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Although allelic variation is ubiquitous in natural populations, our theoretical models are poor at predicting the existence and properties of these observed polymorphisms. In this study, inspired by Van Valen's Red Queen hypothesis, we modeled the effect of viability selection in a deteriorating environment on the properties of allelic variation in populations subject to recurrent mutation. In Monte Carlo simulations, we found that levels of polymorphism consistently built up over time. We censused the simulated populations after 10,000 generations of mutation and selection, revealing that, compared with models assuming a constant environment, the mean number of alleles was greater, as was the range of allele numbers. These results were qualitatively robust to the addition of genetic drift and to the relaxation of the assumption that the viabilities of phenogenotypes containing a new mutation are independent of each other (i.e. incorporating a model of generalized dominance). The broad range of allele numbers realized in the simulated populations-from monomorphisms to highly polymorphic populations-more closely corresponds to the observed range from numerous surveys of natural populations than previously found in theoretical studies. This match suggests that, contrary to the views of some writers, selection may actively maintain genetic variation in natural populations, particularly if the selective environment is gradually becoming harsher. Our simulations also generated many populations with heterozygote advantage, a mismatch with real data that implies that this selective property must arise extremely rarely in natural populations., Competing Interests: Conflicts of interest The author(s) declare no conflicts of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)

Background: The Australian black swan (Cygnus atratus) is an iconic species with contrasting plumage to that of the closely related northern hemisphere white swans. The relative geographic isolation of the black swan may have resulted in a limited immune repertoire and increased susceptibility to infectious diseases, notably infectious diseases from which Australia has been largely shielded. Unlike mallard ducks and the mute swan (Cygnus olor), the black swan is extremely sensitive to highly pathogenic avian influenza. Understanding this susceptibility has been impaired by the absence of any available swan genome and transcriptome information., Results: Here, we generate the first chromosome-length black and mute swan genomes annotated with transcriptome data, all using long-read based pipelines generated for vertebrate species. We use these genomes and transcriptomes to show that unlike other wild waterfowl, black swans lack an expanded immune gene repertoire, lack a key viral pattern-recognition receptor in endothelial cells and mount a poorly controlled inflammatory response to highly pathogenic avian influenza. We also implicate genetic differences in SLC45A2 gene in the iconic plumage of the black swan., Conclusion: Together, these data suggest that the immune system of the black swan is such that should any avian viral infection become established in its native habitat, the black swan would be in a significant peril., (© 2023. The Author(s).)

Natural history collections worldwide contain a plethora of mollusc shells. Recent studies have detailed the sequencing of DNA extracted from shells up to thousands of years old and from various taphonomic and preservational contexts. However, previous approaches have largely addressed methodological rather than evolutionary research questions. Here, we report the generation of DNA sequence data from mollusc shells using such techniques, applied to Haliotis virginea Gmelin, 1791, a New Zealand abalone, in which morphological variation has led to the recognition of several forms and subspecies. We successfully recovered near-complete mitogenomes from 22 specimens including 12 dry-preserved shells up to 60 years old. We used a combination of palaeogenetic techniques that have not previously been applied to shell, including DNA extraction optimized for ultra-short fragments and hybridization-capture of single-stranded DNA libraries. Phylogenetic analyses revealed three major, well-supported clades comprising samples from: (1) The Three Kings Islands; (2) the Auckland, Chatham and Antipodes Islands; and (3) mainland New Zealand and Campbell Island. This phylogeographic structure does not correspond to the currently recognized forms. Critically, our nonreliance on freshly collected or ethanol-preserved samples enabled inclusion of topotypes of all recognized subspecies as well as additional difficult-to-sample populations. Broader application of these comparatively cost-effective and reliable methods to modern, historical, archaeological and palaeontological shell samples has the potential to revolutionize invertebrate genetic research., (© 2022 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.)

An endolithic lifestyle in mineralized substrates has evolved multiple times in various phyla including Bryozoa. The family Penetrantiidae includes one genus with ten extant and two fossil species. They predominantly colonize the shells of molluscs and establish colonies by chemical dissolution of calcium carbonate. Based on several morphological characters, they were described to be either cheilostome or ctenostome bryozoans. For more than 40 years, neither the characters of species identity and systematics nor the problem of their phylogeny was approached. Consequently, the aim of this study is to reevaluate species identities and the systematic position of the genus Penetrantia by analyzing at least six different species from eight regions with the aid of modern methods such as confocal laser scanning microscopy and 3D-reconstruction techniques. This study demonstrates that the musculature associated with the operculum and brood chamber shows significant differences from the cheilostome counterparts and seems to have evolved independently. Together with the presence of other ctenostome-like features such as true polymorphic stolons and uncalcified body wall, this finding supports a ctenostome affinity. Operculum morphology reveals many new species-specific characters, which, together with information about gonozooid morphology, tentacle number, and zooid size ranges, will enhance species identification. It also revealed a probable new species in Japan as well as potential cryptic species in France and New Zealand. In addition, this study increases the known distribution range of the family and its substrate diversity. Altogether, the new information collated here provides the basis for future work on a neglected taxon., Supplementary Information: The online version contains supplementary material available at 10.1007/s13127-023-00612-z., Competing Interests: Conflict of interestThe authors declare no competing interests., (© The Author(s) 2023.)

