ORCID Profile
0000-0002-3429-8699
Current Organisation
University of Waikato
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Genomics | Population, Ecological and Evolutionary Genetics | Genetics | Biological Adaptation
Control of Plant Pests, Diseases and Exotic Species in Farmland, Arable Cropland and Permanent Cropland Environments | Expanding Knowledge in the Biological Sciences |
Publisher: The Company of Biologists
Date: 22-08-2014
DOI: 10.1242/BIO.20148888
Abstract: Low temperature is a primary determinant of growth and survival among organisms and almost all animals need to withstand temperature fluctuations in their surroundings. We used the hermaphroditic nematode Pristionchus pacificus to examine variation in cold tolerance in s les collected from 18 widespread locations. S les were challenged by exposure to both direct and gradual low temperature after culture in the laboratory at 20°C. A short-term acclimation treatment was also applied to assess cold tolerance following a pre-exposure cold treatment. Finally, genotype-by-environment (G × E) analysis was performed on a subset of s les cultured at two additional temperatures (15°C and 25°C). P. pacificus displayed a high degree of natural variation in cold tolerance, corresponding to the presence of three distinct phenotypic classes among s les: cold tolerant, non-cold tolerant, cold tolerant plastic. Survival of gradual cold exposure was significantly higher than survival of direct exposure to low temperature and a cold exposure pre-treatment significantly enhanced cold tolerance in some s les. By focusing on a sub-set of well-s led locations from tropical La Réunion Island, we found evidence of significant effects of genotype and environment on cold tolerance, and we also showed that, within the different Réunion locations s led, all three phenotypic classes are generally well represented. Taken together, our results show that P. pacificus exhibits a highly plastic tolerance to cold exposure that may be partly driven by differential trait sensitivity in erse environments.
Publisher: Wiley
Date: 20-12-2005
Publisher: Wiley
Date: 28-10-2019
DOI: 10.1111/MEC.15269
Abstract: Antarctica is isolated, surrounded by the Southern Ocean and has experienced extreme environmental conditions for millions of years, including during recent Pleistocene glacial maxima. How Antarctic terrestrial species might have survived these glaciations has been a topic of intense interest, yet many questions remain unanswered, particularly for Antarctica's invertebrate fauna. We examine whether genetic data from a widespread group of terrestrial invertebrates, springtails (Collembola, Isotomidae) of the genus Cryptopygus, show evidence for long-term survival in glacial refugia along the Antarctic Peninsula. We use genome-wide SNP analyses (via genotyping-by-sequencing, GBS) and mitochondrial data to examine population ersity and differentiation across more than 20 sites spanning >950 km on the Peninsula, and from islands both close to the Peninsula and up to ~1,900 km away. Population structure analysis indicates the presence of strong local clusters of ersity, and we infer that patterns represent a complex interplay of isolation in local refugia coupled with occasional successful long-distance dispersal events. We identified wind and degree days as significant environmental drivers of genetic ersity, with windier and warmer sites hosting higher ersity. Thus, we infer that refugial areas along the Antarctic Peninsula have allowed populations of indigenous springtails to survive in situ throughout glacial periods. Despite the difficulties of dispersal in cold, desiccating conditions, Cryptopygus springtails on the Peninsula appear to have achieved multiple long-distance colonization events, most likely through wind-related dispersal events.
Publisher: Wiley
Date: 18-08-2009
Publisher: The Royal Society
Date: 24-02-2016
Abstract: Wild isolates of the nematode Caenorhabditis elegans perform social behaviours, namely clumping and bordering, to avoid hyperoxia under laboratory conditions. In contrast, the laboratory reference strain N2 has acquired a solitary behaviour in the laboratory, related to a gain-of-function variant in the neuropeptide Y-like receptor NPR-1. Here, we study the evolution and natural variation of clumping and bordering behaviours in Pristionchus pacificus nematodes in a natural context, using strains collected from 22 to 2400 metres above sea level on La Réunion Island. Through the analysis of 106 wild isolates, we show that the majority of strains display a solitary behaviour similar to C. elegans N2, whereas social behaviours are predominantly seen in strains that inhabit high-altitude locations. We show experimentally that P. pacificus social strains perform clumping and bordering to avoid hyperoxic conditions in the laboratory, suggesting that social strains may have adapted to or evolved a preference for the lower relative oxygen levels available at high altitude in nature. In contrast to C. elegans , clumping and bordering in P. pacificus do not correlate with locomotive behaviours in response to changes in oxygen conditions. Furthermore, QTL analysis indicates clumping and bordering to represent complex quantitative traits. Thus, clumping and bordering behaviours represent an ex le of phenotypic convergence with a different evolutionary history and distinct genetic control in both nematode species.
Publisher: Wiley
Date: 11-01-2007
Publisher: The Royal Society
Date: 16-10-2023
Publisher: Informa UK Limited
Date: 09-2009
Publisher: Wiley
Date: 18-10-2016
DOI: 10.1111/MEC.13841
Abstract: Helicoverpa armigera is a major agricultural pest that is distributed across Europe, Asia, Africa and Australasia. This species is hypothesized to have spread to the Americas 1.5 million years ago, founding a population that is at present, a distinct species, Helicoverpa zea. In 2013, H. armigera was confirmed to have re-entered South America via Brazil and subsequently spread. The source of the recent incursion is unknown and population structure in H. armigera is poorly resolved, but a basic understanding would highlight potential biosecurity failures and determine the recent evolutionary history of region-specific lineages. Here, we integrate several end points derived from high-throughput sequencing to assess gene flow in H. armigera and H. zea from populations across six continents. We first assemble mitochondrial genomes to demonstrate the phylogenetic relationship of H. armigera with other Heliothine species and the lack of distinction between populations. We subsequently use de novo genotyping-by-sequencing and whole-genome sequences aligned to bacterial artificial chromosomes, to assess levels of admixture. Primarily, we find that Brazilian H. armigera are derived from erse source populations, with strong signals of gene flow from European populations, as well as prevalent signals of Asian and African ancestry. We also demonstrate a potential field-caught hybrid between H. armigera and H. zea, and are able to provide genomic support for the presence of the H. armigera conferta subspecies in Australasia. While structure among the bulk of populations remains unresolved, we present distinctions that are pertinent to future investigations as well as to the biosecurity threat posed by H. armigera.
Publisher: The Royal Society
Date: 2023
Abstract: Models are mathematical representations of systems, processes or phenomena. In biomechanics, finite-element modelling (FEM) can be a powerful tool, allowing biologists to test form–function relationships in silico , replacing or extending results of in vivo experimentation. Although modelling simplifications and assumptions are necessary, as a minimum modelling requirement the results of the simplified model must reflect the biomechanics of the modelled system. In cases where the three-dimensional mechanics of a structure are important determinants of its performance, simplified two-dimensional modelling approaches are likely to produce inaccurate results. The vertebrate mandible is one among many three-dimensional anatomical structures routinely modelled using two-dimensional FE analysis. We thus compare the stress regimes of our published three-dimensional model of the chimpanzee mandible with a published two-dimensional model of the chimpanzee mandible and identify several fundamental differences. We then present a series of two-dimensional and three-dimensional FE modelling experiments that demonstrate how three key modelling parameters, (i) dimensionality, (ii) symmetric geometry, and (iii) constraints, affect deformation and strain regimes of the models. Our results confirm that, in the case of the primate mandible (at least), two-dimensional FEM fails to meet this minimum modelling requirement and should not be used to draw functional, ecological or evolutionary conclusions.
