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opencc-zeroFeb 2022View details →

A genome for Bidens hawaiensis: a member of a hexaploid Hawaiian plant adaptive radiation

Abstract The plant genus Bidens (Asteraceae or Compositae; Coreopsidae) is a species-rich and circumglobally distributed taxon. The 19 hexaploid species endemic to the Hawaiian Islands are considered an iconic example of adaptive radiation, of which many are imperiled and of high conservation concern. Until now, no genomic resources were available for this genus, which may serve as a model system for understanding the evolutionary genomics of explosive plant diversification. Here, we present a high-quality reference genome for the Hawai'i Island endemic species B. hawaiensis A. Gray reconstructed from long-read, high-fidelity sequences generated on a Pacific Biosciences Sequel II System. The haplotype-aware, draft genome assembly consisted of ~6.67 Giga bases (Gb), close to the holoploid genome size estimate of 7.56 Gb (± 0.44 SD) determined by flow cytometry. After removal of alternate haplotigs and contaminant filtering, the consensus haploid reference genome was comprised of 15,904 contigs containing ~3.48 Gb, with a contig N50 value of 422,594. The high interspersed repeat content of the genome, approximately 74%, along with hexaploid status, contributed to assembly fragmentation. Both the haplotype-aware and consensus haploid assemblies recovered >96% of Benchmarking Universal Single-copy Orthologs. Yet, the removal of alternate haplotigs did not substantially reduce the proportion of duplicated benchmarking genes (~79% versus ~68%). This reference genome will support future work on the speciation process during adaptive radiation, including resolving evolutionary relationships, determining the genomic basis of trait evolution, and supporting ongoing conservation efforts.

opencc-zeroFeb 2022View details →

Climate change and alpine-adapted insects: modelling environmental envelopes of a grasshopper radiation

Mountains create steep environmental gradients that are sensitive barometers of climate change. We modelled the environmental envelopes of twelve predominantly alpine, flightless grasshopper species in Aotearoa New Zealand, using current conditions and two future global climate change scenarios: representative concentration pathway (RCP) 2.6 (1.0 °C raise) and RCP8.5 (3.7 °C raise). Two thirds of our models suggested a reduced potential range across species by 2070, but surprisingly, for six species we predict an increase in potential suitable habitat under mild (+1.0°C) or severe global warming (+3.7°C). However, when we consider the limited dispersal ability of these grasshoppers, all twelve species studied are predicted to suffer extreme reductions in range, with a quarter likely to go extinct due to a 96-100% reduction in suitable habitat. Alpine species are particularly vulnerable to the impacts of climatic shifts, and species that have limited migratory ability will be particularly at risk of habitat loss, fragmentation and local extinction. Here we present the predicted outcomes for an endemic radiation of alpine taxa as an exemplar of the challenges that alpine species, both in New Zealand, and internationally, will face in light of anthropogenic climate change

opencc-zeroJun 2022View details →

Data from: Compensatory adaptation and diversification subsequent to evolutionary rescue in a model adaptive radiation

Biological populations may survive lethal environmental stress through evolutionary rescue. The rescued populations typically suffer a reduction in growth performance and harbour very low genetic diversity compared with their parental populations. The present study addresses how population size and within-population diversity may recover through compensatory evolution, using the experimental adaptive radiation of bacterium Pseudomonas fluorescens. We exposed bacterial populations to an antibiotic treatment; and then imposed a one-individual-size population bottleneck on those surviving the antibiotic stress. During the subsequent compensatory evolution, population size increased and leveled off very rapidly. The increase of diversity was of slower paces and persisted longer. In the very early stage of compensatory evolution, populations of large sizes had a greater chance to diversify; however, this productivity-diversification relationship was not observed in later stages. Population size and diversity from the end of the compensatory evolution was not contingent on initial population growth performance. We discussed the possibility that our results be explained by the emergence of a "holey" fitness landscape under the antibiotic stress.

opencc-zeroSep 2022View details →

Sexual dimorphism in an adaptive radiation: Does intersexual niche differentiation result in ecological character displacement?

