Circumpolar phylogeography and demographic history of beluga whales reflect past climatic fluctuations

The direction, timing and demography of Popillia japonica (Coleoptera) invasion reconstructed using complete mitochondrial genomes

The Japanese beetle Popillia japonica is a pest insect that feeds on hundreds of species of wild and cultivated plants including important fruit, vegetable, and field crops. Native to Japan, the pest has invaded large areas of the USA, Canada, the Azores (Portugal), Italy, and Ticino (Switzerland), and it is considered a priority for control in the European Union. We determined the complete mitochondrial genome sequence in 86 individuals covering the entire distribution of the species. Phylogenetic analysis supports a major division between South Japan and Central/North Japan, with invasive samples coming from the latter. The origin of invasive USA samples is incompatible, in terms of the timing of the event, with a single introduction, with multiple Japanese lineages having been introduced and one accounting for most of the population expansion locally. The origin of the two invasive European populations is compatible with two different invasions followed by minimal differentiation locally. Population analyses provide the possibility to estimate the rate of sequence change from the data and to date major invasion events. Demographic analysis identifies a population expansion followed by a period of contraction prior to the invasion. The present study adds a time and demographic dimension to available reconstructions.

Contrasting new and available reference genomes to highlight uncertainties in assemblies and areas for future improvement: an example with monodontid species

BACKGROUND

Reference genomes provide a foundational framework for evolutionary investigations, ecological analysis, and conservation science, yet uncertainties in the assembly of reference genomes are difficult to assess, and by extension rarely quantified. Reference genomes for monodontid cetaceans span a wide spectrum of data types and analytical approaches, providing the context to derive broader insights related to discrepancies and regions of uncertainty in reference genome assembly. We generated three beluga (Delphinapterus leucas) and one narwhal (Monodon monoceros) reference genomes and contrasted these with published chromosomal scale assemblies for each species to quantify discrepancies associated with genome assemblies.

RESULTS

The new reference genomes achieved chromosomal scale assembly using a combination of PacBio long reads, Illumina short reads, and Hi-C scaffolding data. For beluga, we identified discrepancies in the order and orientation of contigs in 2.2-3.7% of the total genome depending on the pairwise comparison of references. In addition, unsupported higher order scaffolding was identified in published reference genomes. In contrast, we estimated 8.2% of the compared narwhal genomes featured discrepancies, with inversions being notably abundant (5.3%). Discrepancies were linked to repetitive elements in both species.

CONCLUSIONS

We provide several new reference genomes for beluga (Delphinapterus leucas), while highlighting potential avenues for improvements. In particular, additional layers of data providing information on ultra-long genomic distances are needed to resolve persistent errors in reference genome construction. The comparative analyses of monodontid reference genomes suggested that the three new reference genomes for beluga are more accurate compared to the currently published reference genome, but that the new narwhal genome is less accurate than one published. We also present a conceptual summary for improving the accuracy of reference genomes with relevance to end-user needs and how they relate to levels of assembly quality and uncertainty.

Guidelines and quantitative standards for improved cetacean taxonomy using full mitochondrial genomes

In many organisms, especially those of conservation concern, traditional lines of evidence for taxonomic delineation, such as morphological data, are often difficult to obtain. In these cases, genetic data are often the only source of information available for taxonomic studies. In particular, population surveys of mitochondrial genomes offer increased resolution and precision in support of taxonomic decisions relative to conventional use of the control region or other gene fragments of the mitochondrial genome. To improve quantitative guidelines for taxonomic decisions in cetaceans, we build on a previous effort targeting the control region and evaluate, for whole mitogenome sequences, a suite of divergence and diagnosability estimates for pairs of recognized cetacean populations, subspecies, and species. From this overview, we recommend new guidelines based on complete mitogenomes, combined with other types of evidence for isolation and divergence, which will improve resolution for taxonomic decisions, especially in the face of small sample sizes or low levels of genetic diversity. We further use simulated data to assist interpretations of divergence in the context of varying forms of historical demography, culture, and ecology.

Whole genome analyses reveal weak signatures of population structure and environmentally associated local adaptation in an important North American pollinator, the bumble bee Bombus vosnesenskii

Studies of species that experience environmental heterogeneity across their distributions have become an important tool for understanding mechanisms of adaptation and predicting responses to climate change. We examine population structure, demographic history and environmentally associated genomic variation in Bombus vosnesenskii, a common bumble bee in the western USA, using whole genome resequencing of populations distributed across a broad range of latitudes and elevations. We find that B. vosnesenskii exhibits minimal population structure and weak isolation by distance, confirming results from previous studies using other molecular marker types. Similarly, demographic analyses with Sequentially Markovian Coalescent models suggest that minimal population structure may have persisted since the last interglacial period, with genomes from different parts of the species range showing similar historical effective population size trajectories and relatively small fluctuations through time. Redundancy analysis revealed a small amount of genomic variation explained by bioclimatic variables. Environmental association analysis with latent factor mixed modelling (LFMM2) identified few outlier loci that were sparsely distributed throughout the genome and although a few putative signatures of selective sweeps were identified, none encompassed particularly large numbers of loci. Some outlier loci were in genes with known regulatory relationships, suggesting the possibility of weak selection, although compared with other species examined with similar approaches, evidence for extensive local adaptation signatures in the genome was relatively weak. Overall, results indicate B. vosnesenskii is an example of a generalist with a high degree of flexibility in its environmental requirements that may ultimately benefit the species under periods of climate change.

