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Data from: Time-limited environments affect the evolution of egg - body size allometry

Initial offspring size is a fundamental component of absolute growth rate, where large offspring will reach a given adult body size faster than smaller offspring. Yet, our knowledge regarding the co-evolution between offspring and adult size is limited. In time-constrained environments, organisms need to reproduce at a high rate and reach a reproductive size quickly. In order to rapidly attain a large adult body size, we hypothesize that, in seasonal habitats, large species are bound to having a large initial size, and consequently, the evolution of egg size will be tightly matched to that of body size, compared to less time-limited systems. We tested this hypothesis in killifishes, and found a significantly steeper allometric relationship between egg size and body size in annual, compared to non-annual species. We also found higher rates of evolution of egg and body size in annual compared to non-annual species. Our results suggest that time-constrained environments impose strong selection on rapidly reaching a species-specific body size, and reproduce at a high rate, which in turn imposes constraints on the evolution of egg sizes. In combination, these distinct selection pressures result in different relationships between egg and body size among species in time-constrained versus permanent habitats.

Data from: Revised time scales of RNA virus evolution based on spatial information

The time scales of pathogen evolution are of major concern in the context of public and veterinary health, epidemiology and evolutionary biology. Dating the emergence of a pathogen often relies on estimates of evolutionary rates derived from nucleotide sequence data. For many viruses, this has yielded estimates of evolutionary origins only a few hundred years in the past. Here we demonstrate through the incorporation of geographic information from virus sampling that evolutionary age estimates of two European hantaviruses are severely underestimated because of pervasive mutational saturation of nucleotide sequences. We detected very strong relationships between spatial distance and genetic divergence for both Puumala and Tula hantavirus – irrespective whether nucleotide or derived amino acid sequences were analyzed. Extrapolations from these relationships dated the emergence of these viruses most conservatively to at least 3,700 and 2,500 years ago, respectively. Our minimum estimates for the age of these hantaviruses are ten to a hundred times older than results from current non-spatial methods and in much better accordance with the biogeography of these viruses and their respective hosts. Spatial information can thus provide valuable insights on the deeper time scales of pathogen evolution and improve our understanding of disease emergence.

opencc-zeroDec 2013View details →

Data from: Phylogenomics resolves the timing and pattern of insect evolution

Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight to the Early Devonian (~406 Ma), of major extant lineages to the Mississippian (~345 Ma), and the major diversification of holometabolous insects to the Early Cretaceous. Our phylogenomic study provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects.

opencc-zeroDec 2012View details →

Data from: Hemocyanin gene family evolution in spiders (Araneae), with implications for phylogenetic relationships and divergence times in the infraorder Mygalomorphae

Hemocyanins are multimeric copper-containing hemolymph proteins involved in oxygen binding and transport in all major arthropod lineages. Most arachnids have seven primary subunits (encoded by paralogous genes a–g), which combine to form a 24-mer (4 × 6) quaternary structure. Within some spider lineages, however, hemocyanin evolution has been a dynamic process with extensive paralog duplication and loss. We have obtained hemocyanin gene sequences from numerous representatives of the spider infraorders Mygalomorphae and Araneomorphae in order to infer the evolution of the hemocyanin gene family and estimate spider relationships using these conserved loci. Our hemocyanin gene tree is largely consistent with the previous hypotheses of paralog relationships based on immunological studies, but reveals some discrepancies in which paralog types have been lost or duplicated in specific spider lineages. Analyses of concatenated hemocyanin sequences resolved deep nodes in the spider phylogeny and recovered a number of clades that are supported by other molecular studies, particularly for mygalomorph taxa. The concatenated data set is also used to estimate dates of higher-level spider divergences and suggests that the diversification of extant mygalomorphs preceded that of extant araneomorphs. Spiders are diverse in behavior and respiratory morphology, and our results are beneficial for the comparative analyses of spider respiration. Lastly, the conserved hemocyanin sequences allow for the inference of spider relationships and ancient divergence dates.

opencc-zeroDec 2015View details →

Data from: Uncovering the genetic signature of quantitative trait evolution with replicated time series data

