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opencc-zeroDec 2016View details →

Data from: Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches

Genomic comparisons of closely related species have identified "islands" of locally elevated sequence divergence. Genomic islands may contain functional variants involved in local adaptation or reproductive isolation and may therefore play an important role in the speciation process. However, genomic islands can also arise through evolutionary processes unrelated to speciation, and examination of their properties can illuminate how new species evolve. Here, we performed scans for regions of high relative divergence (FST) in 12 species pairs of Darwin's finches at different genetic distances. In each pair, we identify genomic islands that are, on average, elevated in both relative divergence (FST) and absolute divergence (dXY). This signal indicates that haplotypes within these genomic regions became isolated from each other earlier than the rest of the genome. Interestingly, similar numbers of genomic islands of elevated dXY are observed in sympatric and allopatric species pairs, suggesting that recent gene flow is not a major factor in their formation. We find that two of the most pronounced genomic islands contain the ALX1 and HMGA2 loci, which are associated with variation in beak shape and size, respectively, suggesting that they are involved in ecological adaptation. A subset of genomic island regions, including these loci, appears to represent anciently diverged haplotypes that evolved early during the radiation of Darwin's finches. Comparative genomics data indicate that these loci, and genomic islands in general, have exceptionally low recombination rates, which may play a role in their establishment.

opencc-zeroJan 2024View details →

A lack of genetic diversity and minimal adaptive evolutionary divergence in introduced Mysis shrimp after 50 years

The successes of introduced populations in novel habitats often provide powerful examples of evolution and adaptation. In the 1950's, opossum shrimp (Mysis diluviana) individuals from Clearwater Lake in Minnesota, USA were transported and introduced to Twin Lakes in Colorado, USA by fisheries managers to supplement food sources for trout. Shrimp were subsequently introduced from Twin Lakes into numerous lakes throughout Colorado. Because managers kept detailed records of the timing of the introductions, we had the opportunity to test for evolutionary divergence within a known time interval. Here, we used reduced representation genomic data to investigate patterns of genetic diversity and test for genetic divergence between populations and for evidence of adaptive evolution within the introduced populations in Colorado. We found overall very low levels of genetic diversity across all populations, with evidence for some genetic divergence between the Minnesota source population and the introduced populations in Colorado. There was also little differentiation among the Colorado populations, consistent with the known provenance of a single founding population, with the exception of the population from Gross Reservoir, Colorado. Demographic modeling suggests that the population in Gross Reservoir is of hybrid origin, with an earlier founding population from an unknown source being later supplemented from another population. Despite the overall low genetic diversity we observed, FST outlier and environmental association analyses identified multiple loci exhibiting signatures of selection and adaptive variation related to elevation and lake depth. The success of introduced species is thought to be limited by genetic variation, but our results imply that populations with limited genetic variation can become established in a wide range of novel environments.

opencc-zeroApr 2024View details →

Data from: Genomic landscapes of divergence among island bird populations: evidence of parallel adaptation but at different loci?

When populations colonise new environments they may be exposed to novel selection pressures but also suffer from extensive genetic drift due to founder effects, small population sizes, and limited interpopulation gene flow. Genomic approaches enable us to study how these factors drive divergence, and disentangle neutral effects from differentiation at specific loci due to selection. Here, we investigate patterns of genetic diversity and divergence using whole-genome resequencing (> 22X coverage) in Berthelot's pipit (Anthus berthelotii), a passerine endemic to the islands of three north Atlantic archipelagos. Strong environmental gradients, including in pathogen pressure, across populations in the species range, make it an excellent system in which to explore traits important in adaptation and/or incipient speciation. Firstly, we quantify how genomic divergence accumulates across the speciation continuum, i.e., among Berthelot's pipit populations, between subspecies across archipelagos, and between Berthelot's pipit and its mainland ancestor, the tawny pipit (Anthus campestris). Across these colonisation timeframes (2.1 million – ca. 8,000 years ago), we identify highly differentiated loci within genomic islands of divergence and conclude that the observed distributions align with expectations for non-neutral divergence. Characteristic signatures of selection are identified in loci associated with craniofacial/bone and eye development, metabolism, and immune response between population comparisons. Interestingly, we find limited evidence for repeated divergence of the same loci across the colonisation range but do identify different loci putatively associated with the same biological traits in different populations, likely due to parallel adaptation. Incipient speciation across these island populations, in which founder effects and selective pressures are strong, may therefore be repeatedly associated with morphology, metabolism, and immune defence.

opencc-zeroApr 2022View details →

Habitat-linked genetic variation supports microgeographic adaptive divergence in an island-endemic bird species

