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1.  Repeated stressors in adulthood increase the rate of biological ageing 
Frontiers in Zoology  2015;12:4.
Background
Individuals of the same age can differ substantially in the degree to which they have accumulated tissue damage, akin to bodily wear and tear, from past experiences. This accumulated tissue damage reflects the individual’s biological age and may better predict physiological and behavioural performance than the individual‘s chronological age. However, at present it remains unclear how to reliably assess biological age in individual wild vertebrates.
Methods
We exposed hand-raised adult Eurasian blackbirds (Turdus merula) to a combination of repeated immune and disturbance stressors for over one year to determine the effects of chronic stress on potential biomarkers of biological ageing including telomere shortening, oxidative stress load, and glucocorticoid hormones. We also assessed general measures of individual condition including body mass and locomotor activity.
Results
By the end of the experiment, stress-exposed birds showed greater decreases in telomere lengths. Stress-exposed birds also maintained higher circulating levels of oxidative damage compared with control birds. Other potential biomarkers such as concentrations of antioxidants and glucocorticoid hormone traits showed greater resilience and did not differ significantly between treatment groups.
Conclusions
The current data demonstrate that repeated exposure to experimental stressors affects the rate of biological ageing in adult Eurasian blackbirds. Both telomeres and oxidative damage were affected by repeated stress exposure and thus can serve as blood-derived biomarkers of biological ageing.
Electronic supplementary material
The online version of this article (doi:10.1186/s12983-015-0095-z) contains supplementary material, which is available to authorized users.
doi:10.1186/s12983-015-0095-z
PMCID: PMC4336494
Biomarker; Repeated stressors; Eurasian blackbird; Oxidative stress; Glucocorticoid; Telomere
2.  The power of oral and nasal calls to discriminate individual mothers and offspring in red deer, Cervus elaphus 
Frontiers in Zoology  2015;12:2.
Background
In most species, acoustical cues are crucial for mother-offspring recognition. Studies of a few species of ungulates showed that potential for individual recognition may differ between nasal and oral contact calls.
Results
Vocalizations of 28 hinds and 31 calves of farmed Iberian red deer (Cervus elaphus hispanicus) were examined with discriminant function analyses (DFA) to determine whether acoustic structure of their oral and nasal contact calls encodes information about the caller’s identity. Contact calls were elicited by brief separation of individually identified animals by a distance over 10 m or by a bar fence. Both oral and nasal calls of both hinds and calves showed high potential to discriminate individuals. In hinds, individuality was significantly higher in the oral than in the nasal calls, whereas in calves, individuality was equally well expressed in both oral and nasal calls. For calves, the maximum fundamental frequency was higher and the duration was longer in oral calls than in nasal calls. For hinds, the maximum fundamental frequency and the duration were indistinguishable between oral and nasal calls. Compared to the pooled sample of oral and nasal calls, separate oral or nasal call samples provided better classifying accuracy to individual in either hinds or calves. Nevertheless, in both hinds and calves, even in the pooled sample of oral and nasal calls, the degree of individual identity was 2–3 times greater than expected by chance. For hinds that provided calls in both years, cross-validation of calls collected in 2012 with discriminant functions created with calls from 2011 showed a strong decrease of classifying accuracy to individual.
Conclusions
These results suggest different potentials of nasal and oral calls to allow the discrimination of individuals among hinds, but not among red deer calves. The high potential of individual recognition even with the pooled sample of oral and nasal calls allows mother and young to remember only one set of acoustic variables for mutual vocal recognition. Poor between-year stability of individual characteristics of hind oral and nasal calls would require updating keys to individual recognition each calving season.
Electronic supplementary material
The online version of this article (doi:10.1186/s12983-014-0094-5) contains supplementary material, which is available to authorized users.
doi:10.1186/s12983-014-0094-5
PMCID: PMC4301055  PMID: 25610491
Acoustic communication; Individuality; Mother-offspring recognition; Ungulate; Iberian red deer; Cervus elaphus hispanicus; Separation calls
3.  Myoinhibitory peptide regulates feeding in the marine annelid Platynereis 
Frontiers in Zoology  2015;12:1.
Background
During larval settlement and metamorphosis, marine invertebrates undergo changes in habitat, morphology, behavior and physiology. This change between life-cycle stages is often associated with a change in diet or a transition between a non-feeding and a feeding form. How larvae regulate changes in feeding during this life-cycle transition is not well understood. Neuropeptides are known to regulate several aspects of feeding, such as food search, ingestion and digestion. The marine annelid Platynereis dumerilii has a complex life cycle with a pelagic non-feeding larval stage and a benthic feeding postlarval stage, linked by the process of settlement. The conserved neuropeptide myoinhibitory peptide (MIP) is a key regulator of larval settlement behavior in Platynereis. Whether MIP also regulates the initiation of feeding, another aspect of the pelagic-to-benthic transition in Platynereis, is currently unknown.
Results
Here, we explore the contribution of MIP to the regulation of feeding behavior in settled Platynereis postlarvae. We find that in addition to expression in the brain, MIP is expressed in the gut of developing larvae in sensory neurons that densely innervate the hindgut, the foregut, and the midgut. Activating MIP signaling by synthetic neuropeptide addition causes increased gut peristalsis and more frequent pharynx extensions leading to increased food intake. Conversely, morpholino-mediated knockdown of MIP expression inhibits feeding. In the long-term, treatment of Platynereis postlarvae with synthetic MIP increases growth rate and results in earlier cephalic metamorphosis.
Conclusions
Our results show that MIP activates ingestion and gut peristalsis in Platynereis postlarvae. MIP is expressed in enteroendocrine cells of the digestive system suggesting that following larval settlement, feeding may be initiated by a direct sensory-neurosecretory mechanism. This is similar to the mechanism by which MIP induces larval settlement. The pleiotropic roles of MIP may thus have evolved by redeploying the same signaling mechanism in different aspects of a life-cycle transition.
Electronic supplementary material
The online version of this article (doi:10.1186/s12983-014-0093-6) contains supplementary material, which is available to authorized users.
doi:10.1186/s12983-014-0093-6
PMCID: PMC4307165  PMID: 25628752
4.  Transcriptional profiling of reproductive development, lipid storage and molting throughout the last juvenile stage of the marine copepod Calanus finmarchicus 
Frontiers in Zoology  2014;11(1):91.
