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389 results for “ancestral”
A new method for integrating ecological niche modeling with phylogenetics to estimate ancestral distributions
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Data For: The developing bird pelvis passes through ancestral Archosaurian and Dinosaurian conditions
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Reconstructing development of the earliest seed integuments raises a new hypothesis for the evolution of ancestral seed‐bearing structures
<p>This dataset contains three-dimensional model files for <em>Genomosperma</em> specimens LM19 (K1; Long, 1960), LM22, LM1 (L1; Long, 1960), and LM23, supporting the paper ‘Reconstructing development of the earliest seed integuments raises a new hypothesis for the evolution of ancestral seed‐bearing structures' published in New Phytologist <a href="https://doi.org/10.1111/nph.16792">https://doi.org/10.1111/nph.16792</a>.</p> <p>These models are saved in a single ZIP compressed folder as four SPV files and also four VAXML datasets in separate folders. All files are labelled with the working/specimen number they represent. SPV files are able to be viewed in SPIERSview, part of the free SPIERS software package (http://spiers-software.org/). The VAXML datasets comprise a VAXML file that provides metadata specifying how to put together accompanying STL files which define the geometry of the objects in the dataset. [Unzipped total size 1.74GB].</p>
Data from: Shared ancestral polymorphism and chromosomal rearrangements as potential drivers of local adaptation in a marine fish
<p>Gene flow has tremendous importance on local adaptation, by influencing the fate of <i>de novo</i> mutations, maintaining standing genetic variation, and driving adaptive introgression. Furthermore, structural variation as chromosomal rearrangements may facilitate adaptation despite high gene flow. However, our understanding of evolutionary mechanisms impending or favoring local adaptation in the presence of gene flow is still limited to a restricted number of study systems. In this study, we examined how demographic history, shared ancestral polymorphism, and gene flow among glacial lineages contribute to local adaptation to sea conditions in a marine fish, the capelin (<i>Mallotus villosus</i>). We first assembled a 490 Mbp draft genome of <i>M. villosus</i> to map our RAD sequence reads. Then, we used a large dataset of genome-wide single nucleotide polymorphisms (25,904 filtered SNPs) genotyped in 1,310 individuals collected from 31 spawning sites in the northwest Atlantic. We reconstructed the history of divergence among three glacial lineages and showed that they likely diverged from 3.8 to 1.8 MyA and experienced secondary contacts. Within each lineage, our analyses provided evidence for large <i>N</i><sub><i>e</i></sub> and high gene flow among spawning sites. Within the NWA lineage, we detected a polymorphic chromosomal rearrangement leading to the occurrence of three haplogroups. Genotype-environment associations revealed molecular signatures of local adaptation to environmental conditions prevailing at spawning sites. Our study also suggests that, both shared polymorphism among lineages, resulting from standing genetic variation or introgression, and chromosomal rearrangements may contribute to local adaptation in the presence of high gene flow.</p>
Supplementary material 5 from: Hundsdoerfer AK, Kitching IJ (2020) Morphological evolution in Hyles Hübner, 1819 hawkmoths (Lepidoptera, Sphingidae): reconstructing the ancestral Hyles habitus. Nota Lepidopterologica 43: 181-210. https://doi.org/10.3897/nl.43.49512
Figure S2
Supplementary material 1 from: Hundsdoerfer AK, Kitching IJ (2020) Morphological evolution in Hyles Hübner, 1819 hawkmoths (Lepidoptera, Sphingidae): reconstructing the ancestral Hyles habitus. Nota Lepidopterologica 43: 181-210. https://doi.org/10.3897/nl.43.49512
Table S1
Supplementary material 3 from: Hundsdoerfer AK, Kitching IJ (2020) Morphological evolution in Hyles Hübner, 1819 hawkmoths (Lepidoptera, Sphingidae): reconstructing the ancestral Hyles habitus. Nota Lepidopterologica 43: 181-210. https://doi.org/10.3897/nl.43.49512
Table S3
Supplementary material 2 from: Hundsdoerfer AK, Kitching IJ (2020) Morphological evolution in Hyles Hübner, 1819 hawkmoths (Lepidoptera, Sphingidae): reconstructing the ancestral Hyles habitus. Nota Lepidopterologica 43: 181-210. https://doi.org/10.3897/nl.43.49512
Table S2
Supplementary material 4 from: Hundsdoerfer AK, Kitching IJ (2020) Morphological evolution in Hyles Hübner, 1819 hawkmoths (Lepidoptera, Sphingidae): reconstructing the ancestral Hyles habitus. Nota Lepidopterologica 43: 181-210. https://doi.org/10.3897/nl.43.49512
Figure S1
Genome-wide SNP analysis of Siamese cobra (Naja kaouthia) reveals the molecular basis of transitions between Z and W sex chromosomes and supports the presence of an ancestral super-sex chromosome in amniotes
