Pepijn Wilhelmus Kooij

Pepijn Wilhelmus Kooij
São Paulo State University | Unesp · Centro Estudos Insetos Sociais - CEIS

PhD

About

63
Publications
22,706
Reads
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540
Citations
Additional affiliations
February 2020 - present
São Paulo State University
Position
  • Researcher
May 2015 - January 2020
Royal Botanic Gardens, Kew
Position
  • Fellow
May 2014 - April 2015
University of Copenhagen
Position
  • PostDoc Position
Education
October 2010 - April 2014
University of Copenhagen
Field of study
  • Evolution of fungus-growing ants fungal symbionts
September 2003 - September 2009

Publications

Publications (63)
Article
Full-text available
The mutualism between leaf-cutting ants and their fungal symbionts revolves around processing and inoculation of fresh leaf pulp in underground fungus gardens, mediated by ant fecal fluid deposited on the newly added plant substrate. As herbivorous feeding often implies that growth is nitrogen limited, we cloned and sequenced six fungal proteases f...
Article
Full-text available
The genera Atta and Acromyrmex are often grouped as leaf-cutting ants for pest management assessments and ecological surveys, although their mature colony sizes and foraging niches may differ substantially. Few studies have addressed such interspecific differences at the same site, which prompted us to conduct a comparative study across six sympatr...
Article
Full-text available
Innovative evolutionary developments are often related to gene or genome duplications. The crop fungi of attine fungus-growing ants are suspected to have enhanced genetic variation reminiscent of polyploidy, but this has never been quantified with cytological data and genetic markers. We estimated the number of nuclei per fungal cell for 42 symbion...
Article
Full-text available
Obligate mutualistic symbioses rely on mechanisms that secure host-symbiont commitments to maximize host benefits and prevent symbiont cheating. Previous studies showed that somatic incompatibilities correlate with neutral-marker-based genetic distances between fungal symbionts of Panamanian Acromyrmex leaf-cutting ants, but the extent to which thi...
Article
Full-text available
Each day, as the amount of genomic data and bioinformatics resources grows, researchers are increasingly challenged with selecting the most appropriate approach to analyse their data. In addition, the opportunity to undertake comparative genomic analyses is growing rapidly. This is especially true for fungi due to their small genome sizes (i.e. mea...
Article
Fungus-farming ants cultivate multiple lineages of fungi for food, but, because fungal cultivar relationships are largely unresolved, the history of fungus-ant coevolution remains poorly known. We designed probes targeting >2000 gene regions to generate a dated evolutionary tree for 475 fungi and combined it with a similarly generated tree for 276...
Article
The naturally selected fungal crop (Leucoagaricus gongylophorus) farmed by leafcutter ants shows striking parallels with artificially selected plant crops domesticated by humans (e.g., polyploidy, engorged nutritional rewards, dependence on cultivation). To date, poorly resolved L. gongylophorus genome assemblies based on short-read sequencing have...
Preprint
Full-text available
The naturally selected fungal crop ( Leucoagaricus gongylophorus ) farmed by leafcutter ants shows striking parallels with artificially selected plant crops domesticated by humans (e.g., polyploidy, engorged nutritional rewards, dependence on cultivation). To date, poorly resolved L. gongylophorus genomes based on short-read sequencing have constra...
Preprint
Full-text available
Multipartite symbioses are inherently complex, involving dynamic ecological interactions between organisms with intertwined yet distinct evolutionary histories. The fungus-growing (attine) ants facilitate maintenance of a symbiotic species network through maternal vertical transmission of an obligate fungal symbiont. While the gut microbiomes of fu...
Article
Full-text available
Fungus-growing attine ants rely on an obligatory nutritional mutualism with fungi. Most attine ant genera cultivate fungi in the basidiomycete tribe Leucocoprineae (Agaricales: Agaricaceae). Although fungal partners show high genetic diversity, only two fungal species cultivated by leaf-cutting ants were formerly described. This is partly due to th...
Article
Full-text available
Leaf-cutting ants and their fungal crops are a textbook example of a long-term obligatory mutualism. Many microbes continuously enter their nest containing the fungal cultivars, destabilizing the symbiosis and, in some cases, outcompeting the mutual-istic partners. Preferably, the ant workers should distinguish between different microorganisms to r...
Article
Full-text available
Fungus-growing attine ants maintain a mutualistic relationship with basidiomycete fungi which they cultivate for food. In addition to the fungal partner, attine ant colonies harbor a myriad of microorganisms, including the genus Escovopsis, fungal parasites of the ant crops. Because Escovopsioides nivea is phylogenetically close to Escovopsis, prev...
Article
Full-text available
