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opencc-zeroDec 2013View details →

Data from: Genetic control of contagious asexuality in the pea aphid

Although evolutionary transitions from sexual to asexual reproduction are frequent in eukaryotes, the genetic bases of such shifts toward asexuality remain largely unknown. We addressed this issue in an aphid species where both sexual and obligate asexual lineages coexist in natural populations. These sexual and asexual lineages may occasionally interbreed because some asexual lineages maintain a residual production of males potentially able to mate with the females produced by sexual lineages. Hence, this species is an ideal model to study the genetic basis of the loss of sexual reproduction with quantitative genetic and population genomic approaches. Our analysis of the co-segregation of ~300 molecular markers and reproductive phenotype in experimental crosses pinpointed an X-linked region controlling obligate asexuality, this state of character being recessive. A population genetic analysis (>400-marker genome scan) on wild sexual and asexual genotypes from geographically distant populations under divergent selection for reproductive strategies detected a strong signature of divergent selection in the genomic region identified by the experimental crosses. These population genetic data confirm the implication of the candidate region in the control of reproductive mode in wild populations originating from 700 km apart. Patterns of genetic differentiation along chromosomes suggest bidirectional gene flow between populations with distinct reproductive modes, supporting contagious asexuality as a prevailing route to permanent parthenogenesis in pea aphids. This genetic system provides new insights into the mechanisms of coexistence of sexual and asexual aphid lineages.

opencc-zeroDec 2015View details →

Data from: A case for a joint strategy of diversified bet hedging and plasticity in the pea aphid wing polyphenism

Phenotypic plasticity and diversified bet hedging are strategies for coping with variable environments. Plasticity is favoured when an organism can predict future conditions using environmental cues, while bet hedging is favoured when predictive cues are not available. Theoretical analyses suggest that many organisms should use a mixture of both strategies, because environments often present both scenarios. Here, we examine if the pea aphid wing polyphenism, a well-known case of plasticity, is potentially a mixture of plasticity and bet hedging. In this polyphenism, asexual females produce more winged offspring in crowded conditions, and wingless offspring in uncrowded conditions. We find that pea aphids use plasticity to respond to crowding and we find considerable genetic variation for this response. We further show that individual aphids produce both winged and wingless offspring, consistent with the variability expected in a bet hedging trait. We conclude that the pea aphid wing polyphenism system is probably a mixture of plasticity and bet hedging. Our study adds to a limited list of empirical studies examining mixed strategy usage, and suggests that mixed strategies may be common in dispersal traits.

opencc-zeroDec 2011View details →

Data from: Twentieth-century changes in the genetic composition of Swedish field pea metapopulations

Landrace crops are formed by local adaptation, genetic drift and gene flow through seed exchange. In reverse, the study of genetic structure between landrace populations can reveal the effects of these forces over time. We present here the analysis of genetic diversity in 40 Swedish field pea (Pisum sativum L.) populations, either available as historical seed samples from the late nineteenth century or as extant gene bank accessions assembled in the late twentieth century. The historical material shows constant high levels of within-population diversity, whereas the extant accessions show varying, and overall lower, levels of within-population diversity. Structure and principal component analysis cluster most accessions, both extant and historical, in groups after geographical origin. County-wise analyses of the accessions show that the genetic diversity of the historical accessions is largely overlapping. In contrast, most extant accessions show signs of genetic drift. They harbor a subset of the alleles found in the historical accessions and are more differentiated from each other. These results reflect how, historically present metapopulations have been preserved during the twentieth century, although as genetically isolated populations.

opencc-zeroDec 2013View details →

Data from: Genomic regions repeatedly involved in divergence among plant-specialized pea aphid biotypes

