Agrobiodiversity change in a saharan desert oasis, 1919–2006: Historic shifts in tasiwit (Berber) and Bedouin crop inventories of Siwa, Egypt

This study of changes in agrobiodiversity documents the domesticated species and, to a limited degree, the landraces, cultivated in the Siwa oasis of Egypt in 1919, 1924, 1968–1969, and 2004–2006. Siwa is eco-geographically and culturally isolated by more than 300 kilometers (km) from other agrarian communities and, perhaps because of this, detailed observations were made there by a number of agricultural scientists and geographers in a way that provides time-series data lacking from many other agrarian landscapes. Although I have drawn upon Siwan names for crops first published in 1890, this report may be the first substantive record of Tasiwit (Eastern Berber) folk names for traditional crops that allows ethno-linguistic comparisons with Cairene Arabic and other Northern Berber (Tamazight) dialects in North Africa. The perennial crop inventory of Siwan Berbers has remained relatively stable through time and few traditionally cultivated annual species or landraces have been lost. However, additional crop species from other parts of Egypt have been adopted since a paved road was completed to Siwa in 1986 and more Awlad Ali Bedouins have settled and begun dooryard gardens. The reasons for the relative stability of Siwan agrobiodiversity are discussed, and may relate to both the need for crop ecotypes adapted to the challenging alkaline conditions found in Siwan agroecosystems and Siwan pride in and adherence to its traditional cuisine.     

Weeds flora demographic analysis of date palm orchards in El-Bahariya,El-Frafra and Siwa oases

Oases are a specific ecosystems which date palm Phoenix dactylifera are the mainly crop growing for its fruits and others tree parts. Palm orchards are infested by many pests, including weeds species and exposed within time to the challenging invasive weeds to control. The heavy incidence of weeds negatively affects palm productivity, especially in small plantation and divergent distances, while the established orchards, palm trees shading cause deprives from the process of weeds photosynthesis to be lower competitive. The survey was conducted in El-Bahariya and El-Frafra than Siwa oases of which 375 plots were taken. Vegetative analysis in oases altogether demonstrate 91 weed specimens were encountered of which 18 perennial, 42 were broad leaved, and 30 narrow leaved as well as one parasitic weed species belonging to 22 families, whereas Poaceae is the most plentiful family displayed by 38.5% from all families, occurred in date palm orchards during the study. The geographical differentiation affected coefficient of similarity whereas, it in oases recorded the highest between El-Bahariya and El-Frafra than Siwa and El-Bahariya, while El-Frafra Oasis was the most diverse and richness than the others which have the middle soil properties, fertility, and structure. The correlation analysis of weed flora between both El-Bahariya and El-Frafra was higher and more than El-Bahariya and Siwa oases. Under the unique closed agroenvironment of oases, weeds population dynamics are a stable approximately. Regardless of the diversity of annual weed species, perennials species represent the highest dominant number and the pattern of grown weeds was more dominant than wild desert and some invasive weed species. The control action should be taken of perennial weeds and proactive as well as long term prevention for invasive species.     

Indicators for the on-farm assessment of crop cultivar and livestock breed diversity: a survey-based participatory approach

Agrobiodiversity plays a fundamental role in guaranteeing food security. However, still little is known about the diversity within crop and livestock species: the genetic diversity. In this paper we present a set of indicators of crop accession and breed diversity for different farm types at farm-level, which may potentially supply a useful tool to assess and monitor farming system agrobiodiversity in a feasible and relatively affordable way. A generic questionnaire was developed to capture the information on crops and livestock in 12 European case study regions and in Uganda by 203 on-farm interviews. Through a participatory approach, which involved a number of stakeholders, eight potential indicators were selected and tested. Five of them are recommended as potentially useful indicators for agrobiodiversity monitoring per farm: (1) crop-species richness (up to 16 crop species), (2) crop-cultivar diversity (up to 15 crop cultivars, 1–2 on average), (3) type of crop accessions (landraces accounted for 3 % of all crop cultivars in Europe, 31 % in Uganda), (4) livestock-species diversity (up to 5 livestock species), and (5) breed diversity (up to five cattle and eight sheep breeds, on average 1–2).We demonstrated that the selected indicators are able to detect differences between farms, regions and dominant farm types. Given the present rate of agrobiodiversity loss and the dramatic effects that this may have on food production and food security, extensive monitoring is urgent. A consistent survey of crop cultivars and livestock breeds on-farm will detect losses and help to improve strategies for the management and conservation of on-farm genetic resources.     

