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opencc-zeroOct 2023View details →

Data from: The genetic basis of traits associated with the evolution of serpentine endemism in monkeyflowers

The floras on chemically and physically challenging soils, such as gypsum, shale, and serpentine, are characterized by narrowly endemic species. The evolution of edaphic endemics may be facilitated or constrained by genetic correlations among traits contributing to adaptation and reproductive isolation across soil boundaries. The yellow monkeyflowers in the Mimulus guttatus species complex are an ideal system in which to examine these evolutionary patterns. To determine the genetic basis of adaptive and prezygotic isolating traits, we performed genetic mapping experiments with F2 hybrids derived from a cross between a serpentine endemic, M. nudatus, and its close relative M. guttatus. Few large effect and many small effect QTL contribute to interspecific divergence in life history, floral and leaf traits, and a history of directional selection contributed to trait divergence. Loci contributing to adaptive traits and prezygotic reproductive isolation overlap, and their allelic effects are largely in the direction of species divergence. These loci contain promising candidate genes regulating flowering time and plant organ size. Together our results suggest that genetic correlations among traits can facilitate the evolution of adaptation and speciation and may be a common feature of the genetic architecture of divergence between edaphic endemics and their widespread relatives.

opencc-by-4.0Aug 2013View details →

Fig. 7. Vertebral character trait evolution across phocoenids and related delphinoids. A. Character 2, thoracic vertebral counts. B. Character 8 in New fossil remains from the Pliocene Koetoi Formation of northern Japan provide insights into growth rates and the vertebral evolution of porpoises

Fig. 7. Vertebral character trait evolution across phocoenids and related delphinoids. A. Character 2, thoracic vertebral counts. B. Character 8, ratio of centrum length/centrum height of lumbar vertebrae. C. Character 12, height of neural spine. D. Character 14, regional anterior inclination of neural arches. See Table 2 for detailed character descriptions.

opencc-zeroMay 2024View details →

Data from: Fast mvSLOUCH: Multivariate Ornstein-Uhlenbeck-based models of trait evolution on large phylogenies

The PCMBase R package is a powerful computational tool that enables efficient calculations of likelihoods for a wide range of phylogenetic Gaussian models. Taking advantage of it, we redesigned the R package mvSLOUCH. Here, we demonstrate how the new version of the package can be used to thoroughly examine the evolution and adaptation of traits in a large dataset of 1252 vascular plants through the use of multivariate Ornstein-Uhlenbeck processes. The results of our analysis demonstrate the ability of the modeling framework to distinguish between various alternative hypotheses regarding the evolution of functional traits in angiosperms.

Fig. 1 in Assessing troglomorphic and phylogenetically informative traits in troglobionts: a new cave-dwelling centipede illuminates the evolution of a soil-dwelling lineage (Chilopoda: Geophilidae)

Fig. 1 Hypothetical phylogeny with an evolutionarily relict species and different cases of character state reconstruction. Different shapes indicated different characters. Empty shapes indicate an ancestral state, black shapes indicate a derived state, and gray shapes indicate an intermediate (possibly transitional) state. For the circle-character, the relict species shares a derived state with the most closely related species (synapomorphy). For the square-character, it shares an ancestral state with the other more distantly related species (symplesiomorphy). For the triangle-character, it has an apparently intermediate state between an ancestral state and a derived state (possibly transitional)

Fig. 6 Comparison between Plutogeophilus gen.n in Assessing troglomorphic and phylogenetically informative traits in troglobionts: a new cave-dwelling centipede illuminates the evolution of a soil-dwelling lineage (Chilopoda: Geophilidae)

Fig. 6 Comparison between Plutogeophilus gen.n., Macronicophilus, and another Geophilidae: a–c forcipular segment, ventral view; d–f forcipular segment, dorsal view; g–i ultimate leg-bearing segment of adult ♀, without telopodites, ventral view; j–o, right leg of the ultimate pair, ventral view. Line drawings from photos, setae omitted: a, d, g, j PD-G 1359; b, e, m ISLA 11879; c, f, i, n PD-G 230; h, l ISLA 12866; o PD-G 1510. Redrawn from: k Pereira et al., 2000

Fig. 2 in Assessing troglomorphic and phylogenetically informative traits in troglobionts: a new cave-dwelling centipede illuminates the evolution of a soil-dwelling lineage (Chilopoda: Geophilidae)

Fig. 2 Living specimen of Plutogeophilus jurupariquibaba gen.n. sp.n. in the Areias de Cima cave, 7.IV.2012 (photo by Robson Zampaulo)

Fig. 7 Comparison between Plutogeophilus gen.n in Assessing troglomorphic and phylogenetically informative traits in troglobionts: a new cave-dwelling centipede illuminates the evolution of a soil-dwelling lineage (Chilopoda: Geophilidae)

