Molecular Ecology and Systematics of Blue Mussels (Genus Mytilus) (Mytilidae; Bivalvia; Mollusca) in the Southern Hemisphere

<p>The Mytilus edulis species complex, comprised of M. edulis, M. galloprovincialis and M. trossulus, is antitropically distributed in temperate coastal regions of all oceans and main seas of the world. This genus has been heavily studied in the Northern hemisphere but Southern hemisphere populations have received much less attention. This thesis aims to place Southern hemisphere blue mussels into global evolutionary relationships among Mytilus species and investigate aspects of their molecular ecology, including, effects of non-native Northern hemisphere species introductions, biogeography across the Southern hemisphere, regional phylogeographic patterns and population genetics within New Zealand. Southern hemisphere blue mussel phylogenetic reconstruction resulted in the detection of a monophyletic M. galloprovincialis lineage. Two new molecular markers developed with specificity for this lineage and congruence among phylogenetic investigations indicates a panhemispheric distribution of this M. galloprovincialis lineage with implications for naming a new sibling species of the M. edulis complex. This proposed new species, M. meridianus, is distributed in South America, the Kerguelen Islands, New Zealand and Australia at latitudes between ~ 30°S and ~ 55°S. Non-native M. galloprovincialis introduced from the Northern hemisphere have been present in NZ, Australia and Chile for at least ten years and hybridise with native blue mussels. Introgression is observed in New Zealand and Australian but not Chilean hybrid regions. The limited number of introduced mussels in Australia induces hybrid swamping of non-native alleles but an interlineage gender bias towards non-native maternal parents may result in eventual loss of the unique genomic content of native blue mussels in NZ. Southern hemisphere blue mussels form a monophyletic sister clade to a haplogroup shared by Northern hemisphere M. edulis and M. galloprovincialis. Although single gene histories are not congruent with respect to evolutionary relationships within the Northern hemisphere due to introgressive hybridisation after speciation, it is clear that Southern hemisphere blue mussels arose from a species native to the northeast Atlantic Ocean after speciation of the three ‘M. edulis complex’ members. Within the Southern hemisphere monophyletic clade lies three reciprocally monophyletic clades restricted to the geographic regions South America/Kerguelen Islands, New Zealand and Australia. Phylogeographic analysis indicates past gene flow between South American/Kerguelen Islands and New Zealand populations that has ceased at present day and ongoing gene flow between South America and the Kerguelen Islands likely via the West Wind Drift. Within NZ, population subdivision inferred from mtDNA indicates genetic variation is distributed within an east-west phylogeographic split on the North Island. These populations experienced gene flow in the past that has ceased at present day. Microsatellite allele frequencies indicate a different population subdivision within the northwest North Island that has been narrowed down to a 15 km stretch of coastline in a sheltered bay. The abrupt discontinuity within a small geographic area does not conform to classic population subdivision in this broad-cast spawning species, therefore, further investigation into the genomic content of northwest North Island mussels with respect to introgressed non-native genes is warranted. Resolving complex phylogenetic patterns from interspecific introgression is key to understanding the evolutionary history of Southern hemisphere M. galloprovincialis. Further characterisation of hybrid introgression would increase accuracy of (1) inferences of processes contributing to hybridisation dynamics and (2) population subdivision in NZ. Probing the basis for variation of hybridisation dynamics would help to predict the outcomes of Northern hemisphere M. galloprovincialis introductions in other areas of the world.</p>

Molecular Ecology and Systematics of Blue Mussels (Genus Mytilus) (Mytilidae; Bivalvia; Mollusca) in the Southern Hemisphere