Understanding the genetic bases of biological diversification is a long-standing goal in evolutionary biology. Here we investigate whether replicated cases of adaptive divergence involve the same genomic regions in the pea aphid, Acyrthosiphon pisum, a large complex of genetically differentiated biotypes, each specialized on different species of legumes. A previous study identified genomic regions putatively involved in host-plant adaptation and/or reproductive isolation by performing a hierarchical genome scan in three biotypes. This led to the identification of 11 FST outliers among 390 polymorphic microsatellite markers. In this study, the outlier status of these 11 loci was assessed in eight biotypes specialized on other host plants. Four of the 11 previously identified outliers showed greater genetic differentiation among these additional biotypes than expected under the null hypothesis of neutral evolution (α<0.01). Whether these hotspots of genomic divergence result from adaptive events, intrinsic barriers or reduced recombination is discussed.

opencc-zeroDec 2013View details →

Data from: Dynamics of copy number variation in host races of the pea aphid

Copy number variation (CNV) makes a major contribution to overall genetic variation and is suspected to play an important role in adaptation. However, aside from a few model species, the extent of CNV in natural populations has seldom been investigated. Here, we report on CNV in the pea aphid Acyrthosiphon pisum, a powerful system for studying the genetic architecture of host plant adaptation and speciation thanks to multiple host races forming a continuum of genetic divergence. Recent studies have highlighted the potential importance of chemosensory genes, including the gustatory and olfactory receptor gene families (Grs and Ors, respectively), in the process of host race formation. We used targeted re-sequencing to achieve a very high depth of coverage, and thereby revealed the extent of CNV of 434 genes, including 150 chemosensory genes, in 104 individuals distributed across eight host races of the pea aphid. We found that CNV was widespread in our global sample, with a significantly higher occurrence in multigene families, especially in Ors, and a decrease in the probability of complete gene duplication or deletion (CDD) with increase in coding sequence length. Genes with CDD variants were usually more polymorphic for copy number, especially in the P450 gene family where toxin resistance may be related to gene dosage. We found that Grs were over-represented among genes discriminating host races, as were CDD genes and pseudogenes. Our observations shed new light on CNV dynamics and are consistent with CNV playing a role in both local adaptation and speciation.

opencc-zeroDec 2011View details →

Data from: Predation drives stable coexistence ratios between red and green pea aphid morphs

We conducted field surveys and experiments to evaluate the hypothesis that predation is an important driving factor determining the degree of coexistence between red and green morphs of the pea aphid Acyrthosiphon pisum. Theory suggests that the different colour morphs are differentially susceptible to natural enemies and selection by predation which in turn leads to variable relative abundances of red and green morphs among host plants across landscapes. Our field surveys on pea and alfalfa revealed, however, that the colour morphs tended to coexist closely in a ratio of one red to three green aphids across fields with different host plant monocultures. Experimentation involving manipulation of the relative abundances of the two colour morphs on host plants pea and alfalfa with and without predator presence revealed that red morphs had higher or same fitness (per capita reproduction) than green morphs on both pea and alfalfa only when in the proportion of one red/three green proportion. Moreover, experimentation evaluating predator efficiency revealed that red morphs are safest from predation when in a 1 : 3 ratio with green morphs. These results suggest that in addition to predation selection effects, red morphs may behaviourally choose to associate with green morphs in a narrow 1 : 3 ratio to maximize their fitness. This evidence, along with existing published data on red and green morph anti-predator behaviour indicates that a 1 : 3 red and green morph coexistence ratio is driven by a balance between predation pressure and behavioural assorting by red morphs across landscapes. In this way predators may have ecological-evolutionary consequences for traits that affect the colour morphs' proportion and tolerances to selective pressure.

Dataset for Quantitative Trait Loci Associated with Lodging in Dry Field Peas. Data for PR Population (Carerra x Striker).

Dataset for Quantitative Trait Loci Associated with Lodging in Dry Field Peas. Data for PR Population (Carerra x Striker). Here is data on lodging, height, stem diameter, side branch diameter, and epicotyl diameter for both site years with the PR population.