Publisher: Cold Spring Harbor Laboratory
Date: 04-07-2019
DOI: 10.1101/692632
Abstract: Within-species skull shape variation of marsupial mammals is widely considered low and strongly size-dependent (allometric), possibly due to developmental constraints arising from the altricial birth of marsupials. However, species whose skulls are impacted by strong muscular stresses – particularly those produced through mastication of tough food items – may not display such intrinsic patterns very clearly because of the known plastic response of bone to muscle activity of the in idual. In such cases, shape variation should not be dominated by allometry ordination of shape in a geometric morphometric context through principal component analysis (PCA) should reveal main variation in areas under masticatory stress (incisor region/zygomatic arches/mandibular ramus) but this main variation should emerge from high in idual variability and thus have low eigenvalues. We assessed the evidence for high in idual variation through 3D geometric morphometric shape analysis of crania and mandibles of thre species of grazing-specialized wombats, whose diet of tough grasses puts considerable strain on their masticatory system. As expected, we found little allometry and low Principal Component 1 (PC1) eigenvalues within crania and mandibles of all three species. Also as expected, the main variation was in the muzzle, zygomatic arches, and masticatory muscle attachments of the mandibular ramus. We then implemented a new test to ask if the landmark variation reflected on PC1 was reflected in in iduals with opposite PC1 scores and with opposite shapes in Procrustes space. This showed that correspondence between in idual and ordinated shape variation was limited, indicating high levels of in idual variability in the masticatory apparatus. Our results are inconsistent with hypotheses that skull shape variation within marsupial species reflects a constraint pattern. Rather, they support suggestions that in idual plasticity can be an important determinant of within-species shape variation in marsupials (and possibly other mammals) with high masticatory stresses, making it difficult to understand the degree to which intrinsic constraint act on shape variation at the within-species level. We conclude that studies that link micro- and macroevolutionary patterns of shape variation might benefit from a focus on species with low-impact mastication, such as carnivorous or frugivorous species.
Publisher: Wiley
Date: 30-08-2023
Abstract: Invasive species threaten native biota, putting fragile ecosystems at risk and having a large‐scale impact on primary industries. Growing trade networks and the popularity of personal travel make incursions a more frequent risk, one only compounded by global climate change. With increasing publication of whole‐genome sequences lies an opportunity for cross‐species assessment of invasive potential. However, the degree to which published sequences are accompanied by satisfactory spatiotemporal data is unclear. We assessed the metadata associated with 199 whole‐genome assemblies of 89 invasive terrestrial invertebrate species and found that only 38% of these were derived from field‐collected s les. Seventy‐six assemblies (38%) reported an ‘undescribed’ s le origin and, while further examination of associated literature closed this gap to 23.6%, an absence of spatial data remained for 47 of the total assemblies. Of the 76 assemblies that were ultimately determined to be field‐collected, associated metadata relevant for invasion studies was predominantly lacking: only 35% (27 assemblies) provided granular location data, and 33% ( n = 25) lacked sufficient collection date information. Our results support recent calls for standardized metadata in genome sequencing data submissions, highlighting the impact of missing metadata on current research in invasion biology (and likely other fields). Notably, large‐scale consortia tended to provide the most complete metadata submissions in our analysis—such cross‐institutional collaborations can foster a culture of increased adherence to improved metadata submission standards and a standard of metadata stewardship that enables reuse of genomes in invasion science.
Publisher: PeerJ
Date: 14-07-2016
DOI: 10.7717/PEERJ.2164
Abstract: Horse racing is a multi-billion-dollar industry that has raised welfare concerns due to injured and euthanized animals. Whilst the cause of musculoskeletal injuries that lead to horse morbidity and mortality is multifactorial, pre-existing pathologies, increased speeds and substrate of the racecourse are likely contributors to foot disease. Horse hooves have the ability to naturally deform during locomotion and dissipate locomotor stresses, yet farriery approaches are utilised to increase performance and protect hooves from wear. Previous studies have assessed the effect of different shoe designs on locomotor performance however, no biomechanical study has hitherto measured the effect of horseshoes on the stresses of the foot skeleton in vivo . This preliminary study introduces a novel methodology combining three-dimensional data from biplanar radiography with inverse dynamics methods and finite element analysis (FEA) to evaluate the effect of a stainless steel shoe on the function of a Thoroughbred horse’s forefoot during walking. Our preliminary results suggest that the stainless steel shoe shifts craniocaudal, mediolateral and vertical GRFs at mid-stance. We document a similar pattern of flexion-extension in the PIP (pastern) and DIP (coffin) joints between the unshod and shod conditions, with slight variation in rotation angles throughout the stance phase. For both conditions, the PIP and DIP joints begin in a flexed posture and extend over the entire stance phase. At mid-stance, small differences in joint angle are observed in the PIP joint, with the shod condition being more extended than the unshod horse, whereas the DIP joint is extended more in the unshod than the shod condition. We also document that the DIP joint extends more than the PIP after mid-stance and until the end of the stance in both conditions. Our FEA analysis, conducted solely on the bones, shows increased von Mises and Maximum principal stresses on the forefoot phalanges in the shod condition at mid-stance, consistent with the tentative conclusion that a steel shoe might increase mechanical loading. However, because of our limited s le size none of these apparent differences have been tested for statistical significance. Our preliminary study illustrates how the shoe may influence the dynamics and mechanics of a Thoroughbred horse’s forefoot during slow walking, but more research is needed to quantify the effect of the shoe on the equine forefoot during the whole stance phase, at faster speeds/gaits and with more in iduals as well as with a similar focus on the hind feet. We anticipate that our preliminary analysis using advanced methodological approaches will pave the way for new directions in research on the form/function relationship of the equine foot, with the ultimate goal to minimise foot injuries and improve animal health and welfare.
Publisher: Wiley
Date: 09-04-2019
DOI: 10.1002/JMOR.20989
Abstract: The biomechanics of the sauropod dinosaur pes is poorly understood, particularly among the earliest members of the group. To date, reasonably complete and articulated pedes in Early Middle Jurassic sauropods are rare, limited to a handful of taxa. Of these, Rhoetosaurus brownei, from eastern Australia, is currently the only one from the Gondwanan Middle Jurassic that preserves an articulated pes. Using Rhoetosaurus brownei as a case exemplar, we assessed its paleobiomechanical capabilities and pedal posture. Physical and virtual manipulations of the pedal elements were undertaken to evaluate the range of motion between the pedal joints, under both bone-to-bone and cartilaginous scenarios. Using the results as constraints, virtual reconstructions of all possible pedal postures were generated. We show that Rhoetosaurus brownei was capable of significant digital mobility at the osteological metatarsophalangeal and distal interphalangeal joints. We assume these movements would have been restricted by soft tissue in life but that their presence would have helped in the support of the animal. Further insights based on anatomy and theoretical mechanical constraints restricted the skeletal postures to a range encompassing digitigrade to subunguligrade stances. The approach was extended to additional sauropodomorph pedes, and some validation was provided via the bone data of an African elephant pes. Based on the resulting pedal configurations, the in-life plantar surface of the sauropod pes is inferred to extend caudally from the digits, with a soft tissue pad supporting the elevated metatarsus. The plantar pad is inferred to play a role in the reduction of biomechanical stresses, and to aid in support and locomotion. A pedal pad may have been a key biomechanical innovation in early sauropods, ultimately resulting in a functionally plantigrade pes, which may have arisen during the Early to Middle Jurassic. Further mechanical studies are ultimately required to permit validation of this long-standing hypothesis.
Publisher: Elsevier BV
Date: 02-2009
DOI: 10.1016/J.JINSPHYS.2008.10.009
Abstract: Terrestrial systems in Antarctica are characterized by substantial spatial and temporal variation. However, few studies have addressed the paucity of data on metabolic responses to the unpredictable Antarctic environment, particularly with regard to terrestrial biota. This study measured metabolic rate variation for in idual springtails at a continental Antarctic site using a fiber-optic closed respirometry system incorporating a custom-made respiration chamber. Concurrent measures of (behavioural) activity were made via daily pitfall counts. Metabolic rate of Gomphiocephalus hodgsoni measured at constant temperature varied systematically with progression through the austral summer, and was greatest mid-season. This finding of clear intra-seasonal and temperature-independent variation in mass-specific metabolic rate in G. hodgsoni is one of very few such reports for a terrestrial invertebrate (and the only such study for Antarctica), and parallels physiological studies in the Antarctic marine environment linking metabolic rate elevation with biological function rather than temperature adaptation per se. However, response to temperature at relatively short time-scales is also likely to be an important part of the life history strategy of Antarctic terrestrial invertebrates such as G. hodgsoni, which appears capable of both physiologically and behaviourally 'tuning' in to short-term thermal variability to respond appropriately to the local unpredictable Antarctic habitat.
