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95 results for “evolutionary lineages”
Figure 1 in Phylogeography and evolutionary lineage diversity in the small-eared greater galago, Otolemur garnettii (Primates: Galagidae)
Figure 1. Illustrations of the recently recognized Otolemur garnettii subspecies (A), their geographic range according to the IUCN red list (B), and localities sampled in this study (C). It is worth noting that illustrations represent the extremes of variation found in the subspecies and the overall range of distribution should be interpreted as areas in which they might be expected to occur. Otolemur g. lasiotis, in particular, is known to occur in highly discontinuous distributions.
Figure 2. Haplotype median joining network estimated from dataset 1, comprising 76 in Phylogeography and evolutionary lineage diversity in the small-eared greater galago, Otolemur garnettii (Primates: Galagidae)
Figure 2. Haplotype median joining network estimated from dataset 1, comprising 76 samples of partial cytochrome b (402 bp).
Data from: Cryptic divergent lineages of Pultenaea pauciflora M.B. Scott (Fabaceae, Mirbelieae) exhibit different evolutionary history
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Data from: A worldwide phylogeography of the whiteworm lichen Thamnolia vermicularis reveals three lineages with distinct habitats and evolutionary histories
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Data from: Pleistocene diversification in an ancient lineage: a role for glacial cycles in the evolutionary history of Dioon Lindl. (Zamiaceae).
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Non-adaptive evolutionary processes governed the diversification of a temperate conifer lineage after its migration into the tropics
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Lineage-specific variation in the evolutionary stability of coral photosymbiosis.
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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..
A new method for quantifying heterochrony in evolutionary lineages
The occupation of new environments by evolutionary lineages is frequently associated with morphological changes. This co-variation of ecotype and phenotype is expected due to the process of natural selection, whereby environmental pressures lead to the proliferation of morphological variants that are a better fit for the prevailing abiotic conditions. One primary mechanism by which phenotypic variants are known to arise is through changes in the timing or duration of organismal development resulting in alterations to adult morphology, a process known as heterochrony. While numerous studies have demonstrated heterochronic trends in association with environmental gradients, few have done so within a phylogenetic context. Understanding species interrelationships is necessary to determine whether morphological change is due to heterochronic processes; however, research is hampered by the lack of a quantitative metric with which to assess the degree of heterochronic traits expressed within and among species. Here I present a new metric for quantifying heterochronic change, expressed as a heterochronic weighting, and apply it to xiphosuran chelicerates within a phylogenetic context to reveal concerted independent heterochronic trends. These trends correlate with shifts in environmental occupation from marine to non-marine habitats, resulting in a macroevolutionary ratchet. Critically, the distribution of heterochronic weightings among species shows evidence of being influenced by both historical, phylogenetic processes and external ecological pressures. Heterochronic weighting proves to be an effective method to quantify heterochronic trends within a phylogenetic framework and is readily applicable to any group of organisms that have well-defined morphological characteristics, ontogenetic information, and resolved internal relationships.
Data from: Ecological and evolutionary dynamics of coexisting lineages during a long-term experiment with E. coli
Closely related organisms usually occupy similar ecological niches, leading to intense competition and even extinction. Such competition also can promote rapid phenotypic evolution and ecological divergence. This process may end with the stable occupation of distinct niches or, alternatively, may entail repeated bouts of evolution. Here we examine two Escherichia coli lineages, called L and S, that coexisted for more than 30,000 generations after diverging from a common ancestor. Both lineages underwent sustained phenotypic evolution based on global transcription and resource utilization profiles, with L seeming to encroach over time on the catabolic profile of S. Reciprocal invasion experiments with L and S clones from the same or different generations revealed evolutionary changes in their interaction, including an asymmetry that confirmed the encroachment by L on the niche of the S lineage. In general, L and S clones from the same generation showed negative frequency-dependent effects, consistent with stable coexistence. However, L clones could invade S clones from both earlier and later generations, whereas S clones could invade only L clones from earlier generations. In this system, the long-term coexistence of competing lineages evidently depended on successive rounds of evolution, rather than on initial divergence followed by a static equilibrium.
