Significant Phylogenetic Clustering Research Articles

Functional trait mismatch between native and introduced bee pollinators servicing a global fruit crop

BackgroundUnderstanding connections between biodiversity and ecosystem services can be enhanced by shifting focus from species richness to functional trait-based approaches, that when paired with comparative phylogenetic methods can provide even deeper insights. We investigated the functional ecology and phylogenetic diversity of pollination services provided by hymenopteran insects visiting apple flowers in orchards surrounded by either ‘natural’ or ‘disturbed’ landscapes in New South Wales, Australia. We assessed whether morphological and behavioural traits (hairiness, body size, glossa length, pollen load purity, and probability of loose pollen) exhibited non-random phylogenetic patterns. Then, explored whether bees, the primary pollinators in this system, filled unique or overlapping functional entities (FEs). For each landscape, we calculated phylogenetic diversity and used FEs to assess functional richness, evenness, and diversion.ResultsA phylogenomic matrix based on ultraconserved elements (UCEs; 1,382,620 bp from 1,969 loci) was used to infer a fully-resolved and well-supported maximum likelihood phylogeny for 48 hymenopteran morphospecies. There was no significant difference in species richness between landscape categories. Pollinator communities at natural sites had higher phylogenetic complexity (X = 2.37) and functional divergence (x̄ = 0.74 ± 0.02 s.e.) than disturbed sites (X = 1.65 and x̄ = 0.6 ± 0.01 s.e.). Hairiness showed significant phylogenetic clustering (K = 0.94), whereas body size, glossa length, and loose pollen showed weaker non-random phylogenetic patterns (K between 0.3–0.5). Pollen load purity showed no association with phylogeny. The assemblage of 17 bee morphospecies comprised nine FEs: eight FEs consisted of native bees with three containing 65% of all native bee taxa. The introduced honey bee (Apis mellifera) occupied a unique FE, likely due to its different evolutionary history. Both landscape types supported six FEs each with three overlapping: two native bee FEs and the honey bee FE.ConclusionsBee hairiness was the only functional trait to exhibit demonstrable phylogenetic signal. Despite differences in species richness, and functional and phylogenetic diversity between orchard landscape types, both maintained equal bee FE numbers. While no native bee taxon was analogous to the honey bee FE, four native bee FEs shared the same hairiness level as honey bees. Health threats to honey bee populations in Australia will likely disrupt pollination services to apple, and other pollination-dependent food crops, given the low level of functional redundancy within the investigated pollinator assemblages.

Evolutionary clustering in Neotropical biocultural heritage: the Huastec Mayan useful plants

Abstract Biodiversity in the Neotropics includes an extraordinary diversity of plant variation produced by evolution that is useful for human well-being. Traditional knowledge of the Tenek, a Huastec Mayan culture, represents an important biocultural heritage for this realm. Here, we used the information about their useful plants to explore evolutionary biocultural patterns occurring in Neotropics. Our goal was to analyse the phylogenetic distribution of usage guilds, their degree of evolutionary clustering, significant associations, and phylogenetic overlap between guilds to test the hypothesis that Tenek selection of plants is not random but phylogenetically clustered. We found significant phylogenetic clustering in all usage guilds except ceremonial and medicine. Tenek people use a variety of relatively deep plant lineages providing specific services that biocultural processes have promoted in the ecosystems they inhabit. The lineages Asterales, Caryophyllales, Fabales, Lamiales, Malpighiales, and Malvales in eudicots and Poales and Asparagales in monocots concentrated most of the Huastec Mayan useful plants. Multi-functional hot nodes, including Asterales, Fabales, Lamiales, Malvales, Poaceae Sapindales, and Solanales, with phylogenetic overlap between usage guilds, should be major priority targets in conservation planning.

