Genomic evidence of speciation by fusion linked to trophic niche expansion in a recent radiation of grasshoppers

Mapping Intimacies ◽

10.1101/2021.12.26.474180 ◽

2021 ◽

Author(s):

Victor Noguerales ◽

Joaquin Ortego

Keyword(s):

Mechanistic Explanation ◽

Trophic Niche ◽

Hybrid Origin ◽

Phylogenetic Position ◽

Hybrid Speciation ◽

Phenotypic Data ◽

Climatic Oscillations ◽

Adaptive Introgression ◽

Hybrid Swarms ◽

Genetic Clustering

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 (scrub legumes and gramineous herbs) of the taxonomically controversial grasshopper Chorthippus saulcyi algoaldensis resulted from hybridization between two sister taxa that exhibit contrasting host-plant specializations: C. binotatus (scrub legumes) and C. saulcyi (gramineous herbs). Genetic clustering analyses and inferences from coalescent-based demographic simulations confirmed that C. s. algoaldensis represents a uniquely evolving lineage and supported the ancient hybrid origin of this taxon (ca. 1.4 Ma), which provides a mechanistic explanation for its broader trophic niche and sheds light on its uncertain phylogenetic position. 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.

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Genetic status of the putative hybrid swarms of mountain dwarf pine and Scots pine in contact zones of their distribution in Slovakia

Biologia ◽

10.1515/biolog-2015-0153 ◽

2015 ◽

Vol 70 (10) ◽

Author(s):

Peter Maňka ◽

Andrej Kormuťák ◽

Martin Galgóci ◽

Dušan Gömöry

Keyword(s):

Genetic Structure ◽

Scots Pine ◽

Molecular Level ◽

Natural Populations ◽

Hybrid Origin ◽

Putative Hybrid ◽

Hybrid Swarm ◽

Pure Species ◽

Hybrid Swarms ◽

History Of

AbstractGenetic structure of the mountain dwarf pine (Pinus mugo) and Scots pine (P. sylvestris) natural populations along with their 4 putative hybrid swarms in Slovakia were analyzed using 12 enzyme loci. The study aimed in evaluation of postulated hybrid status of the swarms on molecular level. Based on semidiagnostic allele frequencies of the MDH B, MDH C, 6PGDH B, ADH 1 and F-EST loci in their megagametophytes and vegetative buds, the conspicuous genetic differences were detected between P. mugo and P. sylvestris populations. The putative hybrid swarms seem to incline by their genetic structure to P. mugo rather than to P. sylvestris. Obtained results indicate independent developmental history of each of the scored hybrid swarms. The putative hybrid swarm in Sucha Hora was found to be a mixed stand consisting prevailingly of pure-species individuals of P. mugo and P. sylvestris. On the contrary, the putative hybrid swarms in Habovka, Tisovnica and Terchova are supposed to be of hybrid origin.

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EVOLUCIÓN RETICULADA POR HIBRIDACIÓN EN CORALES

Bulletin of Marine and Coastal Research ◽

10.25268/bimc.invemar.2014.43.2.2 ◽

2016 ◽

Vol 43 (2) ◽

Cited By ~ 1

Author(s):

Olga Lucía Torres Suárez

Keyword(s):

Introgressive Hybridization ◽

Reticulate Evolution ◽

Hybrid Speciation ◽

Reproductive Barriers ◽

Ancestral Polymorphism ◽

Adaptive Introgression ◽

Intermediate Morphology ◽

New Methodologies ◽

The Caribbean ◽

Published Research

Hybrid speciation and adaptive introgression have been recognized as mechanisms promoting biodiversity in animals. For corals with high morphological variation, hybridization is being considered as a possible explanation of phylogenetic incongruences. For instance, in the Caribbean Sea, it has been shown that Acropora prolifera contains a haplotype from each of its parents (A. cervicornis and A. palmata) and intermediate morphology. Because of the polyphyly and paraphyly, in addition to crosses between species, it is suggested that hybridization has an important role in the evolution of Acropora and other corals. Moreover, it has been proposed that the evolution of Acropora is in a reticulate pattern owing to a syngameon. Nevertheless, in some cases it has not been possible to state the reason of morphological and genetic variation since it was not possible to differentiate between introgressive hybridization and other process such as incomplete linage sorting, convergence and ancestral polymorphism selectively maintained. To review the empiric evidence of reticulate evolution by hybridization in corals, here, I reviewed published research on the morphologic and phylogenetic evidence of possible events of hybridization. Additionally, I analyzed the reproductive barriers and the results of interspecifi crosses of species that synchronically spawn their gametes. Moreover, I reviewed the effect of hybridization on coral biodiversity and a possible adaptation of corals under climate change. In conclusion, up today, there is no evidence of hybrid speciation in corals. Thus, the use of new methodologies of next generation is needed as a way to looking for hybridization or introgression signals in order to state whether hybrid speciation and/or adaptive introgression are forces driving the great coral diversity.

