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opencc-zeroNov 2023View details →

Data for: Pollinator and habitat-mediated selection as potential contributors to ecological speciation in two closely related species

In ecological speciation, incipient species diverge due to natural selection that is ecologically based. In flowering plants, different pollinators could mediate that selection (pollinator-mediated divergent selection) or other features of the environment that differ between habitats of two species could do so (environment-mediated divergent selection). Although these mechanisms are well understood, they have received little rigorous testing, as few studies of divergent selection across sites of closely related species include both floral traits that influence pollination and vegetative traits that influence survival. This study employed common gardens in sites of the two parental species and a hybrid site, each containing advanced generation hybrids along with the parental species, to test these forms of ecological speciation in plants of the genus Ipomopsis. Three vegetative traits (specific leaf area, leaf trichomes, and photosynthetic water-use efficiency) and five floral traits (corolla length and width, anther insertion, petal color, nectar production) were analyzed for impacts on fitness components (survival to flowering and seeds per flower, respectively). These traits exhibited strong clines across the elevational gradient in the hybrid zone, with narrower clines in theory reflecting stronger selection or higher genetic variance. Plants with long corollas and inserted anthers had higher seeds per flower at the I. tenuituba site, whereas selection favored the reverse condition at the I. aggregata site, a signature of divergent selection. In contrast, no divergent selection due to variation in survival was detected on any vegetative trait. Selection within the hybrid zone most closely resembled selection within the I. aggregata site. Across traits, the strength of divergent selection was not significantly correlated with width of the cline, which was better predicted by evolvability (standardized genetic variance). These results support the role of pollinator-mediated divergent selection in ecological speciation and illustrate the importance of genetic variance in determining divergence across hybrid zones.

opencc-by-4.0Nov 2023View details →

A step towards understanding plastic complexity: antimony speciation in consumer plastics and synthetic textiles revealed by XAS - supporting data

This dataset contains all data related to "A step towards understanding plastic complexity: antimony speciation in consumer plastics and synthetic textiles revealed by XAS"

opencc-by-4.0May 2019View details →

FIGURE 2 in Speciation with gene flow in marine systems

FIGURE 2 Cladogram of the hypotheses of Animalia (after Dunn et al., 2014) and Chromista (after CavalierSmith, 2018) phylogenies. Animalia and Chromista clades in which marine species have been described, are marked blue, with clades in which potential cases of ecological speciation with gene flow Downloaded from Brill.com 12/12/2023 03:01:49PM have been identified in orangevia. Open LettersAccess refer.toThis examples is an of openspecies accessshown articlein fig. 1. distributed under the terms of the prevailing CC-BY license at the time of publication. http://creativecommons.org/licenses/by-nc/4.0

opencc-by-4.0May 2019View details →

FIGURE 1 in Speciation with gene flow in marine systems

FIGURE 1 Examples of some species which potentially arose through ecological speciation with gene flow. The octocoral Eunicea flexuosa (a; photo by Y.W. Lau), the Caribbean hamlet Hypoplectrus unicolor (b; photo by O. Puebla), the intertidal gastropod Littorina saxatilis (c; photo by P. Larsson), the nudibranch Phestilla minor (d; photo by A. Fritts-Penniman), the Japanese greenling Hexagrammos otakii (e; photo by Z. Kanamoto), the corallivorous gastropod Coralliophila violacea (f; photo by S.E. Simmonds), the Downloaded from Brill.com 12/12/2023 03:01:49PM seahorse Hippocampus erectus (via g; Open photo by Access E.. RoseThis), the is an snapping open access shrimparticle Alpheus armatus distributed(h;under photothe terms by A. Anker), the undescribed, coral-associated of gobytheGobiodon prevailingsp. B (CC-BY i; photo licenseby P. at L. the Mundaytime),of and the publication. Caribbean sponge Chondrilla caribensis (j; photo by N.J. de Voogdhttp):. //creativecommons.org/licenses/by-nc/4.0

opencc-by-4.0May 2019View details →

FIGURE 3 in Speciation with gene flow in marine systems

FIGURE 3 Genetic mechanisms of single traits driving divergence. Disruptive selection acting on a mating cue (e.g., colour pattern or body size) targeted by a preference locus elsewhere in the genome ('classic magic trait', after Servedio et al., 2011) results into assortative mating (a). In case of habitat or host differentiation and mating on the host species, disruptive selection may directly lead to assortative mating (b), without the need for a preference locus ('automatic magic trait'). Figures after Servedio et al. (2011). Downloaded from Brill.com 12/12/2023 03:01:49PM via Open Access. This is an open access article distributed under the terms of the prevailing CC-BY license at the time of publication. http://creativecommons.org/licenses/by-nc/4.0

opencc-zeroJan 2024View details →

Pronounced differentiation on the Z chromosome and parts of the autosomes in crowned sparrows contrasts with mitochondrial paraphyly: implications for speciation

