Examples Of Sympatric Speciation Research Articles

Ecological speciation in sympatric palms: 5. Evidence for pleiotropic speciation genes using gene knockout and high-throughput phenotyping

Abstract Theoretical models predict that sympatric, ecological speciation may be facilitated more readily when so-called ‘magic traits’ are present, linking traits under divergent selection with assortative mating. Such traits might be encoded by pleiotropic genes, that is, genes that affect multiple, apparently unrelated, phenotypes. However, few convincing examples of sympatric speciation exist, and empirical evidence for the role of magic traits in driving such speciation is rare. One of the strongest cases of sympatric speciation is the Howea palms of Lord Howe Island, Australia, comprising the sister species Howea belmoreana and Howea forsteriana, which have diverged due to soil substrate preferences and flowering time displacement. Here we investigate the role that pleiotropy may have played in the speciation process by carrying out high-throughput phenotyping experiments using 1830 Arabidopsis thaliana plants with knockouts of candidate Howea ‘speciation genes’. We identify several genes that show signatures of adaptive divergence between the Howea species and demonstrate pleiotropic roles in soil stress tolerance and flowering time, consistent with the Howea speciation scenario—notably, Howea orthologues of the A. thaliana loci At2-MMP, DCL1, RCD1, SAL1, and SIZ1. Empirical evidence is provided, therefore, for a range of pleiotropic genes with the potential to have driven sympatric speciation by generating magic traits which link divergent selection to non-random mating.

Sympatric speciation driving evolution of Late Ordovician brachiopod Zygospira in eastern North America

AbstractThe morphology of Zygospira, an early atrypide brachiopod, was analyzed using a multivariate approach. Principal component analysis and discriminant analysis clearly differentiated species as they are currently defined primarily based on differences in shell size and ornamentation but not in terms of overall shell shape. The older Zygospira modesta was able to persist into the late Katian (Richmondian) while smaller early species in other brachiopod lineages mostly went extinct. This may have been possible through niche partitioning because the smaller shells have been found attached to other filter feeders and no larger species have been found in these associations so far. This could represent a rare example of sympatric speciation preserved in the fossil record. In the future, detailed study of the spiralia and their associated structures may provide clues as to the ultimate evolutionary affinities of this group in relation to the other atrypide brachiopods evolving at this time.

Molecular and Morphological Investigations of Two Giant Diatom Cymbella Species from the Transbaikal Area (Russia, Siberia) with Comments on Their Distributions.

For the first time, a giant diatom species of the genus Cymbella from Lake Baikal was studied using molecular methods. Molecular and morphological investigations allowed to us to described one new species, Cymbella baicalaspera Glushchenko, Kulikovskiy and Kociolek sp. nov. This species is both morphologically similar and phylogenetically close to a second giant Cymbella species that we investigated here, identified by us as Cymbella himalaspera Jüttner and Van de Vijver in Jüttner et al. 2010. This species was first described from Nepal on the basis of a morphological investigation. Small morphological differences exist between the type population and specimens from Lake Baikal, but otherwise the two are identical. These very interesting results show that some Baikalian diatoms can be distributed more widely and are not only endemic to this ancient lake. Similarity between Cymbella baicalaspera sp. nov. and Cymbella himalaspera on the basis of both morphological features and their close phylogenetic relationships suggested by molecular data indicate they are sister species and an example of sympatric speciation. These results also suggest an early development of a species flock. This species group warrants additional research in terms of. their diversification and biogeography.

Trophic specialization on unique resources despite limited niche divergence in a celebrated example of sympatric speciation.

Trophic niche partitioning is observed in many adaptive radiations and is hypothesized to be a central process underlying species divergence. However, patterns of dietary niche partitioning are inconsistent across radiations and there are few studies of niche partitioning in putative examples of sympatric speciation. Here, we conducted the first quantitative study of dietary niche partitioning using stomach contents and stable isotope analyses in one of the most celebrated examples of sympatric speciation: the cichlid radiation from crater lake Barombi Mbo, Cameroon. We found little evidence for trophic niche partitioning among cichlids, including the nine species coexisting in the narrow littoral zone. Stable isotope analyses supported these conclusions of substantial dietary overlap. Our data, however, did reveal that five of eleven species consume rare dietary items, including freshwater sponge, terrestrial ants, and nocturnal foraging on shrimp. Stomach contents of the spongivore (Pungu maclareni) were 20% freshwater sponge, notable considering that only 0.04% of all fishes consume sponges. Overall, we conclude that cichlid species in lake Barombi Mbo overlap considerably in broad dietary niches-in part due to the large proportion of detritus in the stomach contents of all species-but there is evidence for divergence among species in their diet specializations on unique resources. We speculate that these species may utilize these additional specialized resources during periods of low resource abundance in support of Liem's paradox.

