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238 results for “evolutionary relationships”
Data from: Evolutionary relationships within the Triops (Notostraca: Branchiopoda) using complete mitochondrial genomes
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Data from: Anchored phylogenomics improves the resolution of evolutionary relationships in the rapid radiation of Protea L.
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Supplementary material 1 from: Patterson BD, Webala PW, Lavery TH, Agwanda BR, Goodman SM, Kerbis Peterhans JC, Demos TC (2020) Evolutionary relationships and population genetics of the Afrotropical leaf-nosed bats (Chiroptera, Hipposideridae). ZooKeys 929: 117-161. https://doi.org/10.3897/zookeys.929.50240
Figure S1. Geographic distribution of voucher specimens used in this analysis
Figure 2 from: Patterson BD, Webala PW, Lavery TH, Agwanda BR, Goodman SM, Kerbis Peterhans JC, Demos TC (2020) Evolutionary relationships and population genetics of the Afrotropical leaf-nosed bats (Chiroptera, Hipposideridae). ZooKeys 929: 117-161. https://doi.org/10.3897/zookeys.929.50240
Figure 2 Parts A and B. Phylogeny of Hipposideridae based on Bayesian analysis of 303 cyt-b sequences. Colored lines denote well supported clades and symbols denote nodal support: red circles, BS ≥ 70%, PP ≥ 0.95; black circles BS ≥ 70%, PP ≤ 0.95; open circles BS ≤ 70%, PP ≥ 0.95.
Figure 1 from: Patterson BD, Webala PW, Lavery TH, Agwanda BR, Goodman SM, Kerbis Peterhans JC, Demos TC (2020) Evolutionary relationships and population genetics of the Afrotropical leaf-nosed bats (Chiroptera, Hipposideridae). ZooKeys 929: 117-161. https://doi.org/10.3897/zookeys.929.50240
Figure 1 Type localities for Afrotropical hipposiderids: Doryrhina, blue symbols; Hipposideros, white symbols; Macronycteris, black symbols. Stars denote valid species, whereas circles indicate taxa considered as subspecies or synonyms. Localities are projected onto the biome map of Olson et al. (2001). Taxa depicted are: Hipposideros abae J. A. Allen,1917; †Hipposideros (Pseudorhinolophus) amenhotepos Gunnell, Winkler, Miller, Head, El-Barkooky, Gawad, Sanders & Gingerich, 2015; Phyllorhina angolensis Seabra, 1898; Hipposideros caffer var. aurantiaca De Beaux, 1924; Hipposideros beatus K. Andersen, 1906; †Hipposideros besaoka Samonds, 2007; Phyllorrhina bicornis Heuglin, 1861; Hipposideros braima Monard, 1939; Hipposideros caffer Sundevall, 1846; Phyllorhina caffra Peters, 1852; Hipposideros camerunensis Eisentraut, 1956; Hipposideros caffer centralis K. Andersen, 1906; Rhinolophus Commersonii É. Geoffroy, 1813; Hipposideros cryptovalorona Goodman, Schoeman, Rakotoarivelo & Willows-Munro, 2016; Hipposideros curtus G. M. Allen, 1921; Phyllorrhina cyclops Temminck, 1853; Phyllorrhina fuliginosa Temminck, 1853; Hipposideros gigas gambiensis K. Andersen, 1906; Rhinolophus gigas Wagner, 1845; Phyllorrhina gracilis Peters, 1852; Hipposideros caffer guineensis K. Andersen, 1906; Hipposideros jonesi Hayman, 1947; †Hipposideros kaumbului Wesselman, 1984; Hipposideros lamottei Brosset, 1985; Hipposideros langi J. A. Allen, 1917; Hipposideros marisae Aellen, 1954; Phyllorhina Commersoni, var. marungensis Noack, 1887; Hipposideros beatus maximus Verschuren, 1957; Phyllorrhina megalotis Heuglin, 1861; Rhinolophus micaceus de Winton, 1897; HipposiderosCommersoni mostellum Thomas, 1904; Hipposideros nanus J. A. Allen, 1917; Hipposideros gigas niangarae J. A. Allen, 1917; Hipposideros caffer niapu J. A. Allen, 1917; Phyllorrhina rubra Noack, 1893; Hipposideros sandersoni Sanderson, 1937; Hipposideros tephrus Cabrera, 1906; Phyllorhina Commersoni, var. thomensis Bocage, 1891; Hipposideros gigas viegasi Monard, 1939; Phyllorhina vittata Peters, 1852.