Littorinid snails are present in most coastal areas globally, playing a significant role in the ecology of intertidal communities. Laevilitorina is a marine gastropod genus distributed exclusively in the Southern Hemisphere, with 21 species reported from South America, the sub-Antarctic islands, Antarctica, New Zealand, Australia and Tasmania. Here, an updated database of 21 species generated from a combination of sources is presented: 1) new field sampling data; 2) published records; 3) the Global Biodiversity Information Facility (GBIF) and The Atlas of Living Australia (ALA), to provide a comprehensive description of the known geographic distribution of the genus and detailed occurrences for each of the 21 species. The database includes 813 records (occurrences), 53 from field sampling, 174 from the literature, 128 from GBIF, and 458 from ALA. West Antarctica had the highest species richness (8 species), followed by sub-Antarctic islands of New Zealand (4 species) and the south-east shelf of Australia (4 species). The provinces of Magellan, New Zealand South Island, and sub-Antarctic Islands of the Indian Ocean include two species each. This study specifically highlights reports of L.pygmaea and L.venusta , species that have been almost unrecorded since their description. Recent advances in molecular studies of L.caliginosa showed that this species does not correspond to a widely distributed taxon, but to multiple divergent lineages distributed throughout the Southern Ocean. Ongoing molecular and taxonomic studies are necessary for a better understanding of the diversity and biogeography of this genus., (Sebastián Rosenfeld, Claudia S. Maturana, Hamish G. Spencer, Peter Convey, Thomas Saucède, Paul Brickle, Francisco Bahamonde, Quentin Jossart, Elie Poulin, Claudio Gonzalez-Wevar.)

Speciation is less likely to occur when there is gene flow between nascent species. Natural selection can oppose gene flow and promote speciation if there is variation in ecological conditions among the nascent species' locations. Previous theory on ecological speciation with gene flow has focused primarily on the role of genetic variation in ecological traits, largely neglecting the role of nongenetic inheritance or transgenerational plasticity. Here, we build and analyze models incorporating both genetic and epigenetic inheritance, the latter representing a form of nongenetic inheritance. We investigate the rate of speciation for a population that inhabits two patches connected by migration, and find that adaptively biased epigenetic induction can speed up or slow down speciation, depending on the form of the map from genotype and epigenotype to phenotype. While adaptively relevant epigenetic variation can speed up speciation by reducing the fitness of migrants and hybrids, it can also slow down speciation. This latter effect occurs when the epialleles are able to achieve adaptation faster than the genetic alleles, thereby weakening selection on the latter., (© 2022 The Authors. Evolution published by Wiley Periodicals LLC on behalf of The Society for the Study of Evolution.)

Predictive adaptive responses (PARs) are a form of developmental plasticity in which the developmental response to an environmental cue experienced early in life is delayed and yet, at the same time, the induced phenotype anticipates (i.e., is completely developed before) exposure to the eventual environmental state predicted by the cue, in which the phenotype is adaptive. We model this sequence of events to discover, under various assumptions concerning the cost of development, what lengths of delay, developmental time, and anticipation are optimal. We find that in many scenarios modeled, development of the induced phenotype should be completed at the exact same time that the environmental exposure relevant to the induced phenotype begins: that is, in contrast to our observed cases of PARs, there should be no anticipation. Moreover, unless slow development is costly, development should commence immediately after the cue: there should be no delay. Thus, PARs, which normally have non-zero delays and/or anticipation, are highly unusual. Importantly, the exceptions to these predictions of zero delays and anticipation occurred when developmental time was fixed and delaying development was increasingly costly. We suggest, therefore, that PARs will only evolve under three kinds of circumstances: (i) there are strong timing constraints on the cue and the environmental status, (ii) delaying development is costly, and development time is either fixed or slow development is costly, or (iii) when the period between the cue and the eventual environmental change is variable and the cost of not completing development before the change is high. These predictions are empirically testable.

Rapid environmental changes are putting numerous species at risk of extinction. For migration-limited species, persistence depends on either phenotypic plasticity or evolutionary adaptation (evolutionary rescue). Current theory on evolutionary rescue typically assumes linear environmental change. Yet accelerating environmental change may pose a bigger threat. Here, we present a model of a species encountering an environment with accelerating or decelerating change, to which it can adapt through evolution or phenotypic plasticity (within-generational or transgenerational). We show that unless either form of plasticity is sufficiently strong or adaptive genetic variation is sufficiently plentiful, accelerating or decelerating environmental change increases extinction risk compared to linear environmental change for the same mean rate of environmental change.

The Hill-Robertson effect describes how, in a finite panmictic diploid population, selection at one diallelic locus reduces the fixation probability of a selectively favoured allele at a second, linked diallelic locus. Here we investigate the influence of population structure on the Hill-Robertson effect in a population of size N . We model population structure as a network by assuming that individuals occupy nodes on a graph connected by edges that link members who can reproduce with each other. Three regular networks (fully connected, ring and torus), two forms of scale-free network and a star are examined. We find that (i) the effect of population structure on the probability of fixation of the favourable allele is invariant for regular structures, but on some scale-free networks and a star, this probability is greatly reduced; (ii) compared to a panmictic population, the mean time to fixation of the favoured allele is much greater on a ring, torus and linear scale-free network, but much less on power-2 scale-free and star networks; (iii) the likelihood with which each of the four possible haplotypes eventually fix is similar across regular networks, but scale-free populations and the star are consistently less likely and much faster to fix the optimal haplotype; (iv) increasing recombination increases the likelihood of fixing the favoured haplotype across all structures, whereas the time to fixation of that haplotype usually increased, and (v) star-like structures were overwhelmingly likely to fix the least fit haplotype and did so significantly more rapidly than other populations. Last, we find that small ( N < 64) panmictic populations do not exhibit the scaling property expected from Hill & Robertson (1966 Genet. Res. 8 , 269-294. (doi:10.1017/S0016672300010156))., (© 2021 The Authors.)

