Evaluating and interpreting cross-taxon congruence: Potential pitfalls and solutions

Understanding processes underlying cross-taxon congruence in species composition along elevational gradients

Changes in species diversity of different taxa along environmental gradients are usually correlated, resulting in a pattern called cross-taxon congruence. This pattern can be due to functional relationships between taxa, a common response to niche-related processes, or stochastic processes. However, it remains unclear the extent to which they contribute to the association among patterns of changes in species composition, (i.e., beta diversity), and whether these changes are related to species nestedness and turnover. Here we described patterns of change in the taxonomic composition of plant and orthopteran assemblages along an elevational gradient in Cordoba province, central Argentina. We assessed cross-taxon congruence and identified the main environmental variables accounting for such patterns. Mantel correlations showed congruence between the patterns of taxonomic dissimilarity of plants and orthopterans. According Generalized disiimilarity models (GDM) the main environmental variables driving the patterns were temperature for both taxa, and changes in soil nutrient content for plants, spatial effects were also found. Beta diversity was mainly due to species turnover for orthopterans and plants, indicating replacement by species adapted to elevational conditions. Niche-related process, such as environmetal filtering, along with neutral processes may have contributed to cross-taxon congruence in beta diversity.

Environmental drivers of forest biodiversity in temperate mixed forests - A multi-taxon approach

Harmonization of timber production and forest conservation is a major challenge of modern silviculture. For the establishment of ecologically sustainable forest management, the management-related environmental drivers of multi-taxon biodiversity should be explored. Our study reveals those environmental variables related to tree species diversity and composition, stand structure, litter and soil conditions, microclimate, landscape, and land-use history that determine species richness and composition of 11 forest-dwelling organism groups. Herbs, woody regeneration, ground-floor and epiphytic bryophytes, epiphytic lichens, terricolous saprotrophic, ectomycorrhizal, and wood-inhabiting macrofungi, spiders, carabid beetles, and birds were sampled in West Hungarian mature mixed forests. The correlations among the diversities and compositions of different organism groups were also evaluated. Drivers of organism groups were principally related to stand structure, tree species diversity and composition, and microclimate, while litter, soil, landscape, and land-use historical variables were less influential. The complex roles of the shrub layer, deadwood, and the size of the trees in determining the diversity and composition of various taxa were revealed. Stands with more tree species sustained higher stand-level species richness of several taxa. Besides, stands with different dominant tree species harbored various species communities of organism groups. Therefore, landscape-scale diversity of dominant tree species may enhance the diversity of forest-dwelling communities at landscape level. The effects of the overstory layer on forest biodiversity manifested in many cases via microclimate conditions. Diversity of organism groups showed weaker relationship with the diversity of other taxa than with environmental variables. According to our results, the most influential drivers of forest biodiversity are under the direct control of the actual silvicultural management. Heterogeneous stand structure and tree species composition promote the different organism groups in various ways. Therefore, the long-term maintenance of the structural and compositional heterogeneity both at stand and landscape scale is an important aspect of ecologically sustainable forest management.

Cross-taxon congruence of aquatic microbial communities across geological ages in Iceland: Stochastic and deterministic processes

Biotic groups usually have nonrandom cross-taxon relationships in their biodiversity or compositions across sites, but it is poorly known how such congruence varies across long-term ecosystem development, and what are the ecological processes underlying biodiversity patterns. Here, we examined the cross-taxon congruence in diversity and compositions of bacteria, fungi and diatoms in streams from four regions with different geological ages in Iceland, and further studied their community assembly processes. Bacteria and fungi showed contrasting trends in alpha and gamma diversities across geological ages, while their beta diversity patterns were consistent, being the lowest in the oldest region. The three taxonomic groups had the strongest cross-taxon congruence of beta diversity in the oldest region, while the weakest for intermediate-aged regions. Although environmental variables played important roles in shaping their congruence, biotic interaction had nonnegligible influences. Deterministic processes, being dominant for bacteria and fungi, had the highest relative influence in intermediate-aged regions, whereas diatoms showed higher stochasticity. We proposed a four-phase conceptual model to show how the balance of deterministic and stochastic processes changes across geological ages. Taken together, our results provide an advanced understanding of cross-taxon congruence and community assembly processes for aquatic communities over long-term periods of geological age.

