Speciation articles within Nature Communications

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  • Article
    | Open Access

    Little is known about the genetic basis of the rhythmic component of bird song, an important trait in sexual selection and species recognition. By studying a system with innate vocalizations, the Pogoniulus tinkerbirds, this study finds candidate genes that underlie differences in speed in vocal rhythm in this system.

    • Matteo Sebastianelli
    • , Sifiso M. Lukhele
    •  & Alexander N. G. Kirschel

  • Article
    | Open Access

    Hawaiian endemic mints represent the second largest plant radiation in the archipelago. Here, the authors present a reference genome and numerous resequenced individuals to uncover evidence for polyploidy, geographic speciation and localized hybridization underlying diversification in this lineage

    • Crystal M. Tomlin
    • , Sitaram Rajaraman
    •  & Charlotte Lindqvist

  • Article
    | Open Access

    In nature, soil, pollinators, and herbivores are the main drivers of plant adaptation and diversification. This study reveals that the interaction between soil and biotic pollination causes divergent evolution where pollinators play a key role, leading to strong divergence among plants in different soils.

    • Thomas Dorey
    •  & Florian P. Schiestl

  • Article
    | Open Access

    The relative importance of the various mechanisms that can drive microbial speciation is poorly understood. Here, Stanojković et al. explore the diversification of the soil cyanobacterium Microcoleus, showing that this genus represents a global speciation continuum of at least 12 lineages, with lineage divergence driven by selection, geographical distance, and the environment.

    • Aleksandar Stanojković
    • , Svatopluk Skoupý
    •  & Petr Dvořák

  • Article
    | Open Access

    The evolutionary origin of the domestic dog is uncertain. Here, the authors sequence the whole genomes of 9 extinct Japanese wolves and 11 modern Japanese dogs, applying a phylogenetic analysis to show that dogs may have originated in East Asia from a common ancestor with the Japanese wolf.

    • Jun Gojobori
    • , Nami Arakawa
    •  & Yohey Terai

  • Article
    | Open Access

    The origins of alpine plant diversity are unclear. Here, the authors provide a time-calibrated molecular phylogenetic tree for Saxifraga, a diverse alpine plant clade, and show that upslope biome shifts into the alpine zone occurred more often than dispersal between alpine regions.

    • Tom Carruthers
    • , Michelangelo S. Moerland
    •  & Wolf L. Eiserhardt

  • Article
    | Open Access

    Niche theory is often invoked to explain biodiversity, but it does not explain how species evolve to exploit unique niches. Using a combination of experimental and computational approaches, this study shows that resource competition can deform fitness landscapes, opening new pathways that promote ecological speciation.

    • Michael B. Doud
    • , Animesh Gupta
    •  & Justin R. Meyer

  • Article
    | Open Access

    Interactions with angiosperms are thought to have had a significant impact on insect diversification. Here, the authors use a Bayesian process-based approach to find that angiosperm radiation played a dual role that changed through time, mitigating insect extinction in the Cretaceous and promoting insect origination in the Cenozoic.

    • David Peris
    •  & Fabien L. Condamine

  • Article
    | Open Access

    The mechanisms generating montane biodiversity remain incompletely understood. Here, the authors study the passerine avifauna of Indo-Pacific island mountains, finding that Eurasian-origin species colonized directly from other mountains, while Australo-Papuan-origin species made upslope range shifts from the lowlands.

    • Andrew Hart Reeve
    • , Jonathan David Kennedy
    •  & Knud Andreas Jønsson

  • Article
    | Open Access

    Global spatiotemporal patterns of plant diversification are unclear. Here, the authors use a genus-level phylogeny and global distribution data for 14,244 flowering plant genera, finding a negative correlation between spatial patterns of diversification and genus diversity.

    • Dimitar Dimitrov
    • , Xiaoting Xu
    •  & Zhiheng Wang

  • Article
    | Open Access

    Scleractinian corals are important in both shallow and deep ecosystems. Here, the authors use global spatial distribution data with a phylogenetic approach to examine directionality and speed of colonization during depth diversification, finding an offshore-onshore pattern of evolution and that depth dispersion is associated with phenotypic innovations.

    • Ana N. Campoy
    • , Marcelo M. Rivadeneira
    •  & Chris Venditti

  • Article
    | Open Access

    While speciation rates vary across regions, the causes of this disparity and its impact on biodiversity patterns still puzzle scientists. Studying South American fish speciation, Cerezer et al. uncover key associations of body size evolution—especially rapid changes in uplands—with accelerated speciation.

    • Felipe O. Cerezer
    • , Cristian S. Dambros
    •  & Catherine H. Graham

  • Article
    | Open Access

    Do species with large ranges diversify faster? While there have been some studies suggesting the opposite pattern, this study indicates that large-ranged mammals indeed diversify faster in general, but that there are important geographic domains deviating from this pattern.

