Estimating biodiversity change across the planet in the context of widespread human modification is a critical challenge. Here, we review how biodiversity has changed in recent decades across scales and taxonomic groups, focusing on four diversity metrics: species richness, temporal turnover, spatial beta-diversity and abundance. At local scales, change across all metrics includes many examples of both increases and declines and tends to be centred around zero, but with higher prevalence of declining trends in beta-diversity (increasing similarity in composition across space or biotic homogenization) and abundance. The exception to this pattern is temporal turnover, with changes in species composition through time observed in most local assemblages. Less is known about change at regional scales, although several studies suggest that increases in richness are more prevalent than declines. Change at the global scale is the hardest to estimate accurately, but most studies suggest extinction rates are probably outpacing speciation rates, although both are elevated. Recognizing this variability is essential to accurately portray how biodiversity change is unfolding, and highlights how much remains unknown about the magnitude and direction of multiple biodiversity metrics at different scales. Reducing these blind spots is essential to allow appropriate management actions to be deployed. This article is part of the theme issue ‘Detecting and attributing the causes of biodiversity change: needs, gaps and solutions’.
more »
« less
Diversity in biology: definitions, quantification and models
Abstract Diversity indices are useful single-number metrics for characterizing a complex distribution of a set of attributes across a population of interest. The utility of these different metrics or sets of metrics depends on the context and application, and whether a predictive mechanistic model exists. In this topical review, we first summarize the relevant mathematical principles underlying heterogeneity in a large population, before outlining the various definitions of ‘diversity’ and providing examples of scientific topics in which its quantification plays an important role. We then review how diversity has been a ubiquitous concept across multiple fields, including ecology, immunology, cellular barcoding experiments, and socioeconomic studies. Since many of these applications involve sampling of populations, we also review how diversity in small samples is related to the diversity in the entire population. Features that arise in each of these applications are highlighted.
more »
« less
- Award ID(s):
- 1814364
- PAR ID:
- 10360337
- Publisher / Repository:
- IOP Publishing
- Date Published:
- Journal Name:
- Physical Biology
- Volume:
- 17
- Issue:
- 3
- ISSN:
- 1478-3967
- Page Range / eLocation ID:
- Article No. 031001
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Islands have long represented natural laboratories for studying many aspects of ecology and evolutionary biology, from speciation to community assembly. One aspect that has been well documented is the correlation between island size and taxonomic diversity, likely due to decreased complexity and population size on small islands. This same logic can apply to genetic diversity, which should predictably decrease with effective population size. The island size–diversity correlation has received support over the years but often focuses on single metrics of genetic diversity. Here, we useZosteropswhite-eyes in the Solomon Islands to study the correlation between island size and various metrics related to genetic diversity, including runs of homozygosity and fixation of transposable elements. We find that almost all these metrics strongly correlate with island size, and in turn with each other. We infer that island size is independently correlated with these different variables, demonstrating that population size impacts genomic metrics of diversity in a variety of ways across temporal and hierarchical scales.more » « less
-
Abstract Genetic diversity plays a key role in maintaining population viability by preventing inbreeding depression and providing the building blocks for adaptation. Understanding how genetic diversity varies across space is, therefore, of key interest in conservation and population genetics.Here, we introducewingen, anrpackage for calculating continuous maps of genetic diversity, including nucleotide diversity, allelic richness, and heterozygosity, from standard genotypic and spatial data using a spatial moving window approach. We provide functions to account for variation in sample size across space using rarefaction, to create kriging‐interpolated maps of genetic diversity, and to mask any areas that are outside the area of interest.Tests with simulated and empirical datasets demonstrate thatwingencan successfully capture variation in genetic diversity across landscapes from both reduced‐representation and whole genome sequencing datasets. For reduced‐representation datasets,wingen's functions can be run easily on a standard laptop computer, and we provide options for parallelization to increase the efficiency of running larger whole genome datasets.wingenprovides novel and computationally tractable tools for creating informative maps of genetic diversity with applications for conservation prioritization as well as population and landscape genetic analyses.more » « less
-
Abstract Most heritable information in eukaryotic cells is encoded in the nuclear genome, with inheritance patterns following classic Mendelian segregation. Genomes residing in the cytoplasm, however, prove to be a peculiar exception to this rule. Cytoplasmic genetic elements are generally maternally inherited, although there are several exceptions where these are paternally, biparentally or doubly-uniparentally inherited. In this review, we examine the diversity and peculiarities of cytoplasmically inherited genomes, and the broad evolutionary consequences that non-Mendelian inheritance brings. We first explore the origins of vertical transmission and uniparental inheritance, before detailing the vast diversity of cytoplasmic inheritance systems across Eukaryota. We then describe the evolution of genomic organisation across lineages, how this process has been shaped by interactions with the nuclear genome and population genetics dynamics. Finally, we discuss how both nuclear and cytoplasmic genomes have evolved to co-inhabit the same host cell via one of the longest symbiotic processes, and all the opportunities for intergenomic conflict that arise due to divergence in inheritance patterns. In sum, we cannot understand the evolution of eukaryotes without understanding hereditary symbiosis.more » « less
-
Abstract BackgroundMacArthur and Wilson's theory of island biogeography has been a foundation for obtaining testable predictions from models of community assembly and for developing models that integrate across scales and disciplines. Historically, however, these developments have focused on integration across ecological and macroevolutionary scales and on predicting patterns of species richness, abundance distributions, trait data and/or phylogenies. The distribution of genetic variation across species within a community is an emerging pattern that contains signatures of past population histories, which might provide an historical lens for the study of contemporary communities. As intraspecific genetic diversity data become increasingly available at the scale of entire communities, there is an opportunity to integrate microevolutionary processes into our models, moving towards development of a genetic theory of island biogeography. Motivation/goalWe aim to promote the development of process‐based biodiversity models that predict community genetic diversity patterns together with other community‐scale patterns. To this end, we review models of ecological, microevolutionary and macroevolutionary processes that are best suited to the creation of unified models, and the patterns that these predict. We then discuss ongoing and potential future efforts to unify models operating at different organizational levels, with the goal of predicting multidimensional community‐scale data including a genetic component. Main conclusionsOur review of the literature shows that despite recent efforts, further methodological developments are needed, not only to incorporate the genetic component into existing island biogeography models, but also to unify processes across scales of biological organization. To catalyse these developments, we outline two potential ways forward, adopting either a top‐down or a bottom‐up approach. Finally, we highlight key ecological and evolutionary questions that might be addressed by unified models including a genetic component and establish hypotheses about how processes across scales might impact patterns of community genetic diversity.more » « less
An official website of the United States government