<p>The Mytilus edulis species complex, comprised of M. edulis, M. galloprovincialis and M. trossulus, is antitropically distributed in temperate coastal regions of all oceans and main seas of the world. This genus has been heavily studied in the Northern hemisphere but Southern hemisphere populations have received much less attention. This thesis aims to place Southern hemisphere blue mussels into global evolutionary relationships among Mytilus species and investigate aspects of their molecular ecology, including, effects of non-native Northern hemisphere species introductions, biogeography across the Southern hemisphere, regional phylogeographic patterns and population genetics within New Zealand. Southern hemisphere blue mussel phylogenetic reconstruction resulted in the detection of a monophyletic M. galloprovincialis lineage. Two new molecular markers developed with specificity for this lineage and congruence among phylogenetic investigations indicates a panhemispheric distribution of this M. galloprovincialis lineage with implications for naming a new sibling species of the M. edulis complex. This proposed new species, M. meridianus, is distributed in South America, the Kerguelen Islands, New Zealand and Australia at latitudes between ~ 30°S and ~ 55°S. Non-native M. galloprovincialis introduced from the Northern hemisphere have been present in NZ, Australia and Chile for at least ten years and hybridise with native blue mussels. Introgression is observed in New Zealand and Australian but not Chilean hybrid regions. The limited number of introduced mussels in Australia induces hybrid swamping of non-native alleles but an interlineage gender bias towards non-native maternal parents may result in eventual loss of the unique genomic content of native blue mussels in NZ. Southern hemisphere blue mussels form a monophyletic sister clade to a haplogroup shared by Northern hemisphere M. edulis and M. galloprovincialis. Although single gene histories are not congruent with respect to evolutionary relationships within the Northern hemisphere due to introgressive hybridisation after speciation, it is clear that Southern hemisphere blue mussels arose from a species native to the northeast Atlantic Ocean after speciation of the three ‘M. edulis complex’ members. Within the Southern hemisphere monophyletic clade lies three reciprocally monophyletic clades restricted to the geographic regions South America/Kerguelen Islands, New Zealand and Australia. Phylogeographic analysis indicates past gene flow between South American/Kerguelen Islands and New Zealand populations that has ceased at present day and ongoing gene flow between South America and the Kerguelen Islands likely via the West Wind Drift. Within NZ, population subdivision inferred from mtDNA indicates genetic variation is distributed within an east-west phylogeographic split on the North Island. These populations experienced gene flow in the past that has ceased at present day. Microsatellite allele frequencies indicate a different population subdivision within the northwest North Island that has been narrowed down to a 15 km stretch of coastline in a sheltered bay. The abrupt discontinuity within a small geographic area does not conform to classic population subdivision in this broad-cast spawning species, therefore, further investigation into the genomic content of northwest North Island mussels with respect to introgressed non-native genes is warranted. Resolving complex phylogenetic patterns from interspecific introgression is key to understanding the evolutionary history of Southern hemisphere M. galloprovincialis. Further characterisation of hybrid introgression would increase accuracy of (1) inferences of processes contributing to hybridisation dynamics and (2) population subdivision in NZ. Probing the basis for variation of hybridisation dynamics would help to predict the outcomes of Northern hemisphere M. galloprovincialis introductions in other areas of the world.</p>

Ichthyoplankton DNA metabarcoding: challenges and perspectives

DNA metabarcoding has been widely used to access and monitor species. However, several challenges remain open for its mainstream application in ecological studies, particularly when dealing with a quantitative approach. In a from the Cover article in this issue of Molecular Ecology, Cédric et al. (2021) report species-level ichthyoplankton dynamics for 97 fish species from two Amazon river basins using a clever quantitative metabarcoding approach employing a probe capture method. They clearly show that most species spawned during the rainy season when the floods started, but interestingly, species from the same genus reproduced in distinct periods (i.e., inverse phenology). Opportunistically, Cédric et al. (2021) reported that during an intense hydrological anomaly, several species had a sharp reduction in spawning activity, demonstrating a quick response to environmental cues. This is an interesting result since the speed at which fish species can react to environmental changes, during the spawning period, is largely unknown. Thus, this study brings remarkable insights into basic life history information that is imperative for proposing strategies that could lead to a realistic framework for sustainable fisheries management practices and conservation, fundamental for an under-studied and threatened realm, such as the Amazon River basin.

A lizard with two tales: what diversification within Sceloporus occidentalis teaches us about species formation

In 1859, Charles Darwin proposed that species are not fundamentally different from subspecies or the varieties from which they evolve. A century later, Dobzhansky (1958) suggested that many such lineages are ephemeral and are likely to revert differentiation through introgression (Fig. 1A); only a few evolve complete reproductive isolation and persist in sympatry. In this issue of Molecular Ecology, Bouzid et al. (2021) show how new analytical methods, when applied to genome data, allow us to more precisely determine whether or not species formation follows the paths outlined by Darwin and Dobzhansky (Fig. 1B). The authors study the diversification of the lizard Sceloporus occidentalis, finding a continuum of genetic interactions between the preservation of genetic identity to genetic merger, analogous to what is exemplified by ring species. In doing so, they teach us two tales on species formation: that lineages are fractal byproducts of evolutionary processes such as genetic drift and selection, and that lineages are often ephemeral and do not always progress into species. Studying ephemeral lineages like those in S. occidentalis allows us to capture divergence at its earliest stages, and potentially to determine the factors that allow lineages to remain distinct despite pervasive gene flow. These lineages thus serve as a natural laboratory to address long standing hypotheses on species formation.

