Adaptive radiation into ecological niches with eruptive dynamics: a comparison of tenthredinid and diprionid sawflies

The effect of the Cretaceous–Palaeogene (K–Pg) mass extinction on the evolution of many groups, including placental mammals, has been hotly debated. The fossil record suggests a sudden adaptive radiation of placentals immediately after the event, but several recent quantitative analyses have reconstructed no significant increase in either clade origination rates or rates of character evolution in the Palaeocene. Here we use stochastic methods to date a recent phylogenetic analysis of Cretaceous and Palaeocene mammals and show that Placentalia likely originated in the Late Cretaceous, but that most intraordinal diversification occurred during the earliest Palaeocene. This analysis reconstructs fewer than 10 placental mammal lineages crossing the K–Pg boundary. Moreover, we show that rates of morphological evolution in the 5 Myr interval immediately after the K–Pg mass extinction are three times higher than background rates during the Cretaceous. These results suggest that the K–Pg mass extinction had a marked impact on placental mammal diversification, supporting the view that an evolutionary radiation occurred as placental lineages invaded new ecological niches during the Early Palaeocene.

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Why are There so Many Bee-Orchid Species? Adaptive Radiation by Intraspecific Competition for Mnemonic Pollinators

10.20944/preprints201910.0204.v1 ◽

2019 ◽

Cited By ~ 1

Author(s):

Michel Baguette ◽

Joris Bertrand ◽

Virginie M. Stevens ◽

Bertrand Schatz

Keyword(s):

Adaptive Radiation ◽

Evolutionary Dynamics ◽

Evolutionary Relationship ◽

Ecological Niches ◽

Local Diversity ◽

Pollinator Species ◽

Main Driver ◽

Adaptive Radiations ◽

Suitable Habitats ◽

Species Specific

Adaptive radiations occur mostly in response to environmental variation through the evolution of key eco-morphological innovations that allow emerging species to occupy new ecological niches. However, rapid phenotypic evolution and the evolution of key novelties are likely to also occur when a couple or few species are engaged into narrow ecological interactions. To demonstrate coevolution is a difficult task; only elusive evidences confirm that coevolution is a driver of speciation and diversiﬁcation. Here we propose that the adaptive radiation of the Mediterranean orchid genus Ophrys, which gave rise to ca. 350 species since the apparition of the genus is due to the particular co-evolutionary dynamics between these plants and their pollinators. We suggest that the pollination by sexual swindle used by Ophrys orchids is the main driver of this coevolution. Flowers of each Ophrys species mimic sexually receptive females of one particular insect species, mainly bees. Male bees are attracted by pseudo-pheromones emitted by Ophrys flowers that are similar to the sexual pheromones of their females. Males lured by the flower shape, color and hairiness attempt to copulate with the flower, which glues pollen on their bodies. Pollen is eventually transferred to the stigma of another flower of the same Ophrys species during similar copulation attempts. Three observations led us to propose the scenario of an asymmetric co-evolutionary relationship between Ophrys and their pollinators. Firstly, there is a strong intra-specific competition among Ophrys individuals for the attraction of their species-specific pollinators, which is due to the high learning and memorization abilities of bees that record the pheromone signatures of kin or of previously courted partner to avoid (further) copulation attempts. Mnemonic pollinators induce thus a strong selective pressure for variation in the pseudo-pheromones emitted by individual flowers, which will potentially generate shifts in pollinator species, and hence Ophrys speciation. These pollinator shifts are adaptive for new Ophrys species because they may benefit from a competitor-free space. Secondly, such shifts in pollinator species are due to the random crossing of peaks in the olfactory landscape of the pollinator guild that is syntopic to each particular Ophrys population. This selective process on individual, random variation in pseudo-pheromone bouquets is followed by directional selection on flower phenotypes that will reinforce the attraction of the new pollinator. Thirdly, pollinators use the pseudo-pheromones emitted by Ophrys to locate suitable habitats from a distance within complex landscapes. Pollinators stay fixed for a while in these habitats by the local diversity of pseudo-pheromones, which increases their probability of encounter with a receptive female and hence the reproduction probability of both sexes. Conversely, pollinators disperse out of small suitable habitats once they have memorized the local diversity of sexual pseudo-pheromone bouquet or if fecundated Ophrys flowers repel pollinators, which decreases the probability of geitonogamy (plant advantage) but limit pollinator mating with locally emergent insect females, thus limiting inbreeding and favoring gene flow (pollinator advantage). Finally, we propose several research avenues that emerged according to this scenario of adaptive radiation by assymetric coevolution between Ophrys species and their pollinators.

