Secondary contact followed by gene flow between divergent mitochondrial lineages of a widespread Neotropical songbird (Zonotrichia capensis)

Abstract Correct discrimination between courtship signals could help to maintain genetic integrity between closely related species. However, asymmetric usage of signals might cause asymmetric gene flow across the contact zone. Buergeria choui and B. otai are sibling-species with a parapatric distribution pattern in Taiwan, having two narrow contact zones on the east and west sides of the island. Combining behavioural experiments with genome-wide RAD-seq analyses, we test whether the ability of signal recognition influences genetic introgression across their species boundary. The playback experiments show that all B. choui populations respond strongest to their own ‘cricket’ trills, while the western population of B. otai have evolved a strong level of reproductive character displacement by showing the inclusive usage of the unique ‘chicken’ signals. In contrast, the eastern B. otai population uses both ‘chicken’ and ‘cricket’ trills, and has a stronger preference for the latter. The weak reproductive character displacement in the eastern population has led to asymmetry genetic introgression from B. choui toward B. otai. Our results support the prediction that a more specialized signal-user, compared to its sibling, generalized signal-user, might have a higher probability of maintaining their genetic integrity in the secondary contact region.

Resource partitioning as a factor limiting gene flow in hybridizing populations of Dolly Varden char (Salvelinus malma) and bull trout (Salvelinus confluentus)

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/f01-141 ◽

2001 ◽

Vol 58 (10) ◽

pp. 2037-2047 ◽

Cited By ~ 24

Author(s):

John Hagen ◽

Eric B Taylor

Keyword(s):

Life History ◽

Gene Flow ◽

Secondary Contact ◽

Life History Stage ◽

Bull Trout ◽

Dolly Varden ◽

Salvelinus Malma ◽

Salvelinus Confluentus ◽

Dolly Varden Char ◽

Northwestern North America

Dolly Varden char (Salvelinus malma) and bull trout (Salvelinus confluentus) hybridize in areas of secondary contact in northwestern North America but maintain their genetic integrity in spite of gene flow. We examined juvenile stream ecology and adult reproductive ecology of these species in sympatry to test for specializations to alternative niches that may act as a basis for natural selection against hybrids. Juvenile Dolly Varden occupied deeper, faster water and foraged more during daytime in the drift, whereas bull trout used shallower, slower water and made more nighttime foraging attempts towards the substrate. The species showed extensive diet overlap (Schoener's index = 0.70.9), and we found evidence for density compensation between species among sites. Our results suggest no obvious basis for selection against hybrids at the juvenile stream-rearing life-history stage. Bull trout, however, are adfluvial, whereas Dolly Varden are permanent stream residents. Bull trout are also much larger at maturity (5080 cm vs. 1215 cm) and build redds in faster, deeper water using larger substrate sizes. Consequently, hybrid genotypes may be selected against in these alternative life-history niches or during reproduction owing to their intermediate size at maturity and size-dependent spawning habitat use and mate choice.

Playbacks revisited: asymmetry in behavioural response across an acoustic boundary between two parapatric bird species

Behaviour ◽

10.1163/1568539x-00003309 ◽

2015 ◽

Vol 152 (14) ◽

pp. 1933-1951 ◽

Cited By ~ 7

Author(s):

Tamsin Burbidge ◽

Thari Parson ◽

Paula C. Caycedo-Rosales ◽

Carlos Daniel Cadena ◽

Hans Slabbekoorn

Keyword(s):

