Evaluating summary statistics used to test for incomplete lineage sorting: mito‐nuclear discordance in the reef sponge <i><scp>C</scp>allyspongia vaginalis</i>

DeBiasse, Melissa B.; Nelson, Bradley J.; Hellberg, Michael E.

doi:10.1111/mec.12584

Cited by 30 publications

(33 citation statements)

References 101 publications

(101 reference statements)

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“…The occurrence of incomplete lineage sorting to explain mito-nuclear discordance has been describer for an increasing number of case studies [78–80]. Thus, the failure of nuclear genome to diverge as a consequence of its slower diverging rate and higher population size appear the most plausible interpretation to explain such pattern rather than sex-biased gene flow [81–83].…”

Section: Discussionmentioning

confidence: 99%

A combination of long term fragmentation and glacial persistence drove the evolutionary history of the Italian wall lizard Podarcis siculus

et al. 2017

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BackgroundThe current distribution of genetic diversity is the result of a vast array of microevolutionary processes, including short-term demographic and ecological mechanisms and long-term allopatric isolation in response to Quaternary climatic fluctuations. We investigated past processes that drove the population differentiation and spatial genetic distribution of the Italian wall lizard Podarcis siculus by means of sequences of mitochondrial cytb (n = 277 from 115 localities) and nuclear mc1r and β-fibint7genes (n = 262 and n = 91, respectively) from all its distribution range. The pattern emerging from the genetic data was compared with current and past (last glacial maximum) species distribution modeling (SDM).ResultsWe identified seven deeply divergent parapatric clades which presumably remained isolated in different refugia scattered mainly throughout the Tyrrhenian coast. Conversely, the Adriatic coast showed only two haplogroups with low genetic variability. These results appear to agree with the SDM prediction at the last glacial maximum (LGM) indicating a narrow area of habitat suitability along the Tyrrhenian coast and much lower suitability along the Adriatic one. However, the considerable land exposure of the Adriatic coastline favored a glacial colonization of the Balkan Peninsula.ConclusionsOur population-level historical demography showed a common trend consistent with glacial expansions and regional persistence during the last glacial maximum. This complex genetic signature appears to be inconsistent with the expectation of the expansion-contraction model and post-LGM (re)colonizations from southern refugia. Hence it is one of an increasing number of cases in which these assumptions are not met, indicating that long-term fragmentation and pre-LGM events such as glacial persistence were more prominent in shaping genetic variation in this temperate species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0847-1) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

A combination of long term fragmentation and glacial persistence drove the evolutionary history of the Italian wall lizard Podarcis siculus

et al. 2017

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“…These patterns are consistent with previous sponge studies employing a variety of markers, which often attribute genetic differentiation to limited larval dispersal (Blanquer et al ., ; López‐Legentil & Pawlik, ; Blanquer & Uriz, ; Dailianis et al ., ; Pérez‐Portela et al ., ; Chaves‐Fonnegra et al ., ). Our previous work on C. vaginalis in Florida at a smaller spatial scale showed genomically discordant patterns of structure: COI haplotypes were geographically subdivided, while nuclear alleles were panmictic (DeBiasse et al ., , ). Coalescent simulations and neutrality tests supported population bottlenecks and sperm‐biased dispersal as possible drivers of mitonuclear discordance in C. vaginalis (DeBiasse et al ., ).…”

Section: Discussionmentioning

confidence: 99%

“…() and six nuclear protein‐coding genes (catalase, cata ; cathepsin, cps ; cirhin, cir ; elongation factor 1 alpha, ef ; filamin, fil ; macrophage expressed protein, mep ) in a subset of individuals in each location ( n = 100) using protocols in DeBiasse et al . (). Sequences were aligned in Geneious 4.5.5 (Drummond et al ., ).…”

Section: Methodsmentioning

confidence: 99%

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Shared phylogeographical breaks in a Caribbean coral reef sponge and its invertebrate commensals

