Find research datasets worth reusing

opencc-by-4.0Dec 2017View details →

Fig. 1 in Molecular characterization of Babesia peircei and Babesia ugwidiensis provides insight into the evolution and host specificity of avian piroplasmids

Fig. 1. Maximum likelihood phylogenetic tree of the 18S rRNA gene sequences (1450 bp) of the studied Babesia lineages. Sequences obtained in this study are emphasized in red, and those of other avian-infecting lineages are shown in blue. For each sequence, the following information is provided: morphospecies (individual identification or GenBank code) host species. For avian-infecting lineages, the host order is indicated with colored circles (see legend). Branch lengths are drawn proportionally to evolutionary distance. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

opencc-by-4.0Dec 2008View details →

Text-fig. 1. D&E tree of Endress and Doyle (2009), from the combined morphological and molecular analysis of Doyle and Endress (2000), with modifications based on more recent data, showing the inferred evolution of the reticulum grading character (39). Boxes under names of taxa indicate their character state; shading of branches indicates their reconstructed state based on parsimony optimization with MacClade (Maddison and Maddison 2003). Nymph = Nymphaeales, Aust = Austrobaileyales, Chlor = Chloranthaceae, Piper = Piperales, Ca = Canellales, Magnol = Magnoliales. in Early Cretaceous Monocots: A Phylogenetic Evaluation

Text-fig. 1. D&E tree of Endress and Doyle (2009), from the combined morphological and molecular analysis of Doyle and Endress (2000), with modifications based on more recent data, showing the inferred evolution of the reticulum grading character (39). Boxes under names of taxa indicate their character state; shading of branches indicates their reconstructed state based on parsimony optimization with MacClade (Maddison and Maddison 2003). Nymph = Nymphaeales, Aust = Austrobaileyales, Chlor = Chloranthaceae, Piper = Piperales, Ca = Canellales, Magnol = Magnoliales.

Fig. 7 in On ''Molecular Phylogeny of Vespidae (Hymenoptera) and the Evolution of Sociality in Wasps''

Fig. 7. Screen display of same portion of the 28S alignment as in figure 6, with the show character statistics toggle of Winclada set to on. See text for explanation of the numbers displayed.

Fig. 6 in On ''Molecular Phylogeny of Vespidae (Hymenoptera) and the Evolution of Sociality in Wasps''

Fig. 6. Portion of 28S alignment of Schmitz and Moritz (1998) as displayed on the screen by Winclada.

Fig. 2. Cladogram for the 28S in On ''Molecular Phylogeny of Vespidae (Hymenoptera) and the Evolution of Sociality in Wasps''

Fig. 2. Cladogram for the 28S rDNA alignment of Schmitz and Moritz (1998). The length is 302 steps; consistency index = 0.76 and retention index = 0.80.

Fig. 3. Cladogram for the combined 16S in On ''Molecular Phylogeny of Vespidae (Hymenoptera) and the Evolution of Sociality in Wasps''

Fig. 3. Cladogram for the combined 16S data and the morphological and behavioral characters (see appendix 1). The length is 652 steps; consistency index = 0.64 and retention index = 0.69.

Fig. 4. Consensus tree for the combined 28S in On ''Molecular Phylogeny of Vespidae (Hymenoptera) and the Evolution of Sociality in Wasps''

Fig. 4. Consensus tree for the combined 28S data and the morphological and behavioral characters (see appendix 1). The length is of the two underlying cladograms is 458 steps; consistency index = 0.81 and retention index = 0.85.

