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opencc-by-4.0Apr 2020View details →

Demo dataset for diploid genome assembly pipeline

<p>Small-scale demo data to test the diploid genome assembly pipeline. The tar archive contains PacBio HiFi/CCS and Strand-seq reads, plus a reduced genome reference. For instructions how to run the demo data, please refer to the documentation hosted in the pipeline repository (see related identifiers).</p>

opencc-zeroAug 2020View details →

Polyploids increase overall diversity despite higher turnover than diploids in the Brassicaceae

<p>Although polyploidy is widespread across the plant Tree of Life, its long-term evolutionary significance is still poorly understood. Here we examine the effects of polyploidy in explaining the large-scale evolutionary patterns within angiosperms by focusing on a single family exhibiting extensive inter-specific variation in chromosome numbers. We inferred ploidy from haploid chromosome numbers for 80% of species in the most comprehensive species-level chronogram for the Brassicaceae. After evaluating a total of 94 phylogenetic models of diversification, we found that ploidy influences diversification rates across the Brassicaceae. We also found that despite diversifying at a similar rate to diploids, polyploids have played a significant role in driving present-day differences in species richness among clades. Overall, in addition to highlighting the complexity in the evolutionary consequences of polyploidy, our results suggest that rare successful polyploids persist while significantly contributing to the long-term evolution of clades. Our findings further indicate that polyploidy has played a major role in driving the long-term evolution of the Brassicaceae and highlight the potential of polyploidy in shaping present-day diversity patterns across the plant Tree of Life.</p>

opencc-zeroNov 2019View details →

Eco-genetic additivity of diploids in allopolyploid wild wheats

Underpinnings of the distribution of allopolyploid species (hybrids with duplicated genome) along spatial and ecological gradients are elusive. As allopolyploid speciation combines the range of genetic and ecological characteristics of divergent diploids, allopolyploids initially show their additivity and are predicted to evolve differentiated ecological niches to establish in face of their competition. Here, we use four diploid wild wheats that differentially combined into four independent allopolyploid species to test for such additivity and assess the impact of ecological constraints on species ranges. Divergent genetic variation from diploids being fixed in heterozygote allopolyploids supports their genetic additivity. Spatial integration of comparative phylogeography and modeling of climatic niches supports ecological additivity of locally adapted diploid progenitors into allopolyploid species which subsequently colonized wide ranges. Allopolyploids fill suitable range to a larger extent than diploids and conservative evolution following the combination of divergent species appears to support their expansion under environmental changes.

opencc-zeroDec 2014View details →

Data from: Genetic diversity and distribution patterns of diploid and polyploid hybrid water frog populations (Pelophylax esculentus complex) across Europe

Polyploidization is a rare yet sometimes successful way for animals to rapidly create geno- and phenotypes that may colonize new habitats and quickly adapt to environmental changes. In this study, we use water frogs of the Pelophylax esculentus complex, comprising two species (Pelophylax lessonae, genotype LL; Pelophylax ridibundus, RR) and various diploid (LR) and triploid (LLR, LRR) hybrid forms, summarized as P. esculentus, as a model for studying recent hybridization and polyploidization in the context of speciation. Specifically, we compared the geographic distribution and genetic diversity of diploid and triploid hybrids across Europe to understand their origin, maintenance and potential role in hybrid speciation. We found that different hybrid and parental genotypes are not evenly distributed across Europe. Rather, their genetic diversity is structured by latitude and longitude and the presence/absence of parental species but not of triploids. Highest genetic diversity was observed in central and eastern Europe, the lowest in the northwestern parts of Europe. This gradient can be explained by the decrease in genetic diversity during postglacial expansion from southeastern glacial refuge areas. Genealogical relationships calculated on the basis of microsatellite data clearly indicate that hybrids are of multiple origin and include a huge variety of parental genomes. Water frogs in mixed-ploidy populations without any parental species (i.e. all-hybrid populations) can be viewed as evolutionary units that may be on their way towards hybrid speciation. Maintenance of such all-hybrid populations requires a continuous exchange of genomes between diploids and triploids, but scenarios for alternative evolutionary trajectories are discussed.

opencc-zeroDec 2009View details →

Data from: Conservation genetics of Neotropical pollinators revisited: microsatellite analysis suggests that diploid males are rare in orchid bees

