How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels

AbstractThe Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study “replicated” instances of secondary contact between closely-related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry-informative panel of such SNPs. We then compared their frequencies in newly-sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bistable variants (Dobzhansky-Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact.

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The distribution and biogeography of slow worms (Anguis, Squamata) across the Western Palearctic, with an emphasis on secondary contact zones

Amphibia-Reptilia ◽

10.1163/15685381-bja10069 ◽

2021 ◽

pp. 1-12

Author(s):

Daniel Jablonski ◽

Neftalí Sillero ◽

Oleksandra Oskyrko ◽

Adriana Bellati ◽

Andris Čeirāns ◽

...

Keyword(s):

Natural History ◽

Genetic Data ◽

Secondary Contact ◽

Hybrid Zones ◽

Grey Zone ◽

Contact Zones ◽

Distribution Maps ◽

Western Palearctic ◽

Southern Balkans

Abstract The slow-worm lizards (Anguis) comprise five species occurring throughout most of the Western Palearctic. Although these species are relatively uniform morphologically – with the exception of A. cephallonica, which exhibits a quite unique morphology – they are genetically deeply divergent. Here, we provide detailed distribution maps for each species and discuss their biogeography and conservation based on updated genetic data and a robust distribution database. We pay particular attention to the so called ‘grey zone’, which typically represents secondary contact zones and in some cases confirmed or presumed hybrid zones. Four of the five species live in parapatry, while only two species, A. cephallonica and A. graeca from the southern Balkans occur in partial sympatry. Further research should focus on the eco-evolutionary interactions between species in contact, including their hybridization rates, to reveal deeper details of the slow-worm evolutionary and natural history.

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A revision of the shield-back katydid genus Neduba (Orthoptera: Tettigoniidae: Tettigoniinae: Nedubini)

Zootaxa ◽

10.11646/zootaxa.4910.1.1 ◽

2021 ◽

Vol 4910 (1) ◽

pp. 1-92

Author(s):

JEFFREY A. COLE ◽

DAVID B. WEISSMAN ◽

DAVID C. LIGHTFOOT ◽

NORIHIRO UESHIMA ◽

ELŻBIETA WARCHAŁOWSKA-ŚLIWA ◽

...

Keyword(s):

Phylogenetic Analysis ◽

New Species ◽

Junior Synonym ◽

Species Boundaries ◽

Secondary Contact ◽

Conservation Priorities ◽

Hybrid Zones ◽

Environmental Disturbance ◽

Western North America ◽

Molecular Phylogenetic

The Nearctic shield-back katydid genus Neduba is revised. Species boundaries were demarcated by molecular phylogenetic analysis, morphology, quantitative analysis of calling songs, and karyotypes. Nine previously described species are redescribed: N. carinata, N. castanea, N. convexa, N. diabolica, N. extincta, N. macneilli, N. propsti, N. sierranus, and N. steindachneri, and twelve new species are described: N. ambagiosa sp. n., N. arborea sp. n., N. cascadia sp. n., N. duplocantans sp. n., N. inversa sp. n., N. longiplutea sp. n., N. lucubrata sp. n., N. oblongata sp. n., N. prorocantans sp. n., N. radicata sp. n., N. radocantans sp. n., and N. sequoia sp. n. We chose a lectotype for N. steindachneri and transferred N. picturata from a junior synonym of N. diabolica to a junior synonym of N. steindachneri. Diversification in this relict group reflects cycles of allopatric isolation and secondary contact amidst the tumultuous, evolving geography of western North America. The taxonomy and phylogenies presented in this revision lay the groundwork for studies of speciation, biogeography, hybrid zones, and behavioral evolution. Given that one Neduba species is already extinct from human environmental disturbance, we suggest conservation priorities for the genus.

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Wxlv, the Ancestral Allele of Rice Waxy Gene

Proceedings ◽

10.3390/proceedings2019036140 ◽

2020 ◽

Vol 36 (1) ◽

pp. 140 ◽

Cited By ~ 1

Author(s):

Changquan Zhang ◽

Jihui Zhu ◽

Shengjie Chen ◽

Qiaoquan Liu

Keyword(s):

