How to fail at species delimitation

Molecular Ecology, Journal Year: 2013, Volume and Issue: 22(17), P. 4369 - 4383

Published: July 16, 2013

Abstract Species delimitation is the act of identifying species‐level biological diversity. In recent years, field has witnessed a dramatic increase in number methods available for delimiting species. However, most investigations only utilize handful (i.e. 2–3) methods, often unstated reasons. Because parameter space that potentially relevant to species far exceeds parameterization any existing method, given method necessarily makes simplifying assumptions, one which could be violated particular system. We suggest researchers should apply wide range analyses their data and place trust delimitations are congruent across methods. Incongruence results from different evidence either difference power detect cryptic lineages or more approaches used delimit indicate assumptions have been violated. case, inferences drawn studies conservative, contexts it better fail than falsely entities do not represent actual evolutionary lineages.

Language: Английский

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The emergence and promise of functional biogeography

Proceedings of the National Academy of Sciences, Journal Year: 2014, Volume and Issue: 111(38), P. 13690 - 13696

Published: Sept. 15, 2014

Understanding, modeling, and predicting the impact of global change on ecosystem functioning across biogeographical gradients can benefit from enhanced capacity to represent biota as a continuous distribution traits. However, this is challenge for field biogeography historically grounded species concept. Here we focus newly emergent functional biogeography: study geographic trait diversity organizational levels. We show how bridges species-based earth science provide ideas tools help explain in multifaceted (including species, functional, phylogenetic diversities), predict services worldwide, infuse regional conservation programs with basis. Although much recent progress has been made possible because rising multiple data streams, new developments ecoinformatics, methodological advances, future directions should theoretical comprehensive framework scaling biotic interactions trophic levels its ecological implications.

Language: Английский

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Cryptic species as a window into the paradigm shift of the species concept

Molecular Ecology, Journal Year: 2018, Volume and Issue: 27(3), P. 613 - 635

Published: Jan. 15, 2018

The species concept is the cornerstone of biodiversity science, and any paradigm shift in delimitation affects many research fields. Many biologists now are embracing a new "species" as separately evolving populations using different criteria. Individual criteria can emerge during periods speciation; some may never evolve. As such, relates to this inherent heterogeneity speciation process category-which fundamentally overlooked research. Cryptic fall within shift: they continuously being reported from diverse animal phyla but poorly considered current tests ecological evolutionary theory. aim review integrate cryptic science. In first section, we address that absence morphological diversification an phenomenon, "process" counterpart long-studied mechanisms diversification. next section regarding taxonomy, show molecular heavily biased towards distance-based methods. We also stress importance formally naming for better integration into fields use units analysis. Finally, incorporating leads novel insights patterns processes, including large-scale assessments, geographic variation distribution coexistence. It time multicriteria approaches aiming understand across space taxa, thus allowing conservation while accommodating uncertainty.

Language: Английский

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Genetic Management of Fragmented Animal and Plant Populations

Oxford University Press eBooks, Journal Year: 2017, Volume and Issue: unknown

Published: July 13, 2017

Abstract The biological diversity of the planet is being rapidly depleted due to direct and indirect consequences human activity. As size animal plant populations decrease fragmentation increases, loss genetic reduces their ability adapt changes in environment, with inbreeding reduced fitness inevitable for many species. Many small isolated are going extinct unnecessarily. In cases, such can be genetically rescued by gene flow into them from another population within species, but this very rarely done. This novel authoritative book addresses issues involved management fragmented populations, including depression, elevated extinction risk augmentation flow, rescue, causes outbreeding depression predicting its occurrence, desirability implementation translocations cope climate change, defining diagnosing species conservation purposes.

Language: Английский

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Bayesian species delimitation combining multiple genes and traits in a unified framework

Evolution, Journal Year: 2014, Volume and Issue: 69(2), P. 492 - 507

Published: Dec. 15, 2014

Delimitation of species based exclusively on genetic data has been advocated despite a critical knowledge gap: how might such approaches fail because they rely alone, and would their accuracy be improved by using multiple types. We provide here the requisite framework for addressing these key questions. Because both phenotypic molecular can analyzed in common Bayesian with our program iBPP, we compare delimited taxa alone versus when integrated data. also evaluate integration improve delimitation divergence occurs gene flow and/or is selectively driven. These two realities speciation process are ignored currently available approaches. Our model accommodates characters that exhibit different degrees divergence, allowing neutral traits under selection. found greater estimated boundaries data, strong beneficial influence from selection involves flow. results highlight benefits types, but draws into question rationale

Language: Английский

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Demographic and genetic approaches to study dispersal in wild animal populations: A methodological review

Molecular Ecology, Journal Year: 2018, Volume and Issue: 27(20), P. 3976 - 4010

Published: Aug. 29, 2018

Abstract Dispersal is a central process in ecology and evolution. At the individual level, three stages of dispersal (i.e., emigration, transience immigration) are affected by complex interactions between phenotypes environmental factors. Condition‐ context‐dependent have far‐reaching consequences, both for demography genetic structuring natural populations adaptive processes. From an applied point view, also deeply affects spatial dynamics their ability to respond land‐use changes, habitat degradation climate change. For these reasons, has received considerable attention from ecologists evolutionary biologists. Demographic methods allow quantifying non‐effective followed or not successful reproduction) effective with investigate how factors affect different process. Over past decade, demographic designed quantify rapidly evolved but researchers two fields limited. We here review recent developments study wild animal populations. present strengths limits, as well applicability depending on objectives population characteristics. propose unified framework allowing combine select more suitable tools address broad range important topics about evolution its consequences genetics.

