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opencc-zeroMay 2024View details →

Data from: Evolutionary patterns of ploidy and genome size variations show positive correlations with taxonomic diversity in tropical gingers (Zingiberaceae)

Premise: Cytogenetic traits such as an organism's chromosome number and genome size are taxonomically critical and can define angiosperm diversity. Variations in these cytogenetic traits by evolutionary processes such as polyploidization are known to be common, although underexplored in tropical plants. Zingiberaceae is a pantropical monocot family with ~1500 species where cytogenetic characters have often been used to define taxonomic boundaries, but a family-wide synthesis of cytogenetic patterns is absent. Methods: A time-calibrated Bayesian phylogenetic tree was constructed to test for different models of chromosome number and genome size evolution in Zingiberaceae. We next tested how chromosome number and genome size variations differed with lineage-age, taxonomic diversity, and distributional range at two taxonomic ranks: within the family Zingiberaceae, and in the genus Hedychium using correlations, generalized linear models and phylogenetic least square models. Key results: The most frequent changes in chromosome number within Zingiberaceae were demi-polyploidization and polyploidization (~57 % of the time), followed by ascending dysploidy (~27 %). The subfamily Zingiberoideae showed descending dysploidy at its base, while Alpinioideae showed polyploidization at its internal nodes. Although chromosome counts and genome sizes did not corroborate with each other, suggesting that they are not equivalent, at both taxonomic ranks, higher chromosome number variations and higher genome size variations were associated with higher taxonomic diversity and wider biogeographic distribution. Conclusions: Within Zingiberaceae, multiple incidences of polyploidization were discovered, and these cytogenetic events appear to have impacted the morphology, decreased genome sizes, and increased taxonomic diversity, distributional range and invasiveness of plants within this family.

FIGURE 2 in Morphological, genome-size and molecular analyses of Apostasia fogangica (Apostasioideae, Orchidaceae), a new species from China

FIGURE 2. The flow picture estimating the genome size of A. fogangica. A. Leaf: 2C=1.91 pg. B. Ovaries: 2C=2 pg. C. Pollen: 2C=1.8 pg. D. Phalaenopsis aphrodite (as reference standard) pollen: 2C=2.65.

FIGURE 1 in Morphological, genome-size and molecular analyses of Apostasia fogangica (Apostasioideae, Orchidaceae), a new species from China

FIGURE 1. Phylogenetic tree of Apostasioideae based on combined nuclear ITS rDNA and plastid DNA (matK and trnL-F) analyses. The

FIGURE 4. Apostasia fogangica. A. Flowering and fruiting plant. B. Inflorescence. C. Flower, front view. D. Flower, side view. E in Morphological, genome-size and molecular analyses of Apostasia fogangica (Apostasioideae, Orchidaceae), a new species from China

FIGURE 4. Apostasia fogangica. A. Flowering and fruiting plant. B. Inflorescence. C. Flower, front view. D. Flower, side view. E. Stamen and style, showing the stigma with a cavity. F. Column, showing honey in the nectary. G. Anthers, back view. H. Fruits. I. Flowering and fruiting plant of A. shenzhenica.

FIGURE 3. Apostasia fogangica. A. Flowering plant. B. Flower, front view. C. Flower, side view. D. Sepal and petal. E in Morphological, genome-size and molecular analyses of Apostasia fogangica (Apostasioideae, Orchidaceae), a new species from China

FIGURE 3. Apostasia fogangica. A. Flowering plant. B. Flower, front view. C. Flower, side view. D. Sepal and petal. E. Column, stamen and style, front view. F. Column, stamen and style, back view. G. Column, stamen and style, side view.

FIGURE 1 in Diploid and tetraploid cytotypes and subspecies of Odontarrhena tortuosa (Brassicaceae) in Pannonia: differences in morphology, ecology and genome size

FIGURE 1. Map of sample sites of Pannonian populations of Odontarrhena tortuosa under study. Population codes follow Table 1. Taxa (O. tortuosa subsp. heterophylla and O. tortuosa subsp. tortuosa), ploidy levels and the type of substrate are indicated by symbol colours and shapes.