Members of the trochoidean genus Margarella (Calliostomatidae) are broadly distributed across Antarctic and sub-Antarctic ecosystems. Here we used novel mitochondrial and nuclear gene sequences to clarify species boundaries and phylogenetic relationships among seven nominal species distributed on either side of the Antarctic Polar Front (APF). Molecular reconstructions and species-delimitation analyses recognized only four species: M. antarctica (the Antarctic Peninsula), M. achilles (endemic to South Georgia), M. steineni (South Georgia and Crozet Island) and the morphologically variable M. violacea (=M. expansa, M. porcellana and M. pruinosa), with populations in southern South America, the Falkland/Malvinas, Crozet and Kerguelen Islands. Margarella violacea and M. achilles are sister species, closely related to M. steineni, with M. antarctica sister to all these. This taxonomy reflects contrasting biogeographic patterns on either side of the APF in the Southern Ocean. Populations of Margarella north of the APF (M. violacea) showed significant genetic variation but with many shared haplotypes between geographically distant populations. By contrast, populations south of the APF (M. antarctica, M. steineni and M. achilles) exhibited fewer haplotypes and comprised three distinct species, each occurring across a separate geographical range. We hypothesize that the biogeographical differences may be the consequence of the presence north of the APF of buoyant kelps - potential long-distance dispersal vectors for these vetigastropods with benthic-protected development - and their near-absence to the south. Finally, we suggest that the low levels of genetic diversity within higher-latitude Margarella reflect the impact of Quaternary glacial cycles that exterminated local populations during their maxima., (Copyright © 2020 Elsevier Inc. All rights reserved.)

Details are provided on 16 land snail genera, eight freshwater molluscan species, one estuarine species, 47 land snail species and varieties from New Zealand, and a further three land snail species putatively from New Zealand, which were described by Frederick Wollaston Hutton between 1879 and 1904. Original primary type material of 54 species was located during the present study. Lectotypes are designated for: Amphidoxa cornea Hutton, 1882, Amphidoxa jacquenetta Hutton, 1883, Amphidoxa perdita Hutton, 1883, Charopa cassandra Hutton, 1883, Cyclotus charmian Hutton, 1883, Fruticicola adriana Hutton, 1883, Gerontia cordelia Hutton, 1883, Gerontia pantherina Hutton, 1882, Microphysa pumila Hutton, 1882, Patula jessica Hutton, 1883, Patula lucetta Hutton, 1884, Patula sylvia Hutton, 1883, Patula tapirina Hutton, 1882, Pfeifferia cressida Hutton, 1883, Phrixgnathus celia Hutton, 1883, Phrixgnathus haasti Hutton, 1883, Phrixgnathus marginatus Hutton, 1882, Phrixgnathus phrynia Hutton, 1883, Rhytida australis Hutton, 1882, Strobila leiodon Hutton, 1882, Thalassia propinqua Hutton, 1882, Therasia thaisa Hutton, 1883, Therasia valeria Hutton, 1883 and Zonites helmsii Hutton, 1882. A neotype is designated for Rhytida citrina Hutton, 1882. Primary type material of the following taxa is figured herein for the first time: Amphidoxa lavinia Hutton, 1883, Cyclotus charmian Hutton, 1883, Fruticicola adriana Hutton, 1883, Leptopoma pannosa Hutton, 1882, Patula lucetta Hutton, 1884, Patula sylvia Hutton, 1883, Patula tapirina Hutton, 1882, Phacussa helmsi var. maculata Hutton, 1884, Phrixgnathus ariel Hutton, 1883, Phrixgnathus celia Hutton, 1883, Rhytida australis Hutton, 1882, Rissoa vana Hutton, 1873, Testacella vagans Hutton, 1882, Trochomorpha hermia Hutton, 1883 and Zonites helmsii Hutton, 1882. New taxonomic combinations introduced herein include Phacussa lucetta (Hutton, 1884) and Therasia propinqua (Hutton, 1882). Amphidoxa lavinia Hutton, 1883, Charopa cassandra Hutton, 1883, Patula timandra Hutton, 1883 and Trochomorpha hermia Hutton, 1883 are treated as junior synonyms of Tasmaphena sinclairii (Pfeiffer, 1846), Phacussa fulminata (Hutton, 1882), Fectola infecta (Reeve, 1852) and Advena campbellii (Gray, 1834), respectively.

While in recent years environmental DNA (eDNA) metabarcoding surveys have shown great promise as an alternative monitoring method, the integration into existing marine monitoring programs may be confounded by the dispersal of the eDNA signal. Currents and tidal influences could transport eDNA over great distances, inducing false-positive species detection, leading to inaccurate biodiversity assessments and, ultimately, mismanagement of marine environments. In this study, we determined the ability of eDNA metabarcoding surveys to distinguish localized signals obtained from four marine habitats within a small spatial scale (<5 km) subject to significant tidal and along-shore water flow. Our eDNA metabarcoding survey detected 86 genera, within 77 families and across 11 phyla using three established metabarcoding assays targeting fish (16S rRNA gene), crustacean (16S rRNA gene) and eukaryotic (cytochrome oxidase subunit 1) diversity. Ordination and cluster analyses for both taxonomic and OTU data sets show distinct eDNA signals between the sampled habitats, suggesting dispersal of eDNA among habitats was limited. Individual taxa with strong habitat preferences displayed localized eDNA signals in accordance with their respective habitat, whereas taxa known to be less habitat-specific generated more ubiquitous signals. Our data add to evidence that eDNA metabarcoding surveys in marine environments detect a broad range of taxa that are spatially discrete. Our work also highlights that refinement of assay choice is essential to realize the full potential of eDNA metabarcoding surveys in marine biodiversity monitoring programs., (© 2018 John Wiley & Sons Ltd.)

