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Data from: Contrasting patterns of divergence at the regulatory and sequence level in European Daphnia galeata natural populations
Understanding the genetic basis of local adaptation has long been the focus of evolutionary biology. Recently there has been increased interest in deciphering the evolutionary role of Daphnia's plasticity and the molecular mechanisms of local adaptation. Using transcriptome data, we assessed the differences in gene expression profiles and sequences within and between four European Daphnia galeata populations. To distinguish neutral from adaptive differentiation, we corrected for phylogenetic differentiation of Daphnia populations. We also applied a "transcriptome scan" approach to investigate the role of natural selection in shaping divergent expression profiles among populations. Furthermore, a SNP analysis allowed inferring population structure and the distribution of genetic variation. Using sequence information, the transcripts were annotated using a comparative genomics approach. In total, ~33% of 32903 transcripts were differentially expressed between populations. Among 10280 differentially expressed transcripts, 5209 transcripts deviated from neutral expectations and were likely involved in local adaptation. The population divergence at the sequence level was higher than at the gene expression level by several orders of magnitude and revealed very distinct clusters according to population origin. Our analysis revealed the respective roles of genetic drift and selection in the four Daphnia populations. This study is a first attempt to understand the genetic background of adaptation to environmental changes in a key species of aquatic ecosystems in absence of any laboratory induced stressor.
Data from: Comparative species divergence across eight triplets of spiny lizards (Sceloporus) using genomic sequence data
Species divergence is typically thought to occur in the absence of gene flow, but many empirical studies are discovering that gene flow may be more pervasive during species formation. Although many examples of divergence with gene flow have been identified, only few clades have been investigated in a comparative manner, and fewer have been studied using genome-wide sequence data. We contrast species divergence genetic histories across eight triplets of North American Sceloporus lizards using a maximum likelihood implementation of the isolation–migration (IM) model. Gene flow at the time of species divergence is modeled indirectly as variation in species divergence time across the genome or explicitly using a migration rate parameter. Likelihood ratio tests (LRTs) are used to test the null model of no gene flow at speciation against these two alternative gene flow models. We also use the Akaike information criterion to rank the models. Hundreds of loci are needed for the LRTs to have statistical power, and we use genome sequencing of reduced representation libraries to obtain DNA sequence alignments at many loci (between 340 and 3,478; mean 1⁄4 1,678) for each triplet. We find that current species distributions are a poor predictor of whether a species pair diverged with gene flow. Interrogating the genome using the triplet method expedites the comparative study of species divergence history and the estimation of genetic parameters associated with speciation.
Data from: The transcriptomics of sympatric dwarf and normal lake whitefish (Coregonus clupeaformis spp., Salmonidae) divergence as revealed by next-generation sequencing
Gene expression divergence is one of the mechanisms thought to be involved in the emergence of incipient species. Next-generation sequencing has become an extremely valuable tool for the study of this process by allowing whole transcriptome sequencing, or RNA-Seq. We have conducted a 454 GS-FLX pyrosequencing experiment in order to refine our understanding of adaptive divergence between dwarf and normal lake whitefish species (Coregonus clupeaformis spp.). The objectives were to: (1) investigate transcriptomic divergence as measured by liver RNA-Seq; (2) test the correlation between divergence in expression and sequence polymorphism and (3) investigate the extent of allelic imbalance. We also compared the results of RNA-seq with those of a previous microarray study performed on the same fish. Following de novo assembly, results showed that normal whitefish over-expressed more contigs associated with protein synthesis while dwarf fish over-expressed more contigs related to energy metabolism, immunity and DNA replication and repair. Moreover, 63 SNPs showed significant allelic imbalance, and this phenomenon prevailed in the recently diverged dwarf whitefish. Results also showed an absence of correlation between gene expression divergence as measured by RNA-Seq and either polymorphism rate or sequence divergence between normal and dwarf whitefish. This study reiterates an important role for gene expression divergence, and provides evidence for allele-specific expression divergence as well as evolutionary decoupling of regulatory and coding sequences in the adaptive divergence of normal and dwarf whitefish. It also demonstrates how next-generation sequencing can lead to a more comprehensive understanding of transcriptomic divergence in a young species pair.
Data from: RAD sequencing reveals genomewide divergence between independent invasions of the European green crab (Carcinus maenas) in the Northwest Atlantic
Genomic studies of invasive species can reveal both invasive pathways and functional differences underpinning patterns of colonization success. The European green crab (Carcinus maenas) was initially introduced to eastern North America nearly 200 years ago where it expanded northwards to eastern Nova Scotia. A subsequent invasion to Nova Scotia from a northern European source allowed further range expansion, providing a unique opportunity to study the invasion genomics of a species with multiple invasions. Here, we use restriction-site-associated DNA sequencing-derived SNPs to explore fine-scale genomewide differentiation between these two invasions. We identified 9137 loci from green crab sampled from 11 locations along eastern North America and compared spatial variation to mitochondrial COI sequence variation used previously to characterize these invasions. Overall spatial divergence among invasions was high (pairwise FST ~0.001 to 0.15) and spread across many loci, with a mean FST ~0.052 and 52% of loci examined characterized by FST values >0.05. The majority of the most divergent loci (i.e., outliers, ~1.2%) displayed latitudinal clines in allele frequency highlighting extensive genomic divergence among the invasions. Discriminant analysis of principal components (both neutral and outlier loci) clearly resolved the two invasions spatially and was highly correlated with mitochondrial divergence. Our results reveal extensive cryptic intraspecific genomic diversity associated with differing patterns of colonization success and demonstrates clear utility for genomic approaches to delineating the distribution and colonization success of aquatic invasive species.
