Field Of Molecular Ecology Research Articles

The future of molecular ecology in Aotearoa New Zealand: an early career perspective

ABSTRACT The skills, insights, and genetic data gathered by molecular ecologists are pivotal to addressing many contemporary biodiversity, environmental, cultural, and societal challenges. Concurrently, the field of molecular ecology is being revolutionised by rapid technological development and diversification in the scope of its applications. Hence, it is timely to review the future opportunities of molecular ecological research in Aotearoa New Zealand, and to reconcile them with philosophies of open science and the implications for Indigenous data sovereignty and benefit sharing. Future molecular ecologists need to be interdisciplinary, equipped to embrace innovation, and informed about the broader societal relevance of their research, as well as advocates of best practice. Here, we present an ideal future for molecular ecology in Aotearoa, based on the perspectives of 23 early career researchers from tertiary institutions, Crown Research Institutes, research consultancies, and government agencies. Our article provides: a guide for molecular ecologists embarking on genetic research in Aotearoa, and a primer for individuals in a position to support early career molecular ecologists in Aotearoa. We outline our goals and highlight specific considerations – for molecular ecology and the scientific community in Aotearoa – based on our own experience and aspirations, and invite other researchers to join this dialogue.

Who are you? A framework to identify and report genetic sample mix-ups.

Sample mix-ups occur when samples have accidentally been duplicated, mislabelled or swapped. When samples are subsequently genotyped or sequenced, this can lead to individual IDs being incorrectly linked to genetic data, resulting in incorrect or biased research results, or reduced power to detect true biological patterns. We surveyed the community and found that almost 80% of responding researchers have encountered sample mix-ups. However, many recent studies in the field of molecular ecology do not appear to systematically report individual assignment checks as part of their publications. Although checks may be done, lack of consistent reporting means that it is difficult to assess whether sample mix-ups have occurred or been detected. Here, we present an easy-to-follow sample verification framework that can utilise existing metadata, including species, population structure, sex and pedigree information. We demonstrate its application to a data set representing individuals of a threatened Aotearoa New Zealand bird species, the hihi, genotyped on a 50K SNP array. We detected numerous incorrect genotype-ID associations when comparing observed and genetic sex or comparing to relationships in a verified microsatellite pedigree. The framework proposed here helped to confirm 488 individuals (39%), correct another 20 bird-genotype links, and detect hundreds of incorrect sample IDs, emphasizing the value of routinely checking genetic and genomic data sets for their accuracy. We therefore promote the implementation and reporting of this simple yet effective sample verification framework as a standardized quality control step for studies in the field of molecular ecology.

Victoria L. Sork—Recipient of the 2020 Molecular Ecology Prize

Victoria L. Sork—Recipient of the 2020 Molecular Ecology Prize

Building a global genomics observatory: Using GEOME (the Genomic Observatories Metadatabase) to expedite and improve deposition and retrieval of genetic data and metadata for biodiversity research.

Genetic data represent a relatively new frontier for our understanding of global biodiversity. Ideally, such data should include both organismal DNA-based genotypes and the ecological context where the organisms were sampled. Yet most tools and standards for data deposition focus exclusively either on genetic or ecological attributes. The Genomic Observatories Metadatabase (GEOME: geome-db.org) provides an intuitive solution for maintaining links between genetic data sets stored by the International Nucleotide Sequence Database Collaboration (INSDC) and their associated ecological metadata. GEOME facilitates the deposition of raw genetic data to INSDCs sequence read archive (SRA) while maintaining persistent links to standards-compliant ecological metadata held in the GEOME database. This approach facilitates findable, accessible, interoperable and reusable data archival practices. Moreover, GEOME enables data management solutions for large collaborative groups and expedites batch retrieval of genetic data from the SRA. The article that follows describes how GEOME can enable genuinely open data workflows for researchers in the field of molecular ecology.

Genomic data reveal deep genetic structure but no support for current taxonomic designation in a grasshopper species complex.

