A Unifying Model for the Analysis of Phenotypic, Genetic, and Geographic Data

Guillot, Gilles; Renaud, Sabrina; Ledevin, Ronan; Michaux, Johan; Julien, Claude

doi:10.1093/sysbio/sys038

Cited by 139 publications

(126 citation statements)

References 68 publications

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“…Unlike other methods described here, the unified model of Guillot et al (2012) can analyse nongenetic data (phenotypical, geographical, behavioural) in addition to genetic data. Their approach implemented a Bayesian clustering algorithm that assumes that each cluster in a geographical domain can be approximated by polygons that are centred around points generated by a Poisson process.…”

Section: Box 1 Systems In Which Species Delimitation Methods Are Applmentioning

confidence: 99%

How to fail at species delimitation

et al. 2013

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

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Section: Box 1 Systems In Which Species Delimitation Methods Are Applmentioning

confidence: 99%

How to fail at species delimitation

et al. 2013

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“…A thorough examination of the statistical methods to be applied in species delimitation based on phenotypic data alone or in combination with genotypic caracters can be found elsewhere (Wiens & Servedio 2000;Guillot et al 2012;Solís-Lemus et al 2015) and it is beyond the scope of the present compilation. As a general rule, a choice on a given statistical test will usually require some assumptions to be met by the data and deviations from these could produce spurious results.…”

Section: Usage Of Statistics In Call Comparisonsmentioning

confidence: 99%

The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice

Köhler

Jansen

Rodríguez³

et al. 2017

Zootaxa

479

410

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Vocalizations of anuran amphibians have received much attention in studies of behavioral ecology and physiology, but also provide informative characters for identifying and delimiting species. We here review the terminology and variation of frog calls from a perspective of integrative taxonomy, and provide hands-on protocols for recording, analyzing, comparing, interpreting and describing these sounds. Our focus is on advertisement calls, which serve as premating isolation mechanisms and, therefore, convey important taxonomic information. We provide recommendations for terminology of frog vocalizations, with call, note and pulse being the fundamental subunits to be used in descriptions and comparisons. However, due to the complexity and diversity of these signals, an unequivocal application of the terms call and note can be challenging. We therefore provide two coherent concepts that either follow a note-centered approach (defining uninterrupted units of sound as notes, and their entirety as call) or a call-centered approach (defining uninterrupted units as call whenever they are separated by long silent intervals) in terminology. Based on surveys of literature, we show that numerous call traits can be highly variable within and between individuals of one species. Despite idiosyncrasies of species and higher taxa, the duration of calls or notes, pulse rate within notes, and number of pulses per note appear to be more static within individuals and somewhat less affected by temperature. Therefore, these variables might often be preferable as taxonomic characters over call rate or note rate, which are heavily influenced by various factors. Dominant frequency is also comparatively static and only weakly affected by temperature, but depends strongly on body size. As with other taxonomic characters, strong call divergence is typically indicative of species-level differences, whereas call similarities of two populations are no evidence for them being conspecific. Taxonomic conclusions can especially be drawn when the general advertisement call structure of two candidate species is radically different and qualitative call differences are thus observed. On the other hand, quantitative differences in call traits might substantially vary within and among conspecific populations, and require careful evaluation and analysis. We provide guidelines for the taxonomic interpretation of advertisement call differences in sympatric and allopatric situations, and emphasize the need for an integrative use of multiple datasets (bio-acoustics, morphology, genetics), particularly for allopatric scenarios. We show that small-sized frogs often emit calls with frequency components in the ultrasound spectrum, although it is unlikely that these high frequencies are of biological relevance for the majority of them, and we illustrate that detection of upper harmonics depends also on recording distance because higher frequencies are attenuated more strongly. Bioacoustics remains a prime approach in integrative taxonomy of anurans if uncertainty due to possible intraspecific variation and technical artifacts is adequately considered and acknowledged.

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“…The clustering approach can combine data on genotypic polymorphism with geographic coordinates projected on a rasterized map. The optimal number of clusters k and the posterior probabilities of cluster membership for any unit of the sampling map were identified by a Markov chain Monte Carlo procedure under the assumption that there is no admixture between populations and that populations are at Hardy-Weinberg equilibrium with linkage equilibrium between loci (Guillot et al, 2012). Here, we assumed that allele frequencies of the cts gene were independent between samples.…”

Section: Inference Of Population Structures By Landscape Clusteringmentioning

confidence: 99%

Features of air masses associated with the deposition of Pseudomonas syringae and Botrytis cinerea by rain and snowfall

Monteil¹,

Bardin²,

Morris³

2014

The ISME Journal

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Clarifying the role of precipitation in microbial dissemination is essential for elucidating the processes involved in disease emergence and spread. The ecology of Pseudomonas syringae and its presence throughout the water cycle makes it an excellent model to address this issue. In this study, 90 samples of freshly fallen rain and snow collected from 2005-2011 in France were analyzed for microbiological composition. The conditions favorable for dissemination of P. syringae by this precipitation were investigated by (i) estimating the physical properties and backward trajectories of the air masses associated with each precipitation event and by (ii) characterizing precipitation chemistry, and genetic and phenotypic structures of populations. A parallel study with the fungus Botrytis cinerea was also performed for comparison. Results showed that (i) the relationship of P. syringae to precipitation as a dissemination vector is not the same for snowfall and rainfall, whereas it is the same for B. cinerea and (ii) the occurrence of P. syringae in precipitation can be linked to electrical conductivity and pH of water, the trajectory of the air mass associated with the precipitation and certain physical conditions of the air mass (i.e. temperature, solar radiation exposure, distance traveled), whereas these predictions are different for B. cinerea. These results are pertinent to understanding microbial survival, emission sources and atmospheric processes and how they influence microbial dissemination.

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A Unifying Model for the Analysis of Phenotypic, Genetic, and Geographic Data

Cited by 139 publications

References 68 publications

How to fail at species delimitation

How to fail at species delimitation

The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice

Features of air masses associated with the deposition of Pseudomonas syringae and Botrytis cinerea by rain and snowfall

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