Data from: Lineage-specific sequence evolution and exon edge conservation partially explain the relationship of evolutionary rate and expression level in A. thaliana
Rapidly evolving proteins can aid the identification of genes underlying phenotypic adaptation across taxa, but functional and structural elements of genes can also affect evolutionary rates. In plants, the 'edges' of exons, flanking intron junctions, are known to contain splice enhancers and to have a higher degree of conservation compared to the remainder of the coding region. However, the extent to which these regions may be masking indicators of positive selection or account for the relationship between dN/dS and other genomic parameters is unclear. We investigate the effects of exon edge conservation on the relationship of dN/dS to various sequence characteristics and gene expression parameters in the model plant Arabidopsis thaliana. We also obtain lineage-specific dN/dS estimates, making use of the recently sequenced genome of Thellungiella parvula, the second closest sequenced relative after the sister species Arabidopsis lyrata. Overall, we find that the effect of exon edge conservation, as well as the use of lineage-specific substitution estimates, upon dN/dS ratios partly explains the relationship between the rates of protein evolution and expression level. Furthermore, the removal of exon edges shifts dN/dS estimates upwards, increasing the proportion of genes potentially under adaptive selection. We conclude that lineage-specific substitutions and exon edge conservation have an important effect on dN/dS ratios and should be considered when assessing their relationship with other genomic parameters..
Data from: Antagonistic relationships between intron content and codon usage bias of genes in three mosquito species: functional and evolutionary implications
Genome biology of mosquitoes holds potential in developing knowledge-based control strategies against vector-borne diseases such as malaria, dengue, West Nile Virus and others. Although the genomes of three major vector mosquitoes have been sequenced, attempts to elucidate the relationship between intron and codon usage bias across species in phylogenetic contexts are limited. In this study, we investigated the relationship between intron content and codon bias of orthologous genes among three vector mosquito species. We found an antagonistic relationship between codon usage bias and the intron number of genes in each mosquito species. The pattern is further evident among the intronless and the intron-containing orthologous genes associated with either low or high codon bias among the three species. Furthermore, the co-variance between codon bias and intron number has a directional component associated with the species phylogeny when compared with other non-mosquito insects. By applying a maximum likelihood based continuous regression method, we show that codon bias and intron content of genes vary among the insects in a phylogeny dependent manner but with no evidence of adaptive radiation or species-specific adaptation. We discuss the functional and evolutionary significance of antagonistic relationships between intron content and codon bias.
Data from: Evolutionary relationships, cospeciation, and host switching in avian malaria parasites
We used phylogenetic analyses of cytochrome b sequences of malaria parasites and their avian hosts to assess the coevolutionary relationships between host and parasite lineages. Many lineages of avian malaria parasites have broad host distributions, which tend to obscure cospeciation events. The hosts of a single parasite or of closely related parasites were nonetheless most frequently recovered from members of the same host taxonomic family, more so than expected by chance. However, global assessments of the relationship between parasite and host phylogenetic trees, using Component and ParaFit, failed to detect significant cospeciation. The event-based approach employed by TreeFitter revealed significant cospeciation and duplication with certain cost assignments for these events, but host switching was consistently more prominent in matching the parasite tree to the host tree. The absence of a global cospeciation signal despite conservative host distribution most likely reflects relatively frequent acquisition of new hosts by individual parasite lineages. Understanding these processes will require a more refined species concept for malaria parasites and more extensive sampling of parasite distributions across hosts. If parasites can disperse between allopatric host populations through alternative hosts, cospeciation may not have a strong influence on the architecture of host–parasite relationships. Rather, parasite speciation may happen more often in conjunction with the acquisition of new hosts followed by divergent selection between host lineages in sympatry. Detailed studies of the phylogeographic distributions of hosts and parasites are needed to characterize these events.