We present evidence for and investigate potential mechanisms driving habitat-linked genetic divergence within a bird species endemic to a single 250 km2 island. The island scrub-jay (Aphelocoma insularis) exhibits microgeographic divergence in bill morphology across pine-oak ecotones on Santa Cruz Island, California (USA) similar to adaptive differences described in mainland congeners over much larger geographic scales. To test whether individuals exhibit genetic differentiation related to habitat type and divergence in bill length, we genotyped over 3,000 single nucleotide polymorphisms (SNPs) in 123 adult island scrub-jay males from across Santa Cruz Island using restriction site-associated DNA sequencing (RADseq). Neutral landscape genomic analyses revealed that genome-wide genetic differentiation was primarily related to geographic distance and differences in habitat composition. We also found 168 putatively adaptive loci associated with habitat type using multivariate redundancy analysis (RDA) while controlling for spatial effects. Finally, two genome-wide association analyses revealed a polygenic basis to variation in bill length with multiple loci detected in or near genes known to affect bill morphology in other birds. Our findings support the hypothesis that divergent selection at microgeographic scales can cause adaptive divergence in the presence of ongoing gene flow.

opencc-zeroApr 2022View details →

Adaptation to environmental temperature in divergent clades of the nematode Pristionchus pacificus

Because of ongoing climate change, populations of organisms are being subjected to stressful temperatures more often. This is especially problematic for ectothermic organisms, which are likely to be more sensitive to changes in temperature. Therefore, we need to know if ectotherms have adapted to environmental temperature and, if so, what are the evolutionary mechanisms behind such adaptation. Here, we use the nematode Pristionchus pacificus as a case study to investigate thermal adaptation on the Indian Ocean island of La Réunion, which experiences a range of temperatures from coast to summit. We study the evolution of high temperature tolerance by constructing a phylogenetic tree of strains collected from many different thermal niches. We show that populations of P. pacificus at low altitudes have higher fertility at warmer temperatures. Most likely, this phenotype has arisen recently and at least twice independently, consistent with parallel evolution. We also studied low temperature tolerance and showed that populations from high altitudes have increased their fertility at cooler temperatures. Together, these data indicate that P. pacificus strains on La Réunion are subject to divergent selection, adapting to hot and cold niches at the coast and summit of the volcano. Precisely defining these thermal niches provides essential information for models that predict the impact of future climate change on these populations.

opencc-by-4.0Aug 2022View details →

Supplementary Data of "Introgression between highly divergent sea squirt genomes: an adaptive breakthrough?"

Datasets used in the analyses (see Table S5 for a detailed description). ► Dataset #1: phased SNPs with offspring. joint_bwa_mem_mdup_IR_recal_variants_refine_HQ_denovo_Oad18ad31ad2.clean.biallelic.noindels_filter_phased_phasedBeagle.vcf ► Dataset #2: all SNPs with missing data. joint_bwa_mem_mdup_IR_recal_variants_refine_HQ_denovo_Oad18ad31ad2.clean.biallelic.noindels_filter_parents_oNA5.vcf ► Dataset #3a: phased SNPs. joint_bwa_mem_mdup_IR_recal_variants_refine_HQ_denovo_Oad18ad31ad2.clean.biallelic.noindels_filter_phased_phasedBeagle_parents.vcf ► Dataset #3b: CDS version of “phased SNPs”. joint_bwa_mem_mdup_IR_recal_variants_refine_HQ_denovo_Oad18ad31ad2.clean.biallelic.noindels_filter_phased_phasedBeagle_parents_SNP_CHRall.orf.cds ► Dataset #3c: FASTA version of “phased SNPs”. joint_bwa_mem_mdup_IR_recal_variants_refine_HQ_denovo_Oad18ad31ad2.clean.biallelic.noindels_filter_phased_phasedBeagle_parents_SNP_chr5.sub_${START}-${END}.fasta ► Dataset #4: ancestry informative phased SNPs. joint_bwa_mem_mdup_IR_recal_variants_refine_HQ_denovo_Oad18ad31ad2.clean.biallelic.noindels_filter_phased_phasedBeagle_parents.frq.fixed.vcf ► Dataset #5: all SNPs. joint_bwa_mem_mdup_IR_recal_variants_refine_HQ_denovo_Oad18ad31ad2.clean.biallelic.noindels_filter_parents_oNA.vcf ► Dataset #6: all polarized SNPs. joint_bwa_mem_mdup_IR_recal_variants_refine_HQ_denovo_Oad18ad31ad2.clean.biallelic.noindels_filter_parents_raw_refine_HQ_edwardsi_oNA3_polar.vcf ► Dataset #7: unfiltered mapping files. ciona_bwa-mapping_${IND}_bwa_mem_mdup_IR_chromosome5:700000-1500000_sorted_nodup.bam

opencc-by-4.0Aug 2022View details →

Supplementary Information of "Introgression between highly divergent sea squirt genomes: an adaptive breakthrough?"