Amylose Content ◽

Waxy Gene ◽

Evolutionary Analysis ◽

Ancestral Allele ◽

Cultivated Rice ◽

Functional Sites ◽

Wx Locus ◽

Wx Gene ◽

Shed Light

In rice endosperms, the Waxy (Wx) gene is important for amylose synthesis, and various Wx alleles control the amylose content and affect the taste of cooked rice. Herein, we report the cloning of the ancestral allele Wxlv of the Wx locus, which affects the mouthfeel of rice grains by modulating the size of amylose molecules. Using evolutionary analysis, we demonstrated that Wxlv originated directly from wild rice, and the three major Wx alleles in cultivated rice (Wxb, Wxa, and Wxin) differentiated after the substitution of one base pair at the functional sites. These data indicate that the Wxlv allele played an important role in artificial selection and domestication. The findings also shed light on the evolution of various Wx alleles, which have greatly contributed to improving the eating and cooking quality of rice.

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Genomics of isolation in hybrids

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2011.0196 ◽

2012 ◽

Vol 367 (1587) ◽

pp. 439-450 ◽

Cited By ~ 88

Author(s):

Zachariah Gompert ◽

Thomas L. Parchman ◽

C. Alex Buerkle

Keyword(s):

Reproductive Isolation ◽

Genetic Architecture ◽

Large Scale ◽

Empirical Studies ◽

Hybrid Zones ◽

Direct Measure ◽

Fitness Effects ◽

Outlier Loci ◽

Admixed Population ◽

Genome Level

Hybrid zones are common in nature and can offer critical insights into the dynamics and components of reproductive isolation. Hybrids between diverged lineages are particularly informative about the genetic architecture of reproductive isolation, because introgression in an admixed population is a direct measure of isolation. In this paper, we combine simulations and a new statistical model to determine the extent to which different genetic architectures of isolation leave different signatures on genome-level patterns of introgression. We found that reproductive isolation caused by one or several loci of large effect caused greater heterogeneity in patterns of introgression than architectures involving many loci with small fitness effects, particularly when isolating factors were closely linked. The same conditions that led to heterogeneous introgression often resulted in a reasonable correspondence between outlier loci and the genetic loci that contributed to isolation. However, demographic conditions affected both of these results, highlighting potential limitations to the study of the speciation genomics. Further progress in understanding the genomics of speciation will require large-scale empirical studies of introgression in hybrid zones and model-based analyses, as well as more comprehensive modelling of the expected levels of isolation with different demographies and genetic architectures of isolation.

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Designation of a neotype for the Brazilian porcupine, Coendou prehensilis (Linnaeus, 1758)

Zootaxa ◽

10.11646/zootaxa.2791.1.2 ◽

2011 ◽

Vol 2791 (1) ◽

pp. 30 ◽

Cited By ~ 10

Author(s):

YURI L. R. LEITE ◽

VILACIO CALDARA JÚNIOR ◽

ANA CAROLINA LOSS ◽

LEONORA PIRES COSTA ◽

ÉVERTON R. A. MELO ◽

...

Keyword(s):

Mitochondrial Dna ◽

Geographic Distribution ◽

Related Species ◽

Taxonomic Revision ◽

Type Specimen ◽

Northeastern Brazil ◽

Closely Related Species ◽

Geographic Ranges ◽

Central Brazil ◽

Shed Light

The Brazilian porcupine was one of several species described and illustrated by the 17 th -century naturalist Georg Marcgrave, whose text was among the primary references upon which Linnaeus based his Hystrix prehensilis. As currently understood, Coendou prehensilis is a wide-ranging polytypic taxon that has never been revised and may represent a complex of closely related species. Given that no name-bearing type specimen of C. prehensilis is believed to be extant, and in order to avoid ambiguous application of this name, we designate a specimen collected at the type locality in Pernambuco, northeastern Brazil, as the neotype for Hystrix prehensilis Linnaeus. The geographic distribution of mitochondrial DNA haplotypes suggests that specimens from west-central Brazil previously identified as “Coendou prehensilis” belong to a different species, but only a comprehensive taxonomic revision of the genus will shed light on species limits and the geographic ranges of C. prehensilis and other congeneric forms.

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Extensive introgression despite Haldane’s rule: insights from grasshopper hybrid zones

10.22541/au.163785413.32517525/v1 ◽

2021 ◽

Author(s):

Linda Hagberg ◽

Enrique Celemin ◽

Iker Irisarri ◽

Oliver Hawlitschek ◽

J L Bella ◽

...