Dataset for Quantitative Trait Loci Associated with Lodging, Stem Strength, Yield, and Other Important Agronomic Traits in Dry Field Peas, All SNP markers

Dataset for Quantitative Trait Loci Associated with Lodging, Stem Strength, Yield, and Other Important Agronomic Traits in Dry Field Peas. All SNP markers were included in the dataset. U designates a missing datapoint. The data was not inputed.

Dataset for Quantitative Trait Loci Associated with Lodging, Stem Strength, Yield, and Other Important Agronomic Traits in Dry Field Peas with data for 330 markers

Dataset for Quantitative Trait Loci Associated with Lodging, Stem Strength, Yield, and Other Important Agronomic Traits in Dry Field Peas with data for 330 markers. This dataset is associated with the dissertation entitled, Quantitative Trait Loci Associated with Lodging, Stem Strength, Yield, and Other Important Agronomic Traits in Dry Field Peas.

opencc-by-4.0Nov 2023View details →

The importance of management on the productivity of cereal-pea intercrops

Poster presented at the Internal Legume Conference, Granada, September 2023

opencc-by-4.0Mar 2022View details →

The World's First Climate Positive Gin - made using peas - Nàdar (Nature).

A brief introduction to the development of Nadar Gin (and Nadar vodka) by Arbikie Distillery (Scotland) in collaboration with Abertay University, and the James Hutton Institute. Nadar Gin is the worlds first climate-positive spirit, and it was made using 100% peas.

opencc-zeroMar 2022View details →

Phylogeny and disparate selection signatures suggest two genetically independent domestication events of pea (Pisum L.)

Domestication is considered a model of adaptation that can be used to draw conclusions about the modus operandi of selection in natural systems. Investigating domestication may give insights into how plants react to different intensities of human manipulation, which has direct implication for the continuing efforts of crop improvement. Therefore, scientists of various disciplines study domestication-related questions to understand the biological and cultural bases of the domestication process. We employed restriction site-associated DNA sequencing (RAD-seq) of 494 Pisum sativum (pea) samples from all wild and domesticated groups to analyze the genetic structure of the collection. Patterns of ancient admixture were investigated by analysis of admixture graphs. We used two complementary approaches, one diversity based and one based on differentiation, to detect the selection signatures putatively associated with domestication. An analysis of the subpopulation structure of wild P. sativum revealed five distinct groups with a notable geographic pattern. Pisum abyssinicum clustered unequivocally within the P. sativum complex, without any indication of hybrid origin. We detected 32 genomic regions putatively subjected to selection: 29 in P. sativum ssp. sativum and three in P. abyssinicum. The two domesticated groups did not share regions under selection and did not display similar haplotype patterns within those regions. Wild P. sativum is structured into well-diverged subgroups. Although Pisum sativum ssp. humile is not supported as a taxonomic entity, the so-called 'southern humile' is a genuine wild group. Introgression did not shape the variation observed within the sampled germplasm. The two domesticated pea groups display distinct genetic bases of domestication, suggesting two genetically independent domestication events.

opennotspecifiedMay 2022View details →

FIGURE 1 in Redescription of Arcotheres tivelae (Gordon, 1936), a pea crab endemic to the Persian Gulf and Gulf of Oman (Crustacea: Decapoda: Brachyura: Pinnotheridae)

FIGURE 1. Arcotheres tivelae (Gordon, 1936). A–C, holotype female (13.6 × 11.5 mm) (NHM 1936.6.19.9), Muscat; D–F, G, I, A–D, F, female (11.2 × 9.8 mm) (ZRC 2009.0831), Iran; H, female (10.1 × 9.1 mm) (ZRC 2016.162), Iran. A, D, overall dorsal view; B, E, frontal view of cephalothorax; C, F, ventral view of cephalothorax; G, right third maxilliped; H, right chela; I, right P5 (ventral view). Scales: 1.0 mm.

opennotspecifiedMay 2022View details →

FIGURE 2 in Redescription of Arcotheres tivelae (Gordon, 1936), a pea crab endemic to the Persian Gulf and Gulf of Oman (Crustacea: Decapoda: Brachyura: Pinnotheridae)

