Lionfish (Pterois spp.) invade the upper-bathyal zone in the western Atlantic
Non-native lionfish have been recorded throughout the western Atlantic on both shallow and mesophotic reefs, where they have been linked to declines in reef health. In this study we report the first lionfish observations from the deep sea (>200 m) in Bermuda and Roatan, Honduras, with lionfish observed to a maximum depth of 304 m off the Bermuda platform, and 250 m off West End, Roatan. Placed in the context of other deeper lionfish observations and records, our results imply that lionfish may be present in the 200–300 m depth range of the upper-bathyal zone across many locations in the western Atlantic, but currently are under-sampled compared to shallow habitats. We highlight the need for considering deep-sea lionfish populations in future invasive lionfish management.
Gress et al. (2017) Lionfish (Pterois spp.) invade the upper-bathyal zone in the western Atlantic. PeerJ 5:e3683 https://doi.org/10.7717/peerj.3683
Energetics and evasion dynamics of large predators and prey: pumas vs. hounds
Quantification of fine-scale movement, performance, and energetics of hunting by large carnivores is critical for understanding the physiological underpinnings of trophic interactions. This is particularly challenging for wide-ranging terrestrial canid and felid predators, which can each affect ecosystem structure through distinct hunting modes. To compare free-ranging pursuit and escape performance from group-hunting and solitary predators in unprecedented detail, we calibrated and deployed accelerometer-GPS collars during predator-prey chase sequences using packs of hound dogs (Canis lupus familiaris, 26 kg, n = 4–5 per chase) pursuing simultaneously instrumented solitary pumas (Puma concolor, 60 kg, n = 2). We then reconstructed chase paths, speed and turning angle profiles, and energy demands for hounds and pumas to examine performance and physiological constraints associated with cursorial and cryptic hunting modes, respectively. Interaction dynamics revealed how pumas successfully utilized terrain (e.g., fleeing up steep, wooded hillsides) as well as evasive maneuvers (e.g., jumping into trees, running in figure-8 patterns) to increase their escape distance from the overall faster hounds (avg. 2.3× faster). These adaptive strategies were essential to evasion in light of the mean 1.6× higher mass-specific energetic costs of the chase for pumas compared to hounds (mean: 0.76 vs. 1.29 kJ kg−1 min−1, respectively). On an instantaneous basis, escapes were more costly for pumas, requiring exercise at ≥90% of predicted $\dot {\mathrm{V }}{\mathrm{O}}_{2\mathrm{MAX}}$ V ̇ O 2 MAX and consuming as much energy per minute as approximately 5 min of active hunting. Our results demonstrate the marked investment of energy for evasion by a large, solitary carnivore and the advantage of dynamic maneuvers to postpone being overtaken by group-hunting canids.
Bryce et al. (2017) Energetics and evasion dynamics of large predators and prey: pumas vs. hounds. PeerJ 5:e3701 https://doi.org/10.7717/peerj.3701
Diversity, abundance, and host relationships of avian malaria and related haemosporidians in New Mexico pine forests
Avian malaria and related haemosporidian parasites (genera Haemoproteus, Plasmodium, and Leucocytozoon) affect bird demography, species range limits, and community structure, yet they remain unsurveyed in most bird communities and populations. We conducted a community-level survey of these vector-transmitted parasites in New Mexico, USA, to describe their diversity, abundance, and host associations. We focused on the breeding-bird community in the transition zone between piñon-juniper woodland and ponderosa pine forests (elevational range: 2,150–2,460 m). We screened 186 birds representing 49 species using both standard PCR and microscopy techniques to detect infections of all three avian haemosporidian genera. We detected infections in 68 out of 186 birds (36.6%), the highest proportion of which were infected with Haemoproteus (20.9%), followed by Leucocytozoon (13.4%), then Plasmodium (8.0%). We sequenced mtDNA for 77 infections representing 43 haplotypes (25 Haemoproteus, 12 Leucocytozoon, 6 Plasmodium). When compared to all previously known haplotypes in the MalAvi and GenBank databases, 63% (27) of the haplotypes we recovered were novel. We found evidence for host specificity at the avian clade and species level, but this specificity was variable among parasite genera, in that Haemoproteus and Leucocytozoon were each restricted to three avian groups (out of six), while Plasmodium occurred in all groups except non-passerines. We found striking variation in infection rate among host species, with nearly universal infection among vireos and no infection among nuthatches. Using rarefaction and extrapolation, we estimated the total avian haemosporidian diversity to be 70 haplotypes (95% CI [43–98]); thus, we may have already sampled ∼60% of the diversity of avian haemosporidians in New Mexico pine forests. It is possible that future studies will find higher diversity in microhabitats or host species that are under-sampled or unsampled in the present study. Fortunately, this study is fully extendable via voucher specimens, frozen tissues, blood smears, parasite images, and documentation provided in open-access databases (MalAvi, GenBank, and ARCTOS).
