Journal of Heredity

BackgroundAnimal mitochondrial genomes are typically circular, 14-20 kb in length, maternally inherited, contain 13 coding genes, two ribosomal genes and are homoplasmic. In contrast, plant mitogenomes display frequent gene rearrangements, often contain greatly expanded repetitive regions, encode various open reading frames of unknown function and may be heteroplasmic due to differential repeat expansions between molecules. Error correction by recombination is common in plant mitochondria and has been proposed as the driver behind the rearrangements and repeat expansions that are often observed. In contrast, most animal mitochondria never or only very seldomly recombine and their utilisation of other repair mechanisms for mitochondrial genome error correction is a potential driver of their non-coding DNA reduction. ResultsUsing PacBio long reads for genome assembly and structural variant detection, we identify evidence of heteroplasmy in the form of variable repeat lengths within two blocks of repetitive DNA within the expanded 46 kb mitochondrial genome of the bivalve mollusc, quagga mussel, Dreissena rostriformis. The quagga mussel also has a greatly expanded repertoire of coding genes in comparison to most animals which includes an additional nine open reading frames (ORFs) encoding predicted transmembrane peptides of unknown orthology. ConclusionsThe genome size, repeat content and coding gene repertoire of the quagga mussel mitogenome closely resemble those of plants and the identification of repeat-associated heteroplasmy is consistent with the utilisation of plant-like recombination-based error correction mechanisms. Given the frequency of mitochondrial repeat expansions within the Bivalvia, recombination may be an underappreciated mechanism for mitogenomic error correction within this and other animal lineages. Significance StatementUnlike most animals, the mitochondrial genomes of many bivalve molluscs are often greatly expanded and contain large non-coding regions and additional predicted genes of unknown function. While these features are uncommon in other animal groups, they are common features of plant mitochondrial genomes. Here we show that the mitochondrial genome of the bivalve mollusc, the quagga mussel, displays many plant-like features and additionally, shows evidence of variability in the repeat lengths between mitochondrial molecules within an individual mussel. We propose that similar error correction mechanisms in plants and bivalves may play a role in these observed commonalities.

Sturgeon and paddlefish represent some of the most early diverging branches of ray-finned fishes and have undergone at least one global and several lineage-specific whole genome duplication events. White sturgeon (Acipenser transmontanus), the largest freshwater fish in North America, have experienced at least two rounds of whole genome duplication, and may exhibit both di- and multi-valent meiotic segregation. Moreover, they exhibit contemporary ploidy variants due to spontaneous autopolyploidy, particularly in aquaculture. Nonetheless, as a species with several population segments that exhibit chronic recruitment failure, conservation aquaculture is an important part of their management. To facilitate the development of genetic tools to aid white sturgeon conservation, as well as a basis to understand how ploidy changes and variation historically and contemporarily shape the evolution of this species, we present a genome assembly for a white sturgeon from the Snake River, Idaho, USA. Analysis of sequence data used for assembly indicated a haploid genome size of approximately 1.5Gbp, implying tetraploidy (4N), while analysis of heterozygous k-mers from 21 to 41 bp suggest the genome reflects both 4N and 8N variants. The final genome assembly, scaffolded using linkage maps constructed from Fraser River and Snake River F1 families, contained 6.26Gbp in 832,145 scaffolds, consistent with published genome size estimates. Conserved ortholog completeness for this genome (90.5%; 22.8% single-copy and 67.7% duplicated) was similar to the putatively diploid sterlet sturgeon, and the largest linkage map-based scaffold was 55.2Gbp, though the N50 for this assembly was only 416Kbp, indicating the assembly remains fragmented. We demonstrate the utility of this assembly by identifying genomic regions significantly associated with sex. Genetic markers, designed for inclusion in an amplicon genotyping panel, predicted sex 96.6% and 81.5% correctly in females and males, respectively, providing a strong overall association ({square}2 p-value < 2.7x10-37) with some variation by geographic region. Article summaryFunctional polysomes (more than two chromosomes that pair in meiosis) are rare among vertebrates. White sturgeon, the largest freshwater fish in North America, are tetraploid and occasionally hexaploid. Several populations of this species are stagnant or declining, requiring aquaculture to bolster reproduction. We analyzed whole genomic data and assembled the genome of an individual from the unique Snake River, Idaho, population. Results indicate most genetic variants are consistent with tetraploidy, and the genome assembly, while fragmented, is largely complete. We demonstrate its utility by designing genetic markers for sex for use in conservation and commercial aquaculture.

