Ultraconserved elements-based phylogenomic systematics of the snake superfamily Elapoidea, with the description of a new Afro-Asian family

The highly diverse snake superfamily Elapoidea is considered to be a classic example of ancient, rapid radiation. Such radiations are challenging to fully resolve phylogenetically, with the highly diverse Elapoidea a case in point. Previous attempts at inferring a phylogeny of elapoids produced highly incongruent estimates of their evolutionary relationships, often with very low statistical support. We sought to resolve this situation by sequencing over 4,500 ultraconserved element loci from multiple representatives of every elapoid family/sub-family level taxon and inferring their phylogenetic relationships with multiple methods. Concatenation and multispecies coalescent based species trees yielded largely congruent and well-supported topologies. Hypotheses of a hard polytomy were not retained for any deep branches. Our phylogenies recovered Cyclocoridae and Elapidae as diverging early within Elapoidea. The Afro-Malagasy radiation of elapoid snakes, classified as multiple subfamilies of an inclusive Lamprophiidae by some earlier authors, was found to be monophyletic in all analyses. The genus Micrelaps was consistently recovered as sister to Lamprophiidae. We establish a new family, Micrelapidae fam. nov., for Micrelaps and assign Brachyophis to this family based on cranial osteological syn-apomorphy. We estimate that Elapoidea originated in the early Eocene and rapidly diversified into all the major lineages during this epoch. Ecological opportunities presented by the post-Cretaceous-Paleogene mass extinction event may have promoted the explosive radiation of elapoid snakes.Peer reviewe

Phylogenetic Relationships and Evolution of Snakes

Snakes represent an impressive evolutionary radiation of over 3,500 widely-distributed species, categorized into 515 genera, encompassing a diverse range of morphologies and ecologies. This diversity is likely attributable to their distinctive morphology, which has allowed them to populate a wide range of habitat types within most major ecosystems. In my first chapter, I provide the largest-yet estimate of the snake tree of life using maximum likelihood on a supermatrix of 1745 taxa (1652 snake species + 7 outgroup taxa) and 9,523 base pairs from 10 loci (5 nuclear, 5 mitochondrial), including previously unsequenced genera (2) and species (61). I then use this phylogeny to test hypotheses regarding heterogeneity in diversification rates and how this shaped overall patterns of snake diversity in Chapter 2. I also used the species-level phylogeny to test the evolution of habitat use in snakes, morphological variation, and whether distantly-related species exhibit morphological convergence in Chapter 3. Finally, in Chapter 4 I investigate how prehensile tails effect striking performance in arboreal snakes

