Biodiversity metrics on ecological networks: Demonstrated with animal gastrointestinal microbiomes

Biodiversity has become a terminology familiar to virtually every citizen in modern societies.It is said that ecology studies the economy of nature,and economy studies the ecology of humans;then measuring biodiversity should be similar with measuring national wealth.Indeed,there have been many parallels between ecology and economics,actually beyond analogies.For example,arguably the second most widely used biodiversity metric,Simpson(1949)’s diversity index,is a function of familiar Gini-index in economics.One of the biggest challenges has been the high“diversity”of diversity indexes due to their excessive“speciation”-there are so many indexes,similar to each country’s sovereign currency-leaving confused diversity practitioners in dilemma.In 1973,Hill introduced the concept of“numbers equivalent”,which is based on Renyi entropy and originated in economics,but possibly due to his abstruse interpretation of the concept,his message was not widely received by ecologists until nearly four decades later.What Hill suggested was similar to link the US dollar to gold at the rate of$35 per ounce under the Bretton Woods system.The Hill numbers now are considered most appropriate biodiversity metrics system,unifying Shannon,Simpson and other diversity indexes.Here,we approach to another paradigmatic shift-measuring biodiversity on ecological networks-demonstrated with animal gastrointestinal microbiomes representing four major invertebrate classes and all six vertebrate classes.The network diversity can reveal the diversity of species interactions,which is a necessary step for understanding the spatial and temporal structures and dynamics of biodiversity across environmental gradients.

Plant diversity and community history shift colonization success from early- to mid-successional species

Aims Functional traits are supposed to play an important role in deter-mining the colonization success of new species into established communities.short-term experimental studies have documented higher resistance of more diverse grasslands against coloni-zation by new species.However,little is known about which traits colonizers should have to successfully invade diverse plant communities in the longer term and how community his-tory may modify the resistance of diverse communities against colonization.Methods In a grassland biodiversity experiment(Jena Experiment)established with different species richness(s;1,2,4,8 and 16)and functional group(Fg)number and composition(1 to 4;legumes,grasses,small herbs,tall herbs),we studied colonization of naturally dispersed species in split-plots(i)with different duration of weeding(never weeded,weeded for 3 or 6 years and then un-weeded for 1 year)and(ii)with different duration of colonization(7 years,4 years and 1 year after cessation of weeding).Important Findingsresistance against colonization by new species declined with increased duration of weeding(on average 13,17 and 22 col-onizer species in 1-,4-and 7-year-old communities,respec-tively).Communities established at low diversity accumulated more colonizer species with a longer duration of weeding than more diverse communities.Duration of colonization had only small effects on the number of colonizer species.Colonizers with early successional traits,i.e.annual life cycle,reproduction by seeds,small seeds,long-lived seeds and an earlier start of a longer flowering period,were favoured in species-poor newly established experimental plant communities(short duration of weeding)and early after cessation of weeding(short duration of colonization).a change from early-to mid-successional traits,i.e.taller growth,perennial life cycle,vegetative reproduction,characterized colonization at increased plant diversity and in communities with legumes or without grasses.legume absence/grass presence and increased duration of weeding led to a shift in colonizer strategies from rapid nutrient uptake and cycling(higher specific leaf area)to nutrient retention and symbiotic N2 fixation.our study shows that non-random trait spectra of naturally dispersed colonizers encompass trade-offs between different functions(reproduction,persistence,growth)reflected in a change from early-to mid-successional traits at increasing plant diversity,with a longer duration of weeding and a longer time of colonization.

A cautionary note on some phylogenetic dissimilarity measures

Aims Measures of plot-to-plot phylogenetic dissimilarity and beta diversity are providing a powerful tool for understanding the complex ecolog-ical and evolutionary mechanisms that drive community assembly.Methods Here,we review the properties of some previously published dis-similarity measures that are based on minimum or average phylo-genetic dissimilarity between species in different plots.Important Findings We first show that some of these measures violate the basic condi-tion that for two identical plots the measures take the value zero.They also violate the condition that the dissimilarity between two identical plots should always be lower than that between two differ-ent plots.Such erratic behavior renders these measures unsuitable for measuring plot-to-plot phylogenetic dissimilarity.We next pro-pose a new measure that satisfies these conditions,thus providing a more reasonable way for measuring phylogenetic dissimilarity.