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Speciation by polyploidy

Speciation by polyploidy


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Speciation can occur by polyploidy. My understanding of the process is as follows:

'polyploidy is when the number of chromosomes in an organism's cell doubles. This means that the organism has more chromosomes than other individuals of the same species, meaning it cannot mate with other individuals. The polyploidy organism then evolves, eventually leading to it becoming a separate species'.

I realise this may not be exactly correct. Is someone able to provide a better description of speciation by polyploidy?


By definition, polyploidy just means that a cell or organism contains more than 2 pairs of homologous chromosomes (or is more than 2n). This is more common in plants than it is in animals. The plant, as shown below, undergoes failed meiosis, which means that the diploid (2n) cells never become haploid (n). As a result, a plant ends up with more than 2n when it self-polinates. The shown result is tetraploidy (4n), but there are other possible results (3n, 5n, etc).

Multiple plants within a population can end up with the same polyploidy number. They can then reproduce with each other but not with the original plants or any other plants. As a result, they become biologically isolated from the original group of plants and are considered a different species. It is a type of sympatric speciation, which means that it occurs without geographic isolation.


In the genus Rhododendron polyploid species are common especially in deciduous azaleas and lepidotes. Yet complete reproductive isolation of the poylpoid species from the closely related diploid species is the exception rather than the rule.

Closely related diploid and tetraploid species interact in natural contact zones to create triploids and some triploids are able to reproduce with both populations.

Hybrid triploid lepidotes seem to freely set small amounts of viable open pollinated seed.

Tetraploid and hexaploid species and hybrids appear to interact even more freely than diploids and tetraploids. Pentaploids are often semi-fertile.

For Rhododendron, ploidy level creates a barrier to sexual interaction but that barrier is not absolute and is sometimes surprising porous. In fact the triploids may act as a pathway in the transition from diploid to tetraploid in that 2x (reduced) X 2x (unreduced) can create 3x and 2x (reduced) X 3x (unreduced) can create 4x. Moreover, C D Darlington established that triploids can throw 1x and 2x gametes so 3x (reduced to 2x) X 3x (reduced to 2x) can produce 4x or 3x (reduced to 1x) X 3x (unreduced) can produce 4x. Darlington documents the historical development of garden hyacinths from diploid species to triploid and then to tetraploids using a triploid pathway. The development of tetraploid hybrid elepidote Rhododendron 'Countess of Derby' also illustrates a triploid pathway.

One cannot rule out the possibility that the ability of the diploid species to interact with newly created polyploids actually contributes to the creation of the tetraploid species.

The diagram below illustrates how the triploid 'Pink Pearl' has produced diploid, triploid, and tetraploid offspring when interacting with diploids and has produced a tetraploid offspring by interacting with another triploid.

The flow cytometry for this research on the genus Rhododendon was performed by Dr. João Loureiro, Dr. Silvia Castro, José Cerca, and Mariana Castro Plant Ecology and Evolution Group, Centre for Functional Ecology, Department of Life Sciences, Faculty of Science and Technology, University of Coimbra, Portugal.

References

Meiosis in Polyploids by W. C. F. Newton and C. D. Darlington in Journal of Genetics 1929

The history of the garden hyacinths by C D Darlington, J B Hair and R Hurcombe in Heredity 1951

Ploidy level estimations in deciduous and elepidote hybrids of Rhododendron by José Cerca de Oliveira, Mariana Castro, Francisco J. do Nascimento, Sílvia Castro, John Perkins,Sally Perkins, João Loureiro in Jornadas Portuguesas de Genética, Coimbra, Portugal; 05/2011

Weighing in: Discovering the ploidy of hybrid elepidote rhododendrons by Sally Perkins, John Perkins, José Monteiro de Oliveira, Mariana Castro, Sílvia Castro, João Loureiro in Rhododendrons, Camellias and Magnolias, Royal Horticultural Society, Editors: Simon Maughan, pp.34-48 2012

Untersuchung des Ploidiegrades elepidoter Rhododendron-Hybriden by Sally Perkins, John Perkins, Mariana Castro, José Cerca De Oliveira, Silvia Castro, João Loureiro in Rhododendron und Immergrüne , Deutsche Rhododendron-Gesellschaft e.V. , Seite 21: pages 21-42; 11/2013


Categories of Speciation (With Diagram) | Ecology

Allopatric speciation occurs when the new species evolves in geo­graphic isolation from the parent species. The species range, becomes subdivided by a bar­rier such as a new mountain range or the change in the course of a river.

Gene flow between the two subpopulations becomes im­possible allowing evolution to proceed inde­pendently in each. Natural selection may favour different genotypes on either side of the barrier and random genetic drift and mu­tation could contribute to divergence.

Over time, divergence may proceed to the point that were the two populations to meet again, they would not be able to interbreed and speciation would be complete. This form of speciation may take place most readily in small populations at the extreme edge of a species range. The peripheral popu­lation could become isolated, for example, during contraction of the main species range in response to changing climate.

The isolated population would be subject to the founded effect and could be genetically different from the parent population. The combined effect of a small atypical population and extreme environmental conditions can cause rapid and extensive genetic reorganization through ran­dom genetic drift and strong natural selection, or, in other words a genetic revolution.

Category # 2. Parapatric Speciation:

This form of specia­tion occurs where the speciating populations are contiguous and hence only partially geo­graphically isolated. They are able to across a common boundary during the speciation pro­cess. Where a species occupies a large geo­graphical range it may become adapted to dif­ferent environmental (e.g. climatic) conditions in different parts of that range.