Strategies for agrobiodiversity conservation and promotion: a case from Yunnan, China

This paper deals with strategies for agrobiodiversity conservation and promotion based on studies on four plant groups (selected from 50 plant groups) occurring in the Yunnan Province of China. These plants are edible konjac (Amorphophallus), medicinal Paris, Musella lasiocarpa and wild tea (Camellia sinensis and its wild relatives), including their cultivars and wild populations. After analyzing the target plants, we conclude that the following strategies should be adopted to conserve and promote agrobiodiversity: (1) in situ conservation of agrobiodiversity, including habitat protection of wild populations, maintenance of native species and varieties in traditional agroecosystems, and relevant environmental education; (2) ex situ conservation and promotion of agrobiodiversity, including establishment of living collections and germplasm banks, and introduction of species and varieties into agroecosystems for agricultural practice; and (3) promotion and conservation of agrobiodiversity through sustainable uses, including technique development of propagation, cultivation, pest and disease control, on farm and off farm management, and other activities such as new variety breeding and scientific studies. Strategies developed here will be helpful to conserve and promote agrobiodiversity at agroecosystem, species, variety or landrace, and management system levels.     

Homegardens on Amazonian Dark Earths,Non-anthropogenic Upland,and Floodplain Soils along the Brazilian Middle Madeira River Exhibit Diverging Agrobiodiversity<Superscript>1</Superscript>

Homegardens on Amazonian Dark Earths, Non-anthropogenic Upland, and Floodplain Soils along the Brazilian Middle Madeira River Exhibit Diverging Agrobiodiversity. We test the hypothesis that the agrobiodiversity associated with homegardens on three different soils—upland Amazonian Dark Earths (ADE) and Oxisols (OX), and Fluvent Entisols (FL)—commonly found along the middle Madeira River in the municipality of Manicoré, Amazonas State, Brazil, is different due to the contrasting biotic, abiotic, and cultural settings specific to each of these soils. Using data from interviews with 63 farmers about food and utility species, we compare structural and floristic characteristics of homegarden agrobiodiversity. The density of individuals is higher on ADE than on the other soils (mean ± standard deviation: 715 ± 363 on ADE, 474 ± 283 on OX, 642 ± 399 on FL). ADE and OX have higher species richness (28.2 ± 5.6 on ADE, 25 ± 3.7on OX, 23.6 ± 5 on FL), while ADE and FL have a greater degree of domestication (2 ± 0.6 on ADE, 1.3 ± 0.5 on OX, 2.3 ± 0.6 on FL). ADE and OX have greater proportions of richness, density, and coverage composed of South American species, while FL has greater proportions of richness and density composed of Old World species. ADE has higher proportions of density and coverage of Mesoamerican species. Floristic composition is also different between soils: ADE occupies an intermediate position, composed of species associated with each of the other soil types and species that are most common on ADE. These differences in agrobiodiversity emerge through the interaction of human agency, plant responses, and the unique properties of soils in relation to socioeconomic and historical trajectories over time.     

Insights into the historical biogeography of the date palm (Phoenix dactylifera L.) using geometric morphometry of modern and ancient seeds

Aim The main purpose of this work is to understand the origin, history, historical biogeography and mechanisms of date palm (Phoenix dactylifera L.) domestication. Location Seeds of uncultivated Phoenix individuals from isolated Oman populations, cultivated date palm varieties of various geographical origins and other related Phoenix species were analysed. Additionally, well‐preserved seeds from Egyptian archaeological sites (14th century bc to 8th century ad ) were compared with the morphometric reference model based on the analysis of modern material. Methods Elliptic Fourier transforms (EFT), a morphometric method applied to shape outline analysis, were used to characterize seed shape and to quantify morphological diversity in P. dactylifera and related species. Results Analysis of seed outlines by EFT (1) showed that P. dactylifera can be differentiated from other Phoenix species and (2) enabled the quantification of patterns of shape differentiation in the genus Phoenix at different taxonomic, geographical and chronological levels. Date palm agrobiodiversity, partitioned in distinct morphotypes, appeared to be complex in terms of geographical structure. Allocation of archaeological seeds to different modern Phoenix forms and date palm morphotypes allowed us to reveal ancient forms consumed and/or exploited in Egypt and finally to determine spatial and temporal changes in agrobiodiversity. Main conclusions Based on the morphological diversity quantified in P. dactylifera and related species, we characterized ancestral seed shape features present in uncultivated populations. The geographical distribution pattern of seed shapes points to human dispersal routes that spread cultivation from one or more initial ‘domestication centres’. Finally, this work provides a powerful tool to identify ancient forms as demonstrated by the analysis of well‐preserved Egyptian archaeological seeds, dating from the 14th century bc to the 8th century ad . Results open new and fascinating perspectives on the investigation of the origins and chrono‐geographical fluctuation of date palm agrobiodiversity.     