Allozyme analyses have suggested that Neotropical orchid bee (Euglossini) pollinators are vulnerable because of putative high frequencies of diploid males, a result of loss of sex allele diversity in small hymenopteran populations with single locus complementary sex determination. Our analysis of 1010 males from 27 species of euglossine bees sampled across the Neotropics at 2-11 polymorphic microsatellite loci revealed only 5 diploid males at an overall frequency of 0.005 (95% CIs 0.002-0.010); errors through genetic non-detection of diploid males were likely small. In contrast to allozyme-based studies, we detected very weak or insignificant population genetic structure, even for a pair of populations >500 km apart, possibly accounting for low diploid male frequencies. Technical flaws in previous allozyme-based analyses have probably led to considerable overestimation of diploid male production in orchid bees. Other factors may have a more immediate impact on population persistence than the genetic load imposed by diploid males on these important Neotropical pollinators.

opencc-zeroDec 2015View details →

Data from: Unidirectional diploid–tetraploid introgression among British birch trees with shifting ranges shown by restriction site-associated markers

Hybridization may lead to introgression of genes among species. Introgression may be bidirectional or unidirectional, depending on factors such as the demography of the hybridizing species, or the nature of reproductive barriers between them. Previous microsatellite studies suggested bidirectional introgression between diploid Betula nana (dwarf birch) and tetraploid B. pubescens (downy birch) and also between B. pubescens and diploid B. pendula (silver birch) in Britain. Here, we analyse introgression among these species using 51 237 variants in restriction site-associated (RAD) markers in 194 individuals, called with allele dosages in the tetraploids. In contrast to the microsatellite study, we found unidirectional introgression into B. pubescens from both of the diploid species. This pattern fits better with the expected nature of the reproductive barrier between diploids and tetraploids. As in the microsatellite study, introgression into B. pubescens showed clear clines with increasing introgression from B. nana in the north and from B. pendula in the south. Unlike B. pendula alleles, introgression of B. nana alleles was found far from the current area of sympatry or allopatry between B. nana and B. pubescens. This pattern fits a shifting zone of hybridization due to Holocene reduction in the range of B. nana and expansion in the range of B. pubescens.

opencc-zeroDec 2012View details →

Data from: Adaptation of diploid and tetraploid Chamerion angustifolium to elevation but not local environment

Polyploid organisms often have different geographic ranges than their diploid relatives. However, it is unclear whether this divergence is maintained by adaptation or results from historical differences in colonization. Here we conducted a reciprocal transplant experiment with diploid and autotetraploid Chamerion angustifolium to test for adaptation at the ploidy and population level. In the Rocky Mountains, pure diploid populations occur at high elevations and pure autotetraploid populations occur at low elevations with mixed-ploidy populations between. We planted 3134 seedlings in 2004 and 3890 juveniles (bolting) in 2005 among nine plots, three in each of the diploid, mixed-ploidy and tetraploid zones, and monitored survival until 2008. For both seedlings and juvenile plants, elevation significantly influenced survival. The juvenile plants also showed a significant ploidy by elevation interaction, indicating that diploids and tetraploids survived best at their native elevations. In contrast, we found no evidence of local adaptation to plot within elevation. This suggests that the current distribution of diploids and tetraploids across elevations is the result of adaptation and that genome duplication may have facilitated the invasion of lower elevation habitats by limiting the movement of maladapted alleles from diploid populations at higher elevations.

opencc-zeroDec 2018View details →

Data from: Fitness of an allopolyploid rupicolous fern compared to its diploid progenitors: From sporogenesis to sporophyte formation

PREMISE OF THE STUDY: When two populations of related cytotypes grow in sympatry, the rarer cytotype tends to be excluded due to a frequency-dependent mating disadvantage. Evolutionary models predict that polyploids, which are typically the rarer cytotype upon first formation, should have higher relative fitness and/or higher selfing rates to establish and then coexist with diploid parents. METHODS: We compared performance in early recruitment among three co-occurring rupicolous fern species: the allotetraploid Cheilanthes tinaei and its diploid ancestors, C. hispanica and C. maderensis. We made culture experiments with fresh spores and samples of soil spore banks to test for variation among cytotypes in germination, survival, growth and fecundity, and mating system of gametophytes. KEY RESULTS: Compared to its diploid parents, C. tinaei fresh spores had: higher abortion percentages, worselower dispersal ability due to larger spores, and similar vigor at germination. As for gametophytes from soil spore banks, C. tinaei showed high survival as C. maderensis, but its , similar germination percentage and similar time taken to germinate at each incubation temperature. Regarding soil spore banks, C. tinaei showed more abundant germination than both diploids, which supports greater spore deposition under sporophytes of the allotetraploid. Its gender expression resembles that of C. hispanica, with a high proportion of males. Patterns of sporophyte formation by females and bisexuals indicate that the polyploid does not have increased intragametophytic selfing rates. Gametophytes were larger in C. tinaei, but its reproductive success (sporophyte formation) was intermediate relative to diploids. CONCLUSIONS: Our results indicate that the allopolyploid show similar or even lower fitness than diploid progenitors show no evidence of higher selfing or fitness advantage of the allopolyploid over both diploid parents at any stage of early recruitment. In addition, all three species may have similar selfing rates. These two unexpected findings suggest that further factors, such as niche differentiation, play a more important role in cytotype coexistence.