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Evolution and adaptive radiation in the chydoridae (crustacea: cladocera): a study in comparative functional morphology and ecology

Philosophical Transactions of the Royal Society of London Series B Biological Sciences ◽

10.1098/rstb.1968.0017 ◽

1968 ◽

Vol 254 (795) ◽

pp. 221-384 ◽

Cited By ~ 182

Keyword(s):

Functional Morphology ◽

Adaptive Radiation ◽

Basic Mechanism ◽

Ecological Niches ◽

Anatomical Features ◽

Progressive Development ◽

The Family ◽

Ways Of Life ◽

Great Complexity ◽

Original Type

(Numbers given in the summary refer to certain key figures in the text which facilitate understanding.) An account is given of the functional morphology, ecology, habits and feeding mechanisms, of a representative series of anomopod cladocerans of the family Chydoridae, embracing some 22 species belonging to 15 genera. Of these genera two are defined as new on the basis of this investigation. Habits, which often depend on anatomical specializations of great complexity, are more diverse than has been supposed, and permit the exploitation of a diversity of ecological niches. The functional significance of many anatomical features is described. Carapace specializations, previously almost unstudied, are extremely important. Fundamental homologies not only within the Chydoridae but within the Anomopoda as a whole, can now be recognized and the feeding mechanism of all species can be related to one original type. By subtle modification of its various components, however, this basic mechanism has been adapted to very different ways of life and to different functions. The various species are described in a sequence which in part illustrates the progressive development of specialized ways of life rather than phylogeny, but light has been thrown on affinities, or lack of affinity, between certain species.

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Evolution and adaptive radiation in the Macrothricidae (Crustacea: Cladocera): A study in comparative functional morphology and ecology

Philosophical Transactions of the Royal Society of London Series B Biological Sciences ◽

10.1098/rstb.1974.0044 ◽

1974 ◽

Vol 269 (898) ◽

pp. 137-274 ◽

Cited By ~ 89

Keyword(s):

Functional Morphology ◽

Adaptive Radiation ◽

Basic Structure ◽

Ecological Niches ◽

Mechanical Handling ◽

The Family ◽

Primitive Feature ◽

Trunk Limbs ◽

Ways Of Life ◽

Great Complexity

An account is given of the functional morphology, ecology, habits and - in most cases - feeding mechanisms of representatives of 13 genera of anomopod cladocerans of the family Macrothricidae. As in the Chydoridae, habits, which often depend on anatomical specializations of great complexity, are diverse, and permit the exploitation of a wide variety of ecological niches. In general, locomotion is less specialized than in the Ghydoridae and most species neither swim nor creep so efficiently as do chydorids. So far as is known only one species, Macrothrix triseal , has evolved a chydorid-like method of crawling by means of the first trunk limbs but others have acquired means of locomotion peculiar to themselves. In only a few cases is the post-abdomen used for pushing, its lack of such employment and the lack of a joint between it and the trunk being primitive features. In basic structure and arrangement the trunk limbs are similar to those of the Chydoridae and the principles involved in many of the feeding mechanisms are the same in both families. By numerous, sometimes subtle, sometimes profound modifications of the components involved, this basic arrangement has been adapted to widely differing ways of life and different functions. Many macrothricids use the first trunk limbs for food collection rather than the second as in most chydorids. This is interpreted as a primitive feature. Acantholeberis curvirostris (figures 1-6), a frequenter of peaty pools, is primitive in several respects; for example, it lacks a headshield and is unable to push effectively with its post-abdomen, but exhibits several specializations. The antennae, which also serve as props and levers, are the principal means of locomotion, and have massive protopods flexed at about 90°. Progression is by means of intermittent ‘leaps’: steady swimming is not practised. Crawling by use of the first trunk limbs in a manner that foreshadows the efficient crawling of certain anomopods is feebly developed. Food collected by the first trunk limbs is dragged into the chamber made up by these and other trunk limbs (figures 8, 9), both mechanical handling and filtration being involved in its manipulation

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Adaptive introgression and de novo mutations increase access to novel fitness peaks on the fitness landscape during a vertebrate adaptive radiation