When a single species evolves into multiple descendent species, some parts of the genome can play a key role in the evolution of reproductive isolation while other parts flow between the evolving species via interbreeding. Genomic evolution during the speciation process is particularly interesting when major components of the genome—for instance, sex chromosomes vs. autosomes vs. mitochondrial DNA—show widely differing patterns of relationships between three diverging populations. The golden-crowned sparrow (Zonotrichia atricapilla) and the white-crowned sparrow (Zonotrichia leucophrys) are phenotypically differentiated sister species that are largely reproductively isolated despite possessing similar mitochondrial genomes, likely due to recent introgression. We assessed variation in more than 45,000 single nucleotide polymorphisms (SNPs) to determine the structure of nuclear genomic differentiation between these species and between two hybridizing subspecies of Z. leucophrys. The two Z. leucophrys subspecies showed moderate levels of relative differentiation and patterns consistent with a history of recurrent selection in both ancestral and daughter populations, with much of the sex chromosome Z and a large region on the autosome 1A showing increased differentiation compared to the rest of the genome. The two species Z. leucophrys and Z. atricapilla show high relative differentiation and strong heterogeneity in the level of differentiation among various chromosomal regions, with a large portion of the sex chromosome (Z) showing highly divergent haplotypes between these species. Studies of speciation often emphasize mitochondrial DNA differentiation, but speciation between Z. atricapilla and Z. leucophrys appears primarily associated with Z chromosome divergence and more moderately associated with autosomal differentiation, whereas mitochondria appear highly similar due apparently to recent introgression. These results add to the growing body of evidence for highly heterogeneous patterns of genomic differentiation during speciation, with some genomic regions showing lack of gene flow between populations many hundreds of thousands of years before other genomic regions.

opencc-zeroJan 2024View details →

Data from: Mating environments mediate the evolution of behavioral isolation during ecological speciation

The evolution of behavioral isolation is often the first step towards speciation. While past studies show that behavioral isolation will sometimes evolve as a by-product of divergent ecological selection, we lack a more nuanced understanding of factors that may promote or hamper its evolution. The environment in which mating occurs may be important in mediating whether behavioral isolation evolves for two reasons. Ecological speciation could occur as a direct outcome of different sexual interactions being favored in different mating environments. Alternatively, mating environments may vary in the constraint they impose on traits underlying mating interactions, such that populations evolving in a 'constraining' mating environment would be less likely to evolve behavioral isolation than populations evolving in a less constraining mating environment. In the latter, mating environment is not the direct cause of behavioral isolation but rather permits its evolution only if other drivers are present. We test these ideas with a set of 28 experimental fly populations, each of which evolved under one of two mating environments and one of two larval environments. Counter to the prediction of ecological speciation by mating environment, behavioral isolation was not maximal between populations evolved in different mating environments. Nonetheless, mating environment was an important factor as behavioral isolation evolved among populations from one mating environment but not among populations from the other. Though one mating environment was conducive to the evolution of behavioral isolation, it was not sufficient: assortative mating only evolved between populations adapting to different larval environments within that mating environment, indicating a role for ecological speciation. Intriguingly, the mating environment that promoted behavioral isolation is characterized by less sexual conflict compared to the other mating environment. Our results suggest that mating environments plays a key role in mediating ecological speciation via other axes of divergent selection.

Data and code used in "Adaptive expansion of ERVK solo-LTRs is associated with Passeriformes speciation events"

Data and code used in "Adaptive expansion of ERVK solo-LTRs is associated with Passeriformes speciation events"

Fig. 9 in Cryptic Speciation And Characteristics Of The Transition Bias Following An Example Of The Cytb Gene In Palearctic Mammals

Fig. 9. Variation of summarized tv/ts-index in micro- (1) and macromammals (2) depending on nucleotide substitution level. Thick lines illustrate exponential approximation.

