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

The evolution of diet in the Lamprophiidae

A dissertation submitted in fulfilment of the requirements of the degree of Master of Science to the School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa . July 2017.Studying feeding biology in a phylogenetic context helps elucidate the factors that significantly influenced the evolutionary history of organisms. The snake lineage is one of the most morphologically and ecologically diverse clades of vertebrates due to a variety of traits (e.g. venom, body shape, gape size and habitat use) that have enabled their exceptional radiation. Recently, the Deep History Hypothesis (DHH) has been used to explain how divergence, deep in the evolutionary history of snakes, has resulted in present day niche preferences. The Competition-Predation Hypothesis (CPH) contrastingly attributes current ecological traits to recent species interactions. Diet has been a key factor in shaping snake diversity and ecology, and it has often been used as a proxy to understand current snake community structure and evolutionary trends in snakes. I tested the validity of the two evolutionary hypotheses in the Lamprophiidae, a family of primarily African snakes. Furthermore, the evolution of lifestyle, fang types and body size in the Lamprophiidae was examined. Having sourced dietary data for ~300 species, a Hierarchical Cluster Analysis was performed, to group diet into eight broad clusters. A generalist diet comprised of lizards, aquatic vertebrates, small mammals, snakes and reptile eggs, was characteristic of 46% of extant species. Stochastic Character Mapping was performed to generate 50 possible evolutionary hypotheses, the majority of which suggested a generalist ancestral feeding condition with a tendency towards specialisation. Although the generalist feeding trait has largely been retained in many extant lamprophids, some species have a more specialised diet. From the phylogenetic reconstruction, it is evident that the ancestral lamprophid consumed a generalist diet in a terrestrial environment with a relatively small body size (400-600 mm) and possessed back fangs. Body size and fang morphology were correlated with diet indicating that these selective pressures have influenced the variety in prey consumption. A phylogenetic signal from Pagel’s lambda confirmed the divergence in diet while traits such as lifestyle, fang types and body size were constrained. Thus, the validity of DHH and CPH depends on the characters assessed and in this case, a combination of historical and contemporary influences is responsible for shaping the lamprophid community as a whole. The divergence in diet in the lamprophids is most likely influenced by competition or predation, as their interactions with other species within their habitat could be responsible for shaping their diet. This proves to be the case for the lamprophidae, however, studies on other groups of snakes, in different regions of the world have found that phylogeny is more influential on diet patterns. This study shows the importance in understanding ecological factors as a determinant of community ecology. Key words: Divergent evolution, snake ecology, morphological trait reconstructionLG201

Lois et règlements sur la faune sauvage à Madagascar : Progrès accomplis et besoins du futur

In many countries wildlife species are threatened by hunting for meat or collection for the pet trade. Wildlife laws which control where these activities can occur, limit the timing of exploitation, or provide strict protection for some species are therefore an important component of the conservation strategy. However it is important that these wildlife laws reflect the ecology and threat status of the species concerned, and that they are aligned with any relevant international conventions. In this article we discuss the legal framework for exploiting and protecting tetrapod species in Madagascar. We review the 2006 update to wildlife legislation with respect to international treaties, other national legislation and the IUCN Red List of Threatened Species. We also present a summary of the different categories of hunting (sport, commercial, scientific, and subsistence) and the control of hunting in protected areas. Madagascar has a sound legal framework for the use and protection of wildlife and the classification of species into protected, pest and legally hunted is clear and mostly fits well with the species’ classification according to the IUCN Red List and CITES. A revision of the protected species list managed is needed however to (i) include marine mammals that are protected by fisheries law and the Convention on Migratory Species and to (ii) better reflect the rights of people whose livelihoods rely heavily on the income or protein derived from hunting animals. Renewed effort to communicate and enforce wildlife legislation is needed, especially regarding the illegal hunting and export of protected species. This would also support the ongoing initiative to expand the protected area system and could be integrated into a revised National Biodiversity Strategy and Action Plan that Madagascar should produce for 2011-2020 as part of its commitment to implementing the Convention on Biological Diversity. RÉSUMÉLes lois et règlements déterminant les niveaux de protection des espèces de la faune et de la flore sauvages sont des indicateurs importants de l’importance qu’accorde un pays à la conservation de sa biodiversité. Dans cette revue, nous évaluons la cohérence entre les lois et règlements portant sur la gestion de la faune sauvage à Madagascar, en considérant la législation nationale, les conventions internationales ratifiées et la Liste Rouge de l’UICN pour les confronter aux réalités locales. Suite à nos analyses, nous pouvons conclure que Madagascar dispose d’un cadre juridique adéquat pour réglementer la protection et l’exploitation des animaux sauvages. Cependant, des révisions et mises à jour sont nécessaires, particulièrement en ce qui concerne la liste des espèces dans les différentes catégories et la facilitation de la mise en application de la loi

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

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

An overview of the venom apparatus in venomous snakes (Squamata, Serpentes) of the world

Zmije su kroz svoju evoluciju razvile niz prilagodbi za savladavanje plijena. Neke su evoluirale mehanizam za trovanje različitog stupnja složenosti i time postale životinje otrovnice, ali ne i otrovne. Cilj ovog seminara je razjasniti neke pojmove vezane uz mehanizam za trovanje zmija otrovnica, dati kratki pregled njegovih varijacija kod zmija otrovnica svijeta i ukazati na neke probleme koji kompliciraju tematiku.Snakes have developed through their evolution a wide range of adaptations for overcoming their prey. Some evolved a venom apparatus, with varying complexity, and with that became venomous animals, but not poisonous. The goal of this seminar is to explain some of the terms associated with snake venom apparatuses, give a brief overview of its variations in snakes of the world and point out some of the problems complicating the subject at hand

First Large-Scale DNA Barcoding Assessment of Reptiles in the Biodiversity Hotspot of Madagascar, Based on Newly Designed COI Primers

BACKGROUND: DNA barcoding of non-avian reptiles based on the cytochrome oxidase subunit I (COI) gene is still in a very early stage, mainly due to technical problems. Using a newly developed set of reptile-specific primers for COI we present the first comprehensive study targeting the entire reptile fauna of the fourth-largest island in the world, the biodiversity hotspot of Madagascar. METHODOLOGY/PRINCIPAL FINDINGS: Representatives of the majority of Madagascan non-avian reptile species (including Squamata and Testudines) were sampled and successfully DNA barcoded. The new primer pair achieved a constantly high success rate (72.7-100%) for most squamates. More than 250 species of reptiles (out of the 393 described ones; representing around 64% of the known diversity of species) were barcoded. The average interspecific genetic distance within families ranged from a low of 13.4% in the Boidae to a high of 29.8% in the Gekkonidae. Using the average genetic divergence between sister species as a threshold, 41-48 new candidate (undescribed) species were identified. Simulations were used to evaluate the performance of DNA barcoding as a function of completeness of taxon sampling and fragment length. Compared with available multi-gene phylogenies, DNA barcoding correctly assigned most samples to species, genus and family with high confidence and the analysis of fewer taxa resulted in an increased number of well supported lineages. Shorter marker-lengths generally decreased the number of well supported nodes, but even mini-barcodes of 100 bp correctly assigned many samples to genus and family. CONCLUSIONS/SIGNIFICANCE: The new protocols might help to promote DNA barcoding of reptiles and the established library of reference DNA barcodes will facilitate the molecular identification of Madagascan reptiles. Our results might be useful to easily recognize undescribed diversity (i.e. novel taxa), to resolve taxonomic problems, and to monitor the international pet trade without specialized expert knowledge

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