DNA extraction from environmental samples (environmental DNA; eDNA) for metabarcoding-based biodiversity studies is gaining popularity as a noninvasive, time-efficient, and cost-effective monitoring tool. The potential benefits are promising for marine conservation, as the marine biome is frequently under-surveyed due to its inaccessibility and the consequent high costs involved. With increasing numbers of eDNA-related publications have come a wide array of capture and extraction methods. Without visual species confirmation, inconsistent use of laboratory protocols hinders comparability between studies because the efficiency of target DNA isolation may vary. We determined an optimal protocol (capture and extraction) for marine eDNA research based on total DNA yield measurements by comparing commonly employed methods of seawater filtering and DNA isolation. We compared metabarcoding results of both targeted (small taxonomic group with species-level assignment) and universal (broad taxonomic group with genus/family-level assignment) approaches obtained from replicates treated with the optimal and a low-performance capture and extraction protocol to determine the impact of protocol choice and DNA yield on biodiversity detection. Filtration through cellulose-nitrate membranes and extraction with Qiagen's DNeasy Blood & Tissue Kit outperformed other combinations of capture and extraction methods, showing a ninefold improvement in DNA yield over the poorest performing methods. Use of optimized protocols resulted in a significant increase in OTU and species richness for targeted metabarcoding assays. However, changing protocols made little difference to the OTU and taxon richness obtained using universal metabarcoding assays. Our results demonstrate an increased risk of false-negative species detection for targeted eDNA approaches when protocols with poor DNA isolation efficacy are employed. Appropriate optimization is therefore essential for eDNA monitoring to remain a powerful, efficient, and relatively cheap method for biodiversity assessments. For seawater, we advocate filtration through cellulose-nitrate membranes and extraction with Qiagen's DNeasy Blood & Tissue Kit or phenol-chloroform-isoamyl for successful implementation of eDNA multi-marker metabarcoding surveys.

The Indian Cormorant (Phalacrocorax fuscicollis) is a common avian piscivore that occurs throughout the Indian subcontinent and east to southern Vietnam. Its evolutionary relationships, however, have remained obscure, largely because of a lack of material available for either osteological or genetic analysis. Here we show using DNA-sequence data from both nuclear and mitochondrial genes that this species is sister to the allopatric Little Black Cormorant (P. sulcirostris), which occurs from Java in the west through southern Indonesia and New Guinea to Australia and New Zealand in the south. We estimate this split to have happened 2.5-3.2 million years ago, during the late Pliocene. We also report on genetic variation within the mitochondrial control region, which suggests that this part of the genome may be useful in investigating if there is genetic structure across the geographical range of the Indian Cormorant., (Copyright © 2018 Elsevier Inc. All rights reserved.)

Transgenerational plasticity (TGP) occurs when offspring exhibit plasticity in traits induced by the environments experienced by their parents, and represents a nongenetic mechanism of inheritance. Evidence that traits can be transmitted to future generations by means other than genetic inheritance has caused a surge of interest in epigenetic inheritance, but evidence for epigenetic modifications being both adaptive and heritable remains scarce. What features would make a species most prone to evolve a system of epigenetically mediated adaptive TGP? Here, we use population-genetic models modified to include epigenetic induction and inheritance to investigate if and when epigenetically mediated adaptive TGP would be expected to evolve for a population subdivided between two habitats connected by migration. We show that differences in the direction of selection between the two habitats drives the evolution of epigenetically mediated adaptive TGP. With low migration, the strength of indirect selection in favor of epigenetically mediated adaptive TGP increases with migration rate. Yet, with higher migration, the opposite trend is observed. We predict that species subdivided between habitats that differ in the direction of selection with moderate migration rates between the habitats would be most likely to evolve epigenetically mediated adaptive TGP if costs of producing such systems are not too high., (© 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.)

New Zealand's endemic King Shag (Leucocarbo carunculatus) has occupied only a narrow portion of the northeastern South Island for at least the past 240years. However, pre-human Holocene fossil and archaeological remains have suggested a far more widespread distribution of the three Leucocarbo species (King, Otago, Foveaux) on mainland New Zealand at the time of Polynesian settlement in the late 13th Century CE. We use modern and ancient DNA, and morphometric and osteological analyses, of modern King Shags and Holocene fossil Leucocarbo remains to assess the pre-human distribution and taxonomic status of the King Shag on mainland New Zealand, and the resultant conservation implications. Our analyses show that the King Shag was formerly widespread around southern coasts of the North Island and the northern parts of the South Island but experienced population and lineage extinctions, and range contraction, probably after Polynesian arrival. This history parallels range contractions of other New Zealand seabirds. Conservation management of the King Shag should take into account this species narrow distribution and probable reduced genetic diversity. Moreover, combined genetic, morphometric and osteological analyses of prehistoric material from mainland New Zealand suggest that the now extinct northern New Zealand Leucocarbo populations comprised a unique lineage. Although these distinctive populations were previously assigned to the King Shag (based on morphological similarities and geographic proximity to modern Leucocarbo populations), we herein describe them as a new species, the Kohatu Shag (Leucocarbo septentrionalis). The extinction of this species further highlights the dramatic impacts Polynesians and introduced predators had on New Zealand's coastal and marine biodiversity. The prehistoric presence of at least four species of Leucocarbo shag on mainland NZ further highlights its status as a biodiversity hotspot for Phalacrocoracidae., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Genomic imprinting is a form of epigenetic modification involving parent-of-origin-dependent gene expression, usually the inactivation of one gene copy in some tissues, at least, for some part of the diploid life cycle. Occurring at a number of loci in mammals and flowering plants, this mode of non-Mendelian expression can be viewed more generally as parentally-specific differential gene expression. The effects of natural selection on genetic variation at imprinted loci have previously been examined in a several population-genetic models. Here we expand the existing one-locus, two-allele population-genetic models of viability selection with genomic imprinting to include sex-limited imprinting, i.e., imprinted expression occurring only in one sex, and differential viability between the sexes. We first consider models of complete inactivation of either parental allele and these models are subsequently generalized to incorporate differential expression. Stable polymorphic equilibrium was possible without heterozygote advantage as observed in some prior models of imprinting in both sexes. In contrast to these latter models, in the sex-limited case it was critical whether the paternally inherited or maternally inherited allele was inactivated. The parental origin of inactivated alleles had a different impact on how the population responded to the different selection pressures between the sexes. Under the same fitness parameters, imprinting in the other sex altered the number of possible equilibrium states and their stability. When the parental origin of imprinted alleles and the sex in which they are inactive differ, an allele cannot be inactivated in consecutive generations. The system dynamics became more complex with more equilibrium points emerging. Our results show that selection can interact with epigenetic factors to maintain genetic variation in previously unanticipated ways., (Copyright © 2017 Elsevier Inc. All rights reserved.)

