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Nucleic Acids Research Jan 2021Alternative splicing is widespread throughout eukaryotic genomes and greatly increases transcriptomic diversity. Many alternative isoforms have functional roles in...
Alternative splicing is widespread throughout eukaryotic genomes and greatly increases transcriptomic diversity. Many alternative isoforms have functional roles in developmental processes and are precisely temporally regulated. To facilitate the study of alternative splicing in a developmental context, we created MeDAS, a Metazoan Developmental Alternative Splicing database. MeDAS is an added-value resource that re-analyses publicly archived RNA-seq libraries to provide quantitative data on alternative splicing events as they vary across the time course of development. It has broad temporal and taxonomic scope and is intended to assist the user in identifying trends in alternative splicing throughout development. To create MeDAS, we re-analysed a curated set of 2232 Illumina polyA+ RNA-seq libraries that chart detailed time courses of embryonic and post-natal development across 18 species with a taxonomic range spanning the major metazoan lineages from Caenorhabditis elegans to human. MeDAS is freely available at https://das.chenlulab.com both as raw data tables and as an interactive browser allowing searches by species, tissue, or genomic feature (gene, transcript or exon ID and sequence). Results will provide details on alternative splicing events identified for the queried feature and can be visualised at the gene-, transcript- and exon-level as time courses of expression and inclusion levels, respectively.
Topics: Alternative Splicing; Amphibians; Animals; Caenorhabditis elegans; Cephalochordata; Databases, Genetic; Exons; Gene Expression Regulation, Developmental; Genome; High-Throughput Nucleotide Sequencing; Humans; Internet; Introns; Mammals; RNA, Messenger; Reptiles; Software; Transcriptome; Urochordata; Zebrafish
PubMed: 33084905
DOI: 10.1093/nar/gkaa886 -
Global Change Biology Sep 2023Shifts between native and alien climatic niches pose a major challenge for predicting biological invasions. This is particularly true for insular species because...
Shifts between native and alien climatic niches pose a major challenge for predicting biological invasions. This is particularly true for insular species because geophysical barriers could constrain the realization of their fundamental niches, which may lead to underestimates of their invasion potential. To investigate this idea, we estimated the frequency of shifts between native and alien climatic niches and the magnitude of climatic mismatches using 80,148 alien occurrences of 46 endemic insular amphibian, reptile, and bird species. Then, we assessed the influence of nine potential predictors on climatic mismatches across taxa, based on species' characteristics, native range physical characteristics, and alien range properties. We found that climatic mismatch is common during invasions of endemic insular birds and reptiles: 78.3% and 55.1% of their respective alien records occurred outside of the environmental space of species' native climatic niche. In comparison, climatic mismatch was evident for only 16.2% of the amphibian invasions analyzed. Several predictors significantly explained climatic mismatch, and these varied among taxonomic groups. For amphibians, only native range size was associated with climatic mismatch. For reptiles, the magnitude of climatic mismatch was higher for species with narrow native altitudinal ranges, occurring in topographically complex or less remote islands, as well as for species with larger distances between their native and alien ranges. For birds, climatic mismatch was significantly larger for invasions on continents with higher phylogenetic diversity of the recipient community, and when the invader was more evolutionarily distinct. Our findings highlight that apparently common niche shifts of insular species may jeopardize our ability to forecast their potential invasions using correlative methods based on climatic variables. Also, we show which factors provide additional insights on the actual invasion potential of insular endemic amphibians, reptiles, and birds.
Topics: Animals; Introduced Species; Ecosystem; Phylogeny; Amphibians; Reptiles; Birds
PubMed: 37395619
DOI: 10.1111/gcb.16849 -
BMC Ecology and Evolution Dec 2023Vertebrate brains show extensive variation in relative size. The expensive brain hypothesis argues that one important source of this variation is linked to a species'...
Vertebrate brains show extensive variation in relative size. The expensive brain hypothesis argues that one important source of this variation is linked to a species' ability to generate the energy required to sustain the brain, especially during periods of unavoidable food scarcity. Here we ask whether this hypothesis, tested so far in endothermic vertebrates, also applies to ectotherms, where ambient temperature is an additional major aspect of energy balance. Phylogenetic comparative analyses of reptiles and amphibians support the hypothesis. First, relative brain size increases with higher body temperature in those species active during the day that can gain free energy by basking. Second, relative brain size is smaller among nocturnal species, which generally face less favorable energy budgets, especially when maintaining high body temperature. However, we do not find an effect of seasonal variation in ambient temperature or food on brain size, unlike in endotherms. We conclude that the factors affecting energy balance in ectotherms and endotherms are overlapping but not identical. We therefore discuss the idea that when body temperatures are seasonally very low, cognitive benefits may be thwarted and selection on larger brain size may be rare. Indeed, mammalian hibernators may show similarities to ectotherms.