EVOLUÇÃO CARIOTÍPICA DE SERPENTES REVISITADA

Karyotype evolution of snakes revisited. Cytogenetic analyzes have proved been valuable tool for characterization, evolutionary mechanisms and phylogenetic relationships in several species. Most of cytogenetic studies on snakes are restricted to analyzes of chromosome number and morphology. Despite this, a chromosomal characterization, is important for heterochromatin analysis and / or chromosomal location of specific sequences, such as DNA and telomeric and has contributed significantly to the studies of systematics and phylogeny in various groups of snakes. This work aimed to perform a literature review of the cytogenetics studies of snakes, aiming to provide subsets for a better understanding of the theme. The snakes present a bimodal karyotype, with presence of macrochromosomes and microchromosomes. The diploid number within the group ranges from 2n = 24 to 2n = 50, where 2n = 36 is considered the common karyotype and is present in most species. Despite being considered conserved in relation to the diploid number, the snakes karyotype has shown the difference in the pattern of distribution of bands and specific sequences as the DNAr and telomeric regions. The main mechanism of chromosome evolution within the group is given by events involving centric fusions and fissions. The pattern of heterochromatin distribution has been shown to be an important cytotaxonomic marker within families. The differentiation of ZZ / ZW or multiple sex chromosomes occurs in more derived species where there are few or no cases of heteromorphism in basal lines.As análises citogenéticas têm se mostrado uma valiosa ferramenta para caracterização, mecanismos evolutivos e relações filogenéticas em várias espécies. A maioria dos trabalhos de citogenética em serpentes estão restritos a análises do número e morfologia cromossômica. Apesar disso, a caracterização cromossômica, principalmente quando são utilizadas as análises da heterocromatina e/ou localização cromossômicas de sequências específicas, como as de DNAr e as teloméricas, tem contribuído de forma significativa para os estudos da sistemática e filogenia em diversos grupos de serpentes. Este trabalho teve como objetivo realizar uma revisão de literatura dos estudos de citogenética de serpentes, visando fornecer subsídios para uma melhor compreensão sobre o tema. As serpentes apresentam um carióipo bimodal, com presença de macrocromossomos e microcromossomos. O número diploide dentro do grupo varia de 2n=24 à 2n=50, onde 2n=36 é considerado o cariótipo comum e se encontra presente na maioria das espécies. Apesar de ser considerado conservado, em relação ao número diploide, o cariótipo das serpentes vem mostrando diferenciação quanto ao padrão de distribuição de bandas e sequências específicas como de DNAr e regiões teloméricas. O principal mecanismo de evolução cromossômica dentro do grupo se dá por eventos envolvendo fusões e fissões cêntricas. O padrão de distribuição de heterocromatina tem se mostrado importante marcador citotaxonômico dentro das famílias. A diferenciação dos cromossomos sexuais, do tipo ZZ/ZW ou múltiplos, acontecem em espécies mais derivadas onde há poucos ou nenhum caso de heteromorfismo em linhas mais basais

Envenomation by the Malagasy colubrid snake Langaha madagascariensis

This report documents a case of envenomation by a Malagasy opisthoglyphous snake, Langaha madagascariensis. The snake bit the finger of a healthy adult man who was attempting to record its morphological measurements as part of a biodiversity survey which was being conducted in the extreme north of Madagascar. Symptoms of this case included severe local pain accompanied by observable swelling which lasted for several days. The present observations indicate that bite by L. madagascariensis potentially causes notable physiological effects in humans although the snake is generally calm and reluctant to bite unless provoked

Comparing species tree estimation with large anchored phylogenomic and small Sanger-sequenced molecular datasets: an empirical study on Malagasy pseudoxyrhophiine snakes