Fig. 8 in Cryptic Speciation And Characteristics Of The Transition Bias Following An Example Of The Cytb Gene In Palearctic Mammals

Fig. 8. Variation of transition (upper lines) and transversion (lower lines) frequencies accordingly to substitution frequencies level. Think lines are empirical data for each subfamily/family, thick ones — polynomial approximations of averaged data.

Fig. 2 in Cryptic Speciation And Characteristics Of The Transition Bias Following An Example Of The Cytb Gene In Palearctic Mammals

Fig. 2. Average frequencies of nucleotide substitutions frequencies (sub) and its standard errors of the three taxonomical levels in micromammals (black) and macromammals (gray).

T a b l e 1 in Cryptic Speciation And Characteristics Of The Transition Bias Following An Example Of The Cytb Gene In Palearctic Mammals

T a b l e 1. Average (M), sample deviations (SD) of nucleotide substitution, ts/tv and F indexes of different taxonomical levels within 15 Palearctic mammal families/subfamilies

opencc-zeroNov 2021View details →

Competition and geography underlie speciation and morphological evolution in Indo-Australasian monitor lizards

How biotic and abiotic factors act together to shape biological diversity is a major question in evolutionary biology. The recent availability of large datasets and development of new methodological approaches provide new tools to evaluate the predicted effects of ecological interactions and geography on lineage diversification and phenotypic evolution. Here, we use a near complete phylogenomic-scale phylogeny and a comprehensive morphological dataset comprising more than a thousand specimens to assess the role of biotic and abiotic processes in the diversification of monitor lizards (Varanidae). This charismatic group of lizards shows striking variation in species richness among its clades and multiple instances of endemic radiation in Indo-Australasia (i.e., the Indo-Australian Archipelago and Australia), one of Earth's most biogeographically complex regions. We found heterogeneity in diversification dynamics across the family. Idiosyncratic biotic and geographic conditions appear to have driven diversification and morphological evolution in three endemic Indo-Australasian radiations. Furthermore, incumbency effects partially explain patterns in the biotic exchange between Australia and New Guinea. Our results offer insight into the dynamic history of Indo-Australasia, the evolutionary significance of competition, and the long-term consequences of incumbency effects.

opencc-zeroDec 2021View details →

Data for: Faster evolution of a premating reproductive barrier is not associated with faster speciation rates in New World passerine birds

Why are speciation rates so variable across the tree of life? One hypothesis is that this variation is explained by how rapidly reproductive barriers evolve. We tested this hypothesis by conducting a comparative study of the evolution of bird song, a premating barrier to reproduction. Speciation in birds is typically initiated when geographically isolated (allopatric) populations evolve reproductive barriers. We measured the strength of song as a premating barrier between closely related allopatric populations by conducting 2,339 field experiments to measure song discrimination for 175 taxon pairs of allopatric or parapatric New World passerine birds, and estimated recent speciation rates from a global molecular phylogeny of birds. Taxon pairs with high song discrimination in allopatry failed to regularly interbreed in parapatry, evidence that song discrimination is indeed an important reproductive barrier. However, evolutionary rates of song discrimination were not associated with recent speciation rates, and song discrimination evolves faster in suboscine passerines than their more species-rich sister clade, the oscines. Our findings support the long-held idea that song is a key premating reproductive barrier in birds, but show that faster evolution of this reproductive barrier between populations does not result in faster diversification betweeen species.

opencc-zeroDec 2021View details →

Acaulescence promotes speciation and shapes the distribution patterns of palms in Neotropical seasonally dry habitats

Rainforests have been a source of lineages to open and seasonally dry habitats throughout Angiosperm evolution, especially in the Neotropics. However, the underlying mechanisms that allow such shifts remain poorly understood at large spatial scales. Here, we test whether acaulescence (an underground stem or a very short stem concealed in the ground) has affected the colonization and speciation in Neotropical seasonally dry habitats by cocosoid palms (Cocoseae). Acaulescent species maintain their growth underground, which increases their chances of survival from prolonged seasonal dry season and frequent fires. We use an integrative approach based on trait‐dependent diversification models, phylogenetic comparative methods, and ecological niche models. We found that shifts towards acaulescent growth form were accompanied by evolutionary transitions to seasonally dry habitats. Acaulescent lineages had higher speciation rates than non-acaulescent ones. However, the interaction between acaulescence and seasonally dry habitats had no significant effect on Cocoseae speciation rates. Acaulescent palms are primarily distributed in Neotropical seasonally dry habitats and non-acaulescent palms are concentrated in Amazonian rainforests. Our results suggest that an underground stem, with high carbohydrate and water storage capacity, is a preadaptation by which rainforest lineages were able to colonize and diversify in new fire-prone, increasingly seasonal and drier adaptive zones. The projected global expansion of dry seasonal habitats requires an understanding of how drought-avoidance functional traits evolve and how they are linked to seasonally dry habitats. Our results are, thus, a step forward in determining plant response mechanisms to drier and seasonal conditions.