Introduction
Calanus finmarchicus, a highly abundant copepod that is an important primary consumer in North Atlantic ecosystems, has a flexible life history in which copepods in the last juvenile developmental stage (fifth copepodid, C5) may either delay maturation and enter diapause or molt directly into adults. The factors that regulate this developmental plasticity are poorly understood, and few tools have been developed to assess the physiological condition of individual copepods.
Results
We sampled a cultured population of C. finmarchicus copepods daily throughout the C5 stage and assessed molt stage progression, gonad development and lipid storage. We used high-throughput sequencing to identify genes that were differentially expressed during progression through the molt stage and then used qPCR to profile daily expression of individual genes. Based on expression profiles of twelve genes, samples were statistically clustered into three groups: (1) an early period occurring prior to separation of the cuticle from the epidermis (apolysis) when expression of genes associated with lipid synthesis and transport (FABP and ELOV) and two nuclear receptors (ERR and HR78) was highest, (2) a middle period of rapid change in both gene expression and physiological condition, including local minima and maxima in several nuclear receptors (FTZ-F1, HR38b, and EcR), and (3) a late period when gonads were differentiated and expression of genes associated with molting (Torso-like, HR38a) peaked. The ratio of Torso-like to HR38b strongly differentiated the early and late groups.
Conclusions
This study provides the first dynamic profiles of gene expression anchored with morphological markers of lipid accumulation, development and gonad maturation throughout a copepod molt cycle. Transcriptomic profiling revealed significant changes over the molt cycle in genes with presumed roles in lipid synthesis, molt regulation and gonad development, suggestive of a coupling of these processes in Calanus finmarchicus. Finally, we identified gene expression profiles that strongly differentiate between early and late development within the C5 copepodid stage. We anticipate that these findings and continued development of robust gene expression biomarkers that distinguish between diapause preparation and continuous development will ultimately enable novel studies of the intrinsic and extrinsic factors that govern diapause initiation in Calanus finmarchicus.
Electronic supplementary material
The online version of this article (doi:10.1186/s12983-014-0091-8) contains supplementary material, which is available to authorized users.
doi:10.1186/s12983-014-0091-8
PMCID: PMC4285635  PMID: 25568661
Arthropod; Crustacean; Gene expression; Molt cycle; Transcriptomics
5.  The nervous system of Paludicella articulata - first evidence of a neuroepithelium in a ctenostome ectoproct 
Frontiers in Zoology  2014;11(1):89.
Introduction
Comparatively few data are available concerning the structure of the adult nervous system in the Ectoprocta or Bryozoa. In contrast to all other ectoprocts, the cerebral ganglion of phylactolaemates contains a central fluid-filled lumen surrounded by a neuroepithelium. Preliminary observations have shown a small lumen within the cerebral ganglion of the ctenostome Paludicella articulata. Ctenostome-grade ectoprocts are of phylogenetic relevance since they are considered to have retained ancestral ectoproct features. Therefore, the ctenostome Paludicella articulata was analyzed in order to contribute to the basal neural bauplan of ctenostomes and the Ectoprocta in general.
Results
The presence of a lumen and a neuroepithelial organization of the nerve cells within the cerebral ganglion are confirmed. Four tentacle nerves project from the cerebral ganglion into each tentacle. Three of the tentacle nerves (one abfrontal and two latero-frontal nerves) have an intertentacular origin, whereas the medio-frontal nerve arises from the cerebral ganglion. Six to eight visceral nerves and four tentacle sheath nerves are found to emanate from the cerebral ganglion and innervate the digestive tract and the tentacle sheath, respectively.
Conclusions
The situation in P. articulata corresponds to the situation found in other ctenostomes and supports the notion that four tentacle nerves are the ancestral configuration in Ectoprocta and not six as proposed earlier. The presence of a lumen in the ganglion represents the ancestral state in Ectoprocta which disappears during ontogeny in all except in adult Phylactolaemata and P. articulata. It appears likely that it has been overlooked in earlier studies owing to its small size.
doi:10.1186/s12983-014-0089-2
PMCID: PMC4269932  PMID: 25525454
6.  Opponent familiarity and contest experience jointly influence contest decisions in Kryptolebias marmoratus 
Frontiers in Zoology  2014;11(1):92.
Introduction
Individual recognition and winner/loser effects both play important roles in animal contests, but how their influences are integrated to affect an individual’s contest decisions in combination remains unclear. Individual recognition provides an animal with relatively precise information about its ability to defeat conspecifics that it has fought previously. Winner/loser effects, conversely, rely on sampling information about how an animal’s ability to win compares with those of others in the population. The less precise information causing winner/loser effects should therefore be more useful to an individual facing an unfamiliar opponent. In this study, we used Kryptolebias marmoratus, a hermaphroditic mangrove killifish, to test whether winner/loser effects do depend on opponent familiarity. In addition, as previous studies have shown that subordinates that behave aggressively sometimes suffer post-retreat retaliation from contest winners, we also explored this aspect of contest interaction in K. marmoratus.
Results
In the early stages of a contest, subordinates facing an unfamiliar dominant were more likely to signal their aggressiveness with either gill displays or attacks rather than retreating immediately. A winning experience then increased the likelihood that the most aggressive behavioral pattern the subordinates exhibited would be attacks rather than gill displays, irrespective of their opponents’ familiarity. Dominants that received a losing experience and faced an unfamiliar opponent were less likely than others to launch attacks directly. And subordinates that challenged dominants with more aggressive tactics but still lost received more post-retreat attacks from their dominant opponents.
Conclusions
Subordinates’ contest decisions were influenced by both their contest experience and the familiarity of their opponents, but these influences appeared at different stages of a contest and did not interact significantly with each other. The influence of a losing experience on dominants’ contest decisions, however, did depend on their subordinate opponents’ familiarity. Subordinates and dominants thus appeared to integrate information from the familiarity of their opponents and the outcome of previous contests differently, which warrants further investigation. The higher costs that dominants imposed on subordinates that behaved more aggressively toward them may have been to deter them from either fighting back or challenging them in the future.
doi:10.1186/s12983-014-0092-7
PMCID: PMC4271475  PMID: 25530793
Animal contest; Information; Winner-loser effect; Individual recognition; Familiarity; Kryptolebias marmoratus
7.  Developmental dynamics of myogenesis in the shipworm Lyrodus pedicellatus (Mollusca: Bivalvia) 
Frontiers in Zoology  2014;11(1):90.
