Is my study system good enough? A case study for identifying maternal effects

In this paper, we demonstrate how simulation studies can be used to answer questions about identifiability and consequences of omitting effects from a model. The methodology is presented through a case study where identifiability of genetic and/or individual (environmental) maternal effects is explored. Our study system is a wild house sparrow (Passer domesticus) population with known pedigree. We fit pedigree‐based (generalized) linear mixed models (animal models), with and without additive genetic and individual maternal effects, and use deviance information criterion (DIC) for choosing between these models. Pedigree and R‐code for simulations are available. For this study system, the simulation studies show that only large maternal effects can be identified. The genetic maternal effect (and similar for individual maternal effect) has to be at least half of the total genetic variance to be identified. The consequences of omitting a maternal effect when it is present are explored. Our results indicate that the total (genetic and individual) variance are accounted for. When an individual (environmental) maternal effect is omitted from the model, this only influences the estimated (direct) individual (environmental) variance. When a genetic maternal effect is omitted from the model, both (direct) genetic and (direct) individual variance estimates are overestimated.     

Is there a density compensation effect in plant communities in extreme habitats?

The occurrence of a density compensation effect (DCE) has been estimated in north Caucasian areas of extreme habitats occupied by communities of vascular plants, mosses, and lichens. The species densities have been estimated according to their frequency. The correlation between species number and frequency in the studied areas has failed to confirm the assumption that extreme environmental conditions alone is responsibile for the DCE, at least locally.     

Is MHC diversity a better marker for conservation than neutral genetic diversity? A case study of two contrasting dolphin populations

Genetic diversity is essential for populations to adapt to changing environments. Measures of genetic diversity are often based on selectively neutral markers, such as microsatellites. Genetic diversity to guide conservation management, however, is better reflected by adaptive markers, including genes of the major histocompatibility complex (MHC). Our aim was to assess MHC and neutral genetic diversity in two contrasting bottlenose dolphin (Tursiops aduncus) populations in Western Australia—one apparently viable population with high reproductive output (Shark Bay) and one with lower reproductive output that was forecast to decline (Bunbury). We assessed genetic variation in the two populations by sequencing the MHC class II DQB, which encompasses the functionally important peptide binding regions (PBR). Neutral genetic diversity was assessed by genotyping twenty‐three microsatellite loci. We confirmed that MHC is an adaptive marker in both populations. Overall, the Shark Bay population exhibited greater MHC diversity than the Bunbury population—for example, it displayed greater MHC nucleotide diversity. In contrast, the difference in microsatellite diversity between the two populations was comparatively low. Our findings are consistent with the hypothesis that viable populations typically display greater genetic diversity than less viable populations. The results also suggest that MHC variation is more closely associated with population viability than neutral genetic variation. Although the inferences from our findings are limited, because we only compared two populations, our results add to a growing number of studies that highlight the usefulness of MHC as a potentially suitable genetic marker for animal conservation. The Shark Bay population, which carries greater adaptive genetic diversity than the Bunbury population, is thus likely more robust to natural or human‐induced changes to the coastal ecosystem it inhabits.     

Making remote sense of biodiversity: What grassland characteristics make spectral diversity a good proxy for taxonomic diversity?

Aim

The spectral variability hypothesis (SVH) predicts that spectral diversity, defined as the variability of radiation reflected from vegetation, increases with biodiversity. While confirmation of this hypothesis would pave the path for use of remote sensing to monitor biodiversity, support in herbaceous ecosystems is mixed. Methodological aspects related to scale have been the predominant explanation for the mixed support, yet biological characteristics that vary among herbaceous systems may also affect the strength of the relationship. Therefore, we examined the influence of three biological characteristics on the relationship between spectral and taxonomic diversity: vegetation density, spatial species turnover and invasion by non-native species. We aimed to understand when and why spectral diversity may serve as an indicator of taxonomic diversity and be useful for monitoring.

Location

Continental U.S.A.

Time Period

Peak greenness in 2017.

Major Taxa Studied

Grassland and herbaceous ecosystems.