Commerson's dolphin population structure: evidence for female phylopatry and male dispersal

A key in species conservation is understanding the amount and distribution of genetic diversity and how environmental changes that occurred in the recent past may have influenced current patterns of population structure. Commerson's dolphin, Cephalorhynchus commersonii, has two subspecies, one of which is endemic to South America (C. commersonii commersonii) and little is known about its population genetics. Our objective was to investigate the population genetics of this subspecies throughout its distribution. Using 70 skin samples and information available in GenBank, 308 mitochondrial DNA sequences and 28 species-specific microsatellites were analyzed. The species presented low genetic diversity when compared to other dolphin species, but was consistent with other species within the genus. Strong population structure based on mitochondrial DNA was exhibited throughout its entire distribution, a pattern consistent with female philopatry. However, this pattern was not detected when using microsatellites, suggesting male-mediated gene flow. Demographic tests suggested a population expansion beginning approximately 15,000 years ago, after the Last Glacial Maximum. In a climate change scenario, we recommended considering each sampling location as an independent population management unit in order to evaluate the impact of possible environmental changes on the distribution of genetic information within the species.

Climate change and cetacean health: impacts and future directions

Climate change directly impacts the foraging opportunities of cetaceans (e.g. lower prey availability), leads to habitat loss, and forces cetaceans to move to other feeding grounds. The rise in ocean temperature, low prey availability and loss of habitat can have severe consequences for cetacean survival, particularly those species that are already threatened or those with a limited habitat range. In addition, it is predicted that the concentration of contaminants in aquatic environments will increase owing to Arctic meltwater and increased rainfall events leading to higher rates of land-based runoff in downstream coastal areas. These persistent and mobile contaminants can bioaccumulate in the ecosystem, and lead to ecotoxicity with potentially severe consequences on the reproductive organs, immune system and metabolism of marine mammals. There is a need to measure and assess the cumulative impact of multiple stressors, given that climate change, habitat alteration, low prey availability and contaminants do not act in isolation. Human-caused perturbations to cetacean foraging abilities are becoming a pervasive and prevalent threat to many cetacean species on top of climate change-associated stressors. We need to move to a greater understanding of how multiple stressors impact the metabolism of cetaceans and ultimately their population trajectory. This article is part of the theme issue 'Nurturing resilient marine ecosystems'.

205 newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates

Mitochondrial DNA remains a cornerstone for molecular ecology, especially for study species from which high‐quality tissue samples cannot be easily obtained. Methods using mitochondrial markers are usually reliant on reference databases, but these are often incomplete. Furthermore, available mitochondrial genomes often lack crucial metadata, such as sampling location, limiting their utility for many analyses. Here, we assembled 205 new mitochondrial genomes for platyrrhine primates, most from the Amazon and with known sampling locations. We present a dated mitogenomic phylogeny based on these samples along with additional published platyrrhine mitogenomes, and use this to assess support for the long‐standing riverine barrier hypothesis (RBH), which proposes that river formation was a major driver of speciation in Amazonian primates. Along the Amazon, Negro, and Madeira rivers, we found mixed support for the RBH. While we identified divergences that coincide with a river barrier, only some occur synchronously and also overlap with the proposed dates of river formation. The most compelling evidence is for the Amazon river potentially driving speciation within bearded saki monkeys (Chiropotes spp.) and within the smallest extant platyrrhines, the marmosets and tamarins. However, we also found that even large rivers do not appear to be barriers for some primates, including howler monkeys (Alouatta spp.), uakaris (Cacajao spp.), sakis (Pithecia spp.), and robust capuchins (Sapajus spp.). Our results support a more nuanced, clade‐specific effect of riverine barriers and suggest that other evolutionary mechanisms, besides the RBH and allopatric speciation, may have played an important role in the diversification of platyrrhines.

Larger body size leads to greater female beluga whale ovarian reproductive activity at the southern periphery of their range

Identification of phenotypic characteristics in reproductively successful individuals provides important insights into the evolutionary processes that cause range shifts due to environmental change. Female beluga whales (Delphinapterus leucas) from the Baffin Bay region (BB) of the Canadian Arctic in the core area of the species' geographic range have larger body size than their conspecifics at the southern range periphery in Hudson Bay (HB). We investigated the mechanism for this north and south divergence as it relates to ovarian reproductive activity (ORA = total corpora) that combines morphometric data with ovarian corpora counted from female reproductive tracts. Our study aim was to assess the relative influence of age and body size of female beluga whale on ORA in the two populations. Female beluga whale ORA increased more quickly with age (63% partial variation explained) in BB than in HB (41%). In contrast, body length in HB female beluga whales accounted for considerably more of the total variation (12% vs. 1%) in ORA compared to BB whales. We speculate that female HB beluga whale ORA was more strongly linked with body length due to higher population density resulting in food competition that favors the energetic advantages of larger body size during seasonal food limitations. Understanding the evolutionary mechanism of how ORA varies across a species' range will assist conservation efforts in anticipating and mitigating future challenges associated with a warming planet.