Taxonomy has traditionally relied on morphological and ecological traits to interpret and classify biological diversity. Over the last decade, technological advances and conceptual developments in the field of molecular ecology and systematics have eased the generation of genomic data and changed the paradigm of biodiversity analysis. Here we illustrate how traditional taxonomy has led to species designations that are supported neither by high throughput sequencing data nor by the quantitative integration of genomic information with other sources of evidence. Specifically, we focus on Omocestus antigai and Omocestus navasi, two montane grasshoppers from the Pyrenean region that were originally described based on quantitative phenotypic differences and distinct habitat associations (alpine vs. Mediterranean-montane habitats). To validate current taxonomic designations, test species boundaries, and understand the factors that have contributed to genetic divergence, we obtained phenotypic (geometric morphometrics) and genome-wide SNP data (ddRADSeq) from populations covering the entire known distribution of the two taxa. Coalescent-based phylogenetic reconstructions, integrative Bayesian model-based species delimitation, and landscape genetic analyses revealed that populations assigned to the two taxa show a spatial distribution of genetic variation that do not match with current taxonomic designations and is incompatible with ecological/environmental speciation. Our results support little phenotypic variation among populations and a marked genetic structure that is mostly explained by geographic distances and limited population connectivity across the abrupt landscapes characterizing the study region. Overall, this study highlights the importance of integrative approaches to identify taxonomic units and elucidate the evolutionary history of species.

MIPE: A metagenome-based community structure explorer and SSU primer evaluation tool.

An understanding of microbial community structure is an important issue in the field of molecular ecology. The traditional molecular method involves amplification of small subunit ribosomal RNA (SSU rRNA) genes by polymerase chain reaction (PCR). However, PCR-based amplicon approaches are affected by primer bias and chimeras. With the development of high-throughput sequencing technology, unbiased SSU rRNA gene sequences can be mined from shotgun sequencing-based metagenomic or metatranscriptomic datasets to obtain a reflection of the microbial community structure in specific types of environment and to evaluate SSU primers. However, the use of short reads obtained through next-generation sequencing for primer evaluation has not been well resolved. The software MIPE (MIcrobiota metagenome Primer Explorer) was developed to adapt numerous short reads from metagenomes and metatranscriptomes. Using metagenomic or metatranscriptomic datasets as input, MIPE extracts and aligns rRNA to reveal detailed information on microbial composition and evaluate SSU rRNA primers. A mock dataset, a real Metagenomics Rapid Annotation using Subsystem Technology (MG-RAST) test dataset, two PrimerProspector test datasets and a real metatranscriptomic dataset were used to validate MIPE. The software calls Mothur (v1.33.3) and the SILVA database (v119) for the alignment and classification of rRNA genes from a metagenome or metatranscriptome. MIPE can effectively extract shotgun rRNA reads from a metagenome or metatranscriptome and is capable of classifying these sequences and exhibiting sensitivity to different SSU rRNA PCR primers. Therefore, MIPE can be used to guide primer design for specific environmental samples.

RAD sequencing resolves fine-scale population structure in a benthic invertebrate: implications for understanding phenotypic plasticity.

The field of molecular ecology is transitioning from the use of small panels of classical genetic markers such as microsatellites to much larger panels of single nucleotide polymorphisms (SNPs) generated by approaches like RAD sequencing. However, few empirical studies have directly compared the ability of these methods to resolve population structure. This could have implications for understanding phenotypic plasticity, as many previous studies of natural populations may have lacked the power to detect genetic differences, especially over micro-geographic scales. We therefore compared the ability of microsatellites and RAD sequencing to resolve fine-scale population structure in a commercially important benthic invertebrate by genotyping great scallops (Pecten maximus) from nine populations around Northern Ireland at 13 microsatellites and 10 539 SNPs. The shells were then subjected to morphometric and colour analysis in order to compare patterns of phenotypic and genetic variation. We found that RAD sequencing was superior at resolving population structure, yielding higher Fst values and support for two distinct genetic clusters, whereas only one cluster could be detected in a Bayesian analysis of the microsatellite dataset. Furthermore, appreciable phenotypic variation was observed in size-independent shell shape and coloration, including among localities that could not be distinguished from one another genetically, providing support for the notion that these traits are phenotypically plastic. Taken together, our results suggest that RAD sequencing is a powerful approach for studying population structure and phenotypic plasticity in natural populations.

