Ylenia Chiari

George Mason University | GMU · Department of Biology

RNA sequencing (RNA-Seq) is a popular method for measuring gene expression in non-model organisms, including wild populations. While RNA-Seq can measure gene expression variation among wild-caught individuals and can yield important biological insights into organism function, sampling methods may also influence gene expression estimates. We examine...

Cancer rates vary widely across vertebrate groups. Identifying species with lower-than-expected cancer prevalence can help establish new models for unraveling the biological mechanisms underlying cancer resistance. Theoretical predictions suggest that cancer prevalence should be positively associated with body mass and longevity in animals. Yet, in...

Pseudemys alabamensis is one of the most endangered freshwater turtle species in the United States due to its restricted geographic distribution in coastal Alabama and Mississippi. Populations of P. alabamensis are geographically isolated from one another by land and saltwater, which could act as barriers to gene flow. It is currently unknown how d...

Animals are exposed to different visual stimuli that influence how they perceive and interact with their environment. Visual information such as shape and colour can help animals detect, discriminate, and make appropriate behavioural decisions for mate selection, communication, camouflage, and foraging. Previous research indicates that at least som...

The Galapagos Archipelago is recognized as a natural laboratory for studying evolutionary processes. San Cristóbal was one of the first islands colonized by tortoises, which radiated from there across the archipelago to inhabit 10 islands. Here, we sequenced the mitochondrial control region from six historical giant tortoises from San Cristóbal (fi...

Nearly 90% of flowering plants depend on animals for reproduction. One of the main rewards plants offer to pollinators for visitation is nectar. Nesocodon mauritianus (Campanulaceae) produces a blood-red nectar that has been proposed to serve as a visual attractant for pollinator visitation. Here, we show that the nectar’s red color is derived from...

There are many costs associated with increased body size and longevity in animals, including the accumulation of genotoxic and cytotoxic damage that comes with having more cells and living longer. Yet, some species have overcome these barriers and have evolved remarkably large body sizes and long lifespans, sometimes within a narrow window of evolu...

Pseudemys alabamensis is one of the most endangered turtle species in the United States due to its small population size and restricted geographic distribution in coastal Alabama and Mississippi. Increased urbanization and climate change impacts in the region further threaten this species. Populations of P. alabamensis are geographically isolated f...

Animal color patterns are widely studied in ecology, evolution, and through mathematical modeling. Patterns may vary among distinct body parts such as the head, trunk or tail. As large amounts of photographic data is becoming more easily available, there is a growing need for general quantitative methods for capturing and analyzing the full complex...

• The Kemp’s ridley (Lepidochelys kempii) is the world’s most endangered sea turtle species. Predominately nesting at only one beach in Mexico, this species declined to an estimated 300 females in the mid-1980s. Conservation efforts in the United States and Mexico, including a head start programme in southern Texas in which hatchlings were reared i...

There are many costs associated with increased body size and longevity in animals, including the accumulation of genotoxic and cytotoxic damage that comes with having more cells and living longer. Yet, some species have overcome these barriers and have evolved remarkably large body sizes and long lifespans, sometimes within a narrow window of evolu...

Cadmium (Cd) accumulates with aging and is elevated in long-lived species. Metallothioneins (MTs), small cysteine-rich proteins involved in metal homeostasis and Cd detoxification, are known to be related to longevity. However, the relationship between Cd accumulation, the role of MTs, and aging is currently unclear. Specifically, we do not know if...

Nesocodon mauritianus (Campanulaceae) produces a blood-red nectar that has been proposed to serve as a visual attractant for pollinator visitation. Here we show that the nectar’s red color is derived from a novel alkaloid termed nesocodin. The first nectar produced is acidic and pale yellow in color, but slowly becomes alkaline before taking on its...

Animal color patterns are widely studied in ecology, evolution, and through mathematical modeling. Patterns may vary among distinct body parts such as the head, trunk or tail. As large amounts of photographic data is becoming more easily available, there is a growing need for general quantitative methods for capturing and analyzing the full complex...

Animals are exposed to different visual stimuli that influence how they perceive and interact with their environment. Visual information such as shape and colour can help the animal detect, discriminate and make appropriate behavioural decisions for mate selection, communication, camouflage, and foraging. In all major vertebrate groups, it has been...

RNA sequencing (RNA-Seq) is becoming a popular method for measuring gene expression in non-model organisms, including wild populations sampled in the field. While RNA-Seq can be used to measure gene expression variation among wild-caught individuals and can yield important biological insights into organismal function, technical variables may also i...

