Speciation articles within Nature Communications

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  • Article
    | Open Access

    Acoustic communication is widespread, but not universal, across terrestrial vertebrates. Here, the authors show that acoustic communication evolved anciently, but independently, in most tetrapod groups and that these origins were associated with nocturnal activity.

    • Zhuo Chen
    •  & John J. Wiens

  • Article
    | Open Access

    Male orchid bees collect scents from the environment to attract females for mating. Here, Brand et al. combine population genomic, perfume chemistry, and functional analyses to show how divergence in odorant receptor genes may be driving reproductive divergence between two orchid bee species.

    • Philipp Brand
    • , Ismael A. Hinojosa-Díaz
    •  & Santiago R. Ramírez

  • Article
    | Open Access

    Recent studies have suggested that hybridization can facilitate adaptive radiations. Here, the authors show that opportunity for hybridization differentiates Lake Mweru, where cichlids radiated, and Lake Bangweulu, where cichlids did not radiate despite ecological opportunity in both lakes.

    • Joana I. Meier
    • , Rike B. Stelkens
    •  & Ole Seehausen

  • Article
    | Open Access

    Models of mate choice have mainly focused on the implications of female mate choice for reproductive isolation. Here, Aubier et al. develop a population genetic model of coevolution between female and male mate choice, which can lead the population to oscillate between assortative and random mating.

    • Thomas G. Aubier
    • , Hanna Kokko
    •  & Mathieu Joron

  • Article
    | Open Access

    Ecological speciation can proceed rapidly, but the origin of genetic variation facilitating it has remained elusive. Here, the authors show that secondary contact and introgression between deeply diverged lineages of stickleback fish facilitated rapid ecological speciation into lake and stream ecotypes in Lake Constance.

    • David A. Marques
    • , Kay Lucek
    •  & Ole Seehausen

  • Article
    | Open Access

    Hybridization across species can lead to offspring with reduced fertility. Here, the authors experimentally evolve yeast and show that whole-genome duplication during asexual reproduction can restore fertility in hybrids over a relatively short evolutionary timespan.

    • Guillaume Charron
    • , Souhir Marsit
    •  & Christian R. Landry

  • Article
    | Open Access

    The viviparity driven conflict hypothesis predicts the evolution of the placenta will suppress the evolution of traits associated with pre-copulatory mate choice and accelerate speciation rate. Furness et al. support the former and disprove the latter predictions with comparative analyses of the poecilid fishes.

    • Andrew I. Furness
    • , Bart J. A. Pollux
    •  & David N. Reznick

  • Article
    | Open Access

    Hybridization can contribute to diversity from the genomic to the species level. Here, Eberlein, Hénault et al. investigate genomic, transcriptomic and phenotypic variation among wild lineages of the yeast Saccharomyces paradoxus and suggest that an incipient species has formed by recurrent hybridization.

    • Chris Eberlein
    • , Mathieu Hénault
    •  & Christian R. Landry

  • Article
    | Open Access

    Turnovers in sex determination systems occur quite frequently, yet the evolutionary drivers of these turnovers are not well understood. Here, the authors study the sex determination systems in sticklebacks and propose chromosomal inversions as a possible driver of the evolution of sex determination.

    • Heini M. Natri
    • , Juha Merilä
    •  & Takahito Shikano

  • Article
    | Open Access

    Plants and fungi interact widely and in diverse ways, from mutualism to parasitism and decomposition. Here, Lutzoni et al. analyse the timing of plant and fungal evolutionary radiations and identify four major periods in which plant-fungal interactions likely drove lineage diversification.

    • François Lutzoni
    • , Michael D. Nowak
    •  & Susana Magallón

  • Article
    | Open Access

    The history and patterns of species diversity are shaped by a variety of ecological and evolutionary factors. Here, the authors develop a computational model to predict clade diversification dynamics and rates of speciation and extinction under the influences of resource competition, genetic differentiation, and random landscape fluctuation.

    • Robin Aguilée
    • , Fanny Gascuel
    •  & Regis Ferriere

  • Article
    | Open Access

    The speciation process tends to generate ‘genomic islands’ of increased divergence. Here, the authors use haplotype–resolved whole-genome sequences of European sea bass lineages to infer divergence history and show that linked selection generated genomic islands that resist introgression at secondary contact.

    • Maud Duranton
    • , François Allal
    •  & Pierre-Alexandre Gagnaire

  • Article
    | Open Access

    Speciation reversal is known mainly from recently diverged lineages that have come into secondary contact following anthropogenic disturbance. Here, Kearns et al. use genomic and phylogenomic analyses to show that the Common Raven (Corvus corax) was formed by the ancient fusion of two non-sister lineages of ravens.

