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opencc-zeroDec 2014View details →

Data from: Transient dynamics reveal the importance of early life survival to the response of a tropical tree to harvest

Exploitation of non-timber forest products can contribute to the alleviation of poverty. However, overexploitation can also lead to species decline. Studies on the sustainability of harvest often use stationary population growth rates to assess harvesting effects. For such frequently harvested systems, transient analysis can provide new insights into the response of populations to harvest. To test the prediction that the effect of harvest differs between transient and asymptotic phases, I used four years of demographic data to compare the impact of harvesting bark and foliage on the short- and long-term dynamics of African dry zone Mahogany Khaya senegalensis in West Africa. The effect of harvest was stronger in the short term than in the long term, particularly in the moist region. Patterns of transient elasticities also differed from the elasticities of long-term growth rates to perturbation of vital rates. Survival at early life stages was more important for short-term dynamics than for long-term population dynamics. Synthesis and applications. This study illustrates that using the asymptotic growth rates to assess the impact of harvest may underestimate the short-term effects of harvest. Short-term management plans based on the elasticity analysis of long-term growth rates will be suboptimal given the relative importance of the survival of non-reproductive stages for population dynamics in the near term. Managers should use results from elasticity analysis of both long-term and short-term population dynamics to develop more realistic management plans.

opencc-zeroJun 2021View details →

Larger cells have relatively smaller nuclei across the Tree of Life

Larger cells have larger nuclei, but the precise relationship between cell size and nucleus size remains unclear, and the evolutionary forces that shape this relationship are debated. We compiled data for almost 900 species – from yeast to mammals – at three scales of biological organisation: among‐species, within‐species, and among‐lineages of a species that was artificially selected for cell size. At all scales, we showed that the ratio of nucleus size to cell size (the 'N: C' ratio) decreased systematically in larger cells. Size evolution appears more constrained in nuclei than cells: cell size spans across six orders of magnitude, whereas nucleus size varies by only three. The next important challenge is to determine the drivers of this apparently ubiquitous relationship in N:C ratios across such a diverse array of organisms.

opencc-zeroDec 2013View details →

Data from: Taxon-rich phylogenomic analyses resolve the eukaryotic tree of life and reveal the power of subsampling by sites

Most eukaryotic lineages are microbial, and many have only recently been sampled for phylogenetic studies or remain in the 'dark area' of the tree of life where there are no molecular data. To assess relationships among eukaryotic lineages, we perform a taxon-rich phylogenomic analysis including 232 eukaryotes selected to maximize taxonomic diversity and up to 1554 genes chosen as vertically inherited based on their broad distribution among eukaryotes. We also include sequences from 486 bacteria and 84 archaea to assess the impact of endosymbiotic gene transfer (EGT) from plastids and to detect contamination. Overall, our analyses are consistent with other less taxon-rich estimates of the eukaryotic tree of life and we recover strong support for five major clades: Amoebozoa, Excavata (without the genus Malawimonas), Opisthokonta, Archaeplastida and SAR (Stramenopila, Alveolata and Rhizaria). Our analyses also highlight the existence of 'orphan' lineages, lineages that lack robust placement in the eukaryotic tree of life and indicate the possibility of as yet undiscovered diversity. In analyses including bacteria and archaea, we find that ~10% of the 1554 genes, which we choose because they are found in four or five of the five major eukaryotic clades and hence may be more likely to be inherited vertically, appear to have been acquired from cyanobacteria through EGT in photosynthetic lineages. Removing these EGT genes places the green algae as sister to the glaucophytes instead of the red algae, suggesting that unknowingly including of genes of plastid origin, and combining them with genes of nuclear origin, may mislead phylogenetic estimates. Finally, the large size of our dataset allows comparative analyses of subsets of data; alignments built from randomly sampled sites provide greater support, particularly for deep relationships, than do equivalent sized datasets built from randomly sampled genes.