The genetic architecture of adaptation in natural populations has not yet been resolved: it is not clear to what extent the spread of beneficial mutations (selective sweeps) or the response of many quantitative trait loci drive adaptation to environmental changes. Although much attention has been given to the genomic footprint of selective sweeps, the importance of selection on quantitative traits is still not well studied, as the associated genomic signature is extremely difficult to detect. We propose 'Evolve and Resequence' as a promising tool, to study polygenic adaptation of quantitative traits in evolving populations. Simulating replicated time series data we show that adaptation to a new intermediate trait optimum has three characteristic phases that are reflected on the genomic level: (1) directional frequency changes towards the new trait optimum, (2) plateauing of allele frequencies when the new trait optimum has been reached and (3) subsequent divergence between replicated trajectories ultimately leading to the loss or fixation of alleles while the trait value does not change. We explore these 3 phase characteristics for relevant population genetic parameters to provide expectations for various experimental evolution designs. Remarkably, over a broad range of parameters the trajectories of selected alleles display a pattern across replicates, which differs both from neutrality and directional selection. We conclude that replicated time series data from experimental evolution studies provide a promising framework to study polygenic adaptation from whole-genome population genetics data.

opencc-zeroDec 2014View details →

Data from: Prepupal building behavior in Drosophila melanogaster and its evolution under resource and time constraints

Structures built by animals are a widespread and ecologically important 'extended phenotype'. While its taxonomic diversity has been well described, factors affecting short-term evolution of building behavior within a species have received little experimental attention. Here we describe how, given the opportunity, wandering Drosophila melanogaster larvae often build long tunnels in agar substrates and embed their pupae within them. These embedded larvae are characterized by a longer egg-to-pupariation developmental time than larvae that pupate on the surface. Assuming that such building behaviors are likely to be energetically costly and/or time consuming, we hypothesized that they should evolve to be less pronounced under resource or time limitation. In accord with this prediction, larvae from populations evolved for 160 generations under a regime that combines larval malnutrition with limited developmental time dug shorter tunnels than larvae from control unselected populations. However, the proportion of larvae that embedded before pupation did not differ between the malnutrition-adapted and control populations, suggesting that tunnel length and likelihood of embedding before pupation are controlled by different genetic loci. The behaviors exhibited by wandering larvae of Drosophila melanogaster prior to pupation offer a model system to study evolution of animal building behaviors because the tunneling and embedding phenotypes are simple, facultative and highly variable.

opencc-zeroDec 2008View details →

Data from: Mammalian evolution: timing and implications from using the LogDeterminant transform for proteins of differing amino acid composition

We explore the tree of mammalian mtDNA sequences, using particularly the LogDet transform on amino acid sequences, the distance Hadamard transform, and the Closest Tree selection criterion. The amino acid composition of different species show significant differences, even within mammals. After compensating for these differences, nearest-neighbor bootstrap results suggest that the tree is locally stable, though a few groups show slightly greater rearrangements when a large proportion of the constant sites are removed. Many parts of the trees we obtain agree with those on published protein ML trees. Interesting results include a preference for rodent monophyly. The detection of a few alternative signals to those on the optimal tree were obtained using the distance Hadamard transform (with results expressed as a Lento plot). One rearrangement suggested was the interchange of the position of primates and rodents on the optimal tree. The basic stability of the tree, combined with two calibration points (whale/cow and horse/rhinoceros), together with a distant secondary calibration from the mammal/bird divergence, allows inferences of the times of divergence of putative clades. Allowing for sampling variances due to finite sequence length, most major divergences amongst lineages leading to modern orders, appear to occur well before the Cretaceous/Tertiary (K/T) boundary. Implications arising from these early divergences are discussed, particularly the possibility of competition between the small dinosaurs and the new mammal clades.

opencc-zeroDec 2015View details →

Data from: Synergism and antagonism of proximate mechanisms enable and constrain the response to simultaneous selection on body size and development time: an empirical test using experimental evolution

