scholarly journals There and Back to the Present: An Evolutionary Tale on Biological Diversity

2021 ◽  
Author(s):  
Leandro Duarte ◽  
Gabriel Nakamura ◽  
Vanderlei Debastiani ◽  
Renan Maestri ◽  
Maria Joao Veloso da Costa Ramos Pereira ◽  
...  
Keyword(s):  
Biological Diversity ◽  
Environmental Gradients ◽  
Dispersal Limitation ◽  
R Package ◽  
Analytical Framework ◽  
Niche Evolution ◽  
Ecological Patterns ◽  
Local Species ◽  
Individual Based Simulation ◽  
Approximate Bayesian

Ecologists often agree on the importance of macroevolution for niche-mediated distribution of biological diversity along environmental gradients. Yet, macroevolutionary diversification and dispersal in time and space generate uneven geographic distribution of phylogenetic pools, which affects the imprint let by macroevolution on local species pools. In this article we introduce an individual-based simulation approach coupled to Approximate Bayesian Computation (ABC) that allows to parameterize the adaptation rate of species niche positions along the evolution of a monophyletic lineage, and the intensity of dispersal limitation, associated with the distribution of biological diversity between assemblages potentially connected by dispersal (metacommunity). The analytical tool was implemented in an R package called mcfly. We evaluated the statistical performance of the analytical framework using simulated datasets, which confirmed the suitability of the analysis to estimate adaptation rate and dispersal limitation parameters. Further, we evaluated the role played by niche evolution and dispersal limitation on species diversity distribution of Phyllostomidae bats across the Neotropics. The framework proposed here shed light on the links between niche evolution, dispersal limitation and the distribution of biological diversity, and thereby improved our understanding of evolutionary imprints on ecological patterns. Perhaps more importantly, it offers new possibilities for solving the eco-evolutionary puzzle.

scholarly journals metabaR : an R package for the evaluation and improvement of DNA metabarcoding data quality

2020 ◽  
Author(s):  
Lucie Zinger ◽  
Clément Lionnet ◽  
Anne-Sophie Benoiston ◽  
Julian Donald ◽  
Céline Mercier ◽  
...  
Keyword(s):  
Data Quality ◽  
Large Scale ◽  
Environmental Gradients ◽  
R Package ◽  
Data Curation ◽  
Environmental Research ◽  
List Type ◽  
Sequencing Platform ◽  
Dna Metabarcoding ◽  
Ecological Patterns

AbstractDNA metabarcoding is becoming the tool of choice for biodiversity studies across taxa and large-scale environmental gradients. Yet, the artefacts present in metabarcoding datasets often preclude a proper interpretation of ecological patterns. Bioinformatic pipelines removing experimental noise have been designed to address this issue. However, these often only partially target produced artefacts, or are marker specific. In addition, assessments of data curation quality and the appropriateness of filtering thresholds are seldom available in existing pipelines, partly due to the lack of appropriate visualisation tools.Here, we present metabaR, an R package that provides a comprehensive suite of tools to effectively curate DNA metabarcoding data after basic bioinformatic analyses. In particular, metabaR uses experimental negative or positive controls to identify different types of artefactual sequences, i.e. reagent contaminants and tag-jumps. It also flags potentially dysfunctional PCRs based on PCR replicate similarities when those are available. Finally, metabaR provides tools to visualise DNA metabarcoding data characteristics in their experimental context as well as their distribution, and facilitate assessment of the appropriateness of data curation filtering thresholds.metabaR is applicable to any DNA metabarcoding experimental design but is most powerful when the design includes experimental controls and replicates. More generally, the simplicity and flexibility of the package makes it applicable any DNA marker, and data generated with any sequencing platform, and pre-analysed with any bioinformatic pipeline. Its outputs are easily usable for downstream analyses with any ecological R package.metabaR complements existing bioinformatics pipelines by providing scientists with a variety of functions with customisable methods that will allow the user to effectively clean DNA metabarcoding data and avoid serious misinterpretations. It thus offers a promising platform for automatised data quality assessments of DNA metabarcoding data for environmental research and biomonitoring.

scholarly journals Three points of consideration before testing the effect of patch connectivity on local species richness: patch delineation, scaling and variability of metrics