Cloacal microbiota are biogeographically structured in larks from desert, tropical and temperate areas

BackgroundIn contrast with macroorganisms, that show well-documented biogeographical patterns in distribution associated with local adaptation of physiology, behavior and life history, strong biogeographical patterns have not been found for microorganisms, raising questions about what determines their biogeography. Thus far, large-scale biogeographical studies have focused on free-living microbes, paying little attention to host-associated microbes, which play essential roles in physiology, behavior and life history of their hosts. Investigating cloacal gut microbiota of closely-related, ecologically similar free-living songbird species (Alaudidae, larks) inhabiting desert, temperate and tropical regions, we explored influences of geographical location and host species on α-diversity, co-occurrence of amplicon sequence variants (ASVs) and genera, differentially abundant and dominant bacterial taxa, and community composition. We also investigated how geographical distance explained differences in gut microbial community composition among larks.ResultsGeographic location did not explain variation in richness and Shannon diversity of cloacal microbiota in larks. Out of 3798 ASVs and 799 bacterial genera identified, 17 ASVs (< 0.5%) and 43 genera (5%) were shared by larks from all locations. Desert larks held fewer unique ASVs (25%) than temperate zone (31%) and tropical larks (34%). Five out of 33 detected bacterial phyla dominated lark cloacal gut microbiomes. In tropical larks three bacterial classes were overrepresented. Highlighting the distinctiveness of desert lark microbiota, the relative abundances of 52 ASVs differed among locations, which classified within three dominant and 11 low-abundance phyla. Clear and significant phylogenetic clustering in cloacal microbiota community composition (unweighted UniFrac) showed segregation with geography and host species, where microbiota of desert larks were distinct from those of tropical and temperate regions. Geographic distance was nonlinearly associated with pairwise unweighted UniFrac distances.ConclusionsWe conclude that host-associated microbiota are geographically structured in a group of widespread but closely-related bird species, following large-scale macro-ecological patterns and contrasting with previous findings for free-living microbes. Future work should further explore if and to what extent geographic variation in host-associated microbiota can be explained as result of co-evolution between gut microbes and host adaptive traits, and if and how acquisition from the environmental pool of bacteria contributes to explaining host-associated communities.

Spatial and phylogenetic structure of Alpine stonefly assemblages across seven habitats using DNA-species.

Stream ecosystems are spatially heterogeneous, with many different habitat patches distributed within a small area. The influence of this heterogeneity on the biodiversity of benthic insect communities is well documented; however, studies of the role of habitat heterogeneity in species coexistence and assembly remain limited. Here, we investigated how habitat heterogeneity influences spatial structure (beta biodiversity) and phylogenetic structure (evolutionary processes) of benthic stonefly (Plecoptera, Insecta) communities. We sampled 20 sites along two Alpine rivers, including seven habitats in four different reaches (headwaters, meandering, bar-braided floodplain, and lowland spring-fed). We identified 21 morphological species and delineated 52 DNA-species based on sequences from mitochondrial cox1 and nuclear ITS markers. Using DNA-species, we first analysed the patterns of variation in richness, diversity, and assemblage composition by quantifing the contribution of each reach and habitat to the overall DNA-species diversity using an additive partition analysis and distance-based redundancy analysis. Using gene-tree phylogenies, we assessed whether environmental filtering could lead to the co-occurrence of DNA-species using a two-step analysis to detect a phylogenetic signal. All four reaches significantly contributed to DNA-species richness, with the meandering reach having the highest contribution. Habitats had an effect on DNA-species diversity, where glide, riffle and, pool influenced the spatial structure of stonefly assemblage possibly due to the high habitat heterogeneity. Among the habitats, the pool showed significant phylogenetic clustering, suggesting high levels of evolutionary adaptation and strong habitat filtering. This assemblage structure may be caused by long-term stability of the habitat and the similar requirements for co-occurring species. Our study shows the importance of different habitats for the spatial and phylogenetic structure of stonefly assemblage and sheds light on the habitat-specific diversity that may help improve conservation practices.

Plant community assembly is jointly shaped by environmental and dispersal filtering along elevation gradients in a semiarid area, China.