Two-Variance-Component Model Improves Genetic Prediction in Family Datasets

Genetic prediction based on either identity by state (IBS) sharing or pedigree information has been investigated extensively with best linear unbiased prediction (BLUP) methods. Such methods were pioneered in plant and animal-breeding literature and have since been applied to predict human traits, with the aim of eventual clinical utility. However, methods to combine IBS sharing and pedigree information for genetic prediction in humans have not been explored. We introduce a two-variance-component model for genetic prediction: one component for IBS sharing and one for approximate pedigree structure, both estimated with genetic markers. In simulations using real genotypes from the Candidate-gene Association Resource (CARe) and Framingham Heart Study (FHS) family cohorts, we demonstrate that the two-variance-component model achieves gains in prediction r² over standard BLUP at current sample sizes, and we project, based on simulations, that these gains will continue to hold at larger sample sizes. Accordingly, in analyses of four quantitative phenotypes from CARe and two quantitative phenotypes from FHS, the two-variance-component model significantly improves prediction r² in each case, with up to a 20% relative improvement. We also find that standard mixed-model association tests can produce inflated test statistics in datasets with related individuals, whereas the two-variance-component model corrects for inflation.     

Assessing the Impacts of Agrobiodiversity Maintenance on Food Security Among Farming Households in Sri Lanka’s Dry Zone

Farmers’ maintenance of agrobiodiversity is fundamental to global food security, particularly in a world increasingly affected by climate change. Biodiversity helps to buffer agroecosystems from stresses like climatic variability, and the crop genetic diversity conserved with biodiverse agroecosystems is critical for plant breeding both locally and globally. Yet, despite these benefits, few studies have directly assessed the implications of household–level agrobiodiversity maintenance on household food security. Drawing on survey data collected in Sri Lanka’s Hambantota District, we evaluated the plant diversity maintained by small–scale farming households in both homegardens and crop fields and determined the relationships between this diversity and their households’ food security. We also considered how a suite of additional demographic, household, community, and farm characteristics relate to both the plant diversity maintained by a household and their food security. Similar to previous studies, the age of the agricultural decision-maker and the age and size of households’ homegardens positively correlated with the overall species richness of farming systems. Older homegardens were also identified to be more evenly distributed in their species abundance, and market–oriented households had significantly higher species richness but lower Shannon Indices. Most notably, household socioeconomic status and material wealth were important to both agrobiodiversity maintenance and household food security, while no significant relationships between species richness and food security measures were detected. These findings suggest that effort aiming to increase the food security of small–scale farming households in Sri Lanka, and elsewhere, should target those farming households with a paucity of socioeconomic assets, as these households lack both agroecological and economic resources to overcome shocks, such as those associated with climate change.     

Crop identity and memory effects on aboveground arthropods in a long‐term crop rotation experiment

Agricultural landscapes are globally dominated by monocultures under intensive management. This is one of the main reasons for biodiversity loss and insect population decline in many regions all over the world. Agroecosystem biodiversity in these areas can be enhanced by cropping system diversification, such as crop rotations. Yet, long‐term studies on effects of crop rotations on aboveground agrobiodiversity are lacking. We set up a 10‐year long‐term crop rotation experiment in Central Germany and monitored the temporal dynamics of aboveground arthropods over a full cultivation period to investigate influence of current and preceding crop identity and cropping system diversification on activity density, species richness, and community structure. We found that species composition was strongly influenced by currently grown crop although effect on arthropods varied between species groups. Especially, winter oilseed rape strongly affects arthropod community structure. Interestingly, we were also able to show an influence of the preceding crops, indicating an ecological memory effect in the aboveground arthropod community. Our results show that crop identity of both currently and previously grown crops in crop rotations may lead to an increase in arthropod activity density and changes in species composition. Diversified crop rotations including appropriate crops can be an easily implemented tool to increase arthropod biodiversity and biomass at large spatial and temporal scales, particularly in areas dominated by a single crop (e.g., wheat, maize). Our results may help to design optimized crop rotations for large‐scale enhancement of insect biodiversity in agroecosystems.     