Intermediate or hybrids, will be found but the large distances involved prevent the two types from merging completely.

For example, the herring gull Larus argentatus is a ring species whose distribution covers a large geographical area. Westwards from Brit­ain toward North America its appearance changes gradually, but it is still recognizable herring gull. Further west in Siberia it begins to look more like the lesser black-backed gull Larus fuscus.

From Siberia to Russia and into northern Europe it becomes progressively more like the lesser black-backed gull. The ends of the ring meet in Europe and the two geographical extremes appear to be two good biological species.

Category # 3. Sympatric Speciation:

Sympatric speciation describes a situation where there is no geo- graphical separation between the speciating populations. All individuals are, in theory, able to meet each other during the speciation pro­cess. This model usually requires a change in host preference, food preference or habitat preference in order to prevent the new spe­cies being swamped by gene flow.

Whether sympatric speciation happens at all is a contentious issue. In theory it can occur where there is a polymorphism in the popula­tion conferring adaptation to two different habitats or niches. Reproductive isolation could then arise if the two morphs had a pref­erence for ‘their’ habitat.

There is some evi­dence for this in natural populations. For ex­ample, caterpillars of the ermine moth, Yponomeuta padellus, feed on apple and haw­thorn trees. Females prefer to lay their eggs on the species on which they were raised.

Cat­erpillars also prefer to feed on the plant on which their mothers were raised and adult moths prefer to mate with individuals from the same plant. The apple and hawthorn types are not completely isolated, but may represent an intermediate point in on-going sympatric speciation.

An un-contentious example of sympatric spe­ciation occurs in plants through polyploidy. Polyploidy is the spontaneous duplication of the entire genome resulting in an individual with a multiple of the original chromosome number. Polyploidy is common in plants, where it often results in larger, more vigorous forms.

It is usually fatal in animals, although some amphibians are polyploids. The polyp­loid plant is no longer sexually compatible with the parent population but is able to establish a distinct population which may occupy a dif­ferent habitat. The sand dune grass, Spartina townsendii, is a polyploid derived from the origi­nal S. anglica. It is more vigorous than the par­ent and has colonized large areas of sand dune in Britain.

Category # 4. Alloparapatric Speciation:

It is specialised kind of speciation where differentiation in iso­lation takes place through barrier breakdown processes, as influenced by gradual environ­mental variation. The details of different kinds of speciation mechanisms are shown in Fig. 2.1.


Polyploidy and interspecific hybridization: partners for adaptation, speciation and evolution in plants

Background: Polyploidy or whole-genome duplication is now recognized as being present in almost all lineages of higher plants, with multiple rounds of polyploidy occurring in most extant species. The ancient evolutionary events have been identified through genome sequence analysis, while recent hybridization events are found in about half of the world's crops and wild species. Building from this new paradigm for understanding plant evolution, the papers in this Special Issue address questions about polyploidy in ecology, adaptation, reproduction and speciation of wild and cultivated plants from diverse ecosystems. Other papers, including this review, consider genomic aspects of polyploidy.

Approaches: Discovery of the evolutionary consequences of new, evolutionarily recent and ancient polyploidy requires a range of approaches. Large-scale studies of both single species and whole ecosystems, with hundreds to tens of thousands of individuals, sometimes involving 'garden' or transplant experiments, are important for studying adaptation. Molecular studies of genomes are needed to measure diversity in genotypes, showing ancestors, the nature and number of polyploidy and backcross events that have occurred, and allowing analysis of gene expression and transposable element activation. Speciation events and the impact of reticulate evolution require comprehensive phylogenetic analyses and can be assisted by resynthesis of hybrids. In this Special Issue, we include studies ranging in scope from experimental and genomic, through ecological to more theoretical.

Conclusions: The success of polyploidy, displacing the diploid ancestors of almost all plants, is well illustrated by the huge angiosperm diversity that is assumed to originate from recurrent polyploidization events. Strikingly, polyploidization often occurred prior to or simultaneously with major evolutionary transitions and adaptive radiation of species, supporting the concept that polyploidy plays a predominant role in bursts of adaptive speciation. Polyploidy results in immediate genetic redundancy and represents, with the emergence of new gene functions, an important source of novelty. Along with recombination, gene mutation, transposon activity and chromosomal rearrangement, polyploidy and whole-genome duplication act as drivers of evolution and divergence in plant behaviour and gene function, enabling diversification, speciation and hence plant evolution.

Keywords: Polyploidy adaptation angiosperms bryophytes chromosomes crops ecology evolution genomics hybrids phylogeny speciation weeds whole-genome duplication (WGD).

© The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: [email protected]

Figures

Simplified phylogeny of the green…

Simplified phylogeny of the green plant lineage focusing on the occurrence of WGD…

Metaphase chromosomes of diploid, tetraploid…

Metaphase chromosomes of diploid, tetraploid and hexaploid wheats stained with the DNA stain…


2 Main Types of Speciation | Evolution | Biology

Speciation is the method of formation of new species. A species can be defined as one or more populations of interbreeding organisms that are reproductively isolated in nature from all other organisms. As natural selection adapts populations occupying different environments, they will diverge into races, subspecies, and finally separate species. When populations no longer interbreed, they are thought to be separate species.

Speciation is of two types:

Type # 1. Allopatric Speciation:

Allopatric speciation is the evolution of species in a population that occupy different geographical areas. Geographic isolation is often the first step in allopatric speciation. Other isolating mechanism may also operate that further restrict reproduction between populations. An example of allopatric speciation is the Darwin’s finches. The finches varied from each other mainly in shape and size of beak and colour of the feathers or plumage.