Publisher: Wiley
Date: 30-06-2022
DOI: 10.1111/EVO.14520
Abstract: Because of ongoing climate change, populations of organisms are being subjected to stressful temperatures more often. This is especially problematic for ectothermic organisms, which are likely to be more sensitive to changes in temperature. Therefore, we need to know if ectotherms have adapted to environmental temperature and, if so, what are the evolutionary mechanisms behind such adaptation. Here, we use the nematode Pristionchus pacificus as a case study to investigate thermal adaptation on the Indian Ocean island of La Réunion, which experiences a range of temperatures from coast to summit. We study the evolution of high-temperature tolerance by constructing a phylogenetic tree of strains collected from many different thermal niches. We show that populations of P. pacificus at low altitudes have higher fertility at warmer temperatures. Most likely, this phenotype has arisen recently and at least twice independently, consistent with parallel evolution. We also studied low-temperature tolerance and showed that populations from high altitudes have increased their fertility at cooler temperatures. Together, these data indicate that P. pacificus strains on La Réunion are subject to ergent selection, adapting to hot and cold niches at the coast and summit of the volcano. Precisely defining these thermal niches provides essential information for models that predict the impact of future climate change on these populations.
Publisher: MDPI AG
Date: 30-12-2022
DOI: 10.3390/D15010047
Abstract: Climate change is expected to impact the global distribution and ersity of arthropods, with warmer temperatures forcing species to relocate, acclimate, adapt, or go extinct. The Arctic and Antarctic regions are extremely sensitive to climate change and have displayed profound and variable changes over recent decades, including decreases in sea ice extent, greening of tundra, and changes to hydrological and biogeochemical cycles. It is unclear how polar-adapted arthropods will respond to such changes, though many are expected to be at great risk of extinction. Here, we review the adaptive mechanisms that allow polar arthropods to persist in extreme environments and discuss how the effects of climate change at the poles will likely favour non-native species or those with the ability to rapidly evolve and/or acclimate. We find that physiological, behavioural, plastic, and genetic data are limited in scope for polar arthropods and research on adaptive responses to change is scarce. This restricts our ability to predict how they may respond to a warming climate. We call for a greater investment in research that specifically targets the ecology and evolution of these taxa, including genomic and transcriptomic approaches that can evaluate the potential for plastic and evolved environmental responses.
Publisher: Cold Spring Harbor Laboratory
Date: 15-12-2020
DOI: 10.1101/2020.12.15.422848
Abstract: Telomeres are repetitive sequences located at the end of chromosomes in eukaryotes that protect against loss of important sequences during the cell replication process. Telomere length (TL) shortens with every round of cell ision. When a telomere becomes too short, cells can no longer proliferate and this triggers the cell apoptosis process. Apart from cell replication, the length of telomeres can be affected by factors such as sex, genetics, and stress levels. Oxidative stress in particular can cause damage to telomeres and telomere maintenance processes, resulting in TL shortening. This phenomenon occurs in humans and many vertebrates, especially endothermic species. However, the ways in which various stress types affect the TL of invertebrate species remains ambiguous. Here, we examined the effects of development and oxidative stress on TL in the invertebrate pest moth, Helicoverpa armigera . In the former case, we extracted genomic DNA from three developmental stages (1-day old egg, 4th instar, and first-day emerged moths) and measured TL by qPCR. In the latter, we chronically exposed in iduals to paraquat – an organic herbicide that induces oxidative stress - and then measured TL as per our development methodology. In addition, we examined TL in a subset of published whole genome short-read sequencing data of caterpillars and moths using the software, Computel. In our experimental work, we found that TL in H. armigera was significantly longer at the early stages of development and shortens in later stages. However, oxidative stress does not appear to shorten TL in H. armigera following chronic exposure to paraquat. In our Computel analysis, we found that caterpillars had longer mean TL than moths but this difference was not significant due to the high variation among s les. Collectively, our research provides new data on TL in an underrepresented group, adding new insights into the progression of TL shortening with development and the effects of oxidative stress on TL, while also more generally highlighting the value of applying complementary approaches to TL measurement.
Publisher: Oxford University Press (OUP)
Date: 03-04-2014
DOI: 10.1111/BIJ.12255
Publisher: PeerJ
Date: 15-05-2019
DOI: 10.7717/PEERJ.6881
Abstract: White rhinoceroses ( Ceratotherium simum ) are odd-toed ungulates that belong to the group Perissodactyla. Being second only to elephants in terms of large body mass amongst extant tetrapods, rhinoceroses make fascinating subjects for the study of how large land animals support and move themselves. Rhinoceroses often are kept in captivity for protection from ivory poachers and for educational/touristic purposes, yet a detrimental side effect of captivity can be foot disease (i.e., enthesopathies and osteoarthritis around the phalanges). Foot diseases in large mammals are multifactorial, but locomotor biomechanics (e.g., pressures routinely experienced by the feet) surely can be a contributing factor. However, due to a lack of in vivo experimental data on rhinoceros foot pressures, our knowledge of locomotor performance and its links to foot disease is limited. The overall aim of this study was to characterize peak pressures and center of pressure trajectories in white rhinoceroses during walking. We asked two major questions. First, are peak locomotor pressures the lowest around the fat pad and its lobes (as in the case of elephants)? Second, are peak locomotor pressures concentrated around the areas with the highest reported incidence of pathologies? Our results show a reduction of pressures around the fat pad and its lobes, which is potentially due to the material properties of the fat pad or a tendency to avoid or limit “heel” contact at impact. We also found an even and gradual concentration of foot pressures across all digits, which may be a by-product of the more horizontal foot roll-off during the stance phase. While our exploratory, descriptive s le precluded hypothesis testing, our study provides important new data on rhinoceros locomotion for future studies to build on, and thus impetus for improved implementation in the care of captive/managed rhinoceroses.
Publisher: Springer Science and Business Media LLC
Date: 11-2019
DOI: 10.1186/S12983-019-0338-5
Abstract: Within-species skull shape variation of marsupial mammals is widely considered low and strongly size-dependent (allometric), possibly due to developmental constraints arising from the altricial birth of marsupials. However, species whose skulls are impacted by strong muscular stresses – particularly those produced through mastication of tough food items – may not display such intrinsic patterns very clearly because of the known plastic response of bone to muscle activity of the in idual. In such cases, allometry may not dominate within-species shape variation, even if it is a driver of evolutionary shape ergence ordination of shape in a geometric morphometric context through principal component analysis (PCA) should reveal main variation in areas under masticatory stress (incisor region/zygomatic arches/mandibular ramus) but this main variation should emerge from high in idual variability and thus have low eigenvalues. We assessed the evidence for high in idual variation through 3D geometric morphometric shape analysis of crania and mandibles of three species of grazing-specialized wombats, whose diet of tough grasses puts considerable strain on their masticatory system. As expected, we found little allometry and low Principal Component 1 (PC1) eigenvalues within crania and mandibles of all three species. Also as expected, the main variation was in the muzzle, zygomatic arches, and masticatory muscle attachments of the mandibular ramus. We then implemented a new test to ask if the landmark variation reflected on PC1 was reflected in in iduals with opposite PC1 scores and with opposite shapes in Procrustes space. This showed that correspondence between in idual and ordinated shape variation was limited, indicating high levels of in idual variability in the masticatory apparatus. Our results are inconsistent with hypotheses that skull shape variation within marsupial species reflects a constraint pattern. Rather, they support suggestions that in idual plasticity can be an important determinant of within-species shape variation in marsupials (and possibly other mammals) with high masticatory stresses, making it difficult to understand the degree to which intrinsic constraints act on shape variation at the within-species level. We conclude that studies that link micro- and macroevolutionary patterns of shape variation might benefit from a focus on species with low-impact mastication, such as carnivorous or frugivorous species.
