scholarly journals Expected differences in diversity and rarity between communities containing sexually versus asexually reproducing taxa

2018 ◽  
Author(s):  
Cristina M. Herren
Keyword(s):  
Confounding Factor ◽  
Empirical Studies ◽  
Emergent Properties ◽  
Extinction Rate ◽  
Mate Finding ◽  
Markov Chain Models ◽  
Macro Scale ◽  
Population Sizes ◽  
Mate Limitation ◽  
Emergent Community

AbstractRecent studies evaluating the community structures of microorganisms and macro-organisms have found greater diversity and rarity within micro-scale communities, compared to macro-scale communities. However, reproductive method has been a confounding factor in these comparisons; the microbes considered generally reproduce asexually, while the macro-organisms considered generally reproduce sexually. Sexual reproduction imposes the constraint of mate finding, which can have significant demographic consequences by depressing birth rates at low population sizes. Here, I examine theoretically how the effects of mate finding in sexual populations translate to the emergent community properties of diversity, rarity, and dominance. Using continuous-time Markov chain models, I compare communities with and without constraints of mate limitation. In mate-limited sexual populations, the decreased growth rates at low population densities translates to a much higher extinction rate. In communities consisting of sexually reproducing taxa, the increased extinction rate due to mate limitation decreases expected diversity. Furthermore, mate limitation has a disproportionately strong effect on taxa with low population density, leading to fewer rare taxa. These shifts in community structure mirror recent empirical studies of micro versus macro communities, indicating that reproductive method may contribute to observed differences in emergent properties between communities at these two scales.

scholarly journals Asexual Reproduction Can Account for the High Diversity and Prevalence of Rare Taxa Observed in Microbial Communities

2019 ◽  
Vol 85 (15) ◽  
Author(s):  
Cristina M. Herren
Keyword(s):  
Microbial Communities ◽  
Asexual Reproduction ◽  
Growth Rates ◽  
Extinction Rate ◽  
Population Densities ◽  
Mate Finding ◽  
Rare Taxa ◽  
Micro Scale ◽  
Macro Scale ◽  
Mate Limitation

ABSTRACTRecent studies evaluating the community structures of microorganisms and macroorganisms have found greater diversity and rarity within micro-scale communities, compared to macro-scale communities. However, reproductive method has been a confounding factor in these comparisons; the microbes considered generally reproduce asexually, while the macroorganisms considered generally reproduce sexually. Sexual reproduction imposes the constraint of mate finding, which can have significant demographic consequences by depressing birth rates at low population sizes. First, I construct an island biogeography model to study the organization of ecological communities under neutral stochastic processes. Then, I examine theoretically how the effects of mate finding in sexual populations translate to the emergent community properties of diversity, rarity, and dominance (size of the largest population). In mate-limited sexual populations, the decreased growth rates at low population densities translate to a higher extinction rate; this increased extinction rate had a disproportionately strong effect on taxa with low population densities. Thus, mate limitation decreased diversity, primarily by excluding small populations from communities. However, the most abundant taxa were minimally affected by mate limitation. Therefore, mate limitation affected the diversity and rarity of taxa in communities but did not alter the dominance of the largest population. The observed shifts in community structure mirror recent empirical studies of micro-scale versus macro-scale communities, which have shown that microbial communities have greater diversity and rarity than macrobial communities but are not different in dominance. Thus, reproductive method may contribute to observed differences in emergent properties between communities at these two scales.IMPORTANCEThere have been numerous recent efforts to integrate microbes into broad-scale ecological theories. Microbial communities are often structurally distinct from macrobial communities, but it is unclear whether these differences are real or whether they are due to the different methodologies used to study communities at these two scales. One major difference between macroorganisms and microorganisms is that microbes are much more likely to reproduce asexually. Sexually reproducing taxa have diminished growth rates at low population size, because they must encounter another member of their species before reproducing. This study shows that communities of asexually reproducing taxa are expected to be more diverse, because taxa persist longer. Furthermore, asexually reproducing taxa can exist at much lower densities than sexually reproducing taxa. Thus, asexual reproduction by microbes can account for two major differences between microbial and macrobial communities, namely, greater diversity and greater prevalence of rare taxa for microbes.