Natural selection acts on multiple traits simultaneously. How mechanisms underlying such traits enable or constrain their response to simultaneous selection is poorly understood. We show how antagonism and synergism among three traits at the developmental level enable or constrain evolutionary change in response to simultaneous selection on two focal traits at the phenotypic level. After 10 generations of 25% simultaneous directional selection on all four combinations of body size and development time in Manduca sexta (Sphingidae), the changes in the three developmental traits predict 93% of the response of development time and 100% of the response of body size. When the two focal traits were under synergistic selection, the response to simultaneous selection was enabled by juvenile hormone and ecdysteroids and constrained by growth rate. When the two focal traits were under antagonistic selection, the response to selection was due primarily to change in growth rate and constrained by the two hormonal traits. The approach used here reduces the complexity of the developmental and endocrine mechanisms to three proxy traits. This generates explicit predictions for the evolutionary response to selection that are based on biologically informed mechanisms. This approach has broad applicability to a diverse range of taxa, including algae, plants, amphibians, mammals, and insects.

opencc-zeroDec 2018View details →

Data from: The evolution of traits and functions in herbivorous coral reef fishes through space and time

Herbivory by fishes has been identified as a key ecological process shaping coral reefs through time. Although taxonomically limited, herbivorous reef fishes display a wide range of traits, which results in varied ecosystem functions on reefs around the world. Yet, we understand little about how these trait combinations and functions in ecosystems changed through time and across biogeographic realms. Here we used fossils and phylogenies in a functional ecological framework to reveal temporal changes in nominally herbivorous fish assemblages among oceanic basins in both trait space and lineage richness among functions. We show that the trait space occupied by extant herbivorous fishes in the Indo-Pacific resulted from an expansion of traits from the ancestral Tethyan assemblages. By contrast, trait space in the Atlantic is the result of lineage turnover, with relatively recent colonization by lineages that arose in the east Tethys/Indo-Pacific. From an ecosystem function perspective, the Atlantic supports a depauperate fauna, with few extant herbivorous reef fish lineages performing each function. Indo-Pacific fishes support both more functions and more lineages within each function, with a marked Miocene to Pleistocene expansion. These disparities highlight the importance of history in explaining global variation in fish functional composition on coral reefs.

Data from: The biased evolution of generation time

Many life-history traits are important determinants of the generation time. For instance, semelparous species whose adults reproduce only once have shorter generation times than iteroparous species that reproduce on several occasions – assuming equal development duration. A shorter generation time ensures a higher growth rate in stable environments where resources are in excess, and is therefore a positively selected feature in this situation. In a stable and limiting environment, all combinations of traits that produce the same number of viable offspring are selectively equivalent. Here we study the neutral evolution of life-history strategies with different generation times, and show that the slowest strategy represents the most likely evolutionary out- come when mutation is considered. Indeed, strategies with longer generation times generate fewer mutants per time unit, which makes them less likely to be replaced within a given time period. This 'turnover bias' favors the evolution of strategies with long generation times. Its real impact, however, depends on both the population size and the nature of selection on life-history strategies. The latter is primarily impacted by the relationships between life- history traits whose estimation will be crucial to understand the evolution of life-history strategies.

Data from: Lineage-independent retrotransposition of UTP14 associated with male fertility has occurred multiple times throughout mammalian evolution

In mammals, gamete production is essential for reproductive success. This is particularly true for males where large quantities of sperm are produced to fertilize a limited number of eggs released by the female. Because of this, new genes associated with increased spermatogenic efficiency have been accumulating throughout the evolution of therian mammals. Many of these new genes are testis-specific retrotransposed copies of housekeeping genes located on the X chromosome. Of particular interest are retrotransposed copies of UTP14 that are present in many distantly related eutherian mammals. Analysis of genomic data available in ENSEMBL indicates that these UTP14 retrogenes have arisen independently in the various eutherian clades. They represent an interesting aspect of evolution whereby new homologues of UTP14 have become independently fixed in multiple mammalian lineages due to the reproductive advantage that may be conferred to males. Surprisingly, these genes may also be lost, even after being present within a lineage for millions of years. This phenomenon may potentially be used to delineate evolutionary trees in closely related groups of mammals, particularly in the case of South American primates. Studying these retrogenes will yield new insights into the evolutionary history of male gamete production and the phylogeny of eutherian mammals.

opencc-zeroFeb 2024View details →

Supplementary material 1 from: Gruntman M, Segev U (2024) Effect of residence time on trait evolution in invasive plants: review and meta-analysis. NeoBiota 91: 99-124. https://doi.org/10.3897/neobiota.91.109251

