number of available niches and competition to occupy these niches. At the local scale, this is reflected in a negative SRPR probably driven by competition, whereas with increasing scale the positive influence of productivity emerges. This represents the first evidence that productivity and competition affect the diversity of tropical herb assemblages at the plot scale.