Background
The shipworm Lyrodus pedicellatus is a wood-boring bivalve with an unusual vermiform body. Although its larvae are brooded, they retain the general appearance of a typical bivalve veliger-type larva. Here, we describe myogenesis of L. pedicellatus revealed by filamentous actin labelling and discuss the data in a comparative framework in order to test for homologous structures that might be part of the bivalve (larval) muscular ground pattern.
Results
Five major muscle systems were identified: a velum retractor, foot retractor, larval retractor, a distinct mantle musculature and an adductor system. For a short period of larval life, an additional ventral larval retractor is present. Early in development, a velum muscle ring and an oral velum musculature emerge. In late stages the lateral and dorsal mantle musculature, paired finger-shaped muscles, an accessory adductor and a pedal plexus are formed. Similar to other bivalve larvae, L. pedicellatus exhibits three velum retractor muscles, but in contrast to other species, one of them disappears in early stages of L. pedicellatus. The remaining two velum retractors are considerably remodelled during late larval development and are most likely incorporated into the elaborate mantle musculature of the adult.
Conclusions
To our knowledge, this is the first account of any larval retractor system that might contribute to the adult bodyplan of a (conchiferan) mollusk. A comparative analysis shows that a pedal plexus, adductors, a larval velum ring, velum retractors and a ventral larval retractor are commonly found among bivalve larvae, and thus most likely belong to the ground pattern of the bivalve larval musculature.
Electronic supplementary material
The online version of this article (doi:10.1186/s12983-014-0090-9) contains supplementary material, which is available to authorized users.
doi:10.1186/s12983-014-0090-9
PMCID: PMC4282732  PMID: 25558273
Teredinid; Mollusk; Evodevo; Evolution; Ontogeny; Larva; Veliger; Lophotrochozoa
9.  Behavioural response of a migratory songbird to geographic variation in song and morphology 
Frontiers in Zoology  2014;11(1):85.
Introduction
Sexually selected traits contribute substantially to evolutionary diversification, for example by promoting assortative mating. The contributing traits and their relevance for reproductive isolation differ between species. In birds, sexually selected acoustic and visual signals often undergo geographic divergence. Clines in these phenotypes may be used by both sexes in the context of sexual selection and territoriality. The ways conspecifics respond to geographic variation in phenotypes can give insights to possible behavioural barriers, but these may depend on migratory behaviour. We studied a migratory songbird, the Stonechat, and tested its responsiveness to geographic variation in male song and morphology. The traits are acquired differently, with possible implications for population divergence. Song can evolve quickly through cultural transmission, and thus may contribute more to the establishment of geographic variation than inherited morphological traits. We first quantified the diversity of song traits from different populations. We then tested the responses of free-living Stonechats of both sexes to male phenotype with playbacks and decoys, representing local and foreign stimuli derived from a range of distances from the local population.
Results
Both sexes discriminated consistently between stimuli from different populations, responding more strongly to acoustic and morphological traits of local than foreign stimuli. Time to approach increased, and time spent close to the stimuli and number of tail flips decreased consistently with geographic distance of the stimulus from the local population. Discriminatory response behaviour was more consistent for acoustic than for morphological traits. Song traits of the local population differed significantly from those of other populations.
Conclusions
Evaluating an individual’s perception of geographic variation in sexually selected traits is a crucial first step for understanding reproductive isolation mechanisms. We have demonstrated that in both sexes of Stonechats the responsiveness to acoustic and visual signals decreased with increasing geographic distance of stimulus origin. These findings confirm consistent, fine discrimination for both learned song and inherited morphological traits in these migratory birds. Maintenance or further divergence in phenotypic traits could lead to assortative mating, reproductive isolation, and potentially speciation.
Electronic supplementary material
The online version of this article (doi:10.1186/s12983-014-0085-6) contains supplementary material, which is available to authorized users.
doi:10.1186/s12983-014-0085-6
PMCID: PMC4256809  PMID: 25484906
Sexual selection; Population divergence; Reproductive isolation; Phenotypic traits; Geographic clines; Simulated territorial intrusion; Saxicola torquata; Songbird; Behavioural isolation barrier
10.  Evolutionary history of Chaetognatha inferred from molecular and morphological data: a case study for body plan simplification 
Frontiers in Zoology  2014;11(1):84.
Background
Chaetognatha are a phylum of marine carnivorous animals which includes more than 130 extant species. The internal systematics of this group have been intensively debated since it was discovered in the 18th century. While they can be traced back to the earlier Cambrian, they are an extraordinarily homogeneous phylum at the morphological level - a fascinating characteristic that puzzled many a scientist who has tried to clarify their taxonomy. Recent studies which have attempted to reconstruct a phylogeny using molecular data have relied on single gene analyses and a somewhat restricted taxon sampling. Here, we present the first large scale phylogenetic study of Chaetognatha based on a combined analysis of nearly the complete ribosomal RNA (rRNA) genes. We use this analysis to infer the evolution of some morphological characters. This work includes 36 extant species, mainly obtained from Tara Oceans Expedition 2009/2012, that represent 16 genera and 6 of the 9 extant families.
Results
Cladistic and phenetic analysis of morphological characters, geometric morphometrics and molecular small subunit (SSU rRNA) and large subunit (LSU rRNA) ribosomal genes phylogenies provided new insights into the relationships and the evolutionary history of Chaetognatha. We propose the following clade structure for the phylum: (((Sagittidae, Krohnittidae), Spadellidae), (Eukrohniidae, Heterokrohniidae)), with the Pterosagittidae included in the Sagittidae. The clade (Sagittidae, Krohnittidae) constitutes the monophyletic order of Aphragmophora. Molecular analyses showed that the Phragmophora are paraphyletic. The Ctenodontina/Flabellodontina and Syngonata/Chorismogonata hypotheses are invalidated on the basis of both morphological and molecular data. This new phylogeny also includes resurrected and modified genera within Sagittidae.
