The genetic equidistance result:misreading by the molecular clock and neutral theory and reinterpretation nearly half of a century later

In 1963,Margoliash discovered the unexpected genetic equidistance result after comparing cytochrome c sequences from different species.This finding,together with the hemoglobin analyses of Zuckerkandl and Pauling in 1962,directly inspired the ad hoc molecular clock hypothesis.Unfortunately,however,many biologists have since mistakenly viewed the molecular clock as a genuine reality,which in turn inspired Kimura,King,and Jukes to propose the neutral theory of molecular evolution.Many years of studies have found numerous contradictions to the theory,and few today believe in a universal constant clock.What is being neglected,however,is that the failure of the molecular clock hypothesis has left the original equidistance result an unsolved mystery.In recent years,we fortuitously rediscovered the equidistance result,which remains unknown to nearly all researchers.Incorporating the proven virtues of existing evolutionary theories and introducing the novel concept of maximum genetic diversity,we proposed a more complete hypothesis of evolutionary genetics and reinterpreted the equidistance result and other major evolutionary phenomena.The hypothesis may rewrite molecular phylogeny and population genetics and solve major biomedical problems that challenge the existing framework of evolutionary biology.

Age structure in neutral theory resolves inconsistencies related to reproductive-size threshold

Aims Neutral theory consists of a suite of models that assume ecological equivalence among individual organisms.They have been most commonly applied to tropical forest tree communities either as null models or as approximations.Neutral models typically only include reproductive adults;therefore,fitting to empirical tree community data requires defining a reproductive-size threshold,which for trees is usually set arbitrarily to a diameter at breast height(DBH)of 100 mm.The inevitable exclusion of some reproductive adults and inclusion of some saplings cause a non-random sampling bias in neutral model fits.Here,we investigate this problem and resolve it by introducing simple age structure into a neutral model.Methods We compared the performance and sensitivity of DBH threshold of three variants of a spatially explicit neutral model:the traditional model,a model incorporating random sampling and a model with two distinct age classes—reproductive adults and saplings.In the age-structured model,saplings are offspring from adults that disperse according to a Gaussian dispersal kernel around the adults.The only extra parameter is the ratio of adults to saplings,which is not a free parameter but directly measurable.We used species–area relationships(SARs)to explore the predicted effect of saplings on the species richness at different scales in our model.We then evaluated the three model variations to find the parameters required to maintain the observed level of species richness in the 50-ha plot on Barro Colorado Island(BCI).We repeated our analysis filtering the data at different minimum tree-size thresholds in order to find the effect this threshold has on our results.Lastly,we used empirical species–individual relationships(SIRs)to test the pre-existing hypothesis that environmental filtering is the primary cause of differences between the assemblage of saplings and that of adults on BCI.Important Findings Our age-structured neutral model was characterized by SARs that were insensitive to the presence of saplings at large scales and highly sensitive to them at small scales.Both models without age structure were highly sensitive to the DBH threshold chosen in a way that could not be explained based on random samplings alone.The age-structured neutral model,which allowed for non-random sampling based on life stage,was consistent with species richness observations.Our analysis of empirical SIRs did not support environmental filtering as a dominant force,but it did show evidence for other differences between age classes.Age can now be easily incorporated into future studies of neutral models whenever there is a concern that a sample is not entirely composed of reproductive adult individuals.More generally,we suggest that modeling studies using tree data subject to a minimum size threshold should consider the sensitivity of their results to that threshold.

Neutral theory in community ecology

One of the central goals of community ecology is to understand the forces that maintain species diversity within communities.The traditional niche-assembly theory asserts that species live together in a community only when they differ from one another in resource uses.But this theory has some difficulties in explaining the diversity often observed in specie-rich communities such as tropical forests.As an alternative to the niche theory,Hubbell and other ecologists introduced a neutral model.Hubbell argues that the number of species in a community is controlled by species extinction and immigration or speciation of new species.Assuming that all individuals of all species in a trophically similar com-munity are ecologically equivalent,Hubbell’s neutral theory predicts two important statistical distributions.One is the asymptotic log-series distribution for the metacommunities under point mutation speciation,and the other is the zero-sum multinomial distribution for both local communities under dispersal limitation and metacommunities under random fission speciation.Unlike the niche-assembly theory,the neutral theory takes similarity in species and individuals as a starting point for investigating species diversity.Based on the fundamental processes of birth,death,dispersal and spe-ciation,the neutral theory provided the first mechanistic explanation of species abundance distribution commonly observed in natural communities.Since the publication of the neutral theory,there has been much discussion about it,pro and con.In this paper,we summarize recent progress in the assumption,prediction and speciation mode of the neutral theory,including progress in the theory itself,tests about the assumption of the theory,prediction and speciation mode at the metacommunity level.We also suggest that the most important task in the future is to bridge the niche-assembly theory and the neutral theory,and to add species differences to the neutral theory and more stochasticity to the niche theory.