According to Darwin, the species in the South American mainland were the original species from which different forms migrated to different islands of the Galapagos and became adapted to the environmental conditions of these islands. The adapted forms eventually became the new species (Fig. 34).

In the case of the finches, geographical isolation led to the development of reproductive isolation and thereby to the origin of new species.

Type # 2. Sympatric Speciation:

Speciation within a population that occupies the same geographic environment by either ecological isolation (differing habitats) or by chromosomal aberrations as seen in plants is known as sympatric speciation. Sympatric speciation happens when members of a population develop genetic differences that prevent them from reproducing with the parent type.

Polyploidy in plants and hybridisation are two methods of introducing reproductive isolation. Polyploidy is the phenomenon when organism has more than two sets of chromo­somes – 3n, 4n, 5n and so on. Polyploidy is a mechanism that can lead to the formation of new species very rapidly. Polyploidy does not occur in animals naturally.

This mechanism is best understood in plants, where failure to reduce chromosome number results in polyploid plants that reproduce successfully only with other polyploids. Reproduction with their parent population (the diploids) produces sterile offspring. For example, the wheat variety, Triticum aestivum is a hexaploid that has been developed by polyploidy.


Polyploidy in animals

Polyploidy is much rarer in animals. It is found in some insects, fishes, amphibians, and reptiles. Until recently, no polyploid mammal was known. However, the 23 September 1999 issue of Nature reported that a polyploid (tetraploid 4n = 102) rat has been found in Argentina.

Polyploid cells are larger than diploid ones not surprising in view of the increased amount of DNA in their nucleus. The liver cells of the Argentinian rat are larger than those of its diploid relatives, and its sperm are huge in comparison. Normal mammalian sperm heads contain some 3.3 picograms (10 -12 g) of DNA the sperm of the rat contains 9.2 pg.


Results

We obtained a total of about 720 kb of DNA sequence data from 6 pairs of duplicate nuclear loci in 92 C. bursa-pastoris accessions from eastern and western Eurasia, and for the corresponding 6 loci in 21 C. rubella accessions from Europe ( fig. 1, supplementary Supplementary Data , Supplementary Material online).

Mean nucleotide diversity (π) of C. bursa-pastoris was an order of magnitude higher in western than in eastern Eurasia (2.5 × 10 −3 vs. 2.2 × 10 −4 ) and the difference was significant (Wilcoxon signed-rank test V = 7.5, P= 0.015). Estimates of π ranged from 0 to 0.012 across loci and values of Watterson's estimate of the population mutation rate, θw, ranged from 0 to 0.006 ( table 1, supplementary Supplementary Data , Supplementary Material online). In the C. bursa-pastoris sample from western Eurasia, there were a total of 34 genotypes, whereas 19 genotypes were found in the sample from eastern Eurasia. In our smaller sample of 21 C. rubella accessions, there were 9 genotypes. The total number of haplotypes observed at each locus in C. bursa-pastoris ranged from 2 (for CRY1 B) to 6 (for FRI A), excluding indels (see supplementary Supplementary Data , Supplementary Material online for numbers of haplotypes per locus and region). We found haplotype sharing between C. bursa-pastoris and C. rubella in western but not in eastern Eurasia. In samples from western Eurasia, C. bursa-pastoris accessions shared haplotypes with C. rubella at one of the homoeologs of 4 nuclear genes: Adh, CRY1, LD, and PI. For each of these genes, this C. bursa-pastoris homoeolog was also the least divergent from C. rubella in the C. bursa-pastoris sample from eastern Eurasia (supplementary Supplementary Data , Supplementary Material online). In western Eurasia, shared haplotypes were found in frequencies ranging from 12% to 30% (Adh A: 0.24, CRY1 A: 0.30, LD A: 0.18, PI A: 0.12 see Material and Methods for naming of homoelogous loci). For several loci, these haplotypes were present in C. bursa-pastoris accessions north of the current C. rubella range in Europe (supplementary Supplementary Data , Supplementary Material online). Distributions of Tajima's D values in western and eastern Eurasian samples of C. bursa-pastoris were significantly different (V = 2, P= 0.023) with values ranging from −1.58 to 2.94 in the former and only negative values, ranging from −1.48 to −0.41, in the latter (supplementary Supplementary Data , Supplementary Material online).

Population Genetic Summary Statistics and Neutrality Test Statistics (Significance Indicated by Asterisks) for Capsella bursa-pastoris (Cbp) A-Homoeologs in Western Eurasia and for Capsella rubella (Cr)