Conclusions
The distribution of some morphological characters traditionally used in systematics and for species diagnosis suggests that the diversity in Chaetognatha was produced through a process of mosaic evolution. Moreover, chaetognaths have mostly evolved by simplification of their body plan and their history shows numerous convergent events of losses and reversions. The main morphological novelty observed is the acquisition of a second pair of lateral fins in Sagittidae, which represents an adaptation to the holoplanktonic niche.
Electronic supplementary material
The online version of this article (doi:10.1186/s12983-014-0084-7) contains supplementary material, which is available to authorized users.
doi:10.1186/s12983-014-0084-7
PMCID: PMC4254178  PMID: 25473413
Chaetognatha; Phylogenetics; Systematics; Procrustes surimposition; Homoplasy; Body plan simplification
11.  The role of osmotic stress transcription factor 1 in fishes 
Frontiers in Zoology  2014;11(1):86.
Osmotic stress transcription factor 1 (Ostf1) was first discovered by subtractive hybridization in the gills of Mozambique tilapia (Oreochromis mossambicus) transferred from fresh water (FW) to seawater (SW). It is a putative transcriptional regulator and the “early hyperosmotic regulated protein”. In the 2 hours after FW to SW transfer, ostf1 mRNA levels increase six fold. It is believed that, as a fast-response gene, Ostf1 plays a critical role in fish osmoregulation. Since its discovery, numerous studies have been performed to understand the nature and osmoregulatory mechanism of Ostf1. A decade has passed since the discovery of Ostf1, and it is a good time to summarize our current understanding of this gene. Different fish models have been used to study Ostf1, which is not limited to the traditional euryhaline fishes, such as eels and tilapia. Ostf1 can be found in modern fish models such as medaka and zebrafish. This review covers and summarizes the findings from different fishes, and provides a perspective for future Ostf1 studies.
doi:10.1186/s12983-014-0086-5
PMCID: PMC4240841  PMID: 25419222
Gill; Osmoregulation; Osmosensing; Osmotic stress
12.  FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies 
Frontiers in Zoology  2014;11(1):81.
Background
Phylogenetic and population genetic studies often deal with multiple sequence alignments that require manipulation or processing steps such as sequence concatenation, sequence renaming, sequence translation or consensus sequence generation. In recent years phylogenetic data sets have expanded from single genes to genome wide markers comprising hundreds to thousands of loci. Processing of these large phylogenomic data sets is impracticable without using automated process pipelines. Currently no stand-alone or pipeline compatible program exists that offers a broad range of manipulation and processing steps for multiple sequence alignments in a single process run.
Results
Here we present FASconCAT-G, a system independent editor, which offers various processing options for multiple sequence alignments. The software provides a wide range of possibilities to edit and concatenate multiple nucleotide, amino acid, and structure sequence alignment files for phylogenetic and population genetic purposes. The main options include sequence renaming, file format conversion, sequence translation between nucleotide and amino acid states, consensus generation of specific sequence blocks, sequence concatenation, model selection of amino acid replacement with ProtTest, two types of RY coding as well as site exclusions and extraction of parsimony informative sites. Convieniently, most options can be invoked in combination and performed during a single process run. Additionally, FASconCAT-G prints useful information regarding alignment characteristics and editing processes such as base compositions of single in- and outfiles, sequence areas in a concatenated supermatrix, as well as paired stem and loop regions in secondary structure sequence strings.
Conclusions
FASconCAT-G is a command-line driven Perl program that delivers computationally fast and user-friendly processing of multiple sequence alignments for phylogenetic and population genetic applications and is well suited for incorporation into analysis pipelines.
Electronic supplementary material
The online version of this article (doi:10.1186/s12983-014-0081-x) contains supplementary material, which is available to authorized users.
doi:10.1186/s12983-014-0081-x
PMCID: PMC4243772  PMID: 25426157
Multiple sequence alignment; Phylogenetic reconstruction; Sequence processing; Consensus sequence; Sequence translation; Sequence concatenation; File format conversion
13.  Sensing deep extreme environments: the receptor cell types, brain centers, and multi-layer neural packaging of hydrothermal vent endemic worms 
Frontiers in Zoology  2014;11(1):82.
Introduction
Deep-sea alvinellid worm species endemic to hydrothermal vents, such as Alvinella and Paralvinella, are considered to be among the most thermotolerant animals known with their adaptability to toxic heavy metals, and tolerance of highly reductive and oxidative stressful environments. Despite the number of recent studies focused on their overall transcriptomic, proteomic, and metabolic stabilities, little is known regarding their sensory receptor cells and electrically active neuro-processing centers, and how these can tolerate and function in such harsh conditions.
Results
We examined the extra- and intracellular organizations of the epidermal ciliated sensory cells and their higher centers in the central nervous system through immunocytochemical, ultrastructural, and neurotracing analyses. We observed that these cells were rich in mitochondria and possessed many electron-dense granules, and identified specialized glial cells and serial myelin-like repeats in the head sensory systems of Paralvinella hessleri. Additionally, we identified the major epidermal sensory pathways, in which a pair of distinct mushroom bodies-like or small interneuron clusters was observed. These sensory learning and memory systems are commonly found in insects and annelids, but the alvinellid inputs are unlikely derived from the sensory ciliary cells of the dorsal head regions.
Conclusions
Our evidence provides insight into the cellular and system-wide adaptive structure used to sense, process, and combat the deep-sea hydrothermal vent environment. The alvinellid sensory cells exhibit characteristics of annelid ciliary types, and among the most unique features were the head sensory inputs and structure of the neural cell bodies of the brain, which were surrounded by multiple membranes. We speculated that such enhanced protection is required for the production of normal electrical signals, and to avoid the breakdown of the membrane surrounding metabolically fragile neurons from oxidative stress. Such pivotal acquisition is not broadly found in the all body parts, suggesting the head sensory inputs are specific, and these heterogenetic protection mechanisms may be present in alvinellid worms.
