Successful reproduction and pheromone production by the spruce bark beetle in evolutionary naïve spruce hosts with familiar terpenoid defences

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Genetic analysis of a successful repatriation programme: giant Galápagos tortoises

As natural populations of endangered species dwindle to precarious levels, remaining members are sometimes brought into captivity, allowed to breed and their offspring returned to the natural habitat. One goal of such repatriation programmes is to retain as much of the genetic variation of the species as possible. A taxon of giant Galápagos tortoises on the island of Espa?ola has been the subject of a captive breeding-repatriation programme for 33 years. Core breeders, consisting of 12 females and three males, have produced more than 1200 offspring that have been released on Espa?ola where in situ reproduction has recently been observed. Using microsatellite DNA markers, we have determined the maternity and paternity of 132 repatriated offspring. Contributions of the breeders are highly skewed. This has led to a further loss of genetic variation that is detrimental to the long-term survival of the population. Modifications to the breeding programme could alleviate this problem.     

Mapping quantitative trait loci in selected breeding populations: A segregation distortion approach

Quantitative trait locus (QTL) mapping is often conducted in line-crossing experiments where a sample of individuals is randomly selected from a pool of all potential progeny. QTLs detected from such an experiment are important for us to understand the genetic mechanisms governing a complex trait, but may not be directly relevant to plant breeding if they are not detected from the breeding population where selection is targeting for. QTLs segregating in one population may not necessarily segregate in another population. To facilitate marker-assisted selection, QTLs must be detected from the very population which the selection is targeting. However, selected breeding populations often have depleted genetic variation with small population sizes, resulting in low power in detecting useful QTLs. On the other hand, if selection is effective, loci controlling the selected trait will deviate from the expected Mendelian segregation ratio. In this study, we proposed to detect QTLs in selected breeding populations via the detection of marker segregation distortion in either a single population or multiple populations using the same selection scheme. Simulation studies showed that QTL can be detected in strong selected populations with selected population sizes as small as 25 plants. We applied the new method to detect QTLs in two breeding populations of rice selected for high grain yield. Seven QTLs were identified, four of which have been validated in advanced generations in a follow-up study. Cloned genes in the vicinity of the four QTLs were also reported in the literatures. This mapping-by-selection approach provides a new avenue for breeders to improve breeding progress. The new method can be applied to breeding programs not only in rice but also in other agricultural species including crops, trees and animals.     

Microsatellites as DNA markers in Sitka spruce

Nine microsatellite loci were found by screening a genomic DNA library of Sitka spruce (Picea sitchensis) with the four oligonucleotide probes (TG), (CAC), (GATA) and (AT). Pairs of flanking primers were generated for seven microsatellites. Five primer pairs were used to screen up to 58 Sitka spruce clones. The five loci SStg3a, SStg4, SStg4a, SStg4c and SSgataS were found to have 15, 13, 4, 3 and 6 different length alleles respectively, and in using a combination of them almost all 58 Sitka spruce genotypes could be identified. The five primer pairs were successful in amplifying DNA from two other spruce species (Picea albutilia and Picea smithiana), while only one primer pair could amplify DNA from the pine species, Pinus sylvestris and Pinus latifolia. The inheritance of microsatellites in Sitka spruce was co-dominant Mendelian.     

Investigating the abundance and flight period of bark beetles (Coleoptera: Curculionidae: Scolytinae) over elevational gradients in Sitka spruce forests

1. A warming climate, as predicted under current climate change projections, is likely to influence the population dynamics of many forest insect species. Numerous bark beetle species in both Europe and North America have already responded to a warming climate by significantly expanding their geographical ranges.
2. The aim of the current study was to investigate how populations of bark beetles within stands of Sitka spruce, a widely planted non-native commercial plantation tree species in the U.K., were likely to respond to a warming climate. Experimental plots were established in stands of Sitka spruce over elevational gradients in two commercial forest plantations, and the abundance and emergence times of key bark beetle species were assessed over a 3-year period using flight interception traps. The air temperature difference between the lowest and highest experimental plot in each forest was consistently >1°C throughout the 3-year period.
3. In general, the abundance of the most dominant bark beetle species (e.g. Trypodendron, Dryocoetes, Hylastes spp.) was higher, and emergence times tended to be earlier in the year at the lower elevation plots, where temperatures were higher, although not all bark beetle species responded in the same manner.
4. The results of the study indicated that, under the projected future climate warming scenarios, monoculture Sitka spruce stands at low elevations may potentially be more vulnerable to significant outbreak events from existing or invasive bark beetle species. Hence, consideration of establishing more resilient forests of Sitka spruce by diversifying the species composition and structure of Sitka spruce stands is discussed.