Gene Species n a L b S c π d θw e h f Hd g DTajima h DFu&Li i
AdhCbp50 351 4 0.00424 0.00254 2 0.372 1.514 0.743
Cr21 558 0 0 0 1 0
CRY1Cbp50 466 4 0.00341 0.00192 3 0.620 1.763 1.014
Cr21 465 0 0 0 1 0
FLCCbp50 509 2 0.00065 0.00088 3 0.316 −0.463 0.743
Cr21 680 3 0.00067 0.00123 3 0.267 −1.186 −0.200
FRICbp50 834 3 0.00073 0.0008 4 0.541 −0.177 −0.441
Cr21 810 5 0.00317 0.00172 2 0.514 2.562** 1.004*
LDCbp50 562 8 0.00473 0.00318 4 0.516 1.330 1.276
Cr21 559 1 0.00092 0.0005 2 0.514 1.505 0.620
PICbp50 392 5 0.0023 0.00285 3 0.251 −0.465 0.116
Cr21 938 9 0.00218 0.00267 6 0.738 −0.615 0.889
Gene Species n a L b S c π d θw e h f Hd g DTajima h DFu&Li i
AdhCbp50 351 4 0.00424 0.00254 2 0.372 1.514 0.743
Cr21 558 0 0 0 1 0
CRY1Cbp50 466 4 0.00341 0.00192 3 0.620 1.763 1.014
Cr21 465 0 0 0 1 0
FLCCbp50 509 2 0.00065 0.00088 3 0.316 −0.463 0.743
Cr21 680 3 0.00067 0.00123 3 0.267 −1.186 −0.200
FRICbp50 834 3 0.00073 0.0008 4 0.541 −0.177 −0.441
Cr21 810 5 0.00317 0.00172 2 0.514 2.562** 1.004*
LDCbp50 562 8 0.00473 0.00318 4 0.516 1.330 1.276
Cr21 559 1 0.00092 0.0005 2 0.514 1.505 0.620
PICbp50 392 5 0.0023 0.00285 3 0.251 −0.465 0.116
Cr21 938 9 0.00218 0.00267 6 0.738 −0.615 0.889

Total number of sequences.

Number of sites considered (excluding sites with indels or missing data).

Number of segregating sites.

Average number of pairwise differences.

Watterson's estimator of the population mutation rate.

Fu and Li's D calculated with an outgroup.

Population Genetic Summary Statistics and Neutrality Test Statistics (Significance Indicated by Asterisks) for Capsella bursa-pastoris (Cbp) A-Homoeologs in Western Eurasia and for Capsella rubella (Cr)

Gene Species n a L b S c π d θw e h f Hd g DTajima h DFu&Li i
AdhCbp50 351 4 0.00424 0.00254 2 0.372 1.514 0.743
Cr21 558 0 0 0 1 0
CRY1Cbp50 466 4 0.00341 0.00192 3 0.620 1.763 1.014
Cr21 465 0 0 0 1 0
FLCCbp50 509 2 0.00065 0.00088 3 0.316 −0.463 0.743
Cr21 680 3 0.00067 0.00123 3 0.267 −1.186 −0.200
FRICbp50 834 3 0.00073 0.0008 4 0.541 −0.177 −0.441
Cr21 810 5 0.00317 0.00172 2 0.514 2.562** 1.004*
LDCbp50 562 8 0.00473 0.00318 4 0.516 1.330 1.276
Cr21 559 1 0.00092 0.0005 2 0.514 1.505 0.620
PICbp50 392 5 0.0023 0.00285 3 0.251 −0.465 0.116
Cr21 938 9 0.00218 0.00267 6 0.738 −0.615 0.889
Gene Species n a L b S c π d θw e h f Hd g DTajima h DFu&Li i
AdhCbp50 351 4 0.00424 0.00254 2 0.372 1.514 0.743
Cr21 558 0 0 0 1 0
CRY1Cbp50 466 4 0.00341 0.00192 3 0.620 1.763 1.014
Cr21 465 0 0 0 1 0
FLCCbp50 509 2 0.00065 0.00088 3 0.316 −0.463 0.743
Cr21 680 3 0.00067 0.00123 3 0.267 −1.186 −0.200
FRICbp50 834 3 0.00073 0.0008 4 0.541 −0.177 −0.441
Cr21 810 5 0.00317 0.00172 2 0.514 2.562** 1.004*
LDCbp50 562 8 0.00473 0.00318 4 0.516 1.330 1.276
Cr21 559 1 0.00092 0.0005 2 0.514 1.505 0.620
PICbp50 392 5 0.0023 0.00285 3 0.251 −0.465 0.116
Cr21 938 9 0.00218 0.00267 6 0.738 −0.615 0.889

Total number of sequences.

Number of sites considered (excluding sites with indels or missing data).

Number of segregating sites.

Average number of pairwise differences.

Watterson's estimator of the population mutation rate.

Fu and Li's D calculated with an outgroup.

The isolation-with-migration model assumes independence of loci, no intralocus recombination, and selective neutrality. Linkage disequilibrium between putatively unlinked loci was low, with mean r 2 values between loci of 0.03 and 0.07 in C. bursa-pastoris from eastern and western Eurasia, respectively, and 0.12 in C. rubella. We found no evidence of intralocus recombination based on the minimum number of recombination events ( Hudson and Kaplan 1985) or the nonparameteric likelihood permutation test ( McVean et al. 2002) (not shown). However, there was evidence for gene conversion between PI homoeologs (GENECONV global score = 3.431, P= 0.019) in C. bursa-pastoris from western Eurasia. Tajima's D was also significantly positive for PI B in C. bursa-pastoris from western Eurasia (DTajima= 2.94, P < 0.001), possibly as a result of gene conversion. Because of these violations of model assumptions, PI was excluded from all analyses using the isolation-with-migration model. Apart from PI, only one other gene, FRI, deviated significantly from neutrality ( table 1, supplementary Supplementary Data , Supplementary Material online). Signs of selection were found for this gene in C. rubella, for FRI B in western Eurasia, and for FRI A in eastern Eurasia. To assess whether this had a substantial effect on the results, all isolation-with-migration analyses were run both with and without FRI.