Disentangling the role of environment in cross-taxon congruence of species richness along elevational gradients

Spatial patterns of species richness have been found to be positively associated, a phenom called cross-taxon congruence. This may be explained by a common response to environment or by ecological interactions between taxa. Spatial changes in species richness are related to energy and environmental heterogeneity but their roles in cross-taxon congruence remain poorly explored. Elevational gradients provide a great opportunity to shed light on the underlying drivers of species richness patterns. We study the joint influence of environment and biotic interactions in shaping the cross-taxon congruence of plants and orthopterans species richness, along three elevational gradients in Sierras Grandes, central Argentina. Elevational patterns of species richness of orthopterans and plants were congruent, being temperature the best single predictor of both patterns supporting the energy-related hypotheses. Using a structural equation model, we found that temperature explained plant richness directly and orthopteran richness indirectly via orthopteran abundance. Cross-taxon congruence is likely due to a common response of both taxa to temperature although via different theoretical mechanisms, possibly, range limitations for plants and foraging activity for orthopterans. We disentangled the role of temperature in determining the cross-taxon congruence of plants and orthopterans by showing that a common response to the environment may mask different mechanisms driving the diversity of different taxonomic groups.

Congruence, but no cascade-Pelagic biodiversity across three trophic levels in Nordic lakes

Covariation in species richness and community structure across taxonomical groups (cross-taxon congruence) has practical consequences for the identification of biodiversity surrogates and proxies, as well as theoretical ramifications for understanding the mechanisms maintaining and sustaining biodiversity. We found there to exist a high cross-taxon congruence between phytoplankton, zooplankton, and fish in 73 large Scandinavian lakes across a 750 km longitudinal transect. The fraction of the total diversity variation explained by local environment alone was small for all trophic levels while a substantial fraction could be explained by spatial gradient variables. Almost half of the explained variation could not be resolved between local and spatial factors, possibly due to confounding issues between longitude and landscape productivity. There is strong consensus that the longitudinal gradient found in the regional fish community results from postglacial dispersal limitations, while there is much less evidence for the species richness and community structure gradients at lower trophic levels being directly affected by dispersal limitation over the same time scale. We found strong support for bidirectional interactions between fish and zooplankton species richness, while corresponding interactions between phytoplankton and zooplankton richness were much weaker. Both the weakening of the linkage at lower trophic levels and the bidirectional nature of the interaction indicates that the underlying mechanism must be qualitatively different from a trophic cascade.

Investigating microbial associations from sequencing survey data with co-correspondence analysis

Microbial communities, which drive major ecosystem functions, consist of a wide range of interacting species. Understanding how microbial communities are structured and the processes underlying this is crucial to interpreting ecosystem responses to global change but is challenging as microbial interactions cannot usually be directly observed. Multiple efforts are currently focused to combine next-generation sequencing (NGS) techniques with refined statistical analysis (e.g., network analysis, multivariate analysis) to characterize the structures of microbial communities. However, most of these approaches consider a single table of sequencing data measured for several samples. Technological advances now make it possible to collect NGS data on different taxonomic groups simultaneously for the same samples, allowing us to analyse a pair of tables. Here, an analytical framework based on co-correspondence analysis (CoCA) is proposed to study the distributions, assemblages and interactions between two microbial communities. We show the ability of this approach to highlight the relationships between two microbial communities, using two data sets exhibiting various types of interactions. CoCA identified strong association patterns between autotrophic and heterotrophic microbial eukaryote assemblages, on the one hand, and between microalgae and viruses, on the other. We demonstrate also how CoCA can be used, complementary to network analysis, to reorder co-occurrence networks and thus investigate the presence of patterns in ecological networks.

Alternatives for the biomonitoring of fish and phytoplankton in tropical streams

Biomonitoring programs need to balance accurate responses in assessments of changes in biological communities with sampling that is fast and low cost. In this study, we evaluated the concordance among fish and phytoplankton communities of streams. We tested the cross-taxa surrogacy, taxonomic, numerical resolution and ecological substitute group (habitat use and trophic guilds) resolution with Procrustes analyses aim of simplifying the biomonitoring process. We collect a total fish abundance of 8,461 individuals, represented by the ecological classes of habitat, including benthic, nektonic, nektobenthic, marginal and trophic guilds by detritivore, terrestrial invertivore, aquatic invertivore, piscivore, algivore and herbivore. We sampled a phytoplankton total density of 1,466.68 individuals/ml, represented by four Morphology-Based Functional Groups and nine Reynolds Functional Groups. Our results don’t support the use of substitute groups among fish and phytoplankton. For fish, habitat use and trophic guild are good surrogates for species-level data. Additionally, our results don’t support the use of functional groups as surrogates for phytoplankton. We suggest the use of higher taxonomic levels (genus and family) and record only the occurrence of species and/or genus for fish and phytoplankton. Our findings contribute to decreasing the costs and time of biomonitoring programs assessments and/or conservation plans on fish and phytoplankton communities of headwater streams.