DeBiasse

Richards

Shivji

et al. 2016

Journal of Biogeography

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Aim To test whether phylogeographical barriers in the brooding sponge Callyspongia vaginalis match breaks previously identified in the Caribbean. We also compared patterns of subdivision in the sponge to those of three of its commensals, the broadcast spawning brittle star Ophiothrix suensonii and the brooding amphipods Leucothoe ashleyae and L. kensleyi, and tested whether any shared breaks arose simultaneously. Location Florida, Bahamas and the Caribbean. Methods Subdivision of C. vaginalis populations was inferred from one mitochondrial (COI) and six nuclear loci using clustering analyses. We identified phylogeographical breaks in the sponge and its invertebrate commensals by determining geographical patterns of genetic variation and tested simultaneous population divergence across barriers shared among taxa using hierarchical approximate Bayesian computation. Results Sponge populations were partitioned into western and eastern groups across the Caribbean, with hierarchical subdivision within regions. The sponge and its commensals shared barriers across their ranges despite differences in dispersal strategy: C. vaginalis, L. ashleyae and O. suensonii populations in Central America were isolated from the remainder of the Caribbean, and all four taxa shared a break between Florida and the Bahamas, although simultaneous population divergence could not be inferred with statistical certainty. Our results also suggest cryptic speciation within C. vaginalis. Main conclusions Phylogeographical patterns in C. vaginalis largely matched barriers previously identified at the Florida Straits, Mona Passage and Bay of Honduras in other Caribbean taxa. Oceanographic features such as deep water between locations, strong currents, and eddies are likely mechanisms responsible for these breaks.

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“…Simulation-based techniques are also commonly applied to empirical systems, either to test competing hypotheses such as introgression and lineage sorting (e.g., refs. [12][13][14] or to test phylogeographic hypotheses against a null model (e.g., refs. [15][16][17].…”

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Phylogeographic model selection leads to insight into the evolutionary history of four-eyed frogs

Thomé

Carstens

2016

Proc. Natl. Acad. Sci. U.S.A.

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Phylogeographic research investigates biodiversity at the interface between populations and species, in a temporal and geographic context. Phylogeography has benefited from analytical approaches that allow empiricists to estimate parameters of interest from the genetic data (e.g., θ = 4Neμ, population divergence, gene flow), and the widespread availability of genomic data allow such parameters to be estimated with greater precision. However, the actual inferences made by phylogeographers remain dependent on qualitative interpretations derived from these parameters' values and as such may be subject to overinterpretation and confirmation bias. Here we argue in favor of using an objective approach to phylogeographic inference that proceeds by calculating the probability of multiple demographic models given the data and the subsequent ranking of these models using information theory. We illustrate this approach by investigating the diversification of two sister species of four-eyed frogs of northeastern Brazil using single nucleotide polymorphisms obtained via restriction-associated digest sequencing. We estimate the composite likelihood of the observed data given nine demographic models and then rank these models using Akaike information criterion. We demonstrate that estimating parameters under a model that is a poor fit to the data is likely to produce values that lead to spurious phylogeographic inferences. Our results strongly imply that identifying which parameters to estimate from a given system is a key step in the process of phylogeographic inference and is at least as important as being able to generate precise estimates of these parameters. They also illustrate that the incorporation of model uncertainty should be a component of phylogeographic hypothesis tests. information theory | model selection | Pleurodema | site frequency spectrum | Caatinga I n biological populations with interbreeding individuals, allele frequencies will inevitably change with time, both in stochastic and systematic manners, through neutral and adaptive processes. These processes-genetic drift, gene flow, mutation, recombination, and natural selection -constitute observable phenomena that lead directly to population structure, population divergence, and eventually speciation. Phylogeography is ideally situated to investigate systems where the microevolutionary processes that act within gene pools begin to form macroevolutionary patterns and has been described as the bridge between population genetics and phylogenetics (1). The power of the discipline comes from the consideration of geographic origin of individuals and populations along the continuum between populations and species (2, 3).Phylogeographic research has progressed through several stages since Avise et al.(1) introduced the term. Initial studies were based on information that can be gathered from the genetic data under few assumptions, for example by calculating summary statistics or estimating gene trees. Inferences were then derived from qualitative interpretations ...

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Evaluating summary statistics used to test for incomplete lineage sorting: mito‐nuclear discordance in the reef sponge Callyspongia vaginalis

Cited by 30 publications

References 101 publications

A combination of long term fragmentation and glacial persistence drove the evolutionary history of the Italian wall lizard Podarcis siculus

A combination of long term fragmentation and glacial persistence drove the evolutionary history of the Italian wall lizard Podarcis siculus

Shared phylogeographical breaks in a Caribbean coral reef sponge and its invertebrate commensals

Phylogeographic model selection leads to insight into the evolutionary history of four-eyed frogs

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