Publisher: Wiley
Date: 06-11-2023
DOI: 10.1111/MEC.16740
Abstract: Invasive species are increasingly threatening ecosystems and agriculture by rapidly expanding their range and adapting to environmental and human‐imposed selective pressures. The genomic mechanisms that underlie such rapid changes remain unclear, especially for agriculturally important pests. Here, we used genome‐wide polymorphisms derived from native, invasive, and intercepted s les and populations of the brown marmorated stink bug (BMSB), Halyomorpha halys , to gain insights into population genomics processes that have promoted the successful global invasion of this polyphagous pest. Our analysis demonstrated that BMSB exhibits spatial structure but admixture rates are high among introduced populations, resulting in similar levels of genomic ersity across native and introduced populations. These spatial genomic patterns suggest a complex invasion scenario, potentially with multiple bridgehead events, posing a challenge for accurately assigning BMSB incursions to their source using reduced‐representation genomic data. By associating allele frequencies with the invasion status of BMSB populations, we found significantly differentiated single nucleotide polymorphisms (SNPs) located in close proximity to genes for insecticide resistance and olfaction. Comparing variations in allele frequencies among populations for outlier SNPs suggests that BMSB invasion success has probably evolved from standing genetic variation. In addition to being a major nuisance of households, BMSB has caused significant economic losses to agriculture in recent years and continues to expand its range. Despite no record of BMSB insecticide resistance to date, our results show high capacity for potential evolution of such traits, highlighting the need for future sustainable and targeted management strategies.
Publisher: PeerJ
Date: 17-12-2015
DOI: 10.7287/PEERJ.PREPRINTS.1590V1
Abstract: Herman Melville’s novel Moby Dick was inspired by historical instances in which large sperm whales (Physeter macrocephalus L.) sank 19th century whaling ships by ramming them with their foreheads. The immense forehead of sperm whales is possibly the largest, and one of the strangest, anatomical structures in the animal kingdom. It contains two large oil-filled compartments, known as the “spermaceti organ” and “junk”, that constitute up to one-quarter of body mass and extend one-third of the total length of the whale. Recognized as playing an important role in echolocation, previous studies have also attributed the complex structural configuration of the spermaceti organ and junk to acoustic sexual selection, acoustic prey debilitation, buoyancy control, and aggressive ramming. Of these additional suggested functions, ramming remains the most controversial, and the potential mechanical roles of the structural components of the spermaceti organ and junk in ramming remain untested. Here we explore the aggressive ramming hypothesis using a novel combination of structural engineering principles and probabilistic simulation to determine if the unique structure of the junk significantly reduces stress in the skull during quasi-static impact. Our analyses indicate that the connective tissue partitions within the junk reduce stress across the skull during impact stress reduction is greatest in the anterior aspect of the skull and removal of the connective tissue partitions increases stress concentrations on the tip of the skull, possibly making it prone to fracture. Although the unique structure of the junk certainly serves multiple functions, our results are consistent with the hypothesis that the structure also evolved to function as a massive battering ram during male-male competition.
Publisher: PeerJ
Date: 02-02-2014
DOI: 10.7287/PEERJ.PREPRINTS.231V1
Abstract: Horses and elephants have extreme foot designs horses have an unguligrade foot posture with small, single-toed, rigid hooves housing a small fibrous digital cushion, whereas elephants have large, multi-toed, functionally plantigrade, compliant feet with large adipose filled digital cushions. The morphology of the digital cushion is ergent in these species, in terms of its size, shape, volume, composition and organisation. In the context of foot-ground contact this is interesting, because feet nonetheless have to perform similar mechanical functions in all terrestrial species. How well the digital cushion functions under load may contribute to the aetiopathogenesis of foot disease a sub-optimal digital cushion is less likely to distribute (and thus reduce) high pressures, moderate impact shock and vibration, or prevent unwarranted bone displacement. In this study, we seek to understand how the digital cushion morphologies evident in horse and elephant feet influence internal and external foot pressures. Our novel use of invasive blood pressure monitoring equipment, combined with a pressure pad and force plate, enabled measurements of ( ex vivo ) digital cushion pressure under increasing axial loads in seven horse and six elephant forefeet. Linear mixed effects models (LMER) revealed that internal digital cushion pressures increase under load and differ depending on region elephant feet experienced higher magnitudes of medial digital cushion pressure, whereas horse feet experienced higher magnitudes of centralised digital cushion pressure. Direct comparison of digital cushion pressure magnitudes in both species, at equivalent loads relative to body weight, revealed that medial and lateral pressures increased more rapidly with load in elephant limbs. Within the same approximate region, internal pressures exceeded external, palmar pressures (on the sole of the foot), supporting previous Finite Element (FE) predictions. High pressures and large variations in pressure may relate to the development of foot pathology, which is a major concern in horses and elephants in a captive/domestic environment. We suggest that heterogeneity within the digital cushion allows it to perform conflicting mechanical functions during locomotion different digital cushion regions may be responsible for specific functions and therefore feature appropriate properties to do so. Determining how internal structures such as the digital cushion respond to locomotor loading is essential to understanding foot health and pathology, as well as the functional consequences of evolutionary changes in foot morphology.
Publisher: Oxford University Press (OUP)
Date: 09-05-2016
Abstract: Understanding how new species form requires investigation of evolutionary forces that cause phenotypic and genotypic changes among populations. However, the mechanisms underlying speciation vary and little is known about whether genomes ersify in the same ways in parallel at the incipient scale. We address this using the nematode, Pristionchus pacificus, which resides at an interesting point on the speciation continuum (distinct evolutionary lineages without reproductive isolation), and inhabits heterogeneous environments subject to ergent environmental pressures. Using whole genome re-sequencing of 264 strains, we estimate FST to identify outlier regions of extraordinary differentiation (∼1.725 Mb of the 172.5 Mb genome). We find evidence for shared ergent genomic regions occurring at a higher frequency than expected by chance among populations of the same evolutionary lineage. We use allele frequency spectra to find that, among lineages, 53% of ergent regions are consistent with adaptive selection, whereas 24% and 23% of such regions suggest background selection and restricted gene flow, respectively. In contrast, among populations from the same lineage, similar proportions (34-48%) of ergent regions correspond to adaptive selection and restricted gene flow, whereas 13-22% suggest background selection. Because speciation often involves phenotypic and genomic ergence, we also evaluate phenotypic variation, focusing on pH tolerance, which we find is erging in a manner corresponding to environmental differences among populations. Taking a genome-wide association approach, we functionally validate a significant genotype-phenotype association for this trait. Our results are consistent with P. pacificus undergoing heterogeneous genotypic and phenotypic ersification related to both evolutionary and environmental processes.