2019 ◽  
Author(s):  
Fabien Laroche ◽  
Manon Balbi ◽  
Théophile Grébert ◽  
Franck Jabot ◽  
Frédéric Archaux
Keyword(s):  
Species Richness ◽  
Empirical Studies ◽  
Structural Connectivity ◽  
Dispersal Limitation ◽  
Dispersal Distance ◽  
Habitat Amount ◽  
Local Species Richness ◽  
Theory Of Island Biogeography ◽  
Local Species ◽  
Patch Connectivity

AbstractThe Theory of Island Biogeography (TIB) promoted the idea that species richness within sites depends on site connectivity, i.e. its connection with surrounding potential sources of immigrants. TIB has been extended to a wide array of fragmented ecosystems, beyond archipelagoes, surfing on the analogy between habitat patches and islands and on the patch-matrix framework. However, patch connectivity often little contributes to explaining species richness in empirical studies. Before interpreting this trend as questioning the broad applicability of TIB principles, one first needs a clear identification of methods and contexts where strong effects of patch structural connectivity are likely to occur. Here, we use spatially explicit simulations of neutral metacommunities to show that patch connectivity effect on local species richness is maximized under a set of specific conditions: (i) patch delineation should be fine enough to ensure that no dispersal limitation occurs within patches, (ii) patch connectivity indices should be scaled according to target organisms’ dispersal distance and (iii) the habitat amount around sampled sites (within a distance adapted to organisms’ dispersal) should be highly variable. When those three criteria are met, the absence of an effect of connectivity on species richness should be interpreted as contradicting TIB hypotheses

scholarly journals strandCet: R package for estimating natural and non-natural mortality-at-age of cetaceans from age-structured strandings

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5768 ◽  
Author(s):  
Camilo Saavedra
Keyword(s):  
Total Mortality ◽  
R Package ◽  
Analytical Framework ◽  
Population Projections ◽  
Sources Of Information ◽  
Mortality Models ◽  
Credible Intervals ◽  
Leslie Matrices ◽  
Age Structured ◽  
Derived Data

Mortality is one of the most important parameters for the study of population dynamics. One of the main sources of information to calculate the mortality of cetaceans arises from the observed age-structure of stranded animals. A method based on an adaptation of a Heligman-Pollard model is proposed. A freely accessible package of functions (strandCet) has been created to apply this method in the statistical software R. Total, natural, and anthropogenic mortality-at-age is estimated using only data of stranded cetaceans whose age is known. Bayesian melding estimation with Incremental Mixture Importance Sampling is used for fitting this model. This characteristic, which accounts for uncertainty, further eases the estimation of credible intervals. The package also includes functions to perform life tables, Siler mortality models to calculate total mortality-at-age and Leslie matrices to derive population projections. Estimated mortalities can be tested under different scenarios. Population parameters as population growth, net production or generation time can be derived from population projections. The strandCet R package provides a new analytical framework to assess mortality in cetacean populations and to explore the consequences of management decisions using only stranding-derived data.

scholarly journals Evolutionary origins for ecological patterns in space

2020 ◽  
Vol 117 (30) ◽  
pp. 17482-17490 ◽  
Author(s):  
Mark C. Urban ◽  
Sharon Y. Strauss ◽  
Fanie Pelletier ◽  
Eric P. Palkovacs ◽  
Mathew A. Leibold ◽  
...  
Keyword(s):  
Local Adaptation ◽  
Environmental Gradients ◽  
Spatial Scales ◽  
Keystone Species ◽  
Future Research ◽  
Evolutionary Divergence ◽  
Patch Selection ◽  
Fully Integrated ◽  
Evolutionary Origins ◽  
Ecological Patterns