Could taxonomic misnaming threaten the ex situ conservation and the usage of plant genetic resources?

Ex situ conservation of plant germplasm, especially seed banking, is a favourable and widely used method for the conservation of plant genetic resources (PGR). The long-term conservation of these resources is fundamental for food security and plant breeding in order to stem the losses in agrobiodiversity and to meet the global challenges that agriculture is facing. The conservation and accessibility of PGR relies on their correct taxonomic labelling and on the building of a searchable database that links ex situ collections together. In the current study, we analysed the impact of taxonomic misnaming in the two major PGR databases (Genesys PGR, EURISCO), listing accessions conserved worldwide. The aim was to understand if taxonomic misnaming issues prevent PGR conservation. We chose as a case-study seed collections of accessions of the genus Citrullus (watermelon genepool), the taxonomy and nomenclature of which have been largely revised in recent times. We observed that taxonomic misnaming greatly limits PGR conservation with only 3% of the accessions listed in the databases correctly named; moreover, 28% were affected by taxonomic errors that prevent the establishment of the accessions’ taxonomic identity, with consequences on their conservation and exploitation. The existence of the problem was also confirmed by the experimental propagation of three misnamed accessions. We suggest herein a series of actions that, put in place, could solve the extant misnaming issues in the databases and prevent their reoccurrence, allowing the correct conservation and the usability by the stakeholders of all the accessions.     

Genetic similarity, breeding distribution range and sexual selection

Large populations with extensive breeding distributions may sustain greater genetic variability, thus producing a positive relationship between genetic variation and population size. Levels of genetic variability may also be affected by sexual selection, which could either reduce levels because a small fraction of males contribute to the following generation, or augment them by generating genetic variability through elevated rates of mutations. We investigated to what extent genetic variability, as estimated from band sharing coefficients for minisatellite markers, could be predicted by breeding distribution range, population size and intensity of sexual selection (as reflected by degree of polygyny and extra-pair paternity). Across a sample of 62 species of birds in the Western Palearctic, we found extensive interspecific variation in band sharing coefficients. High band sharing coefficients (implying low local genetic variability among individuals) were associated with restricted breeding distributions, a conclusion confirmed by analysis of statistically independent linear contrasts. Independently, species with large population sizes had small band sharing coefficients. Furthermore, bird species with a high richness of subspecies for their breeding distribution range had higher band sharing coefficients. Finally, bird species with high levels of polygyny and extra-pair paternity had small band sharing coefficients. These results suggest that breeding distribution range, population size and intensity of sexual selection are important predictors of levels of genetic variability in extant populations.     

SCoT-marker analysis of Oryzaephilus surinamensis L. (Coleoptera: Silvanidae) and stored date kernels of Phoenix dactylifera (L.) fumigated with ozone and phosphine gases

Oryzaephilus surinamensis, a common grain product pest around the world, particularly causing great damage and losses to the date crops available in the storage. It has been traditionally resisted by using organic pesticides despite suspicions of their harmful effects on dates. This study aimed at the evaluation of the usage of ozone gas as an effective pesticide and also focuses on the safety alternatives provided by the respective method as compared to the usage of phosphine as a pesticide. While studying the ozone effects, the O. surinamensis was exposed to the gas for a variety of time scales (2, 4 and 6 h), distinctly for every life stages of the insect such as egg, larva and adults, infested the Phoenix dactylifera L date palm species present in the Siwa oasis. The obtained results showed that the adult insects had high resistance to ozone gas, while the larvae and egg stages were less resistant. The reduction rate of vital insect was 100% in all stages. Start codon analysis of DNA also showed that there are some SCoT primers can be identified and differentiated between the different treatments and control. On the other hand, the percentage of polymorphisms in insects was 50% while in date kernels 25% by six SCoT primers used. This study highlighted higher efficacy and safety regarding the usage of ozone gas in effectively controlling the manifestation of O. Surinamensis and thereby reducing the loss of stored date crops as compared to the phosphine.     