Publisher: Cold Spring Harbor Laboratory
Date: 29-12-2016
DOI: 10.1101/096727
Abstract: Studying the effect of temperature on fertility is particularly important in the light of ongoing climate change. We need to know if organisms can adapt to higher temperatures and, if so, what are the evolutionary mechanisms behind such adaptation. Such studies have been h ered by the lack different populations of sufficient sizes with which to relate the phenotype of temperature tolerance to the underlying genotypes. Here, we examined temperature adaptation in populations of the nematode Pristionchus pacificus , in which in idual strains are able to successfully reproduce at 30°C. Analysis of the frequency of heat tolerant strains in different temperature zones on La Réunion supports that this trait is subject to natural selection. Reconstruction of ancestral states along the phylogeny of highly differentiated P. pacificus clades suggests that heat tolerance evolved multiple times independently. This is further supported by genome wide association studies showing that heat tolerance is a polygenic trait and that different loci are used by in idual P. pacificus clades to develop heat tolerance. More precisely, analysis of allele frequencies indicated that most genetic markers that are associated with heat tolerance are only polymorphic in in idual clades. While in some P. pacificus clades, parallel evolution of heat tolerance can be explained by ancestral polymorphism or by gene flow across clades, we observe at least one clearly distinct and independent scenario where heat tolerance emerged by de novo mutation. Thus, temperature tolerance evolved at least two times independently in the evolutionary history of this species. Our data suggest that studies of wild populations of P. pacificus will reveal distinct cellular mechanisms driving temperature adaptation.
Publisher: Wiley
Date: 28-11-2013
DOI: 10.1002/ECE3.902
Publisher: Cold Spring Harbor Laboratory
Date: 07-06-2020
DOI: 10.1101/2020.06.06.137729
Abstract: The characterization of developmental phenotypes often relies on the accurate linear measurement of structures that are small and require laborious preparation. This is tedious and prone to errors, especially when repeated for the multiple replicates that are required for statistical analysis, or when multiple distinct structures have to be analysed. To address this issue, we have developed a pipeline for characterization of long-bone length and inter-vertebral distance using X-ray microtomography (XMT) scans. The pipeline involves semi-automated algorithms for automatic thresholding and fast interactive isolation and 3D-model generation of the main limb bones, using either the open-source ImageJ plugin BoneJ or the commercial Mimics Innovation Suite package. The tests showed the appropriate combination of scanning conditions and analysis parameters yields fast and comparable length results, highly correlated with the measurements obtained via ex vivo skeletal preparations. Moreover, since XMT is not destructive, the s les can be used afterwards for histology or other applications. Our new pipelines will help developmental biologists and evolutionary researchers to achieve fast, reproducible and non-destructive length measurement of bone s les from multiple animal species. Beltran Diaz et al. present a semi-automated pipeline for fast and versatile characterization of bone length from micro-CT images of mouse developmental s les.
Publisher: Public Library of Science (PLoS)
Date: 15-03-2010
Publisher: Springer Science and Business Media LLC
Date: 23-02-2017
Publisher: Elsevier BV
Date: 2010
DOI: 10.1016/J.JINSPHYS.2009.09.003
Abstract: Spatial and temporal environmental variation in terrestrial Antarctic ecosystems are known to impact species strongly at a local scale, but the ways in which organisms respond (e.g. physiologically, behaviourally) to such variation are poorly understood. Further, very few studies have attempted to assess inter-annual variability of such responses. Building on previous work demonstrating intra-seasonal variation in standard metabolic rate in the springtail Gomphiocephalushodgsoni, we investigated variation in metabolic activity of G. hodgsoni across two austral summer periods at Cape Bird, Ross Island. We also examined the influence of spatial variation by comparing metabolic rates of G. hodgsoni at Cape Bird with those from two other isolated continental locations within Victoria Land (Garwood and Taylor Valleys). We found significant differences between metabolic rates across the 2 years of measurement at Cape Bird. In addition, standard metabolic rates of G. hodgsoni obtained from Garwood and Taylor Valleys were significantly higher than those at Cape Bird where habitats are comparable, but environmental characteristics differ (e.g. microclimatic temperatures are higher). We discuss potential underlying causes of these metabolic rate variation patterns, including those related to differences among in iduals (e.g. physiological and genetic differences), locations (e.g. habitat quality and microclimatic regime differences) and populations (e.g. acclimation differences among G. hodgsoni populations in the form of metabolic cold adaptation (MCA)).
Publisher: Wiley
Date: 13-10-2022
DOI: 10.1002/JBM4.10559
Abstract: Lower jaw (mandible) fractures significantly impact patient health and well‐being due to pain and difficulty eating, but the best technique for repairing the most common subtype—angle fractures—and rehabilitating mastication is unknown. Our study is the first to use realistic in silico simulation of chewing to quantify the effects of Ch y and biplanar techniques of angle fracture fixation. We show that more rigid, biplanar fixation results in lower strain magnitudes in the miniplates, the bone around the screws, and in the fracture zone, and that the mandibular strain regime approximates the unfractured condition. Importantly, the strain regime in the fracture zone is affected by chewing laterality, suggesting that both fixation type and the patient's post‐fixation masticatory pattern—ipsi‐ or contralateral to the fracture— impact the bone healing environment. Our study calls for further investigation of the impact of fixation technique on chewing behavior. Research that combines in vivo and in silico approaches can link jaw mechanics to bone healing and yield more definitive recommendations for fixation, hardware, and postoperative rehabilitation to improve outcomes. © 2021 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.
Publisher: Cold Spring Harbor Laboratory
Date: 15-01-2020
DOI: 10.1101/2020.01.14.906958
Abstract: Stress is a widespread phenomenon that all organisms must endure. Common in nature is oxidative stress, which can interrupt cell homeostasis to cause cell damage and may be derived from respiration or from environmental exposure thought diet. As a result of the routine exposure from respiration, many organisms can mitigate the effects of oxidative stress, but less is known about responses to oxidative stress from other sources. Helicoverpa armigera is a major agricultural pest moth that causes significant damage to crops worldwide. Here, we examined the effects of oxidative stress on H. armigera by chronically exposing in iduals to paraquat - a free radical producer - and measuring changes in development (weight, developmental rate, lifespan), and gene expression. We found that oxidative stress strongly affected development in H. armigera , with stressed s les spending more time as caterpillars than control s les ( vs. ∼15 days, respectively) and living longer overall. We found 1,618 up- and 761 down-regulated genes, respectively, in stressed vs. control s les. In the up-regulated gene set were genes associated with cell senescence and apoptosis and an over-representation of biological processes related to cuticle and chitin development, glycine metabolism, and oxidation-reduction. Oxidative stress clearly impacts physiology and biochemistry in H. armigera and the interesting finding of an extended lifespan in stressed in iduals could demonstrate hormesis, the process whereby toxic compounds can actually be beneficial at low doses. Collectively, our findings provide new insights into genomic responses to oxidative stress in invertebrates.
Publisher: The Royal Society
Date: 10-2016
DOI: 10.1098/RSOS.160203
Abstract: Elephants, the largest living land mammals, have evolved a specialized foot morphology to help reduce locomotor pressures while supporting their large body mass. Peak pressures that could cause tissue damage are mitigated passively by the anatomy of elephants' feet, yet this mechanism does not seem to work well for some captive animals. This study tests how foot pressures vary among African and Asian elephants from habitats where natural substrates predominate but where foot care protocols differ. Variations in pressure patterns might be related to differences in husbandry, including but not limited to trimming and the substrates that elephants typically stand and move on. Both species' s les exhibited the highest concentration of peak pressures on the lateral digits of their feet (which tend to develop more disease in elephants) and lower pressures around the heel. The trajectories of the foot's centre of pressure were also similar, confirming that when walking at similar speeds, both species load their feet laterally at impact and then shift their weight medially throughout the step until toe-off. Overall, we found evidence of variations in foot pressure patterns that might be attributable to husbandry and other causes, deserving further examination using broader, more comparable s les.