Genetics of reintroduced populations of the narrowly endemic thistle, Cirsium pitcheri (Asteraceae)

Botany ◽  
2013 ◽  
Vol 91 (5) ◽  
pp. 301-308 ◽  
Author(s):  
Jeremie B. Fant ◽  
Andrea Kramer ◽  
Eileen Sirkin ◽  
Kayri Havens
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Empirical Studies ◽  
Small Population ◽  
Native Plant ◽  
Effective Population ◽  
Term Survival ◽  
Inbreeding Coefficients ◽  
Native Populations ◽  
Population Sizes

The aim of any reintroduction is to provide sufficient genetic variability to buffer against changing selection pressures and ensure long-term survival. To date, few empirical studies have compared levels of genetic diversity in reintroduced and native plant populations. Using microsatellite markers, we measured the genetic diversity within reintroduced and native populations of the threatened Cirsium pitcher (Eaton) Torrey and Gray. We found that the use of local mixed source was successful in establishing populations with significantly higher genetic diversity (P < 0.005) than the native populations (allelic richness is 3.39 in reintroduced and 1.84 in native populations). However, the reintroduced populations had significantly higher inbreeding coefficients (P < 0.002) (FIS is 0.405 and 0.213 in reintroduced and in native populations, respectively), despite having multiple genetic founders, population sizes equivalent to native populations and a positive growth rate. These results may be due to inbreeding or the Wahlund effect, driven by genetic substructuring. This suggests that the small population size of these reintroduced populations may lead to genetic issues in the future, given the low number of flowering individuals each year. This highlights the importance of considering not only the number of source individuals but the effective population size of the reintroduction.

scholarly journals Universal structure motifs in biominerals: a lesson from nature for the efficient design of bioinspired functional materials

2017 ◽  
Vol 7 (4) ◽  
pp. 20160120 ◽  
Author(s):  
Joe Harris ◽  
Corinna F. Böhm ◽  
Stephan E. Wolf
Keyword(s):  
Composite Structure ◽  
Functional Materials ◽  
Structural Diversity ◽  
Emergent Properties ◽  
Efficient Design ◽  
Link Type ◽  
Macro Scale ◽  
Scale Properties ◽  
Universal Structure ◽  
Design Motifs

Biominerals are typically indispensable structures for their host organism in which they serve varying functions, such as mechanical support and protection, mineral storage, detoxification site, or as a sensor or optical guide. In this perspective article, we highlight the occurrence of both structural diversity and uniformity within these biogenic ceramics. For the first time, we demonstrate that the universality–diversity paradigm, which was initially introduced for proteins by Buehler et al . (Cranford & Buehler 2012 Biomateriomics ; Cranford et al. 2013 Adv. Mater. 25 , 802–824 ( doi:10.1002/adma.201202553 ); Ackbarow & Buehler 2008 J. Comput. Theor. Nanosci. 5 , 1193–1204 ( doi:10.1166/jctn.2008.001 ); Buehler & Yung 2009 Nat. Mater. 8 , 175–188 (doi:10.1038/nmat2387)), is also valid in the realm of biomineralization. A nanogranular composite structure is shared by most biominerals which rests on a common, non-classical crystal growth mechanism. The nanogranular composite structure affects various properties of the macroscale biogenic ceramic, a phenomenon we attribute to emergence. Emergence, in turn, is typical for hierarchically organized materials. This is a clear call to renew comparative studies of even distantly related biomineralizing organisms to identify further universal design motifs and their associated emergent properties. Such universal motifs with emergent macro-scale properties may represent an unparalleled toolbox for the efficient design of bioinspired functional materials.

scholarly journals Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes

2006 ◽  
Vol 361 (1475) ◽  
pp. 2009-2021 ◽  
Author(s):  
Martin F Polz ◽  
Dana E Hunt ◽  
Sarah P Preheim ◽  
Daniel M Weinreich
Keyword(s):  
Microbial Communities ◽  
Division Of Labour ◽  
Population Diversity ◽  
Nutrient Concentrations ◽  
Emergent Properties ◽  
Marine Microbes ◽  
Whole Genomes ◽  
Population Sizes ◽  
Underlying Mechanisms ◽  
Diverse Groups

Microbes in the ocean dominate biogeochemical processes and are far more diverse than anticipated. Thus, in order to understand the ocean system, we need to delineate microbial populations with predictable ecological functions. Recent observations suggest that ocean communities comprise diverse groups of bacteria organized into genotypic (and phenotypic) clusters of closely related organisms. Although such patterns are similar to metazoan communities, the underlying mechanisms for microbial communities may differ substantially. Indeed, the potential among ocean microbes for vast population sizes, extensive migration and both homologous and illegitimate genetic recombinations, which are uncoupled from reproduction, challenges classical population models primarily developed for sexually reproducing animals. We examine possible mechanisms leading to the formation of genotypic clusters and consider alternative population genetic models for differentiation at individual loci as well as gene content at the level of whole genomes. We further suggest that ocean bacteria follow at least two different adaptive strategies, which constrain rates and bounds of evolutionary processes: the ‘opportuni-troph’, exploiting spatially and temporally variable resources; and the passive oligotroph, efficiently using low nutrient concentrations. These ecological lifestyle differences may represent a fundamental divide with major consequences for growth and predation rates, genome evolution and population diversity, as emergent properties driving the division of labour within microbial communities.