The main aim of this study was to test whether haplotype sharing between C. rubella and C. bursa-pastoris is best explained by retention of ancestral polymorphism or by introgression. To answer this question, we analyzed data for 5 nuclear loci, Adh A, CRY1 A, FLC A, FRI A, and LD A using a coalescent-based isolation-with-migration model that allows population size change and thus constitutes a realistic scenario for polyploid speciation ( fig. 2). Our prediction was that, if haplotype sharing between C. rubella and C. bursa-pastoris is only due to retention of ancestral polymorphism, then estimates of gene flow between these species should be zero. If, on the other hand, hybridization and introgression have occurred, then some estimates of gene flow between species should be nonzero. Indeed, we found the latter to be true. In western Eurasia, where C. bursa-pastoris and C. rubella are partially sympatric and share haplotypes at 3 of the analyzed loci, there was evidence for unidirectional gene flow from C. rubella to C. bursa-pastoris ( fig. 3, table 2). In eastern Eurasia, where C. rubella is absent, there was no evidence for gene flow in either direction ( fig. 3, table 2). Analyses of both geographical samples supported a scenario where the origin of the tetraploid C. bursa-pastoris constituted a severe bottleneck ( table 2, supplementary Supplementary Data , Supplementary Material online), after which the species underwent a strong population expansion to a current effective population size of about 30,000 ( table 2). The mode of the marginal posterior probability density for the time since the split (t) between C. rubella and C. bursa-pastoris was located at about 1.2 MYA in analyses of the eastern Eurasian sample, but the probability of observing higher values of t remained high (supplementary Supplementary Data , Supplementary Material online). The time of the split was poorly resolved in analyses of the western Eurasian sample, where marginal posterior probabilities were low for very recent values of t (less than about 500 ka) and higher but unresolved for higher values of t (supplementary Supplementary Data , Supplementary Material online). Because no credibility intervals are available for the time since the split, these estimates should be viewed with caution. Results from analyses without FRI A were qualitatively similar to results from analyses with all 5 loci (not shown).

Model Parameter Estimates and 90% HPD Intervals (in Parentheses, Where Available) for Analyses of Pairs of Populations/Species: Capsella bursa-pastoris Samples from Western and Eastern Eurasia (W Cbp and E Cbp), and Capsella rubella (Cr)

Population 1 Population 2 m1 a m2 a N1 b N2 b sNA b NA c t c, d
W Cbp Cr 0.408 (0.118–0.903) 0.0025 (0–0.333) 32.9 (14.6–56.7) 28.6 (13.5–60.0) 0.540 (0–270) 1.62 3925.7
E Cbp Cr 0.0025 (0–0.278) 0.0025 (0–0.328) 28.9 (11.1–57.4) 24.7 (11.1–53.2) 0.527 (0–298) 1.58 1206.8
W Cbp E Cbp 0.005 (0–4.03) 2.165 c 8.1 (2.3–22.5) 17.1 (6.5–43.1) 11.5 67.7
Population 1 Population 2 m1 a m2 a N1 b N2 b sNA b NA c t c, d
W Cbp Cr 0.408 (0.118–0.903) 0.0025 (0–0.333) 32.9 (14.6–56.7) 28.6 (13.5–60.0) 0.540 (0–270) 1.62 3925.7
E Cbp Cr 0.0025 (0–0.278) 0.0025 (0–0.328) 28.9 (11.1–57.4) 24.7 (11.1–53.2) 0.527 (0–298) 1.58 1206.8
W Cbp E Cbp 0.005 (0–4.03) 2.165 c 8.1 (2.3–22.5) 17.1 (6.5–43.1) 11.5 67.7

N OTE .—The 2 comparisons involving C. rubella are based on A homoeolog data, whereas the comparison within C. bursa-pastoris is based on B homoeolog data.

Estimates of gene flow (forward in time) from population 1 to population 2 (m2) and from population 2 to population 1 (m1), scaled by the geometric mean of the mutation rate for all loci.

Effective population size estimates in numbers of individuals × 10 −3 . NA, ancestral effective population size s, population splitting parameter, which accounts for the proportion of the ancestral population that found descendant population 1.

90% HPD interval not available.

Estimated time of the split (ka).

Model Parameter Estimates and 90% HPD Intervals (in Parentheses, Where Available) for Analyses of Pairs of Populations/Species: Capsella bursa-pastoris Samples from Western and Eastern Eurasia (W Cbp and E Cbp), and Capsella rubella (Cr)

Population 1 Population 2 m1 a m2 a N1 b N2 b sNA b NA c t c, d
W Cbp Cr 0.408 (0.118–0.903) 0.0025 (0–0.333) 32.9 (14.6–56.7) 28.6 (13.5–60.0) 0.540 (0–270) 1.62 3925.7
E Cbp Cr 0.0025 (0–0.278) 0.0025 (0–0.328) 28.9 (11.1–57.4) 24.7 (11.1–53.2) 0.527 (0–298) 1.58 1206.8
W Cbp E Cbp 0.005 (0–4.03) 2.165 c 8.1 (2.3–22.5) 17.1 (6.5–43.1) 11.5 67.7
Population 1 Population 2 m1 a m2 a N1 b N2 b sNA b NA c t c, d
W Cbp Cr 0.408 (0.118–0.903) 0.0025 (0–0.333) 32.9 (14.6–56.7) 28.6 (13.5–60.0) 0.540 (0–270) 1.62 3925.7
E Cbp Cr 0.0025 (0–0.278) 0.0025 (0–0.328) 28.9 (11.1–57.4) 24.7 (11.1–53.2) 0.527 (0–298) 1.58 1206.8
W Cbp E Cbp 0.005 (0–4.03) 2.165 c 8.1 (2.3–22.5) 17.1 (6.5–43.1) 11.5 67.7

N OTE .—The 2 comparisons involving C. rubella are based on A homoeolog data, whereas the comparison within C. bursa-pastoris is based on B homoeolog data.