Gene Flow ◽

Response Pattern ◽

Bird Species ◽

Elevational Gradient ◽

High Elevation ◽

Secondary Contact ◽

Potential Contribution ◽

Asymmetric Response ◽

Singing Style ◽

The Impact

Behavioural barriers to gene flow can play a key role in speciation and hybridisation. Birdsong is well-known for its potential contribution to such behavioural barriers as it may affect gene flow through an effect on territorial and mating success across population boundaries. Conspecific recognition and heterospecific discrimination of acoustic variation can prevent or limit hybridization in areas where closely related species meet. Here we tested the impact of song differences on territorial response levels between two adjacent Henicorhina wood-wren species along an elevational gradient in Colombia. In an earlier study, playback results had revealed an asymmetric response pattern, with low-elevation H. leucophrys bangsi responding strongly to any conspecific or heterospecific song variant, whereas high-elevation H. anachoreta birds discriminated, responding more strongly to their own songs than to those of bangsi. However, in that study we could not exclude a role for relative familiarity to the song stimuli. In the current study we confirm the asymmetric response pattern with song stimuli recorded close to and on both sides of the distinct acoustic boundary. Furthermore, we also show a previously unnoticed divergence in singing style between these two wood-wren species, which may contribute to an acoustically guided barrier to hybridization in this secondary contact zone.

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.

Population genomics of Cryptosporidium hominis across five continents identifies two subspecies that have diverged and recombined during 500 years of evolution

10.1101/2021.09.09.459610 ◽

2021 ◽

Author(s):

Swapnil Tichkule ◽

Simone M. Cacciò ◽

Guy Robinson ◽

Rachel M. Chalmers ◽

Ivo Mueller ◽

...

Keyword(s):

Gene Flow ◽

Low Income ◽

Population Genomics ◽

Balancing Selection ◽

Public Health Problem ◽

High Income ◽

Secondary Contact ◽

Middle Income ◽

Middle Income Countries ◽

Low And Middle Income

AbstractCryptosporidium is a significant public health problem and one of the primary causes of diarrhoea in humans, particularly in very young children living in low- and middle-income countries. While the zoonotic Cryptosporidium parvum and anthroponotic C. hominis species collectively account for most cases globally, the latter is predominant in low- and middle-income countries. Here, we present a comprehensive whole genome study of C. hominis, comprising 114 isolates from 16 countries within five continents. We detect two highly diverged lineages with a distinct biology and demography that have diverged circa 500 years ago. We consider these lineages as two subspecies, and provisionally propose the names C. hominis hominis (clade 1) and C. hominis aquapotentis (clade 2 or gp60 subtype IbA10G2). C. h. hominis is mostly found in low-income countries in Africa and Asia, and it appears to have recently undergone population contraction. In marked contrast, C. h. aquapotentis was found in high-income countries, mainly in Europe, North America and Oceania, and we reveal a signature of population expansion. Moreover, we detected genomic regions of introgression representing gene flow after a secondary contact between the subspecies from low- and high-income countries. We demonstrate that this gene flow resulted in genomic island of high diversity and divergence, and that this diversity at potential virulence genes is maintained by balancing selection, suggesting that they are involved in a coevolutionary arms race.

Outcrossing rates in an experimentally admixed population of self-compatible and self-incompatible Arabidopsis lyrata

Heredity ◽

10.1038/s41437-021-00489-8 ◽

2021 ◽

Author(s):

Christina Steinecke ◽

Courtney E. Gorman ◽

Marc Stift ◽

Marcel E. Dorken

Keyword(s):

Gene Flow ◽

Natural Populations ◽

Secondary Contact ◽

Uniform Density ◽

Evolutionary Divergence ◽

Arabidopsis Lyrata ◽

Multiple Origins ◽

Outcrossing Rates ◽

Self Fertilization ◽

Self Compatibility

AbstractThe transition to self-compatibility from self-incompatibility is often associated with high rates of self-fertilization, which can restrict gene flow among populations and cause reproductive isolation of self-compatible (SC) lineages. Secondary contact between SC and self-incompatible (SI) lineages might re-establish gene flow if SC lineages remain capable of outcrossing. By contrast, intrinsic features of SC plants that reinforce high rates of self-fertilization could maintain evolutionary divergence between lineages. Arabidopsis lyrata subsp. lyrata is characterized by multiple origins of self-compatibility and high rates of self-fertilization in SC-dominated populations. It is unclear whether these high rates of selfing by SC plants have intrinsic or extrinsic causes. We estimated outcrossing rates and examined patterns of pollinator movement for 38 SC and 40 SI maternal parents sampled from an admixed array of 1509 plants sourced from six SC and six SI populations grown under uniform density. Although plants from SI populations had higher outcrossing rates (mean tm = 0.78 ± 0.05 SE) than plants from SC populations (mean tm = 0.56 ± 0.06 SE), outcrossing rates among SC plants were substantially higher than previous estimates from natural populations. Patterns of pollinator movement appeared to contribute to lower outcrossing rates for SC plants; we estimated that 40% of floral visits were geitonogamous (between flowers of the same plant). The relatively high rates of outcrossing for SC plants under standardized conditions indicate that selfing rates in natural SC populations of A. lyrata are facultative and driven by extrinsic features of A. lyrata, including patterns of pollinator movement.

