Abstract Background Whole genome duplication (polyploidization) is a dominant force in sympatric speciation, particularly in plants. Genome doubling instantly poses a barrier to gene flow owing to the strong crossing incompatibilities between individuals differing in ploidy. The strength of the barrier, however, varies from species to species and recent genetic investigations revealed cases of rampant interploidy introgression in multiple ploidy-variable species. Scope Here, we review novel insights into the frequency of interploidy gene flow in natural systems and summarize the underlying mechanisms promoting interploidy gene flow. Field surveys, occasionally complemented by crossing experiments, suggest frequent opportunities for interploidy gene flow, particularly in the direction from diploid to tetraploid, and between (higher) polyploids. However, a scarcity of accompanying population genetic evidence and a virtual lack of integration of these approaches leave the underlying mechanisms and levels of realized interploidy gene flow in nature largely unknown. Finally, we discuss potential consequences of interploidy genome permeability on polyploid speciation and adaptation and highlight novel avenues that have just recently been opened by the very first genomic studies of ploidy-variable species. Standing in stark contrast with rapidly accumulating evidence for evolutionary importance of homoploid introgression, similar cases in ploidy-variable systems are yet to be documented. Conclusions The genomics era provides novel opportunity to re-evaluate the role of interploidy introgression in speciation and adaptation. To achieve this goal, interdisciplinary studies bordering ecology and population genetics and genomics are needed. 

Ploidy as a leaky reproductive barrier: mechanisms, rates and evolutionary significance of interploidy gene flow

Understanding speciation has long been a fundamental goal of evolutionary biology. It is widely accepted that speciation requires an interruption of gene flow to generate strong reproductive isolation between species. The mechanism of how speciation in sexually dichromatic species operates in the face of gene flow remains an open question. Two species in the genus Chrysolophus, the Golden Pheasant (C. pictus) and Lady Amherst's Pheasant (C. amherstiae), both of which exhibit significant plumage dichromatism, are currently parapatric in southwestern China with several hybrid recordings in field. In this study, we estimated the pattern of gene flow during the speciation of the two pheasants using the Approximate Bayesian Computation (ABC) method based on data from multiple genes. Using a newly assembled de novo genome of Lady Amherst's Pheasant and resequencing of widely distributed individuals, we reconstructed the demographic history of the two pheasants by the PSMC (pairwise sequentially Markovian coalescent) method. The results provide clear evidence that the gene flow between the two pheasants was consistent with the predictions of the isolation with migration model during divergence, indicating that there was long-term gene flow after the initial divergence (ca. 2.2 million years ago). The data further support the occurrence of secondary contact between the parapatric populations since around 30 kya with recurrent gene flow to the present, a pattern that may have been induced by the population expansion of the Golden Pheasant in the late Pleistocene. The results of the study support the scenario of speciation between the Golden Pheasant and Lady Amherst's Pheasant with cycles of mixing-isolation-mixing, possibly due to the dynamics of geographical context in the late Pleistocene. The two species provide a good research system as an evolutionary model for testing reinforcement selection in speciation. 

Parapatric speciation with recurrent gene flow of two sexual dichromatic pheasants

Thamnocalamus spathiflorus is a shrubby woody bamboo invigorating at the alpine and sub-alpine region of the northwestern Himalayas. The present investigation was conducted to map the potential distribution of Th. spathiflorus in the western Himalayas for current and future climate scenario using Ecological Niche Modelling (ENM). In total, 125 geo-coordinates were collected for the species presence from Himachal Pradesh (HP) and Uttarakhand (UK) states of India and modelled to predict the current distribution using the Maximum Entropy (MaxEnt) model, along with 13 bioclimatic variables selected after multi-collinearity test. Model output was supported with a significant value of the Area Under the “Receiver Operating Characteristics” Curve (AUC = 0.975 ± 0.019), and other confusion matrix-derived accuracy measures. The variables, namely precipitation seasonality (Bio 15), precipitation (Prec), annual temperature range (Bio 7), and altitude (Alt) showed highest level of percentage contribution (72.2%) and permutation importance (60.9%) in predicting the habitat suitability of Th. spathiflorus. The actual (1 km2 buffer zone) and predicted estimates of species cover were ~136 km2 and ~982 km2, respectively. The predicted range was extended from Chamba (HP) in the north to Pithoragarh (UK) in southeast, which further protracted to Nepal. Furthermore, the distribution modelling under future climate change scenarios (RCP 8.5) for year 2050 and 2070 showed an eastern centroidal shift with slight decline of the species area by ~16 km2 and ~46 km2, respectively. This investigation employed the Model for Interdisciplinary Research on Climate (MIROC6)–shared socio-economics pathways (SSP245) for cross-validation purposes. The model was used to determine the habitat suitability and potential distribution of Th. spathiflorus in relation to the current distribution and RCP 8.5 future scenarios for the years 2021–2040 and 2061–2080, respectively. It showed a significant decline in the distribution area of the species between year 2030 and 2070. Overall, this is the pioneer study revealing the eco-distribution prediction modelling of this important high-altitude bamboo species. 