FIGURE 4 in Diploid and tetraploid cytotypes and subspecies of Odontarrhena tortuosa (Brassicaceae) in Pannonia: differences in morphology, ecology and genome size

FIGURE 4. Canonical discriminant analysis (CDA 1) of 329 individuals of Odontarrhena tortuosa based on 27 morphological characters and three predefined groups corresponding to populations from three geographic regions differing in the type of substrate: (1) sand dunes in southwestern Slovakia, central Hungary and northern Serbia (tetraploid populations 24GRE, 244ORK, 471MCL, 473UZO, 539KIS, 540KSH), (2) sandy and rocky screes in central Hungary (diploid populations 13PIL, 447TOK, 537DOR, 538CSI), (3) calcareous rocks in eastern Slovakia (diploid populations 201JBV, 552KRV, 553HRH). 95 % isodensity circles are depicted. Population codes follow Table 1. For total canonical structure, see Table 5.

FIGURE 5 in Diploid and tetraploid cytotypes and subspecies of Odontarrhena tortuosa (Brassicaceae) in Pannonia: differences in morphology, ecology and genome size

FIGURE 5. Canonical discriminant analyses (CDA) of 329 individuals of Odontarrhena tortuosa based on 27 morphological characters. A. CDA 2 with diploids (black) and tetraploids (white) as two predefined groups, B. CDA 3 with O. tortuosa subsp. tortuosa (white) and O. tortuosa subsp. heterophylla (black) as two predefined groups. For total canonical structure, see Table 5.

FIGURE 3 in Diploid and tetraploid cytotypes and subspecies of Odontarrhena tortuosa (Brassicaceae) in Pannonia: differences in morphology, ecology and genome size

FIGURE 3. Principal coordinate analysis (PCoA) of 13 populations of Odontarrhena tortuosa based on 27 morphological characters and population means. The first three components explain 46.3%, 18.5% and 10.1% of the variation, respectively. Different colours and symbols are used to mark the two ploidy levels, two subspecies and populations from three regions differing in the type of substrate: diploids of O. tortuosa subsp. heterophylla from rocks of the Slovak Karst and Vihorlat Mts in eastern Slovakia (black squares), diploids of O. tortuosa subsp. tortuosa from habitats with sandy and rocky screes in the Gerecse, Pilis and Buda Mts in the northern part of central Hungary (black circles), and tetraploids of O. tortuosa subsp. tortuosa from sand dunes in southwestern Slovakia, central Hungary and northern Serbia (white circles).

FIGURE 2 in Diploid and tetraploid cytotypes and subspecies of Odontarrhena tortuosa (Brassicaceae) in Pannonia: differences in morphology, ecology and genome size

FIGURE 2. Monoploid relative genome size variation of Pannonian populations of Odontarrhena tortuosa sorted into groups based on three criteria: ploidy level (A), assignment to a subspecies (B) and the type of substrate (C). Boxes define the 25th and 75th percentiles, vertical lines within boxes indicate medians, and whiskers extend from minimum to maximum values.

FIGURE 6 in Alyssum rossetii (Brassicaceae), a new species from the Aosta Valley in Italy based on morphological and genome size data

FIGURE 6. Morphology of Alyssum rossetii (A-H) and of inner and outer filaments of A. montanum (I), A. rhodanense (J), A. flexicaule (K) and A. orophilum (L). A—habitus, B—fruiting raceme, C—silicule, D—flower, E—morphology of a silicule trichome, H–L—filaments. Drawings by Zlata Komárová.

FIGURE 5 in Alyssum rossetii (Brassicaceae), a new species from the Aosta Valley in Italy based on morphological and genome size data

FIGURE 5. Relative monoploid genome size variation of Alyssum species under study. Boxes define the 25th and 75th percentiles, vertical lines within boxes indicate medians, and whiskers span the whole range of values.

FIGURE 7 in Alyssum rossetii (Brassicaceae), a new species from the Aosta Valley in Italy based on morphological and genome size data

FIGURE 7. Variation of the indumentum on the lower surface of middle cauline leaves among Alyssum rossetii (A, B; pop. 560FEU), A. montanum (C, D; pop. 293CHA), A. flexicaule (E, F, 274VEX), A. orophilum (G, H; pop. 316MGR) and A. rhodanense (I, J, 254TAI). Scale bars: 100 μm (B, D, F, H, J) and 200 μm (A, C, E, G, I). SEM microphotographs by V. Cetlová and S. Španiel.

