Elephants as an animal model for self-domestication.

Humans are unique in their sophisticated culture and societal structures, their complex languages, and their extensive tool use. According to the human self-domestication hypothesis, this unique set of traits may be the result of an evolutionary process of self-induced domestication, in which humans evolved to be less aggressive and more cooperative. However, the only other species that has been argued to be self-domesticated besides humans so far is bonobos, resulting in a narrow scope for investigating this theory limited to the primate order. Here, we propose an animal model for studying self-domestication: the elephant. First, we support our hypothesis with an extensive cross-species comparison, which suggests that elephants indeed exhibit many of the features associated with self-domestication (e.g., reduced aggression, increased prosociality, extended juvenile period, increased playfulness, socially regulated cortisol levels, and complex vocal behavior). Next, we present genetic evidence to reinforce our proposal, showing that genes positively selected in elephants are enriched in pathways associated with domestication traits and include several candidate genes previously associated with domestication. We also discuss several explanations for what may have triggered a self-domestication process in the elephant lineage. Our findings support the idea that elephants, like humans and bonobos, may be self-domesticated. Since the most recent common ancestor of humans and elephants is likely the most recent common ancestor of all placental mammals, our findings have important implications for convergent evolution beyond the primate taxa, and constitute an important advance toward understanding how and why self-domestication shaped humans' unique cultural niche.

Interpreting the Evolutionary Echoes of a Protein Complex Essential for Inner-Ear Mechanosensation.

The sensory epithelium of the inner ear, found in all extant lineages of vertebrates, has been subjected to over 500 million years of evolution, resulting in the complex inner ear of modern vertebrates. Inner-ear adaptations are as diverse as the species in which they are found, and such unique anatomical variations have been well studied. However, the evolutionary details of the molecular machinery that is required for hearing are less well known. Two molecules that are essential for hearing in vertebrates are cadherin-23 and protocadherin-15, proteins whose interaction with one another acts as the focal point of force transmission when converting sound waves into electrical signals that the brain can interpret. This "tip-link" interaction exists in every lineage of vertebrates, but little is known about the structure or mechanical properties of these proteins in most non-mammalian lineages. Here, we use various techniques to characterize the evolution of this protein interaction. Results show how evolutionary sequence changes in this complex affect its biophysical properties both in simulations and experiments, with variations in interaction strength and dynamics among extant vertebrate lineages. Evolutionary simulations also characterize how the biophysical properties of the complex in turn constrain its evolution and provide a possible explanation for the increase in deafness-causing mutants observed in cadherin-23 relative to protocadherin-15. Together, these results suggest a general picture of tip-link evolution in which selection acted to modify the tip-link interface, although subsequent neutral evolution combined with varying degrees of purifying selection drove additional diversification in modern tetrapods.

Mechanism of Cardiac Troponin C Calcium Sensitivity Modulation by Small Molecules Illuminated by Umbrella Sampling Simulations.

Cardiac troponin C (cTnC) binds intracellular calcium and subsequently cardiac troponin I (cTnI), initiating cardiac muscle contraction. Due to its role in contraction, cTnC has been a therapeutic target in the search for small molecules to treat conditions that interfere with normal muscle contraction like the heritable cardiomyopathies. Structural studies have shown the binding location of small molecules such as bepridil, dfbp-o, 3-methyldiphenylamine (DPA), and W7 to be a hydrophobic pocket in the regulatory domain of cTnC (cNTnC) but have not shown the influence of these small molecules on the energetics of opening this domain. Here we describe an application of an umbrella sampling method used to elucidate the impact these calcium sensitivity modulators have on the free energy of cNTnC hydrophobic patch opening. We found that all these molecules lowered the free energy of opening in the absence of the cTnI, with bepridil facilitating the least endergonic transformation. In the presence of cTnI, however, we saw a stabilization of the open configuration due to DPA and dfbp-o binding, and a destabilization of the open configuration imparted by bepridil and W7. Predicted poor binding molecule NSC34337 left the hydrophobic patch in under 3 ns in conventional MD simulations suggesting that only hydrophobic patch binders stabilized the open conformation. In conclusion, this study presents a novel approach to study the impact of small molecules on hydrophobic patch opening through umbrella sampling, and it proposes mechanisms for calcium sensitivity modulation.

Rapid evolution of genes with anti-cancer functions during the origins of large bodies and cancer resistance in elephants.