Nestedness of bird assemblages in the karst forest fragments of southwestern Guangxi, China

The limestone region in southwestern Guangxi contains the most typical karst landforms in the world. Due to their destruction, the original forests mainly survive in nature reserves in the form of fragmented areas. From June 2009 to September 2010 we conducted an investigation of 13 relatively isolated habitats or sites, selected from each of the 13 nature reserves in southwestern Guangxi, with the least amount of anthropological activity and the largest presence of the original vegetation, in order to study the distribution of birds on forest fragments. The distribution patterns of the birds and the factors which affect them were analyzed by using the 'BINMATNEST' software and the Spearman’s rank correlation analysis, to determine: 1) whether nested patterns of birds in the karst area of southwestern Guangxi exist or not and 2) which factors are correlated with the nested patterns and the effect of these factors on forming nested patterns. The results show that the birds had statistically significant nested patterns in the karst area and the specificity of the habitat of the birds had a significant effect on the nested patterns. We suggest possible reasons for these results, based on the characteristics of the seasonal tropical rain forests in the study area and on neutral theory. We also urgently recommend that close attention be paid to the protection of the diversity of the environment for birds in all fragmented habitats.

Integrity of Four Theories on Natural Selection Unit

[Objective] The aim was to study the internal relationship of the four theories on natural selection unit. [Method] The value field of fitness of heterozygote was investigated by constructing mathematical models, to clarify the internal relations of the four theories on natural selection unit. [Result] According to mathematical modes constructed in the study, only the mutated genes meet the requirements of natural selection on heterozygous and homozygous aspects, as well as show high fitness in heterozygous condition, could the mutated genes be kept, giving consideration to both individual and population adaptation. Thus, this methodology theoretically inte- grates the theories of individual selection, collective selection, and genetic selection as well as Kimura＇s neutral theory of health information. [Conclusion] The result of this study suggested that the four theories on natural selection unit can co-exist, and share common premises.

Multi-scale analysis on species diversity within a 40-ha old-growth temperate forest

In order to better explore the maintenance mechanisms of biodiversity, data collected from a 40-ha undisturbed Pinus forest were applied to the Individual Species-Area Relationship model(ISAR) to determine distribution patterns for species richness. The ecological processes influencing species abundance distribution patterns were assessed by applying the same data set to five models: a LogNormal Model(LNM), a Broken Stick Model(BSM), a Zipf Model(ZM), a Niche Preemption Model(NPM), and a Neutral Model(NM). Each of the five models was used at six different sampling scales(10 m×10 m, 20 m×20 m, 40 m×40 m, 60 m×60 m, 80 m×80 m, and 100 m×100 m). Model outputs showed that:(1) Accumulators and neutral species strongly influenced species diversity, but the relative importance of the two types of species varied across spatial scales.(2) Distribution patterns of species abundance were best explained by the NPM at small scales(10 m-20 m), whereas the NM was the best fit model at large spatial scales.(3) Species richness and abundance distribution patterns appeared to be driven by similar ecological processes. At small scales, the niche theory could be applied to describe species richness and abundance, while at larger scales the neutral theory was more applicable.