Resource partitioning is not coupled with assortative mating in sympatrically divergent ricefish in a Wallacean ancient lake.

Sympatric speciation is considered to be difficult without the coupling between ecological traits that allow resource partitioning and reproductive traits that allow assortative mating. Such "magic traits" are known to be involved in most of the compelling examples of sympatric speciation. In this study, we report a possible case of sympatric speciation without magic traits. Three species of ricefish (genus Oryzias) are suggested to have diverged sympatrically within Lake Poso, an ancient lake in Sulawesi. An analysis of genome-wide single-nucleotide polymorphisms showed that these three species are reproductively isolated from each other throughout the lake. Stable isotope analyses revealed that the three species use different food resources, which reflect differences in their feeding morphologies (gill rakers and digestive tracts) and feeding sites. Field and laboratory observations showed that O.nebulosus and O.orthognathus share a mating habitat of cobbles, where they scatter fertilized eggs, whereas this site is never used by O.nigrimas, indicating that assortative mating is partly achieved by spatial isolation. The small, less-adhesive eggs of O.nebulosus and O.orthognathus probably reflect their adaptation to spawning on cobble beaches. Laboratory mating experiments showed strong prezygotic isolation between O.nebulosus and O.orthognathus, which is achieved by strong species recognition presumably by both sexes based on species-specific mating dances and nuptial coloration. In summary, the assortative mating of O.nebulosus and O.orthognathus is probably not coupled to resource partitioning. We discussed how sympatric speciation among these species might have been achieved even without magic traits.

Genomic signatures of sympatric speciation with historical and contemporary gene flow in a tropical anthozoan (Hexacorallia: Actiniaria).

Sympatric diversification is recognized to have played an important role in the evolution of biodiversity. However, an in situ sympatric origin for codistributed taxa is difficult to demonstrate because different evolutionary processes can lead to similar biogeographic outcomes, especially in ecosystems that can readily facilitate secondary contact due to a lack of hard barriers to dispersal. Here we use a genomic (ddRADseq), model-based approach to delimit a species complex of tropical sea anemones that are codistributed on coral reefs throughout the Tropical Western Atlantic. We use coalescent simulations in fastsimcoal2 and ordinary differential equations in Moments to test competing diversification scenarios that span the allopatric-sympatric continuum. Our results suggest that the corkscrew sea anemone Bartholomea annulata is a cryptic species complex whose members are codistributed throughout their range. Simulation and model selection analyses from both approaches suggest these lineages experienced historical and contemporary gene flow, supporting a sympatric origin, but an alternative secondary contact model receives appreciable model support in fastsimcoal2. Leveraging the genome of the closely related Exaiptasia diaphana, we identify five loci under divergent selection between cryptic B.annulata lineages that fall within mRNA transcripts or CDS regions. Our study provides a rare empirical, genomic example of sympatric speciation in a tropical anthozoan and the first range-wide molecular study of a tropical sea anemone, underscoring that anemone diversity is under-described in the tropics, and highlighting the need for additional systematic studies into these ecologically and economically important species.

Speciation in Howea Palms Occurred in Sympatry, Was Preceded by Ancestral Admixture, and Was Associated with Edaphic and Phenological Adaptation.