Electronic supplementary material
The online version of this article (doi:10.1186/s12983-014-0082-9) contains supplementary material, which is available to authorized users.
doi:10.1186/s12983-014-0082-9
PMCID: PMC4261566  PMID: 25505488
Deep-sea; Sensory cells; Brain; Nervous system; Glia; Annelids; Evolution
14.  Song characteristics track bill morphology along a gradient of urbanization in house finches (Haemorhous mexicanus) 
Frontiers in Zoology  2014;11(1):83.
Introduction
Urbanization can considerably impact animal ecology, evolution, and behavior. Among the new conditions that animals experience in cities is anthropogenic noise, which can limit the sound space available for animals to communicate using acoustic signals. Some urban bird species increase their song frequencies so that they can be heard above low-frequency background city noise. However, the ability to make such song modifications may be constrained by several morphological factors, including bill gape, size, and shape, thereby limiting the degree to which certain species can vocally adapt to urban settings. We examined the relationship between song characteristics and bill morphology in a species (the house finch, Haemorhous mexicanus) where both vocal performance and bill size are known to differ between city and rural animals.
Results
We found that bills were longer and narrower in more disturbed, urban areas. We observed an increase in minimum song frequency of urban birds, and we also found that the upper frequency limit of songs decreased in direct relation to bill morphology.
Conclusions
These findings are consistent with the hypothesis that birds with longer beaks and therefore longer vocal tracts sing songs with lower maximum frequencies because longer tubes have lower-frequency resonances. Thus, for the first time, we reveal dual constraints (one biotic, one abiotic) on the song frequency range of urban animals. Urban foraging pressures may additionally interact with the acoustic environment to shape bill traits and vocal performance.
Electronic supplementary material
The online version of this article (doi:10.1186/s12983-014-0083-8) contains supplementary material, which is available to authorized users.
doi:10.1186/s12983-014-0083-8
PMCID: PMC4243808  PMID: 25426158
Urban impacts; Bill shape; Singing behavior; Noise pollution; Vocal communication
15.  Reproductive responses of birds to experimental food supplementation: a meta-analysis 
Frontiers in Zoology  2014;11(1):80.
Introduction
Food availability is an important environmental cue for animals for deciding how much to invest in reproduction, and it ultimately affects population size. The importance of food limitation has been extensively studied in terrestrial vertebrate populations, especially in birds, by experimentally manipulating food supply. However, the factors explaining variation in reproductive decisions in response to food supplementation remain unclear. By performing meta-analyses, we aim to quantify the extent to which supplementary feeding affects several reproductive parameters in birds, and identify the key factors (life-history traits, behavioural factors, environmental factors, and experimental design) that can induce variation in laying date, clutch size and breeding success (i.e., number of fledglings produced) in response to food supplementation.
Results
Food supplementation produced variable but mostly positive effects across reproductive parameters in a total of 201 experiments from 82 independent studies. The outcomes of the food effect were modulated by environmental factors, e.g., laying dates advanced more towards low latitudes, and food supplementation appeared not to produce any obvious effect on bird reproduction when the background level of food abundance in the environment was high. Moreover, the increase in clutch size following food addition was more pronounced in birds that cache food, as compared to birds that do not. Supplementation timing was identified as a major cause of variation in breeding success responses. We also document the absence of a detectable food effect on clutch size and breeding success when the target species had poor access to the feed due to competitive interactions with other animals.
Conclusions
Our findings indicate that, from the pool of bird species and environments reviewed, extra food is allocated to immediate reproduction in most cases. Our results also support the view that bird species have evolved different life-history strategies to cope with environmental variability in food supply. However, we encourage more research at low latitudes to gain knowledge on how resource allocation in birds changes along a latitudinal gradient. Our results also emphasize the importance of developing experimental designs that minimise competition for the supplemented food and the risk of reproductive bottle-necks due to inappropriate supplementation timings.
Electronic supplementary material
The online version of this article (doi:10.1186/s12983-014-0080-y) contains supplementary material, which is available to authorized users.
doi:10.1186/s12983-014-0080-y
PMCID: PMC4222371  PMID: 25386221
Effect size; Feeding experiment; Population regulation; Reproductive performance; Resource competition; Wildlife management
16.  Differentiated adaptive evolution, episodic relaxation of selective constraints, and pseudogenization of umami and sweet taste genes TAS1Rs in catarrhine primates 
Frontiers in Zoology  2014;11(1):79.
Background
Umami and sweet tastes are two important basic taste perceptions that allow animals to recognize diets with nutritious carbohydrates and proteins, respectively. Until recently, analyses of umami and sweet taste were performed on various domestic and wild animals. While most of these studies focused on the pseudogenization of taste genes, which occur mostly in carnivores and species with absolute feeding specialization, omnivores and herbivores were more or less neglected. Catarrhine primates are a group of herbivorous animals (feeding mostly on plants) with significant divergence in dietary preference, especially the specialized folivorous Colobinae. Here, we conducted the most comprehensive investigation to date of selection pressure on sweet and umami taste genes (TAS1Rs) in catarrhine primates to test whether specific adaptive evolution occurred during their diversification, in association with particular plant diets.
Results
We documented significant relaxation of selective constraints on sweet taste gene TAS1R2 in the ancestral branch of Colobinae, which might correlate with their unique ingestion and digestion of leaves. Additionally, we identified positive selection acting on Cercopithecidae lineages for the umami taste gene TAS1R1, on the Cercopithecinae and extant Colobinae and Hylobatidae lineages for TAS1R2, and on Macaca lineages for TAS1R3. Our research further identified several site mutations in Cercopithecidae, Colobinae and Pygathrix, which were detected by previous studies altering the sensitivity of receptors. The positively selected sites were located mostly on the extra-cellular region of TAS1Rs. Among these positively selected sites, two vital sites for TAS1R1 and four vital sites for TAS1R2 in extra-cellular region were identified as being responsible for the binding of certain sweet and umami taste molecules through molecular modelling and docking.
Conclusions
Our results suggest that episodic and differentiated adaptive evolution of TAS1Rs pervasively occurred in catarrhine primates, most concentrated upon the extra-cellular region of TAS1Rs.