Topics: Animals; Phylogeny; Reptiles; Amphibians; Vertebrates; Mammals; Brain
PubMed: 38114918
DOI: 10.1186/s12862-023-02188-w -
Biology Letters Jun 2023Over the past two decades, there has been an astounding growth in the documentation of vertebrate facultative parthenogenesis (FP). This unusual reproductive mode has...
Over the past two decades, there has been an astounding growth in the documentation of vertebrate facultative parthenogenesis (FP). This unusual reproductive mode has been documented in birds, non-avian reptiles-specifically lizards and snakes-and elasmobranch fishes. Part of this growth among vertebrate taxa is attributable to awareness of the phenomenon itself and advances in molecular genetics/genomics and bioinformatics, and as such our understanding has developed considerably. Nonetheless, questions remain as to its occurrence outside of these vertebrate lineages, most notably in Chelonia (turtles) and Crocodylia (crocodiles, alligators and gharials). The latter group is particularly interesting because unlike all previously documented cases of FP in vertebrates, crocodilians lack sex chromosomes and sex determination is controlled by temperature. Here, using whole-genome sequencing data, we provide, to our knowledge, the first evidence of FP in a crocodilian, the American crocodile, . The data support terminal fusion automixis as the reproductive mechanism; a finding which suggests a common evolutionary origin of FP across reptiles, crocodilians and birds. With FP now documented in the two main branches of extant archosaurs, this discovery offers tantalizing insights into the possible reproductive capabilities of the extinct archosaurian relatives of crocodilians and birds, notably members of Pterosauria and Dinosauria.
Topics: Animals; Alligators and Crocodiles; Biological Evolution; Genomics; Dinosaurs; Turtles; Birds; Parthenogenesis
PubMed: 37282490
DOI: 10.1098/rsbl.2023.0129 -
Anais Da Academia Brasileira de Ciencias 2024Fishermen-hunter-gatherers of sambaquis (Brazilian shell mounds) had an intimate affinity with marine-coastal environments, where they exploited a great variety of fish...
Fishermen-hunter-gatherers of sambaquis (Brazilian shell mounds) had an intimate affinity with marine-coastal environments, where they exploited a great variety of fish and mollusks that comprise the best documented fauna from sambaquis. However, other groups of animals as mammals, birds, reptiles, and amphibians are also present in these sites, but are relatively less studied. This paper is the first one focused exclusively on the Tetrapoda biodiversity of sambaquis and aimed to identify tetrapods of ten sites from southern Brazil. We present a faunal inventory and data regarding animal capture and environmental exploitation. We identified the specimens anatomically and taxonomically, analyzed them concerning fragmentation, and quantified the data for the number of identified specimens (NISP) and minimum number of individuals (MNI). Despite the high degree of fragmentation of remains, we identified 46 taxa. As expected, most were from marine animals: cetaceans (total NISP = 2,568 and MNI = 27), otariids (total NISP = 248 and MNI = 32), and seabirds (total NISP = 65 and MNI = 23), indicating great relevance of marine tetrapod fauna as a resource for sambaqui builders (79.39% of NISP). We thus document the close bond between fishermen-hunter-gatherers of sambaquis and the marine tetrapods in southern Brazil.
Topics: Animals; Brazil; Biodiversity; Birds; Reptiles; Cetacea
PubMed: 38747839
DOI: 10.1590/0001-3765202420230901 -
PLoS Neglected Tropical Diseases Feb 2021We assessed the presence of Rickettsia spp., Coxiella burnetii and Anaplasma phagocytophilum in reptiles, their ectoparasites and in questing ticks collected in a nature...