FIGURE 2. Arcotheres tivelae (Gordon, 1936), female (11.2 × 9.8 mm) (ZRC 2009.0831), Iran. A, right MXP3 (denuded); B–E, right P2–P5, respectively; F–I, left P2–P5, respectively. Scales: A = 0.5 mm; B–I = 1.0 mm.

opennotspecifiedMay 2022View details →

FIGURE 4 in Redescription of Arcotheres tivelae (Gordon, 1936), a pea crab endemic to the Persian Gulf and Gulf of Oman (Crustacea: Decapoda: Brachyura: Pinnotheridae)

FIGURE 4. Arcotheres tivelae (Gordon, 1936), male (5.7 × 5.6 mm) (ZRC 2011.0155), Iran. A, left MXP3 (denuded); B–E, left P2–P5, respectively; F, right G1 (ventral view); G, right G1 (dorsal view); H, distal part of right G1 (denuded, ventral view); I, distal part of right G1 (denuded, dorsal view); J, left G2. Scales: A, F, G, J = 0.2 mm; B–E = 0.5 mm; H, I = 0.1 mm.

FIGURE 4. Pinnixa plectrophoros Glassell, 1935, A–G in Redescription of the poorly known pea crab, Pinnixa plectrophoros Glassell, 1935 (Decapoda: Pinnotheridae), from the Gulf of California

FIGURE 4. Pinnixa plectrophoros Glassell, 1935, A–G, male from Bahía Santa María–La Reforma (ICML-EMU 10575). A– B, third maxilliped, A, external view, B, internal view, exopod and setae omitted but marking the line of points where the long plumose setae emerge; C, sternite, abdomen and telson; D–E fourth walking leg, D, posterior side, E, anterior side; F, male abdomen and telson; G, left gonopod; H, abdomen of female from Bahía Santa María—La Reforma, Sinaloa (A–B, G, scale bar = 0. 5 mm; C–F, H, scale bar = 1 mm).

FIGURE 3. Pinnixa plectrophoros, 1935 in Redescription of the poorly known pea crab, Pinnixa plectrophoros Glassell, 1935 (Decapoda: Pinnotheridae), from the Gulf of California

FIGURE 3. Pinnixa plectrophoros, 1935, Glassell Male from Bahía Santa María–La Reforma, Sinaloa (ICML-EMU 10575); A, Carapace, dorsal view; B–C, left cheliped, setae omitted in C; D, right first walking leg, posterior view; E, right second walking leg, posterior view; F–G, right third walking leg, F, posterior view; G, anterior view. (Scale bar = 1 mm).

FIGURE 1. Pinnixa plectrophoros, 1935 in Redescription of the poorly known pea crab, Pinnixa plectrophoros Glassell, 1935 (Decapoda: Pinnotheridae), from the Gulf of California

FIGURE 1. Pinnixa plectrophoros, 1935, Glassell Male holotype (SDNHM 3894), Puerto Peñasco, Sonora, México, A, anterodorsal view; B, ventral view; C, propodus and dactyl of second walking leg, arrows point the subproximal tubercles; D, third walking leg, arrows point spur on ventral side of merus and spine and granules in propodus and dactylus.

FIGURE 2. Pinnixa plectrophoros, 1935 in Redescription of the poorly known pea crab, Pinnixa plectrophoros Glassell, 1935 (Decapoda: Pinnotheridae), from the Gulf of California

FIGURE 2. Pinnixa plectrophoros, 1935, Glassell Male from Bahía Santa María–La Reforma (ICML-EMU 10575), color in life. (Scale bar = 1 mm).

A Model Predicting The Relationships Between Seed Size, Yield, and Actual Yield in Dry Field Peas

This is a model that predicts yield and actual yield in dry pea based on seed size. Seeding rate, seed cost, pod length, and expected grain yield can be varied in the model. The ideal seed size is displayed at the vertex of the curve in three different graphs.