Data from: Phylogenomics resolves evolutionary relationships among ants, bees, and wasps
Eusocial behavior has arisen in few animal groups, most notably in the aculeate Hymenoptera, a clade comprising ants, bees, and stinging wasps. Phylogeny is crucial to understanding the evolution of the salient features of these insects, including eusociality. Yet the phylogenetic relationships among the major lineages of aculeate Hymenoptera remain contentious. We address this problem here by generating and analyzing genomic data for a representative series of taxa. We obtain a single well-resolved and strongly supported tree, robust to multiple methods of phylogenetic inference. Apoidea (spheciform wasps and bees) and ants are sister groups, a novel finding that contradicts earlier views that ants are closer to ectoparasitoid wasps. Vespid wasps (paper wasps, yellow jackets, and relatives) are sister to all other aculeates except chrysidoids. Thus, all eusocial species of Hymenoptera are contained within two major groups, characterized by transport of larval provisions and nest construction, likely prerequisites for the evolution of eusociality. These two lineages are interpolated among three other clades of wasps whose species are predominantly ectoparasitoids on concealed hosts, the inferred ancestral condition for aculeates. This phylogeny provides a new framework for exploring the evolution of nesting, feeding, and social behavior within the stinging Hymenoptera.
Data from: Heterogeneity in local density allows a positive evolutionary relationship between self-fertilisation and dispersal
Despite empirical evidence for a positive relationship between dispersal and self-fertilisation (selfing), theoretical work predicts that these traits should always be negatively correlated, and the Good Coloniser Syndrome of high dispersal and selfing (Cf. Baker's Law) should not evolve. Critically, previous work assumes that adult density is spatiotemporally homogeneous, so selfing results in identical offspring production for all patches, eliminating the benefit of dispersal for escaping from local resource competition. We investigate the joint evolution of dispersal and selfing in a demographically structured metapopulation model where local density is spatiotemporally heterogeneous due to extinction-recolonisation dynamics. Selfing alleviates outcrossing failure due to low local density (an Allee Effect) while dispersal alleviates competition through dispersal of propagules from high- to low-density patches. Because local density is spatiotemporally heterogenous in our model, selfing does not eliminate heterogeneity in competition, so dispersal remains beneficial even under full selfing. Hence the Good Coloniser Syndrome is evolutionarily stable under a broad range of conditions, and both negative and positive relationships between dispersal and selfing are possible, depending on the environment. Our model thus accommodates positive empirical relationships between dispersal and selfing not predicted by previous theoretical work and provides additional explanations for negative relationships.
Data from: Information content is more important than sensory system or physical distance in guiding the long-term evolutionary relationships between signaling modalities in Sceloporus lizards
Long-term signal evolution is shaped by a variety of selective pressures including the need to convey additional information or to improve message transfer to specific receivers or through multiple environments. Here, we test the relative importance of information and sensory modality in shaping the long-term evolution of multimodal signals in Sceloporus lizards. To broadcast identity at territorial boundaries, male Sceloporus use both visual motion (headbob) and chemical signals, whereas they use color (blue belly patches) to signal aggression. Using modern phylogenetic comparative methods, we found a negative correlation between evolutionary changes in visual motion (headbobs) and chemical (femoral pore) signals, but only indirect ties between the evolution of color and motion signals (both of which are perceived visually) through viviparity, and no evidence of an evolutionary link between color and chemical signals. We also find a negative correlation between arboreality and chemical signals. Thus, information content (in this case, broadcasting individual identity versus signaling aggression) appears to play a more important role than sensory modality or physical distance in guiding long-term signal evolution. Additional insights into the underlying evolutionary processes are described, illustrating the utility of a phylogenetic approach.