Cross Taxon Congruence Between Lichens and Vascular Plants in a Riparian Ecosystem

Despite that congruence across taxa has been proved as an effective tool to provide insights into the processes structuring the spatial distribution of taxonomic groups and is useful for conservation purposes, only a few studies on cross-taxon congruence focused on freshwater ecosystems and on the relations among vascular plants and lichens. We hypothesized here that, since vascular plants could be good surrogates of lichens in these ecosystems, it would be possible to assess the overall biodiversity of riparian habitats using plant data only. In this frame, we explored the relationship between (a) species richness and (b) community composition of plants and lichens in a wetland area located in central Italy to (i) assess whether vascular plants are good surrogates of lichens and (ii) to test the congruence of patterns of species richness and composition among plants and lichens along an ecological gradient. The general performance of plant species richness per se, as a biodiversity surrogate of lichens, had poor results. Nonetheless, the congruence in compositional patterns between lichens and vascular plants varied across habitats and was influenced by the characteristics of the vegetation. In general, we discussed how the strength of the studied relationships could be influenced by characteristics of the data (presence/absence vs. abundance), by the spatial scale, and by the features of the habitats. Overall, our data confirm that the more diverse and structurally complex the vegetation is, the more diverse are the lichen communities it hosts.

Congruence between arthropod and plant diversity in a biodiversity hotspot largely driven by underlying abiotic factors

Plants often form the basis of conservation planning and management. The effectiveness of plant diversity as a surrogate for arthropod diversity was assessed in natural areas in the Kogelberg Biosphere Reserve, a floral endemism hotspot in the Cape Floristic Region (CFR), South Africa. Arthropods and plants were sampled across 30 topographically heterogeneous sites in a spatially nested design. The relationship between plants and arthropods were quantified in terms of species richness, assemblage variation, and assemblage turnover. The influence of arthropod trophic groups, habitat association, and spatial scale were also explored. Generalized dissimilarity modelling was used to investigate differential influence of explanatory groups (geology, disturbance, local site characteristics, refuge, mesoclimate, terrain) on arthropod and plant turnover. Congruence in assemblage variation was restricted to local scales, and only present between plants and those arthropods associated with the foliar component of the habitat. Weak congruence in species turnover was due to differences in the relative importance of explanatory groups, with different variables within each explanatory group being important, and similar variables predicting different turnover patterns. For both groups, variables related to geology and fire history were important for assemblage turnover. These variables are already incorporated in conservation planning and management for plant diversity across the CFR. Overall plant diversity was a weak surrogate for the arthropod groups included in this study, suggesting that as an alternative, environmental surrogates for arthropod diversity perform better.

Teamwork makes the dream work: Disentangling cross-taxon congruence across soil biota in black pine plantations

Soil plays a fundamental role in many ecological processes, throughout a complex network of above- and below-ground interactions. This has aroused increasing interest in the use of correlates for biodiversity assessment and has demonstrated their reliability with respect to proxies based on environmental data alone. Although co-variation of species richness and composition in forests has been discussed in the literature, only a few studies have explored these elements in forest plantations, which are generally thought to be poor in biodiversity, being aimed at timber production. Based on this premise our aims were 1) to test if cross-taxon congruence across different groups of organisms (bacteria, vascular plants, mushrooms, ectomycorrhizae, mycelium, carabids, microarthropods, nematodes) is consistent in artificial stands; 2) to evaluate the strength of relationships due to the existing environmental gradients as expressed by abiotic and biotic factors (soil, spatial-topographic, dendrometric variables). Correlations between groups were studied with Mantel and partial Mantel tests, while variance partition analysis was applied to assess the relative effect of environmental variables on the robustness of observed relationships. Significant cross-taxon congruence was observed across almost all taxonomic groups pairs. However, only bacteria/mycelium and mushrooms/mycelium correlations remained significant after removing the environmental effect, suggesting that a strong abiotic influence drives species composition. Considering variation partitioning, the results highlighted the importance of bacteria as a potential indicator: bacteria were the taxonomic group with the highest compositional variance explained by the predictors used; furthermore, they proved to be involved in the only cases where the variance attributed solely to the pure effect of biotic or abiotic predictors was significant. Remarkably, the co-dependent effect of all predictors always explained the highest portion of total variation in all dependent taxa, testifying the intricate and dynamic interplay of environmental factors and biotic interactions in explaining cross-taxon congruence in forest plantations.

