The Effects of Ecological Traits on the Rate of Molecular Evolution in Ray-Finned Fishes: A Multivariable Approach

CanFlyet: habitat zone and diet trait dataset for Diptera species of Canada and Greenland

Background

Flies (Diptera) are an ecologically important group that play a role in agriculture, public health and ecosystem functioning. As researchers continue to investigate this order, it is beneficial to link the growing occurrence data to biological traits. However, large-scale ecological trait data are not readily available for fly species. While some databases and datasets include fly data, many ecologically relevant traits for taxa of interest are not included. In this study, we create a dataset containing ecological traits (habitat and diet) for fly species of Canada and Greenland having occurrence records on the Barcode of Life Data Systems (BOLD). We present a dataset containing trait information from the literature for 981 Diptera species.

New information

Diptera species were chosen for the dataset, based on the occurrence records available for Diptera species from Canada and Greenland on the Barcode of Life Data System (BOLD). Trait data were then compiled and digitised in a standardised format, based on 667 works from literature published before April 2024. Traits were assigned at the lowest taxonomic level available. Three biological traits were included: larval habitat, larval diet type and adult diet. The dataset contains traits for 981 species across 380 genera, 34 subfamilies and 61 families. This dataset allows for assignment of traits to occurrence data for Diptera species and can be used for further research into the ecology, evolution and conservation of this order.

Diversity of lanternfish (Myctophidae) larvae along the Ninety East Ridge, Indian Ocean

Since the 19th century, the impact of seamounts on the distribution of plankton has been a topic of considerable interest. The influence of seamounts on the biogeographic patterns of marine organisms is complex, with some aspects still under debate. It is generally accepted that seamounts can drive the upwelling of nutrient-rich deep waters. Tidal amplification, flow acceleration, and internal waves can further enhance vertical mixing, leading to increased primary productivity near seamounts. Seamounts may also act as barriers to the migration of marine organisms, affecting gene flow. Research on Pacific seamounts suggests these features might serve as "stepping stones" for the dispersal of marine species across the ocean. However, investigations of seamounts in the eastern Indian Ocean remain limited. Focusing on the Ninety East Ridge region in the eastern Indian Ocean, this study collected zooplankton samples using horizontal (surface) and vertical (0-200 m) plankton nets and measured temperature and salinity profiles with a conductivity, temperature, and depth (CTD) sensor. A total of 544 fish larvae were identified, including 260 lanternfish larvae, representing 38 species across 12 genera, determined through COI DNA barcoding. Phylogenetic trees and haplotype networks were constructed to analyze genetic distances and population structures of lanternfish species. Among the samples, intra-specific genetic distances ranged from 0% to 2.99%, while inter-specific distances ranged from 1.88% to 25.71%. Except for Notolychnus valdiviae (Brauer, 1904), the maximum intra-specific distances were lower than the minimum inter-specific distances for all species. Haplotype analysis of nine species revealed significant variations in haplotype number, structure, and spatial distribution. Specifically, Ceratoscopelus warmingii (Lütken, 1892) and N. valdiviae exhibited a notable north-south divergence pattern, consistent with the temperature and salinity distribution of the region's water masses. This conclusion was supported by analysis of molecular variance analysis, suggesting that larval stages of certain lanternfish species may struggle to cross boundaries between water masses. However, the remaining species showed no significant north-south distribution differences, possibly due to their adaptive capabilities, vertical migration patterns, or the duration of their planktonic larval stages. These findings suggest that seamounts and water mass distribution have varying implications for lanternfish species, potentially influencing gene flow and horizontal distribution patterns, which could contribute to speciation. Global climate change-induced alterations in ocean currents may profoundly impact the genetic diversity of fish species. This study provides new insights into the diversity of lanternfish in the Ninety East Ridge region and offers valuable data for understanding the biogeography of seamounts.

