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Figure 2 in Parallel evolution in molar outline of murine rodents: the case of the extinct Malpaisomys insularis (Eastern Canary Islands)

Figure 2. Schematic representation of the modern and fossil murine rodents compared to Malpaisomys. Top, molecular phylogeny after Chevret (1994) and Chevret et al. (2001). A calibration of the time of divergence between taxa is given by reference to the divergence of the Rattus rattus lineage, estimated as having occurred 12 Mya (Chevret et al., 2001). The grey box includes the arvicanthine rodents, characterized by a herbivorous diet. Bottom, fossil lineages with investigated localities. Thick grey lines indicate taxa with stephanodont characteristics, thick black lines, complete stephanodonty. Crosses indicate extinct taxa.

opencc-zeroJan 2024View details →

Rapid in situ diversification rates in Rhamnaceae explain the parallel evolution of high diversity in temperate biomes from global to local scales

The macroevolutionary processes that have shaped biodiversity across the temperate realm remain poorly understood and may have resulted from evolutionary dynamics related to diversification rates, dispersal rates, and colonization times, closely coupled with Cenozoic climate change. We integrated phylogenomic, environmental ordination, and macroevolutionary analyses for the cosmopolitan angiosperm family Rhamnaceae to disentangle the evolutionary processes that have contributed to high species diversity within and across temperate biomes. Our results show independent colonization of environmentally similar but geographically separated temperate regions mainly during the Oligocene, consistent with the global expansion of temperate biomes. High global, regional, and local temperate diversity was the result of high in situ diversification rates, rather than high immigration rates or accumulation time, except for Southern China, which was colonized much earlier than other regions. The relatively common lineage dispersals out of temperate hotspots highlights strong source-sink dynamics across the cosmopolitan distribution of Rhamnaceae. The proliferation of temperate environments since the Oligocene may have provided the ecological opportunity for rapid in situ diversification of Rhamnaceae across the temperate realm. Our study illustrates the importance of high in situ diversification rates for the establishment of modern temperate biomes and biodiversity hotspots across spatial scales.

opencc-zeroNov 2021View details →

Data from: Rapid, parallel evolution of field mustard (Brassica rapa) under experimental drought

Climate change is driving evolutionary and plastic responses in populations, but predicting these responses remains challenging. Studies that combine experimental evolution with ancestor-descendant comparisons allow assessment of the causes, parallelism, and adaptive nature of evolutionary responses, although such studies remain rare, particularly in a climate change context. Here, we created experimental populations of Brassica rapa derived from the same natural population and exposed these replicated populations to experimental drought or watered conditions for four generations. We then grew ancestors and descendants concurrently, following the resurrection approach. Experimental populations under drought showed rapid evolution of earlier flowering time and increased specific leaf area, consistent with a drought escape strategy and observations in natural populations. Evolutionary shifts followed the direction of selection and increased fitness under drought, indicative of adaptive evolution. Evolution to drought also occurred largely in parallel among replicate populations. Further, traits showed phenotypic plasticity to drought, but the direction and effect size of plasticity varied. Our results demonstrate parallel evolution to experimental drought, suggesting that evolution to strong, consistent selection may be predictable. Broadly, our study demonstrates the utility of combining experimental evolution with the resurrection approach to investigate responses to climate change.

opencc-by-4.0Dec 2021View details →

apomixis_parallel_evolution, and Fortunella hindsii (Citrus hindsii )Genome sequencing and assembly

##The assemble(genome) files Citrus hindsii (Mini citrus)Genome assembly Citrus hindsii (Mini citrus)Genome assembly gene model gff3 file Citrus hindsii (Mini citrus)Genome assembly function annotation Citrus hindsii (Mini citrus)Genome assembly TE gff3 file ##The population dataset LD_pur.vcf.gz  //The LD purning SNP vcfs (1.4 M sites) used in analysis log10_auxin.txt //The expression (log10) related to auxin pathway sjg.temergedref.fasta.gz //The TE insertion modify genome in popTE2 analysis SVs.vcf.gz //The SV vcfs  used in the paper te-hierarchy.txt //The TE classfication in popTE2 analysis TPM_count.txt //All samples expression in TMP count unfiltered.vcf.gz //The unfiltered vcfs file (7.3 M sites, within 0.4 M indels)

opencc-zeroJan 2022View details →

Historical museum samples enable the examination of divergent and parallel evolution during invasion

During the Anthropocene, Earth has experienced unprecedented habitat loss, native species decline, and global climate change. Concurrently, greater globalisation is facilitating species movement, increasing the likelihood of alien species establishment and propagation. There is a great need to understand what influences a species' ability to persist or perish within a new or changing environment. Examining genes that may be associated with a species' invasion success or persistence informs invasive species management, assists with native species preservation, and sheds light on important evolutionary mechanisms that occur in novel environments. This approach can be aided by coupling spatial and temporal investigations of evolutionary processes. Here we use the common starling, Sturnus vulgaris, to identify parallel and divergent evolutionary change between contemporary native and invasive range samples and their common ancestral population. To do this, we use reduced-representation sequencing of native samples collected recently in north-western Europe and invasive samples from Australia, together with museum specimens sampled in the UK during the mid-19th Century. We found evidence of parallel selection on both continents, possibly resulting from common global selective forces such as exposure to pollutants. We also identified divergent selection in these populations, which might be related to adaptive changes in response to the novel environment encountered in the introduced Australian range. Interestingly, signatures of selection are equally as common within both invasive and native range contemporary samples. Our results demonstrate the value of including historical samples in genetic studies of invasion and highlight the ongoing and occasionally parallel role of adaptation in both native and invasive ranges.

opencc-by-4.0Apr 2022View details →

Supplementary files for, 'Developmental morphology and anatomy shed light on both parallel and convergent evolution of the umbellate inflorescence in Monocots, underlied by a new variant of metatopy.'