Howea palms are viewed as one of the most clear-cut cases of speciation in sympatry. The sister species Howea belmoreana and H. forsteriana are endemic to the oceanic Lord Howe Island, Australia, where they have overlapping distributions and are reproductively isolated mainly by flowering time differences. However, the potential role of introgression from Australian mainland relatives had not previously been investigated, a process that has recently put other examples of sympatric speciation into question. Furthermore, the drivers of flowering time-based reproductive isolation remain unclear. We sequenced an RNA-seq data set that comprehensively sampled Howea and their closest mainland relatives (Linospadix, Laccospadix), and collected detailed soil chemistry data on Lord Howe Island to evaluate whether secondary gene flow had taken place and to examine the role of soil preference in speciation. D-statistics analyses strongly support a scenario whereby ancestral Howea hybridized frequently with its mainland relatives, but this only occurred prior to speciation. Expression analysis, population genetic and phylogenetic tests of selection, identified several flowering time genes with evidence of adaptive divergence between the Howea species. We found expression plasticity in flowering time genes in response to soil chemistry as well as adaptive expression and sequence divergence in genes pleiotropically linked to soil adaptation and flowering time. Ancestral hybridization may have provided the genetic diversity that promoted their subsequent adaptive divergence and speciation, a process that may be common for rapid ecological speciation.

Searching for Sympatric Speciation in the Genomic Era.

Sympatric speciation illustrates how natural and sexual selection may create new species in isolation without geographic barriers. However, recent genomic reanalyses of classic examples of sympatric speciation reveal complex histories of secondary gene flow from outgroups into the radiation. In contrast, the rich theoretical literature on this process distinguishes among a diverse range of models based on simple genetic histories and different types of reproductive isolating barriers. Thus, there is a need to revisit how to connect theoretical models of sympatric speciation and their predictions to empirical case studies in the face of widespread gene flow. Here, theoretical differences among different types of sympatric speciation and speciation-with-gene-flow models are reviewed and summarized, and genomic analysesare proposed for distinguishing which models apply to case studies based on the timing and function of adaptive introgression. Investigating whether secondary gene flow contributed to reproductive isolation is necessary to test whether predictions of theory are ultimately borne out in nature.

Don't throw out the sympatric speciation with the crater lake water: fine-scale investigation of introgression provides equivocal support for causal role of secondary gene flow in one of the clearest examples of sympatric speciation.

Genomic data has revealed complex histories of colonization and repeated gene flow previously unrecognized in some of the most celebrated examples of sympatric speciation and radiation. However, much of the evidence for secondary gene flow into these radiations comes from summary statistics calculated from sparse genomic sampling without knowledge of which specific genomic regions introgressed. This tells us little about how gene flow potentially influenced sympatric diversification. Here, we investigated whole genomes of Barombi Mbo crater lake cichlids for fine‐scale patterns of introgression with neighboring riverine cichlid populations. We found evidence of secondary gene flow into the radiation scattered across <0.24% of the genome; however, from our analyses, it is not clear if the functional diversity in these regions contributed to the ecological, sexual, and morphological diversity found in the lake. Unlike similar studies, we found no obvious candidate genes for adaptive introgression and we cannot rule out that secondary gene flow was predominantly neutral with respect to the diversification process. We also found evidence for differential assortment of ancestral polymorphisms found in riverine populations between sympatric sister species, suggesting the presence of an ancestral hybrid swarm. Although the history of gene flow and colonization is more complicated than previously assumed, the lack of compelling evidence for secondary gene flow's role in species diversification suggests that we should not yet rule out one of the most celebrated examples of sympatric speciation in nature without a more thorough investigation of the timing and functional role of each introgressed region.

Killer whales differentiating in geographic sympatry facilitated by divergent behavioural traditions.

Foote and Morin (2016) reanalyse data published in our recent RADseq studies (Moura et al., 2014a, 2015) to address questions about the likelihood of differentiation in sympatry among killer whale populations in the North Pacific. However, they describe a demic version of sympatric differentiation, requiring reproductive isolation to evolve by ‘ecologically driven disruptive selection’ from a background of panmixia. As they point out, questions have been raised about the potential for maintaining linkage between loci associated with ecotype and reproductive isolation, though there are some convincing putative examples of sympatric speciation by this mechanism (for example, Gavrilets et al., 2007). However, we emphasise the potential role of spatial/temporal segregation in the process, as have various authors (for example, Mallet et al., 2009). We have consistently described a process for killer whales whereby the ‘social facilitation of prey location and capture’ (Hoelzel et al., 2007) leads resource specialists to differential spatial and temporal habitat use, even while occupying overlapping geographic ranges, and suggested that this promotes assortative mating and differentiation by both genetic drift and selection (for example, Hoelzel et al., 2007; Moura et al., 2014a, 2015).