Estimates of gene flow (forward in time) from population 1 to population 2 (m2) and from population 2 to population 1 (m1), scaled by the geometric mean of the mutation rate for all loci.

Effective population size estimates in numbers of individuals × 10 −3 . NA, ancestral effective population size s, population splitting parameter, which accounts for the proportion of the ancestral population that found descendant population 1.

90% HPD interval not available.

Estimated time of the split (ka).

Probability density estimates for gene flow parameters, scaled by the geometric mean of the per-locus mutation rate. (A) The left plot shows the probability density for gene flow in western Eurasia, with gene flow from Capsella rubella to Capsella bursa-pastoris (forward in time) in black and from C. bursa-pastoris to C. rubella in gray. The right plot shows the marginal posterior probability distribution of gene flow estimates for eastern Eurasia. (B) Probability density for gene flow between eastern and western Eurasian populations of C. bursa-pastoris.

Probability density estimates for gene flow parameters, scaled by the geometric mean of the per-locus mutation rate. (A) The left plot shows the probability density for gene flow in western Eurasia, with gene flow from Capsella rubella to Capsella bursa-pastoris (forward in time) in black and from C. bursa-pastoris to C. rubella in gray. The right plot shows the marginal posterior probability distribution of gene flow estimates for eastern Eurasia. (B) Probability density for gene flow between eastern and western Eurasian populations of C. bursa-pastoris.

We assessed the timing and extent of gene flow from C. rubella to C. bursa-pastoris in western Eurasia in all isolation-with-migration analyses. The posterior probability distribution for migration times and numbers differed between loci where haplotypes were shared between C. rubella and C. bursa-pastoris (Adh A, CRY1 A, and LD A) and loci where no haplotype sharing was found (FLC A and FRI A) (supplementary Supplementary Data , Supplementary Material online). For Adh A, CRY1 A, and LD A, the highest probability was obtained for 2 migration events, whereas for FRI A and FLC A the estimated number of migration events was 1 (supplementary Supplementary Data , Supplementary Material online). Loci with shared haplotypes had a bimodal posterior probability distribution of migration times with a major, sharp peak located at about 10.8–19.4 ka, and a subsidiary, much flatter peak at 300–500 ka ( fig. 4 supplementary Supplementary Data , Supplementary Material online). Probability distributions of migration times for FRI A and FLC A only had one minor, flat peak at around 500 ka (supplementary Supplementary Data , Supplementary Material online). All probability distributions were clearly different from the priors (supplementary Supplementary Data , Supplementary Material online).

Posterior probability distributions of the time of introgression from Capsella rubella to Capsella bursa-pastoris (black) and the time of gene flow from western to eastern Eurasian populations of C. bursa-pastoris (gray), for LD.

Posterior probability distributions of the time of introgression from Capsella rubella to Capsella bursa-pastoris (black) and the time of gene flow from western to eastern Eurasian populations of C. bursa-pastoris (gray), for LD.

To obtain an independent estimate of the timing and direction of worldwide dispersal of C. bursa-pastoris, we analyzed C. bursa-pastoris sequence data for the 5 B-homoeologs (Adh B, CRY1 B, FRI B, FLC B, and LD B) using the standard isolation-with-migration model. This analysis gave somewhat lower estimates of the effective population size of C. bursa-pastoris, although the 90% HPD intervals overlapped with those obtained from the A-homoeologs ( table 2). Consistent with previous hypotheses on the origin and spread of C. bursa-pastoris ( Hurka and Neuffer 1997), there was some evidence for gene flow from western to eastern Eurasia ( fig. 3, table 2). All 5 loci had posterior probability distributions that clearly differed from the priors, and the estimated time of gene flow ranged from 21 to 64 ka ( fig. 4, supplementary Supplementary Data , Supplementary Material online). For Adh, CRY1, and LD, but not for FRI and FLC, the major peak in the probability distribution for the time of gene flow from western to eastern populations of C. bursa-pastoris predated the estimated time of introgression ( fig. 4, supplementary Supplementary Data , Supplementary Material online). Posterior probability distributions for the time since population splitting and the ancestral population size were flat and uninformative, and results for analyses run without FRI B were qualitatively similar to those for all 5 loci (not shown).


ACKNOWLEDGMENTS

The authors would like to thank J. Coyne, J. Evans, and H. A. Orr for stimulating discussion. H. D. Bradshaw, Jr., E. Dittmar, R. Harrison, K. Kay, D. Lowry, N. Martin, P. Nosil, H. A. Orr, H. Rundle, D. Schluter, J. Willis read previous versions of this manuscript and provided invaluable comments. Funding was provided by the National Science Foundation, through a FIBR grant (DBI-0328636) and a Doctoral Dissertation Improvement Grant (DEB-0808447). This is KBS contribution number 1547 from the W. K. Kellogg Biological Station.


Results

Nuclear DNA

The length of the aligned LEAFY sequence was 1017 bp. Two hundred ninety-two haplotypes were identified from 380 LEAFY sequences. Most shared haplotypes were detected within species, such as H2 and H108 in I. yunguiensis, H72 in I. taiwanensis, H92 in I. sinensis and H133 in I. orientalis (Table S3). And one shared haplotype (H51) was found between JD1 and JM from two different species, I. sinensis and I. taiwanensis (Fig. 2a, Table S3).