<p>Elucidation of the process of sex chromosome differentiation is necessary to understand the dynamics of evolutionary mechanisms in organisms. The Siamese cobra (<i>Naja kaouthia</i>) exhibits ZZ/ZW heteromorphic sex chromosomes. The W sex chromosome contains a large number of repeats and shares several amniote sex chromosomal linkages. In conjunction with recent advances in high-throughput sequencing, Diversity Arrays Technology (DArTseq™) provides an effective approach to identify sex-specific loci that are epoch-making, to understand the dynamics of molecular transitions between the Z and W sex chromosomes in a snake lineage. From a total of 543 perfectly sex-linked loci, 90 loci showed partial homology with several amniote sex chromosomal linkages, and 89 loci were homologous to transposable elements, which suggests that recombination suppression may be the crucial step in snake sex chromosome differentiation. Two loci were confirmed as W-specific nucleotides in females but not in males in the population examined by PCR amplification; one of the two loci (locus id: 100002617) was further amplified in females of the Indochinese spitting cobra (<i>N. siamensis</i>) but not in the other 22 snake species examined. Female-specific DArT markers were identified in Siamese cobra. These loci might result from a sex chromosome differentiation process between Z and W and involve putative sex-determination regions in Siamese cobra. Short sequences derived from DArTseq™ technology also shared linkage homologies among amniote sex chromosomes, which supports the hypothesis of an ancestral super-sex chromosome with overlaps of partial sex chromosomal linkages. The locus (id: 100002617) shared in <i>N. kaouthia</i> and <i>N. siamensis</i>, but among 22 other snake species, indicates inheritance from a common ancestor as synapomorphic loci in the <i>Naja</i> lineage. The ease of use of the DArT markers and DArTseq™ platform provides a useful strategy for future research on sex chromosome evolution in snakes.</p>
Ancestral genetic variation in phenotypic plasticity underlies rapid evolutionary changes in resurrected populations of waterfleas
<p>The role that phenotypic plasticity plays in adaptive evolution has been debated for decades. This is because the strength of natural selection is dependent upon the direction and magnitude of phenotypic responses to environmental signals. Therefore, the connection between plasticity and adaptation will depend on the patterns of plasticity harbored by ancestral populations prior to a change in the environment. Yet, few studies have directly assessed ancestral variation in plasticity and tracked phenotypic changes over time. Here we resurrected historic propagules of <i>Daphnia</i> spanning multiple species and lakes in Wisconsin following the invasion and proliferation of a novel predator (spiny waterflea, <i>Bythotrephes</i> <i>longimanus</i>)<i>. </i>This approach revealed extensive genetic variation in predator-induced plasticity in ancestral populations of <i>Daphnia</i>. It is unlikely that the standing patterns of plasticity shielded <i>Daphnia</i> from selection to permit long-term coexistence with a novel predator. Instead, this variation in plasticity provided the raw materials for <i>Bythotrephes</i>-mediated selection to drive rapid shifts in <i>Daphnia</i> behavior and life history. Surprisingly, there was little evidence for the evolution of trait plasticity as genetic variation in plasticity was maintained in the face of a novel predator. Such results provide new insights into the link between plasticity and adaptation and highlight the importance of quantifying genetic variation in plasticity when evaluating the drivers of evolutionary change in the wild. </p>
Data from: Phylogenomic analysis supports the ancestral presence of LPS-outer membranes in the Firmicutes
One of the major unanswered questions in evolutionary biology is when and how the transition between diderm (two membranes) and monoderm (one membrane) cell envelopes occurred in Bacteria. The Negativicutes and the Halanaerobiales belong to the classically monoderm Firmicutes, but possess outer membranes with lipopolysaccharide (LPS-OM). Here, we show that they form two phylogenetically distinct lineages, each close to different monoderm relatives. In contrast, their core LPS biosynthesis enzymes were inherited vertically, as in the majority of bacterial phyla. Finally, annotation of key OM systems in the Halanaerobiales and the Negativicutes shows a puzzling combination of monoderm and diderm features. Together, these results support the hypothesis that the LPS-OMs of Negativicutes and Halanaerobiales are remnants of an ancient diderm cell envelope that was present in the ancestor of the Firmicutes, and that the monoderm phenotype in this phylum is a derived character that arose multiple times independently through OM loss.