Evolutionary radiations are one plausible explanation for the rich biodiversity on Earth. Adaptive radiations are the most studied form of evolutionary radiations and ecological opportunity has been identified as one factor permitting them. Competition among individuals is supposedly highest in populations of conspecifics. Divergent modes of resource use might minimize trophic overlap, and thus intersexual competition, resulting in ecological character displacement between sexes. However, the role of intersexual differentiation in speciation processes is insufficiently studied. The few studies available suggest that sexual niche differentiation exists in adaptive radiations, but their role within the radiation, and the extent of differentiation within the organism itself, remains largely unexplored. Here, we test the hypothesis that multiple morphological structures are affected by sexual niche differentiation in "roundfin" Telmatherina, the first case where sexual niche differentiation was demonstrated in an adaptive fish radiation. We show that sexes of two of the three morphospecies differ in several structural components of the head, all of these are likely adaptive. Sexual differentiation is linked to the respective morphospecies-specific ecology and affects several axes of variation. Trait variation translates into different feeding modes, processing types and habitat usages that add to interspecific variation in all three morphospecies. Intrasexual selection, i.e. male-male competition, may contribute to variation in some of the traits, but appears unlikely in internal structures which are invisible for other individuals. We conclude that intersexual variation adds to the adaptive diversity of roundfins, and might play a key role in minimizing intersexual competition in emerging radiations.

opencc-zeroJul 2024View details →

Adaptive radiation without independent stages of trait evolution in a group of Caribbean anoles

Adaptive radiation involves diversification along multiple trait axes, producing phenotypically diverse, species-rich lineages. Theory generally predicts that multi-trait evolution occurs via a 'stages' model, with some traits saturating early in a lineage's history, and others diversifying later. Despite its multidimensional nature, however, we know surprisingly little about how different suites of traits evolve during adaptive radiation. Here, we investigated the rate, pattern, and timing of morphological and physiological evolution in the anole lizard adaptive radiation from the Caribbean island of Hispaniola. Rates and patterns of morphological and physiological diversity are largely unaligned, belying independent selective pressures associated with structural and thermal niches. Cold tolerance evolution reflects parapatric divergence across elevation, rather than niche partitioning within communities. Heat tolerance evolution and the preferred temperature evolve more slowly than cold tolerance, reflecting behavioral buffering, particularly in edge-habitat species (a pattern associated with the Bogert effect). In contrast to the nearby island of Puerto Rico, closely related anoles on Hispaniola do not sympatrically partition thermal niche space. Instead, allopatric and parapatric separation across biogeographic and environmental boundaries serves to keep morphologically similar close relatives apart. The phenotypic diversity of this island's adaptive radiation accumulated largely as a by-product of time and historical biogeography, with surprisingly few exceptional pulses of trait evolution. A better understanding of the processes that guide multidimensional trait evolution (and nuance therein) will prove key in determining whether the stages model should be considered a common theme of adaptive radiation.

opennotspecifiedDec 2016View details →

Figure 3 in Adaptive Radiation in Socially Advanced Stem-Group Ants from the Cretaceous

Figure 3. Preferred Timescaled Consensus Cladogram of Cretaceous and Exemplar Extant Ants Based on a parsimony-based analysis of 42 morphological characters using implied weighting (K = 6.875) and a crown-group topology con- strained by previous molecular hypotheses [9]. Timescale included to demonstrate range of Cretaceous fauna: nodes and branch lengths do not correspond to actual diversification times or morphological change, although the earliest di- vergences are constrained not to exceed the age of the earliest aculeates (Bethylonymidae) in the very Late Jurassic [42]. Node values represent boot- strap support measures. See Supplemental Infor- mation for details of analytical procedures.

opennotspecifiedMay 2015View details →

Fig. 3 in The hypothesis of adaptive radiation in evolutionary biology: hard facts about a hazy concept

Fig. 3 Systematic characteristics of the groups having possibly radiated. a Number of case studies (potentially several case studies per article) recorded for each category of organism: angiosperms (n =210), nonangiosperm terrestrial plants (n = 36), "algae", non-terrestrial chlorophyllian lineages (n = 9), tetrapods (n = 381), non-tetrapod vertebrates (n =121), hexapods (n =153), non-hexapod invertebrates (n = 90), fungi, Eumycetes (n =22), non-metazoan heterotrophic eukaryotes

opennotspecifiedMay 2015View details →

Fig. 1 in The hypothesis of adaptive radiation in evolutionary biology: hard facts about a hazy concept