scholarly journals Mate‐finding dispersal reduces local mate limitation and sex bias in dispersal

2020 ◽  
Vol 89 (9) ◽  
pp. 2089-2098 ◽  
Author(s):  
Abhishek Mishra ◽  
Sudipta Tung ◽  
V. R. Shree Sruti ◽  
Sahana Srivathsa ◽  
Sutirth Dey
Keyword(s):  
Sex Bias ◽  
Mate Finding ◽  
Local Mate ◽  
Mate Limitation

scholarly journals Fine mapping without phenotyping: Identification of selection targets in secondary Evolve and Resequence experiments

2021 ◽  
Author(s):  
Anna Maria Langmüller ◽  
Marlies Dolezal ◽  
Christian Schlötterer
Keyword(s):  
Population Size ◽  
Experimental Evolution ◽  
Single Gene ◽  
Empirical Studies ◽  
Selection Response ◽  
Founder Population ◽  
Experimental Procedure ◽  
Causative Snps ◽  
Population Sizes ◽  
Candidate Loci

AbstractEvolve and Resequence (E&R) studies investigate the genomic selection response of populations in an Experimental Evolution (EE) setup. Despite the popularity of E&R, empirical studies typically suffer from an excess of candidate loci due to linkage, and single gene or SNP resolution is the exception rather than the rule. Recently, a secondary E&R design – where unevolved founder genotypes are added to a primary E&R study - has been suggested as promising experimental procedure to confirm putative selection targets. Furthermore, secondary E&R provides the opportunity to increase mapping resolution by allowing for additional recombination events, which separate the selection target from neutral hitchhikers. Here, we use computer simulations to assess the effect of crossing scheme, population size, experimental duration, and number of replicates on the power, and resolution of secondary E&R. We find that the crossing scheme, population size, and the experimental duration are crucial factors for the power and resolution of secondary E&R: a simple crossing scheme with few founder lines consistently outcompetes crossing schemes where evolved populations from a primary E&R experiment are mixed with a complex ancestral founder population. Regardless of the experimental design tested, a population size of at least 4,800 individuals, which is roughly 5 times larger than population sizes in typical E&R studies, is required to achieve a power of at least 75%. Our study provides an important step towards improved experimental designs aiming to characterize causative SNPs in EE studies.

scholarly journals The degeneration of Y chromosomes

2000 ◽  
Vol 355 (1403) ◽  
pp. 1563-1572 ◽  
Author(s):  
Brian Charlesworth ◽  
Deborah Charlesworth
Keyword(s):  
Y Chromosome ◽  
Empirical Studies ◽  
Effective Population ◽  
Weak Selection ◽  
Deleterious Alleles ◽  
Y Chromosomes ◽  
Population Sizes ◽  
The Hill ◽  
Future Work ◽  
Active Genes

Y chromosomes are genetically degenerate, having lost most of the active genes that were present in their ancestors. The causes of this degeneration have attracted much attention from evolutionary theorists. Four major theories are reviewed here: Muller's ratchet, background selection, the Hill–Robertson effect with weak selection, and the ‘hitchhiking’ of deleterious alleles by favourable mutations. All of these involve a reduction in effective population size as a result of selective events occurring in a non–recombining genome, and the consequent weakening of the efficacy of selection. We review the consequences of these processes for patterns of molecular evolution and variation at loci on Y chromosomes, and discuss the results of empirical studies of these patterns for some evolving Y–chromosome and neo–Y–chromosome systems. These results suggest that the effective population sizes of evolving Y or neo–Y chromosomes are severely reduced, as expected if some or all of the hypothesized processes leading to degeneration are operative. It is, however, currently unclear which of the various processes is most important; some directions for future work to help to resolve this question are discussed.

scholarly journals An interplay of population size and environmental heterogeneity explains why fitness costs are rare

2020 ◽  
Author(s):  
Yashraj Chavhan ◽  
Sarthak Malusare ◽  
Sutirth Dey
Keyword(s):  
Experimental Evolution ◽  
Environmental Heterogeneity ◽  
Empirical Studies ◽  
Large Population ◽  
Theoretical Models ◽  
Heterogeneous Environments ◽  
Ecological Specialization ◽  
Fitness Costs ◽  
Cost Avoidance ◽  
Population Sizes

AbstractTheoretical models of ecological specialization commonly assume that adaptation to one environment leads to fitness reductions (costs) in others. However, empirical studies often fail to detect such costs. We addressed this conundrum using experimental evolution with Escherichia coli in several homogeneous and heterogeneous environments at multiple population sizes. We found that in heterogeneous environments, smaller populations paid significant costs, but larger ones avoided them altogether. Contrastingly, in homogeneous environments, larger populations paid more costs than the smaller ones. Overall, large population sizes and heterogeneous environments led to cost avoidance when present together but not on their own. Whole-genome whole-population sequencing revealed that the enrichment of multiple mutations within the same lineage (and not subdivision into multiple distinct specialist subpopulations) was the mechanism of cost avoidance. Since the conditions revealed by our study for avoiding costs are widespread, it explains why the costs expected in theory are rarely detected in experiments.

scholarly journals Does deterministic coexistence theory matter in a finite world?