Genome-wide analysis reveals the contributors to fast molecular evolution of the Chinese hook snout carp (Opsariichthys bidens)

Variations in molecular evolutionary rate have been widely investigated among lineages and genes. However, it remains an open question whether fast rate of molecular evolution is driven by natural selection or random drift, and how the fast rate is linked to metabolic rate. Additionally, previous studies on fast molecular evolution have been largely restricted to concatenated matrix of genes or a few specifically selected genes, but less is known for individual genes at the genome-wide level. Here we addressed these questions using more than 5000 single-copy orthologous (SCO) genes through comparative genomic and phylogenetic analyses among fishes, with a special focus on a newly-sequenced clupeocephalan fish the Chinese hook snout carp Opsariichthys bidens. We showed O. bidens displays significantly higher mean substitution rate and more fast-evolving SCO genes (2172 genes) than most fishes studied here. The rapidly evolving genes are enriched in highly conserved and very basic functions such as translation and ribosome that are critical for biological fitness. We further revealed that ∼25 % of these fast-evolving genes exhibit a constant increase of substitution rate from the common ancestor down to the present, suggesting a neglected but important contribution from ancestral states. Model fitting showed that ∼85 % of fast-evolving genes exclusive to O. bidens and related species follow the adaptive evolutionary model rather than random-drift model, and 7.6 % of fast-evolving genes identified in O. bidens have experienced positive selection, both indicating the reflection of adaptive selection. Finally, metabolic rate was observed to be linked with substitution rate in a gene-specific manner. Overall, our findings reveal fast molecular evolution of SCO genes at genome-wide level in O. bidens, and uncover the evolutionary and ecological contributors to it.

Combining Molecular, Macroevolutionary, and Macroecological Perspectives on the Generation of Diversity

Charles Darwin presented a unified process of diversification driven by the gradual accumulation of heritable variation. The growth in DNA databases and the increase in genomic sequencing, combined with advances in molecular phylogenetic analyses, gives us an opportunity to realize Darwin's vision, connecting the generation of variation to the diversification of lineages. The rate of molecular evolution is correlated with the rate of diversification across animals and plants, but the relationship between genome change and speciation is complex: Mutation rates evolve in response to life history and niche; substitution rates are influenced by mutation, selection, and population size; rates of acquisition of reproductive isolation vary between populations; and traits, niches, and distribution can influence diversification rates. The connection between mutation rate and diversification rate is one part of the complex and varied story of speciation, which has theoretical importance for understanding the generation of biodiversity and also practical impacts on the use of DNA to understand the dynamics of speciation over macroevolutionary timescales.

VLF: An R package for the analysis of very low frequency variants in DNA sequences

Here, we introduce VLF, an R package to determine the distribution of very low frequency variants (VLFs) in nucleotide and amino acid sequences for the analysis of errors in DNA sequence records. The package allows users to assess VLFs in aligned and trimmed protein-coding sequences by automatically calculating the frequency of nucleotides or amino acids in each sequence position and outputting those that occur under a user-specified frequency (default of p = 0.001). These results can then be used to explore fundamental population genetic and phylogeographic patterns, mechanisms and processes at the microevolutionary level, such as nucleotide and amino acid sequence conservation. Our package extends earlier work pertaining to an implementation of VLF analysis in Microsoft Excel, which was found to be both computationally slow and error prone. We compare those results to our own herein. Results between the two implementations are found to be highly consistent for a large DNA barcode dataset of bird species. Differences in results are readily explained by both manual human error and inadequate Linnean taxonomy (specifically, species synonymy). Here, VLF is also applied to a subset of avian barcodes to assess the extent of biological artifacts at the species level for Canada goose (Branta canadensis), as well as within a large dataset of DNA barcodes for fishes of forensic and regulatory importance. The novelty of VLF and its benefit over the previous implementation include its high level of automation, speed, scalability and ease-of-use, each desirable characteristics which will be extremely valuable as more sequence data are rapidly accumulated in popular reference databases, such as BOLD and GenBank.

Investigating the reliability of molecular estimates of evolutionary time when substitution rates and speciation rates vary

Background

An accurate timescale of evolutionary history is essential to testing hypotheses about the influence of historical events and processes, and the timescale for evolution is increasingly derived from analysis of DNA sequences. But variation in the rate of molecular evolution complicates the inference of time from DNA. Evidence is growing for numerous factors, such as life history and habitat, that are linked both to the molecular processes of mutation and fixation and to rates of macroevolutionary diversification. However, the most widely used methods rely on idealised models of rate variation, such as the uncorrelated and autocorrelated clocks, and molecular dating methods are rarely tested against complex models of rate change. One relationship that is not accounted for in molecular dating is the potential for interaction between molecular substitution rates and speciation, a relationship that has been supported by empirical studies in a growing number of taxa. If these relationships are as widespread as current evidence suggests, they may have a significant influence on molecular dates.