The dorsal surfaces of many taxonomic groups often feature repetitive pattern elements consisting of stripes, spots or bands. Here we investigate how distinct categories of camouflage pattern work by relating them to ecological and behavioral traits in 439 species of gecko. We use phylogenetic comparative methods to test outstanding hypotheses base...

Genotypic variation, environmental variation, and their interaction may produce variation in the developmental process and cause phenotypic differences among individuals. Developmental noise, which arises during development from stochasticity in cellular and molecular processes when genotype and environment are fixed, also contributes to phenotypic...

Evolution of sample patterns for Gecko #682 and Gecko #772 over 600K simulation time steps for the linear Turing model. The panels (a-f) show the pattern every 100K time steps for a simulation with parameters corresponding to those of Gecko #682. The LALI-type for Gecko #682 is matched at 200K time steps. (TIFF)

Determination of characteristic Fourier wavelength. A: a rectangular section of the pattern for Gecko ID #731. B: the corresponding centered Fourier spectrum. Low-frequency components are shown in the center of the image, high-frequency components on the edges. Lighter colors indicate larger values. C: a plot of radially averaged interpolated absol...

Giant tortoises are among the longest-lived vertebrate animals and, as such, provide an excellent model to study traits like longevity and age-related diseases. However, genomic and molecular evolutionary information on giant tortoises is scarce. Here, we describe a global analysis of the genomes of Lonesome George—the iconic last member of Chelono...

Phenotypic variation in organisms is typically attributed to genotypic variation, environmental variation, and their interaction. Developmental noise, which arises from stochasticity in cellular and molecular processes occurring during development when genotype and environment are fixed, also contributes to phenotypic variation. The potential influ...

Chemical use in society is growing rapidly and is one of the five major pressures on biodiversity worldwide. Since empirical toxicity studies of pollutants generally focus on a handful of model organisms, reliable approaches are needed to assess sensitivity to chemicals across the wide variety of species in the environment. Phylogenetic comparative...

DNA damage has been linked to genomic instability and the progressive breakdown of cellular and organismal homeostasis, leading to the onset of disease and reduced longevity. Insults to DNA from endogenous sources include base deamination, base hydrolysis, base alkylation, and metabolism-induced oxidative damage that can lead to single-strand and d...

Self-righting, the capacity of an animal to self-turn after falling on its back, is a fitness-related trait. Delayed self-righting can result in loss of mating opportunities or death. Traits involved in self-righting may therefore be under selection. Galápagos giant tortoises have two main shell morphologies - saddleback and domed – that have been...

Oceanic islands are often inhabited by endemic species that have undergone substantial morphological evolutionary change due to processes of multiple colonizations from various source populations, dispersal, and local adaptation. Galápagos marine iguanas are an example of an island endemic exhibiting high morphological diversity, including substant...

Seagrass meadows form ecologically and economically valuable coastal habitat on every continental margin except the Antarctic, but their areal extent is declining by approximately 2–5 % per year. Seagrass wasting disease is a contributing factor in these declines, with the protist Labyrinthula identified as the etiologic agent. To help elucidate th...

Amelotin (AMTN) is an ameloblast-secreted protein that belongs to the secretory calcium-binding phosphoprotein (SCPP) family, which originated in early vertebrates. In rodents, AMTN is expressed during the maturation stage of amelogenesis only. This expression pattern strongly differs from the spatiotemporal expression of other ameloblast-secreted...

The taxonomy of giant Galapagos tortoises (Chelonoidis spp.) is currently based primarily on morphological characters and island of origin. Over the last decade, compelling genetic evidence has accumulated for multiple independent evolutionary lineages, spurring the need for taxonomic revision. On the island of Santa Cruz there is currently a singl...

The release of large quantities of chemicals into the environment represents a major source of environmental disturbance. In recent years, the focus of ecotoxicology has shifted from describing the effects of chemical contaminants on individual species to developing more integrated approaches for predicting and evaluating long term effects of chemi...

Genetic diversity is the amount of variation observed between DNA sequences from distinct individuals of a given species. This pivotal concept of population genetics has implications for species health, domestication, management and conservation. Levels of genetic diversity seem to vary greatly in natural populations and species, but the determinan...

The metallothionein (MT) gene superfamily consists of metal-binding proteins involved in various metal detoxification and storage mechanisms. The evolution of this gene family in vertebrates has mostly been studied in mammals using sparse taxon or gene sampling. Genomic databases and available data on MT protein function and expression allow a bett...

The giant Galapagos tortoise, Chelonoidis nigra, is a large-sized terrestrial chelonian of high patrimonial interest. The species recently colonized a small continental archipelago, the Galapagos islands, where it has been facing novel environmental conditions and limited resource availability. To explore the genomic consequences of this ecological...