We assessed the presence of Rickettsia spp., Coxiella burnetii and Anaplasma phagocytophilum in reptiles, their ectoparasites and in questing ticks collected in a nature preserve park in southern Italy, as well as in a peri-urban area in another region. We also investigated the exposure to these pathogens in forestry workers, farmers and livestock breeders living or working in the nature preserve park given the report of anecdotal cases of spotted fever rickettsioses. Rickettsia spp. were molecularly detected in Podarcis muralis and Podarcis siculus lizards (i.e., 3.1%), in Ixodes ricinus (up to 87.5%) and in Neotrombicula autumnalis (up to 8.3%) collected from them as well as in I. ricinus collected from the environment (up to 28.4%). Rickettsia monacensis was the most prevalent species followed by Rickettsia helvetica. An undescribed member of the family Anaplasmataceae was detected in 2.4% and 0.8% of the reptiles and ectoparasites, respectively. Sera from human subjects (n = 50) were serologically screened and antibodies to Rickettsia spp. (n = 4; 8%), C. burnetti (n = 8; 16%) and A. phagocytophilum (n = 11; 22%) were detected. Two ticks collected from two forestry workers were positive for spotted fever group (SFG) rickettsiae. Ixodes ricinus is involved in the transmission of SFG rickettsiae (R. monacensis and R. helvetica) in southern Europe and lizards could play a role in the sylvatic cycle of R. monacensis, as amplifying hosts. Meanwhile, N. autumnalis could be involved in the enzootic cycle of some SFG rickettsiae among these animals. People living or working in the southern Italian nature preserve park investigated are exposed to SFG rickettsiae, C. burnetii and A. phagocytophilum.
Topics: Adult; Aged; Anaplasma phagocytophilum; Anaplasmataceae; Animals; Arthropods; Coxiella burnetii; Europe; Female; Humans; Italy; Ixodes; Male; Middle Aged; One Health; Polymerase Chain Reaction; RNA, Ribosomal, 16S; Reptiles; Rickettsia; Rickettsia Infections; Snakes; Young Adult
PubMed: 33596200
DOI: 10.1371/journal.pntd.0009090 -
Parasites & Vectors Apr 2023Sergentomyia minuta (Diptera: Phlebotominae) is an abundant sand fly species in the Mediterranean basin and a proven vector of reptile parasite Leishmania...
BACKGROUND
Sergentomyia minuta (Diptera: Phlebotominae) is an abundant sand fly species in the Mediterranean basin and a proven vector of reptile parasite Leishmania (Sauroleishmania) tarentolae. Although it feeds preferentially on reptiles, blood meal analyses and detection of Leishmania (Leishmania) infantum DNA in wild-caught S. minuta suggest that occasional feeding may occur on mammals, including humans. Therefore, it is currently suspected as a potential vector of human pathogens.
METHODS
A recently established S. minuta colony was allowed to feed on three reptile species (i.e. lizard Podarcis siculus and geckos Tarentola mauritanica and Hemidactylus turcicus) and three mammal species (i.e. mouse, rabbit and human). Sand fly mortality and fecundity were studied in blood-fed females, and the results were compared with Phlebotomus papatasi, vector of Leishmania (L.) major. Blood meal volumes were measured by haemoglobinometry.
RESULTS
Sergentomyia minuta fed readily on three reptile species tested, neglected the mouse and the rabbit but took a blood meal on human. However, the percentage of females engorged on human volunteer was low in cage (3%) and feeding on human blood resulted in extended defecation times, higher post-feeding mortality and lower fecundity. The average volumes of blood ingested by females fed on human and gecko were 0.97 µl and 1.02 µl, respectively. Phlebotomus papatasi females readily fed on mouse, rabbit and human volunteer; a lower percentage of females (23%) took blood meal on the T. mauritanica gecko; reptilian blood increased mortality post-feeding but did not affect P. papatasi fecundity.
CONCLUSIONS
Anthropophilic behaviour of S. minuta was experimentally demonstrated; although sand fly females prefer reptiles as hosts, they were attracted to the human volunteer and took a relatively high volume of blood. Their feeding times were longer than in sand fly species regularly feeding on mammals and their physiological parameters suggest that S. minuta is not adapted well for digestion of mammalian blood. Nevertheless, the ability to bite humans highlights the necessity of further studies on S. minuta vector competence to elucidate its potential role in circulation of Leishmania and phleboviruses pathogenic to humans.
Topics: Female; Humans; Rabbits; Animals; Mice; Phlebotomus; Psychodidae; Leishmania; DNA; Lizards; Mammals
PubMed: 37055860
DOI: 10.1186/s13071-023-05758-5 -
Ecology Letters Jan 2023An individual's fitness cost associated with environmental change likely depends on the rate of adaptive phenotypic plasticity, and yet our understanding of plasticity...
An individual's fitness cost associated with environmental change likely depends on the rate of adaptive phenotypic plasticity, and yet our understanding of plasticity rates in an ecological and evolutionary context remains limited. We provide the first quantitative synthesis of existing plasticity rate data, focusing on acclimation of temperature tolerance in ectothermic animals, where we demonstrate applicability of a recently proposed analytical approach. The analyses reveal considerable variation in plasticity rates of this trait among species, with half-times (how long it takes for the initial deviation from the acclimated phenotype to be reduced by 50% when individuals are shifted to a new environment) ranging from 3.7 to 770.2 h. Furthermore, rates differ among higher taxa, being higher for amphibians and reptiles than for crustaceans and fishes, and with insects being intermediate. We argue that a more comprehensive understanding of phenotypic plasticity will be attained through increased focus on the rate parameter.