Population genetics employs two major models for conceptualizing genetic relationships among individuals - outcome-driven (coalescent) and process-driven (forward). These models are complementary, but the basic Kingman coalescent and its extensions make fundamental assumptions to allow analytical approximations: a constant effective population size much larger than the sample size. These make the probability of multiple coalescent events per generation negligible. Although these assumptions are often violated in species of conservation concern, conservation genetics often uses coalescent models of effective population sizes and trajectories in endangered species. Despite this, the effect of very small effective population sizes, and their interaction with bottlenecks and sample sizes, on such analyses of genetic diversity remains unexplored. Here, I use simulations to analyze the influence of small effective population size, population decline, and their relationship with sample size, on coalescent-based estimates of genetic diversity. Compared to forward process-based estimates, coalescent models significantly overestimate genetic diversity in oversampled populations with very small effective sizes. When sampled soon after a decline, coalescent models overestimate genetic diversity in small populations regardless of sample size. Such overestimates artificially inflate estimates of both bottleneck and population split times. For conservation applications with small effective population sizes, forward simulations that do not make population size assumptions are computationally tractable and should be considered instead of coalescent-based models. These findings underscore the importance of the theoretical basis of analytical techniques as applied to conservation questions.

Juncus bufonius L. s.l. is a species complex with several ploidy levels, for which species delimitation remains unclear due to a lack of reliable morphological characters and the paucity of molecular studies. To clarify taxonomic and geographic relationships in the complex, we combined genomic, cytometric and morphological data from a broad latitudinal range from England down to Spain. We collected morphometric and cytometric data from 31 populations, and genomic data were obtained through Hyb-Seq using the Angiosperm353 kit for a subset of individuals. These three datasets were combined to explore phylogenetic relationships, population structure, and the validity of four previously proposed morphospecies (J. bufonius s.str., a hexaploid; J. minutulus, a tetraploid; and J. ranarius and J. hybridus, both diploids). Sequencing supported the separation of diploids and polyploids as two distinct taxa, but morphometric characters used previously to describe morphospecies showed continuous variation with no diagnostic value, and were not congruent with genomic and cytometric data. Polyploids likely originated through allopolyploidisation from diploids and tetraploids. Phylogenetic lineages were extensively mixed geographically, both for diploid and polyploid taxa, which suggests repeated long-distance dispersal events for both diploids and polyploids, and no separation of taxa by geography. Splitting of diploids into J. ranarius and J. hybridus was not supported. We recommend J. ranarius be treated as a synonym of J. hybridus, and that tetraploids and hexaploids be grouped under J. bufonius. The observed geographical patterns are consistent with high rates of seed dispersal by migratory waterbirds.

Focal and intelligent passerine songbirds, corvids (Aves: Corvidae) have served as models for research on the genomics of hybridization and cognition. Clarks Nutcracker (Nucifraga columbiana), the sole North American member of its genus, is distributed in mountain forests from northern Mexico to northern British Columbia. A seed predator, N. columbiana is highly reliant on pine nuts from Pinus spp. conifers, which it both consumes directly from cones and caches for future use. Because cached seeds are often forgotten or abandoned, it is a major seed disperser for high elevation pines--in particular Whitebark Pine P. albicaulis. Previous studies of genetic variation in Clarks Nutcracker found range-wide panmixia and generally high levels of heterozygosity at a handful of nuclear and mitochondrial loci, potentially due to seasonal elevational movements and long term dispersal. An earlier genome assembly from low-coverage short read data was highly fragmented and has not to date been used as the basis for population-level resequencing. Here we report on the first chromosome-scale genome assembly for N. colombiana. We generated long-read sequencing and genome conformation mapping data from tissues sampled from a male N. columbiana individual in Wyoming, USA. These data were assembled into a highly contiguous and complete assembly, which showed strong chromosomal synteny with New Caledonian crow (Corvus moneduloides). This genome has relatively low heterozygosity compared to other Corvid genomes and to previous population-level heterozygosity estimates for the species. We also found evidence of a long-term decline in effective population size dating back to the Pleistocene, after accounting for a technical artifact common to demographic inference using the pairwise sequential Markovian coalescent. These findings raise concerns about the future viability of the species and its mutualist P. albicaulis; we hope the assembly will motivate further comparative and conservation genomics research.