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The Phylogenetic Position of Vincetoxicum pannonicum (Borhidi) Holub Supports the Species' Allopolyploid Hybrid Origin

Acta Societatis Botanicorum Poloniae ◽

10.5586/asbp.8931 ◽

2020 ◽

Vol 89 (3) ◽

Cited By ~ 1

Author(s):

Orsolya Horváth ◽

Levente Laczkó ◽

Zsuzsa Lisztes-Szabó ◽

Attila Molnár V. ◽

Agnieszka Popiela ◽

...

Keyword(s):

Genome Size ◽

Hybrid Origin ◽

Phylogenetic Position ◽

Gene Trees ◽

Separate Species ◽

Diploid Parent ◽

Hybridization Event ◽

Pollen Donor ◽

Molecular Phylogenetic ◽

Allotetraploid Hybrid

The Pannonian endemic species Vincetoxicum pannonicum was described from specimens collected in Hungary and occurs at only few locations. It is considered “vulnerable” according to the International Red List. The chromosome set was reported to be tetraploid, and the species was hypothesized to be an allotetraploid hybrid of the Balkan species V. fuscatum and the Adriatic species hirundinaria subsp. adriaticum. We investigated the origin of V. pannonicum using molecular phylogenetic methods by separately analyzing the multicopy nuclear ribosomal internal transcribed spacer (nrITS) and the plastid-encoded trnH-psbA DNA regions and by evaluating discrepancies between the produced gene trees. Paralogs in the nrITS region clustered in two main groups, one of which was closest to V. fuscatum, and the other included V. hirundinaria subsp. adriaticum. According to trnH-psbA sequences, V. pannonicum and V. hirundinaria subsp. adriaticum formed a single group. Our results show that V. pannonicum diversified because of hybrid speciation, in which V. fuscatum was the pollen donor. We discovered a similar placement of V. maeoticum, which suggests a further hybridization event between V. fuscatum and a species of the V. hirundinaria group. Our genome-size estimate indicates almost sixfold larger genome size in V. pannonicum compared to the maternal diploid parent, suggesting hexaploidy; however, V. pannonicum is tetraploid. This may suggest cytological diploidization in the allopolyploid V. pannonicum. We observed substantial genetic distance between V. hirundinaria subsp. adriaticum and all other subspecies of V. hirundinaria, and we therefore propose that V. adriaticum should be regarded as a separate species.

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Evidence for continual hybridization rather than hybrid speciation betweenLigularia duciformisandL. paradoxa(Asteraceae)

PeerJ ◽

10.7717/peerj.3884 ◽

2017 ◽

Vol 5 ◽

pp. e3884 ◽

Cited By ~ 5

Author(s):

Rong Zhang ◽

Xun Gong ◽

Ryan Folk

Keyword(s):