Keyword(s):

Gene Flow ◽

Reproductive Isolation ◽

Male Sterility ◽

Secondary Contact ◽

Hybrid Zones ◽

Hybrid Male ◽

Hybrid Male Sterility ◽

Haldane’S Rule ◽

Haldane's Rule ◽

Species Formation

Although the process of species formation is notoriously idiosyncratic, the observation of pervasive patterns of reproductive isolation across species pairs suggests that generalities, or “rules”, underlie species formation in all animals. Haldane’s rule states that whenever a sex is absent, rare or sterile in a cross between two taxa, that sex is usually the heterogametic sex. Yet, understanding how Haldane’s rule first evolves and whether it is associated to genome wide barriers to gene flow remains a challenging task because this rule is usually studied in highly divergent taxa that no longer hybridize in nature. Here, we address these questions using the meadow grasshopper Pseudochorthippus parallelus where populations that readily hybridize in two natural hybrid zones show hybrid male sterility in laboratorial crosses. Using mitochondrial data, we infer that such populations have diverged some 100,000 years ago, surviving multiple glacial periods in isolated Pleistocenic refugia. Nuclear data shows that secondary contact has led to extensive introgression throughout the species range, including between populations showing hybrid male sterility. We find repeatable patterns of genomic differentiation across the two hybrid zones, yet such patterns are consistent with shared genomic constraints across taxa rather than their role in reproductive isolation. Together, our results suggest that Haldane’s rule can evolve relatively quickly within species, particularly when associated to strong demographic changes. At such early stages of species formation, hybrid male sterility still permits extensive gene flow, allowing future studies to identify genomic regions associated with reproductive barriers.

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A dense linkage map for a large repetitive genome: discovery of the sex-determining region in hybridising fire-bellied toads (Bombina bombina and B. variegata)

10.1101/2020.10.06.328633 ◽

2020 ◽

Author(s):

Beate Nürnberger ◽

Stuart J.E. Baird ◽

Dagmar Čížková ◽

Anna Bryjová ◽

Austin B. Mudd ◽

...

Keyword(s):

Sex Determination ◽

Linkage Map ◽

Large Scale ◽

Sex Chromosome ◽

Repetitive Sequences ◽

Secondary Contact ◽

Gene Pools ◽

Hybrid Zones ◽

Chromosome 5 ◽

Bombina Bombina

AbstractHybrid zones that result from secondary contact between diverged populations offer unparalleled insight into the genetic architecture of emerging reproductive barriers and so shed light on the process of speciation. Natural selection and recombination jointly determine their dynamics, leading to a range of outcomes from finely fragmented mixtures of the parental genomes that facilitate introgression to a situation where strong selection against recombinants retains large unrecombined genomic blocks that act as strong barriers to gene flow. In the hybrid zone between the fire-bellied toads Bombina bombina and B. variegata (Anura: Bombinatoridae), two anciently diverged and ecologically distinct taxa meet and produce abundant, fertile hybrids. The dense linkage map presented here enables genomic analysis of the selection-recombination balance that keeps the two gene pools from merging into one. We mapped 4,775 newly developed marker loci from bait-enriched genomic libraries in F2 crosses. The enrichment targets were selected from a draft assembly of the B. variegata genome, after filtering highly repetitive sequences. We developed a novel approach to infer the most likely diplotype per sample and locus from the raw read mapping data, which is robust to over-merging and obviates arbitrary filtering thresholds. Large-scale synteny between Bombina and Xenopus tropicalis supports the resulting linkage map. By assessing the sex of late-stage F2 tadpoles from histological sections, we also identified the sex-determining region in the Bombina genome to 7 cM on LG5, which is homologous to X. tropicalis chromosome 5, and inferred male heterogamety, suggestive of an XY sex determination mechanism. Interestingly, chromosome 5 has been repeatedly recruited as a sex chromosome in anurans with XY sex determination.

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Assortative mating in hybrid zones is remarkably ineffective in promoting speciation

10.1101/637678 ◽

2019 ◽

Cited By ~ 2

Author(s):

Darren E. Irwin

Keyword(s):