Maintaining symbiosis homeostasis is essential for mutualistic partners. Leaf-cutting ants evolved a long-term symbiotic mutualism with fungal cultivars for nourishment while using vertical asexual transmission across generations. Despite the ants’ efforts to suppress fungal sexual reproduction, scattered occurrences of cultivar basidiomes have bee...
Article
Full-text available
During crop domestication, human farmers traded greater productivity for higher crop vulnerability outside specialized cultivation conditions. We found a similar domestication trade-off across the major co-evolutionary transitions in the farming systems of attine ants. First, the fundamental nutritional niches of cultivars narrowed over ~60 million...
Article
Full-text available
Plant and animal community composition changes at higher elevations on mountains. Plant and animal species richness generally declines with elevation, but the shape of the relationship differs between taxa. There are several proposed mechanisms, including the productivity hypotheses; that declines in available plant biomass confers fewer resources...
Article
Full-text available
Leaf-cutting ants employ diverse behavioral strategies for promoting the growth of fungal cultivars in a structure known as fungus garden. As a nutritionally rich resource for the ants, the fungal crop is threatened by microbial antagonists and pathogens. Strategies for protecting the garden against harmful microbes have been described in detail, a...
Article
Full-text available
Animal gut microbiota affect host physiology and behaviour. In social insects, where colony level integrity is preserved via a nestmate discrimination system based on cuticular hydrocarbon mixtures, microorganismal effects may therefore influence social dynamics. Although nestmate recognition has undergone a thorough exploration during the last fou...
Article
Full-text available
Leaf-cutting ants are often considered agricultural pests, but they can also benefit local people and serve important roles in ecosystems. Throughout their distribution, winged reproductive queens of leaf-cutting ants in the genus Atta Fabricius, 1804 are consumed as a protein-rich food source and sometimes used for medical purposes. Little is know...
Article
In this study, we document and describe the new Cortinarius section Austroamericani. Our results reveal high species diversity within this clade, with a total of 12 recognized species. Of these, only C. rufus was previously documented. Seven species are described as new based on basidiomata collections. The four remaining species are only known fro...
Chapter
Full-text available
HOW ARE DIFFERENT SPECIES RELATED TO EACH OTHER? THIS SIMPLE YET CRITICALLY IMPORTANT QUESTION, WHICH IS ROUTINELY ASKED ABOUT SPECIES IN ALL KINGDOMS OF LIFE, IS ONE OF THE MOST DIFFICULT TO ANSWER FOR FUNGI. This is because building the fungal tree of life has several significant challenges. First, similarities in the physical features of fungi,...
Chapter
Full-text available
THE GENOMES OF FUNGI HAVE LONG BEEN OF INTEREST TO GENETICISTS BECAUSE MANY SPECIES ARE QUICK AND EASY TO GROW, THEIR DNA CAN BE EASILY MANIPULATED, AND BECAUSE MANY OF THEIR ESSENTIAL CELL PROCESSES ARE THE SAME AS IN ALL EUKARYOTES, INCLUDING HUMANS. Indeed, some of the earliest insights into how DNA encodes the information needed to build life c...
Preprint
Full-text available
Animal gut microbiota affect host physiology and behaviour. In eusocial Hymenoptera, where colony-level integrity is preserved via a nestmate discrimination system based on cuticular hydrocarbon mixtures, microorganismal effects may influence social dynamics. Although nestmate recognition has undergone a thorough exploration during the last four de...
Article
How foraging trails are formed and the chemical communication between individual ants is well known. However, communication between partners in mutualistic relationships, such as the leaf-cutting ants (LCA) and their symbiotic fungus, is less studied. There is a feedback mechanism that operates in LCA colonies, with the fungus garden communicating...
Article
Myrteae (c. 2500 species; 51 genera) is the largest tribe of Myrtaceae and an ecologically important groups of angiosperms in the Neotropics. Systematic relationships in Myrteae are complex, hindering conservation initiatives and jeopardizing evolutionary modelling. A well-supported and robust phylogenetic hypothesis was here targeted towards a com...
Article
Full-text available
Significance Early subsistence farming implied significant physiological challenges for Neolithic farmers until they genetically isolated their crops through artificial selection and polyploidization. The attine ants faced analogous challenges when they adopted fungus farming 55–60 Mya. Whereas evolutionarily derived attine lineages irreversibly do...
Article
Full-text available
Background: Xyloglucan is an important component in plant cell walls that herbivores cannot digest without microbial symbionts. Leaf-cutting ants are major insect herbivores in the Neo-Tropics that rely on fungus-garden enzymes for degrading plant cell walls. However, many of these ants discard much of their harvested plant material after partial...