Construction of Multilevel Structure for Avian Influenza Virus System Based on Granular Computing.

Exploring the genetic structure of influenza viruses attracts the attention in the field of molecular ecology and medical genetics, whose epidemics cause morbidity and mortality worldwide. The rapid variations in RNA strand and changes of protein structure of the virus result in low-accuracy subtyping identification and make it difficult to develop effective drugs and vaccine. This paper constructs the evolutionary structure of avian influenza virus system considering both hemagglutinin and neuraminidase protein fragments. An optimization model was established to determine the rational granularity of the virus system for exploring the intrinsic relationship among the subtypes based on the fuzzy hierarchical evaluation index. Thus, an algorithm was presented to extract the rational structure. Furthermore, to reduce the systematic and computational complexity, the granular signatures of virus system were identified based on the coarse-grained idea and then its performance was evaluated through a designed classifier. The results showed that the obtained virus signatures could approximate and reflect the whole avian influenza virus system, indicating that the proposed method could identify the effective virus signatures. Once a new molecular virus is detected, it is efficient to identify the homologous virus hierarchically.

Epigenetic variation among natural populations of the South African sandhopper Talorchestia capensis

Ecological epigenetics is gaining importance within the field of Molecular Ecology, because of its novel evolutionary implications. Linking population ecology to the variation in epigenetic profiles can help explain the effect of environmental conditions on phenotypic differences among populations. While epigenetic changes have largely been investigated through the examination of DNA methylation under laboratory conditions, there is a limited understanding of the extent of DNA methylation variation in wild populations. Assuming that epigenetic variation is important in nature, the conditions experienced by different conspecific populations should result in levels of DNA methylation that are independent of their genetic differentiation. To test this, we investigated levels of DNA methylation among populations of the sandhopper Talorchestia capensis that show phenotypic (physiological) differences in their response to environmental conditions, at the same time evaluating their genetic relationships. Given the high levels of inter-individual physiological variation observed within populations, we further hypothesised that inter-individual differences in methylation would be high. Levels of genetic and epigenetic variation were assessed within and among populations from five localities using the methylation sensitive amplified polymorphism technique. Population differentiation was higher for epigenetics than genetics, with no clear geographical pattern or any relation to biogeography. Likewise, individuals showed greater variability in their epigenetic than their genetic profiles. Four out of five populations showed significant negative relationships between epigenetic and genetic diversity. These results show uncoupling between epigenetic and genetic variation and suggest that: (1) epigenetics are more responsive to local, site-specific environmental conditions than genetics and (2) individual differences in epigenetic profiles drive phenotypic variation within (and most likely among) natural populations. Within populations, epigenetics could offer a level of phenotypic flexibility beyond genetic constraint that allows rapid responses to variable or unpredictable environments, potentially compensating for low genetic variability.

An ecological model organism flies into the genomics era.

Despite the very rapid 'genomicization' of the field of Molecular Ecology in recent years, there have been relatively few annotated whole-genome assemblies of nonmodel organisms published. Instead, molecular ecologists have more frequently utilized next-generation sequencing technologies to develop genome-wide markers or to generate transcriptome data. Whole-genome assemblies are more expensive and require considerable computational resources and bioinformatic expertise. However, the availability of an annotated genome offers exciting opportunities to address fundamental questions in ecology and evolution that are difficult to address with moderate sets of markers or by transcriptome sequencing. Such questions include elucidating the roles of natural and sexual selection in shaping diversity, determining the roles of regulatory and protein-coding change in the evolution of traits, and determining the genomic architecture of sex-specific trait variation. Arguably, these questions are most tractable--and most interesting--in well-characterized species for which there is already some knowledge of natural and sexual selection, and of the traits that are most likely to link to fitness. In this issue, Mueller et al. (2016) present the assembly and annotation of the genome of the blue tit (Cyanistes caeruleus), a model ecological species. In addition, by sequencing the transcriptome of male and female blue tits, the authors identify and annotate sex-biased gene expression and conclude that noncoding RNA genes are likely to play a significant role in sex-biased expression. By making their assembly and annotation publically available and accessible via a genome browser, Mueller et al. (2016) offer exciting possibilities for further research into the genomic basis of adaptation, and investigation of the roles of natural and sexual selection, in this well-studied ecological model species.