Data from: Genotype by sequencing identifies natural selection as a driver of intraspecific divergence in Atlantic populations of the high dispersal marine invertebrate, Macoma petalum
Mitochondrial DNA analyses indicate that the Bay of Fundy population of the intertidal tellinid bivalve Macoma petalum is genetically divergent from coastal populations in the Gulf of Maine and Nova Scotia. To further examine the evolutionary forces driving this genetic break, we performed double digest genotype by sequencing (GBS) to survey the nuclear genome for evidence of both neutral and selective processes shaping this pattern. The resulting reads were mapped to a partial transcriptome of its sister species, M. balthica, to identify single nucleotide polymorphisms (SNPs) in protein-coding genes. Population assignment tests, principle components analyses, analysis of molecular variance, and outlier tests all support differentiation between the Bay of Fundy genotype and the genotypes of the Gulf of Maine, Gulf of St. Lawrence, and Nova Scotia. Although both neutral and non-neutral patterns of genetic subdivision were significant, genetic structure among the regions was nearly 20 times higher for loci putatively under selection, suggesting a strong role for natural selection as a driver of genetic diversity in this species. Genetic differences were the greatest between the Bay of Fundy and all other population samples, and some outlier proteins were involved in immunity-related processes. Our results suggest that in combination with limited gene flow across the mouth of the Bay of Fundy, local adaptation is an important driver of intraspecific genetic variation in this marine species with high dispersal potential.
Fig. 3 in ddRAD Sequencing Sheds Light on Low Interspecific and High Intraspecific mtDNA Divergences in Two Groups of Caddisflies
Fig. 3. Maximum likelihood trees and population structuring of Apatania (A) and Limnephilus (B) based on ddRAD SNP data.ML trees were inferred from RAxML analysis with 1,000 bootstrap replicates. The bootstrap values are indicated near the branches. Results of population STRUCTURE analyses with posterior probability plots of individual assignments to the inferred genetic clusters for K = 6 and 7 for Apatania and K = 4 for Limnephilus.
Fig. 2 in ddRAD Sequencing Sheds Light on Low Interspecific and High Intraspecific mtDNA Divergences in Two Groups of Caddisflies
Fig. 2. Maximum likelihood trees based on mitochondrial COI sequences of Apatania (A) and Limnephilus (B). The bootstrap values are indicated near the branches (only shown for nodes supported with more than 50% of BS).
Supplementary material 1 from: Colihueque N, Gantz A, Rau JR, Parraguez M (2015) Genetic divergence analysis of the Common Barn Owl Tyto alba (Scopoli, 1769) and the Short-eared Owl Asio flammeus (Pontoppidan, 1763) from southern Chile using COI sequence. ZooKeys 534: 135-146. https://doi.org/10.3897/zookeys.534.5953
Pictures of external morphology of specimens of Tyto alba and Asio flammeus collected in southern Chile: Explanation note: Pictures of ventral and dorsal views of specimens showing plumage color and overall appearance. Data on body mass of these specimens are also provided.
Figure 6 in A phylogeny with divergence-time estimation of planthoppers (Hemiptera: Fulgoroidea) based on mitochondrial sequences
Figure 6. Chronogram of Fulgoroidea estimated using the Bayesian phylogenetic by MCMCTREE in paml. Time units are in millions of years. Estimated divergence times are shown near nodes.
Figure 5 in A phylogeny with divergence-time estimation of planthoppers (Hemiptera: Fulgoroidea) based on mitochondrial sequences
Figure 5. BI analysis (PhyloBayes) based on PCG12R–ATP8. Numerals at nodes are Bayesian posterior probabilities (PP). '–' indicates different clades.
Figure 1 in A phylogeny with divergence-time estimation of planthoppers (Hemiptera: Fulgoroidea) based on mitochondrial sequences
Figure 1. Sliding window analysis. The red curve shows the value of nucleotide diversity (Pi). Pi value of each PCG is shown below the arrows.
Figure 4 in A phylogeny with divergence-time estimation of planthoppers (Hemiptera: Fulgoroidea) based on mitochondrial sequences
Figure 4. BI analysis (MrBayes) based on PCG12R–ATP8. Numerals at nodes are Bayesian posterior probabilities (PP). '–' indicates different clades.