Can benthic foraminifera serve as proxies for changes in benthic macrofaunal community structure? Implications for the definition of reference conditions

Benthic macrofauna is one of the most widely used biological groups to assess the ecological status of marine systems. Lately, attention has been paid to similar use of benthic foraminifera. In this study, distribution patterns of benthic foraminiferal and macrofaunal species were investigated simultaneously in 11 fjords in southeastern Norway in order to assess correlations and responses to environmental conditions. Selected fjords allowed to investigate contrasted environmental conditions from low total organic carbon (TOC) content (sediment TOC < 2.7%) in normoxia (bottom-water [O₂] > 2 mL O₂.L^-1) up to high TOC content (> 3.4%) in severe hypoxia (< 0.5 mL O₂.L^-1). Environmental parameters comprised bottom-water dissolved oxygen, grain size, total organic carbon, total nitrogen (TN), pigments and depth below threshold (DBT). Foraminiferal and macrofaunal community data were significantly correlated (Procrustes analysis m² = 0.66, p = 0.001). Hence, benthic foraminiferal distribution patterns mirror those of benthic macrofauna. However, as opposed to the foraminifera, macrofauna was not recorded at the most oxygen-depleted stations and, hence, was more sensitive to severe oxygen depletion. With regard to assigning species to ecological groups for ecological quality status assessment, the results suggest that species, e.g. Spiroplectammina biformis (foraminifera), Scalibregma inflatum (macrofauna), may exhibit different ecological requirements depending on their habitat. Considering the observed congruent patterns of benthic foraminifera and macrofauna, palaeo-communities of benthic foraminifera could be used as indicators of reference conditions for benthic macrofaunal community structure. This would however need further developments of algorithms to perform such a translation.

Effectiveness of amphibians as biodiversity surrogates in pond conservation

Amphibian decline has led to worldwide conservation efforts, including the identification and designation of sites for their protection. These sites could also play an important role in the conservation of other freshwater taxa. In 89 ponds in Switzerland, we assessed the effectiveness of amphibians as a surrogate for 4 taxonomic groups that occur in the same freshwater ecosystems as amphibians: dragonflies, aquatic beetles, aquatic gastropods, and aquatic plants. The ponds were all of high value for amphibian conservation. Cross-taxon correlations were tested for species richness and conservation value, and Mantel tests were used to investigate community congruence. Species richness, conservation value, and community composition of amphibians were weakly congruent with these measures for the other taxonomic groups. Paired comparisons for the 5 groups considered showed that for each metric, amphibians had the lowest degree of congruence. Our results imply that site designation for amphibian conservation will not necessarily provide protection for freshwater biodiversity as a whole. To provide adequate protection for freshwater species, we recommend other taxonomic groups be considered in addition to amphibians in the prioritization and site designation process.

The successional pathway of the tree community and how it shapes the fruit-feeding butterfly community in an Afrotropical forest

The relative importance of different bottom-up-mediated effects in shaping insect communities in tropical secondary forests are poorly understood. Here, we explore the roles of vegetation structure, forest age, local topography (valley vs. hill top) and soil variables in predicting fruit-feeding butterfly and tree community composition, and tree community composition in predicting fruit-feeding butterfly community composition, in different-aged naturally regenerating and primary forests of Kibale National Park, Uganda. We also examine which variables are best predictors of fruit-feeding butterfly species richness or diversity. Butterflies (88 species) were sampled with a banana-baited trap and trees (98 taxa) with a 40 × 20-m sampling plot at 80 sampling sites. The environmental variables explained 31% of the variation in the tree community composition, the best predictors being local topography, forest age and cover of Acanthus pubescens (a shrub possibly arresting succession). The fruit-feeding butterfly community composition was better predicted by tree community composition (explaining 10% of the variation) rather than vegetation structure, local topography or soil factors. Environmental variables and tree species richness (or diversity) were poor predictors of butterfly species richness (or diversity). Our results emphasize the importance of tree community to recovery of herbivorous insect communities in tropical secondary forests.