Results

We simulate phylogenies and molecular sequences under three different realistic rate variation models—one in which speciation rates and substitution rates both vary but are unlinked, one in which they covary continuously and one punctuated model in which molecular change is concentrated in speciation events, using empirical case studies to parameterise realistic simulations. We test three commonly used “relaxed clock” molecular dating methods against these realistic simulations to explore the degree of error in molecular dates under each model. We find average divergence time inference errors ranging from 12% of node age for the unlinked model when reconstructed under an uncorrelated rate prior using BEAST 2, to up to 91% when sequences evolved under the punctuated model are reconstructed under an autocorrelated prior using PAML.

Conclusions

We demonstrate the potential for substantial errors in molecular dates when both speciation rates and substitution rates vary between lineages. This study highlights the need for tests of molecular dating methods against realistic models of rate variation generated from empirical parameters and known relationships.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-02015-8.

Diversification Rate is Associated with Rate of Molecular Evolution in Ray-Finned Fish (Actinopterygii)

Understanding the factors that drive diversification of taxa across the tree of life is a key focus of macroevolutionary research. While the effects of life history, ecology, climate and geography on diversity have been studied for many taxa, the relationship between molecular evolution and diversification has received less attention. However, correlations between rates of molecular evolution and diversification rate have been detected in a range of taxa, including reptiles, plants and birds. A correlation between rates of molecular evolution and diversification rate is a prediction of several evolutionary theories, including the evolutionary speed hypothesis which links variation in mutation rates to differences in speciation rates. If it is widespread, such correlations could also have significant practical impacts, if they are not adequately accounted for in phylogenetic inference of evolutionary rates and timescales. Ray-finned fish (Actinopterygii) offer a prime target to test for this relationship due to their extreme variation in clade size suggesting a wide range of diversification rates. We employ both a sister-pairs approach and a whole-tree approach to test for correlations between substitution rate and net diversification. We also collect life history and ecological trait data and account for potential confounding factors including body size, latitude, max depth and reef association. We find evidence to support a relationship between diversification and synonymous rates of nuclear evolution across two published backbone phylogenies, as well as weak evidence for a relationship between mitochondrial nonsynonymous rates and diversification at the genus level.

Phylogenetic signal of sub-arctic beetle communities

Postglacial dispersal and colonization processes have shaped community patterns in sub-Arctic regions such as Churchill, Manitoba, and Canada. This study investigates evolutionary community structure within the beetle (Coleoptera) families of Churchill and tests whether biological traits have played a role in governing colonization patterns from refugial and southerly geographic regions. This study quantifies sub-Arctic beetle phylogenetic community structure for each family using the net relatedness index (NRI) and nearest taxon index (NTI), calculated using publicly available data from the Barcode of Life Data Systems (BOLD); compares patterns across families with different traits (habitat, diet) using standard statistical analysis (ANOVA) as well as phylogenetic generalized least squares (PGLS) using a family-level beetle phylogeny obtained from the literature; and compares community structure in Churchill with a region in southern Canada (Guelph, Ontario). These analyses were also repeated at a genus level. The dominant pattern detected in our study was that aquatic families were much better represented in Churchill compared to terrestrial families, when compared against richness sampled from across Canada and Alaska. Individually, most families showed significant phylogenetic clustering in Churchill, likely due to the strong environmental filtering present in Arctic environments. There was no significant difference in phylogenetic structure between Churchill and Guelph but with a trend toward stronger clustering in the North. Fungivores were significantly more overdispersed than other feeding modes, predators were significantly more clustered, and aquatic families showed significantly stronger clustering compared to terrestrial. This study contributes to our understanding of the traits and processes structuring insect biodiversity and macroecological trends in the sub-Arctic.