Jack Hearn

Revealing secret liaisons: DNA barcoding changes our understanding of food webs

1. How food webs are structured will affect how species dynamically interact. To date, the construction of quantitative food webs has largely been based on morphological species characters. Yet, recent work suggests that the use of molecular characters may change our perception of both species limits and species identity.

Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae)

Evolutionary radiations are prominent and pervasive across many plant lineages in diverse geographical and ecological settings; in neotropical rainforests there is growing evidence suggesting that a significant fraction of species richness is the result of recent radiations. Understanding the evolutionary trajectories and mechanisms underlying these radiations demands much greater phylogenetic resolution than is currently available for these groups. The neotropical tree genus Inga (Leguminosae) is a good example, with ~300 extant species and a crown age of 2–10 MY, yet over 6 kb of plastid and nuclear DNA sequence data gives only poor phylogenetic resolution among species. Here we explore the use of larger-scale nuclear gene data obtained though targeted enrichment to increase phylogenetic resolution within Inga. Transcriptome data from three Inga species were used to select 264 nuclear loci for targeted enrichment and sequencing. Following quality control to remove probable paralogs from these sequence data, the final dataset comprised 259,313 bases from 194 loci for 24 accessions representing 22 Inga species and an outgroup (Zygia). Bayesian phylogenies reconstructed using either all loci concatenated or a gene-tree/species-tree approach yielded highly resolved phylogenies. We used coalescent approaches to show that the same targeted enrichment data also have significant power to discriminate among alternative within-species population histories within the widespread species I. umbellifera. In either application, targeted enrichment simplifies the informatics challenge of identifying orthologous loci associated with de novo genome sequencing. We conclude that targeted enrichment provides the large volumes of phylogenetically-informative sequence data required to resolve relationships within recent plant species radiations, both at the species level and for within-species phylogeographic studies.

ABC inference of multi-population divergence with admixture from unphased population genomic data

Rapidly developing sequencing technologies and declining costs have made it possible to collect genome‐scale data from population‐level samples in nonmodel systems. Inferential tools for historical demography given these data sets are, at present, underdeveloped. In particular, approximate Bayesian computation (ABC) has yet to be widely embraced by researchers generating these data. Here, we demonstrate the promise of ABC for analysis of the large data sets that are now attainable from nonmodel taxa through current genomic sequencing technologies. We develop and test an ABC framework for model selection and parameter estimation, given histories of three‐population divergence with admixture. We then explore different sampling regimes to illustrate how sampling more loci, longer loci or more individuals affects the quality of model selection and parameter estimation in this ABC framework. Our results show that inferences improved substantially with increases in the number and/or length of sequenced loci, while less benefit was gained by sampling large numbers of individuals. Optimal sampling strategies given our inferential models included at least 2000 loci, each approximately 2 kb in length, sampled from five diploid individuals per population, although specific strategies are model and question dependent. We tested our ABC approach through simulation‐based cross‐validations and illustrate its application using previously analysed data from the oak gall wasp, Biorhiza pallida.

Likelihood-based inference of population history from low-coverage de novo genome assemblies

Short‐read sequencing technologies have in principle made it feasible to draw detailed inferences about the recent history of any organism. In practice, however, this remains challenging due to the difficulty of genome assembly in most organisms and the lack of statistical methods powerful enough to discriminate between recent, nonequilibrium histories. We address both the assembly and inference challenges. We develop a bioinformatic pipeline for generating outgroup‐rooted alignments of orthologous sequence blocks from de novo low‐coverage short‐read data for a small number of genomes, and show how such sequence blocks can be used to fit explicit models of population divergence and admixture in a likelihood framework. To illustrate our approach, we reconstruct the Pleistocene history of an oak‐feeding insect (the oak gallwasp Biorhiza pallida), which, in common with many other taxa, was restricted during Pleistocene ice ages to a longitudinal series of southern refugia spanning the Western Palaearctic. Our analysis of sequence blocks sampled from a single genome from each of three major glacial refugia reveals support for an unexpected history dominated by recent admixture. Despite the fact that 80% of the genome is affected by admixture during the last glacial cycle, we are able to infer the deeper divergence history of these populations. These inferences are robust to variation in block length, mutation model and the sampling location of individual genomes within refugia. This combination of de novo assembly and numerical likelihood calculation provides a powerful framework for estimating recent population history that can be applied to any organism without the need for prior genetic resources.

Eight new species of Cycloneuroterus Melika & Tang gallwasps from Taiwan and mainland China (Hymenoptera: Cynipidae: Cynipini)

Eight new species of cynipid gallwasps, Cycloneuroterus abei Melika & Tang, C. ergei Tang & Melika, C. gilvus Melika & Tang, C. globosus Melika & Tang, C. jianwui Tang & Melika, C. lohsei Melika & Tang, C. tumiclavus Tang & Melika, C. uraianus Tang & Melika, from Taiwan and mainland China are described. Descriptions, diagnoses, biology, and host associations for the new species and a key to all Cycloneuroterus species are given. All taxa are supported by morphological and molecular data. Seven newly described species induce galls on Quercus subgenus Cyclobalanopsis, while one, C. uraianus, induces galls on Castanopsis. This is the first Cycloneuroterus species known to associate with Castanopsis.

New species of cynipid inquilines of the genus Saphonecrus (Hymenoptera: Cynipidae: Synergini) from the Eastern Palaearctic, with a re-appraisal of known species world-wide.