Multispecies Outcomes of Sympatric Speciation after Admixture with the Source Population in Two Radiations of Nicaraguan Crater Lake Cichlids.

The formation of species in the absence of geographic barriers (i.e. sympatric speciation) remains one of the most controversial topics in evolutionary biology. While theoretical models have shown that this most extreme case of primary divergence-with-gene-flow is possible, only a handful of accepted empirical examples exist. And even for the most convincing examples uncertainties remain; complex histories of isolation and secondary contact can make species falsely appear to have originated by sympatric speciation. This alternative scenario is notoriously difficult to rule out. Midas cichlids inhabiting small and remote crater lakes in Nicaragua are traditionally considered to be one of the best examples of sympatric speciation and lend themselves to test the different evolutionary scenarios that could lead to apparent sympatric speciation since the system is relatively small and the source populations known. Here we reconstruct the evolutionary history of two small-scale radiations of Midas cichlids inhabiting crater lakes Apoyo and Xiloá through a comprehensive genomic data set. We find no signs of differential admixture of any of the sympatric species in the respective radiations. Together with coalescent simulations of different demographic models our results support a scenario of speciation that was initiated in sympatry and does not result from secondary contact of already partly diverged populations. Furthermore, several species seem to have diverged simultaneously, making Midas cichlids an empirical example of multispecies outcomes of sympatric speciation. Importantly, however, the demographic models strongly support an admixture event from the source population into both crater lakes shortly before the onset of the radiations within the lakes. This opens the possibility that the formation of reproductive barriers involved in sympatric speciation was facilitated by genetic variants that evolved in a period of isolation between the initial founding population and the secondary migrants that came from the same source population. Thus, the exact mechanisms by which these species arose might be different from what had been thought before.

Structure of "species flocks" in fishes: Channels of the splanchnocranium divergence in endemic lacustrine benthivorous charrs (Salvelinus, Salmonidae, Teleostei) in Lake Kronotskoye, Kamchatka.

The structure of splanchnocranium bones has been studied in four endemic benthivorous charrs (the genus Salvelinus) from Lake Kronotskoe (Kamchatka). It has been found that, according to the whole set of characters of the splanchnocranium structure, the most expressed differences are observed between specialized forms, nosed and largemouth charrs, inhabiting different biotopes of the lake. Differences between small-mouth and white charrs are less pronounced, and the species are characterized by generalized features of the structure of jaws. It can be suggested that, in addition to diverse feeding preferences within a feeding niche, an extremely high diversity of charrs in Lake Kronotskoe is due to a complex geomorphological structure of the water system. Thus, the "species flock" comprising a complex set of diverse benthivorous morphotypes has been formed and exists in Lake Kronotskoe. Charrs from Lake Kronotskoe are a representative example of sympatric speciation by way of formation of new forms differing from each other in morphological, ecological, and trophic features.

The geography of hybrid speciation in plants

AbstractBoth homoploid and polyploid hybrid speciation are commonly considered straightforward examples of sympatric speciation. Based on 28 studies of homoploid and 34 studies of polyploid hybrid species I conclude that lati‐ / longitudinal and/or altitudinal ecogeographical displacement of hybrid lineages from parental lineages has been observed in the majority of cases examined, although more commonly in homoploid than in polyploid hybrid species. This ecogeographical displacement is interpreted as the result of evolutionary novelty in hybrid lineages. As the geographical scale of ecogeographical displacement in relation to gene flow distances may not be large enough to prevent gene flow at the time of initial hybrid formation, I hypothesize that climate‐induced changes of distribution ranges may have played a large role in hybrid species formation. In particular, I hypothesize that hybrid lineages initially remain in the secondary contact area of their parental lineages, whereas the parental lineages, responding to climate change, track their niches and withdraw from this contact area. This results in geographical isolation. I conclude that assessment of hybrid speciation as sympatric may be inappropriate in many cases, and that instead a phase of geographical displacement of hybrid and parental lineages into para‐ / allopatry may often be required.

Complex histories of repeated gene flow in Cameroon crater lake cichlids cast doubt on one of the clearest examples of sympatric speciation.