Figure 2 in A phylogeny with divergence-time estimation of planthoppers (Hemiptera: Fulgoroidea) based on mitochondrial sequences
Figure 2. Genetic distance (on average) and ratio of non-synonymous (Ka) to synonymous (Ks) substitution rates.
Figure 3 in A phylogeny with divergence-time estimation of planthoppers (Hemiptera: Fulgoroidea) based on mitochondrial sequences
Figure 3. ML analysis based on PCG12R–ATP8. Numerals at nodes are bootstrap values (BS). '–' indicates different clades.
FIGURE 3. Boxplots illustrating uncorrected pairwise sequence divergence. Colored boxes represent the 50 in A new species of forest-dwelling Cyrtodactylus Gray (Squamata: Gekkonidae) from the Indawgyi Wildlife Sanctuary, Kachin State, Myanmar
FIGURE 3. Boxplots illustrating uncorrected pairwise sequence divergence. Colored boxes represent the 50% quartiles. Lightblue circles represent mean values.
Fig. 2 Splits graph for ITS sequences from 26 in Allopatric divergence and secondary contacts in Euphorbia spinosa L: Influence of climatic changes on the split of the species
Fig. 2 Splits graph for ITS sequences from 26 ribotypes of E. spinosa. Branch lengths were estimated using the standard implementation of split decomposition (SplitsTree 4.0 beta 06). Ribotype abbreviations are given in Table 3
Data from: Chironomus riparius (Diptera) genome sequencing reveals the impact of minisatellite transposable elements on population divergence
Active transposable elements (TEs) may result in divergent genomic insertion and abundance patterns among conspecific populations. Upon secondary contact, such divergent genetic backgrounds can theoretically give rise to classical Dobzhansky-Muller incompatibilities (DMI), thus contributing to the evolution of endogenous genetic barriers and eventually cause population divergence. We investigated differential TE abundance among conspecific populations of the non-biting midge Chironomus riparius and evaluated their potential role in causing endogenous genetic incompatibilities between these populations. We focussed on a Chironomus-specific TE, the minisatellite-like Cla-element, whose activity is associated with speciation in the genus. Using a newly generated and annotated draft genome for a genomic study with five natural C. riparius populations, we found highly population-specific TE insertion patterns with many private insertions. A significant correlation of the pairwise FST estimated from genome-wide single nucleotide polymorphisms (SNPs) and the FST estimated from TEs, is consistent with drift as the major force driving TE population differentiation. However, the significantly higher Cla-element FST level due to a high proportion of differentially fixed Cla-element insertions also indicates selection against segregating (i.e. heterozygous) insertions. With reciprocal crossing experiments and fluorescent in-situ hybridisation of Cla-elements to polytene chromosomes, we documented phenotypic effects on female fertility and chromosomal mispairings. We propose that the inferred negative selection on heterozygous Cla-element insertions may cause endogenous genetic barriers and therefore acts as DMI among C. riparius populations. The intrinsic genomic turnover exerted by TEs may thus have a direct impact on population divergence that is operationally different from drift and local adaptation.
Supporting data for: Whole genome sequencing reveals fine-scale environment associated divergence near the range limits of a temperate reef fish
<p>Environmental variation is increasingly recognized as an important driver of diversity in marine species despite the lack of physical barriers to dispersal and the presence of pelagic stages in many taxa. A robust understanding of the genomic and ecological processes involved in structuring populations is lacking for most marine species, often hindering management and conservation action. Cunner (<em>Tautogolabrus adspersus</em>), is a temperate reef fish with both pelagic early life history stages and strong site-associated homing as adults; the species is also of interest for use as a cleaner fish in salmonid aquaculture in Atlantic Canada. We aimed to characterize genomic and geographic differentiation of cunner in the Northwest Atlantic. To achieve this, a chromosome-level genome assembly for cunner was produced and used to characterize spatial population structure throughout Atlantic Canada using whole genome resequencing. The genome assembly spanned 0.72 Gbp and 24 chromosomes; whole genome resequencing of 803 individuals from 20 locations from Newfoundland to New Jersey identified approximately 11 million genetic variants. Principal component analysis revealed four regional Atlantic Canadian groups. Pairwise F<sub>ST</sub> and selection scans revealed signals of differentiation and selection at discrete genomic regions, including adjacent peaks on chromosome 10 across multiple pairwise comparisons (<em>i.e.</em>, F<sub>ST</sub> 0.5–0.75). Redundancy analysis suggested association of environmental variables related to benthic temperature and oxygen range with genomic structure. Results suggest regional scale diversity in this temperate reef fish and can directly inform the collection and translocation of cunner for aquaculture applications and the conservation of wild populations throughout the Northwest Atlantic.</p>
Data from: The transcriptomics of sympatric dwarf and normal lake whitefish (Coregonus clupeaformis spp., Salmonidae) divergence as revealed by next-generation sequencing
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Data from: Contrasting patterns of divergence at the regulatory and sequence level in European Daphnia galeata natural populations
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