Fig. 5 in On ''Molecular Phylogeny of Vespidae (Hymenoptera) and the Evolution of Sociality in Wasps''

Fig. 5. Cladogram for the combined sequence datasets and the morphological and behavioral characters. The length is 907 steps; consistency index = 0.68 and retention index = 0.75.

opencc-by-4.0May 2005View details →

Figure 4 in Phylogenetic relationships and evolution of Orbiniidae (Annelida, Polychaeta) based on molecular data

Figure 4. Most parsimonious tree (tree length = 2641, CI = 0.5388) of the maximum parsimony analysis of the combined dataset. The values at each node represent the MP bootstrap support. Taxa which are discussed in detail in the discussion are in bold type.

opencc-by-4.0May 2005View details →

Figure 3 in Phylogenetic relationships and evolution of Orbiniidae (Annelida, Polychaeta) based on molecular data

Figure 3. Maximum likelihood tree of the mitochondrial 16S rRNA gene dataset based on the GTR + G model of sequence evolution (–lnL = 3943.65274). The first value at each node represents the ML bootstrap support, the second the Bayesian posterior probability. Taxa which are discussed in detail in the discussion are in bold type.

opencc-by-4.0Nov 2022View details →

dataset for bioRxiv preprint titled 'Evolution of drug resistance drives progressive destabilizations in functionally conserved molecular dynamics of the flap region of the HIV-1 protease'

This data supports the Figures in the preprint titled Evolution of drug resistance drives progressive destabilizations in functionally conserved molecular dynamics of the flap region of the HIV-1 protease working abstract The HIV-1 protease is one of several common key targets of combination drug therapies for human immunodeficiency virus infection and acquired immunodeficiency syndrome (HIV/AIDS).  During the progression of the disease, some individual patients acquire -drug resistance due to mutational hotspots on the viral proteins targeted by combination drug therapies.  It has recently been discovered that drug-resistant mutations accumulate on the ‘flap region’ of the HIV-1 protease,  which is a critical dynamic region involved in non-specific polypeptide binding  during invasion and infection of the host cell.  In this study, we utilize machine learning assisted comparative molecular dynamics, conducted at single amino acid site resolution, to investigate the dynamic changes that occur during functional dimerization and polypeptide binding of the main protease. We use a multi-agent machine learning model to identify conserved dynamics of the HIV-1 main protease that are preserved across simian and feline protease orthologs (SIV and FIV).  We also investigate changes in dynamics due to common drug-resistant mutations in many patients. We find that a key functional site in the flap region, a solvent-exposed isoleucine (ILE50) and surrounding sites that control flap dynamics is often targeted by drug-resistance mutations, likely leading to malfunctional molecular dynamics affecting the overall flexibility of the flap region. We conclude that better long term patient outcomes may be achieved by designing drugs that target protease regions which are less dependent upon single sites with large functional binding effects.

publicNov 2023View details →

Data from: The role of mutation bias in adaptive molecular evolution: insights from convergent changes in protein function

Open the record for dataset details and reuse information.

publicApr 2020View details →

Data from: Molecular evolution of the proopiomelanocortin system in Barn owl species

Open the record for dataset details and reuse information.

publicNov 2019View details →

Data from: Natural selection and repeated patterns of molecular evolution following allopatric divergence

Open the record for dataset details and reuse information.

publicNov 2024View details →

Data from: High-resolution chromosome-level genome of Scylla paramamosain provides molecular insights into adaptive evolution in crab

Open the record for dataset details and reuse information.

opencc-zeroAug 2020View details →

Heterogeneity in the rate of molecular sequence evolution substantially impacts the accuracy of detecting shifts in diversification rates

As species richness varies along the tree of life, there is a great interest in identifying factors that affect the rates by which lineages speciate or go extinct. To this end, theoretical biologists have developed a suit of phylogenetic comparative methods that aim to identify where shifts in diversification rates had occurred along a phylogeny and whether they are associated with some traits. Using these methods, numerous studies have predicted that speciation and extinction rates vary across the tree of life. In this study we show that asymmetric rates of sequence evolution rates lead to systematic biases in the inferred phylogeny, which in turn lead to erroneous inferences regarding lineage diversification patterns. The results demonstrate that as the asymmetry in sequence evolution rates increases, so does the tendency to select more complicated models that include the possibility of diversification rate shifts. These results thus suggest that any inference regarding shifts in diversification pattern should be treated with great caution, at least until any biases regarding the molecular substitution rate have been ruled out.

opencc-zeroDec 2016View details →

Data from: Targeted enrichment of large gene families for phylogenetic inference: phylogeny and molecular evolution of photosynthesis genes in the Portullugo clade (Caryophyllales)