opencc-by-4.0Jan 2022View details →

Genomic signatures of isolation, hybridization, and selection during speciation of island finches

Data associated to the study Genomic signatures of isolation, hybridization, and selection during speciation of island finches Contents <ul> <li>Table_S9_samples_accession_nos.xlsx: Editable Excel matrix with sample names and accession numbers.</li> <li>RAD_SNPs_stacks_42424_loci.vcf.tar.gz: VCF file (gzip-compressed tarball) containing SNPs in 42,424 loci, based on analyses of restriction site-associated DNA (RAD) sequencing using Stacks.</li> <li>RAD_SNPs_standard_variant_calling.vcf.tar.gz: VCF file (gzip-compressed tarball) containing 131,661 SNPs from standard variant calling pipelines.</li> <li>mitochondrial_markers_full_data.nex: Nexus file containing mitochondrial (mt) sequences used for mt-phylogeny. Partitioned for COX2, tRNA-Lys, ATP8, and ATP6. </li> <li>sequences_nuclear_genotype_with_zebra_finch_TG.tar.gz: Directory (gzip-compressed tarball) containing genotype sequence (heterozygous sites with IUPAC codes) alignments of nuclear markers in nexus files. In addition to the study species, the sequence for zebra finch Taeniopygia guttata is included with sample code TG.</li> <li>sequences_nuclear_phased_and_mitochondrial_haplotypes_matching.tar.gz: Directory (gzip-compressed tarball) containing phased sequence (haplotype) alignments of nuclear markers in nexus files. These include only those individuals that match individuals sequenced for mitochondrial markers (also included here). In case of recombining loci, both the full locus and the largest non-recombining block are represented.</li> <li>sequences_nuclear_phased_haplotypes_all.tar.gz: Directory (gzip-compressed tarball) containing phased sequence (haplotype) alignments of nuclear markers in nexus files. These include all individuals. In case of recombining loci, both the full locus and the largest non-recombining block are represented.</li> <li>microsatellite_dataset.xlsx: Microsatellite datasets for the study species and additional outgroups. <ul> </ul> Sequences and short read datasets available from NCBI; accession numbers in Table S9 (Table_S9_samples_accession_nos.xlsx). </li> </ul>   Study summary Sister species occurring sympatrically on islands are rare and offer unique opportunities to understand how speciation can proceed in the face of gene flow. The São Tomé grosbeak is a massive-billed, ‘giant’ finch endemic to the island of São Tomé in the Gulf of Guinea, where it has diverged from its co-occurring sister species the Príncipe seedeater, an average-sized finch that also inhabits two neighbouring islands. Here, we show that the grosbeak carries a large number of unique alleles different from all three Príncipe seedeater populations, but also shares many alleles with the sympatric São Tomé population of the seedeater, a genomic signature signifying divergence in isolation as well as subsequent introgressive hybridization. Furthermore, genomic segments that remain unique to the grosbeak are situated close to genes, including genes that determine bill morphology, suggesting the preservation of adaptive variation through natural selection during divergence with gene flow. This study reveals a complex speciation process whereby genetic drift, introgression, and selection during periods of isolation and secondary contact all have shaped the diverging genomes of these sympatric island endemic finches.