Language: Английский

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assignPOP: An r package for population assignment using genetic, non‐genetic, or integrated data in a machine‐learning framework

Methods in Ecology and Evolution, Journal Year: 2017, Volume and Issue: 9(2), P. 439 - 446

Published: Sept. 18, 2017

Abstract The use of biomarkers (e.g., genetic, microchemical and morphometric characteristics) to discriminate among assign individuals a population can benefit species conservation management by facilitating our ability understand structure demography. Tools that evaluate the reliability large genomic datasets for discrimination assignment, as well allow their integration with non‐genetic markers same purpose, are lacking. Our r package, POP , provides both functions in supervised machine‐learning framework. uses Monte‐Carlo K ‐fold cross‐validation procedures, principal component analysis, estimate assignment accuracy membership probabilities, using training (i.e., baseline source population) test validation) independent. A user then build specified predictive model based on relative sizes these classification functions, including linear discriminant support vector machine, naïve Bayes, decision tree random forest. any researcher who seeks genetic or data infer individuals. is freely available package under GPL license, be downloaded from CRAN at https://github.com/alexkychen/assignPOP . comprehensive tutorial also found https://alexkychen.github.io/assignPOP/

Language: Английский

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Species Delimitation: A Decade After the Renaissance

InTech eBooks, Journal Year: 2013, Volume and Issue: unknown

Published: Feb. 6, 2013

A decade ago Sites and Marshall [1] described the empirical practice of species delimitation as “a Renaissance issue in systematic biology”. At time there was an odd disconnect be‐ tween two frequently stated goals biology: discovery of: (1) monophyletic groups (clades) relationships within these at all hierarchical levels above species; (2) lineages (species); compared to actual discipline. While much biology had been devoted first goal, second goal until re‐ cently largely ignored [2], despite fact that are routinely used basic units analysis biogeography, ecology, evolutionary biology, conservation [3,4]. However, noted “signs a Renaissance” their view, which precipitated part by others emphasizing need distinguish between non-operational, ontological definition species, versus (operational) data needed test reality [5-7]. De Queiroz [7] (p. 60) “All modern defi‐ nitions either explicitly or implicitly equate with segments population level evolu‐ tionary lineages.” also this revised version Simpson’s “evolutionary concept”, defines lineage (an ancestraldescend‐ ent sequence populations) evolving separately from its own role tendencies” ([8], p. 153), called General Lineage Concept (GLC) ([7], 65). [9] further emphasized multiple criteria simply flect many contingent properties (differences genetic morphological features, adap‐ tive zones ecological niches, mate-recognition systems, reproductive compatibility, monophyly, etc.) diverging populations associated different processes operating various geographic contexts [10,11]. emerging consensus among systematists biologists based on utili‐ ty distinction (ontological vs. [SDL] meth‐

Language: Английский

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Spatiotemporal landscape genetics: Investigating ecology and evolution through space and time

Molecular Ecology, Journal Year: 2019, Volume and Issue: 29(2), P. 218 - 246

Published: Nov. 23, 2019

Genetic time-series data from historical samples greatly facilitate inference of past population dynamics and species evolution. Yet, although climate landscape change are often touted as post-hoc explanations biological change, our understanding influences on evolutionary processes is severely hindered by the limited application methods that directly relate environmental to through time. Increased integration spatiotemporal genetic will revolutionize interpretation quantification recent anthropogenic impacts species, vastly improve prediction responses under future scenarios, yielding widespread revelations across biology, ecology conservation genetics. This review encourages greater use analyses explicitly link landscape, time providing an overview analytical approaches for integrating in five key research areas: structure, demography, phylogeography, metapopulation connectivity adaptation. We also include a tabular summary methodological information, suggest mitigating particular difficulties applying these techniques ancient DNA palaeoclimate data, highlight areas development.

Language: Английский

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Climate change, genetic markers and species distribution modelling

Journal of Biogeography, Journal Year: 2015, Volume and Issue: 42(9), P. 1577 - 1585

Published: June 27, 2015

Abstract Ecologists and biogeographers are currently expending great effort forecasting shifts in species geographical ranges that may result from climate change. However, these efforts problematic because they have mostly relied on presence‐only data ignore within‐species genetic diversity. Technological advances high‐throughput sequencing now made it cost‐effective to survey the structure of populations sampled throughout range a species. These can be used delineate two or more clusters within range, identify admixtures individuals reflect different patterns ancestry. Species distribution models ( SDM s) applied presence absence should provide realistic forecasts take account variability. High‐throughput spatially explicit further refine projections.

Language: Английский

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