Accounting for female space sharing in St. Kilda Soay sheep (Ovis aries) results in little change in heritability estimates

When estimating heritability in free‐living populations, it is common practice to account for common environment effects, because of their potential to generate phenotypic covariance among relatives thereby biasing heritability estimates. In quantitative genetic studies of natural populations, however, philopatry, which results in relatives being clustered in space, is rarely accounted for. The two studies that have been carried out so far suggest absolute declines in heritability estimates of up to 43% when accounting for space sharing by relatives. However, due to methodological limitations these estimates may not be representative. We used data from the St. Kilda Soay sheep population to estimate heritabilities with and without accounting for space sharing for five traits for which there is evidence for additive genetic variance (birthweight, birth date, lamb August weight, and female post‐mortem jaw and metacarpal length). We accounted for space sharing by related females by separately incorporating spatial autocorrelation, and a home range similarity matrix. Although these terms accounted for up to 18% of the variance in these traits, heritability estimates were only reduced by up to 7%. Our results suggest that the bias caused by not accounting for space sharing may be lower than previously thought. This suggests that philopatry does not inevitably lead to a large bias if space sharing by relatives is not accounted for. We hope our work stimulates researchers to model shared space when relatives in their study population share space, as doing so will enable us to better understand when bias may be of particular concern.     

Insights into the molecular correlates modulating functional compensation between monogenic and polygenic disease gene duplicates in human

Functional redundancy by gene duplication appears to be a common phenomenon in biological system and hence understanding its underlying mechanism deserves much attention. Here, we investigated the differences between functional compensation of monogenic and polygenic disease genes which are unexplored till date. We found that the competence of functional buffering varies in the order of non-disease genes>monogenic disease genes>polygenic disease genes. This fact has been explained by the sequence identity, expression profile similarity, shared interaction partners and cellular locations between duplicated pairs. Moreover, we observed an inverse relationship between backup capacity and the non-synonymous substitution rate of disease and non-disease genes while the opposite trend is found for their corresponding paralogs. Logistic regression analysis among sequence identity, sharing of expression profile, interaction partners and cellular locations with backup capacity between duplicated pairs demonstrated that the sharing of expression profile is the most dominant regulator of backup capacity.     

Recombination between similar but not identical DNA sequences during yeast transformation occurs within short stretches of identity.

Interactions between similar but not identical (homeologous) DNA sequences play an important biological role in the evolution of genes and genomes. To gain insight into the underlying molecular mechanism(s) of genetic recombination, we have studied inter- and intramolecular homeologous recombination in S. cerevisiae during transformation. We found that homeologous DNAs recombine efficiently. Hybrid sequences were obtained between two mammalian cytochrome P450 cDNAs, sharing 73% identity, and between the yeast ARG4 gene and its human homeologous cDNA, sharing 52% identity. Sequencing data showed that the preferred recombination events are those corresponding to the overall alignment of the DNA sequences and that the junctions are within stretches of identity of variable length (2-21 nt). We suggest that these events occur by a conventional homologous recombination mechanism.     

Genetic variation in walnuts (Juglans regia and J. sigillata; Juglandaceae): Species distinctions, human impacts, and the conservation of agrobiodiversity in Yunnan, China

Walnuts are a major crop of many countries and mostly cultivated in large-scale plantations with few cultivars. Landraces provide important genetic reservoirs; thus, understanding factors influencing the geographic distribution of genetic variation in crop resources is a fundamental goal of agrobiodiversity conservation. Here, we investigated the role of human settlements and kinship on genetic variation and population structure of two walnut species: Juglans regia, an introduced species widely cultivated for its nuts, and J. sigillata, a native species cultivated locally in Yunnan. The objectives of this study were to characterize sympatric populations of J. regia and J. sigillata using 14 molecular markers and evaluate the role of Tibetan villages and kin groups (related households) on genotypic variation and population structure of J. regia and J. sigillata. Our results based on 220 walnut trees from six Tibetan villages show that although J. regia and J. sigillata are morphologically distinct, the two species are indistinguishable based on microsatellite data. Despite the lack of interspecific differences, AMOVAs partitioned among villages (5.41%, P = 0.0068) and kin groups within villages (3.34%, P = 0.0068) showed significant genetic variation. These findings suggest that village environments and familial relationships are factors contributing to the geographic structure of genetic variation in Tibetan walnuts.     