Marroquin-Flores et al. (2017) Diversity, abundance, and host relationships of avian malaria and related haemosporidians in New Mexico pine forests. PeerJ 5:e3700 https://doi.org/10.7717/peerj.3700
Diversity of compounds in femoral secretions of Galápagos iguanas (genera: Amblyrhynchus and Conolophus), and their potential role in sexual communication in lek-mating marine iguanas (Amblyrhynchus cristatus)
Background Chemical signals are widely used in the animal kingdom, enabling communication in various social contexts, including mate selection and the establishment of dominance. Femoral glands, which produce and release waxy secretions into the environment, are organs of central importance in lizard chemical communication. The Galápagos marine iguana (Amblyrhynchus cristatus) is a squamate reptile with a lek-mating system. Although the lekking behaviour of marine iguanas has been well-studied, their potential for sexual communication via chemical cues has not yet been investigated. Here we describe the diversity of the lipophilic fraction of males’ femoral gland secretions among 11 island populations of marine iguanas, and compare it with the composition of its sister species, the Galápagos land iguana (Conolophus subcristatus). We also conducted behavioural observations in marine iguana territorial males in order to explore the possible function of these substances in the context of male dominance in leks. Methods Femoral secretions were analysed by gas chromatography coupled to mass spectrometry (GC–MS), and chromatography with a flame ionisation detector (GC-FID) in order to characterise the lipophilic composition. To understand the potential role of femoral secretions in marine iguana intraspecific communication, territorial males were sampled for their femoral glands and monitored to record their head bob rate—a territorial display behaviour in males—as well as the number of females present in their leks. Results We found that the gland secretions were composed of ten saturated and unsaturated carboxylic acids ranging in chain length between C16 and C24, as well as three sterols. Cholesterol was the main compound found. Intriguingly, land iguanas have a higher diversity of lipophilic compounds, with structural group of lipids (i.e. aldehydes) entirely absent in marine iguanas; overall the chemical signals of both species were strongly differentiated. Lipid profiles also differed among populations of marine iguanas from different islands, with some islands demonstrating a high diversity of lipophilic compounds (i.e. full spectra of compounds), and others lacking one or more compounds. Among the compounds most frequently found missing were 11- and 13-eicosenoic acids. Gland secretions of males with a better body condition and with a higher dominance status (i.e. those accompanied by females and with higher head bob display) were proportionately richer in C20-unsaturated fatty acids (11-eicosenoic acid). Discussion Land and marine iguanas strongly diverged in their chemical composition of the femoral glands likely due to ecological differences between both species. Despite that marine iguana populations varied in their femoral gland composition that was not related to their genetic structure. Our results indicated that 11-eicosenoic acid may play an important role in intraspecific chemical communication in marine iguanas.
Ibáñez et al. (2017) Diversity of compounds in femoral secretions of Galápagos iguanas (genera: Amblyrhynchus and Conolophus), and their potential role in sexual communication in lek-mating marine iguanas (Amblyrhynchus cristatus). PeerJ 5:e3689 https://doi.org/10.7717/peerj.3689
Late Pleistocene songbirds of Liang Bua (Flores, Indonesia); the first fossil passerine fauna described from Wallacea
Background Passerines (Aves: Passeriformes) dominate modern terrestrial bird communities yet their fossil record is limited. Liang Bua is a large cave on the Indonesian island of Flores that preserves Late Pleistocene–Holocene deposits (∼190 ka to present day). Birds are the most diverse faunal group at Liang Bua and are present throughout the stratigraphic sequence. Methods We examined avian remains from the Late Pleistocene deposits of Sector XII, a 2 × 2 m area excavated to about 8.5 m depth. Although postcranial passerine remains are typically challenging to identify, we found several humeral characters particularly useful in discriminating between groups, and identified 89 skeletal elements of passerines. Results At least eight species from eight families are represented, including the Large-billed Crow (Corvus cf. macrorhynchos), the Australasian Bushlark (Mirafra javanica), a friarbird (Philemon sp.), and the Pechora Pipit (Anthus cf. gustavi). Discussion These remains constitute the first sample of fossil passerines described in Wallacea. Two of the taxa no longer occur on Flores today; a large sturnid (cf. Acridotheres) and a grassbird (Megalurus sp.). Palaeoecologically, the songbird assemblage suggests open grassland and tall forests, which is consistent with conditions inferred from the non-passerine fauna at the site. Corvus cf. macrorhynchos, found in the Homo floresiensis-bearing layers, was likely part of a scavenging guild that fed on carcasses of Stegodon florensis insularis alongside vultures (Trigonoceps sp.), giant storks (Leptoptilos robustus), komodo dragons (Varanus komodoensis), and probably H. floresiensis as well.