    • Anna M. Kearns
    • , Marco Restani
    •  & Kevin E. Omland

  • Article
    | Open Access

    Centromeres and large-scale structural variants evolve and contribute to genome diversity during vertebrate speciation. Here Ichikawa et al perform de novo long-read genome assembly of three inbred medaka strains, and report long-range structure of centromeres and their methylation as well as correlation of structural variants with differential gene expression.

    • Kazuki Ichikawa
    • , Shingo Tomioka
    •  & Shinich Morishita

  • Article
    | Open Access

    The evolution of new sex chromosomes potentially generates reproductive isolation. Here, Bracewell et al. combine crossing experiments with population and functional genomics to characterize neo-sex chromosome evolution and incipient speciation in the mountain pine beetle, Dendroctonus ponderosae.

    • Ryan R. Bracewell
    • , Barbara J. Bentz
    •  & Jeffrey M. Good

  • Article
    | Open Access

    Microbes adapting to broad and specialized ranges of environments (generalists and specialists) have distinct ecological roles and properties. Via meta-analysis of community sequencing datasets, Sriswasdi et al. show that generalists have higher speciation rates and persistence advantage over specialists.

    • Sira Sriswasdi
    • , Ching-chia Yang
    •  & Wataru Iwasaki

  • Article
    | Open Access

    In animals with complex life cycles, selection on one life phase may constrain adaptation in another phase. Here the authors find that, during the adaptive radiation of mantellid frogs, the evolution of tadpole and adult morphologies has been uncoupled through phase-specific gene expression.

    • Katharina C. Wollenberg Valero
    • , Joan Garcia-Porta
    •  & Miguel Vences

  • Article
    | Open Access

    Cichlids underwent a rapid diversification in the Lake Victoria region, expanding to more than 700 species within 150,000 years. Here, Meier and colleagues show that an ancient hybridization between two divergent cichlid lineages generated high genetic diversity that facilitated the rapid radiation.

    • Joana I. Meier
    • , David A. Marques
    •  & Ole Seehausen

  • Article
    | Open Access

    Genetic linkage of ecologically relevant traits has been suggested to facilitate sympatric speciation. Here, Fruciano et al. show in sister species of cichlid fish the genetic non-independence of genomic regions responsible for differentiation in body size and pharyngeal jaw morphology, two characters associated with adaptive divergence in sympatry.

    • Carmelo Fruciano
    • , Paolo Franchini
    •  & Axel Meyer

  • Article
    | Open Access

    Species radiations can be driven by both adaptive and non-adaptive processes, but the relative importance of these drivers is unknown. Here, Nevado et al. show that multiple radiations in the New World lupins were associated with genome-wide accelerations in both coding and regulatory evolution, suggesting a strong influence of adaptive processes.

    • Bruno Nevado
    • , Guy W. Atchison
    •  & Dmitry A. Filatov

  • Article
    | Open Access

    Fruit flies gain valuable information about their environment by sensing chemicals. Here, Arguello et al. show strong signals of recent selection on the chemosensory system of the fruit fly Drosophila melanogaster, consistent with the adaptation of populations to their local chemical environment.

    • J. Roman Arguello
    • , Margarida Cardoso-Moreira
    •  & Richard Benton

  • Article
    | Open Access

    Live birth and an annual life cycle potentially enable access to new ecological niches and subsequent species diversification. Here, Helmstetter et al.build the phylogeny for fish in the order Cyprinodontiformes and find that, though live birth and annualism have each evolved multiple times, only live birth is associated with increased diversification.

    • Andrew J. Helmstetter
    • , Alexander S. T. Papadopulos
    •  & Vincent Savolainen

  • Article
    | Open Access

    Understanding the mechanism underlying the evolution of ecologically relevant traits is challenging. Here the authors show that changes in the Hox protein Ultrabithorax and its target genegiltcontribute to the evolution of long-mid-legs in water striders, a critical trait to escape predators.

    • David Armisén
    • , Peter Nagui Refki
    •  & Abderrahman Khila

  • Article
    | Open Access

    The European sea bass is an economically important fish species, which is subject to intense selective breeding. Here, the authors sequence the genome of the European sea bass and highlight gene family expansions underlying adaptation to salinity change, as well as the genomic architecture of speciation between two divergent sea bass lineages.

    • Mbaye Tine
    • , Heiner Kuhl
    •  & Richard Reinhardt

  • Article |

    Functional integration limits the potential for morphological differences to evolve. Here, the authors show an association between changes in skull morphology and evolutionary integration with feeding behaviour in eels.