Data from: Ancestral polyploidy in seed plants and angiosperms
Whole-genome duplication (WGD), or polyploidy, followed by gene loss and diploidization has long been recognized as an important evolutionary force in animals, fungi and other organisms1, 2, 3, especially plants. The success of angiosperms has been attributed, in part, to innovations associated with gene or whole-genome duplications4, 5, 6, but evidence for proposed ancient genome duplications pre-dating the divergence of monocots and eudicots remains equivocal in analyses of conserved gene order. Here we use comprehensive phylogenomic analyses of sequenced plant genomes and more than 12.6 million new expressed-sequence-tag sequences from phylogenetically pivotal lineages to elucidate two groups of ancient gene duplications—one in the common ancestor of extant seed plants and the other in the common ancestor of extant angiosperms. Gene duplication events were intensely concentrated around 319 and 192 million years ago, implicating two WGDs in ancestral lineages shortly before the diversification of extant seed plants and extant angiosperms, respectively. Significantly, these ancestral WGDs resulted in the diversification of regulatory genes important to seed and flower development, suggesting that they were involved in major innovations that ultimately contributed to the rise and eventual dominance of seed plants and angiosperms.
Data from: Ancient hybridizations among the ancestral genomes of bread wheat
The allohexaploid bread wheat genome consists of three closely related subgenomes (A, B, and D), but a clear understanding of their phylogenetic history has been lacking. We used genome assemblies of bread wheat and five diploid relatives to analyze genome-wide samples of gene trees, as well as to estimate evolutionary relatedness and divergence times. We show that the A and B genomes diverged from a common ancestor ~7 million years ago and that these genomes gave rise to the D genome through homoploid hybrid speciation 1 to 2 million years later. Our findings imply that the present-day bread wheat genome is a product of multiple rounds of hybrid speciation (homoploid and polyploid) and lay the foundation for a new framework for understanding the wheat genome as a multilevel phylogenetic mosaic.
Data from: On the ancestral recruitment of metalloproteinases into the venom of snakes
Tracing the evolutionary history of proteins can reveal insights into gene alterations responsible for changes in structure and function. Here, the origin of snake venom metalloproteinases was rigorously reassessed using phylogenetics and the reconstruction of ancestral sequences. Basal SVMPs are most closely related to ADAM 7, 28 and decysin 1 proteins. Reconstructing the evolutionary history of these proteins and their hypothetical ancestors elucidates progressive alterations in the amino acid composition and structural characteristics of ADAMs/SVMPs through evolutionary time.
Data from: A branch-heterogeneous model of protein evolution for efficient inference of ancestral sequences
Most models of nucleotide or amino acid substitution used in phylogenetic studies assume that the evolutionary process has been homogeneous across lineages and that composition of nucleotides or amino acids has remained the same throughout the tree. These oversimplified assumptions are refuted by the observation that compositional variability characterizes extant biological sequences. Branch-heterogeneous models of protein evolution that account for compositional variability have been developed, but are not yet in common use because of the large number of parameters required, leading to high computational costs and potential overparameterization. Here, we present a new branch-nonhomogeneous and nonstationary model of protein evolution that captures more accurately the high complexity of sequence evolution. This model, henceforth called Correspondence and likelihood analysis (COaLA), makes use of a correspondence analysis to reduce the number of parameters to be optimized through maximum likelihood, focusing on most of the compositional variation observed in the data. The model was thoroughly tested on both simulated and biological data sets to show its high performance in terms of data fitting and CPU time. COaLA efficiently estimates ancestral amino acid frequencies and sequences, making it relevant for studies aiming at reconstructing and resurrecting ancestral amino acid sequences. Finally, we applied COaLA on a concatenate of universal amino acid sequences to confirm previous results obtained with a nonhomogeneous Bayesian model regarding the early pattern of adaptation to optimal growth temperature, supporting the mesophilic nature of the Last Universal Common Ancestor.
Data from: Relaxed phylogenetics and the Palaeoptera problem: resolving deep ancestral splits in the insect phylogeny
The order in which the three groups of winged insects diverged from their common ancestor has important implications for understanding the origin of insect flight. But despite this importance, the split between the Odonata (dragonflies and damselflies), Ephemeroptera (mayflies) and Neoptera (the other winged orders) remains very much unresolved. Indeed, previous studies have obtained strong apparent support for each of the three possible branching patterns. Here, we present a systematic reinvestigation of the basal pterygote split. Our results suggest that outgroup choice and limited taxon sampling have been major sources of systematic error, even for datasets with a large number of characters (e.g., in phylogenomic datasets). In particular, a dataset of 113 taxa provides consistent support for the Palaeoptera hypothesis (the grouping of Odonata with Ephemeroptera), while results from datasets with fewer taxa give inconsistent results, and are highly sensitive to minor changes in data and methods. We also focus on recent methods that exploit temporal information, combined with additional assumptions about the evolutionary process, and so reduce the influence of outgroup choice. These methods are shown to provide more consistent results, for example, supporting Palaeoptera, even for datasets that previously supported other hypotheses. Together, these results have implications for understanding insect origins and for resolving other problematic splits in the tree of life.