    • Jan Smyčka
    • , Anna Toszogyova
    •  & David Storch

  • Article
    | Open Access

    common assumption of evolution is that of an ecological limit to species diversity. This study tests whether sympatry with closely-related species leads to decreasing speciation rates. They find that, for terrestrial vertebrates, the probability of speciation seems to be unaffected by the number of other species of that lineage already present

    • Marcio R. Pie
    • , Raquel Divieso
    •  & Fernanda S. Caron

  • Article
    | Open Access

    The notothenioid radiation is a remarkable group of fish adapted to life in the icy waters of the Southern Ocean. This study investigates the evolutionary history of this group and the basis of their adaption to cold environments through genomic analysis of 24 new genome assemblies.

    • Iliana Bista
    • , Jonathan M. D. Wood
    •  & Richard Durbin

  • Article
    | Open Access

    The evolution and systematics of Madagascar’s extinct elephant birds remains unclear. Here, the authors recover genetic, stable isotope, morphological, and geographic data from fossil eggshell to describe variation among clades, identifying cryptic diversity and potential drivers of speciation.

    • Alicia Grealy
    • , Gifford H. Miller
    •  & Michael Bunce

  • Article
    | Open Access

    The impact of three extinction events during the Permo–Triassic interval on terrestrial invertebrates is unclear. Here, the authors find that key abiotic and biotic factors, including changes in floral assemblages, were correlated with changes in insect diversity through this interval.

    • Corentin Jouault
    • , André Nel
    •  & Fabien L. Condamine

  • Article
    | Open Access

    Here, the authors present a rare example of sympatric homoploid hybrid speciation, without ploidy changes, in the Midas cichlid fishes from Nicaragua. Midas cichlid hybrids occupy a different ecological niche, likely facilitated by body shape adaptations.

    • Melisa Olave
    • , Alexander Nater
    •  & Axel Meyer

  • Article
    | Open Access

    The genus Serratia includes clinically-important and diverse environmental bacteria. Here, Williams et al. assemble and analyse a representative set of 664 genomes from across the genus, including historic isolates, to provide a genome-based phylogenetic framework for a better understanding of the emergence of clinical and environmental lineages of Serratia.

    • David J. Williams
    • , Patrick A. D. Grimont
    •  & Sarah J. Coulthurst

  • Article
    | Open Access

    In this genomic study on Alpine whitefish radiations, the authors reveal details on the genetic architecture underlying the repeated eco-morphological diversification and the role of hybridization in the evolution of endemic whitefish species.

    • Rishi De-Kayne
    • , Oliver M. Selz
    •  & Philine G. D. Feulner

  • Article
    | Open Access

    Here, the authors use full-plastome phylogenomics and multiclade comparative models to reconstruct the tempo and drivers of six European Alpine angiosperm lineages before and during the Pleistocene. They find that geographic divergence and bedrock shifts drive speciation events, while diversification rates remained steady.

    • Jan Smyčka
    • , Cristina Roquet
    •  & Sébastien Lavergne

  • Article
    | Open Access

    Islands and mountaintops are often considered evolutionary dead ends. Using whole genomic data of 18 bird species and demographic models, the authors show that populations become isolated at high elevations, but disjunct montane populations maintain gene flow and thus the capacity for further colonisation.

    • José Martín Pujolar
    • , Mozes P. K. Blom
    •  & Knud Andreas Jønsson

  • Article
    | Open Access

    ‘Here, the authors use dummies of different Morpho butterfly species and sexes to investigate behaviour in patrolling butterflies, finding strong reproductive interference between species despite limited gene flow. They finally show that interference is mitigated by temporal partitioning, hence promoting the coexistence of sympatric Morpho species.’

    • Camille Le Roy
    • , Camille Roux
    •  & Violaine Llaurens

  • Article
    | Open Access

    Trait genetic architecture influences how populations evolve and adapt. Genomic analysis finds that an inversion links genetic variation controlling redpoll finch color and bill shape, allowing the maintenance of latitudinal ecotypes despite a genome largely homogenized by gene flow.

    • Erik R. Funk
    • , Nicholas A. Mason
    •  & Scott A. Taylor

  • Article
    | Open Access

    There are many hypotheses for why the tropics are more biodiverse than higher latitudes. Phylogenomic analyses of 21 montane birds finds that tropical birds disperse less and have more genetically structured populations than their counterparts at higher latitudes, possibly due to a larger elevational climate gradient in the tropics

    • Gregory Thom
    • , Marcelo Gehara
    •  & Fábio Raposo do Amaral

  • Article
    | Open Access

    Tooth morphology has provided many insights into the tempo and mode of dietary evolution in mammals. A study of fossil and extant squamates shows that this group also repeatedly evolved increasingly complex teeth with more flexibility than mammals, and that higher tooth complexity and herbivory likely led to higher speciation rates.

    • Fabien Lafuma
    • , Ian J. Corfe
    •  & Nicolas Di-Poï

  • 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

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