10.1101/2021.07.01.450666 ◽

2021 ◽

Author(s):

Austin H. Patton ◽

Emilie Richards ◽

Katelyn J. Gould ◽

Logan K. Buie ◽

Christopher Herbert Martin

Keyword(s):

Genetic Variation ◽

Adaptive Radiation ◽

De Novo ◽

Fitness Landscape ◽

Adaptive Landscape ◽

Ecological Niches ◽

San Salvador ◽

Adaptive Introgression ◽

Independent Field ◽

Adaptive Walks

Estimating the complex relationship between fitness and genotype or phenotype (i.e. the adaptive landscape) is one of the central goals of evolutionary biology. Empirical fitness landscapes have now been estimated for numerous systems, from phage to proteins to finches. However, the nature of adaptive walks connecting genotypes to organismal fitness, speciation, and novel ecological niches are still poorly understood. One outstanding system for addressing these connections is a recent adaptive radiation of ecologically and morphologically distinct pupfishes (a generalist, molluscivore, and scale-eater) endemic to San Salvador Island, Bahamas. Here, we leveraged whole-genome sequencing of 139 hybrids from two independent field fitness experiments to identify the genomic basis of fitness, visualize the first genotypic fitness networks in a vertebrate system, and infer the contributions of different sources of genetic variation to the accessibility of the fitness landscape. We identified 132 SNPs that were significantly associated with fitness in field enclosures, including six associated genes that were differentially expressed between specialists, and one gene (protein-lysine methyltransferase: METTL21E) misexpressed in hybrids, suggesting a potential intrinsic genetic incompatibility. We then constructed genotypic fitness networks from adaptive alleles and show that only introgressed and de novo variants, not standing genetic variation, increased the accessibility of genotypic fitness paths from generalist to specialists. Our results suggest that adaptive introgression and de novo variants provided key connections in adaptive walks necessary for crossing fitness valleys and triggering the evolution of novelty during adaptive radiation.

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Genomic bases underlying the adaptive radiation of core landbirds

BMC Ecology and Evolution ◽

10.1186/s12862-021-01888-5 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Yonghua Wu ◽

Yi Yan ◽

Yuanqin Zhao ◽

Li Gu ◽

Songbo Wang ◽

...

Keyword(s):

Adaptive Radiation ◽

Strong Support ◽

Bright Light ◽

Ecological Niches ◽

Ecological Diversification ◽

Fat Digestion ◽

Genome Wide ◽

Adaptive Enhancement ◽

Dietary Niche ◽

Dim Light

Abstract Background Core landbirds undergo adaptive radiation with different ecological niches, but the genomic bases that underlie their ecological diversification remain unclear. Results Here we used the genome-wide target enrichment sequencing of the genes related to vision, hearing, language, temperature sensation, beak shape, taste transduction, and carbohydrate, protein and fat digestion and absorption to examine the genomic bases underlying their ecological diversification. Our comparative molecular phyloecological analyses show that different core landbirds present adaptive enhancement in different aspects, and two general patterns emerge. First, all three raptorial birds (Accipitriformes, Strigiformes, and Falconiformes) show a convergent adaptive enhancement for fat digestion and absorption, while non-raptorial birds tend to exhibit a promoted capability for protein and carbohydrate digestion and absorption. Using this as a molecular marker, our results show relatively strong support for the raptorial lifestyle of the common ancestor of core landbirds, consequently suggesting a single origin of raptors, followed by two secondary losses of raptorial lifestyle within core landbirds. In addition to the dietary niche, we find at temporal niche that diurnal birds tend to exhibit an adaptive enhancement in bright-light vision, while nocturnal birds show an increased adaption in dim-light vision, in line with previous findings. Conclusions Our molecular phyloecological study reveals the genome-wide adaptive differentiations underlying the ecological diversification of core landbirds.