Amphibian declines have been documented worldwide. Chytridiomycosis, a disease caused by the aquatic fungus Batrachochytrium dendrobatidis (Bd), is one of the causes associated with these declines. Occurrence, rate of infection and mortality due to chytridiomycosis in amphibians depend on multiple factors including habitat and life-style (aquatic/t...

Pyxis arachnoides is a Critically Endangered Malagasy tortoise for which little data about its natural history and genetic variation are available. This lack of knowledge difficult undertaking conservation measures considering Pyxis genetic diversity. Here, we describe six new microsatellites for Pyxis arachnoides from wild specimens and several lo...

Neutral rates of molecular evolution vary across species, and this variation has been shown to be related to biological traits. One of the first patterns to be observed in vertebrates has been an inverse relationship between body mass (BM) and substitution rates. The effects of three major life-history traits (LHT) that covary with BM - metabolic r...

The morphological peculiarities of turtles have, for a long time, impeded their accurate placement in the phylogeny of amniotes. Molecular data used to address this major evolutionary question have so far been limited to a handful of markers and/or taxa. These studies have supported conflicting topologies, positioning turtles as either the sister g...

Figure S1: Maximum likelihood analyses of the nucleotide dataset. ML phylograms with branch lengths obtained using RAxML with a single concatenated GTR + G model for analysing (a) the complete nucleotide dataset, (b) codon positions 1 + 2, and (c) third codon positions only.

Table S2: Chicken Ensembl gene IDs and official gene names of the 248 markers used in this study.

Table S1: Detailed results of Bayesian relaxed molecular clock analyses obtained under different uncorrelated models for the eight unconstrained nodes.

Figure S2: Analytical pipeline used for assembling the phylogenomic dataset.

Next-generation sequencing (NGS) technologies offer the opportunity for population genomic study of non-model organisms sampled in the wild. The transcriptome is a convenient and popular target for such purposes. However, designing genetic markers from NGS transcriptome data requires assembling gene-coding sequences out of short reads. This is a co...

Detecting the factors that determine the interruption of gene flow between populations is key to understanding how speciation occurs. In this context, caves are an excellent system for studying processes of colonization, differentiation and speciation, since they represent discrete geographical units often with known geological histories. Here, we...

Problems relative to dating estimates for our data. (DOC)

Results of the SAMOVA/AMOVA analyses. Intraspecific genetic structure for each Hydromantes species on the base of the within and among population genetic variance, the geographic location and sampling site. This was not tested for H. sarrabusensis, as only one haplotype network was recovered for this species. Populations belonging to distinct clust...

Genetic p-distances among species (a) and intraspecific clades (b) of Italian Hydromantes. Average p-distances (minimum and maximum p-distances in parenthesis) based on 511 bp of the cytochrome b gene. Numbers with each species refer to clades as in Figure 2. (DOC)

Intraspecific haplotype networks distances. Minimum number of steps (absolute genetic distances) to connect intraspecific single haplotype networks. (DOC)

Molecular biology techniques are useful for taxonomic assignment, but they are not always accessible and can be expensive and time consuming to perform. Morphological methods to identify the origin of individuals could be valuable if they can be performed rapidly, accurately, and with minimal resources. In order to correctly assign the origin of in...

Next Generation Sequencing technologies (NGS) are rapidly invading many evolutionary and ecological fields, such as phylogenomics, molecular evolution, population genomics and molecular ecology. Among the potential targets of NGS is transcriptome sequencing, a fast and relatively cheap way to generate massive amounts of coding sequence data, offeri...

Galápagos tortoises possess two main shell forms, domed and saddleback, that correlate with the biogeographic history of this species group. However, the lack of description of morphological shell variation within and among populations has prevented the understanding of the contribution of evolutionary forces and the potential role of ontogeny in s...

Advanced, transcriptome-based molecular techniques require the use of RNA of high quality and quantity. RNA extraction from nucleated blood of endangered non-model organisms is still problematic due to insufficient starting material or physico-chemical differences between samples from different organisms. Here we evaluate, validate, and suggest mod...

The best documented selection-based hypothesis to explain unequal usage of codons is based on the relative abundance of isoaccepting tRNAs. In unicellular organisms the most used codons are optimally translated by the most abundant tRNAs. The chemical bonding energies are affected by modification of the four traditional bases, in particular in the...

Average nucleotide and amino acid distances. a) Average Tamura-Nei nucleotide distances, and average amino acid p-distances calculated for the 582 sequence dataset and for each part (5' and 3'-ends) of the entire fragment length of the gene. "N" indicates the number of sequences used. Check Table 1 to see the length range of the sequences included....