Animal translocations are becoming increasingly popular as a tool for conservationists. Demographic factors can be crucial determinants dictating translocation viability in the short term. Translocated populations pass through artificial bottlenecks and can suffer from founder effects. Reduction in genetic variation relative to their source populations is likely, limiting their adaptive potential. Founder events can increase frequencies of deleterious alleles due to elevated rates of inbreeding and inbreeding depression. Here, we describe the effects of human-driven, serial population translocations on the genetic diversity of critically endangered Anegada iguanas (Cyclura pinguis) in the British Virgin Islands. Though founding populations were extremely small (N=8, N=4), the census sizes of translocated iguana populations increased dramatically over the first twenty years. This implies that these translocations were successful from a demographic perspective despite the small number of animals used, indicating a genetic paradox. To quantify genetic signatures in these bottlenecked populations, blood samples were collected from the source population and two translocated populations and genotyped at 21 microsatellite loci. We found that allele frequencies in translocated populations differed significantly from those of the source, with the translocated populations having less genetic diversity. However, common methods for estimating presence of genetic bottlenecks were non-significant. Estimates of internal relatedness by age class suggest that inbreeding depression may be elevated after translocation, likely reflecting the small initial population sizes associated with these translocation events. Anecdotally, our work shows that translocations may result in subtle genetic erosion that has long-term population viability impacts, even when census size indicates success.

>Mixed-cytotype populations are ideal to understand polyploid establishment and diversification. We used the orchid Zygopetalum mackayi to understand how facultative apomictic reproduction relates to polyploidy. Sexual diploids and facultative apomictic tetraploids occur under distinct niches, with a contact zone where triploids occur. We hypothesized that facultative apomictic reproduction increases the fitness of tetraploids through reproductive interference between cytotypes. We predict patterns of genetic diversity of allopatric tetraploid populations to be significantly different from contact zone populations as a result of dominant apomictic reproduction in the later. We also describe the contact nature of diploids and tetraploids and the role of the intermediate triploids based on patterns of genetic structure within and among pure and mixed-cytotype populations.\n>We designed eight microsatellite markers and genotyped 155 individuals from six populations resulting in 237 alleles. We described patterns of genetic diversity and structure within and among populations and cytotypes.\n>Genotypic diversity is similarly high among all populations and cytotypes. Each cytotype emerged as a genetically cluster, combining individuals from different populations. Triploids clustered in an intermediate position between diploids andtetraploids.\n>We rejected the hypothesis of reproductive interference between cytotypes of Z. mackayi. Patterns of genetic diversity are incongruent with the occurrence of apomict reproduction in tetraploids. Mixed-cytotype populations originate from secondary contact and triploids are hybrids between diploids and tetraploids and act as a reproductive barrier. We suggest polyploidy rather than facultative apomixis explains higher fitness of tetraploids in this species and, therefore, eco-geographical patterns of distribution.

Although translocations can be effective for augmenting and restoring wild populations, they can disrupt native patterns of genetic structure, diversity, and local adaptation, thereby hampering conservation efforts. Managers must weigh potential costs and benefits of choosing well-differentiated donor individuals that could confer a boost to genetic diversity while avoiding outbreeding depression or ecological mismatch. This decision is more daunting when taxonomy is unclear or debated. For example, bighorn sheep (Ovis canadensis) populations in the United States that have been managed as the "California" lineage (part of the formerly recognized subspecies O. c. californiana) originate from serial translocations sourced from populations in British Columbia, resulting in reduced genetic diversity and elevated risk of inbreeding. After research on skull shape and RFLP analysis of mtDNA failed to find support for that subspecies, some jurisdictions treated the California lineage as part of the Rocky Mountain subspecies (O. c. canadensis) and mixed individuals in subsequent translocations, in part to increase genetic diversity of bottlenecked populations. Yet detailed genetic data addressing validity of those putative lineages were lacking. We reconstructed the genetic history of bighorn sheep by sampling the major putative subspecies or lineages, focusing on native (remnant) genetic variation, and generating high-throughput DNA sequencing data ([~]15,000-25,000 SNPs). Complementary phylogenetic and population genetic analyses supported the distinctiveness of four bighorn lineages at levels corresponding to subspecies. Our results confirm the genetic identity of the no longer putative California bighorn lineage, answering a question that puzzled geneticists and managers for decades. Moving forward, we recommend that managers 1) maintain the natural variation held in native populations by protecting them from intentional translocations or unintentional mixing with nearby populations; 2) prioritize withinlineage translocations for population augmentation or repatriation to previously occupied regions; and 3) cautiously consider any translocations that would lead to mixing of distinct evolutionary lineages.

