Application of CO2 carbon stable isotope analysis to ant trophic ecology

Stable isotope analysis of animal tissues is commonly used to infer diet and trophic position. However, it requires destructive sampling. The analysis of carbon isotopes from exhaled CO₂ is non-invasive and can provide useful ecological information because isotopic CO₂ signatures can reflect the diet and metabolism of an animal. However, this methodology has rarely been used on invertebrates and never on social insects. Here, we first tested whether this method reflects differences in δ¹³C-CO₂ between workers of the Mediterranean ant Crematogaster scutellaris (Olivier) (Hymenoptera: Formicidae, Crematogastrini) fed with sugar from beet (C3; Beta vulgaris L., Amaranthaceae) or cane (C4; Saccharum officinarum L., Poaceae). We found that a significant difference can be obtained after 24 h. Consequently, we used this technique on wild co-occurring ant species with different feeding preferences to assess their reliance on C3 or C4 sources. For this purpose, we sampled workers of C. scutellaris, the invasive garden ant Lasius neglectus (van Loon et al.) (Lasiini), and the harvester ant Messor capitatus (Latreille) (Stenammini). No significant differences in their carbon isotopic signatures were recorded, suggesting that in our study site no niche partitioning occurs based on the carbon pathway, with all species sharing similar resources. However, further analysis revealed that M. capitatus, a seed-eating ant, can be regarded as a C3 specialist, whereas L. neglectus and C. scutellaris are generalists that rely on both C3 and C4 pathways, though with a preference for the former. Our results show that this methodology can be applied even to small animals such as ants and can provide useful information on the diets of generalist omnivores.     

Cave-adapted evolution in the North American amblyopsid fishes inferred using phylogenomics and geometric morphometrics

Cave adaptation has evolved repeatedly across the Tree of Life, famously leading to pigmentation and eye degeneration and loss, yet its macroevolutionary implications remain poorly understood. We use the North American amblyopsid fishes, a family spanning a wide degree of cave adaptation, to examine the impact of cave specialization on the modes and tempo of evolution. We reconstruct evolutionary relationships using ultraconserved element loci, estimate the ancestral histories of eye-state, and examine the impact of cave adaptation on body shape evolution. Our phylogenomic analyses provide a well-supported hypothesis for amblyopsid evolutionary relationships. The obligate blind cavefishes form a clade and the cave-facultative eyed spring cavefishes are nested within the obligate cavefishes. Using ancestral state reconstruction, we find support for at least two independent subterranean colonization events within the Amblyopsidae. Eyed and blind fishes have different body shapes, but not different rates of body shape evolution. North American amblyopsids highlight the complex nature of cave-adaptive evolution and the necessity to include multiple lines of evidence to uncover the underlying processes involved in the loss of complex traits.     

Applying a multiobjective metaheuristic inspired by honey bees to phylogenetic inference

The development of increasingly popular multiobjective metaheuristics has allowed bioinformaticians to deal with optimization problems in computational biology where multiple objective functions must be taken into account. One of the most relevant research topics that can benefit from these techniques is phylogenetic inference. Throughout the years, different researchers have proposed their own view about the reconstruction of ancestral evolutionary relationships among species. As a result, biologists often report different phylogenetic trees from a same dataset when considering distinct optimality principles. In this work, we detail a multiobjective swarm intelligence approach based on the novel Artificial Bee Colony algorithm for inferring phylogenies. The aim of this paper is to propose a complementary view of phylogenetics according to the maximum parsimony and maximum likelihood criteria, in order to generate a set of phylogenetic trees that represent a compromise between these principles. Experimental results on a variety of nucleotide data sets and statistical studies highlight the relevance of the proposal with regard to other multiobjective algorithms and state-of-the-art biological methods.     

Evidence and hypothesis in biogeography

Evidence can provide support for or against a particular biogeographical hypothesis. Treating a hypothesis as if it were evidence or an empirical observation confounds many biogeographical analyses. We focus on two recent publications that address, in part, the evolution of the biota of Sulawesi, the large Indonesian island in the centre of the Indo‐Australian Archipelago. Many biogeographical explanations are hampered by invoking simple notions of mechanism or process – dispersal and vicariance – or constraints, such as dispersal from a centre of origin, and, in so doing, dismiss more complex geological phenomena such as emergent volcanoes within island chains or composite areas as irrelevant. Moreover, they do not search for, therefore never discover, biogeographical patterns that may better explain the distribution of biota through time.     