Fig. 1 Various metrics relative to the study of adaptive radiations over the 2003–2012 time period. a Number of articles extracted from the Web of Science™ database, after the third step of our search procedure (see the "Material and methods" section for details), for each journal and for each year. b Percentage of articles that examined the hypotheses of radiation

opennotspecifiedMay 2015View details →

Fig. 5 in The hypothesis of adaptive radiation in evolutionary biology: hard facts about a hazy concept

Fig. 5 Features of the insular systems investigated in studies about radiations between 2003 and 2012. Numbers and percentages are relative to case studies (potentially several case studies per article). a Location of the possible radiation. b Percentage of case studies for each of the island types identified in the dataset. c The Suski Inselberg, Maripasoula, French Guiana (credit: Corinne Sarthou). d Number of

opencc-zeroDec 2010View details →

Data from: Population genomic tests of models of adaptive radiation in Lake Victoria region cichlid fish.

Adaptive radiation is usually thought to be associated with speciation, but the evolution of intraspecific polymorphisms without speciation is also possible. The radiation of cichlid fish in Lake Victoria is perhaps the most impressive example of a recent rapid adaptive radiation, with 600+ very young species. Key questions about its origin remain poorly characterized, such as the importance of speciation versus polymorphism, whether species persist on evolutionary time scales, and if speciation happens more commonly in small isolated or in large connected populations. We used 320 individuals from 105 putative species from Lakes Victoria, Edward, Kivu, Albert, Nabugabo and Saka, in a radiation-wide AFLP genome scan to address some of these questions. We demonstrate pervasive signatures of speciation supporting the classical model of adaptive radiation associated with speciation. A positive relationship between the age of lakes and the average genomic differentiation of their species, and a significant fraction of molecular variance explained by above-species level taxonomy suggest the persistence of species on evolutionary time scales, with radiation through sequential speciation rather than a single starburst. Finally the large gene diversity retained from colonization to individual species in every radiation suggests large effective population sizes and makes speciation in small geographical isolates unlikely.

opencc-zeroDec 2013View details →

Data from: Expanding the understanding of local community assembly in adaptive radiations

Communities are thought to be assembled by two types of filters: by the environment relating to the fundamental niche and by biotic interactions relating to the realized niche. Both filters include parameters related to functional traits, and their variation along environmental gradients. Here we infer the general importance of environmental filtering of a functional trait determining local community assembly within insular adaptive radiations on the example of Caribbean Anolis lizards. We constructed maps for the probability of presence of Anolis ecomorphs (ecology-morphology-behavior specialists) on the Greater Antilles and overlaid these to estimate ecomorph community completeness (ECC) over the landscape. We then tested for differences in environmental parameter spaces among islands for real and cross-fitted ECC values to see whether the underlying assembly filters are deterministic (i.e., similar among islands). We then compared information-theoretic models of climatic and landscape parameters among Greater Antillean islands and inferred whether body mass as functional trait determines ECC. We found areas with high ECC to be strongly correlated to environmental filters, partly related to elevation. The environmental parameters influencing high ECC differed among islands. With the exception of the Jamaican twig ecomorph (which we suspect to be misclassified), smaller ecomorphs were more restricted to higher elevations than larger ones which might reflect filtering on the basis of differential physiological restrictions of ecomorphs. Our results in Anolis show that local community assembly within adaptive island radiations of animals can be determined by environmental filtering of functional traits, independently from species composition and realized environmental niche space.

opencc-zeroDec 2011View details →

Data from: Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation

Although population genomic studies using next generation sequencing (NGS) data are becoming increasingly common, studies focusing on phylogenetic inference using these data are in their infancy. Here, we use NGS data generated from reduced representation genomic libraries of restriction-site-associated DNA (RAD) markers to infer phylogenetic relationships among 16 species of cichlid fishes from a single rocky island community within Lake Victoria's cichlid adaptive radiation. Previous attempts at sequence-based phylogenetic analyses in Victoria cichlids have shown extensive sharing of genetic variation among species and no resolution of species or higher-level relationships. These patterns have generally been attributed to the very recent origin (<15 000 years) of the radiation, and ongoing hybridization between species. We show that as we increase the amount of sequence data used in phylogenetic analyses, we produce phylogenetic trees with unprecedented resolution for this group. In trees derived from our largest data supermatrices (3 to >5.8 million base pairs in width), species are reciprocally monophyletic with high bootstrap support, and the majority of internal branches on the tree have high support. Given the difficulty of the phylogenetic problem that the Lake Victoria cichlid adaptive radiation represents, these results are striking. The strict interpretation of the topologies we present here warrants caution because many questions remain about phylogenetic inference with very large genomic data set and because we can with the current analysis not distinguish between effects of shared ancestry and post-speciation gene flow. However, these results provide the first conclusive evidence for the monophyly of species in the Lake Victoria cichlid radiation and demonstrate the power that NGS data sets hold to resolve even the most difficult of phylogenetic challenges.