Parental Species ◽

Reproductive Traits ◽

Issr Markers ◽

Natural Hybridization ◽

Hybrid Origin ◽

Phenotypic Traits ◽

Hybrid Species ◽

Network Analyses ◽

Hybrid Swarms ◽

Ssr Loci

BackgroundHybrids possess phenotypic traits that are often intermediate between their parental taxa, which commonly serves as evidence of hybridization in morphological analyses. Natural hybridization has been shown to occur frequently inLigularia(Asteraceae). In a previous study,Ligularia×maoniushanensiswas demonstrated as a natural hybrid species betweenL. duciformisandL.paradoxabased on morphological and reproductive traits.MethodsWe used three chloroplast (cpDNA) fragments (psbA-trnH,trnL-rpl32 andtrnQ-5′rps16), the nuclear ribosomal internal transcribed spacer (nrITS), and co-dominant SSR and dominant ISSR markers to study natural hybridization betweenL. duciformisandL. paradoxagrowing sympatrically in two locations. Parental taxa were inferred using network analyses of cpDNA and nrITS haplotypes. Admixture among individuals was examined using the Bayesian clustering programs STRUCTURE and NewHybrids based on the SSR and ISSR data; and potential introgression in the SSR loci was assessed using the INTROGRESS package.ResultsThe putative parental species were clearly distinguished from other sympatricLigulariaspecies by nrITS data, andL.×maoniushanensisindividuals were confirmed to be the hybrid offspring ofL.duciformisandL.paradoxa. Moreover, introgression was detected among several individuals morphologically identified asL.duciformisorL. paradoxa. Analyses of the cpDNA data revealed primarily unidirectional hybridization betweenL. duciformisandL. paradoxa, withL.paradoxaas the maternal parent in Mt. Maoniu, whereas bidirectional but asymmetrical hybridization was inferred to occur in Heihai Lake. The STRUCTURE analyses based on the SSR data detected two distinct clusters among the three taxa. The NewHybrids analyses showed that individuals circumscribed asL.×maoniushanensiswere dominated by early- and later-generation and backcrossing hybrids. The NewHybrids results based on the ISSR data were congruent with SSR results. In addition, introgression was detected in some SSR loci, and heterogeneity among loci was found in terms of detected patterns of introgression.ConclusionsOur data provide strong evidence for hybridization and introgression betweenL.duciformisandL.paradoxa.Ligularia×maoniushanensiswas demonstrated to be of hybrid origin. Since no evident reproductive isolation was found between the two parental species, detected hybrids appear to be part of hybrid swarms resulting from frequent and ongoing gene flow, which might impede the formation of a new hybrid species.

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Recent hybrid speciation at the origin of the narrow endemic Pulmonaria helvetica

Annals of Botany ◽

10.1093/aob/mcaa145 ◽

2020 ◽

Vol 127 (1) ◽

pp. 21-31 ◽

Cited By ~ 1

Author(s):

Sandra Grünig ◽

Markus Fischer ◽

Christian Parisod

Keyword(s):

Niche Differentiation ◽

Ecological Modelling ◽

Hybrid Origin ◽

Hybrid Speciation ◽

Niche Modelling ◽

Hybrid Species ◽

Intrinsic Factors ◽

Narrow Endemic ◽

Genetic Clusters ◽

Original Number

Abstract Background and Aims Hybridization is known to drive plant speciation through the establishment of homoploid or allopolyploid hybrid species. Here we investigate the origin of Pulmonaria helvetica, a narrow endemic species described across a restricted area of Switzerland that was entirely covered by ice during the last glacial maximum. This species presents an original number of chromosomes (2n = 24) and morphological traits suggestive of a hybrid origin. Methods We sequenced a plastid locus and 1077 double-digest restriction-site-associated DNA (ddRAD) loci in 67 individuals from across the distribution range of P. helvetica and candidate progenitor species growing in the same area. Assignment of genotypes to main genetic clusters within and among taxa using STRUCTURE tested whether P. helvetica represents a genetically differentiated lineage and addressed the hypothesis of its hybrid origin. Comparative ecological modelling further addressed possible niche differentiation among taxa. Key Results Pulmonaria helvetica was highlighted as a genetically homogeneous species distinct from co-occurring taxa. Consistent with a scenario of hybrid speciation, it presented clear evidence of balanced admixture between Pulmonaria officinalis (2n = 16) and Pulmonaria mollis s.l. (2n = 18, 22), which was also highlighted as a maternal progenitor based on plastid sequences. Limited genetic structure within the maternal progenitor is consistent with an origin of P. helvetica through either homoploid hybridization with considerable karyotype changes or via complex scenarios of allopolyploidy involving a dysploid taxon of P. mollis s.l. Comparative niche modelling indicated non-significant ecological differences between P. helvetica and its progenitors, supporting intrinsic factors resulting from hybridization as main drivers of speciation. Conclusions Hybridization appears as a major process having promoted the postglacial origin of the narrow endemic P. helvetica, suggesting hybrid speciation as an effective process that rapidly produces new species under climate changes.