Publisher: The Company of Biologists
Date: 05-2012
DOI: 10.1242/JEB.065862
Abstract: Foot pressure distributions during locomotion have causal links with the anatomical and structural configurations of the foot tissues and the mechanics of locomotion. Elephant feet have five toes bound in a flexible pad of fibrous tissue (digital cushion). Does this specialized foot design control peak foot pressures in such giant animals? And how does body size, such as during ontogenetic growth, influence foot pressures? We addressed these questions by studying foot pressure distributions in elephant feet and their correlation with body mass and centre of pressure trajectories, using statistical parametric mapping (SPM), a neuro-imaging technology. Our results show a positive correlation between body mass and peak pressures, with the highest pressures dominated by the distal ends of the lateral toes (digits 3, 4 and 5). We also demonstrate that pressure reduction in the elephant digital cushion is a complex interaction of its viscoelastic tissue structure and its centre of pressure trajectories, because there is a tendency to avoid rear ‘heel’ contact as an elephant grows. Using SPM, we present a complete map of pressure distributions in elephant feet during ontogeny by performing statistical analysis at the pixel level across the entire plantar almar surface. We hope that our study will build confidence in the potential clinical and scaling applications of mammalian foot pressures, given our findings in support of a link between regional peak pressures and pathogenesis in elephant feet.
Publisher: Oxford University Press (OUP)
Date: 07-2018
DOI: 10.1642/AUK-17-226.1
Publisher: Wiley
Date: 07-02-2013
DOI: 10.1002/ECE3.495
Abstract: The hermaphroditic nematode Pristionchus pacificus is a model organism with a range of fully developed genetic tools. The species is globally widespread and highly erse genetically, consisting of four major independent lineages (lineages A, B, C, and D). Despite its young age (~2.1 Ma), volcanic La Réunion Island harbors all four lineages. Ecological and population genetic research studies suggest that this ersity is due to repeated independent island colonizations by P. pacificus . Here, we use model‐based statistical methods to rigorously test hypotheses regarding the evolutionary history of P. pacificus . First, we employ ergence analyses to date ersification events among the four “world” lineages. Next, we examine demographic properties of a subset of four populations (“a”, “b”, “c”, and “d”), present on La Réunion Island. Finally, we use the results of the ergence and demographic analyses to inform a modeling‐based approximate Bayesian computation ( ABC ) approach, where we test hypotheses about the order and timing of establishment of the Réunion populations. Our dating estimates place the recent common ancestor of P. pacificus lineages at nearly 500,000 generations past. Our demographic analysis supports recent ( ,000 generations) spatial expansion for the island populations, and our ABC approach supports c a b d as the most likely colonization order of the island populations. Collectively, our study comprehensively improves previous inferences about the evolutionary history of P. pacificus .
Publisher: Springer Science and Business Media LLC
Date: 09-04-2011
Publisher: Elsevier BV
Date: 02-2008
DOI: 10.1016/J.YMPEV.2007.10.003
Abstract: We sequenced the mitochondrial (mt) DNA cytochrome c oxidase subunit I gene to examine comparative phylogeographic patterns for the springtail Gomphiocephalus hodgsoni and the mite Stereotydeus mollis throughout their ranges in southern Victoria Land, Antarctica. Our aim was to extend previous genetic work to encompass a large ice-free area in the Dry Valleys. In particular, we sought to determine if this new region harboured high levels of genetic ersity and if patterns of genetic structure were congruent across taxa. Phylogenetic and nested clade analyses for G. hodgsoni and S. mollis showed similar patterns of population sub-structuring among locations and highlighted several potential refugia that may have existed during glacial maxima. We identified greater levels of genetic ergence in S. mollis and suggest that there is a nucleotide substitution (mutation) rate difference between S. mollis and G. hodgsoni, and/or that S. mollis has had a longer association with the Antarctic landscape.
Publisher: Public Library of Science (PLoS)
Date: 30-01-2013
Publisher: PeerJ
Date: 23-02-2016
DOI: 10.7287/PEERJ.PREPRINTS.1779V1
Abstract: Horse racing is a multi-billion-dollar industry that has raised welfare concerns due to disabled and euthanized animals. Whilst the cause of musculoskeletal injuries that lead to horse morbidity and mortality is multifactorial, pre-existing pathologies, increased speeds and substrate of the racecourse are likely contributors to foot disease. The hooves of horses have the ability to naturally deform during locomotion and dissipate locomotor stresses, yet farriery approaches are utilised to increase performance and protect hooves from wear. Previous studies have assessed the effect of different shoe designs on locomotor performance however, no biomechanical study has hitherto measured the effect of horseshoes on the stresses of the foot skeleton in vivo. As there is a need to reduce musculoskeletal injuries in racing and training horses, it is crucial to understand the natural function of the feet of horses and how this is influenced by shoe design. This preliminary study introduces a novel combination of three-dimensional data from biplanar radiography, inverse dynamics, and finite element analysis (FEA) to evaluate the effect of a stainless steel shoe on the function of a Thoroughbred horse’s front foot during walking. Our results show that the stainless steel shoe increases craniocaudal, mediolateral and vertical GRFs at mid-stance. We document a similar pattern of flexion-extension in the PIP (pastern) and DIP (coffin) joint between the unshod and shod conditions, yet variation in the degrees of rotations are encountered throughout the stance phase. In particular, in both the shod and unshod conditions, the PIP joint extends between the 10-40% of the stance phase and flexes before mid-stance and until the end of the stance phase. Similarly the DIP joint extends until the 40% of stance and then flexes until the end of the stance phase. Overall at mid-stance the PIP joint extends more at the shod (-2.9o) than the unshod (-1.5o) horse, whilst the DIP joint extends more at the unshod (-3.6o), than the shod (-2.8o) condition. We also document that the DIP joint flexes more than the PIP after mid-stance and until the end of the stance in both conditions. Our FEA results show increased von Mises stresses on the fore foot phalanges in the shod condition at mid-stance, indicating that the steel shoe increases mechanical loading. Our preliminary study illustrates how the shoe may influence the dynamics and mechanics of a Thoroughbred horse’s forefoot during slow walking, but more research is needed to quantify the effect of the shoe on the equine forefoot during the whole stance phase, at faster speeds/gaits and with more in iduals as well as with a similar focus on the hind feet. We anticipate that our preliminary analysis using advanced methodological approaches will pave the way for new directions in research on the form/function relationship of the equine foot, with the ultimate goal to minimise foot injuries and improve animal health and welfare.
Publisher: Frontiers Media SA
Date: 30-10-2019
Publisher: Informa UK Limited
Date: 21-06-2023
Publisher: Wiley
Date: 29-04-2020
DOI: 10.1002/ECE3.6308
Publisher: Wiley
Date: 08-08-2011
DOI: 10.1002/AJPA.21573
Publisher: Public Library of Science (PLoS)
Date: 31-01-2014
Publisher: Elsevier BV
Date: 10-2017
Publisher: Elsevier BV
Date: 10-2010
DOI: 10.1016/J.YMPEV.2010.06.003
Abstract: We examine the effects of isolation over both ancient and contemporary timescales on evolutionary ersification and speciation patterns of springtail species in circum-Antarctica, with special focus on members of the genus Cryptopygus (Collembola, Isotomidae). We employ phylogenetic analysis of mitochondrial DNA (cox1), and ribosomal DNA (18S and 28S) genes in the programmes MrBayes and RAxML. Our aims are twofold: (1) we evaluate existing taxonomy in light of previous work which found dubious taxonomic classification in several taxa based on cox1 analysis (2) we evaluate the biogeographic origin of our chosen suite of springtail species based on dispersal/vicariance scenarios, the magnitude of genetic ergence among lineages and the age and accessibility of potential habitat. The dubious taxonomic characterisation of Cryptopygus species highlighted previously is confirmed by our multi-gene phylogenetic analyses. Specifically, according to the current taxonomy, Cryptopygus antarcticus subspecies are not completely monophyletic and neither are Cryptopygus species in general. We show that distribution patterns among species/lineages are both dispersal- and vicariance-driven. Episodes of colonisation appear to have occurred frequently, the routes of which may have followed currents in the Southern Ocean. In several cases, the estimated ergence dates among species correspond well with the timing of terrestrial habitat availability. We conclude that these isotomid springtails have a varied and erse evolutionary history in the circum-Antarctic that consists of both ancient and recent elements and is reflected in a dynamic contemporary fauna.