Hybrid enrichment is an increasingly popular approach for obtaining hundreds of loci for phylogenetic analysis across many taxa quickly and cheaply. The genes targeted for sequencing are typically single-copy loci, which facilitate a more straightforward sequence assembly and homology assignment process. However, this approach limits the inclusion of most genes of functional interest, which often belong to multi-gene families. Here we demonstrate the feasibility of including large gene families in hybrid enrichment protocols for phylogeny reconstruction and subsequent analyses of molecular evolution, using a new set of bait sequences designed for the "portullugo" (Caryophyllales), a moderately sized lineage of flowering plants (∼2200 species) that includes the cacti and harbors many evolutionary transitions to C4 and CAM photosynthesis. Including multi-gene families allowed us to simultaneously infer a robust phylogeny and construct a dense sampling of sequences for a major enzyme of C4 and CAM photosynthesis, which revealed the accumulation of adaptive amino acid substitutions associated with C4 and CAM origins in particular paralogs. Our final set of matrices for phylogenetic analyses included 75–218 loci across 74 taxa, with ∼50% matrix completeness across datasets. Phylogenetic resolution was greatly improved across the tree, at both shallow and deep levels. Concatenation and coalescent-based approaches both resolve the sister lineage of the cacti with strong support: Anacampserotaceae + Portulacaceae, two lineages of mostly diminutive succulent herbs of warm, arid regions. In spite of this congruence, BUCKy concordance analyses demonstrated strong and conflicting signals across gene trees. Our results add to the growing number of examples illustrating the complexity of phylogenetic signals in genomic-scale data.

opencc-zeroNov 2023View details →

Data for: The pace of mitochondrial molecular evolution varies with seasonal migration distance

This repository contains data associated with "The pace of mitochondrial molecular evolution varies with seasonal migration distance." This study demonstrates relationships between traits (migration distance, mass, population genetic parameters representing genetic diversity) and molecular evolutionary rates (dS and dN/dS). The main conclusions are based on models from the program Coevol. The files included here are input files necessary to run models with Coevol, as well as selected Coevol output files used for figure generation associated with the manuscript. We also include a copy of a GitHub repository of manuscript code. Other necessary data for replicating analyses in the manuscript are included in the manuscript supplement.

opencc-zeroDec 2023View details →

Molecular phylogeny and morphological perianth evolution in Corymbia (Myrtaceae), and the implications for generic delimitation: data and tree files

Premise: Eucalypts (Myrtaceae tribe Eucalypteae) are currently placed in seven genera. Traditionally, Eucalyptus was defined by its operculum but when phylogenies placed Angophora, with free sepals and petals, as sister to the operculate bloodwood eucalypts, the latter were segregated into a new genus, Corymbia. Yet generic delimitation in the tribe Eucalypteae remains uncertain. Here we address these problems using phylogenetic analysis with the largest molecular dataset to date. Methods: We captured 101 low-copy nuclear exons from 392 samples representing 266 species. Our phylogenetic analysis used maximum likelihood (IQtree) and multi-species coalescent (Astral). At two nodes critical to generic delimitation, we tested alternative relationships among Arillastrum, Angophora, Eucalyptus and Corymbia using Shimodaira's AU test. Phylogenetic mapping was used to explore the evolution of perianth traits. Results: Monophyly of Corymbia relative to Angophora was decisively rejected. All alternative relationships among the seven currently recognised Eucalypteae genera imply homoplasy in evolutionary origins of the operculum. Inferred evolutionary transitions in perianth traits are congruent with divergences between major clades except that expression of separate sepals and petals in Angophora, which is nested within the operculate genus Corymbia, appears to be a reversal to the plesiomorphic perianth structure. Conclusions: Here we formally raise Corymbia subg. Blakella to genus rank and make the relevant new combinations. We also define and name three sections within Blakella (B. sect. Blakella, B. sect. Naviculares and B. sect. Maculatae), and two series within Blakella sect. Maculatae (B. ser. Maculatae and B. ser. Torellianae). Corymbia is reduced to the red bloodwoods.