2018 ◽  
Author(s):  
Sebastian J. Schreiber ◽  
Jonathan M. Levine ◽  
Oscar Godoy ◽  
Nathan J.B. Kraft ◽  
Simon P. Hart
Keyword(s):  
Growth Rates ◽  
Species Coexistence ◽  
Deterministic Model ◽  
Empirical Studies ◽  
Finite Size ◽  
Niche Overlap ◽  
Demographic Stochasticity ◽  
Deterministic Models ◽  
Deterministic Theory ◽  
Population Sizes

AbstractContemporary studies of species coexistence are underpinned by deterministic models that assume that competing species have continuous (i.e. non-integer) densities, live in infinitely large landscapes, and coexist over infinite time horizons. By contrast, in nature species are composed of discrete individuals subject to demographic stochasticity, and occur in habitats of finite size where extinctions occur in finite time. One important consequence of these discrepancies is that metrics of species coexistence derived from deterministic theory may be unreliable predictors of the duration of species coexistence in nature. These coexistence metrics include invasion growth rates and niche and competitive differences, which are now commonly applied in theoretical and empirical studies of species coexistence. Here we test the efficacy of deterministic coexistence metrics on the duration of species coexistence in a finite world. We introduce new theoretical and computational methods to estimate coexistence times in a stochastic counterpart of a classic deterministic model of competition. Importantly, we parameterized this model using experimental field data for 90 pairwise combinations of 18 species of annual plants, allowing us to derive biologically-informed estimates of coexistence times for a natural system. Strikingly, we find that for species expected to deterministically coexist, habitat sizes containing only tens of individuals have predicted coexistence times of greater than 1, 000 years. We also find that invasion growth rates explain 60% of the variation in intrinsic coexistence times, reinforcing their general usefulness in studies of coexistence. However, only by integrating information on both invasion growth rates and species’ equilibrium population sizes could most (> 99%) of the variation in species coexistence times be explained. Moreover, because of a complex relationship between niche overlap/competitive differences and equilibrium population sizes, increasing niche overlap and increasing competitive differences did not always result in decreasing coexistence times as deterministic theory would predict. Nevertheless, our results tend to support the informed use of deterministic theory for understanding the duration of species coexistence, while highlighting the need to incorporate information on species’ equilibrium population sizes in addition to invasion growth rates.

scholarly journals Exploration of social spreading reveals behavior is prevalent among Pedobacter and P. fluorescens isolates, and shows variations in induction of phenotype

2019 ◽  
Author(s):  
Lucy M. McCully ◽  
Jasmine Graslie ◽  
Adam S. Bitzer ◽  
Auður M. Sigurbjörnsdóttir ◽  
Oddur Vilhelmsson ◽  
...  
Keyword(s):  
Social Context ◽  
Microbial Communities ◽  
Soil Bacteria ◽  
Close Contact ◽  
Microbial Interactions ◽  
Emergent Properties ◽  
High Nutrient ◽  
Agar Surface ◽  
Nutritional Environment ◽  
Emergent Community

AbstractWithin soil, bacteria are naturally found in multi-species communities, where interactions can lead to emergent community properties. It is critical that we study bacteria in a social context to investigate community-level functions. We previously showed that when co-cultured, Pseudomonas fluorescens Pf0-1 and Pedobacter sp. V48 engage in interspecies social spreading on a hard agar surface, a behavior which required close contact and was dependent on the nutritional environment. In this study, we investigate whether the ability to participate in social spreading is widespread among P. fluorescens and Pedobacter isolates, and whether the requirements for interaction vary. We find that this phenotype is not restricted to the interaction between P. fluorescens Pf0-1 and Pedobacter sp. V48, but is a more prevalent behavior found in one clade in the P. fluorescens group and two clades in the Pedobacter genus. We also discovered that the interaction with certain Pedobacter isolates occurred without close contact, indicating induction of spreading by a putative diffusible signal. As is the case for ISS by Pf0-1+V48, motility of all interacting pairs is influenced by the environment, with no spreading behaviors observed under high nutrient conditions. While Pf0-1+V48 require low nutrient but high NaCl conditions, in the broader range of interacting pairs this requirement for low nutrient and high salt was variable. The prevalence of motility phenotypes observed in this study and found within the literature indicates that community-induced locomotion in general, and social spreading in particular, is likely important within the environment. It is crucial that we continue to study microbial interactions and their emergent properties to gain a fuller understanding of the functions of microbial communities.

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