The blue mussel, Mytilus edulis is part of the Mytilus edulis species complex, encompassing at least three putative species: M. edulis, M. galloprovincialis and M. trossulus. These three species occur on both sides of the Atlantic and hybridize in nature, and both M. edulis and M. galloprovincialis are important aquaculture species. They are also invasive species in many parts of the world. Here, we present a chromosome-level assembly of Mytilus edulis. We used a combination of PacBio sequencing and Dovetails Omni-C technology to generate an assembly with 14 long scaffolds containing 94% of the predicted length of the M. edulis genome (1.6 out of 1.7 Gb). Assembly statistics were total length 1.65 Gb, N50 = 116 Mb, L50 = 7 and, L90 = 13. BUSCO analysis showed 92.55% eukaryote BUSCOs identified. AB-Initio annotation using RNA-seq from mantle, gills, muscle and foot predicted 47,128 genes. These gene models were combined with Isoseq validation resulting in 65,505 gene models and 129,708 isoforms. Using GBS and shotgun sequencing, we also sequenced 3 North American populations of Mytilus to characterize single-nucleotide as well as structural variance. This high-quality genome for M. edulis provides a platform to develop tools that can be used in breeding, molecular ecology and evolution to address questions of both commercial and environmental perspectives.

Pigeons and doves (family Columbidae) are one of the most diverse extant avian lineages, and many species have served as key models for evolutionary genomics, developmental biology, physiology, and behavioral studies. Building genomic resources for colubids is essential to further many of these studies. Here, we present high-quality genome assemblies and annotations for two columbid species, Columba livia and C. guinea. We simultaneously assembled C. livia and C. guinea genomes from long-read sequencing of a single F1 hybrid individual. The new C. livia genome assembly (Cliv_3) shows improved completeness and contiguity relative to Cliv_2.1, with an annotation incorporating long-read IsoSeq data for more accurate gene models. Intensive selective breeding of C. livia has given rise to hundreds of breeds with diverse morphological and behavioral characteristics, and Cliv_3 offers improved tools for mapping the genomic architecture of interesting traits. The C. guinea genome assembly is the first for this species and is a new resource for avian comparative genomics. Together, these assemblies and annotations provide improved resources for functional studies of columbids and avian comparative genomics in general. ARTICLE SUMMARYPigeons and doves are important models for evolutionary genomics, developmental biology, physiology, and behavioral studies. Here, we present high-quality reference genome assemblies and annotations for two pigeon species, the domestic rock pigeon (Columba livia) and the African speckled pigeon (C. guinea). These assemblies and annotations provide improved resources for both comparative genomics and functional studies.

BackgroundThe central bearded dragon (Pogona vitticeps) is widely distributed in central eastern Australia and adapts readily to captivity. Among other attributes, it is distinctive because it undergoes sex reversal from ZZ genotypic males to phenotypic females at high incubation temperatures. Here, we report an annotated telomere to telomere phased assembly of the genome of a female ZW central bearded dragon. ResultsGenome assembly length is 1.75 Gbp with a scaffold N50 of 266.2 Mbp, N90 of 28.1 Mbp, 26 gaps and 42.2% GC content. Most (99.6%) of the reference assembly is scaffolded into 6 macrochromosomes and 10 microchromosomes, including the Z and W microchromosomes, corresponding to the karyotype. The genome assembly exceeds standard recommended by the Earth Biogenome Project (6CQ40): 0.003% collapsed sequence, 0.03% false expansions, 99.8% k-mer completeness, 97.9% complete single copy BUSCO genes and an average of 93.5% of transcriptome data mappable back to the genome assembly. The mitochondrial genome (16,731 bp) and the model rDNA repeat unit (length 9.5 Kbp) were assembled. Male vertebrate sex genes Amh and Amhr2 were discovered as copies in the small non-recombining region of the Z chromosome, absent from the W chromosome. This, coupled with the prior discovery of differential Z and W transcriptional isoform composition arising from pseudoautosomal sex gene Nr5a1, suggests that complex interactions between these genes, their autosomal copies and their resultant transcription factors and intermediaries, determines sex in the bearded dragon. ConclusionThis high-quality assembly will serve as a resource to enable and accelerate research into the unusual reproductive attributes of this species and for comparative studies across the Agamidae and reptiles more generally. Species TaxonomyEukaryota; Animalia; Chordata; Reptilia; Squamata; Iguania; Agamidae; Amphibolurinae; Pogona; Pogona vitticeps (Ahl, 1926) (NCBI:txid103695). Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=102 SRC="FIGDIR/small/651798v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@1a9d5fforg.highwire.dtl.DTLVardef@1206061org.highwire.dtl.DTLVardef@97acf7org.highwire.dtl.DTLVardef@1dc939d_HPS_FORMAT_FIGEXP M_FIG C_FIG