Electronic supplementary material
The online version of this article (doi:10.1186/s12983-014-0079-4) contains supplementary material, which is available to authorized users.
doi:10.1186/s12983-014-0079-4
PMCID: PMC4226867  PMID: 25389445
Catarrhine primates; TAS1Rs; Adaptive evolution; Positive selection; Episodic relaxation of selective constraints; Pseudogenization
17.  Unveiling the factors shaping the distribution of widely distributed alpine vertebrates, using multi-scale ecological niche modelling of the bat Plecotus macrobullaris 
Frontiers in Zoology  2014;11(1):77.
Several alpine vertebrates share a distribution pattern that extends across the South-western Palearctic but is limited to the main mountain massifs. Although they are usually regarded as cold-adapted species, the range of many alpine vertebrates also includes relatively warm areas, suggesting that factors beyond climatic conditions may be driving their distribution. In this work we first recognize the species belonging to the mentioned biogeographic group and, based on the environmental niche analysis of Plecotus macrobullaris, we identify and characterize the environmental factors constraining their ranges. Distribution overlap analysis of 504 European vertebrates was done using the Sorensen Similarity Index, and we identified four birds and one mammal that share the distribution with P. macrobullaris. We generated 135 environmental niche models including different variable combinations and regularization values for P. macrobullaris at two different scales and resolutions. After selecting the best models, we observed that topographic variables outperformed climatic predictors, and the abruptness of the landscape showed better predictive ability than elevation. The best explanatory climatic variable was mean summer temperature, which showed that P. macrobullaris is able to cope with mean temperature ranges spanning up to 16°C. The models showed that the distribution of P. macrobullaris is mainly shaped by topographic factors that provide rock-abundant and open-space habitats rather than climatic determinants, and that the species is not a cold-adapted, but rather a cold-tolerant eurithermic organism. P. macrobullaris shares its distribution pattern as well as several ecological features with five other alpine vertebrates, suggesting that the conclusions obtained from this study might be extensible to them. We concluded that rock-dwelling and open-space foraging vertebrates with broad temperature tolerance are the best candidates to show wide alpine distribution in the Western Palearctic.
Electronic supplementary material
The online version of this article (doi:10.1186/s12983-014-0077-6) contains supplementary material, which is available to authorized users.
doi:10.1186/s12983-014-0077-6
PMCID: PMC4226887  PMID: 25389444
Alpine distribution; Alpine long-eared bat; Biogeography; Chiroptera; Distribution; Modelling; Mountain long-eared bat; Zoogeography
18.  The role of juvenile hormone in dominance behavior, reproduction and cuticular pheromone signaling in the caste-flexible epiponine wasp, Synoeca surinama 
Frontiers in Zoology  2014;11(1):78.
Background
The popular view on insect sociality is that of a harmonious division of labor among two morphologically distinct and functionally non-overlapping castes. But this is a highly derived state and not a prerequisite for a functional society. Rather, caste-flexibility is a central feature in many eusocial wasps, where adult females have the potential to become queens or workers, depending on the social environment. In non-swarming paper wasps (e.g., Polistes), prospective queens fight one another to assert their dominance, with losers becoming workers if they remain on the nest. This aggression is fueled by juvenile hormone (JH) and ecdysteroids, major factors involved in caste differentiation in most eusocial insects. We tested whether these hormones have conserved aggression-promoting functions in Synoeca surinama, a caste-flexible swarm-founding wasp (Epiponini) where reproductive competition is high and aggressive displays are common.
Results
We observed the behavioral interactions of S. surinama females in field nests before and after we had removed the egg-laying queen(s). We measured the ovarian reproductive status, hemolymph JH and ecdysteroid titers, ovarian ecdysteroid content, and analyzed the cuticular hydrocarbon (CHC) composition of females engaged in competitive interactions in both queenright and queenless contexts. These data, in combination with hormone manipulation experiments, revealed that neither JH nor ecdysteroids are necessary for the expression of dominance behaviors in S. surinama. Instead, we show that JH likely functions as a gonadotropin and directly modifies the cuticular hydrocarbon blend of young workers to match that of a reproductive. Hemolymph ecdysteroids, in contrast, are not different between queens and workers despite great differences in ovarian ecdysteroid content.
Conclusions
The endocrine profile of S. surinama shows surprising differences from those of other caste-flexible wasps, although a rise in JH titers in replacement queens is a common theme. Extensive remodeling of hormone functions is also evident in the highly eusocial bees, which has been attributed to the evolution of morphologically defined castes. Our results show that hormones which regulate caste-plasticity can lose these roles even while caste-plasticity is preserved.
Electronic supplementary material
The online version of this article (doi:10.1186/s12983-014-0078-5) contains supplementary material, which is available to authorized users.
doi:10.1186/s12983-014-0078-5
PMCID: PMC4219083  PMID: 25371699
Cuticular hydrocarbons; Ecdysteroids; Endocrine; Epiponini; Juvenile hormone; Swarm founding; Wasps
19.  Shifty salamanders: transient trophic polymorphism and cannibalism within natural populations of larval ambystomatid salamanders 
Frontiers in Zoology  2014;11(1):76.
Introduction
Many species of ambystomatid salamanders are dependent upon highly variable temporary wetlands for larval development. High larval densities may prompt the expression of a distinct head morphology that may facilitate cannibalism. However, few studies have characterized structural cannibalism within natural populations of larval salamanders. In this study we used two species of larval salamanders, long-toed (Ambystoma macrodactylum) and ringed salamanders (A. annulatum). Head morphometrics and stable isotopic values of carbon (δ13C) and nitrogen (δ15N) were used to identify the presence or absence of structural cannibalism. Weather conditions were also analyzed as a potential factor associated with the expression of cannibalistic morphology.
Results
Populations of salamander larvae did not consistently exhibit cannibalistic morphologies throughout collection periods. Larval long-toed salamanders exhibited trophic polymorphisms when relatively lower precipitation amounts were observed. Larval ringed salamanders were observed to be cannibalistic but did not exhibit polymorphisms in this study.