Supplementary Figures Figure S1 Population genetic statistics calculated in non-overlapping 10 Kb windows along the 14 chromosomes in the sea squirt genome. Figure S2 C. robusta introgression into C. intestinalis shown across the 14 chromosomes. Figure S3 Population genetic statistics of the C. robusta introgressed coding sequences. Figure S4 ABBA-BABA introgression patterns using C. edwardsi as an outgroup. Figure S5 Inference of the divergence history between C. robusta and C. intestinalis with moments. Figure S6 Selection tests. Figure S7 C. robusta ancestry along chromosome 5 in C. intestinalis individuals. Figure S8 Neighbor-joining trees of 50 Kb windows framing the “missing data region” (grey band) at the center of the chromosome 5 hotspot. Figure S9 Copy number variation at candidate SNPs in the introgression hotspot on chromosome 5 (700 Kb - 1.5 Mb). Figure S10 Structural analysis of the “missing data region” on chromosome 5 (from 1,009,000 to 1,055,000 bp).   Supplementary Tables Table S1 Sample information. Table S2 Correlation between chromosomes of the individual C. robusta ancestry fraction. Table S3 Demographic results with moments – excluding chromosome 5. Table S4 Demographic results with moments – including chromosome 5. Table S5 Description of the Supplementary Data.   Supplementary Scripts Bioinformatic pipeline used for genotyping and haplotyping. Script #1: prepare the reference genome for BWA and GATK. reference_bwa_GATK_CF.sh Script #2: mapping the reads to the reference with BWA. mapping_bwa-mem_CF.sh Script #3: indel realignment with GATK. indel_realignment_CF.sh Script #4: individual variant calling in gVCF format with GATK. snpindel_callingGVCF_raw_CF.sh Script #5: joint genotyping with GATK. joint_genotyping_raw_CF.sh Script #6: genotype refinement with GATK. genotype_refinement_raw_CF.sh Script #7: SNPs and indels recalibration with GATK. snpindel_recalibration_CF.sh Script #8: genotype refinement after recalibration with GATK. genotype_refinement_recal_CF.sh Script #9: genotype correction. phase_by_transmission_correctCalling_CF@2020.sh Script #10: phasing with GATK and BEAGLE. phase_by_transmission_clean_CF@2020.sh Pipeline used for the demographic inferences with moments. Script #11: define the demographic models. moments_models_2pop_bb_parallel_folded_2periods.py Script #12: run the demographic inferences. moments_inference_dualanneal_bb_parallel_folded_2periods_bounds.py

opencc-zeroMay 2024View details →

Data for: Selection on the joint action of pairs leads to divergent adaptation and coadaptation of care-giving parents during pre-hatching care

The joint actions of animals in partnerships or social groups evolve under both natural selection, from the wider environment, and social selection, imposed by other members of the pair or group. We used experimental evolution to investigate how jointly expressed actions evolve upon exposure to a new environmental challenge. Our work focused on the evolution of carrion nest preparation by pairs of burying beetles Nicrophorus vespilloides, a joint activity undertaken by the pair but typically led by the male. In previous work, we found that carrion nest preparation evolved to be faster in experimental populations without post-hatching care (No Care lines) than with post-hatching care (Full Care lines). Here we investigate how this joint activity evolved. After 15 generations of experimental evolution, we created heterotypic pairs (No Care females with Full Care males, and No Care males with Full Care females) and compared their carrion nest making with homotypic No Care and Full Care pairs. We found that pairs with No Care males prepared the nest more rapidly than pairs with Full Care males, regardless of the female's line of origin. We discuss how social coadaptations within pairs or groups could act as a post-mating barrier to gene flow.

FIG. 4 in Pollination mechanisms in the African genus Moraea (Iridaceae, Iridoideae): floral divergence and adaptation for pollinators

FIG. 4. — Flowers types in Moraea and some of their pollinators: A, M. tripetala, with an Iris-type flower, being visited by native Apis mellifera; B, M. villosa, showing prominent "beetle marks" and the black hopliine beetle, Anisonyx ursus, with heavy dorsal load of orange pollen; C, M. polyanthos, typical bowl type flower with stamens and style branches held within the deep floral cup; D, M. marlothii, a stellate type flower with stamens and style branches forming and androgynophore supporting anthers well above the flower.