Supplementary file for forth coming manuscript. Consists of Pre-processed microscopy images, FiJI readable annotated stacks and raw laser ablation tomography video data   File name:  MainFigures.zip  File format: .zip, individual images in .bmp format. Description of data: Picolay output of main figure panels.   File name:  Supplementary_File_1 File format: .MOV (video) Description of data: Movie 1 LAT scan of Butomus umbellatus   File name:  Supplementary_File_2 File format: .AVI (video) Description of data: Three-dimensional reconstruction of Butomus umbellatus inflorescence   File name:  Supplementary_File_3 File format: .MOV (video) Description of data: Movie 3 Three-dimensional reconstruction of Butomus umbellatus vasculature   File name:  Supplementary_File_4 File format: .TIFF (Can be opened in FIJI) Description of data: Butomus umbellatus vasculature composite tiff file   File name:  Supplementary_File_5 File format: .MOV (video) Description of data: LAT scan of Ornithogalum umbellatum   File name:  Supplementary_File_6 File format: .TIFF (Can be opened in FIJI) Description of data: Ornithogalum umbellatum vasculature tiff file (Can be opened in FIJI)   File name: Supplementary_File_7 File format: .MOV (video) Description of data: LAT scan of Allium hollandicum inflorescence

opencc-by-4.0Feb 2022View details →

Model data repository of "Styles of Trench-parallel Mid-ocean Ridge Subduction Affect Cenozoic Geological Evolution in circum-Pacific Continental Margins"

This dataset contains the data used in Wu et al. (2022): "Styles of Trench-parallel Mid-ocean Ridge Subduction Affect Cenozoic Geological Evolution in circum-Pacific Continental Margins".

opencc-zeroJun 2022View details →

Scan files, 3D reconstructions, data spreadsheet and supplementary files for Heterochrony and parallel evolution of echinoderm, hemichordate and cephalochordate internal bars

Deuterostomes comprise three phyla with radically different body plans. Phylogenetic bracketing of the living deuterostome clades suggests the latest common ancestor of echinoderms, hemichordates and chordates was a bilaterally symmetrical worm with pharyngeal openings, with these characters lost in echinoderms. Early fossil echinoderms with pharyngeal openings have been described, but their interpretation is highly controversial. Here, we critically evaluate the evidence for pharyngeal structures (gill bars) in the extinct stylophoran echinoderms Lagynocystis pyramidalis and Jaekelocarpus oklahomensis using virtual models based on high-resolution X-ray tomography scans of three-dimensionally preserved fossil specimens. Multivariate analyses of the size, spacing and arrangement of the internal bars in these fossils indicate they are substantially more similar to gill bars in modern enteropneust hemichordates and cephalochordates than to other internal bar-like structures in fossil blastozoan echinoderms. The close similarity between the internal bars of the stylophorans L. pyramidalis and J. oklahomensis and the gill bars of extant chordates and hemichordates is strong evidence for their homology. Differences between these internal bars and bar-like elements of the respiratory systems in blastozoans suggest these structures might have arisen through parallel evolution across deuterostomes, perhaps underpinned by a common developmental genetic mechanism.

Figure 4 in Parallel evolution in molar outline of murine rodents: the case of the extinct Malpaisomys insularis (Eastern Canary Islands)

Figure 4. Cluster analysis of the shape of the upper molar. Euclidean distances between group means were calculated based on Fourier coefficients up to the ninth harmonic (CF9). Clustering method was UPGMA (unweighted pair-group method, arithmetic average). Symbols as per Fig. 3. For locality and sample abbreviations see Table 1.

Figure 7 in Parallel evolution in molar outline of murine rodents: the case of the extinct Malpaisomys insularis (Eastern Canary Islands)

Figure 7. Relationship between time interval and morphological evolution regarding size (A, C) and shape (B, D) of the first upper molars. Size distance is estimated as differences in A0, shape distance as the Euclidean distance calculated based on the Fourier coefficients of the first nine harmonics. (A, B) Log-log relationship between evolutionary rates and time interval. (C, D) Relationship between time interval and morphological distance. Lines correspond to a linear regression on the Occitanomys/Stephanomys lineage (black line), the Paraethomys lineage (light grey line), and modern taxa (dark grey line). Dotted lines P <0.05; solid line P <0.001. (A) pair including Malpaisomys; (Δ) corresponds to the distance between a pair of Malpaisomys samples, Costa Calma and CVA4. Locality or sample abbreviations per Table 1.

Figure 5 in Parallel evolution in molar outline of murine rodents: the case of the extinct Malpaisomys insularis (Eastern Canary Islands)

Figure 5. Morphological differentiation within Malpaisomys. Size of the first upper (A) and lower (B) molars. Shape of the first upper (C) and lower (D) molars, estimated by the scores on the first and second canonical axes of the analysis of Malpaisomys. The dotted ellipses indicate the 95% confidence interval for each sample.