Speciation

  • Article
    | Open Access

    How ecological divergence causes reproductive isolation between populations in close contact remains poorly understood at the genomic level. This study presents a clinal investigation based on whole-genome sequencing to characterize reproductive isolation between threespine stickleback adapted to contiguous but ecologically different lake and stream habitats.

    • Quiterie Haenel
    • , Krista B. Oke
    •  & Daniel Berner
  • Article
    | Open Access

    Little is known on how mitonuclear interactions influence genomic divergence among hybrid and parental lineages. A study of hybridizing wood warbler species complex finds a nuclear gene block with mitochondrial functions coevolves with mitochondrial genome, driven by climate-associated divergent selection underlying hybrid-parental population divergence.

    • Silu Wang
    • , Madelyn J. Ore
    •  & Darren Irwin
  • Article
    | Open Access

    There are relatively few known extant adaptive radiations in Europe that predate the Pleistocene. Here, Borko et al. characterize the diversity and diversification of the subterranean amphipod genus Niphargus, showing evidence for a large adaptive radiation associated with massif uplift 15 million years ago.

    • Špela Borko
    • , Peter Trontelj
    •  & Cene Fišer
  • Article
    | Open Access

    Age-richness rate (ARR) estimates of evolutionary diversification are widely used to study factors that influence species richness among clades. Here the authors show that ARR inference is based on problematic assumptions and recommend against its use in comparison of past diversity or diversification rates across clades.

    • Daniel L. Rabosky
    •  & Roger B. J. Benson
  • Article
    | Open Access

    Many organisms, including moths, use pheromones to attract mates. A study using multiple genomic tools and gene editing identifies a new, neuronal gene underlying mate preference and shows that signal and response loci are in linkage disequilibrium despite being physically unlinked.

    • Melanie Unbehend
    • , Genevieve M. Kozak
    •  & Erik B. Dopman
  • Article
    | Open Access

    Animal signals often encode information on the emitter’s species identity. Using woodpecker drumming as a model, here the authors show that limited signal divergence during a clade radiation does not impair species discrimination, as long as the signals are adapted to local ecological requirements.

    • Maxime Garcia
    • , Frédéric Theunissen
    •  & Nicolas Mathevon
  • Article
    | Open Access

    The genetic mechanisms underlying mate choice decisions can inform our understanding of speciation. A study on Heliconius butterflies identifies 5 candidate genes that would allow sympatric species to evolve distinct preferences without altering their visual perception of the wider environment.

    • Matteo Rossi
    • , Alexander E. Hausmann
    •  & Richard M. Merrill
  • Article
    | Open Access

    Chinese chestnut is widely cultivated for nut production and harbors value as a genetic resource for restoration of American and European chestnut trees destroyed by chestnut blight. Here, the authors reveal the genomic basis of homoploid hybrid speciation within Castanea spp. and find the nonrandom distribution of reproductive barrier loci based on a high-quality reference genome.

    • Yongshuai Sun
    • , Zhiqiang Lu
    •  & Hui Ma
  • Article
    | Open Access

    There is mixed evidence for how temperature affects diversification rates. Here, authors use a supermatrix of nearly 20,000 rosid species, comprising almost a quarter of flowering plants, to show that tropical groups are older and speciated twice as slowly as their counterparts from cooler climates.

    • Miao Sun
    • , Ryan A. Folk
    •  & Robert P. Guralnick
  • Article
    | Open Access

    Both geography and ecology can drive the origins of new species. Siqueira et al. show how geological changes in the structure of Miocene reefs and the concurrent evolution of new feeding strategies combine to explain why coral reefs contain such a diversity of fish species.

    • Alexandre C. Siqueira
    • , Renato A. Morais
    •  & Peter F. Cowman
  • Article
    | Open Access

    It is generally thought many microbes, owing to their ubiquity and dispersal capability, lack biogeographic structuring and clear speciation patterns compared to macroorganisms. However, Pinseel et al. demonstrate multiple cycles of colonization and diversification in Pinnularia borealis, a rare biosphere soil diatom.

    • Eveline Pinseel
    • , Steven B. Janssens
    •  & Wim Vyverman
  • Article
    | Open Access

    Hybrid genomes provide a window into the speciation process over time. Here, Chaturvedi et al. use Lycaeides butterflies from hybrid zones of different ages to show that selection and recombination have repeatable effects on hybrid genome composition across timescales.

    • Samridhi Chaturvedi
    • , Lauren K. Lucas
    •  & Zachariah Gompert
  • 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

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