Application of AFLP markers in fishery and seafood

Several sociological, health and conservation arguments request acorrect labelling of seafood products and fish species. Nowadays, moleculargenetics is a useful tool for food chain traceability, particularly in regardsto species identification. Among the variety of PCRbased molecular markers,AFLPs (Amplified Fragment Length Polymorphisms) have recently been used toinvestigate genomes of different complexities. This paper assesses thepotential use of the AFLP technology to determine fish and seafood species inprocessed commercial products, domestic stocks and research in the field ofmolecular ecology. In particular a species database of fish, molluscs andcrustaceans has been created with the aim to identify species of origin ofseafood products by previously defined AFLP patterns. Researchers in the fieldof molecular ecology and evolution require versatile and low-cost genetictyping methods. The AFLP method was introduced 20 years ago and shows manyfeatures that fulfil these requirements. With good quality genomic DNA at hand,it is relatively easy to generate anonymous multilocus DNA profiles in mostspecies and the start-up time before data can be generated is often less than aweek. These aspects include classical problems such as studies of populationgenetic structure and phylogenetic reconstructions, and also new challengessuch as finding markers for genes governing adaptations in wild populations andmodifications of the protocol that makes it possible to measure expressionvariation of multiple genes (cDNA-AFLP) and the distribution of DNAmethylation. We hope this review will help molecular ecologists to identifywhen AFLP is likely to be superior to other more established methods, such asmicrosatellites, SNP (single nucleotide polymorphism) analyses and multigeneDNA sequencing.

Common misconceptions in molecular ecology: echoes of the modern synthesis

The field of molecular ecology has burgeoned into a large discipline spurred on by technical innovations that facilitate the rapid acquisition of large amounts of genotypic data, by the continuing development of theory to interpret results, and by the availability of computer programs to analyse data sets. As the discipline grows, however, misconceptions have become enshrined in the literature and are perpetuated by routine citations to other articles in molecular ecology. These misconceptions hamper a better understanding of the processes that influence genetic variation in natural populations and sometimes lead to erroneous conclusions. Here, we consider eight misconceptions commonly appearing in the literature: (i) some molecular markers are inherently better than other markers; (ii) mtDNA produces higher F(ST) values than nDNA; (iii) estimated population coalescences are real; (iv) more data are always better; (v) one needs to do a Bayesian analysis; (vi) selective sweeps influence mtDNA data; (vii) equilibrium conditions are critical for estimating population parameters; and (viii) having better technology makes us smarter than our predecessors. This is clearly not an exhaustive list and many others can be added. It is, however, sufficient to illustrate why we all need to be more critical of our own understanding of molecular ecology and to be suspicious of self-evident truths.

Towards a taxonomy ofBacteriaandArchaeabased on interactive and cumulative data repositories

Taxonomy in the second decade of the 21st century is benefiting from technological advances in molecular microbiology, especially those related to genomics. Gene and genome databases are significantly increasing due to intense research activities in the field of molecular ecology and genomics. Taxa, and especially species, are tailored by means of the recognition of a phylogenetic, genomic and phenotypic coherence that reveal their uniqueness in the classification schema. Phylogenetic coherence is mainly revealed by means of 16S rRNA gene analyses for which curated databases such as EzTaxon and LTP provide a valuable tool for tree reconstruction to taxonomy users. On the other hand, in silico full or partial genomic sequence comparisons are called on to substitute cumbersome techniques such as DNA-DNA hybridization (DDH) to genomically circumscribe species. DDH similarity values around 70% would be equivalent to ANI values of 96%. Finally, finding an exclusive phenotypic property for the taxa to be classified is of paramount relevance to producing an operative and predictive classification system. The current methods used for taxonomic classification require significant laboratory experimentation, and generally will not produce interactive databases. The new high-throughput metabolomic technologies, such as ICR-FT and MALDI-TOF mass spectrometry methods, open the door to the construction of metabolic databases for taxonomic purposes. It is to be foreseen that, in the future, taxonomists will benefit significantly from public databases speeding up the classification process. However, serious effort will be needed to harmonize them and to prevent inaccurate material.