Data from: Stochastic character mapping of state-dependent diversification reveals the tempo of evolutionary decline in self-compatible Onagraceae lineages
A major goal of evolutionary biology is to identify key evolutionary transitions that correspond with shifts in speciation and extinction rates. Stochastic character mapping has become the primary method used to infer the timing, nature, and number of character state transitions along the branches of a phylogeny. The method is widely employed for standard substitution models of character evolution. However, current approaches cannot be used for models that specifically test the association of character state transitions with shifts in diversification rates such as state-dependent speciation and extinction (SSE) models. Here we introduce a new stochastic character mapping algorithm that overcomes these limitations, and apply it to study mating system evolution over a time-calibrated phylogeny of the plant family Onagraceae. Utilizing a hidden state SSE model we tested the association of the loss of self-incompatibility with shifts in diversification rates. Confirming long standing theory, we found that self-compatible lineages have higher extinction rates and lower net diversification rates compared to self-incompatible lineages. Furthermore, these results provide empirical evidence for the "senescing" diversification rates predicted in highly selfing lineages: our mapped character histories show that the loss of self-incompatibility is followed by a short-term spike in speciation rates, which declines after a time lag of several million years resulting in negative net diversification. Lineages that have long been self-compatible such as Fuchsia and Clarkia are in a previously unrecognized and ongoing evolutionary decline. Our results demonstrate that stochastic character mapping of SSE models is a powerful tool for examining the timing and nature of both character state transitions and shifts in diversification rates over the phylogeny.
Data from: Evidence for a discrete evolutionary lineage within Equatorial Guinea suggests that the tsetse fly Glossina palpalis palpalis exists as a species complex
Tsetse flies of the palpalis group are major vectors of Human African Trypanosomiasis in Africa. Accurate knowledge of species identity is essential for vector control. Here we combine ribosomal internal transcribed spacer 1 (ITS1), mitochondrial Cytochrome Oxidase 1 (COI) and microsatellites to determine the population structure and phylogenetic relations of G. p. palpalis in Equatorial Guinea. COI sequence data suggest that G. p. palpalis in Equatorial Guinea are a distinct subspecies from previously described G. p. palpalis in West Africa and Democratic Republic of Congo. G. p. palpalis in Equatorial Guinea and DRC share a common ancestor which diverged from West African G. p. palpalis around 1.9 million years ago. Previous ITS1 length polymorphism data suggested the possible presence of hybrids in Equatorial Guinea. However, ITS1 showed incomplete lineage sorting compared to clearly defined COI groups, and data from twelve unlinked microsatellites provided no evidence of hybridization. Microsatellite data indicated moderate but significant differentiation between the populations analysed (Rio Campo, Mbini and Kogo). Moreover, unlike previous studies of G. p. palpalis, there was no evidence for heterozygote deficiency, presence of migrants, or cryptic population structure. Variance effective population size at Rio Campo was estimated at 501 to 731 assuming 8 generations/year. This study of the population genetics of G. p. palpalis in central Africa provides the first estimate of genetic differentiation between geographically separated G. p. palpalis populations.
FIGURE 6 in Unravelling the origin of the brown hyena (Parahyena brunnea) and its evolutionary and paleoecological implications for the Pachycrocuta lineage
FIGURE 6. Bivariate plots of geological age on the scores for the first two principal components of the upper dentition (A) and (B) PC I for fossil individuals and paleontological localities, respectively. C-D, PC II for fossil individuals and paleontological localities, respectively. E: Elandsfontein. G: Gladysvale Cave. K: Kromdraai A. L: Longdan. P: Petralona (circle: PEC 18, triangle: mean for Petralona). S: Ségriès-le Réservoir. At the base of each figure are shown the ranges for the extant species and C. spelaea in each principal component.
FIGURE 3 in Unravelling the origin of the brown hyena (Parahyena brunnea) and its evolutionary and paleoecological implications for the Pachycrocuta lineage
FIGURE 3. Bivariate plots of the scores on the lower dentition two first principal components and their corresponding component loading plots for (A) analysis for fossil individuals and (B) analysis for paleontological localities. Ba: Baihaicum. E: Elandsfontein. L: Longdan.
Figure 9 from: Sukhorukov AP, Sennikov AN, Nilova MV, Mazei Y, Kushunina M, Marchioretto MS, Hanáček P (2019) Evolutionary relationships and taxonomy of Microtea (Microteaceae), a basal lineage in the core Caryophyllales. PhytoKeys 115: 1-50. https://doi.org/10.3897/phytokeys.115.29041
Figure 9 Cross-section of Microteaglochidiata fruit (Brazil, Bahia, Tucano Mun., 20 Feb 1992, A.M. de Carvalho & D.J.N. Hind 3841, PACA). A image of the cross-section B schematic representation. Abbreviations: P – pericarp; T – testa; TE – tegmen.