Data
Binary allele score (A) and allele fragment sizes (B) for 106 identified alleles from AFLP analyses on nine Acromyrmex and nine Atta fungal symbionts. Cutoff for allele identification was set at minimum 50 bp and maximum 500 bp. Columns show colony ID, host ant species, and allele number.
Data
Microsatellite allele scores for nine Acromyrmex and nine Atta fungal symbionts for each of the ten different loci. Columns show colony ID, host ant species, and locus name with respective allele sizes.
Conference Paper
Polyploidy is common in plants, presumably because advantages of increased functional heterozygosity often surpass costs of destabilized mitosis or epigenetic instability, but rare in fungi, where ‘diploid’ cells retain the two parental haploid nuclei rather than merging them into a zygote. Such dikaryotic mycelia are actively maintained in Basidio...
Conference Paper
Full-text available
Polyploidy, the state of having more that 1-2 sets of chromosomes, is widespread in plants and has been shown to increase functional heterozygosity, but also to give mitotic problems and to generate epigenetic instability. However, polyploidy is rare in fungi, possibly because ‘diploid’ cells have two different haploid nuclei rather than a ‘merged’...
Data
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
Data
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
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##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
Data
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
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##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
Data
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
Conference Paper
Research on the mutualism between fungus-growing ants and their symbionts normally views the ants as farmers and the fungi as crops (Weber, 1966). However, there is growing evidence suggesting that the fungus is actually using the ants as a live transportation device for providing substrate and transporting fungal enzymes to the new leaf material t...
Conference Paper
Research on the mutualism between fungus-growing ants and their symbionts normally views the ants as farmers and the fungi as crops (Weber, 1966). However, there is growing evidence suggesting that the fungus is actually using the ants as a live transportation device for providing substrate and transporting fungal enzymes to the new leaf material t...
Conference Paper
Research on the mutualism between fungus-growing ants and their symbionts normally views the ants as farmers and the fungi as crops (Weber, 1966). However, there is growing evidence suggesting that the fungus is actually using the ants as a live transportation device for providing substrate and transporting fungal enzymes to the new leaf material t...
Conference Paper
Research on the mutualism between fungus-growing ants and their symbionts normally views the ants as farmers and the fungi as crops. However, there is growing evidence suggesting that the fungus is actually using the ants as a live transportation device for providing substrate and transporting fungal enzymes to the new leaf material that the ants a...
Article
Though inconspicuous in healthy nests, Pseudoxylaria species are almost always present and overgrow deteriorating fungus-growing termite gardens. Whether these fungi are detrimental to the fungus-garden, benign, or even beneficial is unclear. We hypothesize that Pseudoxylaria is a stowaway that practices a sit-and-wait strategy to survive in the te...
Article
Full-text available
Fungus gardens of the basidiomycete Leucocoprinus gongylophorus sustain large colonies of leaf-cutting ants by degrading the plant material collected by the ants. Recent studies have shown that enzyme activity in these gardens is primarily targeted toward starch, proteins and the pectin matrix associated with cell walls, rather than toward structur...

Questions

Questions (3)
Question
Using IQTREE I received the most optimum models for my data to analyse phylogenetic tree-reconstruction. IQTREE is able to use, aside from the Gamma distribution for heterogeneity across sites also the FreeRate model:
"FreeRate model (Yang, 1995; Soubrier et al., 2012) that generalizes the +G model by relaxing the assumption of Gamma-distributed rates. The number of categories can be specified with e.g. +R6 (default 4 categories if not specified). The FreeRate model typically fits data better than the +G model and is recommended for analysis of large data sets."
Does anyone know if it is possible to use this FreeRate model in MrBayes (or in RevBayes), and if yes, how to I put that in the script?
Question
The terminology on karyotism of fungi is in my opinion very confusing. I'm looking for good explanations of terms like: mono-karyon, homo-karyon, di-karyon, hetero-karyon, multi-karyon, poly-karyon (and others if there are). I find that in different publications the terminology is used for different things, which makes things harder to understand.
Question
I have the sequences in two different sets, but while building the phylogenetic tree I would like to add both sets into the analysis.

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