Historically, many biologists assumed that evolution and ecology acted independently because evolution occurred over distances too great to influence most ecological patterns. Today, evidence indicates that evolution can operate over a range of spatial scales, including fine spatial scales. Thus, evolutionary divergence across space might frequently interact with the mechanisms that also determine spatial ecological patterns. Here, we synthesize insights from 500 eco-evolutionary studies and develop a predictive framework that seeks to understand whether and when evolution amplifies, dampens, or creates ecological patterns. We demonstrate that local adaptation can alter everything from spatial variation in population abundances to ecosystem properties. We uncover 14 mechanisms that can mediate the outcome of evolution on spatial ecological patterns. Sometimes, evolution amplifies environmental variation, especially when selection enhances resource uptake or patch selection. The local evolution of foundation or keystone species can create ecological patterns where none existed originally. However, most often, we find that evolution dampens existing environmental gradients, because local adaptation evens out fitness across environments and thus counteracts the variation in associated ecological patterns. Consequently, evolution generally smooths out the underlying heterogeneity in nature, making the world appear less ragged than it would be in the absence of evolution. We end by highlighting the future research needed to inform a fully integrated and predictive biology that accounts for eco-evolutionary interactions in both space and time.

scholarly journals Evaluation of genetic isolation within an island flora reveals unusually widespread local adaptation and supports sympatric speciation

2014 ◽  
Vol 369 (1648) ◽  
pp. 20130342 ◽  
Author(s):  
Alexander S. T. Papadopulos ◽  
Maria Kaye ◽  
Céline Devaux ◽  
Helen Hipperson ◽  
Jackie Lighten ◽  
...  
Keyword(s):  
Gene Flow ◽  
Local Adaptation ◽  
Plant Species ◽  
Environmental Gradients ◽  
Isolation By Distance ◽  
Model Averaging ◽  
Dispersal Limitation ◽  
Population Divergence ◽  
Environmental Pressures ◽  
Isolation By Environment

It is now recognized that speciation can proceed even when divergent natural selection is opposed by gene flow. Understanding the extent to which environmental gradients and geographical distance can limit gene flow within species can shed light on the relative roles of selection and dispersal limitation during the early stages of population divergence and speciation. On the remote Lord Howe Island (Australia), ecological speciation with gene flow is thought to have taken place in several plant genera. The aim of this study was to establish the contributions of isolation by environment (IBE) and isolation by community (IBC) to the genetic structure of 19 plant species, from a number of distantly related families, which have been subjected to similar environmental pressures over comparable time scales. We applied an individual-based, multivariate, model averaging approach to quantify IBE and IBC, while controlling for isolation by distance (IBD). Our analyses demonstrated that all species experienced some degree of ecologically driven isolation, whereas only 12 of 19 species were subjected to IBD. The prevalence of IBE within these plant species indicates that divergent selection in plants frequently produces local adaptation and supports hypotheses that ecological divergence can drive speciation in sympatry.

scholarly journals Content bias in the cultural evolution of house finch song

2021 ◽  
Author(s):  
Mason Youngblood ◽  
David Lahti
Keyword(s):  
Cultural Evolution ◽  
Cultural Transmission ◽  
Population Level ◽  
R Package ◽  
House Finch ◽  
Population Declines ◽  
Individual Level ◽  
Transmission Mechanisms ◽  
Content Bias ◽  
Approximate Bayesian

In this study, we used a longitudinal dataset of house finch (Haemorhous mexicanus) song recordings spanning four decades in the introduced eastern range to assess how individual-level cultural transmission mechanisms drive population-level changes in birdsong. First, we developed an agent-based model (available as a new R package called TransmissionBias) that simulates the cultural transmission of house finch song given different parameters related to transmission biases, or biases in social learning that modify the probability of adoption of particular cultural variants. Next, we used approximate Bayesian computation and machine learning to estimate what parameter values likely generated the temporal changes in diversity in our observed data. We found evidence that strong content bias, likely targeted towards syllable complexity, plays a central role in the cultural evolution of house finch song in western Long Island. Frequency and demonstrator biases appear to be neutral or absent. Additionally, we estimated that house finch song is transmitted with extremely high fidelity. Future studies should use our simulation framework to better understand how cultural transmission and population declines influence song diversity in wild populations.

scholarly journals The role of environmental filtering, geographic distance and dispersal barriers in shaping the turnover of plant and animal species in Amazonia