Coexistence of nearly neutral species

Aims The neutral theory of biodiversity provides a powerful framework for modeling macroecological patterns and interpreting species assemblages.However,there remain several unsolved problems,including the effect of relaxing the assumption of strict neutrality to allow for empirically observed variation in vital rates and the‘problem of time’—empirically measured coexistence times are much shorter than the prediction of the strictly neutral drift model.Here,we develop a nearly neutral model that allows for differential birth and death rates of species.This model provides an approach to study species coexistence away from strict neutrality.Methods Based on Moran’s neutral model,which assumes all species in a community have the same competitive ability and have identical birth and death rates,we developed a model that includes birth–death trade-off but excludes speciation.This model describes a wide range of asymmetry from strictly neutral to nearly neutral to far from neutral and is useful for analyzing the effect of drift on species coexistence.Specifically,we analyzed the effects of the birth–death trade-off on the time and probability of species coexistence and quantified the loss of biodiversity(as measured by Simpson’s diversity)due to drift by varying species birth and death rates.Important Findings We found(i)a birth–death trade-off operating as an equalizing force driven by demographic stochasticity promotes the coexistence of nearly neutral species.Species near demographic trade-offs(i.e.fitness equivalence)can coexist even longer than that predicted by the strictly neutral model;(ii)the effect of birth rates on species coexistence is very similar to that of death rates,but their compensatory effects are not completely symmetric;(iii)ecological drift over time produces a march to fixation.Trade-off-based neutral communities lose diversity more slowly than the strictly neutral community,while non-neutral communities lose diversity much more rapidly;and(iv)nearly neutral systems have substantially shorter time of coexistence than that of neutral systems.This reduced time provides a promising solution to the problem of time.

Beyond neutrality:adding habitat filtering to neutral models

Background:Understanding the processes that structure species is one of the primary focuses in community ecology.Hubbell’s neutral model shows stochastic processes alone can describe the two macro-ecological patterns,species richness and species-area relationship,of the community.Although Hubbell’s neutral model can explain the macro-ecological patterns of the species at large scales,it paid less attention to construct the spatial structure of the community.Previous studies suggest that such spatial structures are mostly due to habitat filtering processes work at the intermediate spatial scales.Therefore,Hubbell’s neutral model does not explain the full picture of the community structuring due to its fully stochastic nature.Results:In this study,we proposed a two-schema model that has the habitat filtering component and the stochastic component to construct the species assemblages seen in the community level.The proposed model uses one additional parameter(i.e.number of individuals in habitat)in addition to Hubbell’s three-parameter neutral model(i.e.fundamental bio-diversity number(θ),dispersal limitation(m)and speciation(v)).The proposed model works at two spatial scales:habitat filtering at the intermediate scales and stochastic processes at the large and very small spatial scales.The model coupled the local community dynamics with the meta-community dynamics.The local community has a fixed area with carrying capacity that is proportional to the local community size.The number of habitats in the proposed model can vary.Individuals are placed into habitats with probabilities according to the habitat suitability.Species richness and species composition in each habitat were calculated.The model is fitted for differentθvalues,m values,and a different number of habitats.Conclusions:We assume that habitat filtering plays an important role together with stochastic processes to structure species in forests.Therefore,the proposed model with only four parameters can explain a large proportion of the species structuring of the communities.We found that more species can be maintained in a heterogeneous environment than a uniform environment.Therefore,habitat conservation is highly important for maintaining species diversity in forest communities.

Primate phylogeny:molecular evidence for a pongid clade excluding humans and a prosimian clade containing tarsiers

Unbiased readings of fossils are well known to contradict some of the popular molecular groupings among primates,particularly with regard to great apes and tarsiers.The molecular methodologies today are however flawed as they are based on a mistaken theoretical interpretation of the genetic equidistance phenomenon that originally started the field.An improved molecular method the 'slow clock' was here developed based on the Maximum Genetic Diversity hypothesis,a more complete account of the unified changes in genotypes and phenotypes.The method makes use of only slow evolving sequences and requires no uncertain assumptions or mathematical corrections and hence is able to give definitive results.The findings indicate that humans are genetically more distant to orangutans than African apes are and separated from the pongid clade ～17.6 million years ago.Also,tarsiers are genetically closer to lorises than simian primates are.Finally,the fossil times for the radiation of mammals at the K/T boundary and for the Eutheria-Metatheria split in the Early Cretaceous were independently confirmed from molecular dating calibrated using the fossil split times of gorilla-orangutan,mouse-rat,and opossum-kangaroo.Therefore,the re-established primate phylogeny indicates a remarkable unity between molecules and fossils.