FIGURE 4 in Alyssum rossetii (Brassicaceae), a new species from the Aosta Valley in Italy based on morphological and genome size data

FIGURE 4. Total relative genome size variation of Alyssum species under study. Boxes define the 25th and 75th percentiles, vertical lines within boxes indicate medians, and whiskers span the whole range of values.

FIGURE 2 in Alyssum rossetii (Brassicaceae), a new species from the Aosta Valley in Italy based on morphological and genome size data

FIGURE 2. Map of sample sites of analysed Alyssum species. Population codes follow Table 1. Taxa are indicated by symbol colours and ploidy levels of populations are indicated by symbol shapes.

FIGURE 1 in Alyssum rossetii (Brassicaceae), a new species from the Aosta Valley in Italy based on morphological and genome size data

FIGURE 1. Alyssum rossetii: unripe fruits (A), in bloom (B) and the habitat of the holotype between La Tsa and Pas des Feuilles (C, D).

FIGURE 3. A in Alyssum rossetii (Brassicaceae), a new species from the Aosta Valley in Italy based on morphological and genome size data

FIGURE 3. A. Metaphase plate of a root tip of Alyssum rossetii with the chromosome number 2n = 16. Photo by L. Mártonfiová. B. A simultaneous flow cytometric analysis illustrating difference in relative genome size between A. rossetii and diploid A. montanum. For population codes, see Table 1.

opencc-zeroDec 2018View details →

Data from: Improving genomic prediction for two Yorkshire populations with a limited size using single-step method

In this study, we conducted genomic prediction for two Yorkshire purebred populations (Yichun and Chifeng) from two different provinces of China that both had a limited population size. Two growth traits (age adjusted to 100 kg weight, AGE; back‐fat thickness adjusted to 100 kg weight, BF) and one reproduction trait (total number of piglets born, TNB) were analyzed with four prediction strategies: one‐population BLUP, joint two‐population BLUP, one‐population single‐step BLUP (SSBLUP) and joint two‐population SSBLUP. Our results illustrate that accuracies of genomic estimated breeding values were improved for BF and TNB for the Yichun population and for BF for the Chifeng population by genomic prediction (one‐population SSBLUP and joint two‐population SSBLUP). The accuracy of TNB for the Yichun population was increased two fold when comparing the one‐population SSBLUP to the one‐population BLUP prediction. Meanwhile, prediction biases were dramatically reduced for AGE for the Yichun population and for TNB for the Chifeng population. The conclusions of this study are as follows: first, genomic prediction is useful for improving prediction accuracy for purebred pig breeding farms with a limited population size; second, joint genomic prediction for different populations of the same breed with certain genetic links has the trend to further improve prediction accuracy.

opencc-zeroDec 2017View details →

Data from: Roads to isolation: similar genomic history patterns in two species of freshwater crabs with contrasting environmental tolerances and range sizes

Freshwater species often show high levels of endemism and risk of extinction owing to their limited dispersal abilities. This is exemplified by the stenotopic freshwater crab, Johora singaporensis which is one of the world's 100 most threatened species, and currently inhabits less than 0.01 km2 of five low order hill streams within the highly urbanized island city‐state of Singapore. We compared populations of J. singaporensis with that of the non‐threatened, widespread, abundant, and eurytopic freshwater crab, Parathelphusa maculata, and found surprisingly high congruence between their population genomic histories. Based on 2,617 and 2,470 genome‐wide SNPs mined via the double‐digest restriction‐associated DNA sequencing method for ~90 individuals of J. singaporensis and P. maculata, respectively, the populations are strongly isolated (FST = 0.146–0.371), have low genetic diversity for both species (also for COI), and show signatures of recent genetic bottlenecks. The most genetically isolated populations for both species are separated from other populations by one of the oldest roads in Singapore. These results suggest that anthropogenic developments may have impacted stream‐dependent species in a uniform manner, regardless of ubiquity, habitat preference, or dispersal modes of the species. While signs of inbreeding were not detected for the critically endangered species, the genetic distinctiveness and low diversity of the populations call for genetic rescue and connecting corridors between the remaining fragments of the natural habitat.