Supplementary information

opennotspecifiedFeb 2022View details →

Figure 1 in Middle Jurassic origin in India: a new look at evolution of Vermileonidae and time-scaled relationships of lower brachyceran flies

Figure 1. Boxplot of length of each protein-coding gene.

opencc-zeroMay 2022View details →

Reconstruction of reticulate evolution and divergence timing based on RNA-seq: Hippophae as a case

<p>Phylotranscriptomic analysis has successfully been used to reconstruct phylogenies of higher taxa. However, depicting the patterns of phylogenies in more details and, especially, estimating time of introgression for lower taxa remain challenging. Here, we selected Hippophae (Elaeagnaceae), a small genus restricted to the Qinghai-Tibet Plateau (QTP) and adjacent areas, as an example to optimize approaches to investigate reticulate evolution in lower taxa with RNA-seq. Plastid genes and low copy nuclear genes were extracted from RNA-seq data to reconstruct a reliable species tree of Hippophae and estimate the time of species divergence, respectively. Results show that the phylogeny of five Hippophae species has been consistently solved except for H. salicifolia and a potential hybrid species. The divergence time of 5 species ranged from 17.56 Ma to 6.04 Ma, the era of the Himalayas uplift. The inconsistence between gene trees was integrated with the implicit network analysis approaches, such as investigating statistical difference of anomalous gene trees and asymmetry of average most recent common ancestor (MRCA) ages, and explicit network analysis approaches, such as PhyloNet and SNaQ. At least two separate introgression cases were involved in the history of Hippophae: one took place between two basial clades of this genus, in which an early member or common ancestor of H. rhamnoides and H. thibetana lineages experienced introgression with an early member or common ancestor of H. neurocarpa and H. gyantsensis; the other was between H. gyantsensis and H. neurocarpa. Using a MCMC fitting model, we estimated the secondary divergence time after the first introgression, finding two secondary divergence times: one was about 8.79 (7.05-10.64) Ma and between H. rhamnoides and the MRCA of H. neurocarpa and H. gyantsensis, and the other was near 7.76 (5.89-9.58) Ma and between H. tibetana and the MRCA of H. neurocarpa and H. gyantsensis. Furthermore, introgressed gene candidates, including some potential adaptive genes, were found, indicating that even the introgression in small genus is important and functional for species differentiation. Based on the above results and previous studies, the reticulate evolution of Hippophae was highlighted, providing a potential guidance in using RNA-seq data for reconstructing the complex evolution history of lower taxa.</p>

FIGURE 4 in Feeding in marine mammals: An integration of evolution and ecology through time

FIGURE 4. Anatomical features associated with filter feeding in crabeater seal (Lobodon carcinophaga skull, public domain image), and gray whale (Eschrichtius robustus skull, authors' work).

FIGURE 10 in Feeding in marine mammals: An integration of evolution and ecology through time

FIGURE 10. Odontoceti stem and familial level diversity through time. The group "Delphinoidea" includes Delphinidae, Monodontidae, and Phocoenidae, as well as extinct members of this crown group of uncertain phylogenetic placement. The "river dolphins" closely related to these taxa (Inioidea and Lipotidae) are plotted separately to emphasize their diversity in the fossil record compared to the present. "Ziphioidea" includes Ziphiidae and closely related stem taxa as identified by Bianucci et al. (2016). Dashed vertical lines: black, epoch boundaries; gray, age boundaries.

FIGURE 6 in Feeding in marine mammals: An integration of evolution and ecology through time

FIGURE 6. Generic level diversity of marine mammal groups through time. Dashed vertical lines: black, epoch boundaries; gray, age boundaries. All silhouettes used in Figures 6-20 are the authors' own work.

FIGURE 9 in Feeding in marine mammals: An integration of evolution and ecology through time

FIGURE 9. Mysticeti stem and familial level diversity through time. "Cetotheriidae s.l." is a paraphyletic group including all taxa that belong to crown Mysticeti but are not grouped with any of the four living families. Dashed vertical lines: black, epoch boundaries; gray, age boundaries.