There were two major clades in the nuclear phylogenetic tree (Fig. 3). The diploids were exclusively found in either of these clades: I. yunguiensis in Clade I and I. taiwanensis in Clade II. Most populations of I. sinensis were simultaneously located in both clades, for example, JD (JD1 and JD2), XN, NX, and HT. Two populations from I. sinensis, TD and TT were only found in Clade II. And all population of I. orientalis were also located in both clades.

Multiple maternal lineages of Isoetes

The lengths of the aligned sequences of ycf66, atpB-rbcL, petL-psbE and trnS-trnG were 493, 813, 1428 and 836 bp respectively and the concatenated sequences were 3570 bp. Two major clades were inferred in the plastid phylogenetic tree. Clade A was composed of all the populations from I. yunguiensis and the polyploid populations of HT and JD. Clade B consisted of all the populations from I. taiwanensis, and the polyploidy populations of XN, TT, NX, TD, and SY (Fig. 4). And two shared haplotypes were found from different species, I. sinensis and I. orientalis, H21 for populations TD and SY, H24 for populations TD, TT, and SY (Fig. 2b).

Analysis of divergence times

The BEAST dating analysis estimated the crow node of the I. sinensis allopolyploid system was 4.43 Ma (95% HPD: 2.77–6.97 Ma) falling into later Miocene to early Pliocene (Fig. 5). The divergence time between I. sinensis and I. taiwanensis was estimated to 0.65 Ma (95% HPD: 0.26–1.91 Ma) around the Pleistocene of Quaternary (Fig. 5).

Niche variation and quantification in geographical space

The ENMs for I. sinensis and its diploid progenitors showed good performances based on their high AUC values (greater than 0.9 for all models). The predicted current distributions of these species were consistent with their present distributions (Fig. 1 and Fig. 6a, b, c). The niche breadths for I. yunguiensis, I. taiwanensis and I. sinensis were 0.25, 0.014 and 0.008 respectively (Fig. 6d). The Schoener’s D index between I. sinensis and I. yunguiensis was 0.08, 0.26 between I. sinensis and I. taiwanensis, and 0.17 between I. yunguiensis and I. taiwanensis (Fig. 6e).

The map was download from WorldClim 1.4 (www.worldclim.org), and it is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License (http://creativecommons.org/licenses/by-sa/4.0/). Geographical distributions of the sampled populations of Chinese Isoetes complex: hexagons, triangles, circles and squares are used to represent I. orientalis, I. taiwanensis, I. yunguiensis and I. sinensis respectively. The populations colored as grey are extinct. The dotted lines delimit the three distinct elevation stairs (elevation decreases from left to right) in China

Niche variation and quantification in ecological space

The first two principal components (PCs) identified by PCA collectively explained 98.1% of the total variation among the three species (PC1 = 74.1%, PC2 = 24%) and clearly separated these species (Fig. 7). Altitude was strongly associated with PC1 and separated I. yunguiensis from the others along. Annual precipitation showed a high correlation with PC2 and separated I. taiwanensis from the others along. The values of the six retained Bioclim layers of I. yunguiensis, I. taiwanensis and I. sinensis were significantly different (P ≤ 0.05) from each other in four out of the six individual environmental variables (Table 1). The ecology of the polyploid species I. sinensis were characterized by the highest values for temperature annual range (BIO7) and the lowest values for altitude, with intermediate values for annual mean temperature (BIO1) and annual precipitation (Fig. 8). The ecology of the diploid species I. taiwanensis were characterized by the highest values for annual mean temperature, annual precipitation and the lowest values for temperature annual range (Fig. 8). Conversely, the ecology of the diploid species I. yunguiensis showed the lowest values for annual mean temperature and annual precipitation but the highest values for altitude (Fig. 8).


INTRODUCTION

About half of all higher plant species are recognizable as evolutionarily recent polyploids, where multiple whole genomes or sets of chromosomes have come together from close ancestors ( Soltis et al., 2015). Additionally, over evolutionary time, all flowering plants have at least one polyploidy event, also known as a whole-genome duplication (WGD), in their ancestry, from before the divergence of gymnosperms and angiosperms, the ζ (zeta) event (see Fig. 1, and references cited in the legend). Angiosperms, including Amborella and the basal angiosperms (i.e. ANA, for Amborellales, Nymphaeales, Austrobaileyales) that are sisters to all the other angiosperms, have a second polyploidy event in their lineage (ε, epsilon Amborella Genome Project, 2013). Analyses of whole-genome sequences in the last decade have identified additional, and often multiple, polyploidy events in the ancestry of every eudicot and monocot where the genomes have been sequenced (summarized in Fig. 1). Notably, the near-universal occurrence of multiple polyploidy events ( Wendel, 2015) during plant evolution is in contrast to most groups of animals in both recent and long-term evolutionary history (e.g. Hoffmann et al., 2012), marking a significant divergence between evolutionary mechanisms in the two kingdoms.