opencc-zeroDec 2011View details →

Data from: Parsing parallel evolution: ecological divergence and differential gene expression in the adaptive radiations of thick-lipped Midas cichlid fishes from Nicaragua

The study of parallel evolution facilitates the discovery of common rules of diversification. Here, we examine the repeated evolution of thick lips in Midas cichlid fishes (the Amphilophus citrinellus species complex)—from two Great Lakes and two crater lakes in Nicaragua—to assess whether similar changes in ecology, phenotypic trophic traits and gene expression accompany parallel trait evolution. Using next-generation sequencing technology, we characterize transcriptome-wide differential gene expression in the lips of wild-caught sympatric thick- and thin-lipped cichlids from all four instances of repeated thick-lip evolution. Six genes (apolipoprotein D, myelin-associated glycoprotein precursor, four-and-a-half LIM domain protein 2, calpain-9, GTPase IMAP family member 8-like and one hypothetical protein) are significantly underexpressed in the thick-lipped morph across all four lakes. However, other aspects of lips' gene expression in sympatric morphs differ in a lake-specific pattern, including the magnitude of differentially expressed genes (97-510). Generally, fewer genes are differentially expressed among morphs in the younger crater lakes than in those from the older Great Lakes. Body shape, lower pharyngeal jaw size and shape, and stable isotopes (δ13C and δ15N) differ between all sympatric morphs, with the greatest differentiation in the Great Lake Nicaragua. Some ecological traits evolve in parallel (those related to foraging ecology; e.g. lip size, body and head shape) but others, somewhat surprisingly, do not (those related to diet and food processing; e.g. jaw size and shape, stable isotopes). Taken together, this case of parallelism among thick- and thin-lipped cichlids shows a mosaic pattern of parallel and nonparallel evolution.

opencc-zeroJul 2021View details →

Data from: Phylogenomic species delimitation dramatically reduces species diversity in an Antarctic adaptive radiation

Application of genetic data to species delimitation often builds confidence in delimitations previously hypothesized using morphological, ecological, and geographic data and frequently yields recognition of previously-undescribed cryptic diversity. However, a recent critique of genomic data-based species delimitation approaches is that they have the potential to conflate population structure with species diversity, resulting in taxonomic oversplitting. The need for an integrative approach to species delimitation, in which molecular, morphological, ecological, and geographic lines of evidence are evaluated together, is becoming increasingly apparent. Here, we integrate phylogenetic, population genetic, and coalescent analyses of genome-wide sequence data with investigation of variation in multiple morphological traits to delimit species within the Antarctic barbeled plunderfishes (Artedidraconidae: Pogonophryne). Pogonophryne currently comprises 29 valid species, most of which are distinguished solely by variation in ornamentation of the mental barbel that projects from the lower jaw, a structure previously shown to vary widely within a single species. However, our genomic and phenotypic analyses result in a dramatic reduction in the number of distinct species recognized within the clade, providing evidence to support the recognition of no more than six species. We propose to synonymize 24 of the currently recognized species with five species of Pogonophryne. We find genomic and phenotypic evidence for a new species of Pogonophryne from specimens collected in the Ross Sea. Our findings represent a rare example in which application of molecular data provides evidence of taxonomic oversplitting on the basis of morphology, clearly demonstrating the utility of an integrative species delimitation framework.

opencc-zeroDec 2020View details →

Predation shapes behavioral lateralization: insights from an adaptive radiation of livebearing fish