Conclusions
Structural cannibalism may be transient in both species; however in long-toed salamanders this morphology is necessary for cannibalism. Ringed salamanders can be cannibalistic without morphological adaptations; however the cannibal morph may prolong the viable time period for cannibalism. Additionally, weather conditions may alter pond hydroperiod, subsequently influencing head morphology and cannibalism.
doi:10.1186/s12983-014-0076-7
PMCID: PMC4203864  PMID: 25337147
Cannibalism; Larval salamander; Carbon-13; Trophic polymorphism; Nitrogen-15; Stable isotope
20.  Detailed reconstruction of the musculature in Limnognathia maerski (Micrognathozoa) and comparison with other Gnathifera 
Frontiers in Zoology  2014;11:71.
Introduction
Limnognathia maerski is the single species of the recently described taxon, Micrognathozoa. The most conspicuous character of this animal is the complex set of jaws, which resembles an even more intricate version of the trophi of Rotifera and the jaws of Gnathostomulida. Whereas the jaws of Limnognathia maerski previously have been subject to close examinations, the related musculature and other organ systems are far less studied. Here we provide a detailed study of the body and jaw musculature of Limnognathia maerski, employing confocal laser scanning microscopy of phalloidin stained musculature as well as transmission electron microscopy (TEM).
Results
This study reveals a complex body wall musculature, comprising six pairs of main longitudinal muscles and 13 pairs of trunk dorso-ventral muscles. Most longitudinal muscles span the length of the body and some fibers even branch off and continue anteriorly into the head and posteriorly into the abdomen, forming a complex musculature. The musculature of the jaw apparatus shows several pairs of striated muscles largely related to the fibularium and the main jaws. The jaw articulation and function of major and minor muscle pairs are discussed. No circular muscles or intestinal musculature have been found, but some newly discovered muscles may supply the anal opening.
Conclusions
The organization in Limnognathia maerski of the longitudinal and dorso-ventral muscle bundles in a loose grid is more similar to the organization found in rotifers rather than gnathostomulids. Although the dorso-ventral musculature is probably not homologous to the circular muscles of rotifers, a similar function in body extension is suggested. Additionally, a functional comparison between the jaw musculature of Limnognathia maerski, Rotifera and Gnathostomulida, emphasizes the important role of the fibularium in Limnognathia maerski, and suggests a closer functional resemblance to the jaw organization in Rotifera.
doi:10.1186/s12983-014-0071-z
PMCID: PMC4333266
CLSM; 3D reconstructions; Jaw apparatus; F-actin; Trophi; Mastax
21.  Overcoming the fragility – X-ray computed micro-tomography elucidates brachiopod endoskeletons 
Frontiers in Zoology  2014;11(1):65.
Introduction
The calcareous shells of brachiopods offer a wealth of informative characters for taxonomic and phylogenetic investigations. In particular scanning electron microscopy (SEM) has been used for decades to visualise internal structures of the shell. However, to produce informative SEM data, brachiopod shells need to be opened after chemical removal of the soft tissue. This preparation occasionally damages the shell. Additionally, skeletal elements of taxonomic/systematic interest such as calcareous spicules which are loosely embedded in the lophophore and mantle connective tissue become disintegrated during the preparation process.
Results
Using a nondestructive micro-computed tomography (μCT) approach, the entire fragile endoskeleton of brachiopods is documented for the first time. New insights on the structure and position of tissue-bound skeletal elements (spicules) are given as add ons to existing descriptions of brachiopod shell anatomy, thereby enhancing the quality and quantity of informative characters needed for both taxonomic and phylogenetic studies. Here, we present five modern, articulated brachiopods (Rectocalathis schemmgregoryi n. gen., n. sp., Eucalathis sp., Gryphus vitreus, Liothyrella neozelanica and Terebratulina retusa) that were X-rayed using a Phoenix Nanotom XS 180 NF. We provide links to download 3D models of these species, and additional five species with spicules can be accessed in the Supplemental Material. In total, 17 brachiopod genera covering all modern articulated subgroups and 2 inarticulated genera were X-rayed for morphological analysis. Rectocalathis schemmgregoryi n. gen., n. sp. is fully described.
Conclusion
Micro-CT is an excellent non-destructive tool for investigating calcified structures in the exo- and endoskeletons of brachiopods. With high quality images and interactive 3D models, this study provides a comprehensive description of the profound differences in shell anatomy, facilitates the detection of new delicate morphological characters of the endoskeleton and gives new insights into the body plan of modern brachiopods.
Electronic supplementary material
The online version of this article (doi:10.1186/s12983-014-0065-x) contains supplementary material, which is available to authorized users.
doi:10.1186/s12983-014-0065-x
PMCID: PMC4312452  PMID: 25642279
Brachiopoda; Endoskeleton; Spicules; X-ray; Micro-computed tomography (μCT); Interactive 3D model; Rectocalathis schemmgregoryi n. gen., n. sp.
22.  Reproductive cessation and post-reproductive lifespan in Asian elephants and pre-industrial humans 
Frontiers in Zoology  2014;11:54.
Introduction
Short post-reproductive lifespan is widespread across species, but prolonged post-reproductive life-stages of potential adaptive significance have been reported only in few mammals with extreme longevity. Long post-reproductive lifespan contradicts classical evolutionary predictions of simultaneous senescence in survival and reproduction, and raises the question of whether extreme longevity in mammals promotes such a life-history. Among terrestrial mammals, elephants share the features with great apes and humans, of having long lifespan and offspring with long dependency. However, little data exists on the frequency of post-reproductive lifespan in elephants. Here we use extensive demographic records on semi-captive Asian elephants (n = 1040) and genealogical data on pre-industrial women (n = 5336) to provide the first comparisons of age-specific reproduction, survival and post-reproductive lifespan in both of these long-lived species.
Results
We found that fertility decreased after age 50 in elephants, but the pattern differed from a total loss of fertility in menopausal women with many elephants continuing to reproduce at least until the age of 65 years. The probability of entering a non-reproductive state increased steadily in elephants from the earliest age of reproduction until age 65, with the longer living elephants continuing to reproduce until older ages, in contrast to humans whose termination probability increased rapidly after age 35 and reached 1 at 56 years, but did not depend on longevity. Post-reproductive lifespan reached 11–17 years in elephants and 26–27 years in humans living until old age (depending on method), but whereas half of human adult lifespan (of those reproductive females surviving to the age of 5% fecundity) was spent as post-reproductive, only one eighth was in elephants. Consequently, although some elephants have long post-reproductive lifespans, relatively few individuals reach such a phase and the decline in fertility generally parallels declines in survivorship in contrast to humans with a decoupling of senescence in somatic and reproductive functions.