Reconstruction of cranial and hyobranchial muscles in the triassic temnospondyl Gerrothorax provides evidence for akinetic suction feeding

The cranial and hyobranchial muscles of the Triassic temnospondyl Gerrothorax have been reconstructed based on direct evidence (spatial limitations, ossified muscle insertion sites on skull, mandible, and hyobranchium) and on phylogenetic reasoning (with extant basal actinopterygians and caudates as bracketing taxa). The skeletal and soft‐anatomical data allow the reconstruction of the feeding strike of this bottom‐dwelling, aquatic temnospondyl. The orientation of the muscle scars on the postglenoid area of the mandible indicates that the depressor mandibulae was indeed used for lowering the mandible and not to raise the skull as supposed previously and implies that the skull including the mandible must have been lifted off the ground during prey capture. It can thus be assumed that Gerrothorax raised the head toward the prey with the jaws still closed. Analogous to the bracketing taxa, subsequent mouth opening was caused by action of the strong epaxial muscles (further elevation of the head) and the depressor mandibulae and rectus cervicis (lowering of the mandible). During mouth opening, the action of the rectus cervicis muscle also rotated the hyobranchial apparatus ventrally and caudally, thus expanding the buccal cavity and causing the inflow of water with the prey through the mouth opening. The strongly developed depressor mandibulae and rectus cervicis, and the well ossified, large quadrate‐articular joint suggest that this action occurred rapidly and that powerful suction was generated. Also, the jaw adductors were well developed and enabled a rapid mouth closure. In contrast to extant caudate larvae and most extant actinopterygians (teleosts), no cranial kinesis was possible in the Gerrothorax skull, and therefore suction feeding was not as elaborate as in these extant forms. This reconstruction may guide future studies of feeding in extinct aquatic tetrapods with ossified hyobranchial apparatus. J. Morphol., 2013. © 2012 Wiley Periodicals, Inc.     

Comparing methods for metabolic network analysis and an application to metabolic engineering

Bioinformatics tools have facilitated the reconstruction and analysis of cellular metabolism of various organisms based on information encoded in their genomes. Characterization of cellular metabolism is useful to understand the phenotypic capabilities of these organisms. It has been done quantitatively through the analysis of pathway operations. There are several in silico approaches for analyzing metabolic networks, including structural and stoichiometric analysis, metabolic flux analysis, metabolic control analysis, and several kinetic modeling based analyses. They can serve as a virtual laboratory to give insights into basic principles of cellular functions. This article summarizes the progress and advances in software and algorithm development for metabolic network analysis, along with their applications relevant to cellular physiology, and metabolic engineering with an emphasis on microbial strain optimization. Moreover, it provides a detailed comparative analysis of existing approaches under different categories.     

Genome reduction as the dominant mode of evolution

A common belief is that evolution generally proceeds towards greater complexity at both the organismal and the genomic level, numerous examples of reductive evolution of parasites and symbionts notwithstanding. However, recent evolutionary reconstructions challenge this notion. Two notable examples are the reconstruction of the complex archaeal ancestor and the intron‐rich ancestor of eukaryotes. In both cases, evolution in most of the lineages was apparently dominated by extensive loss of genes and introns, respectively. These and many other cases of reductive evolution are consistent with a general model composed of two distinct evolutionary phases: the short, explosive, innovation phase that leads to an abrupt increase in genome complexity, followed by a much longer reductive phase, which encompasses either a neutral ratchet of genetic material loss or adaptive genome streamlining. Quantitatively, the evolution of genomes appears to be dominated by reduction and simplification, punctuated by episodes of complexification.     

The early extinction date of the beaver (Castor fiber) in Britain

This paper re-examines the evidence for the extinction of the beaver (Castor fiber) in South Britain and Scotland. Much of the evidence found by previous scholars is discounted as unreliable or outdated. A new study looks at reliable historical sources and studies references to the beaver in the context of references to comparable mammals, especially the most ecologically comparable [polecat (Mustela putorius), pine marten (Martes martes), otter (Lutra lutra) and badger (Meles meles)]. Each of these mammals was present in every period studied, meaning that medieval authors were reliable witnesses to the species' presence. The beaver is present in comparable numbers to the other mammals in South Britain 1188–1307 and in Scotland 1526–1600, meaning that as a species it was frequently recorded by humans. References to it cease after 1308 in South Britain, except a single anomalous entry, and after 1600 in Scotland. The idea that this reflects a sample bias or random chance is discounted. The paper rejects the late extinction scenario and concludes that the beaver became extinct by 1300 in South Britain and by 1600 in Scotland.     

Reconstruction of the cranial musculature and masticatory function of the Pleistocene panamerican ground sloth Eremotherium laurillardi (Mammalia,Xenarthra, Megatheriidae)

Cranial musculature, dental function and mandibular movement patterns in Eremotherium laurillardi were reconstructed from the examination of crania and dentitions. Size, shape and pattern of muscle divisions were reconstructed from the examination of bony rugosities indicating muscle attachments. Details of masticatory muscle structure and function were based on dissections of the tree sloths Bradypus and Choloepus. Among sloths, masticatory muscles in E. laurillardi demonstrate a different synergist–antagonist pattern, reflecting greater emphasis on mediolateral mandibular movements. Eight cranial character complexes (anterior facial, zygomatic arch, superficial masseter, deep masseter–zygomaticomandibularis, pterygoid, temporal, occipital and occlusal) determined by interrelated contributions of each component made to group functions were identified. An elongate anterior face and predental spout in E. laurillardi allowed protrusion of a long narrow tongue at small degrees of gape, reflecting a probably ancestral xenarthran condition. Gape minimisation, in conjunction with the mediolaterally directed masticatory stroke in E. laurillardi, was a unique solution to increase masticatory efficiency by permitting molariform tooth shearing surfaces to remain in or near occlusion for a greater percentage of each chewing cycle.