Methods

For nine herbaceous sites in the National Ecological Observatory Network, we calculated taxonomic diversity from field surveys of 20 m × 20 m plots and derived spectral diversity for those same plots from airborne hyperspectral imagery with a spatial resolution of 1 m. The strength of the taxonomic diversity–spectral diversity relationship at each site was subsequently assessed against measurements of vegetation density, spatial species turnover and invasion.

Results

We found a significant relationship between taxonomic and spectral diversity at some, but not all, sites. Spectral diversity was more strongly related to taxonomic diversity in sites with high species turnover and low invasion, but vegetation density had no effect on the relationship.

Main Conclusions

Using spectral diversity as a proxy for taxonomic diversity in grasslands is possible in some circumstances but should not just be assumed based on the SVH. It is important to understand the biological characteristics of a community prior to considering spectral diversity to monitor taxonomic diversity.     

Is intensity of plant root mycorrhizal colonization a good proxy for plant growth rate,dominance and decomposition in nutrient poor conditions?

Questions

Mycorrhizae may be a key element of plant nutritional strategies and of carbon and nutrient cycling. Recent research suggests that in natural conditions, intensity of mycorrhizal colonization should be considered an important plant feature. How are inter‐specific variations in mycorrhizal colonization rate, plant relative growth rate (RGR ) and leaf litter decomposability related? Is (arbuscular) mycorrhizal colonization linked to the dominance of plant species in nutrient‐stressed ecosystems?

Location

Teberda State Biosphere Reserve, northwest Caucasus, Russia.

Methods

We measured plant RGR under mycorrhizal limitation and under natural nutrition conditions, together with leaf litter decomposability and field intensity of mycorrhizal colonization across a wide range of plant species, typical for alpine communities of European mountains. We applied regression analysis to test whether the intensity of mycorrhizal colonization is a good predictor of RGR and decomposition rate, and tested how these traits predict plant dominance in communities.

Results

Forb species with a high level of field mycorrhizal colonization had lower RGR under nutritional and mycorrhizal limitation, while grasses were unaffected. Litter decomposition rate was not related to the intensity of mycorrhizal colonization. Dominant species mostly had a higher level of mycorrhizal colonization and lower RGR without mycorrhizal colonization than subordinate species, implying that they were more dependent on mycorrhizal symbionts. There were no differences in litter decomposability.

Conclusions

In alpine herbaceous plant communities dominated by arbuscular mycorrhizae, nutrient dynamics are to a large extent controlled by mycorrhizal symbiosis. Intensity of mycorrhizal colonization is a negative predictor for whole plant RGR . Our study highlights the importance of mycorrhizal colonization as a key trait underpinning the role of plant species in carbon and nutrient dynamics in nutrient‐limited herbaceous plant communities.

     

Do soil phytoliths accurately represent plant communities in a temperate region? A case study of Northeast China

Modern soil phytoliths can potentially provide analogues for phytolith assemblages from archaeological and palaeoecological contexts. To assess the reliability of soil phytoliths for representing different plant communities, we analysed phytoliths in surface soils and parent plants at 65 sites representing five types of regional vegetation in Northeast China. The results demonstrated that surface soil phytolith assemblages could clearly differentiate samples from herbaceous and woody communities, and samples from Poaceae and non-Poaceae communities could be separated statistically. In addition, woody communities could be differentiated into a broadleaf-Poaceae community, a broadleaf-non-Poaceae community and a conifer and broadleaf-non-Poaceae community, except for some overlapping samples. Soil phytolith assemblages are thus able to differentiate regional vegetation types into different plant community types. In the present study, soil phytoliths represented about 30% of the phytoliths present in the aboveground vegetation. In addition, soil phytoliths from different communities reflected the aboveground vegetation with slightly different degrees of accuracy, and in addition different morphotypes exhibited different degrees of representational bias. Some morphotypes (e.g. rondel, elongate psilate, lanceolate) overrepresented the abundance of the associated plant taxa; morphotypes such as tracheid, conical epidermal, stomata and others under-represented the original plant richness; and other morphotypes, e.g. saddle, trapeziform sinuate, scutiform, were in good agreement with the numbers of plant taxa in the plot inventory. Thus, any quantitative palaeovegetation reconstruction using phytoliths should begin with the calibration of soil phytolith assemblages. We conclude that our findings provide improved phytolith analogues for different plant communities, with applications in palaeoenvironmental reconstruction, and they also provide additional insights into the mechanisms of phytolith production and deposition.     