Elephants have emerged as a model system to study the evolution of body size and cancer resistance because, despite their immense size, they have a very low prevalence of cancer. Previous studies have found that duplication of tumor suppressors at least partly contributes to the evolution of anti-cancer cellular phenotypes in elephants. Still, many other mechanisms must have contributed to their augmented cancer resistance. Here, we use a suite of codon-based maximum-likelihood methods and a dataset of 13,310 protein-coding gene alignments from 261 Eutherian mammals to identify positively selected and rapidly evolving elephant genes. We found 496 genes (3.73% of alignments tested) with statistically significant evidence for positive selection and 660 genes (4.96% of alignments tested) that likely evolved rapidly in elephants. Positively selected and rapidly evolving genes are statistically enriched in gene ontology terms and biological pathways related to regulated cell death mechanisms, DNA damage repair, cell cycle regulation, epidermal growth factor receptor (EGFR) signaling, and immune functions, particularly neutrophil granules and degranulation. All of these biological factors are plausibly related to the evolution of cancer resistance. Thus, these positively selected and rapidly evolving genes are promising candidates for genes contributing to elephant-specific traits, including the evolution of molecular and cellular characteristics that enhance cancer resistance.

Pervasive loss of regulated necrotic cell death genes in elephants, hyraxes, and sea cows (Paenungualta).

Gene loss can promote phenotypic differences between species, for example, if a gene constrains phenotypic variation in a trait, its loss allows for the evolution of a greater range of variation or even new phenotypes. Here, we explore the contribution of gene loss to the evolution of large bodies and augmented cancer resistance in elephants. We used genomes from 17 Afrotherian and Xenarthran species to identify lost genes, i.e., genes that have pseudogenized or been completely lost, and Dollo parsimony to reconstruct the evolutionary history of gene loss across species. We unexpectedly discovered a burst of gene losses in the Afrotherian stem lineage and found that the loss of genes with functions in regulated necrotic cell death modes was pervasive in elephants, hyraxes, and sea cows (Paenungulata). Among the lost genes are MLKL and RIPK3, which mediate necroptosis, and sensors that activate inflammasomes to induce pyroptosis, including AIM2, MEFV, NLRC4, NLRP1, and NLRP6. These data suggest that the mechanisms that regulate necrosis and pyroptosis are either extremely derived or potentially lost in these lineages, which may contribute to the repeated evolution of large bodies and cancer resistance in Paenungulates as well as susceptibility to pathogen infection.

Effects of Oregano (Origanum vulgare) Essential Oil Supplementation on Growth Performance of Zebrafish (Danio rerio) Fed a High-Inclusion Soybean Meal Diet.

Soybean meal (SBM) has become a common dietary replacement for fish meal (FM) in aquafeed. However, at high inclusions, SBM has been shown to have negative impacts presenting as reduced feed intake and intestinal inflammation. Medicinal plant extracts, namely essential oils, have been used to promote growth performance and immune response. The objective of this study was to investigate the potential therapeutic effects of oregano (Origanum vulgare) essential oil (OEO) inclusion on utilization of a high-inclusion SBM diet using zebrafish as a model. Five diets were used in this study: reference-FM-based diet, control-55.7% inclusion SBM diet, and three experimental SBM-based diets OEO1, OEO2, and OEO3 that were supplemented with 1%, 2%, or 3% of oregano oil, respectively. The FM group had overall better growth performance when compared with the other treatment groups; however, the OEO3 mean weight and feed conversion ratio were not significantly different from the FM group (p > 0.05) and were significantly improved compared with the SBM group (p < 0.05). Similarly, OEO2 total length was not significantly different from FM (p > 0.05) but significantly higher than the SBM group (p < 0.05). Expression of inflammation-related genes did not significantly differ between the OEO groups and the SBM-only group. However, the OEO2 and OEO3 groups displayed improved growth performance compared with the SBM group, suggesting that inclusion of OEO at or above 2% inclusion may help to alleviate common symptoms induced by a high-inclusion SBM diet.

Phylogenomics reveals an almost perfect polytomy among the almost ungulates (Paenungulata).

