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1. Diploid-dominant life cycles characterize the early evolution of Fungi

   https://doi.org/10.1073/pnas.2116841119  

   Amses, Kevin R. ; Simmons, D. Rabern ; Longcore, Joyce E. ; Mondo, Stephen J. ; Seto, Kensuke ; Jerônimo, Gustavo H. ; Bonds, Anne E. ; Quandt, C. Alisha ; Davis, William J. ; Chang, Ying ; et al ( September 2022 , Proceedings of the National Academy of Sciences)

   Most of the described species in kingdom Fungi are contained in two phyla, the Ascomycota and the Basidiomycota (subkingdom Dikarya). As a result, our understanding of the biology of the kingdom is heavily influenced by traits observed in Dikarya, such as aerial spore dispersal and life cycles dominated by mitosis of haploid nuclei. We now appreciate that Fungi comprises numerous phylum-level lineages in addition to those of Dikarya, but the phylogeny and genetic characteristics of most of these lineages are poorly understood due to limited genome sampling. Here, we addressed major evolutionary trends in the non-Dikarya fungi by phylogenomic analysis of 69 newly generated draft genome sequences of the zoosporic (flagellated) lineages of true fungi. Our phylogeny indicated five lineages of zoosporic fungi and placed Blastocladiomycota, which has an alternation of haploid and diploid generations, as branching closer to the Dikarya than to the Chytridiomyceta. Our estimates of heterozygosity based on genome sequence data indicate that the zoosporic lineages plus the Zoopagomycota are frequently characterized by diploid-dominant life cycles. We mapped additional traits, such as ancestral cell-cycle regulators, cell-membrane– and cell-wall–associated genes, and the use of the amino acid selenocysteine on the phylogeny and found that these ancestral traits thatmore »are shared with Metazoa have been subject to extensive parallel loss across zoosporic lineages. Together, our results indicate a gradual transition in the genetics and cell biology of fungi from their ancestor and caution against assuming that traits measured in Dikarya are typical of other fungal lineages.« less
2. Cophylogenetic analyses of Trachymyrmex ant‐fungal specificity: “One to one with some exceptions”

   https://doi.org/10.1111/mec.16140  

   Beigel, Katherine ; Matthews, Alix E. ; Kellner, Katrin ; Pawlik, Christine V. ; Greenwold, Matthew ; Seal, Jon N. ( September 2021 , Molecular Ecology)

   Over the past few decades, large‐scale phylogenetic analyses of fungus‐gardening ants and their symbiotic fungi have depicted strong concordance among major clades of ants and their symbiotic fungi, yet within clades, fungus sharing is widespread among unrelated ant lineages. Sharing has been explained using a diffuse coevolution model within major clades. Understanding horizontal exchange within clades has been limited by conventional genetic markers that lack both interspecific and geographic variation. To examine whether reports of horizontal exchange were indeed due to symbiont sharing or the result of employing relatively uninformative molecular markers, samples ofTrachymyrmex arizonensisandTrachymyrmex pomonaeand their fungi were collected from native populations in Arizona and genotyped using conventional marker genes and genome‐wide single nucleotide polymorphisms (SNPs). Conventional markers of the fungal symbionts generally exhibited cophylogenetic patterns that were consistent with some symbiont sharing, but most fungal clades had low support. SNP analysis, in contrast, indicated that each ant species exhibited fidelity to its own fungal subclade with only one instance of a colony growing a fungus that was otherwise associated with a different ant species. This evidence supports a pattern of codivergence betweenTrachymyrmexspecies and their fungi, and thus a diffuse coevolutionary model may not accurately predict symbiont exchange.more »These results suggest that fungal sharing across host species in these symbioses may be less extensive than previously thought.

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3. Comparative genomics of Mollicutes-related endobacteria supports a late invasion into Mucoromycota fungi

   https://doi.org/10.1038/s42003-023-05299-8  

   Longley, Reid ; Robinson, Aaron ; Liber, Julian A. ; Bryson, Abigail E. ; Morales, Demosthenes P. ; LaButti, Kurt ; Riley, Robert ; Mondo, Stephen J. ; Kuo, Alan ; Yoshinaga, Yuko ; et al ( September 2023 , Communications Biology)