Conclusions
Our results show that the reproductive and survival patterns of Asian elephants differ from other long-lived animals exhibiting menopause, such as humans, and extreme longevity alone does not promote the evolution of menopause or post-reproductive lifespan, adding weight to the unusual kin-selected benefits suggested to favour such traits in humans and killer whales.
doi:10.1186/s12983-014-0054-0
PMCID: PMC4144032  PMID: 25183990
Ageing; Age-specific fertility; Reproduction; Senescence; Survival
23.  No evidence for assortative mating within a willow warbler migratory divide 
Frontiers in Zoology  2014;11:52.
Introduction
In contact zones, genetic mixing of two taxa can be restricted by prezygotic (e.g. assortative mating) or postzygotic (lower fitness of hybrid offspring) barriers, or a combination of the two. A hybrid zone between two willow warbler subspecies (Phylloscopus trochilus trochilus, P. t. acredula) with distinctive migratory strategies occurs in central Sweden. These subspecies exhibit differences in migratory direction and distance, resulting in geographically distinct wintering areas in Africa. The subspecies may have diverged from a common refuge after the last ice age, and neutral genetic markers are homogeneous across their range. By contrast, several phenotypic traits and genetic markers of two chromosomal regions previously identified show steep clines across the divide. The evolutionary forces that maintain this migratory divide remain unknown. Here we use plumage colour, morphology, genetic markers and feather stable nitrogen-isotopes (δ15N) to assess if assortative mating between migratory phenotypes could be acting as a possible mechanism for keeping the two forms genetically separate and maintaining the migratory divide. We colour-ringed a willow warbler breeding population in the central part of the hybrid zone and observed the breeding population to assess phenotypic and genotypic traits of social pairs.
Results
Our data suggest that wintering area and genetic ancestry had an effect on male arrival time to the breeding grounds which could contribute to assortment. However, evidence for assortative mating could not be detected based on a comparison of plumage colour, morphology and δ15N between social mates.
Conclusion
This finding was strengthened by analyses of subspecies-specific genetic markers, which allowed us to identify the presence of a large proportion of potential hybrids and backcrosses at the study site. Our results supported the hypothesis that pre-mating isolation in willow warblers is weak, resulting in extensive hybridisation across the migratory divide.
doi:10.1186/s12983-014-0052-2
PMCID: PMC4105873  PMID: 25053967
Hybrid zone; Prezygotic selection; Postzygotic selection; Reproductive isolation; Willow warbler; Phylloscopus trochilus; Nitrogen-15
24.  Development and juvenile anatomy of the nemertodermatid Meara stichopi (Bock) Westblad 1949 (Acoelomorpha) 
Frontiers in Zoology  2014;11:50.
Introduction
Nemertodermatida is the sister group of the Acoela, which together form the Acoelomorpha, a taxon that comprises bilaterally symmetric, small aquatic worms. While there are several descriptions of the embryology of acoel species, descriptions of nemertodermatid development are scarce. To be able to reconstruct the ground pattern of the Acoelomorpha it is crucial to gain more information about the development of several nemertodermatid species. Here we describe the development of the nemertodermatid Meara stichopi using light and fluorescent microscopic methods.
Results
We have collected Meara stichopi during several seasons and reconstruct the complex annual reproductive cycle dependent on the sea cucumber Parastichopus tremulus. Using common fluorescent markers for musculature (BODIPY FL-phallacidin) and neurons (antibodies against FMRFamide, serotonin, tyrosinated-tubulin) and live imaging techniques, we followed embryogenesis which takes approximately 9–10 weeks. The cleavage pattern is stereotypic up to the 16-cell stage. Ring- and longitudinal musculature start to develop during week 6, followed by the formation of the basiepidermal nervous system. The juvenile is hatching without mouth opening and has a basiepidermal nerve net with two dorsal neurite bundles and an anterior condensation.
Conclusions
The development of Meara stichopi differs from the development of Acoela in that it is less stereotypic and does not follow the typical acoel duet cleavage program. During late development Meara stichopi does not show a temporal anterior to posterior gradient during muscle and nervous system formation.
doi:10.1186/1742-9994-11-50
PMCID: PMC4094782  PMID: 25024737
Nemertodermatida; Acoelomorpha; Development; Muscle development; Neurogenesis; Cleavage; Cell lineage
25.  Are antimicrobial defences in bird eggs related to climatic conditions associated with risk of trans-shell microbial infection? 
Frontiers in Zoology  2014;11:49.
Introduction
All bird eggs are exposed to microbes in the environment, which if transmitted to the developing embryo, could cause hatching failure. However, the risk of trans-shell infection varies with environmental conditions and is higher for eggs laid in wetter environments. This might relate to generally higher microbial abundances and diversity in more humid environments, including on the surface of eggshells, as well as the need for moisture to facilitate microbial penetration of the eggshell. To protect against microbial infection, the albumen of avian eggs contains antimicrobial proteins, including lysozyme and ovotransferrin. We tested whether lysozyme and ovotransferrin activities varied in eggs of larks (Alaudidae) living along an arid-mesic gradient of environmental aridity, which we used as a proxy for risk of trans-shell infection.
Results
Contrary to expectations, lysozyme activity was highest in eggs from hotter, more arid locations, where we predicted the risk of trans-shell infection would be lower. Ovotransferrin concentrations did not vary with climatic factors. Temperature was a much better predictor of antimicrobial protein activity than precipitation, a result inconsistent with studies stressing the importance of moisture for trans-shell infection.
Conclusions
Our study raises interesting questions about the links between temperature and lysozyme activity in eggs, but we find no support for the hypothesis that antimicrobial protein deposition is higher in eggs laid in wetter environments.
doi:10.1186/1742-9994-11-49
PMCID: PMC4107615  PMID: 25057281
Antimicrobial; Aridity; Humidity; Egg albumen; Lark; Lysozyme; Ovotransferrin

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