The microstructure and mineralogy of chiton valves has been largely ignored in the literature and only described in 29 species to date. Eight species: Acanthochitona zelandica, Notoplax violacea (Family Acanthochitonidae, Suborder Acanthochitonina, Order Chitonida), Chiton glaucus, Onithochiton neglectus, Sypharochiton spelliserpentis, Sypharochiton sinclairi (Family Chitonidae, Suborder, Chitonina, Order Chitonida), Ischnochiton maorianus (Family Ischnochitonidae, Suborder Chitonina, Order Chitonida), and Leptochiton inquinatus (Family Leptochitonidae, Suborder Lepidopleurina, Order Lepidopleurida) were collected from the Otago Peninsula, South Island, New Zealand. The valves of these chitons were analysed with X-ray diffractometry, Raman spectrometry, and Scanning Electron Micrography (SEM) to determine their mineralogy and microstructure. Both the XRD and Raman data show that the valves consisted solely of aragonite. The observed microstructures of the valves were complex, typically composed of four to seven sublayers, and varied among species. The dorsal layer, the tegmentum, of each species was granular and the ventral layer, the articulamentum, was predominately composed of a spherulitic sublayer, a crossed lamellar sublayer, and an acicular sublayer. The chitonids Sypharochiton pelliserpentis and S. sinclairi had the most complex microstructure layering with three crossed lamellar, two spherulitic sublayers, and a ventral acicular sublayer while the acanthochitonids Acanthochitona zelandica and Notoplax violacea as well as the ischnochitonid Ischnochiton maorianus had the simplest structure with one spherulitic, one crossed lamellar sublayer, and a ventral acicular sublayer. Terminal valves were less complex than intermediate valves and tended to be dominated by the crossed lamellar structure. The leptochitonid Leptochiton inquinatus generated a unique crossed lamellar sublayer different from the other analysed chitonids. Acanthochitona zelandica is the only analysed chitonid that utilizes two different crossed lamellar structures. Clearly, many of these properties do not reflect the currently recognized polyplacophoran phylogeny., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Simple models of viability selection acting on variation at a single diploid locus only maintain multiple alleles for very restricted sets of fitnesses. Most of these models assume that fitnesses are independent, even if the genotypes share alleles. Here, we extend this result to a model with generalized dominance interactions, in which fitnesses are strongly affected by what we call the "primary effects" of the genotype's component alleles, so that genotypes with shared alleles have correlated fitnesses. Nevertheless, in keeping with previously reported results, we also show that such fitness sets are easily constructed over time if recurrent mutation is occurring simultaneously. We find that such models maintain less variation over time than do (previous) models with independently sampled fitnesses, especially when the effects of genetic drift are taken into account. We also show that there is a weak tendency for greater weighting of primary effects to evolve over time., (Copyright © 2016 Spencer and Mitchell.)

Digenean parasites infecting four Cominella whelk species (C. glandiformis, C. adspersa, C. maculosa and C. virgata), which inhabit New Zealand's intertidal zone, were analysed using molecular techniques. Mitochondrial 16S and cytochrome oxidase 1 (COI) and nuclear rDNA ITS1 sequences were used to infer phylogenetic relationships amongst digenea. Host species were parasitized by a diverse range of digenea (Platyhelminthes, Trematoda), representing seven families: Echinostomatidae, Opecoelidae, Microphallidae, Strigeidae and three, as yet, undetermined families A, B and C. Each parasite family infected between one and three host whelk species, and infection levels were typically low (average infection rates ranged from 1·4 to 3·6%). Host specificity ranged from highly species-specific amongst the echinostomes, which were only ever observed infecting C. glandiformis, to the more generalist opecoelids and strigeids, which were capable of infecting three out of four of the Cominella species analysed. Digeneans displayed a highly variable geographic range; for example, echinostomes had a large geographic range stretching the length of New Zealand, from Northland to Otago, whereas Family B parasites were restricted to fairly small areas of the North Island. Our results add to a growing body of research identifying wide ranges in both host specificity and geographic range amongst intertidal, multi-host parasite systems.