Environmental filtering (EF) and dispersal filtering (DF) are widely known to shape plant community assembly. Particularly in arid and semi-arid mountainous regions, however, it remains unclear whether EF or DF dominate in the community assembly of different life forms or how they interact along elevational gradients. This research aims to reveal how different ecological processes influence herbaceous and woody community assembly and how they respond to various environmental drivers and elevational gradients. Here we integrated taxonomic diversity (TD), phylogenetic diversity (PD), and ecological drivers across an elevational gradient of 1,420 m in the Helan Mountain Nature Reserve, in typical arid and semi-arid areas of China. This study showed that the TD and PD of herbaceous communities significantly increase linearly with changing elevation gradients, while woody 'TD' showed a unimodal pattern, and there was little relationship between woody 'PD' and elevation. Herbaceous species exhibited significant phylogenetic clustering at low elevations, where they were influenced by climate, aspect, and tree cover. However, woody species exhibited random patterns across elevations. Herbaceous and woody species' taxonomic and phylogenetic beta diversity is governed primarily by spatial turnover rather than nestedness. Spatial turnover is caused primarily by EF and DF's combined influence, but their relative importance differs between herbaceous and woody communities. Therefore, we conclude that the responses of herbaceous and woody plants along elevation gradients in the Helan Mountains are decoupled due to their different adaptation strategies to climate factors in the drylands. These findings are important for understanding the assembly mechanisms driving plant communities in dryland under the context of dramatic increases in drought driven by climate warming.

Evidence for saponin diversity–mycobiome links and conservatism of plant–fungi interaction patterns across Holarctic disjunct Panax species

Although interplays between plant and coevolved microorganisms are believed to drive landscape formation and ecosystem services, the relationships between the mycobiome and phytochemical evolution and the evolutionary characteristics of plant–mycobiome interaction patterns are still unclear. The present study explored fungal communities from 405 multiniche samples of three Holarctic disjunct Panax species. The overall mycobiomes showed compartment-dominated variations and dynamic universality. Neutral models were fitted for each compartment at the Panax genus (I) and species (II) levels to infer the community assembly mechanism and identify fungal subgroups potentially representing different plant–fungi interaction results, i.e., the potentially selected, opposed, and neutral taxa. Selection contributed more to the endosphere than to external compartments. The nonneutral taxa showed significant phylogenetic clustering. In Model I, the opposed subgroups could best reflect Panax saponin diversities (r = 0.69), and genera with highly positive correlations to specific saponins were identified using machine learning. Although mycobiomes in the three species differed significantly, subgroups in Model II were phylogenetically clustered based on potential interaction type rather than plant species, indicating potentially conservative plant–fungi interactions. In summary, the finding of strong links between invaders and saponin diversity can help explore the underlying mechanisms of saponin biosynthesis evolution from microbial insights, which is important to understanding the formation of the current landscape. The potential conservatism of plant–fungi interaction patterns suggests that the related genetic modules and selection pressures were convergent across Panax species, advancing our understanding of plant interplay with biotic environments.

Diet breadth of the aphid predator Chrysoperla rufilabris Burmeister (Neuroptera: Chrysopidae).

The performance (development and reproduction) of generalist predators can vary greatly among the prey species that they use, and these differences can influence the ability of predatory insects to suppress pest populations. The aim of this study was to compare the performance of larvae of the green lacewing Chrysoperla rufilabris (Burmeister, 1839) by offering 16 species of aphids and by assessing the effects of each species on the survival, larval development time, prey consumption, pupal mass and egg load of adult Chr. rufilabris females taking aphid phylogeny into account. Chrysoperla rufilabris larvae preyed on individuals from all 16 aphid species, but complete development, adult emergence and egg load production were achieved only in seven species. As a general pattern, the best levels of performance were achieved for an aphid clade that includes the soybean aphid, Aphis glycines (Matsumara, 1917), and for a milkweed-feeding species, Myzocallis asclepiadis (Monell, 1879). We found significant phylogenetic clustering for most of the performance traits indicating the aspects of specialization in the diet breadth of Chr. rufilabris despite the fact that this species is considered a generalist aphid predator. These findings can help us to understand the interactions of this species in agroecological food webs, where it is commonly found, and provide insights into why natural, conservation biological control or augmentative releases may succeed or fail.