Plant diversity accurately predicts insect diversity in two tropical landscapes

Plant diversity surely determines arthropod diversity, but only moderate correlations between arthropod and plant species richness had been observed until Basset et al. (Science, 338, 2012 and 1481) finally undertook an unprecedentedly comprehensive sampling of a tropical forest and demonstrated that plant species richness could indeed accurately predict arthropod species richness. We now require a high-throughput pipeline to operationalize this result so that we can (i) test competing explanations for tropical arthropod megadiversity, (ii) improve estimates of global eukaryotic species diversity, and (iii) use plant and arthropod communities as efficient proxies for each other, thus improving the efficiency of conservation planning and of detecting forest degradation and recovery. We therefore applied metabarcoding to Malaise-trap samples across two tropical landscapes in China. We demonstrate that plant species richness can accurately predict arthropod (mostly insect) species richness and that plant and insect community compositions are highly correlated, even in landscapes that are large, heterogeneous and anthropogenically modified. Finally, we review how metabarcoding makes feasible highly replicated tests of the major competing explanations for tropical megadiversity.

Disentangling effects of abiotic factors and biotic interactions on cross-taxon congruence in species turnover patterns of plants, moths and beetles

High cross-taxon congruence in species diversity patterns is essential for the use of surrogate taxa in biodiversity conservation, but presence and strength of congruence in species turnover patterns, and the relative contributions of abiotic environmental factors and biotic interaction towards this congruence, remain poorly understood. In our study, we used variation partitioning in multiple regressions to quantify cross-taxon congruence in community dissimilarities of vascular plants, geometrid and arciinid moths and carabid beetles, subsequently investigating their respective underpinning by abiotic factors and biotic interactions. Significant cross-taxon congruence observed across all taxon pairs was linked to their similar responses towards elevation change. Changes in the vegetation composition were closely linked to carabid turnover, with vegetation structure and associated microclimatic conditions proposed causes of this link. In contrast, moth assemblages appeared to be dominated by generalist species whose turnover was weakly associated with vegetation changes. Overall, abiotic factors exerted a stronger influence on cross-taxon congruence across our study sites than biotic interactions. The weak congruence in turnover observed particularly between plants and moths highlights the importance of multi-taxon approaches based on groupings of taxa with similar turnovers, rather than the use of single surrogate taxa or environmental proxies, in biodiversity assessments.

Assessing biodiversity and endemism using phylogenetic methods across multiple taxonomic groups

Identifying geographical areas with the greatest representation of the tree of life is an important goal for the management and conservation of biodiversity. While there are methods available for using a single phylogenetic tree to assess spatial patterns of biodiversity, there has been limited exploration of how separate phylogenies from multiple taxonomic groups can be used jointly to map diversity and endemism. Here, we demonstrate how to apply different phylogenetic approaches to assess biodiversity across multiple taxonomic groups. We map spatial patterns of phylogenetic diversity/endemism to identify concordant areas with the greatest representation of biodiversity across multiple taxa and demonstrate the approach by applying it to the Murray–Darling basin region of southeastern Australia. The areas with significant centers of phylogenetic diversity and endemism were distributed differently for the five taxonomic groups studied (plant genera, fish, tree frogs, acacias, and eucalypts); no strong shared patterns across all five groups emerged. However, congruence was apparent between some groups in some parts of the basin. The northern region of the basin emerges from the analysis as a priority area for future conservation initiatives focused on eucalypts and tree frogs. The southern region is particularly important for conservation of the evolutionary heritage of plants and fishes.

Body size is a significant predictor of congruency in species richness patterns: a meta-analysis of aquatic studies

Biodiversity losses over the next century are predicted to result in alterations of ecosystem functions that are on par with other major drivers of global change. Given the seriousness of this issue, there is a need to effectively monitor global biodiversity. Because performing biodiversity censuses of all taxonomic groups is prohibitively costly, indicator groups have been studied to estimate the biodiversity of different taxonomic groups. Quantifying cross-taxon congruence is a method of evaluating the assumption that the diversity of one taxonomic group can be used to predict the diversity of another. To improve the predictive ability of cross-taxon congruence in aquatic ecosystems, we evaluated whether body size, measured as the ratio of average body length between organismal groups, is a significant predictor of their cross-taxon biodiversity congruence. To test this hypothesis, we searched the published literature and screened for studies that used species richness correlations as their metric of cross-taxon congruence. We extracted 96 correlation coefficients from 16 studies, which encompassed 784 inland water bodies. With these correlation coefficients, we conducted a categorical meta-analysis, grouping data based on the body size ratio of organisms. Our results showed that cross-taxon congruence is variable among sites and between different groups (r values ranging between -0.53 to 0.88). In addition, our quantitative meta-analysis demonstrated that organisms most similar in body size showed stronger species richness correlations than organisms which differed increasingly in size (radj(2) = 0.94, p = 0.02). We propose that future studies applying biodiversity indicators in aquatic ecosystems consider functional traits such as body size, so as to increase their success at predicting the biodiversity of taxonomic groups where cost-effective conservation tools are needed.