Handbook of best practice and standards for 2D+ and 3D imaging of natural history collections

peer reviewedDigitising a collection is key to make it last even after the physical objects are no longer available. Almost all of the techniques currently available to digitise a natural history collection in 2D+ and 3D are listed herein. The techniques are explained in a way that even one without any knowledge on the subject may understand their principle. The strong and weak points of the techniques are discussed, and an overview of suitable collections and specimens are given for each one of them. Also, plenty of examples already digitised with each technique are provided together with the links to visualise them in 3D. After explaining all the different digitisation options, the subsequent chapters provide information on how to improve the 2D+ and 3D digital twins of the specimens and techniques are compared to each other by means of test specimens. These give a fast overview of the capabilities of the digitisation techniques. Possible solutions to avoid digitisation errors are equally provided. Lastly, the dissemination of the results and the data management of the 3D models are briefly discussed in the final chapters. Also, a large chapter is provided with several workflows that can be followed to get the best possible results

Rasprostranjenost vodozemaca i gmazova u Parku prirode »Lastovsko otočje«: mogući biotički i abiotički uzroci

In this paper we examine the distribution of amphibians and reptiles over the islands of the newly founded Lastovo Archipelago Nature Park (Lastovsko otočje), Croatia. On several field trips between 1996 and 2008, we encountered five species of lizards (Podarcis sicula, P. melisellensis, Dalmatolacerta oxycephala, Hemidactylus turcicus and Pseudopus apodus), one species of snake (Dolichophis caspius), one species of sea turtle (Caretta caretta) and one species of toad (Bufo viridis). We confirm literature data on the presence of some of these species on different islands of the archipelago, and add distributional records for several other islands and islets. Logistic regression analyses show that the variables predicting presence/absence from different islands vary among species. Within species, populations from different islands noticeably vary in body size and shape, scalation, dorsal and ventral coloration, behaviour and density. This observation adds to the value of the study area as a »natural laboratory« for future research into the ecology and evolution of island populations. Although most species seem to be doing well presently, we list a number of possible hazards and concerns.U ovom radu istražujemo distribuciju vodozemaca i gmazova novoosnovanog Parka prirode »Lastovsko otočje«, Hrvatska. Tijekom višestrukih terenskih posjeta u periodu od 1996. do 2008. godine zabilježili smo pet vrsta guštera (Podarcis sicula, P. melisellensis, Dalmatolacerta oxycephala, Hemidactylus turcicus i Pseudopus apodus), jednu vrstu zmije (Dolichophis caspius), jednu vrstu morske kornjače (Caretta caretta) i jednu vrstu žabe (Bufo viridis). Potvrdili smo prisutnost određenih vrsta na pojedinim otocima Lastovskog otočja, te dodali nalaze na mnogim drugim otocima i otočićima. Logističkom regresijskom analizom smo pokazali da varijable koje predviđaju prisutnost / odsutnost s različitih otoka variraju između vrsta. Unutar vrste, populacije s različitih otoka zapaženo variraju u veličini i obliku tijela, broju i izgledu pločica, leđnoj i trbušnoj obojenosti, ponašanju i gustoći. Ova opažanja povećavaju vrijednost istraživanog područja kao »prirodnog laboratorija« za buduća istraživanja ekologije i evolucije otočkih populacija. Iako se čini je većina vrsta u dobrom stanju, navodimo listu mogućih opasnih i zabrinjavajućih čimbenika

Cranial osteology of Hypoptophis (Aparallactinae : Atractaspididae: Caenophidia), with a discussion on the evolution of its fossorial adaptations

Fossoriality evolved early in snakes, and has left its signature on the cranial morphology of many extinct Mesozoic and early Caenozoic forms. Knowledge of the cranial osteology of extant snakes is indispensable for associating the crania of extinct lineages with a particular mode of life; this applies to fossorial taxa as well. In the present work, we provide a detailed description of the cranium of Hypoptophis wilsonii, a member of the subfamily Aparallactinae, using micro-computed tomography (CT). This is also the first thorough micro-CT-based description of any snake assigned to this African subfamily of predominantly mildly venomous, fossorial, and elusive snakes. The cranium of Hypoptophis is adapted for a fossorial lifestyle, with increased consolidation of skull bones. Aparallactines show a tendency toward reduction of maxillary length by bringing the rear fangs forward. This development attains its pinnacle in the sister subfamily Atractaspidinae, in which the rear fang has become the "front fang" by a loss of the part of the maxilla lying ahead of the fang. These dentitional changes likely reflect adaptation to subdue prey in snug burrows. An endocast of the inner ear of Hypoptophis shows that this genus has the inner ear typical of fossorial snakes, with a large, globular sacculus. A phylogenetic analysis based on morphology recovers Hypoptophis as a sister taxon to Aparallactus. We also discuss the implications of our observations on the burrowing origin hypothesis of snakes.Peer reviewe