     

Group structure, mating system and extra-group paternity in the co-operatively breeding White-breasted Thrasher Ramphocinclus brachyurus

Avian co-operative breeders show a diverse range of social and reproductive systems. Here we combined microsatellite genotyping with field observations over three consecutive breeding seasons to investigate the social structure and mating system of the White-breasted Thrasher Ramphocinclus brachyurus . Co-operative breeding was facultative in this species, with approximately one-third of nests having helpers. Breeding groups comprised a pair of breeding adults and up to three helpers of either sex. Within co-operative groups, age was associated with parentage in both sexes. Helpers were retained offspring and either rarely or never achieved parentage in current broods. There was no evidence of egg dumping and a relatively small percentage of chicks (7.5%, n  = 67) were fathered by males from outside the co-operative group. The White-breasted Thrasher is a globally Endangered species with a very small and declining population. A captive breeding programme for this species is not recommended at present, but may become necessary in the future, and any such programme should take account of our findings regarding breeding behaviour and group structure.     

Inbreeding dynamics in reintroduced, age-structured populations of highly fecund species

Reintroduction programs aim at reinstalling a self-sustained population into the wild via a period of supplementation with captive-bred individuals. This procedure can rapidly generate inbreeding among offspring because of the mating scheme and this inbreeding might be further enhanced by the reintroduction scenario. First, we used simulations to assess the consequences of breeding designs on mean inbreeding index F among offspring when the genetic diversity of breeders, the number and sex ratios of breeders, and the proportion of successful crosses vary. A high number of breeders, a balanced sex ratio, a high proportion of effective crosses and a genetically diverse source population generally contribute to lower F values. However, moderately high (≥20) numbers of breeders combined with all but the most biased sex ratios produced mean F values near minimal values. The variability in F was negligible in all parameter combinations except for a very small number of breeders (5) and very biased sex ratios (≤ 1M : 19F). We also simulated the long-term inbreeding dynamics in the introduced population under various demographic scenarios. Our main finding was that the annual number of introduced offspring is a decisive factor in establishing long-term F values in the supplemented population. Low supplementation levels (10²) quickly generated an almost completely inbred population whereas high levels (≥10⁴) produced stable F values close to that of the introduced offspring. Simulations were run based on the life history and specific demographics of the bloater (Coregonus hoyi), whose reintroduction in Lake Ontario is being considered.     

Development of a set of highly polymorphic genomic microsatellites (gSSRs) in Sitka spruce (Picea sitchensis (Bong.) Carr.)

Robust, polymorphic microsatellite DNA markers (simple sequence repeats—SSRs) are valuable tools for a range of tree conservation and breeding applications. SSRs are routinely used in the study of population genetic structure and diversity, pedigree reconstruction and genetic linkage mapping. Their abundance in the genome, co-dominant inheritance and potential for cross-species amplification make microsatellites highly prized markers. This paper characterises 22 novel genomic polymorphic microsatellite loci for Sitka spruce (Picea sitchensis (Bong.) Carr.). Amplification of DNA from Sitka spruce material was carried out both with a set of unrelated trees to obtain diversity statistics for each locus, and with the progeny of a full-sib family to test simple Mendelian inheritance. Observed heterozygosity ranged from 0.38 to 0.91 and allele number per locus ranged from 6 to 21, with a mean of 12.2. In addition, the primer pairs were tested with DNA from Norway spruce (P. abies) and white spruce (P. glauca) to investigate their potential for cross-species amplification and ten loci amplified in all three species. The results from these genomic microsatellites are compared to data generated from microsatellites derived from Picea EST libraries. In summary, this novel, highly polymorphic markers represent a significant addition to the rapidly expanding Picea genomics tool-box. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Macrofungal diversity and ecology in four Irish forest types

The macrofungal communities of Irish native tree species (ash and oak) and exotic tree species (Scots pine and Sitka spruce) forests were examined through the collection of sporocarps over 3 yr. Sampling of 27 plots revealed 186 species of macrofungi, including 10 species new to Ireland. The species richness of non-native Sitka spruce and Scots pine forests was similar to that of native oak forests. However, specific communities of macrofungi existed in each of the forest types as confirmed by non-metric multidimensional scaling and multi-response permutation procedure. Indicator species analysis was used to identify macrofungi which are indicative of the four forest types. The oak community lacked certain species/genera known to be distinctive of oak woods in Britain, possibly due to low inoculum availability as a result of historic removal of Ireland’s oak forests. Our results indicate that, while being similar to native forests in species richness, non-native forests of Sitka spruce and Scots pine in Ireland harbour many fungal species which are not typical of native forests, particularly members of the genus Cortinarius.     