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Phylogeny of the rock wallabies, Petrogale (Marsupialia: Macropodidae). Part II: Detection of hybridisation among macropodines

Australian Mammalogy ◽

10.1071/am09017 ◽

2010 ◽

Vol 32 (1) ◽

pp. 67

Author(s):

John A. W. Kirsch ◽

Olivier Gauthier ◽

Antoine Campeau-Péloquin ◽

Mark D. B. Eldridge ◽

François-Joseph Lapointe

Keyword(s):

Parental Species ◽

Phylogenetic Position ◽

Crossing Over ◽

Interspecific Hybridisation ◽

Hybrid Speciation ◽

Detection Criterion ◽

Hybrid Detection ◽

Dna Hybridisation ◽

In Captivity ◽

In The Wild

Phylogenetic relationships among rock-wallabies, Petrogale (Marsupialia: Macropodidae), have proven difficult to resolve. Given the documented interspecific hybridisation in the wild and the ease with which hybrids can be bred in captivity, introgression and hybrid speciation are likely explanations for these difficulties. In this paper, an attempt is made at using a phylogenetic approach to identify Petrogale hybrids of known origin. The Hybrid Detection Criterion (HDC) test is applied to DNA–DNA hybridisation data for 15 full species, two natural yard-bred hybrids, and two artificial hybrids from the same pairs of parental species. While the yard-bred hybrids elude detection with this technique, the artificial hybrids, consisting of equimolar mixture of parental extracts, are easily identified. Moreover, splitsgraphs constructed from five pairs of natural and artificial hybrids, including those evaluated with HDC, and their parents show that, in all cases but one, these two kinds of hybrids do not group together. Because the HDC assumes an intermediate phylogenetic position of the hybrid between its postulated parents, it is likely that unequal crossing-over, or another recombination event, affects the results of the test. These conclusions cast some doubt on the possibility of accurately detecting Petrogale hybrids with a phylogenetic approach.

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The evidence for species—phenotypic and genetic clustering

The Evolutionary Biology of Species ◽

10.1093/oso/9780198749745.003.0003 ◽

2019 ◽

pp. 30-51

Author(s):

Timothy G. Barraclough

Keyword(s):

Genetic Variation ◽

Dna Barcoding ◽

Population Genetic ◽

Genetic Data ◽

Single Locus ◽

Phenotypic Data ◽

Alternative Hypotheses ◽

Complex Models ◽

Genetic Clustering ◽

Rule Out

This chapter discusses how to detect evolutionary species, and how to test whether species are real and to evaluate the alternative hypotheses for the structure of diversity described in chapter 2. After outlining evidence from phenotypic data, such as surveys of morphology, it describes population genetic methods for delimiting species from single-locus genetic data, of the kind gathered by DNA barcoding and taxonomy initiatives. All forms of life display the same pattern of discrete clustering of genetic variation that is indicative of the existence of independently evolving groups, that is, species. This is perhaps the best comprehensive evidence we have for the reality of species, but it leaves open many further questions about the causes of that pattern, and does not rule out more complex models for the structure of diversity.

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Hybridization and genome evolution I: The role of contingency during hybrid speciation

Current Zoology ◽

10.1093/czoolo/59.5.667 ◽

2013 ◽

Vol 59 (5) ◽

pp. 667-674 ◽

Cited By ~ 5

Author(s):

Fabrice Eroukhmanoff ◽

Richard I. Bailey ◽

Glenn-Peter Sætre

Keyword(s):

Chromosome Number ◽

Genome Evolution ◽

Hybrid Speciation ◽

Parent Species ◽

Large Role ◽

Hybrid Species ◽

Intragenomic Conflict ◽

Hybrid Swarms ◽

Homoploid Hybrid

Abstract Homoploid hybrid speciation (HHS) involves the recombination of two differentiated genomes into a novel, functional one without a change in chromosome number. Theoretically, there are numerous ways for two parental genomes to recombine. Hence, chance may play a large role in the formation of a hybrid species. If these genome combinations can evolve rapidly following hybridization and sympatric situations are numerous, recurrent homoploid hybrid speciation is a possibility. We argue that three different, but not mutually exclusive, types of contingencies could influence this process. First, many of these “hopeful monsters” of recombinant parent genotypes would likely have low fitness. Only specific combinations of parental genomic contributions may produce viable, intra-fertile hybrid species able to accommodate potential constraints arising from intragenomic conflict. Second, ecological conditions (competition, geography of the contact zones or the initial frequency of both parent species) might favor different outcomes ranging from sympatric coexistence to the formation of hybrid swarms and ultimately hybrid speciation. Finally, history may also play an important role in promoting or constraining recurrent HHS if multiple hybridization events occur sequentially and parental divergence or isolation differs along this continuum. We discuss under which conditions HHS may occur multiple times in parallel and to what extent recombination and selection may fuse the parent genomes in the same or different ways. We conclude by examining different approaches that might help to solve this intriguing evolutionary puzzle.