Meijer et al. (2017) Late Pleistocene songbirds of Liang Bua (Flores, Indonesia); the first fossil passerine fauna described from Wallacea. PeerJ 5:e3676 https://doi.org/10.7717/peerj.3676
Mesoscale spatiotemporal variability in a complex host-parasite system influenced by intermediate host body size
Background Parasites are essential components of natural communities, but the factors that generate skewed distributions of parasite occurrences and abundances across host populations are not well understood. Methods Here, we analyse at a seascape scale the spatiotemporal relationships of parasite exposure and host body-size with the proportion of infected hosts (i.e., prevalence) and aggregation of parasite burden across ca. 150 km of the coast and over 22 months. We predicted that the effects of parasite exposure on prevalence and aggregation are dependent on host body-sizes. We used an indirect host-parasite interaction in which migratory seagulls, sandy-shore molecrabs, and an acanthocephalan worm constitute the definitive hosts, intermediate hosts, and endoparasite, respectively. In such complex systems, increments in the abundance of definitive hosts imply increments in intermediate hosts’ exposure to the parasite’s dispersive stages. Results Linear mixed-effects models showed a significant, albeit highly variable, positive relationship between seagull density and prevalence. This relationship was stronger for small (cephalothorax length >15 mm) than large molecrabs (<15 mm). Independently of seagull density, large molecrabs carried significantly more parasites than small molecrabs. The analysis of the variance-to-mean ratio of per capita parasite burden showed no relationship between seagull density and mean parasite aggregation across host populations. However, the amount of unexplained variability in aggregation was strikingly higher in larger than smaller intermediate hosts. This unexplained variability was driven by a decrease in the mean-variance scaling in heavily infected large molecrabs. Conclusions These results show complex interdependencies between extrinsic and intrinsic population attributes on the structure of host-parasite interactions. We suggest that parasite accumulation—a characteristic of indirect host-parasite interactions—and subsequent increasing mortality rates over ontogeny underpin size-dependent host-parasite dynamics.
Rodríguez et al. (2017) Mesoscale spatiotemporal variability in a complex host-parasite system influenced by intermediate host body size. PeerJ 5:e3675 https://doi.org/10.7717/peerj.3675
Quercivorol as a lure for the polyphagous and Kuroshio shot hole borers, Euwallacea spp. nr. fornicatus (Coleoptera: Scolytinae), vectors of Fusarium dieback
The polyphagous shot hole borer and Kuroshio shot hole borer, two members of the Euwallacea fornicatus species complex (Coleoptera: Curculionidae: Scolytinae), are invasive ambrosia beetles that harbor distinct species of Fusarium fungal symbionts. Together with the damage caused by gallery construction, these two phytopathogenic Fusarium species are responsible for the emerging tree disease Fusarium dieback, which affects over 50 common tree species in Southern California. Host trees suffer branch dieback as the xylem is blocked by invading beetles and fungi, forcing the costly removal of dead and dying trees in urban areas. The beetles are also threatening natural riparian habitats, and avocado is susceptible to Fusarium dieback as well, resulting in damage to the avocado industries in California and Israel. Currently there are no adequate control mechanisms for shot hole borers. This paper summarizes efforts to find a suitable lure to monitor shot hole borer invasions and dispersal. Field trials were conducted in two counties in Southern California over a span of two years. We find that the chemical quercivorol is highly attractive to these beetles, and perform subsequent field experiments attempting to optimize this lure. We also explore other methods of increasing trap catch and effects of other potential attractants, as well as the deterrents verbenone and piperitone.
Dodge et al. (2017) Quercivorol as a lure for the polyphagous and Kuroshio shot hole borers, Euwallacea spp. nr. fornicatus (Coleoptera: Scolytinae), vectors of Fusarium dieback. PeerJ 5:e3656 https://doi.org/10.7717/peerj.3656
Genome-wide association study identifies novel type II diabetes risk loci in Jordan subpopulations
The prevalence of Type II Diabetes (T2D) has been increasing and has become a disease of significant public health burden in Jordan. None of the previous genome-wide association studies (GWAS) have specifically investigated the Middle East populations. The Circassian and Chechen communities in Jordan represent unique populations that are genetically distinct from the Arab population and other populations in the Caucasus. Prevalence of T2D is very high in both the Circassian and Chechen communities in Jordan despite low obesity prevalence. We conducted GWAS on T2D in these two populations and further performed meta-analysis of the results. We identified a novel T2D locus at chr20p12.2 at genome-wide significance (rs6134031, P = 1.12 × 10−8) and we replicated the results in the Wellcome Trust Case Control Consortium (WTCCC) dataset. Another locus at chr12q24.31 is associated with T2D at suggestive significance level (top SNP rs4758690, P = 4.20 × 10−5) and it is a robust eQTL for the gene, MLXIP (P = 1.10 × 10−14), and is significantly associated with methylation level in MLXIP, the functions of which involves cellular glucose response. Therefore, in this first GWAS of T2D in Jordan subpopulations, we identified novel and unique susceptibility loci which may help inform the genetic underpinnings of T2D in other populations.