Reproductive phenology of a food-hoarding mast-seed consumer: resource- and density-dependent benefits of early breeding in red squirrels

The production of offspring by vertebrates is often timed to coincide with the annual peak in resource availability. However, capital breeders can extend the energetic benefits of a resource pulse by storing food or fat, thus relaxing the need for synchrony between energy supply and demand. Food-hoarding red squirrels (Tamiasciurus hudsonicus) breeding in the boreal forest are reliant on cones from a masting conifer for their nutrition, yet lactation is typically completed before the annual crop of cones is available for consumption such that peaks in energy supply and demand are not synchronized. We investigated the phenological response of red squirrels to annual variation in environmental conditions over a 20-year span and examined how intra- and inter-annual variation in the timing of reproduction affected offspring recruitment. Reproductive phenology was strongly affected by past resource availability with offspring born earlier in years following large cone crops, presumably because this affected the amount of capital available for reproduction. Early breeders had higher offspring survival and were more likely to renest following early litter loss when population density was high, perhaps because late-born offspring are less competitive in obtaining a territory when vacancies are limited. Early breeders were also more likely to renest after successfully weaning their first litter, but renesting predominantly occurred during mast years. Because of their increased propensity to renest and the higher survival rates of their offspring, early breeders contribute more recruits to the population but the advantage of early breeding depends on population density and resource availability.     

Host shifting by Operophtera brumata into novel environments leads to population differentiation in life-history traits

Abstract.  1. Operophtera brumata L. (Lepidoptera: Geometridae), a polyphagous herbivore usually associated with deciduous trees such as oak Quercus robur L . , has expanded its host range to include the evergreen species heather Calluna vulgaris (L.) Hull and, most recently, Sitka spruce Picea sitchensis (Bong.) Carrière.
2. Phenology, morphology, and survival of O. brumata were measured at several life-history stages in populations from the three different host plant communities sampled from a range of geographical locations. The data were used to test for population differences, reflecting the marked differences in host-plant secondary chemistry, growth form, and site factors such as climate. The hypothesis that spruce-feeding populations originated from populations feeding on moorland, commonly sites of coniferous afforestation, was also tested.
3. Altitude, not host plant species, was the major influence on the timing of adult emergence. An effect of insect population independent of altitude was found, implying that additional unidentified factors contribute to this phenological variation. Larval survival and adult size varied between populations reared on different host plant species. Survival of larvae was affected negatively when reared on the novel host plant, Sitka spruce, versus the natal plant (oak or heather) but oak and heather-sourced insects did not differ in survivorship on Sitka spruce.
4. Host range extension into novel environments has resulted in population differentiation to the local climate, demonstrating that host shifts pose challenges to the herbivore population greater than those offered by the host plant alone. The hypothesis that Sitka spruce feeding populations have arisen predominantly from moorland feeding populations was not supported.     

Identification of QTLs influencing combustion quality in <Emphasis Type="Italic">Miscanthus sinensis</Emphasis> Anderss. II. Chlorine and potassium content

Chlorine and potassium content are important traits related to combustion quality of Miscanthus species. These traits were analysed in a cross between F(1.1) and F(1.7) entries of Miscanthus sinensis Anderss, both lines offspring of the cross between MS-90-2 and MS-88-110. Quantitative trait locus (QTL) analyses were performed on a previous linkage map constructed with the offspring cross mapping strategy. The mapqtl 4.0 package was used to perform QTL analyses. Six potential QTLs were detected with data collected over a 2-year period. Of these, four were associated with chlorine and two with potassium. These results could be used as an initial step to develop a marker-aided selection programme for biomass with low mineral content.     