Simplified phylogeny of the green plant lineage focusing on the occurrence of WGD (whole-genome duplication) events. Polyploidy events (yellow diamonds) refer to either single or multiple rounds of WGD (i.e. duplication or triplication) and are labelled where applicable (Greek letters see references below). Complete genome sequences have clearly established that WGD has remarkably shaped the evolutionary history of angiosperms compared with the other major clades of green plants. Estimates for the age of angiosperms have suggested the range of 167–199 million years ago (Mya) ( Bell et al., 2010). Then rapid radiations responsible for the extant angiosperm diversity occurred after the early diversification of Mesangiospermae 139–156 Mya ( Moore et al., 2007 Bell et al., 2010) with a burst of diversification specific for the Cretaceous, <125 Mya (age of the earliest angiosperm macrofossil Cascales-Miñana et al., 2016). Early divergence times are from Bell et al. (2010) and Leliaert et al. (2012) for angiosperms from Fawcett et al. (2009), Jiao et al. (2011) and Li et al. (2016) and for gymnosperms from Lu et al. (2014). Dashed lines indicate imprecise timing or approximate representation of lineage divergence. WGD events are from Jiao et al. (2011) Leliart et al. (2011) D’Hont et al. (2012) Beike et al. (2014) Renny-Byfield and Wendel (2014) Li et al. (2015, 2016) Scott et al. (2016) Shaw et al. (2016) and Bombarely et al. (2016). See corresponding publications for precise estimates of time divergence and occurrence of WGD. AGF, hypothetical ancestral green flagellate ANA, basal angiosperms including Amborellales, Nymphaeales, Austrobaileyales following a standardized method, Greek letters are used to name polyploidy events along the phylogenetic tree, starting from the α (alpha) and β (beta) events that have been identified in the arabidopsis genome ( Bowers et al., 2003).

Simplified phylogeny of the green plant lineage focusing on the occurrence of WGD (whole-genome duplication) events. Polyploidy events (yellow diamonds) refer to either single or multiple rounds of WGD (i.e. duplication or triplication) and are labelled where applicable (Greek letters see references below). Complete genome sequences have clearly established that WGD has remarkably shaped the evolutionary history of angiosperms compared with the other major clades of green plants. Estimates for the age of angiosperms have suggested the range of 167–199 million years ago (Mya) ( Bell et al., 2010). Then rapid radiations responsible for the extant angiosperm diversity occurred after the early diversification of Mesangiospermae 139–156 Mya ( Moore et al., 2007 Bell et al., 2010) with a burst of diversification specific for the Cretaceous, <125 Mya (age of the earliest angiosperm macrofossil Cascales-Miñana et al., 2016). Early divergence times are from Bell et al. (2010) and Leliaert et al. (2012) for angiosperms from Fawcett et al. (2009), Jiao et al. (2011) and Li et al. (2016) and for gymnosperms from Lu et al. (2014). Dashed lines indicate imprecise timing or approximate representation of lineage divergence. WGD events are from Jiao et al. (2011) Leliart et al. (2011) D’Hont et al. (2012) Beike et al. (2014) Renny-Byfield and Wendel (2014) Li et al. (2015, 2016) Scott et al. (2016) Shaw et al. (2016) and Bombarely et al. (2016). See corresponding publications for precise estimates of time divergence and occurrence of WGD. AGF, hypothetical ancestral green flagellate ANA, basal angiosperms including Amborellales, Nymphaeales, Austrobaileyales following a standardized method, Greek letters are used to name polyploidy events along the phylogenetic tree, starting from the α (alpha) and β (beta) events that have been identified in the arabidopsis genome ( Bowers et al., 2003).

With respect to its omnipresence during the evolutionary history of higher plants, polyploidy has been the subject of numerous reviews with emphasis on the genetic and genomic consequences of WGDs ( Soltis et al., 2016). The present review has two main objectives: first, overviewing the papers in this Special Issue ‘Polyploidy in Ecology and Evolution’ and secondly to discuss complementary polyploidy-related topics covered. In the Special Issue, we made the choice not simply to consider the occurrence of polyploidy (or WGD) in plants (including the bryophyte Sphagnum), but also to provide an overview of the consequences of polyploidy in adaptation, speciation and evolution in plants: the relationships between polyploidy and stressful environmental conditions have suggested a major role for polyploidy in adaptation. This has been extensively analysed for cultivated plants, and we review this topic, in the context of concepts related to papers in the Special Issue, many of which present research in the novel area of polyploidy in natural plant populations. With the number of polyploidy events being revealed in plant evolution, the study of its evolutionary significance on wild plant species at the population scale, considering both evolutionarily ancient (deep) phylogenies and recent polyploids (some below the level of species), is now underway. The Special Issue articles consider the success and diversity found in polyploids from the ecological and evolutionary points of view, including developmental and genetic studies. Several papers deal with the relationships of polyploidy to plant reticulate evolution (i.e. natural hybridization), while others bear on the origin and formation of neopolyploids. Some papers discuss the relationships between allopolyploidy and reproductive systems, two major processes driving angiosperm diversification, and other papers highlight the link between polyploidy and adaptation, in a biogeographical context. Finally, a review dedicated to the impact of transposable elements (TEs) on polyploid plant genomes gives consideration to the molecular basis of genomic conflicts, particularly present in genome duplications with hybrid origins. We have specifically developed this renewed interest for the study of polyploidy in plants with new avenues of investigations dedicated to the epigenetic consequences of polyploidy and their role for plasticity and adaptation in plants.


By definition, polyploidy just means that a cell or organism contains more than 2 pairs of homologous chromosomes (or is more than 2n). This is more common in plants than it is in animals. Multiple plants within a population can end up with the same polyploidy number. They can then reproduce with each other but not with the original plants or any other plants. As a result, they become biologically isolated from the original group of plants and are considered a different species.

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