2020 ◽  
Vol 29 (13) ◽  
pp. 3609-3634 ◽  
Author(s):  
Cristian Dambros ◽  
Gabriela Zuquim ◽  
Gabriel M. Moulatlet ◽  
Flávia R. C. Costa ◽  
Hanna Tuomisto ◽  
...  
Keyword(s):  
Community Composition ◽  
Environmental Conditions ◽  
Environmental Gradients ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
Environmental Filtering ◽  
Dispersal Limitation ◽  
Multivariate Techniques ◽  
Time Period ◽  
Dispersal Barriers

Abstract To determine the effect of rivers, environmental conditions, and isolation by distance on the distribution of species in Amazonia. Location: Brazilian Amazonia. Time period: Current. Major taxa studied: Birds, fishes, bats, ants, termites, butterflies, ferns + lycophytes, gingers and palms. We compiled a unique dataset of biotic and abiotic information from 822 plots spread over the Brazilian Amazon. We evaluated the effects of environment, geographic distance and dispersal barriers (rivers) on assemblage composition of animal and plant taxa using multivariate techniques and distance- and raw-data-based regression approaches. Environmental variables (soil/water), geographic distance, and rivers were associated with the distribution of most taxa. The wide and relatively old Amazon River tended to determine differences in community composition for most biological groups. Despite this association, environment and geographic distance were generally more important than rivers in explaining the changes in species composition. The results from multi-taxa comparisons suggest that variation in community composition in Amazonia reflects both dispersal limitation (isolation by distance or by large rivers) and the adaptation of species to local environmental conditions. Larger and older river barriers influenced the distribution of species. However, in general this effect is weaker than the effects of environmental gradients or geographical distance at broad scales in Amazonia, but the relative importance of each of these processes varies among biological groups.

scholarly journals abc: an R package for approximate Bayesian computation (ABC)

2012 ◽  
Vol 3 (3) ◽  
pp. 475-479 ◽  
Author(s):  
Katalin Csilléry ◽  
Olivier François ◽  
Michael G. B. Blum
Keyword(s):  
Approximate Bayesian Computation ◽  
R Package ◽  
Bayesian Computation ◽  
Approximate Bayesian

State of the States: Geographic Patterns of Diversity, Rarity, and Endemism

2000 ◽  
Author(s):  
Geoffrey A. Hammerson ◽  
Larry E. Morse
Keyword(s):  
Biological Diversity ◽  
Dominant Role ◽  
Fish Fauna ◽  
The Future ◽  
Ecological Patterns ◽  
History Of ◽  
Mammal Assemblages ◽  
Southern Florida ◽  
Alaskan Tundra ◽  
Natural Boundaries

The natural geography of the 50 states varies tremendously, supporting an equally varied suite of wild species—from flocks of tropical birds in southern Florida to caribou migrations across the Alaskan tundra. The geography of risk, too, varies across the nation, reflecting the interaction between natural and human history. Similarly, present-day land and water uses will largely determine the future diversity and condition of the flora and fauna. We can learn much, though, from looking at the current condition of a state’s biota, since this both reflects the past and helps illuminate the future. A state’s ecological complexion and the evolutionary history of its biota are the primary determinants of its biological diversity. These environmental factors have encouraged spectacular diversification in many regions: for instance, the freshwater fish fauna in the Southeast, the magnificent conifers along the Pacific cordillera, and the small mammal assemblages of the arid Southwest. Conversely, geological events such as the expansion and contraction of the ice sheets have left other areas of the country with a more modest array of species. States, however, are artificial constructs laid out on the landscape’s natural ecological patterns. While some state lines follow natural boundaries, such as shorelines or major rivers, most cut across the land with no sensitivity to natural features or topography. Nonetheless, urban and rural dwellers alike identify with the major ecological regions within which they live, and this is often the source of considerable pride. Montana is “big sky country,” referring to the vast open plains that sweep up against the eastern phalanx of the Rocky Mountains. California’s moniker “the golden state” now refers more to its tawny hills of summer—unfortunately at present composed mostly of alien species—than to the nuggets first found at Sutter’s Creek. Maryland, home of the Chesapeake Bay, offers the tasty blue crab (Callinectes sapidus) as its unofficial invertebrate mascot. The list could go on, evidenced by the growing number of states that offer vanity license plates celebrating their natural environment. Natural features have always played a dominant role in determining patterns of settlement and land use.

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