    • David C. Collar
    • , Peter C. Wainwright
    •  & Rita S. Mehta

  • Article |

    Similar morphologies can evolve repeatedly in similar environments. Here, the authors show morphological, ecological and genetic differentiation between sympatric ecomorphs across two independent radiations of crater lake cichlids, but a different order of speciation events across radiations.

    • Kathryn R. Elmer
    • , Shaohua Fan
    •  & Axel Meyer

  • Article |

    It is unclear how mimetic radiations, the evolution of a species to resemble different model species, contribute to speciation. Here, the authors show patterns of mating behaviour and genetic divergence, suggesting that mimetic divergence has promoted incipient speciation in a group of Peruvian poison frogs.

    • Evan Twomey
    • , Jacob S. Vestergaard
    •  & Kyle Summers

  • Article |

    PRDM9 is a hybrid sterility gene in mammals; yet its role in primate evolution is unclear. Here, Schwartz et al. identify new PRDM9alleles in 64 primates and show rapid evolution throughout the primate lineage, which suggests that PRDM9 plays a major role in speciation.

    • Jerrod J. Schwartz
    • , David J. Roach
    •  & Jay Shendure

  • Article |

    Competition can promote genetic divergence and speciation, but empirical evidence for this is scarce. Here, Winkelmann et al.show that competition between cichlid fish in Lake Tanganyika promotes the use of rocks or shells for shelter, contributing to morphological and genetic divergence.

    • Kai Winkelmann
    • , Martin J. Genner
    •  & Lukas Rüber

  • Article
    | Open Access

    Hybrids often show poorer performance than their parents due to conflict between parental genes, but the underlying mechanisms are not well understood. Here, Chen et al. identify three genes that activate immune responses and hinder hybrids growth in rice, a finding that may help rice breeding.

    • Chen Chen
    • , Hao Chen
    •  & Hong-Xuan Lin

  • Article |

    Environmental fluctuation is known to promote biodiversity on ecological timescales, but its consequences for the evolution of biodiversity are unknown. Here, the authors report that alternations in environmental conditions help maintain evolved biodiversity in rapidly diversifying bacterial populations.

    • Jiaqi Tan
    • , Colleen K. Kelly
    •  & Lin Jiang

  • Article
    | Open Access

    The loss of flight in some insect lineages may promote allopatric differentiation and result in a high speciation rate. Here, using the carrion beetle, loss of flight is shown to accelerate allopatric speciation with higher genetic differentiation than for flight-capable species.

    • Hiroshi Ikeda
    • , Masaaki Nishikawa
    •  & Teiji Sota

  • Article
    | Open Access

    Populations of the same species living in different habitats can differ in sensory traits driving speciation, but it is not known if this variation limits gene flow. Here, a genetic and acoustic study of the bumblebee bat suggests that geographic distance, instead of echolocation divergence, limits gene flow.

    • Sébastien J. Puechmaille
    • , Meriadeg Ar Gouilh
    •  & Emma C. Teeling

  • Article |

    Harvestmen — Opiliones — are an ancient and diverse arachnid group with a limited fossil record. Here, X-ray micro-tomography of fossils reveals two new Carboniferous harvestmen species, allowing a phylogenetic analysis of these Palaeozoic Opiliones, demonstrating similarities between the fossils and extant groups.

    • Russell J. Garwood
    • , Jason A. Dunlop
    •  & Mark D. Sutton

  • Article |

    Migratory segregation presents a hypothesized barrier to gene flow among seabirds, but its mechanisms are unclear. Rayneret al. find that migratory habitat specialization, associated with breeding asynchrony and philopatry, restricts gene flow between two seabird populations migrating across the Pacific Ocean.

    • Matt J. Rayner
    • , Mark E. Hauber
    •  & Scott A. Shaffer

  • Article |

    The cryptic Wood White butterflies,Leptidea sinapis and Leptidea reali, represent a model for the study of speciation. Dincă et al. use DNA and chromosome data to show that this group, in fact, consists of a triplet of species, a result that provides a new perspective on cryptic biodiversity.

    • Vlad Dincă
    • , Vladimir A. Lukhtanov
    •  & Roger Vila

  • Article
    | Open Access

    A single gene results in either dextral or sinistral snail shell coiling and snails with different coils cannot copulate. Here, the authors provide evidence of how such an allele can become fixed in a population by showing that snails with a counterclockwise sinistral coil are protected from predators.

    • Masaki Hoso
    • , Yuichi Kameda
    •  & Michio Hori

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