Current taxonomic treatments of New Zealand and temperate Australian members of the gastropod subfamily Cantharidinae imply that species on either side of the Tasman Sea are closely related and, in some cases, congeneric. Such a close relationship, however, entails a relatively recent divergence of Australian and New Zealand lineages, which seems inconsistent with what is known about cantharidine larval development in general. In order to address these issues, mitochondrial and nuclear DNA sequences were used to ascertain how cantharidine genera became established over the wide geographical range of temperate Australia and New Zealand, including their subantarctic islands. Our robust and dated phylogenies (based on 16S, COI, 12S and 28S sequences) revealed that Australian and New Zealand species fall into endemic clades that have been separated for, at most, 35million years. This divergence date postdates a vicariant split by around 50million years and we suggest that, once again, long-distance trans-Tasman dispersal has played a pivotal role in molluscan evolution in this part of the world. Our results also show that the current classification requires revision. We recognize three genera (Cantharidus [comprising 2 subgenera: Cantharidus s.str. and Pseudomargarella n. subgen.], Micrelenchus [comprising 2 subgenera: Micrelenchus s.str. and Mawhero] and Roseaplagis n. gen.) for New Zealand cantharidine species. In our dated BEAST tree, these genera form a clade with the endemic Australian Prothalotia and South African Oxystele. Other temperate Australian cantharidines in our study fall into previously recognized genera (Phasianotrochus, Thalotia, Calthalotia), which are all quite distinct from Cantharidus in spite of some authors considering various of them to be possible synonyms. Finally, we remove the Australian genus Cantharidella from the Cantharidinae to the subfamily Trochinae and erect a new genus, Cratidentium n. gen., also in the Trochinae, to accommodate several Australian species previously considered to belong to Cantharidella., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Conservation biologists now realize that parasites of endangered hosts should be conserved for their own sake and as part of their host's natural environment. But parasites should also be conserved because parasitic exposure might be crucial to the host's development of a fully functional immune system and hence to the survival of the host., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

Arguments about the evolutionary modification of genetic dominance have a long history in genetics, dating back more than 100 years. Mathematical investigations have shown that modifiers of the level of dominance at the locus of interest can spread at a reasonable rate only if heterozygotes at that locus are common. One hitherto neglected scenario is that of sexually antagonistic selection, which not only is ubiquitous in sexual species but also can generate stable high frequencies of heterozygotes that would appear to facilitate the spread of such modifiers. Here we present a mathematical model that shows that sexually specific dominance modification is a potential outcome of sexually antagonistic selection. Our model predicts that loci with higher levels of sexual conflict should exhibit greater differentiation between males and females in levels of dominance and that the strength of antagonistic selection experienced by one sex should be proportional to the level of dominance modification. We show that evidence from the literature is consistent with these predictions but suggest that empiricists should be alert to the possibility of there being numerous cases of sex-specific dominance. Further, in order to determine the significance of sexual conflict in the evolution of dominance, we need improved measures of sexual conflict and better characterization of loci that modify dominance of genes with sexually antagonistic fitness effects.

Population geneticists have long been interested in the ability of natural selection to maintain the levels of standing variation observed in natural populations. Here, we study the polymorphism-maintaining properties of maternal selection, in which the fitness of an individual is a function of its own and its mother's genotype. Using a model proposed by Gavrilets, we first estimate the proportion of parameter/state space that preserves allelic variation, before investigating the construction of polymorphism over time through the joint action of mutation and selection. These two methods, the "parameter-space" and "constructionist" approaches, respectively, enable us to draw some general conclusions. We argue that, even though the proportion of parameter-state space allowing multiallele polymorphism is greater under maternal selection than under the standard model of constant viability selection, the former is, in fact, less likely to maintain large numbers of alleles. Nevertheless, variation that is balanced by maternal selection is likely to show elements of heterozygous advantage and be resistant to depletion by genetic drift. We observe that the population mean fitness frequently decreases after the successful invasion of a new mutation, but such declines are usually temporary., (Copyright © 2015 Spencer and Chiew.)

Relationships among the 40 or so extant species of cormorants (family Phalacrocoracidae) have been obscured by their morphological similarities, many of which have recently been shown to be the result of convergent evolution. Previous attempts to derive an evolutionarily justifiable classification for this group of birds using osteological and behavioral data have been hampered by these similarities. We present a well-resolved evolutionary tree for some 40 cormorant taxa based on the results of extensive genetic work that produced over 8000 bases of mitochondrial and nuclear DNA sequence. This tree implies a novel classification for the cormorants, which reflects their evolutionary history and can be implemented using some 7 genera. Some of the relationships among the species are well-known but many are previously unrecognized. Nevertheless, much of the classification makes sense in terms of biogeography., (Copyright © 2014 Elsevier Inc. All rights reserved.)

Theories focused on kinship and the genetic conflict it induces are widely considered to be the primary explanations for the evolution of genomic imprinting. However, there have appeared many competing ideas that do not involve kinship/conflict. These ideas are often overlooked because kinship/conflict is entrenched in the literature, especially outside evolutionary biology. Here we provide a critical overview of these non-conflict theories, providing an accessible perspective into this literature. We suggest that some of these alternative hypotheses may, in fact, provide tenable explanations of the evolution of imprinting for at least some loci.

New Zealand's endemic Stewart Island Shag (Leucocarbo chalconotus) comprises two regional groups (Otago and Foveaux Strait) that show consistent differentiation in relative frequencies of pied versus dark-bronze morphotypes, the extent of facial carunculation, body size and breeding time. We used modern and ancient DNA (mitochondrial DNA control region one), and morphometric approaches to investigate the phylogeography and taxonomy of L. chalconotus and its closely related sister species, the endemic Chatham Island Shag (L. onslowi). Our analysis shows Leucocarbo shags in southern New Zealand comprise two well-supported clades, each containing both pied and dark-bronze morphs. However, the combined monophyly of these populations is not supported, with the L. chalconotus Otago lineage sister to L. onslowi. Morphometric analysis indicates that Leucocarbo shags from Otago are larger on average than those from Foveaux Strait. Principal co-ordinate analysis of morphometric data showed substantial morphological differentiation between the Otago and Foveaux Strait clades, and L. onslowi. The phylogeographic partitioning detected within L. chalconotus is marked, and such strong structure is rare for phalacrocoracid species. Our phylogenetic results, together with consistent differences in relative proportions of plumage morphs and facial carunculation, and concordant differentiation in body size and breeding time, suggest several alternative evolutionary hypotheses that require further investigation to determine the level of taxonomic distinctiveness that best represents the L. chalconotus Otago and Foveaux Strait clades.