Data from: Relationships of diversity, disparity and their evolutionary rates in squirrels (Sciuridae)
Several theories predict that rapidly diversifying clades will also rapidly diverge phenotypically; yet, there are also reasons for suspecting that diversification and divergence might not be correlated. In the widely distributed squirrel clade (Sciuridae), we test for correlations between per-lineage speciation rates, species richness, disparity and a time-invariant measure of disparity that allows for comparing rates when evolutionary modes differ, as they do in squirrels. We find that species richness and speciation rates are not correlated with clade age or with each other. Disparity appears to be positively correlated with clade age because young, rapidly diversifying Nearctic grassland clades are strongly pulled to a single stable optimum but older, slowly diversifying Paleotropical forest clades contain lineages that diverge along multiple ecological and morphological lines. That contrast is likely due to both the environments they inhabit and their phylogenetic community structure. Our results argue against a shared explanation for diversity and disparity in favor of geographically mediated modes of speciation and ecologically mediated modes of phenotypic evolution.
Data from: FlatNJ: a novel network-based approach to visualize evolutionary and biogeographical relationships
Split networks are a type of phylogenetic network that allow visualization of conflict in evolutionary data. We present a new method for constructing such networks called FlatNetJoining (FlatNJ). A key feature of FlatNJ is that it produces networks that can be drawn in the plane in which labels may appear inside of the network. For complex data sets that involve, for example, non-neutral molecular markers, this can allow additional detail to be visualized as compared to previous methods such as split decomposition and NeighborNet. We illustrate the application of FlatNJ by applying it to whole HIV genome sequences, where recombination has taken place, fluorescent proteins in corals, where ancestral sequences are present, and mitochondrial DNA sequences from gall wasps, where biogeographical relationships are of interest. We find that the networks generated by FlatNJ can facilitate the study of genetic variation in the underlying molecular sequence data and, in particular, may help to investigate processes such as intra-locus recombination. FlatNJ has been implemented in Java and is freely available at www.uea.ac.uk/computing/software/flatnj.
Data from: Phylogenomic support for evolutionary relationships of New World direct-developing frogs (Anura: Terraranae)
Phylogenomic approaches have proven able to resolve difficult branches in the tree of life. New World direct-developing frogs (Terraranae) represent a large evolutionary radiation in which interrelationships at key points in the phylogeny have not been adequately determined, affecting evolutionary, biogeographic, and taxonomic interpretations. We employed anchored hybrid enrichment to generate a data set containing 389 loci and >600,000 nucleotide positions for 30 terraranan and several outgroup frog species encompassing all major lineages in the clade. Concatenated maximum likelihood and coalescent species-tree approaches recover nearly identical topologies with strong support for nearly all relationships in the tree. These results are similar to previous phylogenetic results but provide additional resolution at short internodes. Among taxa whose placement varied in previous analyses, Ceuthomantis is shown to be the sister taxon to all other terraranans, rather than deeply embedded within the radiation, and Strabomantidae is monophyletic rather than paraphyletic with respect to Craugastoridae. We present an updated taxonomy to reflect these results, and describe a new subfamily for the genus Hypodactylus.
Data from: Phylogenetic ANCOVA: estimating changes in evolutionary rates as well as relationships between traits
We present a new phylogenetic comparative method—phylogenetic analysis of covariance (PANCOVA)—that uses interspecific data and a phylogeny to estimate the effects of major events on both the rate of phenotypic evolution and the association between traits. It could be used, for example, to model the impact of a key innovation, colonization of a new habitat, or environmental change. The approach is optimized with maximum likelihood and is formulated under the familiar phylogenetic generalized least squares framework, which is flexible and easily extended to incorporate other factors and parameters. As an example, we explore the relationship between parental investment and relative telencephalon size in birds and contrast the results of PANCOVA with those from other phylogenetic comparative methods.