Figure 11 from: Sukhorukov AP, Sennikov AN, Nilova MV, Mazei Y, Kushunina M, Marchioretto MS, Hanáček P (2019) Evolutionary relationships and taxonomy of Microtea (Microteaceae), a basal lineage in the core Caryophyllales. PhytoKeys 115: 1-50. https://doi.org/10.3897/phytokeys.115.29041
Figure 11 Microteadebilis: A general view of the plants (La Selva Biological Station, Costa Rica, 2001) B close-up of the inflorescence (La Selva Biological Station, Costa Rica, 2001). Photographs by Orlando Vargas Ramírez. See also https://sura.ots.ac.cr/florula4/find_sp3.php?key_species_code=LS001515.
Figure 6 from: Sukhorukov AP, Sennikov AN, Nilova MV, Mazei Y, Kushunina M, Marchioretto MS, Hanáček P (2019) Evolutionary relationships and taxonomy of Microtea (Microteaceae), a basal lineage in the core Caryophyllales. PhytoKeys 115: 1-50. https://doi.org/10.3897/phytokeys.115.29041
Figure 6 Fruits and seeds of Microteasulcicaulis and M.bahiensis: A, B fruit of M.sulcicaulis, enclosed in the perianth (Paraguay, Caazapá Dept., Tavai, 7 Dec 1988, F. Mereles 2122, G) C, D seed of M.sulcicaulis (Paraguay, Caazapá Dept., Tavai, 7 Dec 1988, F. Mereles 2122, G) E, F fruit of M.bahiensis (Brazil, Bahia state, Salvador, Dunas de Itapuã, nr Hotel Stella Maris, N from Condomínio Alamedas da Praia, 8 Jun 1993, P. de Queiroz 3211, PACA) G, H seed of M.bahiensis (Brazil, Bahia state, Salvador, Dunas de Itapuã, nr Hotel Stella Maris, N from Condomínio Alamedas da Praia, 8 Jun 1993, P. de Queiroz 3211, PACA). Magnification: A, E – 30×, B, F – 100×, C, G – 50×, D, H – 300×.
Figure 8 from: Sukhorukov AP, Sennikov AN, Nilova MV, Mazei Y, Kushunina M, Marchioretto MS, Hanáček P (2019) Evolutionary relationships and taxonomy of Microtea (Microteaceae), a basal lineage in the core Caryophyllales. PhytoKeys 115: 1-50. https://doi.org/10.3897/phytokeys.115.29041
Figure 8 Fruits and seeds of Microteamaypurensis and M.tenuifolia: A, B fruit of M.maypurensis, enclosed in the perianth (Bolivia, La Paz Dept., Beni river, Jul 1886, H.H. Rusby 1379, LE) C, D seed of M.maypurensis (Bolivia, La Paz Dept., Beni river, Jul 1886, H.H. Rusby 1379, LE) E, F fruit of M.tenuifolia enclosed in the perianth (Brazil, Minas Gerais, Serrra das Vertentes, Jun 1893, A. Glaziou 20437, B) G, H seed of M.tenuifolia (Brazil, Jacobina Mountains in Bahia, 1836, Blanchet 2588, P00798998). Magnification: A, E – 30×, B, F – 100×, C, G – 50×, D, H – 300×.
Figure 10 from: Sukhorukov AP, Sennikov AN, Nilova MV, Mazei Y, Kushunina M, Marchioretto MS, Hanáček P (2019) Evolutionary relationships and taxonomy of Microtea (Microteaceae), a basal lineage in the core Caryophyllales. PhytoKeys 115: 1-50. https://doi.org/10.3897/phytokeys.115.29041
Figure 10 Classification of Microtea species by group average linkage algorithm of cluster analysis based on 13 characters. Black branches connect significantly (P < 0.05) different groups, red branches – insignificantly different groups.
Figure 1 from: Sukhorukov AP, Sennikov AN, Nilova MV, Mazei Y, Kushunina M, Marchioretto MS, Hanáček P (2019) Evolutionary relationships and taxonomy of Microtea (Microteaceae), a basal lineage in the core Caryophyllales. PhytoKeys 115: 1-50. https://doi.org/10.3897/phytokeys.115.29041
Figure 1 The phylogenetic tree from maximum likelihood analysis of matK region sequences. The tree with the highest log likelihood (-2983.53) is shown. The analysis involved 18 nucleotide sequences. Codon positions included were 1st+2nd+3rd+Noncoding. There were a total of 828 positions in the final dataset.
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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.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
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.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.