Phylogenies of traits and functions in soil invertebrate assemblages

AbstractSoil invertebrates are members of terrestrial ecosystems, contributing to the processing of organic matter, resulting in carbon and nutrient cycling that is essential for continuous productivity. By linking species delineations, morphological traits and measured or inferred functional roles, we demonstrate a method for functional identification of soil faunal assemblages based on molecular information. Here we align the genetic inter‐relatedness and functional trait expression in nematodes and springtails. Nematodes were assigned feeding guild, plant parasitic feeding type and coloniser‐persister (c‐p) value, with springtail sequences assigned to soil vertical stratification level, soil moisture preference and a selection of morphological traits.We found that both nematode and springtail feeding preferences show significant phylogenetic clustering. In contrast, greater dispersal was found amongst nematode coloniser‐persister (c‐p) values and springtail soil vertical stratification level and moisture preferences. Minimum patristic (p) distances between species supported the clustering amongst nematode feeding guilds, with plant feeders being separated from all other guilds by at least p = 0.99. Distances between endoparasitic, ectoparasitic and sedentary plant parasitic nematodes were also distinct with minimal distances of p = 0.35–0.72 between parasitic types. Springtail stratification level and soil moisture preferences showed greater dispersion across phylogenies, with negligible between‐group minimum patristic distances. However, nematode c‐p values and springtail moisture preference alignments indicate some genetic conservation at the genus level.These results indicate how ecosystems can direct trait conservation beyond that of environmental stimuli. Being able to assign functional traits to novel sequences will allow individual species' likely contribution to ecosystem functioning to be inferred without the need for exact taxonomic identification. More broadly, such information can advance our understanding of the evolution of soil faunal traits and the contribution of diverse soil assemblages to functional soil systems, particularly those with a high proportion of undescribed species.

Phylogenetic signal of sub‐arctic beetle communities

Postglacial dispersal and colonization processes have shaped community patterns in sub‐Arctic regions such as Churchill, Manitoba, and Canada. This study investigates evolutionary community structure within the beetle (Coleoptera) families of Churchill and tests whether biological traits have played a role in governing colonization patterns from refugial and southerly geographic regions. This study quantifies sub‐Arctic beetle phylogenetic community structure for each family using the net relatedness index (NRI) and nearest taxon index (NTI), calculated using publicly available data from the Barcode of Life Data Systems (BOLD); compares patterns across families with different traits (habitat, diet) using standard statistical analysis (ANOVA) as well as phylogenetic generalized least squares (PGLS) using a family‐level beetle phylogeny obtained from the literature; and compares community structure in Churchill with a region in southern Canada (Guelph, Ontario). These analyses were also repeated at a genus level. The dominant pattern detected in our study was that aquatic families were much better represented in Churchill compared to terrestrial families, when compared against richness sampled from across Canada and Alaska. Individually, most families showed significant phylogenetic clustering in Churchill, likely due to the strong environmental filtering present in Arctic environments. There was no significant difference in phylogenetic structure between Churchill and Guelph but with a trend toward stronger clustering in the North. Fungivores were significantly more overdispersed than other feeding modes, predators were significantly more clustered, and aquatic families showed significantly stronger clustering compared to terrestrial. This study contributes to our understanding of the traits and processes structuring insect biodiversity and macroecological trends in the sub‐Arctic.

Loss and Gain of Gut Bacterial Phylotype Symbionts in Afrotropical Stingless Bee Species (Apidae: Meliponinae).

Stingless bees (Apidae: Meliponini) are the most diverse group of corbiculate bees and are important managed and wild pollinators distributed in the tropical and subtropical regions of the globe. However, little is known about their associated beneficial microbes that play major roles in host nutrition, detoxification, growth, activation of immune responses, and protection against pathogens in their sister groups, honeybees and bumble bees. Here, we provide an initial characterization of the gut bacterial microbiota of eight stingless bee species from sub-Saharan Africa using 16S rRNA amplicon sequencing. Our findings revealed that Firmicutes, Actinobacteria, and Proteobacteria were the dominant and conserved phyla across the eight stingless bee species. Additionally, we found significant geographical and host intra-species-specific bacterial diversity. Notably, African strains showed significant phylogenetic clustering when compared with strains from other continents, and each stingless bee species has its own microbial composition with its own dominant bacterial genus. Our results suggest host selective mechanisms maintain distinct gut communities among sympatric species and thus constitute an important resource for future studies on bee health management and host-microbe co-evolution and adaptation.