Publisher: Elsevier BV
Date: 10-2017
Publisher: Wiley
Date: 04-07-2016
DOI: 10.1111/MEC.13708
Abstract: Genomewide SNP data generated by nontargeted methods such as RAD and GBS are increasingly being used in phylogenetic and phylogeographic analyses. When these methods are used in the absence of a reference genome, however, little is known about the locations and evolution of the SNPs. In using such data to address phylogenetic questions, researchers risk drawing false conclusions, particularly if a representative number of SNPs is not obtained. Here, we empirically test the robustness of phylogenetic inference based on SNP data for closely related lineages. We conducted a genomewide analysis of 75 712 SNPs, generated via GBS, of southern bull-kelp (Durvillaea). Durvillaea chathamensis co-occurs with D. antarctica on Chatham Island, but the two species have previously been found to be so genetically similar that the status of the former has been questioned. Our results show that D. chathamensis, which differs from D. antarctica ecologically as well as morphologically, is indeed a reproductively isolated species. Furthermore, our replicated analyses show that D. chathamensis cannot be reliably distinguished phylogenetically from closely related D. antarctica using subsets (ranging in size from 400 to 10 000 sites) of the 40 912 parsimony-informative SNPs in our data set and that bootstrap values alone can give misleading impressions of the strength of phylogenetic inferences. These results highlight the importance of independently replicating SNP analyses to verify that phylogenetic inferences based on nontargeted SNP data are robust. Our study also demonstrates that modern genomic approaches can be used to identify cases of recent or incipient speciation that traditional approaches (e.g. Sanger sequencing of a few loci) may be unable to detect or resolve.
Publisher: The Royal Society
Date: 11-2022
DOI: 10.1098/RSOS.220438
Abstract: Biomechanical and clinical studies have yet to converge on the optimal fixation technique for angle fractures, one of the most common and controversial fractures in terms of fixation approach. Prior pre-clinical studies have used a variety of animal models and shown abnormal strain environments exacerbated by less rigid (single-plate) Ch y fixation and chewing on the side opposite the fracture (contralateral chewing). However, morphological differences between species warrant further investigation to ensure that these findings are translational. Here we present the first study to use realistically loaded finite-element models to compare the biomechanical behaviour of human and macaque mandibles pre- and post-fracture and fixation. Our results reveal only small differences in deformation and strain regimes between human and macaque mandibles. In the human model, more rigid biplanar fixation better approximated physiologically healthy global bone strains and moments around the mandible, and also resulted in less interfragmentary strain than less rigid Ch y fixation. Contralateral chewing exacerbated deviations in strain, moments and interfragmentary strain, especially under Ch y fixation. Our pre- and post-fracture fixation findings are congruent with those from macaques, confirming that rhesus macaques are excellent animal models for biomedical research into mandibular fixation. Furthermore, these findings strengthen the case for rigid biplanar fixation over less rigid one-plate fixation in the treatment of isolated mandibular angle fractures.
Publisher: Springer Science and Business Media LLC
Date: 28-02-2020
DOI: 10.1186/S12864-020-6594-0
Abstract: Next generation sequencing (NGS) can recover DNA data from valuable extant and extinct museum specimens. However, archived or preserved DNA is difficult to sequence because of its fragmented, damaged nature, such that the most successful NGS methods for preserved specimens remain sub-optimal. Improving wet-lab protocols and comprehensively determining the effects of s le age on NGS library quality are therefore of vital importance. Here, I examine the relationship between s le age and several indicators of library quality following targeted NGS sequencing of ~ 1300 loci using 271 s les of pinned moth specimens ( Helicoverpa armigera ) ranging in age from 5 to 117 years. I find that older s les have lower DNA concentrations following extraction and thus require a higher number of indexing PCR cycles during library preparation. When sequenced reads are aligned to a reference genome or to only the targeted region, older s les have a lower number of sequenced and mapped reads, lower mean coverage, and lower estimated library sizes, while the percentage of adapters in sequenced reads increases significantly as s les become older. Older s les also show the poorest capture success, with lower enrichment and a higher improved coverage anticipated from further sequencing. S le age has significant, measurable impacts on the quality of NGS data following targeted enrichment. However, incorporating a uracil-removing enzyme into the blunt end-repair step during library preparation could help to repair DNA damage, and using a method that prevents adapter-dimer formation may result in improved data yields.
Publisher: Public Library of Science (PLoS)
Date: 11-2018
Publisher: PeerJ
Date: 05-04-2016
DOI: 10.7717/PEERJ.1895
Abstract: Herman Melville’s novel Moby Dick was inspired by historical instances in which large sperm whales ( Physeter macrocephalus L. ) sank 19th century whaling ships by ramming them with their foreheads. The immense forehead of sperm whales is possibly the largest, and one of the strangest, anatomical structures in the animal kingdom. It contains two large oil-filled compartments, known as the “spermaceti organ” and “junk,” that constitute up to one-quarter of body mass and extend one-third of the total length of the whale. Recognized as playing an important role in echolocation, previous studies have also attributed the complex structural configuration of the spermaceti organ and junk to acoustic sexual selection, acoustic prey debilitation, buoyancy control, and aggressive ramming. Of these additional suggested functions, ramming remains the most controversial, and the potential mechanical roles of the structural components of the spermaceti organ and junk in ramming remain untested. Here we explore the aggressive ramming hypothesis using a novel combination of structural engineering principles and probabilistic simulation to determine if the unique structure of the junk significantly reduces stress in the skull during quasi-static impact. Our analyses indicate that the connective tissue partitions in the junk reduce von Mises stresses across the skull and that the load-redistribution functionality of the former is insensitive to moderate variation in tissue material parameters, the thickness of the partitions, and variations in the location and angle of the applied load. Absence of the connective tissue partitions increases skull stresses, particularly in the rostral aspect of the upper jaw, further hinting of the important role the architecture of the junk may play in ramming events. Our study also found that impact loads on the spermaceti organ generate lower skull stresses than an impact on the junk. Nevertheless, whilst an impact on the spermaceti organ would reduce skull stresses, it would also cause high compressive stresses on the anterior aspect of the organ and the connective tissue case, possibly making these structures more prone to failure. This outcome, coupled with the facts that the spermaceti organ houses sensitive and essential sonar producing structures and the rostral portion of junk, rather than the spermaceti organ, is frequently a site of significant scarring in mature males suggest that whales avoid impact with the spermaceti organ. Although the unique structure of the junk certainly serves multiple functions, our results are consistent with the hypothesis that the structure also evolved to function as a massive battering ram during male-male competition.
Publisher: The Royal Society
Date: 11-08-2021
Abstract: Snake fangs are an iconic exemplar of a complex adaptation, but despite striking developmental and morphological similarities, they probably evolved independently in several lineages of venomous snakes. How snakes could, uniquely among vertebrates, repeatedly evolve their complex venom delivery apparatus is an intriguing question. Here we shed light on the repeated evolution of snake venom fangs using histology, high-resolution computed tomography (microCT) and biomechanical modelling. Our examination of venomous and non-venomous species reveals that most snakes have dentine infoldings at the bases of their teeth, known as plicidentine, and that in venomous species, one of these infoldings was repurposed to form a longitudinal groove for venom delivery. Like plicidentine, venom grooves originate from infoldings of the developing dental epithelium prior to the formation of the tooth hard tissues. Derivation of the venom groove from a large plicidentine fold that develops early in tooth ontogeny reveals how snake venom fangs could originate repeatedly through the co-option of a pre-existing dental feature even without close association to a venom duct. We also show that, contrary to previous assumptions, dentine infoldings do not improve compression or bending resistance of snake teeth during biting plicidentine may instead have a role in tooth attachment.