Phylogenetic studies have resolved most relationships among Eutherian Orders. However, the branching order of elephants (Proboscidea), hyraxes (Hyracoidea), and sea cows (Sirenia) (i.e., the Paenungulata) has remained uncertain since at least 1758, when Linnaeus grouped elephants and manatees into a single Order (Bruta) to the exclusion of hyraxes. Subsequent morphological, molecular, and large-scale phylogenomic datasets have reached conflicting conclusions on the branching order within Paenungulates. We use a phylogenomic dataset of alignments from 13,388 protein-coding genes across 261 Eutherian mammals to infer phylogenetic relationships within Paenungulates. We find that gene trees almost equally support the three alternative resolutions of Paenungulate relationships and that despite strong support for a Proboscidea+Hyracoidea split in the multispecies coalescent (MSC) tree, there is significant evidence for gene tree uncertainty, incomplete lineage sorting, and introgression among Proboscidea, Hyracoidea, and Sirenia. Indeed, only 8-10% of genes have statistically significant phylogenetic signal to reject the hypothesis of a Paenungulate polytomy. These data indicate little support for any resolution for the branching order Proboscidea, Hyracoidea, and Sirenia within Paenungulata and suggest that Paenungulata may be as close to a real, or at least unresolvable, polytomy as possible.

Invasive grass (Microstegium vimineum) indirectly benefits spider community by subsidizing available prey.

Invasive plant species cause a suite of direct, negative ecological impacts, but subsequent, indirect effects are more complex and difficult to detect. Where identified, indirect effects to other taxa can be wide-ranging and include ecological benefits in certain habitats or locations.Here, we simultaneously examine the direct and indirect effects of a common, invasive grass species (Microstegium vimineum) on the invertebrate communities of understory deciduous forests in the eastern United States. To do this, we use two complementary analytic approaches to compare invaded and reference plots: (a) community composition analysis of understory arthropod taxa and (b) analysis of isotopic carbon and nitrogen ratios of a representative predatory spider species.Invaded plots contained a significantly greater abundance of nearly all taxa, including predators, herbivores, and detritivores. Spider communities contained over seven times more individuals and exhibited greater species diversity and richness in invaded plots.Surprisingly, however, the abundant invertebrate community is not nutritionally supported by the invasive plant, despite 100% ground cover of M. vimineum. Instead, spider isotopic carbon ratios showed that the invertebrate prey community found within invaded plots was deriving energy from the plant tissue of C3 plants and not the prevalent, aboveground M. vimineum. Synthesis and applications. We demonstrate that invasive M. vimineum can create non-nutritional ecological benefits for some invertebrate taxa, with potential impacts to the nutritional dynamics of invertebrate-vertebrate food webs. These positive impacts, however, may be restricted to habitats that experience high levels of ungulate herbivory or reduced vegetative structural complexity. Our results highlight the importance of fully understanding taxon- and habitat-specific effects of invading plant species when prioritizing invasive species removal or management efforts.

Revisiting Hunter Perceptions toward Chronic Wasting Disease: Changes in Behavior over Time.

Hunter behavior varies in relation to perceived risk of Chronic Wasting Disease (CWD) and changes in perceptions of CWD will lead to changes in behavior over time. During 2018, we surveyed deer (Odocoileus virginianus or Cervus nippon) hunters from Maryland, USA, regarding behavioral changes due to CWD. We matched 477 respondents to their harvest record and created two geographical groups based on harvest history in counties closest to disease presence. We compared the proportion of hunters who claimed to have changed their behavior in each group and estimated the effects of CWD on harvest rate for the 4 years immediately after the discovery of CWD and the following 4-year period. We found no difference between the groups in the proportion of hunters who changed their behavior due to CWD. We found a significant decline in harvest rate for hunters who claimed to change their behavior in the group closest to CWD presence during the period immediately after the discovery of CWD; however, these same hunters increased their harvest rates in the next time period to pre-CWD levels. Overall, we found that time alleviates some perceived risk of CWD and that this is reflected in hunting behavior.

Computational Studies of Cardiac and Skeletal Troponin.