Phylogenetic restriction of plant invasion in drought-stressed environments: Implications for insect-pollinated plant communities in water-limited ecosystems.

BackgroundPlant–pollinator community diversity has been found to decrease under conditions of drought stress; however, research into the temporal dimensions of this phenomenon remains limited. In this study, we investigated the effect of seasonal drought on the temporal niche dynamics of entomophilous flowering plants in a water‐limited ecosystem. We hypothesized that closely related native and exotic plants would tend to share similar life history and that peak flowering events would therefore coincide with phylogenetic clustering in plant communities based on expected phenological responses of plant functional types to limitations in soil moisture availability.LocationGaliano Island, British Columbia, Canada.MethodsCombining methods from pollinator research and phylogenetic community ecology, we tested the influence of environmental filtering over plant community phenology across gradients of landscape disturbance and soil moisture. Floral resource availability and community structure were quantified by counts of flowering shoots. We constructed a robust phylogeny to analyze spatial and temporal variation in phylogenetic patterns across the landscape, testing the significance of the observed patterns against a randomly generated community phylogeny. Phylogenetic metrics were then regressed against factors of disturbance and soil moisture availability.ResultsCritical seasonal fluctuations in floral resources coincided with significant phylogenetic clustering in plant communities, with decreasing plant diversity observed under conditions of increasing drought stress. Exotic plant species in the Asteraceae became increasingly pervasive across the landscape, occupying a late season temporal niche in drought‐stressed environments.Main conclusionResults suggest that environmental filtering is the dominant assembly process structuring the temporal niche of plant communities in this water‐limited ecosystem. Based on these results, and trends seen elsewhere, the overall diversity of plant–pollinator communities may be expected to decline with the increasing drought stress predicted under future climate scenarios.

The phylogenetic diversity and structure of the seasonally dry forests in the Neotropics

AbstractAimExceptions to the quasi‐ubiquitous latitudinal diversity gradient (LDG) have been poorly studied. A reverse LDG, when species richness (SR) increases away from the Equator, has been suggested for several taxa and entire biomes. The Neotropical seasonally dry tropical forests (SDTF) are a well‐known example of a reverse LDG that could be caused by the climatic stability of Pleistocene Refugia and dispersion from distinct source areas. Here, we test these predictions under a spatial and phylogenetic framework.LocationNeotropics.TaxonWoody plants.MethodsWe used a recent species‐level seed plant phylogeny and the DRYFLOR dataset to evaluate the geographic patterns of phylogenetic diversity (PD) and structure of woody plant assemblages associated with the Neotropical SDTFs. We conducted spatial regressions to test the effect of climatic instability since the Last Glacial Maximum (LGM) on assemblages’ residual PD (controlling for SR) and null model analysis to evaluate their phylogenetic structure using the Net Relatedness Index.ResultsPhylogenetic diversity of the Neotropical SDTFs increased away from the Equator, likely driven by SR. This pattern was not related to climatic instability since the LGM. Phylogenetic structure of SDTF assemblages showed considerable spatial patterning, with significant phylogenetic clustering in the Mesoamerica and Caatinga regions.Main conclusionThe reverse latitudinal SR gradient of the Neotropical SDTF assemblages is mirrored by their PD. Phylogenetic history seems to have influenced such patterns differently across the Neotropics with no relationship to climatic stability since the LGM, where particular SDTF nuclei previously suggested as Pleistocene refugia served as cradles and source areas for the current diversity pattern of the biome.

Belowground fungal community diversity, composition and ecological functionality associated with winter wheat in conventional and organic agricultural systems.