One of the most celebrated examples of sympatric speciation in nature are monophyletic radiations of cichlid fishes endemic to Cameroon crater lakes. However, phylogenetic inference of monophyly may not detect complex colonization histories involving some allopatric isolation, such as double invasions obscured by genome-wide gene flow. Population genomic approaches are better suited to test hypotheses of sympatric speciation in these cases. Here, we use comprehensive sampling from all four sympatric crater lake cichlid radiations in Cameroon and outgroups across Africa combined with next-generation sequencing to genotype tens of thousands of SNPs. We find considerable evidence of gene flow between all four radiations and neighboring riverine populations after initial colonization. In a few cases, some sympatric species are more closely related to outgroups than others, consistent with secondary gene flow facilitating their speciation. Our results do not rule out sympatric speciation in Cameroon cichlids, but rather reveal a complex history of speciation with gene flow, including allopatric and sympatric phases, resulting in both reproductively isolated species and incipient species complexes. The best remaining non-cichlid examples of sympatric speciation all involve assortative mating within microhabitats. We speculate that this feature may be necessary to complete the process of sympatric speciation in nature.

Genomic architecture of ecologically divergent body shape in a pair of sympatric crater lake cichlid fishes

Determining the genetic bases of adaptations and their roles in speciation is a prominent issue in evolutionary biology. Cichlid fish species flocks are a prime example of recent rapid radiations, often associated with adaptive phenotypic divergence from a common ancestor within a short period of time. In several radiations of freshwater fishes, divergence in ecomorphological traits - including body shape, colour, lips and jaws - is thought to underlie their ecological differentiation, specialization and, ultimately, speciation. The Midas cichlid species complex (Amphilophus spp.) of Nicaragua provides one of the few known examples of sympatric speciation where species have rapidly evolved different but parallel morphologies in young crater lakes. This study identified significant QTL for body shape using SNPs generated via ddRAD sequencing and geometric morphometric analyses of a cross between two ecologically and morphologically divergent, sympatric cichlid species endemic to crater Lake Apoyo: an elongated limnetic species (Amphilophus zaliosus) and a high-bodied benthic species (Amphilophus astorquii). A total of 453 genome-wide informative SNPs were identified in 240 F2 hybrids. These markers were used to construct a genetic map in which 25 linkage groups were resolved. Seventy-two segregating SNPs were linked to 11 QTL. By annotating the two most highly supported QTL-linked genomic regions, genes that might contribute to divergence in body shape along the benthic-limnetic axis in Midas cichlid sympatric adaptive radiations were identified. These results suggest that few genomic regions of large effect contribute to early stage divergence in Midas cichlids.

Weak Disruptive Selection and Incomplete Phenotypic Divergence in Two Classic Examples of Sympatric Speciation: Cameroon Crater Lake Cichlids

Recent documentation of a few compelling examples of sympatric speciation led to a proliferation of theoretical models. Unfortunately, plausible examples from nature have rarely been used to test model predictions, such as the initial presence of strong disruptive selection. Here I estimated the form and strength of selection in two classic examples of sympatric speciation: radiations of Cameroon cichlids restricted to Lakes Barombi Mbo and Ejagham. I measured five functional traits and relative growth rates in over 500 individuals within incipient species complexes from each lake. Disruptive selection was prevalent in both groups on single and multivariate trait axes but weak relative to stabilizing selection on other traits and most published estimates of disruptive selection. Furthermore, despite genetic structure, assortative mating, and bimodal species-diagnostic coloration, trait distributions were unimodal in both species complexes, indicating the earliest stages of speciation. Long waiting times or incomplete sympatric speciation may result when disruptive selection is initially weak. Alternatively, I present evidence of additional constraints in both species complexes, including weak linkage between coloration and morphology, reduced morphological variance aligned with nonlinear selection surfaces, and minimal ecological divergence. While other species within these radiations show complete phenotypic separation, morphological and ecological divergence in these species complexes may be slow or incomplete outside optimal parameter ranges, in contrast to rapid divergence of their sexual coloration.