Fig. 7 Comparison between Plutogeophilus gen.n., Macronicophilus, and another Geophilidae: a–c labrum, ventral view; d–f, left pretarsus of second maxillae, ventral view; g–i, metasternite at ca. 20% of the antero-posterior series of leg-bearing segments, ventral view. Line drawings from photos, setae omitted: a, d, g PD-G 1359; b, e, h ISLA 11879; c, f, i PD-G 230

opencc-zeroJan 2023View details →

Fast mvSLOUCH: Model comparison for multivariate Ornstein--Uhlenbeck-based models of trait evolution on large phylogenies

These are the Supplementary Material, R scripts and numerical results accompanying Bartoszek, Fuentes Gonzalez, Mitov, Pienaar, Piwczyński, Puchałka, Spalik and Voje "Model Selection Performance in Phylogenetic Comparative Methods under multivariate Ornstein–Uhlenbeck Models of Trait Evolution". The four data files concern two datasets. Ungulates: measurements of muzzle width, unworn lower third molar crown height, unworn lower third molar crown width and feeding style and their phylogeny; Ferula: measurements of ratio of canals, periderm thickness, wing area, wing thickness, and fruit mass, and their phylogeny.

opencc-zeroJul 2023View details →

Diadromy drives elevated rates of trait evolution and ecomorphological convergence in Clupeiformes (herring, shad, and anchovies)

Migration can have a profound influence on rates and patterns of phenotypic evolution. Diadromy is the migration between marine and freshwater habitats for feeding and reproduction that can require individuals to travel tens to thousands of kilometers. The high energetic demands of diadromy are predicted to select for ecomorphological traits that maximize swimming and locomotor efficiency. Intraspecific studies have shown repeated instances of divergence among diadromous and non-diadromous populations in locomotor and foraging traits, which suggests that at a macroevolutionary scale, diadromous lineages may experience convergent evolution onto one or multiple adaptive optima. We tested for differences in rates and patterns of phenotypic evolution among diadromous and non-diadromous lineages in Clupeiformes, a clade that has evolved diadromy more than 10 times. Our results show that diadromous clupeiforms show convergent evolution for some locomotor traits, and faster rates of evolution, which we propose are adaptive responses to the locomotor demands of migration. We also find evidence that diadromous lineages show convergence into multiple regions of multivariate traitspace and suggest these respective traitspaces are associated with differences in migration and trophic ecology. However, not all locomotor traits and no trophic traits show evidence of convergence or elevated rates of evolution associated with diadromy. Our results show that long-distance migration influences the tempo and patterns of phenotypic evolution at macroevolutionary scales, but there is not a single diadromous syndrome.

opencc-by-4.0Jul 2023View details →

Fig. 8 in Morphological trait evolution in Solanum (Solanaceae): Evolutionary lability of key taxonomic characters

Fig. 8. Evolution of the most conserved morphological traits in Solanum with <10 transitions based on species-level analysis using stochastic character mapping. A, Pseudostipules; B, Enlarged anther connectives; C, Anther modifications; D, Pedicel insertion. Results from the best model are shown for each character (see Table 1 and suppl. Table S4 for details) based on 200 simulations. The topology used for mapping was derived from a supermatrix phylogeny with nine loci (two nuclear and seven plastid loci; Gagnon & al., 2022) with 725 species sampled and coded for each trait (58% of all species). All minor clades are labelled; tips reflect the crown nodes of each minor clade. Piecharts indicate likelihood of modelled ancestral states along the nodes, and frequency bars (tips) reflect proportion of species sampled within each clade with each state.

opencc-by-4.0Jul 2023View details →

Fig. 4 in Morphological trait evolution in Solanum (Solanaceae): Evolutionary lability of key taxonomic characters

Fig. 4. Evolution of the most highly labile morphological traits in Solanum with>100 transitions based on species-level analysis using stochastic character mapping. A, Growth form; B, Sympodial unit structure; C, Glandular trichomes; D, Corolla shape; E, Corolla colour; F, Fruit colour. Results from the best model are shown for each character (see Table 1 and suppl. Table S4 for details) based on 200 simulations. The topology used for mapping was derived from a supermatrix phylogeny with nine loci (two nuclear and seven plastid loci; Gagnon & al., 2022) with 725 species sampled and coded for each trait (58% of all species). All minor clades are labelled; tips reflect the crown nodes of each minor clade. Piecharts indicate likelihood of modelled ancestral states along the nodes, and frequency bars (tips) reflect proportion of species sampled within each clade with each state.

opencc-zeroSep 2023View details →

Data from: The sequential direct and indirect effects of mountain uplift, climatic niche and floral trait evolution on diversification dynamics in an Andean plant clade