opencc-zeroDec 2017View details →

Data from: Anchored phylogenomics illuminates the skipper butterfly tree of life

Butterflies (Papilionoidea) are perhaps the most charismatic insect lineage, yet phylogenetic relationships among them remain incompletely studied and controversial. We sequenced nearly 400 loci using Anchored Hybrid Enrichment and sampled all tribes and more than 120 genera of skippers (Hesperiidae), one of the most species-rich and poorly studied butterfly families. Maximum-likelihood, parsimony and coalescent multi-species methods all converged on a novel, robust phylogenetic hypothesis for skippers. Different optimality criteria and methodologies recovered almost identical phylogenetic trees with strong nodal support at nearly all taxonomic levels. Our results support Coeliadinae as the sister group to the remaining skippers, the monotypic Euschemoninae as sister group to all other subfamilies but Coeliadinae, and the monophyly of Eudaminae plus Pyrginae. Within Pyrginae, Celaenorrhinini and Tagiadini are sister groups, the Neotropical firetips, Pyrrhopygini, are sister to all other tribes but Celaenorrhinini and Tagiadini. Achlyodini is recovered as the sister group to Carcharodini, and Erynnini as sister group to Pyrgini. Within Hesperiinae, there is strong support for the monophyly of Aeromachini plus remaining Hesperiinae. The giant skippers (Agathymus and Megathymus) once classified as a single subfamily, are recovered as monophyletic with strong support, but are deeply nested within grass skippers (Hesperiinae). These results enhance understanding of the evolution of one of the most species-rich butterfly families.

opencc-zeroDec 2014View details →

Data from: Building the avian tree of life using a large-scale, sparse supermatrix

Birds are the most diverse tetrapod class, with about 10,000 extant species that represent a remarkable evolutionary radiation in which most taxa arose during a short period of time. There has been a tremendous increase in the amount of molecular data available from birds, and more than two-thirds of these species have some sequence data available. Here we assembled these available sequence data from birds to estimate a large-scale avian phylogeny. We performed an unconstrained maximum likelihood analysis of a sparse supermatrix comprising 22 nuclear loci and seven mitochondrial regions from 6714 species. We inferred a phylogeny with a backbone remarkably similar to that obtained by detailed analyses of multigene datasets, yet with the addition of thousands of more taxa. All orders were monophyletic with generally high support. While most families and genera were well supported, a number of them, especially within the oscine passerines, had little or no support. This likely reflects problems with the circumscription of these genera and families. Our results indicate that the amount of sequence data currently available is sufficient to produce a robust estimate of the avian tree of life using current methods of inference. The availability of a tree that is unconstrained by prior information, with branch lengths that have a direct connection to the underlying data, should be useful for comparative methods, taxonomic revisions, and prioritizing taxa that should be targeted for additional data collection.

opencc-by-4.0May 2024View details →

Bachelorproef toekomst van ons genoom - CpG-eilanden doorheen de tree of life

Deze bestanden zijn supplementaire data van onze bachelorproef aan de Universiteit Gent in de richting Bio-ingenieurswetenschappen (afstudeerrichting cel en gen).

Fig. 18 in The Amphibian Tree Of Life

Fig. 18. Tree of Pelobatoidea and outgroups of GarcíaParís et al. (2003) based on 1,000 bp mitochondrial genes: cytochrome c and 16S rRNA. The sequences were aligned using Clustal X (

Fig. 17 in The Amphibian Tree Of Life

Fig. 17. Tree of amphibians provided by San Mauro et al. (2005). This tree reflects a likelihood analysis of 1,368 bp of the nuclear proteincoding gene RAG1, assuming the GTR I substitution model (as suggested by ModelTest v. 3.6; Posada and Crandall, 1998). Sequence

Fig. 61. Part 6 in The Amphibian Tree Of Life

Fig. 61. Part 6 of anurans from the general tree (fig. 50 [insert]): Microhylidae.