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An unexpected donor in the adaptive introgression candidate Helianthus annuus subsp. texanus

10.1101/2020.11.26.398933 ◽

2020 ◽

Author(s):

Gregory. L Owens ◽

Marco Todesco ◽

Natalia Bercovich ◽

Jean-Sébastien Légaré ◽

Nora Mitchell ◽

...

Keyword(s):

Helianthus Annuus ◽

Entire Range ◽

Common Garden ◽

Whole Genome Sequencing Data ◽

Sequencing Data ◽

Phenotypic Data ◽

Adaptive Introgression ◽

Genome Wide ◽

Potential Test ◽

Donor Species

AbstractHybridization is widely acknowledged as an important mechanism of acquiring adaptive variation. In Texas, the sunflower Helianthus annuus subsp. texanus is thought to have acquired herbivore resistance and morphological traits via introgression from a local congener, H. debilis. Here we test this hypothesis using whole genome sequencing data from across the entire range of H. annuus and possible donor species, as well as phenotypic data from a common garden study. We find that although it is morphologically convergent with H. debilis, H. a. texanus has conflicting signals of introgression. Genome wide tests (Patterson’s D and TreeMix) only find evidence of introgression from H. argophyllus (sister species to H. annuus and also sympatric), but not H. debilis, with the exception of one individual of 109 analysed. We further scanned the genome for localized signals of introgression using PCAdmix and found minimal but non-zero introgression from H. debilis and significant introgression from H. argophyllus. Putative introgressions mainly occur in high recombination regions as predicted by theory if introgressed ancestry contains maladaptive alleles. To reconcile the disparate findings of our analyses, we discuss potential test-specific confounding features, including introgression from other taxa. Given the paucity of introgression from H. debilis, we argue that the morphological convergence observed in Texas is likely independent of introgression.

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Evidence of a Possible Double Hybrid Origin for Two Malagasy Species of Piper L. (Piperaceae)

10.20944/preprints202009.0083.v1 ◽

2020 ◽

Author(s):

Enrico Palchetti ◽

Massimo Gori ◽

Stefano Biricolti ◽

Alessandro Calamai ◽

Lorenzo Bini ◽

...

Keyword(s):

Amino Acid ◽

Hybrid Origin ◽

Phylogenetic Position ◽

Trnl Intron ◽

Unexpected Result ◽

Nuclear Markers ◽

African Species ◽

Asian Species ◽

Hybridization Event ◽

Close Relationship

two new species of genus Piper L. from Madagascar: Piper malgassicum and Piper tsarasotrae, were analyzed to investigate their phylogenetic position and evolutionary history. Both plastidial and nuclear markers were used for sequencing. The plastidial markers (ndhF and the trnL intron) showed a close relationship between the two species with respect to the other species of Piper. Both species appeared phylogenetically related to the African P. guineense and the Malagasian/Mascarenhas endemic P. borbonense. The nuclear marker (G3PDH) amplification produced two separate sets of sequences: “long” sequences, that could be easily translated into an amino acid chain, and “short” sequences, characterized by deletions that did not allowed to translate them correctly to an amino acid sequence. Analyzing together the nuclear sequences, we observed that the “long” sequence of P. tsarasotrae had a stricter relationship to the African accessions of P. guineense, while the accession of P. malgassicum was more strictly related to P. borbonense. On the contrary both “short” sequences of Piper malgassicum and Piper tsaratsotrae resulted phylogenetically related to Asian accessions and more distantly related to the formerly cited species. This unexpected result was tentatively explained with a more ancient hybridization event between an ancestor of P. malgassicum and P. tsarasotrae (and possibly P. borbonense) and an Asian species of Piper. The Asian contribution would have produced the ancestors of the “short” sequences that would eventually have lost functionality by deletions, becoming paralogs. A more recent hybridization event would have led to the separation of Piper malgassicum from Piper tsarasotrae with an African pollen-derived genome contribution from P. guineense or, more probably, an ancestor thereof, to an ancestor of P. tsarasotrae. The chromosome numbers of P. tsarasotrae (2n = about 38) and P. malgassicum (2n = about 46), were more like the Asian species than to the American species. Unfortunately, no chromosome number of the African species P. guineense is currently available, to analyze eventual chromosomal connections.

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