We classify Nepenthes species into 12 functional pitcher types, based on combinations of traits that appear to comprise different syndromes for capturing nutrients, usually from animals. For nine of these types the trapping syndromes are already documented, six targeting live animals (hence carnivorous), and three targeting other nutrient sources (non-carnivorous). Yet, for three pitcher types here is no previous documentation of the syndrome and we do not yet know what sources of nutrients are being targeted. Mapping all these pitcher types on the latest, near comprehensive species-level phylogenomic tree of Nepenthes (Murphy et al. 2019) shows that apart from the ancestral pitcher type 1, most of the remaining pitcher types have evolved independently, in different parts of the phylogenetic tree, usually in several different places. Each of the 12 pitcher types is characterised morphologically and illustrated, its trapping syndrome discussed, and example species are given. An identification key to the 12 pitcher types is presented. The possibility of additional pitcher types being present is discussed. O_FIG O_LINKSMALLFIG WIDTH=96 HEIGHT=200 SRC="FIGDIR/small/852137v1_fig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@bbfa57org.highwire.dtl.DTLVardef@13084e7org.highwire.dtl.DTLVardef@658770org.highwire.dtl.DTLVardef@19eca44_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOType 1 (Fig. 1).C_FLOATNO Ancestral (N. mirabilis) These species have upper pitchers which are more-or-less ovoid-cylindric in shape. The basal, ovoid part, often but not always a little wider than the upper part, is usually separated from the upper, usually cylindrical part by a "hip" or raised ridge that girdles the circumference of the pitcher on the exterior (also present in the six species of pitcher types 7, 8 and 10). Examination of the inner surface shows that the "hip" divides the glossy, broad, basal, fluid-containing, digestive, part (referred to as the "detentive" zone by Macfarlane (1908) because prey are detained here) from the upper opaque, dull, off-white to slightly purple, waxy or "pruinose" zone. This waxy zone is referred to as the "conductive" zone by Macfarlane because it helps conducts the insects downwards to the detentive zone with the digestive fluid. Such type 1 pitchers are shown in Fig. 1, exemplified by the upper pitchers of Nepenthes mirabilis (Lour.) Druce. The waxy zone is so-called because its surface is made up of numerous minute platelets of wax, each platelet like a roof-tile and held on a fragile stalk from the underlying surface. Juniper et al. (1989) documented how the waxy zone functions to prevent animals, usually insects, from leaving the pitchers once they have fallen in. Pressure from a foot placed on a wax "tile" will result in the stalk breaking, so that the insect loses its foothold and may fall back into the pitcher. C_FIG O_FIG O_LINKSMALLFIG WIDTH=111 HEIGHT=200 SRC="FIGDIR/small/852137v1_fig12.gif" ALT="Figure 12"> View larger version (39K): org.highwire.dtl.DTLVardef@1f13b4borg.highwire.dtl.DTLVardef@6bc534org.highwire.dtl.DTLVardef@1600959org.highwire.dtl.DTLVardef@5ee42_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOPitcher type 12. (Fig. 12).C_FLOATNO Flat lip (N. jacquelineae Nepenthes jacquelineae (Sumatra, Sect. Montanae) and N. platychila Ch.C.Lee (Borneo, Sect C.Clarke et al.).. Regiae, Lee 2002) both have all the features of type 3 pitchers: widely funnel-shaped to cup-shaped, non-waxy upper parts of pitchers draining into a more slender cylindrical lower part with viscous liquid. Both species however differ from all type 3 species in their very large, flat, dark red peristomes which can be up to 3.5 cm wide in N. jacquelineae. These peristomes have been speculated to act as a landing platform for large flying insects such as blattid cockroaches and moths, which might act with the contrasting lighter, green pitcher body as a light trap for such prey. It is also possible that such prey are lured into a precarious place above the mouth by the copious nectar produced from the lower surface of the lid from large nectar glands 1.5 mm diam. (Clarke 2001). The morphological convergence between the pitchers of these two species is remarkable. Further investigation of the prey trapped in the wild would be desirable for both species. Nepenthes echinostoma Hook.f. is a species closely related to N. mirabilis but with a remarkably flat and extended peristome which resembles type 3, although it has a different pitcher shape and inner surface C_FIG