Data from: Phylogenetic utility of different types of molecular data used to infer evolutionary relationships among stalk-eyed flies (Diopsidae)
A phylogenetic hypothesis of relationships among 33 species of stalk-eyed flies was generated from a molecular data set comprised of three mitochondrial and three nuclear gene regions. A combined analysis of all the data equally weighted produced a single most parsimonious cladogram with relatively strong support at the majority of nodes. The phylogenetic utility of different classes of molecular data was also examined. In particular, using a number of different measures of utility in both a combined and separate analysis framework, we focus on the distinction between mitochondrial and nuclear genes, and faster-evolving characters and slower-evolving characters. For the first comparison, by nearly any measure of utility, the nuclear genes are substantially more informative for resolving diopsid relationships than are the mitochondrial genes. The nuclear genes exhibit less homoplasy, are less incongruent both with one another and with the combined data, and contribute more support to the combined analysis topology than the mitochondrial genes. Results from the second comparison, however, provide little evidence of a clear difference in utility. Despite indications of rapid divergence and saturation, faster-evolving characters in both the nuclear and mitochondrial data sets still provide substantial phylogenetic signal. In general, inclusion of the more rapidly evolving data consistently improves the congruence among partitions.
Figure 6 from: Patterson BD, Webala PW, Lavery TH, Agwanda BR, Goodman SM, Kerbis Peterhans JC, Demos TC (2020) Evolutionary relationships and population genetics of the Afrotropical leaf-nosed bats (Chiroptera, Hipposideridae). ZooKeys 929: 117-161. https://doi.org/10.3897/zookeys.929.50240
Figure 6 Species tree Hipposideridae based on StarBEAST analysis of four introns. Posterior probabilities appear at all nodes.
Figure 5 from: Patterson BD, Webala PW, Lavery TH, Agwanda BR, Goodman SM, Kerbis Peterhans JC, Demos TC (2020) Evolutionary relationships and population genetics of the Afrotropical leaf-nosed bats (Chiroptera, Hipposideridae). ZooKeys 929: 117-161. https://doi.org/10.3897/zookeys.929.50240
Figure 5 Phylogeny of Hipposideridae based on Bayesian analysis of 103 concatenated nuclear intron sequences. Numbers denote posterior probabilities (BI) and bootstrap percentages (ML); red circles at more terminal nodes indicate BS ≥ 70%, PP ≥ 0.95.
Figure 4 from: Patterson BD, Webala PW, Lavery TH, Agwanda BR, Goodman SM, Kerbis Peterhans JC, Demos TC (2020) Evolutionary relationships and population genetics of the Afrotropical leaf-nosed bats (Chiroptera, Hipposideridae). ZooKeys 929: 117-161. https://doi.org/10.3897/zookeys.929.50240
Figure 4 Substitution network plots for Afrotropical hipposiderids AHipposideros caffer clades 1–4 BHipposideros caffer clades 5–8 CH. ruber clades.
Figure 5 from: Vu TTT, Nguyen AD, Le TML, Peña-Santiago R (2024) Updated taxonomy and new insights into the evolutionary relationships of the genus Sporonchulus Cobb, 1917 (Nematoda, Mononchida) after the study of two Vietnamese species. Zoosystematics and Evolution 100(1): 155-166. https://doi.org/10.3897/zse.100.118675
Figure 5 Bayesian Inference tree from the newly sequenced Sporonchulus ibitiensis (Carvalho, 1951) Andrássy, 1958 based on sequences of the 18S rDNA region. Bayesian posterior probabilities (%) are given for each clade. Scale bar shows the number of substitutions per site.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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