FIG. 2 in Pollination mechanisms in the African genus Moraea (Iridaceae, Iridoideae): floral divergence and adaptation for pollinators

FIG. 2. — Bowl and salver type flowers in Moraea: A, the bowl-shaped flower of M. collina, with the style and stamens forming a column held within the floral cup; B, M. marlothii, showing entire plant, flower with columnar stamens and style branches, with enlarged detail of the androgynophore; C, D, rotate flowers of M. bifida (C) and M. miniata (D) with the androgynophore much enlarged; E, bowl-shaped flower of M. ochroleuca, showing the fly pollination syndrome, with the perianth lacking nectar guides and radiating veins that secrete nectar. Scale bar: 1 cm for flowers, floral dissections variously enlarged. Drawn by Margo BRANCH.

FIG. 3 in Pollination mechanisms in the African genus Moraea (Iridaceae, Iridoideae): floral divergence and adaptation for pollinators

FIG. 3. — Beetle type flowers in Moraea, with examples from three different clades: A, M. villosa, with trilobed inner tepals and dark beetle marks the base of the outer tepals limbs; B, M. elegans, with salver shape and beetle marks on the outer tepals; C, M. insolens, with the base of the tepals and the filament column darkly colored. Note the salver shape in B and C. Scale bar: 1 cm. Drawn by Margo BRANCH.

FIG. 1 in Pollination mechanisms in the African genus Moraea (Iridaceae, Iridoideae): floral divergence and adaptation for pollinators

FIG. 1. — Iris-type flowers in Moraea: A, M. bipartita, whole flower and outer and inner tepal and style branch shown separately with arrow indicating the nectary on the interior (adaxial) surface of the outer tepal; B, M. huttonii, whole flower and the style branches and stamens drawn separately, arrow showing the stigmatic lobe on the abaxial surface of the style branch; C, M. gawleri, entire flower and separated style branch to show stigmatic lobe arching over the anther; D, M. brevistyla (note trilobed inner tepals); E, M. tripetala, with inner tepals reduced to minute cusps; F, M. algoensis, with reduced inner tepals. Scale bar: 1 cm for flowers, floral dissections variously enlarged. Drawn by Margo BRANCH.

opencc-zeroAug 2021View details →

Elucidating gene expression adaptation of phylogenetically divergent coral holobionts under heat stress

As coral reefs struggle to survive under climate change, it is crucial to know whether they have the capacity to withstand changing conditions, particularly increasing seawater temperatures. Thermal tolerance requires the integrative response of the different components of the coral holobiont (coral host, algal photosymbiont, and associated microbiome). Here, using a controlled thermal stress experiment across three divergent Caribbean coral species, we attempt to dissect holobiont member metatranscriptome responses from coral taxa with different sensitivities to heat stress and use phylogenetic ANOVA to study the evolution of gene expression adaptation. We show that coral response to heat stress is a complex trait derived from multiple interactions among holobiont members. We identify host and photosymbiont genes that exhibit lineage-specific expression level adaptation and uncover potential roles for bacterial associates in supplementing the metabolic needs of the coral-photosymbiont duo during heat stress. Our results stress the importance of integrative and comparative approaches across a wide range of species to better understand coral survival under the predicted rise in sea surface temperatures.

opencc-zeroAug 2023View details →

Data from: An adaptive biomolecular condensation response is conserved across environmentally divergent species

Cells must sense and respond to sudden maladaptive environmental changes—stresses—to survive and thrive. Across eukaryotes, stresses such as heat shock trigger conserved responses: growth arrest, a specific transcriptional response, and biomolecular condensation of protein and mRNA into structures known as stress granules under severe stress. The composition, formation mechanism, adaptive significance, and even evolutionary conservation of these condensed structures remain enigmatic. Here we provide an unprecedented view into stress-triggered condensation, its evolutionary conservation and tuning, and its integration into other well-studied aspects of the stress response. Using three morphologically near-identical budding yeast species adapted to different thermal environments and diverged by up to 100 million years, we show that proteome-scale biomolecular condensation is tuned to species-specific thermal niches, closely tracking corresponding growth and transcriptional responses. In each species, poly(A)-binding protein—a core marker of stress granules—condenses in isolation at species-specific temperatures, with conserved molecular features and conformational changes modulating condensation. From the ecological to the molecular scale, our results reveal previously unappreciated levels of evolutionary selection in the eukaryotic stress response, while establishing a rich, tractable system for further inquiry.

publicApr 2022View details →

Adaptation to environmental temperature in divergent clades of the nematode Pristionchus pacificus

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publicApr 2024View details →

Data from: Genomic landscapes of divergence among island bird populations: evidence of parallel adaptation but at different loci?

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publicMay 2024View details →

Data for: Selection on the joint action of pairs leads to divergent adaptation and coadaptation of care-giving parents during pre-hatching care

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