Profound genetic divergence and asymmetric parental genome contributions as hallmarks of hybrid speciation in polyploid toads.

The evolutionary causes and consequences of allopolyploidization, an exceptional pathway to instant hybrid speciation, are poorly investigated in animals. In particular, when and why hybrid polyploids versus diploids are produced, and constraints on sources of paternal and maternal ancestors, remain underexplored. Using the Palearctic green toad radiation (including bisexually reproducing species of three ploidy levels) as model, we generate a range-wide multi-locus phylogeny of 15 taxa and present four new insights: (i) at least five (up to seven) distinct allotriploid and allotetraploid taxa have evolved in the Pleistocene; (ii) all maternal and paternal ancestors of hybrid polyploids stem from two deeply diverged nuclear clades (6 Mya, 3.1-9.6 Mya), with distinctly greater divergence than the parental species of diploid hybrids found at secondary contact zones; (iii) allotriploid taxa possess two conspecific genomes and a deeply diverged allospecific one, suggesting that genomic imbalance and divergence are causal for their partly clonal reproductive mode; (iv) maternal versus paternal genome contributions exhibit asymmetry, with the maternal nuclear (and mitochondrial) genome of polyploids always coming from the same clade, and the paternal genome from the other. We compare our findings with similar patterns in diploid/polyploid vertebrates, and suggest deep ancestral divergence as a precondition for successful allopolyploidization

Phylogeography of Aegean green toads (Bufo viridis subgroup): continental hybrid swarm vs. insular diversification with discovery of a new island endemic

BACKGROUND: Debated aspects in speciation research concern the amount of gene flow between incipient species under secondary contact and the modes by which post-zygotic isolation accumulates. Secondary contact zones of allopatric lineages, involving varying levels of divergence, provide natural settings for comparative studies, for which the Aegean (Eastern Mediterranean) geography offers unique scenarios. In Palearctic green toads (Bufo viridis subgroup or Bufotes), Plio-Pleistocene (~ 2.6 Mya) diverged species show a sharp transition without contemporary gene flow, while younger lineages, diverged in the Lower-Pleistocene (~ 1.9 Mya), admix over tens of kilometers. Here, we conducted a fine-scale multilocus phylogeographic analysis of continental and insular green toads from the Aegean, where a third pair of taxa, involving Mid-Pleistocene diverged (~ 1.5 Mya) mitochondrial lineages, earlier tentatively named viridis and variabilis, (co-)occurs. RESULTS: We discovered a new lineage, endemic to Naxos (Central Cyclades), while coastal islands and Crete feature weak genetic differentiation from the continent. In continental Greece, both lineages, viridis and variabilis, form a hybrid swarm, involving massive mitochondrial and nuclear admixture over hundreds of kilometers, without obvious selection against hybrids. CONCLUSIONS: The genetic signatures of insular Aegean toads appear governed by bathymetry and Quaternary sea level changes, resulting in long-term isolation (Central Cyclades: Naxos) and recent land-bridges (coastal islands). Conversely, Crete has been isolated since the end of the Messinian salinity crisis (5.3 My) and Cretan populations thus likely result from human-mediated colonization, at least since Antiquity, from Peloponnese and Anatolia. Comparisons of green toad hybrid zones support the idea that post-zygotic hybrid incompatibilities accumulate gradually over the genome. In this radiation, only one million years of divergence separate a scenario of complete reproductive isolation, from a secondary contact resulting in near panmixia

From Africa to Europe and back: refugia and range shifts cause high genetic differentiation in the Marbled White butterfly Melanargia galathea