Background Using molecular data generated by high throughput next generation sequencing (NGS) platforms to infer phylogeny is becoming common as costs go down and the ability to capture loci from across the genome goes up. While there is a general consensus that greater numbers of independent loci should result in more robust phylogenetic estimates, few studies have compared phylogenies resulting from smaller datasets for commonly used genetic markers with the large datasets captured using NGS. Here, we determine how a 5-locus Sanger dataset compares with a 377-locus anchored genomics dataset for understanding the evolutionary history of the pseudoxyrhophiine snake radiation centered in Madagascar. The Pseudoxyrhophiinae comprise ~86 % of Madagascar’s serpent diversity, yet they are poorly known with respect to ecology, behavior, and systematics. Using the 377-locus NGS dataset and the summary statistics species-tree methods STAR and MP-EST, we estimated a well-supported species tree that provides new insights concerning intergeneric relationships for the pseudoxyrhophiines. We also compared how these and other methods performed with respect to estimating tree topology using datasets with varying numbers of loci. Methods Using Sanger sequencing and an anchored phylogenomics approach, we sequenced datasets comprised of 5 and 377 loci, respectively, for 23 pseudoxyrhophiine taxa. For each dataset, we estimated phylogenies using both gene-tree (concatenation) and species-tree (STAR, MP-EST) approaches. We determined the similarity of resulting tree topologies from the different datasets using Robinson-Foulds distances. In addition, we examined how subsets of these data performed compared to the complete Sanger and anchored datasets for phylogenetic accuracy using the same tree inference methodologies, as well as the program *BEAST to determine if a full coalescent model for species tree estimation could generate robust results with fewer loci compared to the summary statistics species tree approaches. We also examined the individual gene trees in comparison to the 377-locus species tree using the program MetaTree. Results Using the full anchored dataset under a variety of methods gave us the same, well-supported phylogeny for pseudoxyrhophiines. The African pseudoxyrhophiine Duberria is the sister taxon to the Malagasy pseudoxyrhophiines genera, providing evidence for a monophyletic radiation in Madagascar. In addition, within Madagascar, the two major clades inferred correspond largely to the aglyphous and opisthoglyphous genera, suggesting that feeding specializations associated with tooth venom delivery may have played a major role in the early diversification of this radiation. The comparison of tree topologies from the concatenated and species-tree methods using different datasets indicated the 5-locus dataset cannot beused to infer a correct phylogeny for the pseudoxyrhophiines under any method tested here and that summary statistics methods require 50 or more loci to consistently recover the species-tree inferred using the complete anchored dataset. However, as few as 15 loci may infer the correct topology when using the full coalescent species tree method *BEAST. MetaTree analyses of each gene tree from the Sanger and anchored datasets found that none of the individual gene trees matched the 377-locus species tree, and that no gene trees were identical with respect to topology. Conclusions Our results suggest that ≥50 loci may be necessary to confidently infer phylogenies when using summaryspecies-tree methods, but that the coalescent-based method *BEAST consistently recovers the same topology using only 15 loci. These results reinforce that datasets with small numbers of markers may result in misleading topologies, and further, that the method of inference used to generate a phylogeny also has a major influence on the number of loci necessary to infer robust species trees. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0503-1) contains supplementary material, which is available to authorized users

Factors influencing worldwide zoo collections of lizards, snakes, turtles and crocodiles: effect of conservation status, body size and their attractiveness to humans

Na světě existuje velké množství druhů, každý rok však přibývá těch, které jsou ohrožené. Jednou z možností jejich záchrany je v současné situaci i chov v lidské péči. Dostatečná populace s uspokojivým managementem chovu v zajetí dává mnoha druhům naději jak na samotné přežití (střednědobé), tak i šanci na případný návrat do volné přírody. V současnosti celosvětově nejvýznamnějším sdružením chovatelských zařízení jsou zoologické zahrady WAZA (World Association of Zoos and Aquariums). Protože tyto instituce fungují jako síť umožňující výměnu chovaných jedinců, můžeme populace chované v těchto institucích chápat pro účely ochranářské biologie a dle konceptu tzv. "archy Noemovy" jako celosvětovou populaci daného druhu v lidské péči charakterizovanou svojí velikostí, tj. celkovým počtem jedinců. Ovšem prostor v této novodobé Arše je omezen, proto je důležité, které druhy se vyberou a dostanou šanci na záchranu. Faktorů, které rozhodují o umístění konkrétního zvířete do zoologické zahrady může být celá řada. Podle předchozích studií byly vybrány faktory, které by mohly být významné, a to velikost těla zvířete, taxonomické zařazení a stupeň jeho ohrožení (podle IUCN). Analýza těchto faktorů u hlavních vývojových linií plazů (želvy, krokodýli, ještěři a hadi) by měla naznačit, která zvířata a proč jsou v...There is a large number of species existing in the world; each year, however, the number of the endangered ones rapidly increases. Nowadays, captive breeding becomes an option for their survival in refugees. Sufficient population with satisfactory breeding management gives hope for survival to the endangered species (in mid-term) or even possible future reintroduction to their natural habitat. WAZA is currently the world's leading association of worldwide zoos and similar breeding facilities. Because these institutions operate as a network to facilitate the exchange of reared individuals, for conservation purposes, their captive populations may be seen as one large population characterized by its size, i.e., the total number of individuals. Such view is currently recognized by many conservationists as the so-called concept of Noah's Ark. The space on the Ark is limited, therefore it is needed to heed the characteristics of the species aboard to maximize the conservation potential. Many factors influence the presence of species in zoological gardens. Following previous studies we selected some factors that may be important, i.e., body lenght, taxonomy, and IUCN status. Analysis of these factors among the main reptile clades shall reveal the pattern of reptile composition in worldwide zoos. One of the factors...Katedra zoologieDepartment of ZoologyPřírodovědecká fakultaFaculty of Scienc