Dispersal and recruitment limitation contribute differently to community assembly

Aims The neutral theory of biodiversity has been criticized for being fragile with even slight deviations from its basic assumption of equal fitness among species.In response to this criticism,Hubbell((2001)The Unified Neutral Theory of Biodiversity and Biogeography.Princeton,NJ:Princeton University Press)proposed that competitive exclusion can be infinitely delayed by dispersal and recruitment limitation,thus making species effectively neutral.But the theoretical foundation for this claim still remains unclear and controversial,and the effects of dispersal and recruitment limitation are often confounded,especially in field studies.This study aims to provide an affirmative theoretical answer to the question of whether dispersal limitation and recruitment limitation can separately or jointly overwhelm the effects of fitness differences among species and lead to neutral community dynamics.Methods Computer simulations were used to investigate the effects of dispersal and recruitment limitation on delaying competitive exclusion in a homogeneous habitat in a spatially explicit context.Important Findings We found that even a slight competitive asymmetry would require extremely strong dispersal and recruitment limitation for neutrality to emerge.Most importantly,when the effects of dispersal and recruitment limitation were set apart,it is found that recruitment limitation is more effective in delaying competitive exclusion,whereas dispersal limitation tends to have a stronger impact on the general shape of both species abundance distributions and species–area relationships.

Experimental evidence that soil heterogeneity enhances plant diversity during community assembly

Aims Environmental heterogeneity is a primary mechanism explain-ing species coexistence and extant patterns of diversity.Despite strong theoretical support and ample observational evidence,few experimental studies in plant communities have been able to demonstrate a causal link between environmental heterogene-ity and plant diversity.This lack of experimental evidence sug-gests that either fine-scale heterogeneity has weak effects on plant diversity or previous experiments have been unable to effectively manipulate heterogeneity.Here,we utilize a unique soil manipu-lation to test whether fine-scale soil heterogeneity will increase plant richness through species sorting among experimental patch types.Methods This experiment was conducted in the tallgrass prairie region of south-central Kansas,USA.We utilized the inherent variation found in the vertical soil profile,which varied in both biotic and abiotic characteristics,and redistributed these strata into either homoge-neous or heterogeneous spatial arrangements in 2.4×2.4 m plots.After the soil manipulation,34 native prairie species were sown into all plots.We conducted annual censuses at peak biomass to quantify species composition and plant density by species within the experimental communities.Important Findings After 2 years,species richness was significantly higher in heteroge-neous relative to homogeneous plots and this pattern was independ-ent of total plant density.In the heterogeneous plots,13 species had higher establishment in a specific patch type representing one of the three soil strata.Conversely,no species had greater estab-lishment in the mixed stratum,which comprised the homogene-ous plots,relative to the heterogeneous strata.These species sorting patterns suggest that fine-scale heterogeneity creates opportunities for plant establishment due to niche differences,which translates into increased plant diversity at the plot scale.Species richness was more strongly related to plant density among patches comprising homogenous plots-where fine-scale heterogeneity was minimized,but weak in heterogeneous plots.This pattern is consistent with the idea that richness-density relationships dominate when neutral pro-cesses are important but are weak when niche processes operate.Unlike many previous attempts,our results provide clear,experi-mental evidence that fine-scale soil heterogeneity increases species richness through species sorting during community assembly.

Demographic trade-offs determine species abundance and diversity

Aims Much recent theory has focused on the role of neutral processes in assembling communities,but the basic assumption that all species are demographically identical has found little empirical support.Here,we show that the framework of the current neutral theory can easily be generalized to incorporate species differences so long as fitness equivalence among individuals is maintained through trade-offs between birth and death.Methods Our theory development is based on a careful reformulation of the Moran model of metacommunity dynamics in terms of a non-linear one-step stochastic process,which is described by a master equation.Important Findings We demonstrate how fitness equalization through demographic trade-offs can generate significant macroecological diversity patterns,leading to a very different interpretation of the relation between Fisher’s a and Hubbell’s fundamental biodiversity number.Our model shows that equal fitness(not equal demographics)significantly promotes species diversity through strong selective sieving of community membership against high-mortality species,resulting in a positive association between species abundance and per capita death rate.An important implication of demographic trade-off is that it can partly explain the excessively high speciation rates predicted by the neutral theory of the stronger symmetry.Fitness equalization through demographic trade-offs generalizes neutral theory by considering heterospecific demographic difference,thus representing a significant step toward integrating the neutral and niche paradigms of biodiversity.