Fig. 14 in The Amphibian Tree Of Life

Fig. 14. Narrative tree of relevant anuran taxa by Ford and Cannatella (1993). A branch Hylidae 1 Pseudidae in the original figure is collapsed per errata distributed with reprint. An was used by these authors to denote a metataxon, and quotation marks to denote nonmonophyly

Fig. 36 in The Amphibian Tree Of Life

Fig. 36. Maximum likelihood tree of exemplars of Ranoidea, with a focus on African taxa, by der Meijden et al. (2005), based on mt DNA (12S and 16S rRNA) and nu DNA (RAG1, rhodopsin), for 2,995 bp of sequence. Alignment was made using ClustalW (Thompson et al., with costs not disclosed and gaps and highly variable sites excluded from analysis. The model

Fig. 5 in The Amphibian Tree Of Life

Fig. 5. Tree of salamander families from Gao

Fig. 48 in The Amphibian Tree Of Life

Fig. 48. Consensus of weighted parsimony trees of Rhacophoridae suggested by J.A. Wilkinson al. (2002), with their subfamily taxonomy on right. (This is Mantellidae and Rhacophoridae of authors.) The tree was based on 2kb (of 12S and 16S mt rRNA as well as tRNAVal). Alignment manual, guided by models of secondary structure with ambiguously aligned segments discarded analysis, transversions were weighted twice transitions. Whether reatment of gaps were treated as dence of relationship or as missing data was not stated. Chirixalus eiffingeri was placed in

Fig. 54. Part 1 in The Amphibian Tree Of Life

Fig. 54. Part 1 of anurans from the general tree (fig. 50 [insert]): nonneobatrachian frogs.

Fig. 47. A in The Amphibian Tree Of Life

Fig. 47. A, Rhacophorid and mantellid tree of Liem (1970) based on 36 direct to dendritic mor

Fig. 3 in The Amphibian Tree Of Life

Fig. 3. Currently accepted view of relation

opencc-zeroOct 2021View details →

Distinguishing between dispersal and vicariance: A novel approach using anti-tropical taxa across the fish Tree of Life

Aim: Anti-tropical taxa are species split by the tropics into disjunct northern and southern populations. These distributions occur throughout the Tree of Life, but the mechanisms proposed to drive this pattern are debated and generally fit into two categories: dispersal and vicariance. Here we quantitatively test the prevalence of dispersal and vicariance as plausible drivers of anti-tropical marine distributions using intra-specific anti-tropical marine fishes as a model system. Location: Primarily Indo-Pacific. Major Taxa Studied: Marine fishes. Methods: To test between dispersal and vicariance in latitudinally disjunct marine fishes, we used an ecological niche modeling framework to predict the spatiotemporal suitability of tropical habitats during contemporary and glacial time periods. Three different model configurations were used per species to test: (1) presence of contemporary tropical suitable habitat for northern populations, (2) the same for southern populations, (3) presence of tropical suitable habitat during the last glacial maximum for the entire species. These models were examined in an evolutionary context to determine if there was any phylogenetic signal in biogeographic predictions. Additionally, we tested if life history traits could account for biogeographic predictions. Results: Our analyses resulted in 87 strongly supported models for 29 anti-tropical fishes across the fish Tree of Life (northern population model, southern population model, and full species model for each taxon). Model projections consistently matched predictions of vicariance in 13 fishes and 10 fishes matched predictions of dispersal regardless of thresholding approach. We failed to find any phylogenetic signal for anti-tropicality in general, or for dispersal and vicariant species specifically. Further, dispersal and vicariant tendencies were not found to be correlated with life history traits. Main conclusions: These data quantitatively support both dispersal and vicariance as active mechanisms driving disjunct distributions in marine systems and suggest that they occur stochastically across the fish Tree of Life. This novel approach for examining dispersal and vicariance hypotheses supports the species-specific nature of biogeographic mechanisms structuring distributions, and that a "one-size-fits-all" prediction for current and future species' responses to environmental change is unlikely to be informative.

publicApr 2019View details →

Data from: Organellar phylogenomics inform systematics in the green algal family Hydrodictyaceae (Chlorophyceae) and provide clues to the complex evolutionary history of plastid genomes in the green algal Tree of Life.

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publicOct 2021View details →

Distinguishing between dispersal and vicariance: A novel approach using anti-tropical taxa across the fish Tree of Life

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