Hemispheric brain lateralization can drive the expression of behavioral asymmetry, or laterality, which varies notably both within and among species. To explain these left–right behavioral asymmetries in animals, predator-mediated selection is often invoked. Recent studies have revealed that a relatively high degree of lateralization correlates positively with traits known to confer survival benefits against predators, including escape performance, multitasking abilities, and group coordination. Yet, we still know comparatively little about 1) how consistently predators shape behavioral lateralization, 2) the importance of sex-specific variation, and 3) the degree to which behavioral lateralization is heritable. Here, we take advantage of the model system of the radiation of Bahamas mosquitofish (Gambusia hubbsi) and measure behavioral lateralization in hundreds of wild fish originating from multiple blue holes that differ in natural predation pressure. Moreover, we estimated the heritability of this trait using laboratory-born fish from one focal population. We found that the degree of lateralization but not the particular direction of lateralization (left or right) differed significantly across high and low predation risk environments. Fish originating from high-predation environments were more strongly lateralized, especially females. We further confirmed a genetic basis to behavioral lateralization in this species, with significant additive genetic variation in the population examined. Our results reveal that predation risk represents one key ecological factor that has likely shaped the origin and maintenance of this widespread behavioral phenomenon, even potentially explaining some of the sex-specific patterns of laterality recently described in some animals.

Figure 105 in The tribe Bryocorini (Insecta: Heteroptera: Miridae: Bryocorinae): phylogeny, description of a new genus, and adaptive radiation on ferns

Figure 105. Cladogram based on the topology of Fig. 104 showing tribes and subfamilies. Numbers above nodes indicate Bremer values.

Figures 79–87 in The tribe Bryocorini (Insecta: Heteroptera: Miridae: Bryocorinae): phylogeny, description of a new genus, and adaptive radiation on ferns

Figures 79–87. Aedeagi: 79, Cylapus citus; 80, 81, Bryocoris pteridis, 80, dorsal, 81, lateral; 82, 83, Diplazicoris lombokianus sp. nov., 82, dorsal, 83, lateral; 84, Sinervus baerensprungi; 85, Eurycipitia clarus; 86, Pycnoderes sp.; 87, Nesidiocoris tenuis. Figs 79–81, 85–87 modified from Kerzhner & Konstantinov (1999).

Figure 104. Most parsimonious tree obtained from the analysis using 68 in The tribe Bryocorini (Insecta: Heteroptera: Miridae: Bryocorinae): phylogeny, description of a new genus, and adaptive radiation on ferns

Figure 104. Most parsimonious tree obtained from the analysis using 68 morphological characters (tree length = 213 steps; consistency index, CI = 0.52; retention index, RI = 0.79). Characters are plotted showing fast optimization. Filled circles, non-homoplastic characters mapped by state (discontinuous characters are mapped as homoplasy); open circles, homoplastic characters. Nodes 1–15 are discussed in the text.

Figures 88–103 in The tribe Bryocorini (Insecta: Heteroptera: Miridae: Bryocorinae): phylogeny, description of a new genus, and adaptive radiation on ferns

Figures 88–103. Female genitalia: 88, 89, Diplazicoris lombokianus sp. nov., 88, posterior wall, 89, vulvar area; 90, 91, Hekista laudator, 90, vulvar area, 91, dorsal labiate plate; 92, Sixeonotus sp., vulvar area; 93, Helopeltis clavifer, dorsal labiate plate; 94–103, valvulae – 94, 95, D. lombokianus sp. nov., 94, first, 95, second; 96, 97, Bryocoris pteridis, 96, first, 97, second; 98, 99, Monalocoris filicis, 98, first, 99, second; 100, 101, Hekista laudator, 100, first, 101, second; 102, 103, Pycnoderes sp., 102, first, 103, second.

Figures 1–9 in The tribe Bryocorini (Insecta: Heteroptera: Miridae: Bryocorinae): phylogeny, description of a new genus, and adaptive radiation on ferns

Figures 1–9. Dorsal habitus of Bryocorini: 1, Coballorhynchus convexicollis; 2, Coballorhynchus concavus; 3, Hekista laudator; 4, 5, Bryocoris pteridis – 4, macropterous male, 5, brachypterous female; 6, Diplazicoris lombokianus sp. nov.; 7, Bryocorella emboliata HT; 8, 9, Monalocoris filicis, females – 8, pale form, 9, dark form.