Detecting unknown sequences with DNA microarrays: explorative probe design strategies

Designing environmental DNA microarrays that can be used to survey the extreme diversity of microorganisms existing in nature, represents a stimulating challenge in the field of molecular ecology. Indeed, recent efforts in metagenomics have produced a substantial amount of sequence information from various ecosystems, and will continue to accumulate large amounts of sequence data given the qualitative and quantitative improvements in the next-generation sequencing methods. It is now possible to take advantage of these data to develop comprehensive microarrays by using explorative probe design strategies. Such strategies anticipate genetic variations and thus are able to detect known and unknown sequences in environmental samples. In this review, we provide a detailed overview of the probe design strategies currently available to construct both phylogenetic and functional DNA microarrays, with emphasis on those permitting the selection of such explorative probes. Furthermore, exploration of complex environments requires particular attention on probe sensitivity and specificity criteria. Finally, these innovative probe design approaches require exploiting newly available high-density microarray formats.

Applications and implications of neutral versus non-neutral markers in molecular ecology.

The field of molecular ecology has expanded enormously in the past two decades, largely because of the growing ease with which neutral molecular genetic data can be obtained from virtually any taxonomic group. However, there is also a growing awareness that neutral molecular data can provide only partial insight into parameters such as genetic diversity, local adaptation, evolutionary potential, effective population size, and taxonomic designations. Here we review some of the applications of neutral versus adaptive markers in molecular ecology, discuss some of the advantages that can be obtained by supplementing studies of molecular ecology with data from non-neutral molecular markers, and summarize new methods that are enabling researchers to generate data from genes that are under selection.

Terry Burke - recipient of the 2009Molecular EcologyPrize

Terry Burke - recipient of the 2009<i>Molecular Ecology</i>Prize

Ten years of AFLP in ecology and evolution: why so few animals?

Researchers in the field of molecular ecology and evolution require versatile and low-cost genetic typing methods. The AFLP (amplified fragment length polymorphism) method was introduced 10 years ago and shows many features that fulfil these requirements. With good quality genomic DNA at hand, it is relatively easy to generate anonymous multilocus DNA profiles in most species and the start-up time before data can be generated is often less than a week. Built-in dynamic, yet simple modifications make it possible to find a protocol suitable to the genome size of the species and to screen thousands of loci in hundreds of individuals for a relatively low cost. Until now, the method has primarily been applied in studies of plants, bacteria and fungi, with a strong bias towards economically important cultivated species and their pests. In this review we identify a number of research areas in the study of wild species of animals where the AFLP method, presently very much underused, should be a very valuable tool. These aspects include classical problems such as studies of population genetic structure and phylogenetic reconstructions, and also new challenges such as finding markers for genes governing adaptations in wild populations and modifications of the protocol that makes it possible to measure expression variation of multiple genes (cDNA-AFLP) and the distribution of DNA methylation. We hope this review will help molecular ecologists to identify when AFLP is likely to be superior to other more established methods, such as microsatellites, SNP (single nucleotide polymorphism) analyses and multigene DNA sequencing.

The evolutionary ecology of myco‐heterotrophy

Nonphotosynthetic mycorrhizal plants have long attracted the curiosity of botanists and mycologists, and they have been a target for unabated controversy and speculation. In fact, these puzzling plants dominated the very beginnings of the field of mycorrhizal biology. However, only recently has the mycorrhizal biology of this diverse group of plants begun to be systematically unravelled, largely following a landmark Tansley review a decade ago and crucial developments in the field of molecular ecology. Here I explore our knowledge of these evolutionarily and ecologically diverse plant-fungal symbioses, highlighting areas where there has been significant progress. The focus is on what is arguably the best understood example, the monotropoid mycorrhizal symbiosis, and the overarching goal is to lay out the questions that remain to be answered about the biology of myco-heterotrophy and epiparasitism.