Stochastic processes play more important roles in driving the dynamics of rarer species

Aims One major goal of modern community ecology is to understand how deterministic and stochastic processes combine to drive community assembly.However,little empirical knowledge is known about how their relative importance varies between common and rare species.Methods We exploited two 30-year data sets of plant communities in a temperate steppe using two different methods.One is a null model method,and the other is a recently developed direct-calculation method.Important Findings We found that stochastic processes tended to be more important in influencing rare than common species.This finding suggests that stochastic forces may play a more important role in structuring communities with more rare species,providing a possible solution to the debate on the varied importance of deterministic and stochastic processes among different communities.

Point process models, the dimensions of biodiversity and the importance of small-scale biotic interactions

Aims Recent mechanistic explanations for community assembly focus on the debates surrounding niche-based deterministic and dispersalbased stochastic models.This body of work has emphasized the importance of both habitat filtering and dispersal limitation,and many of these works have utilized the assumption of species spatial independence to simplify the complexity of the spatial modeling in natural communities when given dispersal limitation and/or habitat filtering.One potential drawback of this simplification is that it does not consider species interactions and how they may influence the spatial distribution of species,phylogenetic and functional diversity.Here,we assess the validity of the assumption of species spatial independence using data from a subtropical forest plot in southeastern China.Methods We use the four most commonly employed spatial statistical models—the homogeneous Poisson process representing pure random effect,the heterogeneous Poisson process for the effect of habitat heterogeneity,the homogenous Thomas process for sole dispersal limitation and the heterogeneous Thomas process for joint effect of habitat heterogeneity and dispersal limitation—to investigate the contribution of different mechanisms in shaping the species,phylogenetic and functional structures of communities.Important Findings Our evidence from species,phylogenetic and functional diversity demonstrates that the habitat filtering and/or dispersal-based models perform well and the assumption of species spatial independence is relatively valid at larger scales(50×50 m).Conversely,at local scales(10×10 and 20×20 m),the models often fail to predict the species,phylogenetic and functional diversity,suggesting that the assumption of species spatial independence is invalid and that biotic interactions are increasingly important at these spatial scales.

Large-scale spatial synchrony and the stability of forest biodiversity revisited

Aims Mechanisms contributing to species coexistence have at least one of two modes of action:(i)stabilization of populations through restoring forces and(ii)equalization of fitness across individuals of different species.Recently,ecologists have begun gleaning the relative roles of these by testing the predictions of neutral theory,which predicts the properties of communities under pure fitness equalization.This null hypothesis was rejected for forests of southern Ontario based on large-scale(;100 km)spatial synchrony evident in the fossil pollen record over the entire Holocene,and the argument that a species’relative abundance would instead vary independently at such distances in the absence of stabilizing mechanisms.This test of neutral theory was criticized based on the idea that the synchrony might be produced by dispersal alone.Here,I revisit this test of neutral theory by explicitly calculating the synchrony expected in these forests using a novel simulation method enabling examination of the distribution of a species over large spatial and temporal scales.Methods A novel neutral simulation algorithm tracking only the focal species was used to calculate the neutral expectation for spatial synchrony properties examined empirically by Clark and MacLachlan[(2003)Stability of forest biodiversity.Nature 423:635–8]using fossil pollen data from eight lake sites.The coefficient of variation(CV)in a species’relative abundance across the eight sites(initiated at about 10%with a small CV)was calculated for 10 runs over a 10000 year time interval.The CV reflects the level of spatial synchrony in that less synchronous dynamics should lead to more variation across space(a higher equilibrium CV),and in particular,a greater increase in the CV over time from a small initial value.A‘two dimensional t’fat-tailed dispersal kernel was assumed with parameters set to the median derived from seed trap data for deciduous wind-dispersed trees.Robustness of results to assumed dispersal distance,density of trees on the landscape,site sizes,age at maturity and starting spatial distribution were checked.Important Findings In contrast to the prediction of Clark and MacLachlan that,in the absence of stabilization,the CV across the sites should increase over time from levels observed at the beginning of the Holocene,under fat-tailed dispersal my neutral model robustly predicted only a brief(50 years)and small increase in the CV.I conclude that purely fitnessequalized species coexistence cannot be rejected based on the observed lack of increase in the CV across the eight sites in southern Ontario over the Holocene.Synchronous variation in environmental factors could alternatively explain the observed synchrony without the need for stabilization.However,neither dispersal nor environmental synchrony seems likely explanations for the quick widespread recovery of Tsuga in the Holocene after its seeming decimation,likely due to a pest outbreak.