   Diverse members of early-diverging Mucoromycota, including mycorrhizal taxa and soil-associated Mortierellaceae, are known to harbor Mollicutes-related endobacteria (MRE). It has been hypothesized that MRE were acquired by a common ancestor and transmitted vertically. Alternatively, MRE endosymbionts could have invaded after the divergence of Mucoromycota lineages and subsequently spread to new hosts horizontally. To better understand the evolutionary history of MRE symbionts, we generated and analyzed four complete MRE genomes from two Mortierellaceae genera:Linnemannia(MRE-L) andBenniella(MRE-B). These genomes include the smallest known of fungal endosymbionts and showed signals of a tight relationship with hosts including a reduced functional capacity and genes transferred from fungal hosts to MRE. Phylogenetic reconstruction including nine MRE from mycorrhizal fungi revealed that MRE-B genomes are more closely related to MRE from Glomeromycotina than MRE-L from the same host family. We posit that reductions in genome size, GC content, pseudogene content, and repeat content in MRE-L may reflect a longer-term relationship with their fungal hosts. These data indicateLinnemanniaandBenniellaMRE were likely acquired independently after their fungal hosts diverged from a common ancestor. This work expands upon foundational knowledge on minimal genomes and provides insights into the evolution of bacterial endosymbionts.
4. Closely related tree species support distinct communities of seed‐associated fungi in a lowland tropical forest

   https://doi.org/10.1111/1365-2745.13611  

   Zalamea, Paul‐Camilo ; Sarmiento, Carolina ; Arnold, A. Elizabeth ; Davis, Adam S. ; Ferrer, Astrid ; Dalling, James W. ; Mommer, ed., Liesje ( February 2021 , Journal of Ecology)

   Previous theoretical work has highlighted the potential for natural enemies to mediate the coexistence of species with similar life histories via density‐dependent effects on survivorship. For plant pathogens to play this role, they must differ in their ability to infect or induce disease in different host plant species. In tropical forests characterized by high diversity, these effects must extend to phylogenetically closely related species pairs. Mortality at the seed and seedling stage strongly influences the abundance and distribution of tropical tree species, but the host preferences and spatial distributions of fungi are rarely determined.

   We examined how host species identity, relatedness and seed viability influence the composition of fungal communities associated with seeds of four co‐occurring pioneer trees (Cecropia insignis,C. longipes,C. peltataandJacaranda copaia). Seeds were buried in mesh bags in five common gardens in the understorey of a lowland tropical forest in Panama and retrieved at intervals from 1 to 30 months. A subset of the seeds in each bag was used to determine germination success. One half of each remaining seed was tested for viability; and the other half was used to culture and identify seed‐infecting fungi.

   Seeds were infected by fungi after burial. Although fungal communities differed in viable versusmore »dead seeds, and across burial locations, community composition primarily varied as a function of plant species identity (30.7% of variation in community composition vs. 4.5% for viability and location together), even for congenericCecropiaspecies. Phylogenetic reconstruction showed that relatedness of fungi mostly reflected differences betweenJacaranda(Bignoniaceae) andCecropia(Urticaceae).

   Although the proportion of germinable seeds decreased gradually over time for all species, intraspecific variation in survival was high at the same location (e.g. ranging from 0% to 100% forC. peltata) suggesting variable exposure or susceptibility to seed pathogens.

   Synthesis. Our study provides evidence under field conditions that congeneric tree species with similar life history traits differ markedly in seed‐associated fungal communities when exposed to the same soil‐borne fungi. This is a critical first step supporting pathogen‐mediated coexistence of closely related tree species.

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5. Crocodylomorph cranial shape evolution and its relationship with body size and ecology

   https://doi.org/10.1111/jeb.13540  

   Godoy, Pedro L. ( September 2019 , Journal of Evolutionary Biology)

   Crocodylomorpha, which includes living crocodylians and their extinct relatives, has a rich fossil record, extending back for more than 200 million years. Unlike modern semi‐aquatic crocodylians, extinct crocodylomorphs exhibited more varied lifestyles, ranging from marine to fully terrestrial forms. This ecological diversity was mirrored by a remarkable morphological disparity, particularly in terms of cranial morphology, which seems to be closely associated with ecological roles in the group. Here, I use geometric morphometrics to comprehensively investigate cranial shape variation and disparity in Crocodylomorpha. I quantitatively assess the relationship between cranial shape and ecology (i.e. terrestrial, aquatic, and semi‐aquatic lifestyles), as well as possible allometric shape changes. I also characterize patterns of cranial shape evolution and identify regime shifts. I found a strong link between shape and size, and a significant influence of ecology on the observed shape variation. Terrestrial taxa, particularly notosuchians, have significantly higher disparity, and shifts to more longirostrine regimes are associated with large‐bodied aquatic or semi‐aquatic species. This demonstrates an intricate relationship between cranial shape, body size and lifestyle in crocodylomorph evolutionary history. Additionally, disparity‐through‐time analyses were highly sensitive to different phylogenetic hypotheses, suggesting the description of overall patterns among distinct trees. For crocodylomorphs, most results agreemore »in an early peak during the Early Jurassic and another in the middle of the Cretaceous, followed by nearly continuous decline until today. Since only crown‐group members survived through the Cenozoic, this decrease in disparity was likely the result of habitat loss, which narrowed down the range of crocodylomorph lifestyles.

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