Understanding the impacts of agricultural practices on belowground fungal communities is crucial in order to preserve biological diversity in agricultural soils and enhance their role in agroecosystem functioning. Although fungal communities are widely distributed, relatively few studies have correlated agricultural production practices. We investigated the diversity, composition and ecological functionality of fungal communities in roots of winter wheat (Triticum aestivum) growing in conventional and organic farming systems. Direct and nested polymerase chain reaction (PCR) amplifications spanning the internal transcribed spacer (ITS) region of the rDNA from pooled fine root samples were performed with two different sets of fungal specific primers. Fungal identification was carried out through similarity searches against validated reference sequences (RefSeq). The R package ‘picante’ and FUNGuild were used to analyse fungal community composition and trophic mode, respectively. Either by direct or cloning sequencing, 130 complete ITS sequences were clustered into 39 operational taxonomic units (OTUs) (25 singletons), belonging to the Ascomycota (24), the Basidiomycota (14) and to the Glomeromycota (1). Fungal communities from conventional farming sites are phylogenetically more related than expected by chance. Constrained ordination analysis identified total N, total S and Pcal that had a significant effect on the OTU’s abundance and distribution, and a further correlation with the diversity of the co-occurring vegetation could be hypothesised. The functional predictions based on FUNGuild suggested that conventional farming increased the presence of plant pathogenic fungi compared with organic farming. Based on diversity, OTU distribution, nutrition mode and the significant phylogenetic clustering of fungal communities, this study shows that fungal communities differ across sampling sites, depending on agricultural practices. Although it is not fully clear which factors determine the fungal communities, our findings suggest that organic farming systems have a positive effect on fungal communities in winter wheat crops.

Spatial phylogenetics of the North American flora

AbstractNorth America is a large continent with extensive climatic, geological, soil, and biological diversity. As biota faces threat from habitat destruction and climate change, making a quantitative assessment of biodiversity becomes critically important. Rapid digitization of plant specimen records and accumulation of DNA sequence data enable a much‐needed broad synthesis of species occurrences with phylogenetic data. In this study, the first such synthesis of a flora from such a large and diverse part of the world is attempted, all seed plants from the North American continent (here defined to include Canada, United States, and Mexico), with a focus on examining phylogenetic diversity and endemism. We collected digitized plant specimen records and chose a coarse grain for analysis, recognizing that this grain is currently necessary for reasonable completeness per sampling unit. We found that raw richness and endemism patterns largely support previous hypotheses of biodiversity hotspots. The application of phylogenetic metrics and a randomization test revealed novel results, including a significant phylogenetic clustering across the continent, a striking east–west geographical difference in the distribution of branch lengths, and the discovery of centers of neo‐ and paleoendemism in Mexico, the southwestern USA, and the southeastern USA. Finally, our examination of phylogenetic beta diversity provides a new approach to compare centers of endemism. We discuss the empirical challenges of working at the continental scale and the need for more sampling across large parts of the continent, for both DNA data for terminal taxa and spatial data for poorly understood regions, to confirm and extend these results.

Assembly mechanisms and environmental predictors of the phylogenetic diversity of cricetid rodents in southern Mexico

Understanding the mechanisms that drive the assembly of communities is a central goal in ecology, and phylogenetic approaches allows for the testing of hypotheses related to such mechanisms. We analyzed assembly mechanisms of cricetid rodents in an environmentally heterogeneous region of southern Mexico by assessing their phylogenetic diversity and testing environmental predictors of the phylogenetic structure of local communities. We expected different assembly mechanisms among subprovinces according to their environmental heterogeneity. To test this, we obtained potential communities in cells of 100 km2 by overlapping potential distribution models of 49 species of cricetids. We also estimated a phylogenetic tree using sequences of Cytb obtained from GenBank and used null models to estimate the phylogenetic diversity of communities. We found two phylogenetic diversity patterns: overdispersion in lowlands and clustering in mountains. However, for the majority of the cells, the observed phylogenetic diversity does not differ from that of null models, suggesting that stochastic processes are the main drivers of the Cricetid communities. Only 25% of the communities located in the Sierra Madre de Oaxaca exhibited significant phylogenetic clustering, indicating that habitat filtering structures their composition. According to Generalized Additive Models, all environmental variables (elevation, temperature, precipitation, net primary productivity, and potential evapotranspiration) were highly significant predictors of phylogenetic diversity. Communities at lowest elevations and warmest temperatures showed the highest phylogenetic diversity values. Despite the role of environmental factors and low vagility of cricetids, our results showed that stochastic processes explained the assembly of communities more than deterministic ones, although in mountainous areas habitat filtering was also an outstanding mechanism. This study highlights the importance of including phylogenetic information to understand the mechanisms by which communities of small mammals are assembled.