MaxEnt-Based Potential Distribution Mapping and Range Shift under Future Climatic Scenarios for an Alpine Bamboo Thamnocalamus spathiflorus in Northwestern Himalayas

Genomic patterns of the interspecific gene flow between Pitcairnia staminea and P. albiflos (Bromeliaceae)

Abstract The study of mechanisms that generate new species is considered fundamental for broad areas of ecology and evolution. Speciation is a continuous process in which reproductive isolation is established, and it is of fundamental importance to understand the origins of the adaptations that contribute to this process. Hybrid zones are considered natural laboratories for the study of speciation and represent ideal systems for such studies. Here, we investigated genomic differentiation between hybridizing Neotropical species Pitcairnia staminea (G. Lodd.) and P. albiflos (Herb.). Using thousands of SNPs genotyped through RAD‐seq, we estimate effective population sizes, interspecific gene flow, as well as time of divergence between these two sister species and identify candidate genomic regions for positive selection that may be related to reproductive isolation. We selected different scenarios of speciation and tested them by using approximate Bayesian computation (ABC); we found evidence of divergence with gradual reduction in gene flow between these species over time, compatible with the hypothesis of speciation with gene flow between these Pitcairnia species. The parameter estimates obtained through ABC suggested that the effective population size of P. albiflos was around three times larger than that of P. staminea. Our divergence date estimates showed that these two species diverged during the Pliocene (4.7 Mya; CI = 1.3–8.5 Mya), which has likely allowed this species to accumulate genome‐wide differences. We also detected a total of 17 of 4165 loci which showed signatures of selection with high genetic differentiation (F ST > 0.85), 12 of these loci were annotated in de novo assembled transcriptomes of both species, and 4 candidate genes were identified to be putatively involved in reproductive isolation. These four candidate genes were previously associated with the function of pollen development, pollen tube germination and orientation, abiotic stress, and flower scent in plants, suggesting an interplay between pre‐ and postpollination barriers in the evolution of reproductive isolation between such species.

Speciation with gene flow between two Neotropical sympatric species (Pitcairnia spp.: Bromeliaceae)

Understanding how species diversify is a long-standing question in biology. The allopatric speciation model is a classic hypothesis to explain the speciation process. This model supposes that there is no gene flow during the divergence process of geographically isolated populations. On the contrary, the speciation with gene flow model supposes that gene flow does occur during the speciation process. Whether allopatric species have gene flow during the speciation process is still an open question. We used the genetic information from 31 loci of 24 Chinese Bamboo Partridges (Bambusicola thoracicus) and 23 Taiwan Bamboo Partridges (B. sonorivox) to infer the gene flow model of the two species, using the approximate Bayesian computation (ABC) model. The ecological niche model was used to infer the paleo-distribution during the glacial period. We also tested whether the two species had a conserved ecological niche by means of a background similarity test. The genetic data suggested that the post-divergence gene flow between the two species was terminated before the mid-Pleistocene. Furthermore, our ecological niche modeling suggested that their ecological niches were highly conserved, and that they shared an overlapping potential distribution range in the last glacial maximum. The allopatric speciation model cannot explain the speciation process of the two Bamboo Partridges. The results of this study supported a scenario in which speciation with gene flow occurring between the allopatric species and have contributed to our understanding of the speciation process.

/pdf/multilocus-phylogeography-and-ecological-niche-modeling-1hjk7swxmy.pdf

Multilocus phylogeography and ecological niche modeling suggest speciation with gene flow between the two Bamboo Partridges

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Multilocus phylogeography and ecological niche modeling suggest speciation with gene flow between the two Bamboo Partridges