Small and isolated wildlife populations face numerous threats to extinction, among which is the deterioration of fitness due to an accumulation of deleterious genetic variation. Genomic tools are increasingly used to quantify the impacts of deleterious variation in small populations; however, these approaches remain limited by an inability to accurately predict the selective and dominance effects of individual mutations. Computational simulations of deleterious genetic variation offer an alternative and complementary tool that can help overcome these limitations, though such approaches have yet to be widely employed. In this Perspective, we aim to encourage conservation genomics researchers to adopt greater use of computational simulations to aid in quantifying and predicting the threat that deleterious genetic variation poses to extinction. We first provide an overview of the components of a simulation of deleterious genetic variation, describing the key parameters involved in such models. Next, we clarify several misconceptions about an essential simulation parameter, the distribution of fitness effects (DFE) of new mutations, and review recent debates over what the most appropriate DFE parameters are. We conclude by comparing modern simulation tools to those that have long been employed in population viability analysis, weighing the pros and cons of a genomics-informed simulation approach, and discussing key areas for future research. Our aim is that this Perspective will facilitate broader use of computational simulations in conservation genomics, enabling a deeper understanding of the threat that deleterious genetic variation poses to biodiversity.

Understanding the evolutionary history of diversifying lineages and the delineation of species remain major challenges for evolutionary biology. Here we use single nucleotide polymorphisms (SNPs) and sequence fragment presence-absence (SilicoDArT) data to combine phylogenetics and population genetics to assess species boundaries with a focus on diagnosability. We challenge current and proposed taxonomies in a genus of Australian freshwater turtles (Chelidae: Emydura) from northern Australia and southern New Guinea. In a six-step process, we combine phylogeny with the concept of diagnosability based on fixed allelic differences to select diagnosable lineages as candidate species. Four taxa are supported as diagnosable lineages, two of which we elevate to species status. The nuclear and mitochondrial phylogenies differed in important respects, which we attribute to recent or contemporary lateral transfer of mitochondria during hybridization events, deeper historical hybridization or possibly incomplete lineage sorting of the mitochondrial genome. Taxonomic decisions in cases of allopatry require subjective judgement. Our six-step strategy and the necessary (but not sufficient) criterion of diagnosability adds an additional level of objectivity before that subjectivity is applied, and so reduces the risk of taxonomic inflation that can accompany lineage approaches to species delimitation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=124 SRC="FIGDIR/small/664252v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@1b89bc8org.highwire.dtl.DTLVardef@fb892dorg.highwire.dtl.DTLVardef@1eb09a8org.highwire.dtl.DTLVardef@1c7300c_HPS_FORMAT_FIGEXP M_FIG C_FIG