Is the Natura 2000 network sufficient for conservation of butterfly diversity? A case study in Slovenia

Slovenia has one of the most extensive Natura 2000 networks in Europe with 259 SAC’s covering 31.4% of the country. To determine how well does the current network cover the areas of high butterfly diversity and/or aggregation of the butterfly species of conservation concern, the data from the recent survey for a distribution atlas were used. Altogether 99,423 records of 173 species collated after 1979 were used. The data distribution is slightly biased towards SAC’s, with 44.8% of localities within them, most likely due to sparsely sampled urban areas and intensive farmland areas which are found only outside SAC’s. The diversity and distribution of red listed species was evaluated at a 5 × 5 km grid square level. Additionally the importance of the size of the SAC’s was compared to their butterfly species diversity. In general the high diversity areas also hold the largest aggregation of red listed species with core areas concentrated in SW Slovenia. The SAC’s cover majority of areas with high diversity and the distribution of all but one threatened butterfly species. That species is Colias myrmidone, which is now considered extinct in Slovenia with no records after 1993. The most prominent areas with high conservation value in Slovenia not included in the SAC’s network are the Koro?ka region, Gori?ka Brda region, lower Sava River valley and Slovenske Gorice region. The butterfly diversity in small SAC’s is relatively high with increases in size only gradually increasing the species numbers, thus emphasizing the importance and conservation value of small SAC’s for sustaining high butterfly diversity in Slovenia.     

Do ridge habitats contribute to pteridophyte diversity in tropical montane forests? A case study from southeastern Ecuador

We address the question to which degree ridge habitats in tropical montane forests contribute to overall plant diversity by analysing patterns of pteridophyte (i.e. lycophytes and ferns) assemblages on ridges and slopes in three montane forest sites near Podocarpus National Park, Ecuador. The analyses, which involved 158 pteridophyte species (110 terrestrial, 96 epiphytic, 48 both) from 28 plots of 20 m × 20 m (or an equivalent of 400 m²), showed that more species were typical of one of the three study sites than of one of the two habitats (ridge/slope). As found in previous studies, alpha diversity on ridges was lower than on slopes, accounted for by the absence of numerous species that are found on slopes. Pteridophyte assemblages on ridges were more similar across study sites than those on slopes. Thus, unlike the structurally comparable (i.e. stunted, open) Amazonian forests, the studied montane ridge forests harbour fairly homogenous pteridophytes assemblages with very few specialised species. Our study implies that slope forests are of higher conservation priority for pteridophytes in the study region than ridge habitats. However, comparative studies are needed because other geographical regions and other groups of organisms may not share this pattern. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Does diversity beget diversity? A case study of crops and weeds

Abstract. The ecological literature is ambiguous as to whether the initial diversity of a plant community facilitates or deters the diversity of colonizing species. We experimentally planted annual crop species in monoculture and polyculture, and examined the resulting weed communities. The species composition of weeds was similar among treatments, but the species richness of weeds was significantly higher in the polycultures than in the monocultures. This supports the ‘diversity begets diversity’ hypothesis. Environmental microheterogeneity, diversity promoters, and ecological equivalency do not seem able to explain the observed patterns.     

Is the abundance of species determined by their functional traits? A new method with a test using plant communities

The relation between functional traits and abundance of species has the potential to provide evidence on the mechanisms that structure local ecological communities. The niche-limitation/limiting-similarity hypothesis, derived from MacArthur and Levins’ original concept, predicts that species that are similar to others in terms of functional traits will suffer greater competition and hence be less abundant. On the other hand, the environment-filtering/habitat-optimum hypothesis predicts that groups of species with functional traits that are close to the optimum for that environment, and are therefore similar to other species, will be more abundant. We propose a new niche-assembly model for predicting the relative abundance of species in communities from their functional traits, which can detect the patterns that would be expected from either of these hypotheses. The model was fitted to eight plant communities sampled in the Lake Ohau district of New Zealand. For seven of the sites, the patterns could not be distinguished from that expected under a null model. However, in one site there was highly significant departure from the null model in the direction expected from the niche-limitation hypothesis. The site was probably the most productive of those examined. It is possible that competition for light rather than belowground resources, or faster recovery from disturbance, allowed greater predictability. Surprisingly, the predictability was seen when just the presences of a species’ neighbours in trait space were taken into account, but not when the potential effects of those neighbours were weighted by their abundance. For three of the four model types, the effects of species on each other were consistently negative: a significant trend. These results contradict the various neutral models of ecological communities.     