Dajani et al. (2017) Genome-wide association study identifies novel type II diabetes risk loci in Jordan subpopulations. PeerJ 5:e3618 https://doi.org/10.7717/peerj.3618
RNA sequencing (RNA-Seq) of lymph node, spleen, and thymus transcriptome from wild Peninsular Malaysian cynomolgus macaque (Macaca fascicularis)
The cynomolgus macaque (Macaca fascicularis) is an extensively utilised nonhuman primate model for biomedical research due to its biological, behavioural, and genetic similarities to humans. Genomic information of cynomolgus macaque is vital for research in various fields; however, there is presently a shortage of genomic information on the Malaysian cynomolgus macaque. This study aimed to sequence, assemble, annotate, and profile the Peninsular Malaysian cynomolgus macaque transcriptome derived from three tissues (lymph node, spleen, and thymus) using RNA sequencing (RNA-Seq) technology. A total of 174,208,078 paired end 70 base pair sequencing reads were obtained from the Illumina Hi-Seq 2500 sequencer. The overall mapping percentage of the sequencing reads to the M. fascicularis reference genome ranged from 53–63%. Categorisation of expressed genes to Gene Ontology (GO) and KEGG pathway categories revealed that GO terms with the highest number of associated expressed genes include Cellular process, Catalytic activity, and Cell part, while for pathway categorisation, the majority of expressed genes in lymph node, spleen, and thymus fall under the Global overview and maps pathway category, while 266, 221, and 138 genes from lymph node, spleen, and thymus were respectively enriched in the Immune system category. Enriched Immune system pathways include Platelet activation pathway, Antigen processing and presentation, B cell receptor signalling pathway, and Intestinal immune network for IgA production. Differential gene expression analysis among the three tissues revealed 574 differentially expressed genes (DEG) between lymph and spleen, 5402 DEGs between lymph and thymus, and 7008 DEGs between spleen and thymus. Venn diagram analysis of expressed genes revealed a total of 2,630, 253, and 279 tissue-specific genes respectively for lymph node, spleen, and thymus tissues. This is the first time the lymph node, spleen, and thymus transcriptome of the Peninsular Malaysian cynomolgus macaque have been sequenced via RNA-Seq. Novel transcriptomic data will further enrich the present M. fascicularis genomic database and provide future research potentials, including novel transcript discovery, comparative studies, and molecular markers development.
Ee Uli et al. (2017) RNA sequencing (RNA-Seq) of lymph node, spleen, and thymus transcriptome from wild Peninsular Malaysian cynomolgus macaque (Macaca fascicularis). PeerJ 5:e3566 https://doi.org/10.7717/peerj.3566
Shoreline oiling effects and recovery of salt marsh macroinvertebrates from the Deepwater Horizon Oil Spill
Salt marshes in northern Barataria Bay, Louisiana, USA were oiled, sometimes heavily, in the aftermath of the Deepwater Horizon oil spill. Previous studies indicate that fiddler crabs (in the genus Uca) and the salt marsh periwinkle (Littoraria irrorata) were negatively impacted in the short term by the spill. Here, we detail longer-term effects and recovery from moderate and heavy oiling over a 3-year span, beginning 30 months after the spill. Although neither fiddler crab burrow density nor diameter differed between oiled and reference sites when combined across all sampling events, these traits differed among some individual sampling periods consistent with a pattern of lingering oiling impacts. Periwinkle density, however, increased in all oiling categories and shell-length groups during our sampling period, and periwinkle densities were consistently highest at moderately oiled sites where Spartina alterniflora aboveground biomass was highest. Periwinkle shell length linearly increased from a mean of 16.5 to 19.2 mm over the study period at reference sites. In contrast, shell lengths at moderately oiled and heavily oiled sites increased through month 48 after the spill, but then decreased. This decrease was associated with a decline in the relative abundance of large adults (shell length 21–26 mm) at oiled sites which was likely caused by chronic hydrocarbon toxicity or oil-induced effects on habitat quality or food resources. Overall, the recovery of S. alterniflora facilitated the recovery of fiddler crabs and periwinkles. However, our long-term record not only indicates that variation in periwinkle mean shell length and length-frequency distributions are sensitive indicators of the health and recovery of the marsh, but agrees with synoptic studies of vegetation and infaunal communities that full recovery of heavily oiled sites will take longer than 66 months.
Deis et al. (2017) Shoreline oiling effects and recovery of salt marsh macroinvertebrates from the Deepwater Horizon Oil Spill. PeerJ 5:e3680 https://doi.org/10.7717/peerj.3680