Troponin is a key regulatory protein in muscle contraction, consisting of three subunits troponin C (TnC), troponin I (TnI), and troponin T (TnT). Calcium association to TnC initiates contraction by causing a series of dynamic and conformational changes that allow the switch peptide of TnI to bind and subsequently cross bridges to form between the thin and thick filament of the sarcomere. Owing to its pivotal role in contraction regulation, troponin has been the focus of numerous computational studies over the last decade. These studies elegantly supplemented a large volume of experimental work and focused on the structure, dynamics and function of the whole troponin complex, individual subunits, and even on segments of the thin filament. Molecular dynamics, Brownian dynamics, and free energy simulations have been used to elucidate the conformational dynamics and underlying free energy landscape of troponin, calcium, and switch peptide binding, as well as the effect of disease mutations, small molecules and post-translational modifications such as phosphorylation. Frequently, simulations have been used to confirm or explain experimental observations. Computer-aided drug discovery tools have been employed to identify novel potential calcium sensitizing agents binding to the TnC-TnI interface. Finally, Markov modeling has contributed to simulating contraction within the sarcomere on the mesoscale. Here we are reviewing and classifying the existing computational work on troponin and its subunits, outline current gaps in simulations elucidating troponin's role in contraction and suggest potential future developments in the field.

Genetic diversity and demographic history of introduced sika deer on the Delmarva Peninsula.

The introduction of non-native species can have long-term effects on native plant and animal communities. Introduced populations are occasionally not well understood and offer opportunities to evaluate changes in genetic structure through time and major population changes such as bottleneck and or founder events. Invasive species can often evolve rapidly in new and novel environments, which could be essential to their long-term success. Sika deer are native to East Asia, and their introduction and establishment to the Delmarva Peninsula, USA, is poorly documented, but probably involved ≥1 founder and/or bottleneck events. We quantified neutral genetic diversity in the introduced population and compared genetic differentiation and diversity to the presumed source population from Yakushima Island, Japan, and a captive population of sika deer in Harrington, Delaware, USA. Based on the data from 10 microsatellite DNA loci, we observed reduced genetic variation attributable to founder events, support for historic hybridization events, and evidence that the population did originate from Yakushima Island stocks. Estimates of population structure through Bayesian clustering and demographic history derived from approximate Bayesian computation (ABC), were consistent with the hypothesized founder history of the introduced population in both timing and effective population size (approximately five effective breeding individuals, an estimated 36 generations ago). Our ABC results further supported a single introduction into the wild happening before sika deer spread throughout the Delmarva. We conclude that free-ranging sika deer on Delmarva are descended from ca. five individuals introduced about 100 years ago from captive stocks of deer maintained in the United Kingdom. Free-ranging sika deer on Delmarva have lost neutral diversity due to founder and bottleneck events, yet populations have expanded in recent decades and show no evidence of abnormalities associated with inbreeding. We suggest management practices including increasing harvest areas and specifically managing sika deer outside of Maryland.

Molecular Dynamics and Umbrella Sampling Simulations Elucidate Differences in Troponin C Isoform and Mutant Hydrophobic Patch Exposure.

Troponin C (TnC) facilitates muscle contraction through calcium-binding within its N-terminal region (NTnC). As previously observed using molecular dynamics (MD) simulations, this calcium-binding event leads to an increase in the dynamics of helices lining a hydrophobic patch on TnC. Simulation times of multiple microseconds were required to even see a partial opening of the hydrophobic patch, limiting the ability to thoroughly and quantitatively investigate these rare events. Here we describe the application of umbrella sampling to probe the TnC hydrophobic patch opening in a more targeted and quantitative fashion. Umbrella sampling was utilized to investigate the differences in the free energy of opening between cardiac (cTnC) and fast skeletal TnC (sTnC). We found that, in agreement with previous reports, holo (calcium-bound) sTnC had a lower free energy of opening compared with holo cTnC. Additionally, differences in the free energy of opening of hypertrophic (HCM) and dilated cardiomyopathy (DCM) cTnC systems were investigated. MD simulations and umbrella sampling revealed a lower free energy of opening for the HCM mutations A8V and A31S, as well as the calcium-sensitizing mutation L48Q. The DCM mutations, Y5H, Q50R, and E59D/D75Y, all exhibited a higher free energy of opening. An umbrella sampling simulation of cTnI-bound holo cTnC exhibited the lowest free energy in the open configuration, in agreement with experimental data. In conclusion, this study presents a novel and successful protocol for applying umbrella sampling simulations to quantitatively study the molecular basis of muscle contraction and proposes a mechanism by which HCM and DCM-associated mutations influence contraction.

Rare Osteochondroma Associated with Natural Mortality of a Wild White-Tailed Deer ( Odocoileus virginianus).

Within a 6-mo period, a radio-collared, white-tailed deer ( Odocoileus virginianus) doe from Delaware, US, developed a fatal head mass consistent with osteochondroma. We suspected a retroviral etiology, but test results were negative. Population implications were not suspected, but this case is concerning as these tumors are not thought to cause mortality.