The rates of introgression and barriers to genetic exchange between hybridizing species: sex chromosomes vs. autosomes

10.1101/2020.04.12.038042 ◽

2020 ◽

Author(s):

Christelle Fraïsse ◽

Himani Sachdeva

Keyword(s):

Gene Flow ◽

Sex Chromosomes ◽

Complete Separation ◽

Genetic Exchange ◽

Secondary Contact ◽

Effective Parameters ◽

Ability To Act ◽

Theoretical Predictions ◽

Neutral Gene ◽

Heterogametic Sex

ABSTRACTInterspecific crossing experiments have shown that sex chromosomes play a major role in reproductive isolation between many pairs of species. However, their ability to act as reproductive barriers, which hamper interspecific genetic exchange, has rarely been evaluated quantitatively compared to Autosomes. This genome-wide limitation of gene flow is essential for understanding the complete separation of species, and thus speciation. Here, we develop a mainland-island model of secondary contact between hybridizing species of an XY (or ZW) sexual system. We obtain theoretical predictions for the frequency of introgressed alleles, and the strength of the barrier to neutral gene flow for the two types of chromosomes carrying multiple interspecific barrier loci. Theoretical predictions are obtained for scenarios where introgressed alleles are rare. We show that the same analytical expressions apply for sex chromosomes and autosomes, but with different sex-averaged effective parameters. The specific features of sex chromosomes (hemizygosity and absence of recombination in the heterogametic sex) lead to reduced levels of introgression on the X (or Z) compared to autosomes. This effect can be enhanced by certain types of sex-biased forces, but it remains overall small (except when alleles causing incompatibilities are recessive). We discuss these predictions in the light of empirical data comprising model-based tests of introgression and cline surveys in various biological systems.

Reconstructing the demographic history of divergence between European river and brook lampreys using approximate Bayesian computations

PeerJ ◽

10.7717/peerj.1910 ◽

2016 ◽

Vol 4 ◽

pp. e1910 ◽

Cited By ~ 17

Author(s):

Quentin Rougemont ◽

Camille Roux ◽

Samuel Neuenschwander ◽

Jerome Goudet ◽

Sophie Launey ◽

...

Keyword(s):

Gene Flow ◽

Life Histories ◽

Evolutionary Biology ◽

Demographic History ◽

Secondary Contact ◽

Isolation With Migration ◽

Genome Wide Data ◽

History Of ◽

Parameterized Model ◽

Approximate Bayesian

Inferring the history of isolation and gene flow during species divergence is a central question in evolutionary biology. The European river lamprey (Lampetra fluviatilis) and brook lamprey(L. planeri)show a low reproductive isolation but have highly distinct life histories, the former being parasitic-anadromous and the latter non-parasitic and freshwater resident. Here we used microsatellite data from six replicated population pairs to reconstruct their history of divergence using an approximate Bayesian computation framework combined with a random forest model. In most population pairs, scenarios of divergence with recent isolation were outcompeted by scenarios proposing ongoing gene flow, namely the Secondary Contact (SC) and Isolation with Migration (IM) models. The estimation of demographic parameters under the SC model indicated a time of secondary contact close to the time of speciation, explaining why SC and IM models could not be discriminated. In case of an ancient secondary contact, the historical signal of divergence is lost and neutral markers converge to the same equilibrium as under the less parameterized model allowing ongoing gene flow. Our results imply that models of secondary contacts should be systematically compared to models of divergence with gene flow; given the difficulty to discriminate among these models, we suggest that genome-wide data are needed to adequately reconstruct divergence history.