A survey of the relationship between functional genes and acetaldehyde production characteristics in Streptococcus thermophilus by multilocus sequence typing

Streptococcus thermophilus is an important bacterium used in the production of fermented dairy products. Yogurt with good flavor is preferred by consumers; thus, variation in flavor-formation characteristics among isolates is attracting attention. Here, acetaldehyde production characteristics of 30 isolates were evaluated in parallel with genotyping and multilocus sequence typing of key functional genes involved in acetaldehyde production. The results showed that isolates could be divided into 3 phenotypically distinct groups: high-acetaldehyde-yielding isolates (>10 mg/L), medium-acetaldehyde-yielding isolates (5-10 mg/L) and low-acetaldehyde-yielding (<5 mg/L) based on evaluation of acetaldehyde production during yogurt storage. These groups, distinguishable by phenotypic characteristics, were clustered in corresponding groups based on functional gene multilocus sequence typing analysis. Combining functional gene sequence analysis of 30 Strep. thermophilus isolates with phenotypic evaluation of their flavor-related characteristics (specifically acetaldehyde production) demonstrated that groups of isolates established using genotype data analysis corresponded with groups identified based on their phenotypic traits. Interestingly, the 30 isolates of Strep. thermophilus showed significant phylogenetic clustering in acetaldehyde content by functional gene and acetaldehyde content analysis. A corresponding relationship exists between functional gene phylogenetic clustering and acetaldehyde content variation.

Understorey phylogenetic diversity in thermophilous deciduous forests: overstorey species identity can matter more than species richness

BackgroundUnderstorey vegetation is a key biodiversity component of forest ecosystems. Previous studies examined its relations with the overstorey mainly in terms of taxonomic diversity, composition or productivity. So far, none focused on the phylogenetic aspect, which represents the deepest component of diversity in a community. Here, we explored the relations between overstorey species richness and identity and the phylogenetic structure of the understorey vegetation. As a model system we used a network of 36 plots in thermophilous deciduous forests of central Italy that are part of a European project on forest biodiversity and functions. The plots, characterized by similar site conditions, represent a gradient of overstorey richness from 1 to 4-species mixtures, with variable composition. After surveying the understorey in each plot, measures of phylogenetic diversity and structure (Phylogenetic Diversity, PD; Net Relatedness Index, NRI; and Nearest Taxon Index, NTI) were calculated from a fully resolved seed-plant phylogeny obtained from a ITS-5.8S nrDNA dataset including original sequences from local plant material.ResultsThe resulting understorey phylogenetic tree allowed reliable estimation of PD, NRTI and NTI. Phylogenetic diversity was dependent on species richness and the strength of this relationship did not change along the gradient of overstorey tree species richness. Net Relatedness and Nearest Taxon indices were both mostly positive but non-significant, indicating random phylogenetic structure of the understorey. The presence of Quercus petraea, usually found in more favorable site conditions, was associated with a significant phylogenetic clustering at the species level.ConclusionsOverstorey species richness was not related to understorey phylogenetic structure, while species identity (Q. petraea) was associated with an increase in evolutionary relatedness in this forest layer, possibly due to competitive exclusion in favorable site conditions. Further studies should examine whether and how understory phylogenetic structure is affected by variables such as small scale variations in site conditions and presence of a shrub layer, both present but not accounted for in our model system. A better understanding of the role of these variables and their interaction may contribute to fill the current gap between the theoretical field of phylogenetic ecology and forest management.

Barcoding of estuarine macrophytes and phylogenetic diversity of estuaries along the South African coastline.