Karyotypes in four species of Ranunculus (Ranunculaceae): Karyotypic variation in Mainland China and the Japanese Archipelago

Five species of Ranunculus such as R. brotherusii, R. sieboldii, R. chinensis and R. silerifolius were karyologically studied especially with respect to speciation. Ranunculus brotherusii had the karyotype of 32 small-sized chromosomes (x=8). Ranunculus sieboldii had two different cytotypes such as 2n=48 and 2n=64. The 2n=48 karyotypes of the species from Mainland China were similar to each other and were identical to the 2n=48 karyotype from the Japanese Archipelago. The 2n=48 karyotype consisted of two different chromosomal groups: One chromosomal group comprising 32 and the other chromosomal group comprising 16 chromosomes. The 2n=64 karyotype might be produced by the fertilization of a normal gamete and an unreduced gamete. The karyotypes of R. sieboldii evidenced that the hybridization might play an important role of speciation. Ranunculus chinensis had a single and stable karyotype with 2n=16 under a wide geographical distribution across Mainland China and the Japanese Archipelago. In R. silerifolius specimens from the Mainland China, two different karyotypes such as Mugi and Otaru-C were identified. The Mugi cytotype was widely distributed across Mainland China and the Japanese Archipelago. The new karyotype, Otaru-C, was proposed in specimens from Mainland China. Polymorphism of the cytotype in R. silerifolius in the Japanese Archipelago was pointed out as an example of sympatric speciation.

Swift sympatric adaptation of a species of cattle tick to a new deer host in New Caledonia

The occurrence and frequency of sympatric speciation in natural systems continue to be hotly debated issues in evolutionary biology. This might reflect the timescale over which evolution occurs resulting in there being few compelling observations of the phenomenon (lake fishes, phytophagous insects and Island trees). Despite predictions, few examples of sympatric speciation have been recorded in animal parasites, at least widely accepted as such. Here we show that, in New Caledonia, the monophasic (exploiting one individual host per generation) cattle tick Rhipicephalus microplus has evolved in contact with two sympatric host species into two differentiated genetic pools: on the cattle, its original host and on rusa deer, a new host for this tick. This sympatric isolation has occurred over a relative short period of time (i.e. less than 244 tick generations) as a consequence of differential selection pressure imposed by hosts. It is most likely that this phenomenon has occurred in many other places across the globe where this tick has come in contact with different host species in sympatry with cattle.

Evolution and ecophysiology of the industrial producer Hypocrea jecorina (Anamorph Trichoderma reesei) and a new sympatric agamospecies related to it.

Background Trichoderma reesei, a mitosporic green mould, was recognized during the WW II based on a single isolate from the Solomon Islands and since then used in industry for production of cellulases. It is believed to be an anamorph (asexual stage) of the common pantropical ascomycete Hypocrea jecorina.Methodology/Principal FindingsWe combined molecular evolutionary analysis and multiple methods of phenotype profiling in order to reveal the genetic relationship of T. reesei to H. jecorina. The resulting data show that the isolates which were previously identified as H. jecorina by means of morphophysiology and ITS1 and 2 (rRNA gene cluster) barcode in fact comprise several species: i) H. jecorina/T. reesei sensu stricto which contains most of the teleomorphs (sexual stages) found on dead wood and the wild-type strain of T. reesei QM 6a; ii) T. parareesei nom. prov., which contains all strains isolated as anamorphs from soil; iii) and two other hypothetical new species for which only one or two isolates are available. In silico tests for recombination and in vitro mating experiments revealed a history of sexual reproduction for H. jecorina and confirmed clonality for T. parareesei nom. prov. Isolates of both species were consistently found worldwide in pantropical climatic zone. Ecophysiological comparison of H. jecorina and T. parareesei nom. prov. revealed striking differences in carbon source utilization, conidiation intensity, photosensitivity and mycoparasitism, thus suggesting adaptation to different ecological niches with the high opportunistic potential for T. parareesei nom. prov.ConclusionsOur data prove that T. reesei belongs to a holomorph H. jecorina and displays a history of worldwide gene flow. We also show that its nearest genetic neighbour - T. parareesei nom. prov., is a cryptic phylogenetic agamospecies which inhabits the same biogeographic zone. These two species thus provide a so far rare example of sympatric speciation within saprotrophic fungi, with divergent ecophysiological adaptations and reproductive strategies.

Editorial and retrospective 2010

Editorial and retrospective 2010