Is genomic diversity a useful proxy for census population size? Evidence from a species‐rich community of desert lizards

Species abundance data are critical for testing ecological theory, but obtaining accurate empirical estimates for many taxa is challenging. Proxies for species abundance can help researchers circumvent time and cost constraints that are prohibitive for long‐term sampling. Under simple demographic models, genetic diversity is expected to correlate with census size, such that genome‐wide heterozygosity may provide a surrogate measure of species abundance. We tested whether nucleotide diversity is correlated with long‐term estimates of abundance, occupancy and degree of ecological specialization in a diverse lizard community from arid Australia. Using targeted sequence capture, we obtained estimates of genomic diversity from 30 species of lizards, recovering an average of 5,066 loci covering 3.6 Mb of DNA sequence per individual. We compared measures of individual heterozygosity to a metric of habitat specialization to investigate whether ecological preference exerts a measurable effect on genetic diversity. We find that heterozygosity is significantly correlated with species abundance and occupancy, but not habitat specialization. Demonstrating the power of genomic sampling, the correlation between heterozygosity and abundance/occupancy emerged from considering just one or two individuals per species. However, genetic diversity does no better at predicting abundance than a single day of traditional sampling in this community. We conclude that genetic diversity is a useful proxy for regional‐scale species abundance and occupancy, but a large amount of unexplained variation in heterozygosity suggests additional constraints or a failure of ecological sampling to adequately capture variation in true population size.     

Is vascular plant species diversity a predictor of bryophyte species diversity in Mediterranean forests?

This study aimed to (i) investigate the congruence among the species composition and diversity of bryophytes and vascular plants in forests; (ii) test if site prioritization for conservation aims by the maximization of the pooled number of vascular plant species is effective to maximize the pooled number of bryophyte species. The study was performed in six forests in Tuscany, Italy. Four-hundred and twenty vascular plant species (61 of which were woody) and 128 bryophyte species were recorded in 109 plots. Despite the good predictive value of the compositional patterns of both woody plants and total vascular with respect to the compositional pattern of bryophytes, the species richness of the latter was only marginally related to the species richness of the former two. Bryophyte rare species were not spatially related to rare plant species and neither coincided with the sites of highest plant species richness. The species accumulation curves of bryophytes behaved differently with respect to those of woody plants or total vascular plants. Reserve selection analysis based on the maximization of the pooled species richness of either woody plants or total vascular plants were not effective in maximizing the pooled species richness of bryophytes. This study indicates that species diversity of vascular plants is not likely to be a good indicator of the bryophyte species diversity in Mediterranean forests.     

Does herbivore diversity depend on plant diversity? The case of California butterflies

It is widely believed that the diversity of plants influences the diversity of animals, and this should be particularly true of herbivores. We examine this supposition at a moderate spatial extent by comparing the richness patterns of the 217 butterfly species resident in California to those of plants, including all 5,902 vascular plant species and the 552 species known to be fed on by caterpillars. We also examine the relationships between plant/butterfly richness and 20 environmental variables. We found that although plant and butterfly diversities are positively correlated, multiple regression, path models, and spatial analysis indicate that once primary productivity (estimated by a water-energy variable, actual evapotranspiration) and topographical variability are incorporated into models, neither measure of plant richness has any relationship with butterfly richness. To examine whether butterflies with the most specialized diets follow the pattern found across all butterflies, we repeated the analyses for 37 species of strict monophages and their food plants and found that plant and butterfly richness were similarly weakly associated after incorporating the environmental variables. We condude that plant diversity does not directly influence butterfly diversity but that both are probably responding to similar environmental factors.     