Cost analysis of the application of marker-assisted selection in potato breeding

The primary aim of plant breeders is to develop new cultivars in order to improve productivity and to combat threats from pests and diseases. Recent advances in genomics have been recognised as providing important tools for plant breeders in the form of molecular genetic markers that can be used to tag genes of interest. However, the cost-effective use of marker technology is dependent on the nature and timing of the use of such markers. A conventional potato breeding programme typically creates a large breeding population and then employs phenotypic recurrent selection over a number of generations to identify superior genotypes. Marker-assisted selection (MAS) provides the advantage of being applicable at the seedling or an early generation stage. We have analysed the cost of MAS and compared it to conventional screening, then modelled the respective costs against the breeding population size of the generation in which they would be applied to determine whether MAS in the early generations of a potato breeding programme would be cost-effective. As various potato breeding programmes employ different selection rates in early generations, these rates have also been modelled to determine the effect. Our results indicate that MAS could be applied cost-effectively in the second clonal generation for all models currently employed in potato breeding.     

Identification of QTLs influencing agronomic traits in <Emphasis Type="Italic">Miscanthus sinensis</Emphasis> Anderss. I. Total height,flag-leaf height and stem diameter

We have developed the first quantitative trait locus (QTL) analyses for agronomic traits in a cross between F(1.1) (P1) and F(1.7) (P7) entries of Miscanthus sinensis Anderss. Both lines are offspring of the cross between MS-90-2 and MS-88-110. A map based on random amplified polymorphic DNA markers previously constructed was used to perform the QTL analyses. This map was developed using a new mapping strategy that has been designated offspring cross. Eleven QTLs were detected for height, panicle height and diameter using the programme mapqtl 4.0 and the multiple QTL method. QTL significance was determined using several analyses, including Kruskal-Wallis analyses, empirical determination of LOD critical values using permutation tests, QTLs validation with field data over 2 years and co-localization of QTLs for correlated traits. The results obtained could be the first step in developing a marker-assisted selection programming in this species for biomass production.     

A diallel cross in Sitka spruce assessment of first year characters in an early glasshouse test

Summary The successful pollination of a complete diallel cross among six Sitka spruce (Picea sitchensis (Bong.) Carr.) trees is described, together with the assessment of a range of characters in the first growing-season of an early progeny-test in a glasshouse. Those characters chiefly concerned with tree form were found to be inherited in a predominantly additive fashion, whilst those characters reflecting various aspects of tree vigour were found to be under additive, dominance and maternal control. The results are discussed in the light of selection criteria and current techniques in Sitka spruce breeding.     

No Evidence for Enforced Alloparental Care in a Cooperatively Breeding Parrot

In cooperatively breeding species, in which non‐breeding helpers assist in rearing the offspring of breeding individuals, conflicts of interest commonly occur between breeders and helpers over their respective contributions to offspring care. During such conflicts, breeders might use aggressive behavior to enforce contributions of helpers to offspring care, especially if helpers are not related to the breeders and their offspring and thus do not stand to gain indirect fitness benefits by helping. Using a combination of behavioral and genetic data, we investigated in the cooperatively breeding El Oro parakeet Pyrrhura orcesi (i) whether breeders are commonly dominant over helpers, (ii) whether they use aggressive behavior toward helpers to enforce offspring provisioning, and (iii) whether the relatedness of helpers to the nestlings affects the frequency of—or the reaction of helpers to—such aggressions. Even though breeders were generally dominant over helpers, we found no evidence for the enforcement of alloparental care. This finding was independent of the relatedness between helpers and nestlings, even though distantly related helpers overall contributed little to offspring care. We suggest that the inability of breeders to properly assess the work rates of their helpers at least partly explains the absence of enforcement. More generally, our results add to a body of evidence suggesting that enforcement might be an exceptional rather than a general mechanism underlying the expression of alloparental care in cooperatively breeding species.     

Robust simple sequence repeat markers for spruce (Picea spp.) from expressed sequence tags