Topics: Animals; Acclimatization; Phenotype; Reptiles; Temperature; Amphibians; Crustacea; Fishes
PubMed: 36450612
DOI: 10.1111/ele.14147 -
Zoonoses and Public Health Dec 2022Non-typhoidal Salmonella cause an estimated 1.4 million human illnesses, 26,000 hospitalizations and 400 deaths annually in the United States. Approximately 11% of these...
Non-typhoidal Salmonella cause an estimated 1.4 million human illnesses, 26,000 hospitalizations and 400 deaths annually in the United States. Approximately 11% of these infections are attributed to animal contact. Reptiles and amphibians are known sources of salmonellosis; young children (aged <5 years) are disproportionately affected by reptile- and amphibian-associated salmonellosis (RAAS) outbreaks. We describe multistate RAAS outbreaks to characterize illnesses and inform prevention efforts. RAAS outbreaks were defined as ≥2 culture-confirmed human Salmonella infections with similar pulsed-field gel electrophoresis patterns and epidemiologic, laboratory or traceback evidence linking them to a common reptile/amphibian exposure. Data sources included the Animal Contact Outbreak Surveillance System; CDC Outbreak Response and Prevention Branch's outbreak management database; PulseNet, the national molecular subtyping network for foodborne disease surveillance in the United States; and the National Antimicrobial Resistance Monitoring System. Twenty-six RAAS outbreaks were reported during 2009-2018, resulting in 1465 illnesses and 306 hospitalizations. The outbreaks were associated with turtles (19), lizards (5), snakes (1) and frogs (1). Sixteen (61.5%) outbreaks were linked to small turtles (<4 inches), resulting in 914 illnesses. Forty-nine percent of outbreak-associated patients were aged <5 years. Of 362 patients/caregivers interviewed, 111 (30.7%) were aware that reptiles/amphibians can carry Salmonella. Among 267 patient isolates with antimicrobial susceptibility information, 20 (7.5%) were non-susceptible to ≥1 antibiotic used to treat human salmonellosis. RAAS outbreaks result in considerable morbidity, particularly among young children. Illnesses linked to small turtles are preventable through education, targeted outreach to caregivers and paediatricians, and when appropriate, enforcement. Historically, individual states and jurisdictions have enforced existing or promulgated new authorities to address outbreaks. Preventing future RAAS outbreaks requires addressing challenges related to the illegal sale/distribution of small turtles; and for legal reptile sales, providing information on RAAS risk to consumers at point of sale to support informed pet ownership decisions.
Topics: Humans; United States; Animals; Salmonella Infections; Salmonella Food Poisoning; Salmonella; Disease Outbreaks; Turtles; Lizards; Amphibians; Anti-Infective Agents
PubMed: 36345968
DOI: 10.1111/zph.12990 -
Current Biology : CB Jun 2020Lateralized behaviors have been reported in a variety of extant vertebrates, including birds and reptiles [1-3] and non-human mammals [4-6]. However, evidence of...
Lateralized behaviors have been reported in a variety of extant vertebrates, including birds and reptiles [1-3] and non-human mammals [4-6]. However, evidence of lateralized behaviors in extinct vertebrates is rare, primarily because of the difficulty of identifying such behaviors with confidence in fossils. In rare instances, paleontologists can infer asymmetry in predatory or foraging behavior, including predation scars on trilobites [7], directionality of invertebrate traces [8], and even behavioral asymmetry in fossil non-human primates [9, 10]. Because lateralized behaviors have been linked to hemispheric (brain) lateralization in some vertebrates [11-15], evidence of lateralized behaviors in ancient vertebrates might yield clues about the evolutionary origins of vertebrate brain lateralization. Here, we show the earliest evidence of lateralized behavior in a fossil reptile based on repeatable observations of tooth wear in a large sample of intact jaws. The patterns of dental wear along the tooth rows of nearly one hundred jaws of the small, early Permian (289 million years ago) reptile Captorhinus aguti indicate that it exhibited lateralized behavior, preferring to feed using the right side of the jaw. Discovery of such a feeding behavior in this ancient, terrestrial, and omnivorous animal provides direct evidence of the deep history of directional behavior among amniotes and may indicate an early origin of brain lateralization.
Topics: Animals; Biological Evolution; Feeding Behavior; Fossils; Functional Laterality; Reptiles; Tooth
PubMed: 32413302
DOI: 10.1016/j.cub.2020.04.026