A periodic table for ecology? A chemist's view of plant functional types

Abstract. A functional type approach, in which the complexity found in nature is reduced by grouping organisms that are functionally similar into a single classification, is being promoted in global change research. This paper examines a proposed analogy between this functional type approach in global change ecology and the periodic table of the elements in chemistry. When applied to a ‘bottom-up’ approach for defining functional types in ecology, in which large numbers of organisms are classified into smaller groups based on similarity of certain functions, the analogy fails. Ecological functions are not simple attributes of a biological entity, as electronic structure is for a chemical element, but are themselves complex chemical and physical systems that often interact strongly with the environment. The analogy to the periodic table may be of some use as an organizing tool in a ‘top-down’ approach in which a modelling context is used to define the number of ‘elements’ and their properties. This will be elaborated for plant functional types. Each PFT is assigned characteristics that allow its response to the driving forces of change, e.g. temperature, precipitation, soil nutrients, disturbance, to be predicted. ‘Rules of combination’ determine how the mix of PFTs in a particular ecosystem changes to form different ecosystems, which would correspond in the analogy to chemical compounds. However, these requirements present significant challenges to the usefulness of the analogy, even as an organizing tool in the ‘top-down’ approach.     

Biodiversity and ecosystem services−A case study for the assessment of multiple species and functional diversity levels in a cultural landscape

The expansion of large-scale plantations has a major impact on landscapes in the Tropics and Subtropics. Crops like soy bean, oil palm and rubber have led to drastic changes in land cover over the past decades, thereby altering ecosystem functions and services (ESS). Associated shifts in ESS such as climate regulation, erosion and water cycles, biodiversity as well as soil fertility or the provisioning of raw materials have been assessed through several models and software solutions (InVEST, ARIES, MIMES). However, suitable methods for the integration of a range of biodiversity assessments in agricultural landscapes are scarce.With this study, we introduce a methodology for incorporating multiple levels of species diversity into models to allow an integrated evaluation of ESS. We collected data sets from both published and unpublished sources on the distribution of vascular plants, selected pollinator groups, ground beetles, ungulates as well as amphibians, mammals, reptiles and birds in rubber-dominated landscapes, with a focus on our study sites in Southwest China and Thailand. Based on this information, we developed a common classification scheme that enables the integration of different facets of biodiversity (species diversity and functional diversity) to complement an interdisciplinary ESS assessment.Species diversity data were normalized against the most divers habitats reported (using habitat scores) to assess the impact of rubber cultivation on multiple levels of biodiversity. This resulted in a comparable matrix of different land use types and their suitability as habitat for the respective species groups allowing the aggregation of very diverse indicators. The findings were applied to two alternative land use scenarios in southern China to highlight the potential effects of land use and management decisions on species and functional diversity. Our results highlighted that the conservation oriented scenario did score higher for habitat suitability in both total species (+5%) as well as IUCN Red List species (+6%) assessments compared to the current state or business as usual scenarios (-2% and −3% compared to current state).The process presented here allows for an application within established ESS software programs, in our case InVEST, using aggregated indices while additionally providing enhanced opportunities for comparable, spatially explicit assessments of the expected impact of the analyzed scenarios on specific species groups.     

Is spectral distance a proxy of beta diversity at different taxonomic ranks? A test using quantile regression

Beta diversity represents a powerful indicator of ecological conditions because of its intrinsic relation with environmental gradients. In this view, remote sensing may be profitably used to derive models characterizing or estimating species turnover over an area. While several examples exist using spectral variability to estimate species diversity at several spatial scales, most of these have relied on standard correlation or regression approaches like the common Ordinary Least Square (OLS) regression which are problematic with noisy data. Moreover, very few attempts were made to derive beta diversity characterization models at different taxonomic ranks. In this paper, we performed quantile regression to test if spectral distance represents a good proxy of beta diversity considering different data thresholds and taxonomic ranks. We used plant distribution data from the North and South Carolina including 146 counties and covering a variety of vegetation formations. The dissimilarity in species composition at different taxonomic ranks (using Sørensen distance) among pairs of counties was compared with their distance in NDVI values derived from 23 yearly MODIS images. Our results indicate that (i) spectral variability represents a good proxy of beta diversity when appropriate statistics are applied and (ii) a lower taxonomic rank is important when changes in species composition are examined spatially using remotely sensed data.