Although there is keen interest in the potential adaptive value of epigenetic variation, it is unclear what conditions favor the stability of these variants either within or across generations. Because epigenetic modifications can be environmentally sensitive, existing theory on adaptive phenotypic plasticity provides relevant insights. Our consideration of this theory suggests that stable maintenance of environmentally induced epigenetic states over an organism's lifetime is most likely to be favored when the organism accurately responds to a single environmental change that subsequently remains constant, or when the environmental change cues an irreversible developmental transition. Stable transmission of adaptive epigenetic states from parents to offspring may be selectively favored when environments vary across generations and the parental environment predicts the offspring environment. The adaptive value of stability beyond a single generation of parent-offspring transmission likely depends on the costs of epigenetic resetting. Epigenetic stability both within and across generations will also depend on the degree and predictability of environmental variation, dispersal patterns, and the (epi)genetic architecture underlying phenotypic responses to environment. We also discuss conditions that favor stability of random epigenetic variants within the context of bet hedging. We conclude by proposing research directions to clarify the adaptive significance of epigenetic stability., (© 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.)

Frequency-dependent selection (FDS) remains a common heuristic explanation for the maintenance of genetic variation in natural populations. The pairwise-interaction model (PIM) is a well-studied general model of frequency-dependent selection, which assumes that a genotype's fitness is a function of within-population intergenotypic interactions. Previous theoretical work indicated that this type of model is able to sustain large numbers of alleles at a single locus when it incorporates recurrent mutation. These studies, however, have ignored the impact of the distribution of fitness effects of new mutations on the dynamics and end results of polymorphism construction. We suggest that a natural way to model mutation would be to assume mutant fitness is related to the fitness of the parental allele, i.e., the existing allele from which the mutant arose. Here we examine the numbers and distributions of fitnesses and alleles produced by construction under the PIM with mutation from parental alleles and the impacts on such measures due to different methods of generating mutant fitnesses. We find that, in comparison with previous results, generating mutants from existing alleles lowers the average number of alleles likely to be observed in a system subject to FDS, but produces polymorphisms that are highly stable and have realistic allele-frequency distributions.

The evolution of transgenerational epigenetic adaptation is driven by the invasion and stable inheritance of epialleles. Here, we describe a population-genetic model subject to environmentally-induced epigenetic effects in order to investigate the conditions under which an epigenetically modifiable allele (epiallele) can invade a population insensitive to such cues. Here, epigenetically modifiable individuals have the potential to develop a phenotype that is suitable for their predicted future environment and, provided this prediction is correct, possess a biological advantage compared to their non-modifiable counterpart. However, when individuals experience an environment that 'mismatches' their phenotype, an advantage over unmodifiable individuals may be precluded and instead they experience a decrease in fitness. These epigenetic modifications are then inherited by the next generation which are either epigenetically reset to match their environment or, by resisting environmental cues, maintain their epigenetic status. We found that when environmental cues were common, a severe fitness cost of mismatch between environment and phenotype meant that the disadvantage was too costly and epialleles were less likely to invade. Moreover, for a wide range of parameters, a higher rate of germline epigenetic resetting decreased the likelihood of epiallele invasion. Accordingly, we found that both the frequency of environmental influences and the rate of resetting were central parameters in this system., (Copyright © 2013 Elsevier Inc. All rights reserved.)

Paramutation involves an interaction between homologous alleles resulting in a heritable change in gene expression without altering the DNA sequence. Initially believed to be restricted to plants, paramutation has recently been observed in animal models, and a paramutation-like event has been noted in humans. Despite the accumulating evidence suggesting that trans-acting epigenetic effects can be inherited transgenerationally and therefore generate non-genomic phenotypic variation, these effects have been largely ignored in the context of evolutionary theory. The model presented here incorporates paramutation into the standard model of viability selection at one locus and demonstrates that paramutation can create long-term biological diversity in the absence of genetic change, and even in the absence of the original paramutagenic allele. Therefore, if paramutation is present, attributing evolution to only a traditional genetic model may fail to encompass the broad scope of phenotypic differences observed in nature. Moreover, we show also that an unusual mathematical behaviour, analogous to "Ewens' gap" of the two-locus two-allele symmetric-selection model, occurs: when the rate of one parameter-for example, the rate of paramutation-is increased, a pair of equilibria may disappear only to reappear as this parameter increases further. In summary, by incorporating even the simplest epigenetic parameters into the standard population-genetic model of selection, we show how this type of inheritance system can profoundly alter the course of evolution., (Copyright © 2013 Elsevier Inc. All rights reserved.)

Marine biologists and biogeographers have long been puzzled by apparently non-dispersive coastal taxa that nonetheless have extensive transoceanic distributions. We here carried out a broad-scale phylogeographic study to test whether two widespread Southern Hemisphere species of non-buoyant littoral macroalgae are capable of long-distance dispersal. Samples were collected from along the coasts of southern Chile, New Zealand and several subAntarctic islands, with the focus on high latitude populations in the path of the Antarctic Circumpolar Current or West Wind Drift. We targeted two widespread littoral macroalgal species: the brown alga Adenocystisutricularis (Ectocarpales, Heterokontophyta) and the red alga Bostrychiaintricata (Ceramiales, Rhodophyta). Phylogenetic analyses were performed using partial mitochondrial (COI), chloroplast (rbcL) and ribosomal nuclear (LSU / 28S) DNA sequence data. Numerous deeply-divergent clades were resolved across all markers in each of the target species, but close phylogenetic relationships - even shared haplotypes - were observed among some populations separated by large oceanic distances. Despite not being particularly buoyant, both Adenocystisutricularis and Bostrychiaintricata thus show genetic signatures of recent dispersal across vast oceanic distances, presumably by attachment to floating substrata such as wood or buoyant macroalgae.