opencc-zeroDec 2014View details →

Data from: Ecological differentiation, lack of hybrids involving diploids, and asymmetric gene flow between polyploids in narrow contact zones of Senecio carniolicus (syn. Jacobaea carniolica, Asteraceae)

Areas of immediate contact of different cytotypes offer a unique opportunity to study evolutionary dynamics within heteroploid species and to assess isolation mechanisms governing coexistence of cytotypes of different ploidy. The degree of reproductive isolation of cytotypes, i.e., the frequency of heteroploid crosses and subsequent formation of viable and (partly) fertile hybrids, plays a crucial role for the long-term integrity of lineages in contact zones. Here, we assessed fine-scale distribution, spatial clustering and ecological niches as well as patterns of gene-flow in parental and hybrid cytotypes in zones of immediate contact of di-, tetra- and hexaploid Senecio carniolicus (Asteraceae) in the Eastern Alps. Cytotypes were spatially separated also at the investigated micro-scale; the strongest spatial separation was observed for the fully interfertile tetra- and hexaploids. The three main cytotypes showed highly significant niche differences, which were, however, weaker than across their entire distribution ranges in the Eastern Alps. Individuals with intermediate ploidy levels were found neither in the diploid/tetraploid nor in the diploid/hexaploid contact zones indicating strong reproductive barriers. In contrast, pentaploid individuals were frequent in the tetraploid/hexaploid contact zone, albeit limited to a narrow strip in the immediate contact zone of their parental cytotypes. AFLP fingerprinting data revealed introgressive gene flow mediated by pentaploid hybrids from tetra- to hexaploid individuals, but not vice versa. The ecological niche of pentaploids differed significantly from that of tetraploids but not from hexaploids.

opencc-zeroDec 2015View details →

Data from: The effects of quantitative fecundity in the haploid stage on reproductive success and diploid fitness in the aquatic peat moss Sphagnum macrophyllum

A major question in evolutionary biology is how mating patterns affect the fitness of offspring. However, in animals and seed plants it is virtually impossible to investigate the effects of specific gamete genotypes. In bryophytes, haploid gametophytes grow via clonal propagation and produce millions of genetically identical gametes throughout a population. The main goal of this research was to test whether gamete identity has an effect on the fitness of their diploid offspring in a population of the aquatic peat moss Sphagnum macrophyllum. We observed a heavily male-biased sex ratio in gametophyte plants (ramets) and in multilocus microsatellite genotypes (genets). There was a steeper relationship between mating success (number of different haploid mates) and fecundity (number of diploid offspring) for male genets compared with female genets. At the sporophyte level, we observed a weak effect of inbreeding on offspring fitness, but no effect of brood size (number of sporophytes per maternal ramet). Instead, the identities of the haploid male and haploid female parents were significant contributors to variance in fitness of sporophyte offspring in the population. Our results suggest that intrasexual gametophyte/gamete competition may play a role in determining mating success in this population.

opencc-zeroDec 2015View details →

Data from: Invasion success in polyploids: the role of inbreeding in the contrasting colonization abilities of diploid versus tetraploid populations of Centaurea stoebe s.l