Genetic redundancy resolves invasion paradox in Colorado potato beetle

The paradox of how invasive species cope with novel selective pressures with limited genetic variation is a fundamental question in molecular ecology. Several mechanisms have been proposed, but they can lack generality and predictive power. Here, we introduce an alternative mechanism, genetic redundancy, wherein changes in multiple combinations of loci can achieve a fitness optimum for polygenic traits, and thus the variations left after the founder effect may be sufficient for adaptation. We tested the potential importance of genetic redundancy in environmental adaptation of Colorado potato beetle (CPB) in introduced Eurasia. Population genomic analyses showed substantial genetic depletion following a single introduction event, which supports invasive CPB as a classic system for the paradox study. Genome-environment association analyses revealed a suite of loci and gene functions plausibly related to cold stress. Notably, a substantial portion of loci showed different contributions to similar or identical environments. Such non-parallel evolution indicates their potential redundancy to overall fitness. Furthermore, one important adaptive gene function, “phospholipid production”, was represented by more than one independent linkage cluster, suggesting some gene functional redundancy in cold resistance. Taken together, these results support the hypothesis that genetic redundancy can promote the adaptability of polygenic traits despite strong genetic depletion, thus providing a general mechanism for resolving the genetic paradox of invasion. More broadly, genetic redundancy, as an inherent feature of the genome, may have contributed to the evolutionary success of invasive species in many aspects.

Advancing Genetic Methods in the Study of Parrot Biology and Conservation

Parrots (Psittaciformes) are a well-studied, diverse group of birds distributed mainly in tropical and subtropical regions. Today, one-third of their species face extinction, mainly due to anthropogenic threats. Emerging tools in genetics have made major contributions to understanding basic and applied aspects of parrot biology in the wild and in captivity. In this review, we show how genetic methods have transformed the study of parrots by summarising important milestones in the advances of genetics and their implementations in research on parrots. We describe how genetics helped to further knowledge in specific research fields with a wide array of examples from the literature that address the conservation significance of (1) deeper phylogeny and historical biogeography; (2) species- and genus-level systematics and taxonomy; (3) conservation genetics and genomics; (4) behavioural ecology; (5) molecular ecology and landscape genetics; and (6) museomics and historical DNA. Finally, we highlight knowledge gaps to inform future genomic research on parrots. Our review shows that the application of genetic techniques to the study of parrot biology has far-reaching implications for addressing diverse research aims in a highly threatened and charismatic clade of birds.

A magnet to draw a bright needle out from the haystack -- RADOrgMiner, an automated pipeline to genotype organellar reads from RADseq data

Different versions of Restriction-site Associated DNA sequencing (RADseq) have become powerful and popular tools in molecular ecology. Although RADseq datasets are regarded as representative of the nuclear genome, reduced representation genomic libraries may also sample the organellar (mitochondrial and, in case of plants, plastid) DNA. Extraction of organellar loci from RADseq data can provide additional insights into the phylogenetics of the study group which comes at no additional sequencing effort. Cytoplasmic genetic variance can help better understand the evolutionary history by uncovering past hybridization and identifying the maternal (or, rarely, the paternal) lineage due to rapid lineage sorting. We developed a pipeline in bash that is based on existing bioinformatic tools to automatically mine and genotype organellar loci contained RADseq libraries. The utility of our pipeline is tested on eight, publicly available datasets spanning different phylogenetic levels (i.e. from family-level phylogenies to phylogeography) and RADseq methods (sdRAD, ddRAD, ezRAD, GBS) for genotyping both mitochondrial and plastid loci, which were subject to phylogenetic tree reconstruction. In all cases, organellar phylogenies adequately supplemented the original studies either by corroborating the large-scale picture based on RADseq or by bringing additional evidence on past or contemporary hybridization. RADseq methods designed to achieve a larger horizontal coverage (i.e. ddRAD, ezRAD) evidently yielded longer organellar alignments, but sdRAD and GBS still provided useful polymorphic loci found in the cytoplasmic DNA. Our newly developed pipeline for the above purpose can be run under a Unix-line operating system and is freely accessible at https://github.com/laczkol/RADOrgMiner