Publisher: The Royal Society
Date: 13-08-2021
Abstract: The mechanical behaviour of the mandibles of Pan and Macaca during mastication was compared using finite element modelling. Muscle forces were calculated using species-specific measures of physiological cross-sectional area and scaled using electromyographic estimates of muscle recruitment in Macaca . Loading regimes were compared using moments acting on the mandible and strain regimes were qualitatively compared using maps of principal, shear and axial strains. The enlarged and more vertically oriented temporalis and superficial masseter muscles of Pan result in larger sagittal and transverse bending moments on both working and balancing sides, and larger anteroposterior twisting moments on the working side. The mandible of Pan experiences higher principal strain magnitudes in the ramus and mandibular prominence, higher transverse shear strains in the top of the symphyseal region and working-side corpus, and a predominance of sagittal bending-related strains in the balancing-side mandible. This study lays the foundation for a broader comparative study of Hominidae mandibular mechanics in extant and fossil hominids using finite element modelling. Pan 's larger and more vertical masseter and temporalis may make it a more suitable model for hominid mandibular biomechanics than Macaca .
Publisher: The Royal Society
Date: 10-2022
DOI: 10.1098/RSOS.220701
Abstract: Canine teeth are vital to carnivore feeding ecology, facilitating behaviours related to prey capture and consumption. Forms vary with specific feeding ecologies however, the biomechanics that drive these relationships have not been comprehensively investigated. Using a combination of beam theory analysis (BTA) and finite-element analysis (FEA) we assessed how aspects of canine shape impact tooth stress, relating this to feeding ecology. The degree of tooth lateral compression influenced tolerance of multidirectional loads, whereby canines with more circular cross-sections experienced similar maximum stresses under pulling and shaking loads, while more ellipsoid canines experienced higher stresses under shaking loads. Robusticity impacted a tooth's ability to tolerate stress and appears to be related to prey materials. Robust canines experience lower stresses and are found in carnivores regularly encountering hard foods. Slender canines experience higher stresses and are associated with carnivores biting into muscle and flesh. Curvature did not correlate with tooth stress however, it did impact bending during biting. Our simulations help identify scenarios where canine forms are likely to break and pinpoint areas where this breakage may occur. These patterns demonstrate how canine shape relates to tolerating the stresses experienced when killing and feeding, revealing some of the form–function relationships that underpin mammalian carnivore ecologies.
Publisher: Frontiers Media SA
Date: 26-11-2015
Publisher: Wiley
Date: 26-03-2013
DOI: 10.1111/MEC.12286
Abstract: Comprehensive studies of evolution have historically been h ered by the ision among disciplines. Now, as biology moves towards an '-omics' era, it is more important than ever to tackle the evolution of function and form by considering all those research areas involved in the regulation of phenotypes. Here, we review recent attempts to establish the nematode Pristionchus pacificus as a model organism that allows integrative studies of development and evo-devo, with ecology and population genetics. Originally developed for comparative study with the nematode Caenorhabditis elegans, P. pacificus provided insight into developmental pathways including dauer formation, vulva and gonad development, chemosensation, innate immunity and neurobiology. Its subsequent discovery across a wide geographic distribution in association with scarab beetles enabled its evaluation in a biogeographic context. Development of an evolutionary field station on La Réunion Island, where P. pacificus is present in high abundance across a number of widespread habitat types, allows examination of the microfacets of evolution - processes of natural selection, adaptation and drift among populations can now be examined in this island setting. The combination of laboratory-based functional studies with fieldwork in P. pacificus has the long-term prospective to provide both proximate (mechanistic) and ultimate (evolutionary and ecological) causation and might therefore help to overcome the long-term ide between major areas in biology.
Publisher: Informa UK Limited
Date: 2009
DOI: 10.1080/03014460903019879
Abstract: A fundamental research question for morphologists is how morphological variation in the skeleton relates to function. Traditional approaches have advanced our understanding of form-function relationships considerably but have limitations. Strain gauges can only record strains on a surface, and the geometry of the structure can limit where they can be bonded. Theoretical approaches, such as geometric abstractions, work well on problems with simple geometries and material properties but biological structures typically have neither of these. Finite element analysis (FEA) is a method that overcomes these problems by reducing a complex geometry into a finite number of elements with simple geometries. In addition, FEA allows strain to be modelled across the entire surface of the structure and throughout the internal structure. With advances in the processing power of computers, FEA has become more accessible and as such is becoming an increasingly popular tool to address questions about form-function relationships in development and evolution, as well as human biology generally. This paper provides an introduction to FEA including a review of the sequence of steps needed for the generation of biologically accurate finite element models that can be used for the testing of biological and functional morphology hypotheses.
Publisher: MDPI AG
Date: 06-04-2011
Publisher: Wiley
Date: 20-07-2021
DOI: 10.1111/MEC.15999
Abstract: Studies of invasive species can simultaneously inform management strategies and quantify rapid evolution in the wild. The role of genomics in invasion science is increasingly recognised, and the growing availability of reference genomes for invasive species is paving the way for whole‐genome resequencing studies in a wide range of systems. Here, we survey the literature to assess the application of whole‐genome resequencing data in invasion biology. For some applications, such as the reconstruction of invasion routes in time and space, sequencing the whole genome of many in iduals can increase the accuracy of existing methods. In other cases, population genomic approaches such as haplotype analysis can permit entirely new questions to be addressed and new technologies applied. To date whole‐genome resequencing has only been used in a handful of invasive systems, but these studies have confirmed the importance of processes such as balancing selection and hybridization in allowing invasive species to reuse existing adaptations and rapidly overcome the challenges of a foreign ecosystem. The use of genomic data does not constitute a paradigm shift per se, but by leveraging new theory, tools, and technologies, population genomics can provide unprecedented insight into basic and applied aspects of invasion science.
Publisher: Wiley
Date: 05-10-2022
DOI: 10.1111/JBI.14481
Abstract: We consider the opportunities and challenges comparative phylogeography (CP) faces in the genomic age to determine: (1) how we can maximise the potential of big CP analyses to advance biogeographic and macroevolutionary theory and (2) what we can, and will struggle, to achieve using CP approaches in this era of genomics. World‐wide. All. We review the literature to discuss the future of CP ‐ particularly examining CP insights enabled by genomics that may not be possible for single species and/or few molecular markers. We focus on how geography and species' natural histories interact to yield congruent and incongruent patterns of neutral and adaptive processes in the context of both historical and recent rapid evolution. We also consider how CP genomic data are being stored, accessed, and shared. With the widespread availability of genomic data, the shift from a single‐ to a multi‐locus perspective is resulting in detailed historical inferences and an improved statistical rigour in phylogeography. However, the time and effort required for collecting co‐distributed species and accruing species‐specific ecological knowledge continue to be limiting factors. Bioinformatic skills and user‐friendly analytical tools, alongside the computational infrastructure required for big data, can also be limiting. Over the last ~35 years, there has been much progress in understanding how intraspecific genetic variation is geographically distributed. The next major steps in CP will be to incorporate evolutionary processes and community perspectives to account for patterns and responses among co‐distributed species and across temporal scales, including those related to anthropogenic change. However, the full potential of CP will only be realised if we employ robust study designs within a sound comparative framework. We advocate that phylogeographers adopt such consistent approaches to enhance future comparisons to present‐day findings.
Publisher: Springer Science and Business Media LLC
Date: 23-01-2015
Publisher: Elsevier BV
Date: 07-2021
Publisher: Wiley
Date: 14-02-2019
DOI: 10.1002/ECE3.4971
Publisher: Wiley
Date: 29-11-2011
Publisher: Springer Science and Business Media LLC
Date: 09-02-2010
Start Date: 2024
End Date: 2027
Funder: Marsden Fund
View Funded ActivityStart Date: 2024
End Date: 2027
Funder: Marsden Fund
View Funded ActivityStart Date: 02-2016
End Date: 05-2020
Amount: $372,000.00
Funder: Australian Research Council
View Funded Activity