Plant DNA barcoding serves as an effective approach to building community phylogenies and increasing our understanding of the factors that determine plant community assemblages. The aims of the study were to (i) barcode macrophytes with high estuarine fidelity and (ii) to determine the phylogenetic diversity (PD) of selected South African estuaries for conservation prioritisation. Three DNA barcoding gene regions (rbcLa, matK, and trnH-psbA) were assessed, and community phylogenies were constructed for 270 estuaries. Generally, the matK barcode had the greatest discrimination success rate of 67.4% (parsimony informative sites = 418). Closely related species formed clades that also represent estuarine habitat types. Estuaries with high phylogenetic diversity along the southeast coast were associated with a combination of mangrove and salt marsh habitats. Species richness was strongly and significantly correlated with PD (r = 0.93; p < 0.000). Based on mean pairwise distance (MPD), more temperate estuaries (56) showed significant phylogenetic clustering compared to subtropical estuaries (24) (p < 0.05). Similarly, based on mean nearest taxon distance (MNTD), significant phylogenetic clustering was highest in temperate estuaries (50) compared to subtropical estuaries (12) (p < 0.05). This suggests that the coexistence of plant species in estuaries is structured by both biotic and abiotic interactions.

The insect-focused classification of fruit syndromes in tropical rain forests: An inter-continental comparison

We propose a new classification of rainforest plants into eight fruit syndromes, based on fruit morphology and other traits relevant to fruit-feeding insects. This classification is compared with other systems based on plant morphology or traits relevant to vertebrate fruit dispersers. Our syndromes are based on fruits sampled from 1,192 plant species at three Forest Global Earth Observatory plots: Barro Colorado Island (Panama), Khao Chong (Thailand) and Wanang (Papua New Guinea). The three plots differed widely in fruit syndrome composition. Plant species with fleshy, indehiscent fruits containing multiple seeds were important at all three sites. However, in Panama a high proportion of species had dry fruits, while in New Guinea and Thailand, species with fleshy drupes and thin mesocarps were dominant. Species with dry, winged seeds that do not develop as capsules were important in Thailand, reflecting the local importance of Dipterocarpaceae. These differences can also determine differences among frugivorous insect communities. Fruit syndromes and colours were phylogenetically flexible traits at the scale studied, as only three of the eight seed syndromes, and one of the 10 colours, showed significant phylogenetic clustering at either genus or family levels. Plant phylogeny was, however, the most important factor explaining differences in overall fruit syndrome composition among individual plant families or genera across the three study sites.

Empirical test of the native–nonnative distinction: Native and nonnative assemblages of Anolis lizards are similar in morphology and phylogeny

Abstract Nonnative (“invasive,” “exotic,” “naturalized”) species frequently are vilified. However, some philosophers and ecologists have questioned whether nonnative species and assemblages are objectively, ahistorically identifiable as different entities relative to native species and assemblages, once selection biases are taken into account. We used an unprecedented dataset of morphology, phylogeny and assemblage content for 336 species of Anolis lizard to compare morphological and phylogenetic characteristics of variability and central tendency between native assemblages and those that include nonnative species. Equivalence tests demonstrated significant similarity between native and nonnative assemblages in trait variability, phylogenetic dispersion and mean trait values except for body size; logistic and zero‐inflated regression failed to distinguish native and nonnative assemblages. For most traits, similarity was not due to assemblages being structured randomly but rather to both native and nonnative assemblages including similar species. Without historical information, a naïve observer would be unable to identify Anolis assemblages as native or nonnative based on morphological assemblage structure or most mean assemblage trait values, but would have some success categorizing assemblages based on average body size of species in the assemblage. Significant phylogenetic and morphological clustering in native assemblages likely reflects source pools composed of close relatives that share traits, as well as some environmental filtering effects; the slightly less phylogenetically clustered but equally morphologically clustered nonnative assemblages are less constrained to proximal source pools but still probably subject to filtering. Differences between native and nonnative assemblages in mean body size likely reflect assemblage youth. The ontological status of nonnative species is discussed in the light of these results. A plain language summary is available for this article.