BackgroundMorphological and traditional genetic studies of the young Pliocene genus Hyles have led to the understanding that despite its importance for taxonomy, phenotypic similarity of wing patterns does not correlate with phylogenetic relationship. To gain insights into various aspects of speciation in the Spurge Hawkmoth (Hyles euphorbiae), we assembled a chromosome-level genome and investigated some of its characteristics. ResultsThe genome of a male H. euphorbiae was sequenced using PacBio and Hi-C data, yielding a 504 Mb assembly (scaffold N50 of 18.2 Mb) with 99.9% of data represented by the 29 largest scaffolds forming the haploid chromosome set. Consistent with this, FISH analysis of the karyotype revealed n = 29 chromosomes and a WZ/ZZ (female/male) sex chromosome system. Estimates of chromosome length based on the karyotype image provided an additional quality metric of assembled chromosome size. Rescaffolding the published male H. vespertilio genome resulted in a high-quality assembly (651 Mb, scaffold N50 of 22 Mb) with 98% of sequence data in the 29 chromosomes. The larger genome size of H. vespertilio (average 1C DNA value of 562 Mb) was accompanied by a proportional increase in repeats from 45% in H. euphorbiae (measured as 472 Mb) to almost 55% in H. vespertilio. Several wing pattern genes were found on the same chromosomes in the two species, with varying amounts and positions of repetitive elements and inversions possibly corrupting their function. ConclusionsOur two-fold comparative genomics approach revealed high gene synteny of the Hyles genomes to other Sphingidae and high correspondence to intact Merian elements, the ancestral linkage groups of Lepidoptera, with the exception of three simple fusion events. We propose a standardized approach for genome taxonomy using nucleotide homology via scaffold chaining as the primary tool combined with Oxford plots based on Merian elements to infer and visualize directionality of chromosomal rearrangements. The identification of wing pattern genes promises future understanding of the evolution of forewing patterns in the genus Hyles, although further sequencing data from more individuals are needed. The genomic data obtained provide additional reliable references for further comparative studies in hawkmoths (Sphingidae).

Crossover frequencies often differ substantially between sexes (i.e. heterochiasmy). Although this phenomenon is widespread throughout taxa, the mechanisms that lead to heterochiasmy remain unclear. One pattern that has emerged is that the overall length of the synaptonemal complex likely has a direct influence on the total number of crossovers in each sex. However, this has only been investigated in a handful of species. The threespine stickleback fish (Gasterosteus aculeatus) is an excellent species to explore whether synaptonemal complex length is associated with differences in the total number of crossovers, as females have much longer linkage maps than males. We used an immunocytological approach to quantify synaptonemal complex length in late pachytene female and male meiocytes in two different populations of threespine stickleback fish. Overall, the freshwater population had shorter synaptonemal complex lengths than the marine population. In both populations we observed sexual dimorphism, with females possessing longer axes. Our results support a model where chromosome axis length determines overall crossover frequency and establish the threespine stickleback as a useful species to explore the mechanistic basis of heterochiasmy as well as the genetic basis underlying variation in synaptonemal complex length.

ContextGenetic diversity is essential for the persistence and future adaptation of species. However, human-driven habitat fragmentation results in population isolation, often leading to rapid loss of genetic diversity and adaptive capacity. Genetic management of focal taxa may be overlooked in many threatened species conservation programs. The Endangered southeastern Australian mallee emu-wren Stipiturus mallee is a species that may benefit from genetic management. Its current range encompasses patchily distributed sub-populations, prone to bottlenecks and genetic drift. Thus, the reintroduction to areas from which the species has been locally extirpated requires careful selection of founders to maximise genetic diversity. AimsWe analyse reduced-representation genomic data from seven sampling areas across the global meta-population to design a translocation strategy that maximises heterozygosity and retention of mallee emu-wren allelic diversity. MethodsWe estimated genetic structure, genetic diversity within, and differentiation between subpopulations, thus testing previous inference based on 12 length-variable loci of low population differentiation with 10,840 genome-wide SNP loci. We also estimated effective population sizes to identify populations in need of genetic augmentation, Finally, we used metapop2 simulations to estimate the relative contributions of each population to global genetic diversity of the species and to estimate the source and number of founders that would maximise heterozygosity and allelic richness in a hypothetical newly established population. Key resultsWe found weak genetic structure across all sampling areas, supporting previous conclusions that the global mallee emu-wren population should be considered a single genetic unit for management purposes. Low but significant Weir and Cockerham pairwise FST among locations indicated differentiation between sampling areas, suggesting that contemporary gene flow is restricted. Effective population sizes for the two regions supporting the largest numbers of mallee emu-wrens were below the threshold associated with reduced adaptive potential. ConclusionsThe genetic health and adaptive potential of sampled mallee emu-wren sub-populations are at risk. Implications The global mallee emu-wren meta-population would likely benefit from genetic augmentation, including reciprocal gene flow between extant sub-populations. To maximise genetic diversity in newly established populations, managers should prioritise gene-pool mixing with founders sourced from all sampled areas.