Explanations for the genetic variation ubiquitous in natural populations are often classified by the population-genetic processes they emphasize: natural selection or mutation and genetic drift. Here we investigate models that incorporate all three processes in a spatially structured population, using what we call a construction approach, simulating finite populations under selection that are bombarded with a steady stream of novel mutations. As expected, the amount of genetic variation compared to previous models that ignored the stochastic effects of drift was reduced, especially for smaller populations and when spatial structure was most profound. By contrast, however, for higher levels of gene flow and larger population sizes, the amount of genetic variation found after many generations was greater than that in simulations without drift. This increased amount of genetic variation is due to the introduction of slightly deleterious alleles by genetic drift and this process is more efficient when migration load is higher. The incorporation of genetic drift also selects for fitness sets that exhibit allele-frequency equilibria with larger domains of attraction: they are "more stable." Moreover, the finiteness of populations strongly influences levels of local adaptation, selection strength, and the proportion of allele-frequency vectors that can be distinguished from the neutral expectation.

Dispersal by passive oceanic rafting is considered important for the assembly of biotic communities on islands. However, not much is known about levels of population genetic connectivity maintained by rafting over transoceanic distances. We assess the evolutionary impact of kelp-rafting by estimating population genetic differentiation in three kelp-associated invertebrate species across a system of islands isolated by oceanic gaps for over 5 million years, using mtDNA and AFLP markers. The species occur throughout New Zealand's subantarctic islands, but lack pelagic stages and any opportunity for anthropogenic transportation, and hence must rely on passive rafting for long-distance dispersal. They all have been directly observed to survive transoceanic kelp-rafting journeys in this region. Our analyses indicate that regular gene flow occurs among populations of all three species between all of the islands, especially those on either side of the subtropical front oceanographic boundary. Notwithstanding its perceived sporadic nature, long-distance kelp-rafting appears to enable significant gene flow among island populations separated by hundreds of kilometres of open ocean.

Differences in transgenerational epigenetic stability can result in a diversity of phenotypes among genetically identical individuals. Here we present a model that encapsulates non-genomic phenotypic variation in a population over two distinct environments that each act as a stimulus for epigenetic modification. By allowing different levels of epigenetic resetting, thereby increasing epigenetic diversity, we explore the dynamics of multiple epiallelic states subject to selection in a population-epigenetic model. We find that both epigenetic resetting and the environmental frequency are crucial parameters in this system. Our results illustrate the regions of parameter space that enable up to three equilibria to be simultaneously locally stable. Furthermore, it is clear that both continued environmental induction and epigenetic resetting prevent epigenetic fixation, maintaining phenotypic variation through different epiallelic states. However, unless both environments are reasonably common, levels of epigenetically-maintained variation are low. We argue that it is vital that non-genomic phenotypic diversity is not ignored in evolutionary theory, but instead regarded as distinct epiallelic variants. Ultimately, a critical goal of future experiments should be to determine accurate rates of epigenetic resetting, especially over several generations, in order to establish the long-term significance of epigenetic inheritance., (Copyright © 2012 Elsevier Inc. All rights reserved.)

The pelicans are a charismatic group of large water birds, whose evolutionary relationships have been long debated. Here we use DNA sequence data from both mitochondrial and nuclear genes to derive a robust phylogeny of all the extant species. Our data rejects the widespread notion that pelicans can be divided into white- and brown-plumaged groups. Instead, we find that, in contrast to all previous evolutionary hypotheses, the species fall into three well-supported clades: an Old World clade of the Dalmatian, Spot-billed, Pink-backed and Australian Pelicans, a New World clade of the American White, Brown and Peruvian Pelicans, and monospecific clade consisting solely of the Great White Pelican, weakly grouped with the Old World clade. We discuss possible evolutionary scenarios giving rise to this diversity., (Copyright © 2012 Elsevier Inc. All rights reserved.)

Population-genetic models are developed to investigate the consequences of viability selection at a diallelic X-linked locus subject to genomic imprinting. Under complete paternal-X inactivation, a stable polymorphism is possible under the same conditions as for paternal-autosome inactivation with differential selection on males and females. A necessary but not sufficient condition is that there is sexual conflict, with selection acting in opposite directions in males and females. In contrast, models of complete maternal-X inactivation never admit a stable polymorphism and alleles will either be fixed or lost from the population. Models of complete paternal-X inactivation are more complex than corresponding models of maternal-X inactivation, as inactivation of paternally derived X chromosomes in females screens these chromosomes from selection for a generation. We also demonstrate that polymorphism is possible for incomplete X inactivation, but that the parameter conditions are more restrictive than for complete paternal-X inactivation. Finally, we investigate the effects of recurrent mutation in our models and show that deleterious alleles in mutation-selection balance at imprinted X-linked loci are at frequencies rather similar to those with corresponding selection pressures and mutation rates at unimprinted loci. Overall, our results add to the reasons for expecting less selectively maintained allelic variation on X chromosomes.

Dietary restriction (DR) extends the lifespan of a wide range of species, although the universality of this effect has never been quantitatively examined. Here, we report the first comprehensive comparative meta-analysis of DR across studies and species. Overall, DR significantly increased lifespan, but this effect is modulated by several factors. In general, DR has less effect in extending lifespan in males and also in non-model organisms. Surprisingly, the proportion of protein intake was more important for life extension via DR than the degree of caloric restriction. Furthermore, we show that reduction in both age-dependent and age-independent mortality rates drives life extension by DR among the well-studied laboratory model species (yeast, nematode worms, fruit flies and rodents). Our results suggest that convergent adaptation to laboratory conditions better explains the observed DR-longevity relationship than evolutionary conservation although alternative explanations are possible., (© 2012 The Authors. Aging Cell © 2012 Blackwell Publishing Ltd/Anatomical Society of Great Britain and Ireland.)