Fifteen new species of cynipid inquilines, Saphonecrus chinensis Tang & Schwéger, S. gilvus Melika & Schwéger, S. globosus Schwéger & Tang, S. leleyi Melika & Schwéger, S. lithocarpii Schwéger & Melika, S. longinuxi Schwéger & Melika, S. morii Schwéger & Tang, S. nantoui Tang, Schwéger & Melika, S. nichollsi Schwéger & Melika, S. pachylomai Schwéger, Tang & Melika, S. robustus Schwéger & Melika, S. saliciniai Melika, Tang & Schwéger, S. shanzhukui Melika & Tang, S. symbioticus Melika & Schwéger, and S. taitungi Schwéger, Tang & Melika, from the Eastern Palaearctic are described. Descriptions, diagnoses, biology, and host associations for the new species, and a key to Palaearctic Saphonecrus species are given. All new taxa form distinct units as demonstrated by the molecular phylogenetic analyses of Palaearctic Saphonecrus species. The status of some earlier described Saphonecrus species is discussed also. The Synergini genus Lithonecrus Nieves-Aldrey & Butterill, 2014 is synonymized with Lithosaphonecrus Tang, Melika & Bozsó, 2013. Three Saphonecrus species are transferred to Synergus: Synergus brevis (Weld) comb. nova, Synergus hupingshanensis (Liu, Yang & Zhu) comb. nova, and Synergus yukawai (Wachi, Ide & Abe) comb. nova. Synophrus vietnamensis Abe, Ide, Konishi & Ueno is transferred to Lithosaphonecrus: Lithosaphonecrus vietnamensis Abe, Ide, Konishi & Ueno), comb. nova. The current number of valid Saphonecrus species worldwide is 36.

Whole-genome data reveal the complex history of a diverse ecological community

Significance Widespread biological communities are common, but little is known about how they assemble. A key question is how sets of trophically linked species (predators and their prey, hosts and parasites) spread to occupy current distributions. Do they disperse together, preserving ecological interactions, or separately, such that interactions are interrupted? This is central to assessing the potential for coevolution in a system and requires inference of species associations both over space and through time. Here, we use de novo genomic data and likelihood-based approaches to infer the assembly history of a multispecies community of Western Palearctic insect herbivores and parasitoid natural enemies—the two trophic groups that together comprise 50% of all animal species. How widespread ecological communities assemble remains a key question in ecology. Trophic interactions between widespread species may reflect a shared population history or ecological fitting of local pools of species with very different population histories. Which scenario applies is central to the stability of trophic associations and the potential for coevolution between species. Here we show how alternative community assembly hypotheses can be discriminated using whole-genome data for component species and provide a likelihood framework that overcomes current limitations in formal comparison of multispecies histories. We illustrate our approach by inferring the assembly history of a Western Palearctic community of insect herbivores and parasitoid natural enemies, trophic groups that together comprise 50% of terrestrial species. We reject models of codispersal from a shared origin and of delayed enemy pursuit of their herbivore hosts, arguing against herbivore attainment of “enemy-free space.” The community-wide distribution of species expansion times is also incompatible with a random, neutral model of assembly. Instead, we reveal a complex assembly history of single- and multispecies range expansions through the Pleistocene from different directions and over a range of timescales. Our results suggest substantial turnover in species associations and argue against tight coevolution in this system. The approach we illustrate is widely applicable to natural communities of nonmodel species and makes it possible to reveal the historical backdrop against which natural selection acts.

Genome-wide Methylation Patterns Under Caloric Restriction in Daphnia magna.

The degradation of epigenetic control with age is associated with progressive diseases of ageing, including cancers, immunodeficiency and diabetes. Reduced caloric intake slows the effects of aging and age-related diseases, a process likely to be mediated by the impact of caloric restriction on epigenetic factors such as DNA methylation. We used whole genome bisulphite sequencing to study how DNA methylation patterns change with diet in a small invertebrate, the crustacean Daphnia magna. Daphnia show the classic response of longer life under CR, and they reproduce clonally, which permits the study of epigenetic changes in the absence of genetic variation. Global CpG methylation was 0.7-0.9%, and there was no difference in overall methylation levels between normal and calorie restricted replicates. However, 453 regions were differentially methylated (DMRs) between the normally fed and calorie restricted (CR) replicates. Of these 61% were hypomethylated in the CR group, and 39% were hypermethylated in the CR group. Gene Ontogeny (GO) term enrichment of hyper and hypo-methylated genes showed significant over- and under-representation in three molecular function terms and four biological process GO terms. Notable among these were kinase and phosphorylation activity, which have a well-known functional link to cancers.

Daphnia magna microRNAs respond to nutritional stress and ageing but are not transgenerational

Maternal effects, where the performance of offspring is determined by the condition of their mother, are widespread and may in some cases be adaptive. The crustacean Daphnia magna shows strong maternal effects: offspring size at birth and other proxies for fitness are altered when their mothers are older or when mothers have experienced dietary restriction. The mechanisms for this transgenerational transmission of maternal experience are unknown, but could include changes in epigenetic patterning. MicroRNAs (miRNAs) are regulators of gene expression that have been shown to play roles in intergenerational information transfer, and here, we test whether miRNAs are involved in D. magna maternal effects. We found that miRNAs were differentially expressed in mothers of different ages or nutritional state. We then examined miRNA expression in their eggs, their adult daughters and great granddaughters, which did not experience any treatments. The maternal (treatment) generation exhibited differential expression of miRNAs, as did their eggs, but this was reduced in adult daughters and lost by great granddaughters. Thus, miRNAs are a component of maternal provisioning, but do not appear to be the cause of transgenerational responses under these experimental conditions. MicroRNAs may act in tandem with egg provisioning (e.g., with carbohydrates or fats), and possibly other small RNAs or epigenetic modifications.