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Disentangling incomplete lineage sorting and introgression to refine species-tree estimates for Lake Tanganyika cichlid fishes

10.1101/039396 ◽

2016 ◽

Cited By ~ 4

Author(s):

Britta S Meyer ◽

Michael Matschiner ◽

Walter Salzburger

Keyword(s):

Adaptive Radiation ◽

Lake Tanganyika ◽

Genetic Material ◽

Species Tree ◽

Ecological Niches ◽

Species Flock ◽

Cichlid Fishes ◽

Coalescent Model ◽

Multispecies Coalescent ◽

History Of

Adaptive radiation is thought to be responsible for the evolution of a great portion of the past and present diversity of life. Instances of adaptive radiation, characterized by the rapid emergence of an array of species as a consequence to their adaptation to distinct ecological niches, are important study systems in evolutionary biology. However, because of the rapid lineage formation in these groups, and the occurrence of hybridization between the participating species, it is often difficult to reconstruct the phylogenetic history of species that underwent an adaptive radiation. In this study, we present a novel approach for species-tree estimation in rapidly diversifying lineages, where introgression is known to occur, and apply it to a multimarker dataset containing up to 16 specimens per species for a set of 45 species of East African cichlid fishes (522 individuals in total), with a main focus on the cichlid species flock of Lake Tanganyika. We first identified, using age distributions of most recent common ancestors in individual gene trees, those lineages in our dataset that show strong signatures of past introgression. This led us to formulate three hypotheses of introgression between different lineages of Tanganyika cichlids: the ancestor of Boulengerochromini (or of Boulengerochromini and Bathybatini) received genomic material from the derived H-lineage; the common ancestor of Cyprichromini and Perissodini experienced, in turn, introgression from Boulengerochromini and/or Bathybatini; and the Lake Tanganyika Haplochromini and closely related riverine lineages received genetic material from Cyphotilapiini. We then applied the multispecies coalescent model to estimate the species tree of Lake Tanganyika cichlids, but excluded the lineages involved in these introgression events, as the multispecies coalescent model does not incorporate introgression. This resulted in a robust species tree, in which the Lamprologini were placed as sister lineage to the H-lineage (including the Eretmodini), and we identify a series of rapid splitting events at the base of the H-lineage. Divergence ages estimated with the multispecies coalescent model were substantially younger than age estimates based on concatenation, and agree with the geological history of the Great Lakes of East Africa. Finally, we formally tested the three hypotheses of introgression using a likelihood framework, and find strong support for introgression between some of the cichlid tribes of Lake Tanganyika.

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Selection on old variants drives adaptive radiation of Metrosideros across the Hawaiian Islands

10.1101/2020.11.03.354068 ◽

2020 ◽

Author(s):

Jae Young Choi ◽

Xiaoguang Dai ◽

Julie Z. Peng ◽

Priyesh Rughani ◽

Scott Hickey ◽

...

Keyword(s):

Adaptive Radiation ◽

Recurrent Selection ◽

Balancing Selection ◽

Hawaiian Islands ◽

Ecological Niches ◽

Gene Pools ◽

Ecological Diversity ◽

Founder Populations ◽

Adaptive Radiations ◽

Remote Islands

AbstractSome of the most spectacular adaptive radiations begin with founder populations on remote islands. How genetically limited founder populations give rise to the striking phenotypic and ecological diversity characteristic of adaptive radiations is a paradox of evolutionary biology. We conducted an evolutionary genomic analysis of genus Metrosideros, a landscape-dominant, incipient adaptive radiation of woody plants that spans a striking range of phenotypes and environments across the Hawaiian Islands. Using nanopore-sequencing, we created a chromosome-level genome assembly for M. polymorpha var. incana and analyzed wholegenome sequences of 131 individuals from 11 taxa sampled across the islands. We found evidence of population structure that grouped taxa by island. Demographic modeling showed concordance between the divergence times of island-specific lineages and the geological formation of individual islands. Gene flow was also detected within and between island taxa, suggesting a complex reticulated evolutionary history. We investigated genomic regions with increased differentiation as these regions may harbor variants involved in local adaptation or reproductive isolation, thus forming the genomic basis of adaptive radiation. We discovered differentiation outliers have arisen from balancing selection on ancient divergent haplotypes that formed before the initial colonization of the archipelago. These regions experienced recurrent divergent selection as lineages colonized and diversified on new islands, and hybridization likely facilitated the transfer of these ancient variants between taxa. Balancing selection on multiple ancient haplotypes–or time-tested variants–may help to explain how lineages with limited gene pools can rapidly diversify to fill myriad ecological niches on remote islands.Significance statementSome of the most spectacular adaptive radiations of plants and animals occur on remote oceanic islands, yet such radiations are preceded by founding events that severely limit genetic variation. How genetically depauperate founder populations give rise to the spectacular phenotypic and ecological diversity characteristic of island adaptive radiations is not known. We generated novel genomic resources for Hawaiian Metrosideros––a hyper-variable incipient adaptive radiation of woody taxa—for insights into the paradox of remote island radiations. We found that Metrosideros colonized each island shortly after formation and diversified within islands through recurrent selection on ancient variations that predate the radiation. Recurring use of ancient variants may explain how genetically depauperate lineages can diversify to fill countless niches on remote islands.