opencc-zeroApr 2022View details →

Genomic evidence of speciation by fusion in a recent radiation of grasshoppers

Post-divergence gene flow can trigger a number of creative evolutionary outcomes, ranging from the transfer of beneficial alleles across species boundaries (i.e., adaptive introgression) to the formation of new species (i.e., hybrid speciation). While neutral and adaptive introgression has been broadly documented in nature, hybrid speciation is assumed to be rare and the evolutionary and ecological context facilitating this phenomenon still remains controversial. Through combining genomic and phenotypic data, we evaluate the hypothesis that the dual feeding regime (based on both scrub legumes and gramineous herbs) of the taxonomically controversial grasshopper Chorthippus saulcyi algoaldensis resulted from hybridization between the sister taxa C. binotatus (that exclusively feeds on scrub legumes) and C. saulcyi (that only feeds on gramineous herbs). Genetic clustering analyses and inferences from coalescent-based demographic simulations confirm that C. s. algoaldensis represents an independently evolving lineage and support the ancient hybrid origin of this taxon (ca. 1.4 Ma), which sheds light on its uncertain phylogenetic position and might explain its broader trophic niche. We propose a Pleistocene hybrid speciation model where range shifts resulting from climatic oscillations can promote the formation of hybrid swarms and facilitate its long-term persistence through geographic isolation from parental forms in topographically complex landscapes.

opencc-zeroMay 2022View details →

Whole-genome analysis of multiple wood ant population pairs supports similar speciation histories, but different degrees of gene flow, across their European ranges

The application of demographic history modelling and inference to the study of divergence between species has become a cornerstone of speciation genomics. Speciation histories are usually reconstructed by analysing single populations from each species, assuming that the inferred population history represents the actual speciation history. However, this assumption may not be met when species diverge with gene flow, e.g., when secondary contact may be confined to specific geographic regions. Here, we tested whether divergence histories inferred from heterospecific populations may vary depending on their geographic locations, using the two wood ant species Formica polyctena and F. aquilonia. We performed whole-genome resequencing of 20 individuals sampled in multiple locations across the European ranges of both species. Then, we reconstructed the histories of distinct heterospecific population pairs using a coalescent-based approach. Our analyses always supported a scenario of divergence with gene flow, suggesting that divergence started in the Pleistocene (ca. 500 kya) and occurred with continuous asymmetrical gene flow from F. aquilonia to F. polyctena until a recent time, when migration became negligible (2-19 kya). However, we found support for contemporary gene flow in a sympatric pair from Finland, where the species hybridise, but no signature of recent bidirectional gene flow elsewhere. Overall, our results suggest that divergence histories reconstructed from a few individuals may be applicable at the species level. Nonetheless, the geographical context of populations chosen to represent their species should be taken into account, as it may affect estimates of migration rates between species when gene flow is spatially heterogeneous.

opencc-zeroMay 2022View details →

Data from: Speciation in Nearctic oak gall wasps is frequently correlated with changes in host plant, host organ, or both

Quantifying the frequency of shifts to new host plants within diverse clades of specialist herbivorous insects is critically important to understand whether and how host shifts contribute to the origin of species. Oak gall wasps (Hymenoptera: Cynipidae: Cynipini) comprise a tribe of ~1000 species of phytophagous insects that induce gall formation on various organs of trees in the family Fagacae —primarily the oaks (genus Quercus; ~435 sp). The association of oak gall wasps with oaks is ancient (~50 my), and most oak species are galled by one or more gall wasp species. Despite the diversity of both gall wasp species and their plant associations, previous phylogenetic work has not identified the strong signal of host plant shifting among oak gall wasps that has been found in other phytophagous insect systems. However, most emphasis has been on the Western Palearctic and not the Nearctic where both oaks and oak gall wasps are considerably more species rich. We collected 86 species of Nearctic oak gall wasps from 10 of the 14 major clades of Nearctic oaks and sequenced >1000 Ultra Conserved Elements (UCEs) and flanking sequences to infer wasp phylogenies. We assessed the relationships of Nearctic gall wasps to one another and, by leveraging previously published UCE data, to the Palearctic fauna. We then used phylogenies to infer historical patterns of shifts among host tree species and tree organs. Our results indicate that oak gall wasps have moved between the Palearctic and Nearctic at least four times, that some Palearctic wasp clades have their proximate origin in the Nearctic, and that gall wasps have shifted within and between oak tree sections, subsections, and organs considerably more often than previous data have suggested. Given that host shifts have been demonstrated to drive reproductive isolation between host-associated populations in other phytophagous insects, our analyses of Nearctic gall wasps suggest that host shifts are key drivers of speciation in this clade, especially in hotspots of oak diversity. Though formal assessment of this hypothesis requires further study, two putatively oligophagous gall wasp species in our dataset show signals of host-associated genetic differentiation unconfounded by geographic distance, suggestive of barriers to gene flow associated with the use of alternative host plants.