Multiflora rose invasion amplifies prevalence of Lyme disease pathogen, but not necessarily Lyme disease risk.

BACKGROUND: Forests in urban landscapes differ from their rural counterparts in ways that may alter vector-borne disease dynamics. In urban forest fragments, tick-borne pathogen prevalence is not well characterized; mitigating disease risk in densely-populated urban landscapes requires understanding ecological factors that affect pathogen prevalence. We trapped blacklegged tick (Ixodes scapularis) nymphs in urban forest fragments on the East Coast of the United States and used multiplex real-time PCR assays to quantify the prevalence of four zoonotic, tick-borne pathogens. We used Bayesian logistic regression and WAIC model selection to understand how vegetation, habitat, and landscape features of urban forests relate to the prevalence of B. burgdorferi (the causative agent of Lyme disease) among blacklegged ticks. RESULTS: In the 258 nymphs tested, we detected Borrelia burgdorferi (11.2% of ticks), Borrelia miyamotoi (0.8%) and Anaplasma phagocytophilum (1.9%), but we did not find Babesia microti (0%). Ticks collected from forests invaded by non-native multiflora rose (Rosa multiflora) had greater B. burgdorferi infection rates (mean = 15.9%) than ticks collected from uninvaded forests (mean = 7.9%). Overall, B. burgdorferi prevalence among ticks was positively related to habitat features (e.g. coarse woody debris and total understory cover) favorable for competent reservoir host species. CONCLUSIONS: Understory structure provided by non-native, invasive shrubs appears to aggregate ticks and reservoir hosts, increasing opportunities for pathogen transmission. However, when we consider pathogen prevalence among nymphs in context with relative abundance of questing nymphs, invasive plants do not necessarily increase disease risk. Although pathogen prevalence is greater among ticks in invaded forests, the probability of encountering an infected tick remains greater in uninvaded forests characterized by thick litter layers, sparse understories, and relatively greater questing tick abundance in urban landscapes.

Theileriosis in Multiple Neonatal White-tailed Deer ( Odocoileus virginianus) in Delaware, USA.

Postmortem examination of 21 neonatal white-tailed deer ( Odocoileus virginianus) from Delaware, US identified six fawns with Theileria spp. organisms or suspected infection.

Differential post-fledging habitat use of Nearctic-Neotropical migratory birds within an urbanized landscape.

BACKGROUND: Persistent declines in migratory songbird populations continue to motivate research exploring contributing factors to inform conservation efforts. Nearctic-Neotropical migratory species' population declines have been linked to habitat loss and reductions in habitat quality due to increasing urbanization in areas used throughout the annual cycle. Despite an increase in the number of studies on post-fledging ecology, generally characterized by the period between fledging and dispersal from natal areas or migration, contextual research linking post-fledging survival and habitat use to anthropogenic factors remains limited. METHODS: Here, we examined habitat use of post-fledging habitat-generalist gray catbirds (Dumetella caroliniensis), and habitat-specialist wood thrushes (Hylocichla mustelina), up to 88 days after fledging within an urbanized landscape. These Neotropical migratory species share many life-history traits, exhibit differential degrees of habitat specialization, and co-occur in urbanized landscapes. Starting from daily movement data, we used time-integrated Brownian bridges to generate probability density functions of each species' probability of occurrence, and home range among 16 land cover classes including roads from the US Geological Survey National Land Cover Database for each species. RESULTS: Habitat use differed between pre- and post-independence periods. After controlling for factors that influence habitat use (i.e., pre- or post-independence period, fate (whether individuals survived or not), and land cover class), we found that wood thrushes occupied home ranges containing six times more forest land cover than catbirds. In contrast, catbirds occupied home ranges containing twice the area of roads compared to wood thrushes. Wood thrushes had greater variance for area used (km2) among land cover classes within home ranges compared to catbirds. However, once fledglings achieved independence from parents, wood thrushes had lower variance associated with area used compared to catbirds. CONCLUSIONS: Our findings support predictions that habitat-generalist gray catbirds spend more time in developed areas, less time in forest habitat, and use areas with more roads than the forest-specialist wood thrush. We found strong effects of pre- and post-independence periods on all of the response variables we tested. Species-specific habitat use patterns will likely be affected by projected increases in urbanization over the next several decades leading to further reductions in available forest habitat and increased road density, and will have important implications for the ecology and conservation of these birds.