As a consequence of founder effects, inbreeding can hamper colonization success: First, in species with self-incompatibility controlled by an S-locus, inbreeding may decrease cross-compatibility, mainly due to the sharing of identical S-alleles between closely related mating partners. Secondly, inbreeding can reduce fitness of inbred relative to outbred offspring (i.e. inbreeding depression). Polyploids often show reduced inbreeding depression compared to diploids, which may contribute to the overrepresentation of polyploids among invasive species. This is the first study that tests how the effects of inbreeding differ between geocytotypes (i.e. ploidy levels within a given range). Our model organism, Centaurea stoebe, is strictly self-incompatible and comprises three geocytotypes: diploids are more frequent than tetraploids in the native range, while only tetraploids occur in the invasive range. We conducted a breeding experiment (sib-mating vs. outcrossing) with 14 native diploid, 13 native tetraploid and 15 invasive tetraploid populations. We recorded cross-compatibility and estimated a cumulative index for offspring fitness. Since frequent inbreeding can result in purging of genetic load responsible for inbreeding depression, our analyses included a metric for within-population relatedness, based on eight microsatellite markers, to assess the effect of purging. Inbreeding was found to reduce cross-compatibility, which was similarly pronounced in diploids and tetraploids. It also caused inbreeding depression in cumulative fitness, which was significant in diploids but not in tetraploids. No evidence of purging was observed as inbred fitness was not affected by within-population relatedness. Synthesis. Our results provide new insights into the contrasting invasion success of the cytotypes of C. stoebe. As the effects of cross-compatibility and purging were comparable between cytotypes, both processes can be ruled out to affect the colonization success of diploids versus tetraploids. Our findings are consistent with the hypothesis that polyploidy increases the masking of recessive mutations, which maintains high fitness in inbred tetraploids and may thus facilitate colonization of new ranges. We highlight that reduced inbreeding depression may add to previously acknowledged advantages of polyploids in range expansions, a mechanism that may hitherto have been underestimated due to a lack of data on variation in inbreeding depression across geocytotypes.

Fig. 4 in Morphology and biometry of two Chinese diploid parthenogenetic Artemia populations with a special emphasis on the gonopods and frontal knobs of rare males

Fig. 4. Scatterplots of discriminant analyses. A–D: Using 13 parameters suggested by Hontoria & Amat (1992) and Triantaphyllidis et al. (1997a) (A) female, two dimension plot (B) female, three dimension plot (C) male, two dimension plot (D) male, three dimension plot. E–F: Using 12 parameters of gonopod and frontal knob suggested by Zheng & Sun (2008) (E) two dimension plot (F) three dimension plot. G–H: Using all aforementioned parameters (G) two dimension plot (H) three dimension plot.

Fig. 2 in Morphology and biometry of two Chinese diploid parthenogenetic Artemia populations with a special emphasis on the gonopods and frontal knobs of rare males

Fig. 2. Frontal knobs of rare males of parthenogenetic Artemia (A) GH, lateral view (B) CK-par, lateral view (C) GH, frontal view (D) CK-par, frontal view (E) GH, enlargement to show arrangement of spines (F) CK-par, enlargement to show arrangement of spines.

Fig. 1 in Morphology and biometry of two Chinese diploid parthenogenetic Artemia populations with a special emphasis on the gonopods and frontal knobs of rare males

Fig. 1. Gonopods of rare males of parthenogenetic Artemia and spines on the surface of gonopods (A) the gonopod of GH (B) the gonopod of CK-par; C. basal part of the gonopod of GH (D) exo-lateral spines of GH (E) exo-lateral spines of CK-par (F) the basal gonopod spine of CK-par in detail (G) posterior spines of GH (H) posterior spines of CK-par. BG = basal portion of gonopod. DG = distal portion of gonopod. DA = digitiform apex. ES = exo-lateral spines. PS = posterior spines. BGS = basal gonopod spines.

Fig. 3 in Morphology and biometry of two Chinese diploid parthenogenetic Artemia populations with a special emphasis on the gonopods and frontal knobs of rare males

Fig. 3. Percentage composition of specimens with different LD/SD (ratio of large diameter to small diameter of frontal knob) in 15 Artemia populations.

opennotspecifiedDec 2023View details →

FIGURE 1 in A naturalized diploid Fragaria sp. (Rosaceae) found in southern Chile as revealed by morphological, ploidy and cytogenetic analyses

FIGURE 1. Map of Chile with the locations of the eight accessions of Fragaria chiloensis subsp. chiloensis f. patagonica and Fragaria sp. (Fragaria-MEN) in the Araucania and Los Rios regions. CRC, Curacautin; MAL, Malalcahuello; HUE, Huerquehue; HUE2, Huerquehue 2; HUE3, Huerquehue 3; HUE4, Huerquehue 4; MEN, Menetue; MAM, Mamuil-Malal; NEL, Neltume. Modified from Oñate et al. (2018) and Mora et al. (2016, 2019). For coordinates details of each accession see Table S1.

opennotspecifiedDec 2023View details →

FIGURE 3 in A naturalized diploid Fragaria sp. (Rosaceae) found in southern Chile as revealed by morphological, ploidy and cytogenetic analyses

FIGURE 3. Adaxial and abaxial leaf surfaces of Fragaria chiloensis subsp. chiloensis f. patagonica, Fragaria vesca 'Hawaii' and Fragaria-MEN. Scale = 1 cm.