<p>Abstract</p> <p>Background</p> <p>The glacial-interglacial oscillations caused severe range modifications of biota. Thermophilic species became extinct in the North and survived in southern retreats, e.g. the Mediterranean Basin. These repeated extinction and (re)colonisation events led to long-term isolation and intermixing of populations and thus resulted in strong genetic imprints in many European species therefore being composed of several genetic lineages. To better understand these cycles of repeated expansion and retraction, we selected the Marbled White butterfly <it>Melanargia galathea</it>. Fourty-one populations scattered over Europe and the Maghreb and one population of the sibling taxon <it>M. lachesis </it>were analysed using allozyme electrophoresis.</p> <p>Results</p> <p>We obtained seven distinct lineages applying neighbour joining and STRUCTURE analyses: (i) Morocco, (ii) Tunisia, (iii) Sicily, (iv) Italy and southern France, (v) eastern Balkans extending to Central Europe, (vi) western Balkans with western Carpathian Basin as well as (vii) south-western Alps. The hierarchy of these splits is well matching the chronology of glacial and interglacial cycles since the Günz ice age starting with an initial split between the <it>galathea </it>group in North Africa and the <it>lachesis </it>group in Iberia. These genetic structures were compared with past distribution patterns during the last glacial stage calculated with distribution models.</p> <p>Conclusions</p> <p>Both methods suggest climatically suitable areas in the Maghreb and the southern European peninsulas with distinct refugia during the last glacial period and underpin strong range expansions to the North during the Postglacial. However, the allozyme patterns reveal biogeographical structures not detected by distribution modelling as two distinct refugia in the Maghreb, two or more distinct refugia at the Balkans and a close link between the eastern Maghreb and Sicily. Furthermore, the genetically highly diverse western Maghreb might have acted as source or speciation centre of this taxon, while the eastern, genetically impoverished Maghreb population might result from a relatively recent recolonisation from Europe via Sicily.</p

Genomic Evidence for Cryptic Speciation in Tree Frogs From the Apennine Peninsula, With Description of Hyla perrini sp. nov

Despite increasing appreciation of the speciation continuum, delimiting and describing new species is a major yet necessary challenge of modern phylogeography to help optimize conservation efforts. In amphibians, the lack of phenotypic differences between closely-related taxa, their complex, sometimes unresolved phylogenetic relationships, and their potential to hybridize all act to blur taxonomic boundaries. Here we implement a multi-disciplinary approach to evaluate the nature of two deeply-diverged mitochondrial lineages previously documented in Italian tree frogs (Hyla intermedia s. l.), distributed north and south of the Northern Apennine Mountains. Based on evidence from mitochondrial phylogenetics, nuclear phylogenomics, hybrid zone population genomics, niche modeling analyses, and biometric assessments, we propose that these lineages be considered distinct, cryptic species. Both mitochondrial and nuclear data affirm that they belong to two monophyletic clades of Pliocene divergence (~3.5 My), only admixing over a relatively narrow contact zone restricted to the southeast of the Po Plain (50–100 km). These characteristics are comparable to similarly-studied parapatric amphibians bearing a specific status. Inferred from their current geographic distribution, the two Italian tree frogs feature distinct ecological niches (&lt;15% of niche overlap), raising questions regarding potential adaptive components contributing to their incipient speciation. However, we found no diagnostic morphological and bioacoustic differences between them. This system illustrates the speciation continuum of Western-Palearctic tree frogs and identifies additional cryptic lineages of similar divergence to be treated as separate species (H. cf. meridionalis). We recommend combined approaches using genomic data as applied here for the future taxonomic assessment of cryptic diversity in alloparapatric radiations of terrestrial vertebrates, especially in controversial taxa. Finally, we formally described the northern Italian tree frogs as a new species, Hyla perrini sp. nov

Non-standard errors

In statistics, samples are drawn from a population in a data-generating process (DGP). Standard errors measure the uncertainty in estimates of population parameters. In science, evidence is generated to test hypotheses in an evidence generating process (EGP). We claim that EGP variation across researchers adds uncertainty: Non-standard errors (NSEs). We study NSEs by letting 164 teams test the same hypotheses on the same data. NSEs turn out to be sizable, but smaller for better reproducible or higher rated research. Adding peer-review stages reduces NSEs. We further find that this type of uncertainty is underestimated by participants