Why and how organismal lineages radiate is commonly studied through either assessing abiotic factors (biogeography, geomorphological processes, climate) or biotic factors (traits, interactions). Despite increasing awareness that both abiotic and biotic processes may have important joint effects on diversification dynamics, few attempts have been made to quantify the relative importance and timing of these factors, and their potentially interlinked direct and indirect effects, on lineage diversification. We here combine assessments of historical biogeography, geomorphology, climatic niche, vegetative and floral trait evolution to test whether these factors jointly, or in isolation, explain diversification dynamics of a Neotropical plant clade (Merianieae, Melastomataceae). After estimating ancestral areas and disparification over time in climate and trait space, we employ Phylogenetic Path Analyses as a synthesis tool to test eleven hypotheses on the individual direct and indirect effects of these factors on diversification rates. We find strongest support for interlinked effects of colonization of the uplifting Andes during the mid-Miocene and rapid abiotic climatic niche evolution in explaining a burst in diversification rate in Merianieae. Within Andean habitats, later disparification in floral trait space allowed for the exploitation of wider pollination niches (i.e., shifts from bee to vertebrate pollinators), but did not affect diversification rates. Our approach of including both vegetative and floral trait evolution, rare in assessments of plant diversification in general, highlights important pre-adaptations to mountain colonization, specifically woody habit and larger flowers. Overall, and in concert with the idea that ecological opportunity is a key element of evolutionary radiations, our results suggest that a combination of rapid niche evolution and pre-adapted traits were critical for the exploitation of newly available niche space in the Andes in the mid-Miocene. Further, our results emphasize the importance of incorporating both abiotic and biotic factors into the same analytical framework if we aim to quantify the relative and interlinked effects of these processes on diversification.

opencc-by-4.0Sep 2023View details →

Data from: Alternative measures of trait-niche relationships: a test on dispersal traits in saproxylic beetles (Ecology and Evolution)

Data from: Alternative measures of trait-niche relationships: a test on dispersal traits in saproxylic beetles (Ecology and Evolution) DATA DOI: https://doi.org/10.5281/zenodo.8322080 Associated article DOI: https://doi.org/10.1002/ece3.10588 Ryan C. Burner, Jorg Stephan, Juha Siitonen, Tord Snall, et al. 2023 ryan.c.burner@gmail.com This data release contains data files needed to run the Hmsc models described in the associated publication. It is a subset of the complete beetle capture and environmental covariate dataset maintained by Juha Siitonen (see associated manuscript for references to prior publications). It contains the following four files: 1) Species_detections.csv This site_year x species table has detection/non-detection (1/0) values for each species at each site_year. Beetles were trapped at about 142 sites in Finland forests. Includes only beetle species (n = 212) which are considered saproxylic and which were detected at >=5 sites in the dataset, and for which trait information was available. Species names are as originally identified in the source dataset (see early publications by Juha Siitonen). Row names ('Row_ID'), which consist of [site]_[year], correspond to 'Row_ID' in the 'Site_covariates.csv' file. Species (column) names correspond to species row naes in 'Species_traits.csv' 2) Site_covariates.csv This table has one row for each 'Row_ID' (n = 142) corresponding to rows in 'Species_data.csv'. Covariate columns have been scaled and centered for modeling. Columns are as follows: rowID - [site]_[year] of sampling Year - year of sampling Site - site name/number climID - unique ID for each grid cell from which climate data were extracted lat_WGS84 - latitude (WGS84) lon_WGS84 - longitude (WGS84) VD10 - scaled and centered total pooled volume of local standing and fallen dead trees (originally in m3/ha, before scaling) with a minimum diameter of 10 cm, estimated using transects agedomin - scaled and centered mean age of the five oldest trees in the stand OldFor_1km - scaled and centered volume of living wood in those forests older than 100 years within a one km radius around each site MeanTemp - scaled and centered mean temperature during the trapping period, from mean of all ERA5 hourly estimates of 2m temperature (see manuscript for details) TotalPrecip - scaled and centered total precipitation during the trapping period, from ERA5 summed across all hourly estimates of total precipitation (see manuscript for details) globRad_WHm2 - scaled and centered total solar radiation during the trapping period, summed across all daily values, based on site slope and aspect, calculated using GIS (see manuscript for details). Units were Wh/m2 prior to scaling and centering. log_Nr_traps - scaled and centered log-transformed number of traps used at each capture site  3) Species_traits.csv Trait data, based on trait values in Hagge et al. (2021 - see manuscript for full reference), for beetle species included in model (see species data information, above). In some cases traits are from synonyms used in Hagge that differ from taxonomy of this dataset. Traits have been scaled and centered. Row names are species names that match columns in 'Species_detections.csv'. Columns as follows: wing_length - scaled and centered (log(wing length divided by body length)) wing_load - scaled and centered (log(mass / wing area / body length)) wing_aspect - scaled and centered (log(wing aspect ratio) 4) Phylotree.csv A phylogenetic tree for the species in this dataset, written in the Newick (also known as New Hampshire) format. The tree is based on the species-level insect tree in Chesters et al. (2017) (see manuscript for full citation) but has missing species added randomly to the correct genus (when present) or family or (occassionally) order.