Методология компьютерного моделирования процесса алмазного выглаживания

Приведены результаты компьютерного динамического моделирования процесса алмазного выглаживания методом конечных элементов в программном пакете Third Wave AdvantEdge. Установлено влияние модуля упругости обрабатываемого материала, радиуса выглаживателя, глубины и скорости выглаживания на величину напряжений в зоне обработки.The results of the computer simulation of the process of diamond smoothing by the finite element method in the software package Third Wave AdvantEdge are presented. The effect of the modulus of elasticity of the processed material, the radius of the smoother, the depth and the speed of smoothing on the value of stresses in the treatment zone is established

Rasprostranjenost vodozemaca i gmazova u Parku prirode »Lastovsko otočje«: mogući biotički i abiotički uzroci

In this paper we examine the distribution of amphibians and reptiles over the islands of the newly founded Lastovo Archipelago Nature Park (Lastovsko otočje), Croatia. On several field trips between 1996 and 2008, we encountered five species of lizards (Podarcis sicula, P. melisellensis, Dalmatolacerta oxycephala, Hemidactylus turcicus and Pseudopus apodus), one species of snake (Dolichophis caspius), one species of sea turtle (Caretta caretta) and one species of toad (Bufo viridis). We confirm literature data on the presence of some of these species on different islands of the archipelago, and add distributional records for several other islands and islets. Logistic regression analyses show that the variables predicting presence/absence from different islands vary among species. Within species, populations from different islands noticeably vary in body size and shape, scalation, dorsal and ventral coloration, behaviour and density. This observation adds to the value of the study area as a »natural laboratory« for future research into the ecology and evolution of island populations. Although most species seem to be doing well presently, we list a number of possible hazards and concerns.U ovom radu istražujemo distribuciju vodozemaca i gmazova novoosnovanog Parka prirode »Lastovsko otočje«, Hrvatska. Tijekom višestrukih terenskih posjeta u periodu od 1996. do 2008. godine zabilježili smo pet vrsta guštera (Podarcis sicula, P. melisellensis, Dalmatolacerta oxycephala, Hemidactylus turcicus i Pseudopus apodus), jednu vrstu zmije (Dolichophis caspius), jednu vrstu morske kornjače (Caretta caretta) i jednu vrstu žabe (Bufo viridis). Potvrdili smo prisutnost određenih vrsta na pojedinim otocima Lastovskog otočja, te dodali nalaze na mnogim drugim otocima i otočićima. Logističkom regresijskom analizom smo pokazali da varijable koje predviđaju prisutnost / odsutnost s različitih otoka variraju između vrsta. Unutar vrste, populacije s različitih otoka zapaženo variraju u veličini i obliku tijela, broju i izgledu pločica, leđnoj i trbušnoj obojenosti, ponašanju i gustoći. Ova opažanja povećavaju vrijednost istraživanog područja kao »prirodnog laboratorija« za buduća istraživanja ekologije i evolucije otočkih populacija. Iako se čini je većina vrsta u dobrom stanju, navodimo listu mogućih opasnih i zabrinjavajućih čimbenika

Focus stacking: Comparing commercial top-end set-ups with a semi-automatic low budget approach. A possible solution for mass digitization of type specimens

peer reviewedIn this manuscript we present a focus stacking system, composed of commercial photographic equipment. The system is inexpensive compared to high-end commercial focus stacking solutions. We tested this system and compared the results with several different software packages (CombineZP, Auto-Montage, Helicon Focus and Zerene Stacker). We tested our final stacked picture with a picture obtained from two high-end focus stacking solutions: a Leica MZ16A with DFC500 and a Leica Z6APO with DFC290. Zerene Stacker and Helicon Focus both provided satisfactory results. However, Zerene Stacker gives the user more possibilities in terms of control of the software, batch processing and retouching. The outcome of the test on high-end solutions demonstrates that our approach performs better in several ways. The resolution of the tested extended focus pictures is much higher than those from the Leica systems. The flash lighting inside the Ikea closet creates an evenly illuminated picture, without struggling with filters, diffusers, etc. The largest benefit is the price of the set-up which is approximately € 3,000, which is 8 and 10 times less than the LeicaZ6APO and LeicaMZ16A set-up respectively. Overall, this enables institutions to purchase multiple solutions or to start digitising the type collection on a large scale even with a small budget

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