Past,present, and future research in bipolar lichen‐forming fungi and their photobionts

Compared to other organisms, such as vascular plants or mosses, lichen‐forming fungi have a high number of species occurring in both northern and southern hemispheres but are largely absent from intermediate, tropical latitudes. For instance, ca. 160 Antarctic species also occur in polar areas or mountainous temperate regions of the northern hemisphere. Early interpretations of this particular distribution pattern were made in terms of vicariance or long‐distance dispersal. However, it was not until the emergence of phylogenetics and the possibility of dating past diversification and colonization events that these initial hypotheses started to be evaluated. The premise of a relatively recent colonization of the southern hemisphere by boreal lichens through long‐distance dispersal has gained support in recent studies based on either the comparison of genetic affinities (i.e., tree topology) or more robust, statistical migratory models. Still, the scarcity of such studies and a concern that taxonomic concepts for bipolar lichens are often too broad preclude the generation of sound explanations on the mechanisms and origin of such fascinating disjunct distributions. This review provides an up‐to‐date overview of bipolar distributions in lichen‐forming fungi and their photobionts. Evidence provided by recent, molecular‐based studies as well as data on the type of lichen reproduction, dispersal ability, photobiont identity and availability, and habitat preferences are brought together to discuss how and when these distributions originated and their genetic footprints. Ideas for future prospects and research are also discussed.     

The conservation of agrobiodiversity on-farm: questioning the emerging paradigm

The genetic diversity of traditional varieties of crops is the most economically valuable part of global biodiversity and is of paramount importance for future world crop production. The Biodiversity Convention has given a clear mandate for on-farm conservation. However, very little formal research has been done and no agreed set of scientific principles yet exists for on-farm conservation of genetic resources. This lack of scientific knowledge has not prevented an explosion of recommendations on how to conserve agrobiodiversity on-farm and it is possible to identify an emerging paradigm. Through a review of some of the assumptions on which this paradigm is based, we clearly show that if attempts to conserve agrobiodiversity on-farm are based on these misconceptions, they are likely to fail. By assessing the present activities of farmers, we propose a research agenda to increase the diversity available to farmers and to enhance farmers' capacity to manage this diversity dynamically. Increasing genetic diversification, combined with farmers' experimental abilities, and underpinned by the formal system, will ensure greater on-farm conservation of more useful genetic resources.     

Relocation,high‐latitude warming and host genetic identity shape the foliar fungal microbiome of poplars

Micro‐organisms associated with plants and animals affect host fitness, shape community structure and influence ecosystem properties. Climate change is expected to influence microbial communities, but their reactions are not well understood. Host‐associated micro‐organisms are influenced by the climate reactions of their hosts, which may undergo range shifts due to climatic niche tracking, or may be actively relocated to mitigate the effects of climate change. We used a common‐garden experiment and rDNA metabarcoding to examine the effect of host relocation and high‐latitude warming on the complex fungal endophytic microbiome associated with leaves of an ecologically dominant boreal forest tree (Populus balsamifera L.). We also considered the potential effects of poplar genetic identity in defining the reactions of the microbiome to the treatments. The relocation of hosts to the north increased the diversity of the microbiome and influenced its structure, with results indicating enemy release from plausible pathogens. High‐latitude warming decreased microbiome diversity in comparison with natural northern conditions. The warming also caused structural changes, which made the fungal communities distinct in comparison with both low‐latitude and high‐latitude natural communities, and increased the abundance of plausible pathogens. The reactions of the microbiome to relocation and warming were strongly dependent on host genetic identity. This suggests that climate change effects on host–microbiome systems may be mediated by the interaction of environmental factors and the population genetic processes of the hosts.     

Genetic identity and genotype × genotype interactions between symbionts outweigh species level effects in an insect microbiome

Microbial symbionts often alter the phenotype of their host. Benefits and costs to hosts depend on many factors, including host genotype, symbiont species and genotype, and environmental conditions. Here, we present a study demonstrating genotype-by-genotype (G×G) interactions between multiple species of endosymbionts harboured by an insect, and the first to quantify the relative importance of G×G interactions compared with species interactions in such systems. In the most extensive study to date, we microinjected all possible combinations of five Hamiltonella defensa and five Fukatsuia symbiotica (X-type; PAXS) isolates into the pea aphid, Acyrthosiphon pisum. We applied several ecological challenges: a parasitoid wasp, a fungal pathogen, heat shock, and performance on different host plants. Surprisingly, genetic identity and genotype × genotype interactions explained far more of the phenotypic variation (on average 22% and 31% respectively) than species identity or species interactions (on average 12% and 0.4%, respectively). We determined the costs and benefits associated with co-infection, and how these compared to corresponding single infections. All phenotypes were highly reliant on individual isolates or interactions between isolates of the co-infecting partners. Our findings highlight the importance of exploring the eco-evolutionary consequences of these highly specific interactions in communities of co-inherited species.Subject terms: Microbial ecology, Community ecology, Symbiosis, Microbiome, Evolution