Data from: Elucidating the functional evolution of heat sensors among Xenopus species adapted to different thermal niches by ancestral sequence reconstruction
Ambient temperature fluctuations are detected via the thermosensory system which allows animals to seek preferable thermal conditions or escape from harmful temperatures. Evolutionary changes in thermal perception have thus potentially played crucial roles in niche selection. The genus Xenopus (clawed frog) is suitable for investigating the relationship between thermal perception and niche selection due to their diverse latitudinal and altitudinal distributions. Here we performed comparative analyses of the neuronal heat sensors TRPV1 and TRPA1 among closely related Xenopus species (X. borealis, X. muelleri, X. laevis, and X. tropicalis) to elucidate their functional evolution and to assess whether their functional differences correlate with thermal niche selection among the species. Comparison of TRPV1 among four extant Xenopus species and reconstruction of the ancestral TRPV1 revealed that TRPV1 responses to repeated heat stimulation were specifically altered in the lineage leading to X. tropicalis which inhabits warmer niches. Moreover, the thermal sensitivity of TRPA1 was lower in X. tropicalis than the other species, although the thermal sensitivity of TRPV1 and TRPA1 was not always lower in species that inhabit warmer niches than the species inhabit cooler niches. However, a clear correlation was found in species differences in TRPA1 activity. Heat-evoked activity of TRPA1 in X. borealis and X. laevis, which are adapted to cooler niches, was significantly higher than in X. tropicalis and X. muelleri which are adapted to warmer niches. These findings suggest that the functional properties of heat sensors changed during Xenopus evolution, potentially altering the preferred temperature ranges among species.
Data from: Evolution of the leucine-rich repeat receptor-like protein kinase gene family: Ancestral copy number and functional divergence of BAM1 and BAM2 in Brassicaceae
Gene duplication allows for functional divergence and innovation that provide selective advantages. However, in flowering plants genetic studies have revealed that single-gene mutations affecting one of two or more closely related paralogs often fail to cause detectable morphological defects, suggesting functional redundancy. Flowering plants have hundreds of genes encoding leucine-rich repeat receptor-like protein kinases (LRR-RLKs), several of which play important roles in anther development but little is known about their evolutionary history and possible functional divergence. We investigated the evolutionary relationship of the LRR-RLK gene family by phylogenetic analysis and found that these closely related paralogs resulted from multiple duplication events, such as the one resulting in BAM1 and BAM2. We further used qRT-PCR to verify gene expression changes in immature anthers from the bam1/bam2 single and double mutants compared with wild type providing strong evidence that the BAM1 and BAM2 genes have evolved different functions, with differential effects on anther gene expression. Moreover, careful examination of anther development in bam1 and bam2 single mutants revealed previously unrecognized extra cell division in tapetum cell layers. Thus our results from phylogenetic, molecular and morphological analyses uncover sequence and functional differences between paralogs whose single mutants lack obvious fertility defects, effectively revealing functional divergence of duplicate genes.
Data from: Predicting the ancestral character changes in a tree is typically easier than predicting the root state
Predicting the ancestral sequences of a group of homologous sequences related by a phylogenetic tree has been the subject of many studies, and numerous methods have been proposed for this purpose. Theoretical results are available that show that when the substitution rate become too large, reconstructing the ancestral state at the tree root is no longer feasible. Here, we also study the reconstruction of the ancestral changes that occurred along the tree edges. We show that, depending on the tree and branch length distribution, reconstructing these changes (i.e. reconstructing the ancestral state of all internal nodes in the tree) may be easier or harder than reconstructing the ancestral root state. However, results from information theory indicate that for the standard Yule tree, the task of reconstructing internal node states remains feasible, even for very high substitution rates. Moreover, computer simulations demonstrate that for more complex trees and scenarios, this result still holds. For a large variety of counting, parsimony-based and likelihood-based methods, the predictive accuracy of a randomly selected internal node in the tree is indeed much higher than the accuracy of the same method when applied to the tree root. Moreover, parsimony- and likelihood-based methods appear to be remarkably robust to sampling bias and model mis-specification.
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Allen Brain Atlas
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