Traditionally, simple sequence repeat (SSR) markers have been developed from libraries of genomic DNA. However, the large, repetitive nature of conifer genomes makes development of robust, single-copy SSR markers from genomic DNA difficult. Expressed sequence tags (ESTs), or sequences of messenger RNA, offer the opportunity to exploit single, low-copy, conserved sequence motifs for SSR development. From a 20,275-unigene spruce EST set, we identified 44 candidate EST-SSR markers. Of these, 25 amplified and were polymorphic in white, Sitka, and black spruce; 20 amplified in all 23 spruce species tested; the remaining five amplified in all except one species. In addition, 101 previously described spruce SSRs (mostly developed from genomic DNA), were tested. Of these, 17 amplified across white, Sitka, and black spruce. The 25 EST-SSRs had approximately 9% less heterozygosity than the 17 genomic-derived SSRs (mean H=0.65 vs 0.72), but appeared to have less null alleles, as evidenced by much lower apparent inbreeding (mean F=0.046 vs 0.126). These robust SSRs are of particular use in comparative studies, and as the EST-SSRs are within the expressed portion of the genome, they are more likely to be associated with a particular gene of interest, improving their utility for quantitative trait loci mapping and allowing detection of selective sweeps at specific genes.     

Accuracy of direct genomic breeding values for nationally evaluated traits in US Limousin and Simmental beef cattle

Background

In national evaluations, direct genomic breeding values can be considered as correlated traits to those for which phenotypes are available for traditional estimation of breeding values. For this purpose, estimates of the accuracy of direct genomic breeding values expressed as genetic correlations between traits and their respective direct genomic breeding values are required.

Methods

We derived direct genomic breeding values for 2239 registered Limousin and 2703 registered Simmental beef cattle genotyped with either the Illumina BovineSNP50 BeadChip or the Illumina BovineHD BeadChip. For the 264 Simmental animals that were genotyped with the BovineHD BeadChip, genotypes for markers present on the BovineSNP50 BeadChip were extracted. Deregressed estimated breeding values were used as observations in weighted analyses that estimated marker effects to derive direct genomic breeding values for each breed. For each breed, genotyped individuals were clustered into five groups using K-means clustering, with the aim of increasing within-group and decreasing between-group pedigree relationships. Cross-validation was performed five times for each breed, using four groups for training and the fifth group for validation. For each trait, we then applied a weighted bivariate analysis of the direct genomic breeding values of genotyped animals from all five validation sets and their corresponding deregressed estimated breeding values to estimate variance and covariance components.

Results

After minimizing relationships between training and validation groups, estimated genetic correlations between each trait and its direct genomic breeding values ranged from 0.39 to 0.76 in Limousin and from 0.29 to 0.65 in Simmental. The efficiency of selection based on direct genomic breeding values relative to selection based on parent average information ranged from 0.68 to 1.28 in genotyped Limousin and from 0.51 to 1.44 in genotyped Simmental animals. The efficiencies were higher for 323 non-genotyped young Simmental animals, born after January 2012, and ranged from 0.60 to 2.04.

Conclusions

Direct genomic breeding values show promise for routine use by Limousin and Simmental breeders to improve the accuracy of predicted genetic merit of their animals at a young age and increase response to selection. Benefits from selecting on direct genomic breeding values are greater for breeders who use natural mating sires in their herds than for those who use artificial insemination sires. Producers with unregistered commercial Limousin and Simmental cattle could also benefit from being able to identify genetically superior animals in their herds, an opportunity that has in the past been limited to seed stock animals.     

Genetic Parentage Analysis Confirms a Polygynandrous Breeding System in the European Grayling (Thymallus thymallus)

Knowing the breeding system of a species is important in order to understand individual variation in reproductive success. Large variation in reproductive success and thus reproductive skew strongly impacts on the effective number of breeders and thus the long-term effective population size (N_e). Fishes, in particular species belonging to the salmonid family, exhibit a wide diversity of breeding systems. In general, however, breeding systems are rarely studied in detail in the wild. Here we examine the breeding system of the spring-spawning European grayling Thymallus thymallus from a small Norwegian stream using parentage assignment based on the genotyping of 19 polymorphic microsatellite loci. In total 895 individual grayling fry and 154 mature grayling (57 females and 97 males) were genotyped. A total of 466 offspring were assigned a father, a mother, or a parent pair with a confidence of 90% or higher. Successfully reproducing males had on average 11.9 ± 13.3 (SD) offspring with on average 2.1 ± 1.2 partners, whereas successful females had on average 9.5 ± 12.8 offspring and 2.3 ± 1.5 partners. Parents with more partners also produced more offspring. Thus the grayling breeding system within this small stream revealed a polygynandrous breeding system, similar to what has been observed for many other salmonid fish species. The present study thus unambiguously corroborates a polygynadrous breeding system in the European grayling. This knowledge is critical for managing populations of this species, which has suffered significant local population declines throughout its range over the last several decades.