Assortative Mating ◽

F1 Hybrids ◽

Secondary Contact ◽

Hybrid Zones ◽

Mating Types ◽

Postzygotic Isolation ◽

Small Reduction ◽

Hybrid Fitness ◽

Prezygotic Isolation ◽

Two Populations

AbstractAssortative mating and other forms of partial prezygotic isolation are often viewed as being more important than partial postzygotic isolation (low fitness of hybrids) early in the process of speciation. Here I simulate secondary contact between two populations (‘species’) to examine effects of pre- and postzygotic isolation in preventing blending. A small reduction in hybrid fitness (e.g., 10%) produces a narrower hybrid zone than a strong but imperfect mating preference (e.g., 10x stronger preference for conspecific over heterospecific mates). This is because, in the latter case, rare F1 hybrids find each other attractive (due to assortative mating), leading to the gradual buildup of a full continuum of intermediates between the two species. The cline is narrower than would result from purely neutral diffusion over the same number of generations, largely due to the frequency-dependent mating disadvantage of individuals of rare mating types. Hybrids tend to pay this cost of rarity more than pure individuals, meaning there is an induced postzygotic isolation effect of assortative mating. These results prompt a questioning of the concept of partial prezygotic isolation, since it is not very isolating unless there is also postzygotic isolation.

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Parental population range expansion before secondary contact promotes heterosis

10.1101/2020.04.28.066308 ◽

2020 ◽

Author(s):

Ailene MacPherson ◽

Silu Wang ◽

Ryo Yamaguchi ◽

Loren H. Riesesberg ◽

Sarah P. Otto

Keyword(s):

Reproductive Isolation ◽

Range Expansion ◽

Genomic Analysis ◽

Population Expansion ◽

Ancestral Population ◽

Secondary Contact ◽

Hybrid Zones ◽

Deleterious Alleles ◽

Genomic Divergence ◽

Slightly Deleterious Mutations

AbstractPopulation genomic analysis of hybrid zones is instrumental to our understanding of the evolution of reproductive isolation. Many temperate hybrid zones are formed by the secondary contact between two parental populations that had undergone post-glacial range expansion. Here we show that explicitly accounting for historical parental isolation followed by range expansion prior to secondary contact is fundamental for explaining genetic and fitness patterns in these hybrid zones. Specifically, ancestral population expansion can result in allele surfing, neutral or slightly deleterious mutations drift high frequency at the front of the expansion. If these surfed deleterious alleles are recessive, they can contribute to substantial heterosis in hybrids produced at secondary contact, counteracting negative-epistatic interactions between BDMI loci and hence can deteriorate reproductive isolation. Similarly, surfing at neutral loci can alter the expected pattern of population ancestry and suggests that accounting for historical population expansion is necessary to develop accurate null genomic models in secondary-contact hybrid zones. Furthermore, this process should be incorporated in macroevolutionary models of divergence as well, since such heterosis facilitated by parental-range expansion could dampen genomic divergence established in the past.

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Against the Odds: Hybrid Zones between Mangrove Killifish Species with Different Mating Systems

Genes ◽

10.3390/genes12101486 ◽

2021 ◽

Vol 12 (10) ◽

pp. 1486

Author(s):

Waldir M. Berbel-Filho ◽

Andrey Tatarenkov ◽

George Pacheco ◽

Helder M. V. Espírito-Santo ◽

Mateus G. Lira ◽

...

Keyword(s):

Mating Systems ◽

Sympatric Species ◽

Natural Hybridization ◽

Hybrid Zones ◽

Mating Opportunities ◽

Plant Hybrid ◽

Two Hybrid ◽

Selfing Species ◽

Shed Light ◽

Mangrove Killifish

Different mating systems are expected to affect the extent and direction of hybridization. Due to the different levels of sexual conflict, the weak inbreeder/strong outbreeder (WISO) hypothesis predicts that gametes from self-incompatible (SI) species should outcompete gametes from self-compatible (SC) ones. However, other factors such as timing of selfing and unilateral incompatibilities may also play a role on the direction of hybridization. In addition, differential mating opportunities provided by different mating systems are also expected to affect the direction of introgression in hybrid zones involving outcrossers and selfers. Here, we explored these hypotheses with a unique case of recent hybridization between two mangrove killifish species with different mating systems, Kryptolebias ocellatus (obligately outcrossing) and K. hermaphroditus (predominantly self-fertilizing) in two hybrid zones in southeast Brazil. Hybridization rates were relatively high (~20%), representing the first example of natural hybridization between species with different mating systems in vertebrates. All F1 individuals were sired by the selfing species. Backcrossing was small, but mostly asymmetrical with the SI parental species, suggesting pattern commonly observed in plant hybrid zones with different mating systems. Our findings shed light on how contrasting mating systems may affect the direction and extent of gene flow between sympatric species, ultimately affecting the evolution and maintenance of hybrid zones.

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