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Adaptive Radiation of the Flukes of the Family Fasciolidae Inferred from Genome-Wide Comparisons of Key Species

Molecular Biology and Evolution ◽

10.1093/molbev/msz204 ◽

2019 ◽

Vol 37 (1) ◽

pp. 84-99 ◽

Cited By ~ 4

Author(s):

Young-Jun Choi ◽

Santiago Fontenla ◽

Peter U Fischer ◽

Thanh Hoa Le ◽

Alicia Costábile ◽

...

Keyword(s):

Adaptive Radiation ◽

Fasciola Hepatica ◽

Fasciola Gigantica ◽

Fatty Acid Binding Proteins ◽

Ecological Niches ◽

Secretory Proteins ◽

Effective Population ◽

Fatty Acid Binding ◽

Key Species ◽

The Family

Abstract Liver and intestinal flukes of the family Fasciolidae cause zoonotic food–borne infections that impact both agriculture and human health throughout the world. Their evolutionary history and the genetic basis underlying their phenotypic and ecological diversity are not well understood. To close that knowledge gap, we compared the whole genomes of Fasciola hepatica, Fasciola gigantica, and Fasciolopsis buski and determined that the split between Fasciolopsis and Fasciola took place ∼90 Ma in the late Cretaceous period, and that between 65 and 50 Ma an intermediate host switch and a shift from intestinal to hepatic habitats occurred in the Fasciola lineage. The rapid climatic and ecological changes occurring during this period may have contributed to the adaptive radiation of these flukes. Expansion of cathepsins, fatty-acid-binding proteins, protein disulfide-isomerases, and molecular chaperones in the genus Fasciola highlights the significance of excretory–secretory proteins in these liver-dwelling flukes. Fasciola hepatica and Fasciola gigantica diverged ∼5 Ma near the Miocene–Pliocene boundary that coincides with reduced faunal exchange between Africa and Eurasia. Severe decrease in the effective population size ∼10 ka in Fasciola is consistent with a founder effect associated with its recent global spread through ruminant domestication. G-protein-coupled receptors may have key roles in adaptation of physiology and behavior to new ecological niches. This study has provided novel insights about the genome evolution of these important pathogens, has generated genomic resources to enable development of improved interventions and diagnosis, and has laid a solid foundation for genomic epidemiology to trace drug resistance and to aid surveillance.

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Continental cichlid radiations: functional diversity reveals the role of changing ecological opportunity in the Neotropics

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2016.0556 ◽

2016 ◽

Vol 283 (1836) ◽

pp. 20160556 ◽

Cited By ~ 15

Author(s):

Jessica Hilary Arbour ◽

Hernán López-Fernández

Keyword(s):

Central America ◽

Adaptive Radiation ◽

Morphological Diversity ◽

Evolutionary Rates ◽

Ecological Niches ◽

Ecological Opportunity ◽

Ecological Release ◽

Adaptive Radiations ◽

Lineage Diversification

Adaptive radiations have been hypothesized to contribute broadly to the diversity of organisms. Models of adaptive radiation predict that ecological opportunity and ecological release, the availability of empty ecological niches and the response by adapting lineages to occupy them, respectively, drive patterns of phenotypic and lineage diversification. Adaptive radiations driven by ‘ecological opportunity’ are well established in island systems; it is less clear if ecological opportunity influences continent-wide diversification. We use Neotropical cichlid fishes to test if variation in rates of functional evolution is consistent with changing ecological opportunity. Across a functional morphological axis associated with ram–suction feeding traits, evolutionary rates declined through time as lineages diversified in South America. Evolutionary rates of ram–suction functional morphology also appear to have accelerated as cichlids colonized Central America and encountered renewed opportunity. Our results suggest that ecological opportunity may play an important role in shaping patterns of morphological diversity of even broadly distributed lineages like Neotropical cichlids.

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