O_LIThe relative contributions of heritable versus non-heritable phenotypic variation determine how selection may shape evolutionary responses. While genome-wide association studies can provide some insight into large-effect loci underpinning phenotypes, they potentially miss much of the evolutionarily important variation in polygenic traits because many small-effect loci will contribute to heritable variation. C_LIO_LIGenomic animal models can estimate trait heritability from genomic data but are often difficult to apply to wild organisms. Sampling groups of close kin improves their power, yet this can be logistically challenging in species with large populations and high dispersal. Furthermore, many common approaches for power simulations rely on kin structure in the genomic relationship matrix, A, but such simulations on an unstructured A (comprised of unrelated individuals) are likely uninformative. C_LIO_LIWe developed a novel framework to generate simulated expectations from genomic animal models when applied to samples of unrelated wild organisms. A key innovation of this framework is the use of a phenotypes-from-genotypes approach that allows quantitative traits to be simulated from genotypes, independently of A. This provides clear utility where kin structure is absent. We illustrated the use and flexibility of our phenotypes-from-genotypes simulation approach to explore how the performance of genomic animal models can be influenced by different genetic architectures (clumped vs even genomic distribution of QTLs, and different QTL effect sizes), levels of heritability, and experimental design (sampled individuals and genetic markers). C_LIO_LIWe then applied our framework to a study of head shape traits in a wild marine intertidal fish, Bathygobius cocosensis (Bleeker 1854), for which we acquired SNP genotypes with RADseq. Although our working sample of 297 fish contained no close kin, our framework helped validate the power of genomic animal models, allowing us to confidently infer heritable variation in one head shape trait (estimated h2 = 0.17). C_LIO_LIOur study addresses key methodological gaps for using quantitative genomic approaches on wild organisms, offering a rare example of partitioned heritable and non-heritable contributions to phenotypic variation in a non-model wild marine fish. Our novel phenotypes-from-genotypes approach also provides a new method for simulating QTLs using observed population genetic data. C_LI

The revolution of high-accuracy long reads offers unprecedented quality and contiguity in genome assembly. Pacific Biosciences (PacBio) and Oxford Nanopore Technologies have made significant strides in improving their sequencing technologies, yielding reads with error rates below 1% and lengths ranging from kilobases to megabases. These advancements have prompted the development of assembly tools tailored to leverage the enhanced accuracy of long reads. However, the challenge of collapsing haplotypes into high-quality haploid assemblies persists, especially for highly heterozygous genomes. This raises questions about the feasibility and desirability of phased assemblies versus collapsed haploid assemblies. To address these challenges, we benchmarked five assembly tools on ultra-low input PacBio HiFi and Nanopore R10.4 reads from the parthenogenetic nematode species Plectus sambesii. We propose a comprehensive methodology for assessing phased assemblies, repurposing existing evaluation programs to collect haplotype-relevant statistics. Our evaluation criteria include assembly size, contiguity, and completeness, with a focus on assessing the accuracy of phased assemblies by examining duplicated BUSCO orthologs and k -mer spectra. Additionally, we present strategies for generating collapsed assemblies by purging haplotigs. This study provides valuable insights and guidelines for generating high-quality phased and collapsed de novo genome assemblies from highly accurate long reads, particularly beneficial for non-model species genome assembly projects.

Researchers studying species in nature often find it challenging to apply methods based on simplistic models of reality. Here I consider how some real-world complications influence demographic estimates of effective population size (Ne) when generations overlap. The most widely-used model (by Hill) expresses Ne as a function of variance in lifetime reproductive output (LRO) of the N1 members of a newborn cohort. Hills model assumes stable age structure and constant population size, in which case mean [Formula]. In real-world applications, researchers often ask whether unbiased estimates can be obtained under the following conditions: (1) When [Formula] for empirical data; (2) If cohorts are defined at a later age than newborns; (3) If survival to age at sexual maturity () is not random; (4) When some or all null parents (those with LRO=0) are not sampled. Using analytical methods and computer simulations, I show that: (1) Because variance in offspring number is positively correlated with the mean, [Formula] will be biased using raw data when [Formula], but this bias can be overcome by rescaling var(LRO) to its expected value when [Formula]. (2) The cohort can be defined at any age [&le;], provided that (a) LRO data cover the full lifespan (e.g., production of newborns by newborns, or production of adults by adults), and (b) survival to age is random. (3) If juvenile survival is family-correlated, defining cohorts at age avoids upward bias in [Formula] that occurs if newborn cohorts are used. (4) Missing some or all null parents has no effect on [Formula], provided that data are rescaled to [Formula].