Karyotypes of four species of Xenodontini snakes (Serpentes) and implications for taxonomy

The karyotypes of four South American Xenodontini snake species, Lygophis dilepis, L. meridionalis, L. flavifrenatus and L. anomalus, are here described for the first time. We studied specimens from northeastern Argentina using conventional and silver (Ag-NOR) staining. While the typical ophidian karyotype is 2n= 36, we found that the karyotype of the studied species is 2n=34, with metacentric and submetacentric chromosome pairs. The Ag-NOR staining revealed that nucleolar organizer regions (NORs) are located on one pair of microchromosomes. In L. dilepisand L. anomalus the 4th chromosome pair is heteromorphic, and we suggest that it might be considered as the ZW sex chromosome pair. The optimization of available karyological data on a molecular phylogenetic tree of the tribe Xenodontini shows that the diploid numbers of the three genera (2n= 28, 30 and 34) represent putative synapomorphies for Erythrolamprus, Xenodon and Lygophis, respectively. Our results provide new insights which fill gaps in our knowledge on the cytology in the genus Lygophis and identified a possible diagnostic character for the genus.Los cariotipos de cuatro especies de serpientes, Xenodontini dilepis Lygophis , L . meridionalis , L . flavifrenatus y L . anomalus , se describen aquí por primera vez. Estudiamos especímenes del noreste de Argentina usando tinción convencional y plata (Ag-NOR). Mientras que el cariotipo de ofidio típico es 2n = 36, encontramos que el cariotipo de la especie estudiada es 2n = 34, con pares de cromosomas metacéntricos y submetacéntricos. La tinción de Ag-NOR reveló que las regiones organizadoras nucleolares (NOR) se encuentran en un par de microcromosomas. En L . dilepis y L . anomalusel 4 ° par de cromosomas es heteromorfo, y sugerimos que se lo pueda considerar como el par de cromosomas sexuales ZW. La optimización de los datos disponibles cariológicos sobre un árbol filogenético molecular de la tribu Xenodontini muestra que los números diploides 2n = 28, 30 y 34 representan supuestas sinapomorfías para Erythrolamprus , Xenodon y Lygophis , respectivamente. Nuestros resultados proporcionan nuevos conocimientos que llenan las lagunas en nuestro conocimiento sobre la citología en el género Lygophis e identificaron un posible carácter de diagnóstico para el género.Facultad de Ciencias Naturales y Muse

Isolation of a Neurotoxin (a-colubritoxin) from a Nonvenomous Colubrid: Evidence for Early Origin of Venom in Snakes

Abstract. The evolution of venom in advanced snakes has been a focus of long-standing interest. Here we provide the first complete amino acid sequence of a colubrid toxin, which we have called a-colubritoxin, isolated from the Asian ratsnake Coelognathus radiatus (formerly known as Elaphe radiata), an archetypal nonvenomous snake as sold in pet stores. This potent postsynaptic neurotoxin displays readily reversible, competitive antagonism at the nicotinic receptor. The toxin is homologous with, and phylogenetically rooted within, the three-finger toxins, previously thought unique to elapids, suggesting that this toxin family was recruited into the chemical arsenal of advanced snakes early in their evolutionary history. LC-MS analysis of venoms from most other advanced snake lineages revealed the widespread presence of components of the same molecular weight class, suggesting the ubiquity of three-finger toxins across advanced snakes, with the exclusion of Viperidae. These results support the role of venom as a key evolutionary innovation in the early diversification of advanced snakes and provide evidence that forces a fundamental rethink of the very concept of nonvenomous snake