Contributors:Johnson C.A., Hebblewhite M., Muhly T.B., Neilson E.W., Schmiegelow F., Merrill E., Patterson B.R., McLoughlin P.D., Latham M.C., Fortin D., Musiani M., Fryxell J.M., Latham A.D.M., Scurrah F., Paquet P.C.
Aim: The influence of humans on large carnivores, including wolves, is a worldwide conservation concern. In addition, human‐caused changes in carnivore density and distribution might have impacts on prey and, indirectly, on vegetation. We therefore tested wolf responses to infrastructure related to natural resource development (i.e., human footprint).
Location: Our study provides one of the most extensive assessments of how predators like wolves select habitat in response to various degrees of footprint across boreal ecosystems encompassing over a million square kilometers of Canada.
Methods: We deployed GPS‐collars on 172 wolves, monitored movements and used a generalized functional response (GFR) model of resource selection. A functional response in habitat selection occurs when selection varies as a function of the availability of that habitat. GFRs can clarify how human‐induced habitat changes are influencing wildlife across large, diverse landscapes.
Results: Wolves displayed a functional response to footprint. Wolves were more likely to select forest harvest cutblocks in regions with higher cutblock density (i.e., a positive functional response to high‐quality habitats for ungulate prey) and to select for higher road density in regions where road density was high (i.e., a positive functional response to human‐created travel routes). Wolves were more likely to use cutblocks in habitats with low road densities, and more likely to use roads in habitats with low cutblock densities, except in winter when wolves were more likely to use roads regardless of cutblock density.
Main conclusions: These interactions suggest that wolves trade‐off among human‐impacted habitats, and adaptively switch from using roads to facilitate movement (while also risking encounters with humans), to using cutblocks that may have higher ungulate densities. We recommend that conservation managers consider the contextual and interacting effects of footprints when assessing impacts on carnivores. These effects likely have indirect impacts on ecosystems too, including on prey species.
We develop a spatially explicit model of diversification based on paleohabitat to explore the predictions of four major hypotheses potentially explaining the latitudinal diversity gradient (LDG), namely, the ‘time-area’, ‘tropical niche conservatism’, ‘ecological limits’ and ‘evolutionary speed’ hypotheses. We compare simulation outputs to observed diversity gradients in the global reef fish fauna. Our simulations show that these hypotheses are non-mutually exclusive and that their relative influence depends on the time scale considered. Indeed, simulations suggest that reef habitat dynamics produced the LDG during deep geological time, while ecological constraints shaped the modern LDG, with a strong influence of the reduction in the latitudinal extent of tropical reefs during the Neogene. Overall, this study illustrates how mechanistic models in ecology and evolution can provide a temporal and spatial understanding of the role of speciation, extinction and dispersal in generating contemporary biodiversity patterns.
Contributors:Hamilton, Chris A., St. Laurent, Ryan A., Dexter, Kelly, Kitching, Ian J., Breinholt, Jesse W., Zwick, Andreas, Timmermans, Martijn, Barber, Jesse R., Kawahara, Akito Y.
Background: Silkmoths and their relatives constitute the ecologically and taxonomically diverse superfamily Bombycoidea, which includes some of the most charismatic species of Lepidoptera. Despite displaying spectacular forms and diverse ecological traits, relatively little attention has been given to understanding their evolution and drivers of their diversity. To begin to address this problem, we created a new Bombycoidea-specific Anchored Hybrid Enrichment (AHE) probe set and sampled up to 571 loci for 117 taxa across all major lineages of the Bombycoidea, with a newly developed DNA extraction protocol that allows Lepidoptera specimens to be readily sequenced from pinned natural history collections.Results The well-supported tree was overall consistent with prior morphological and molecular studies, although some taxa (e.g., the bombycid, Arotros Schaus) were misplaced and here formally transferred to Apatelodidae. We identified important evolutionary patterns (e.g., morphology, biogeography, and differences in speciation and extinction), and our analysis of diversification rates highlights the stark increases that exist within the Sphingidae (hawkmoths) and Saturniidae (wild silkmoths).Conclusions Our study establishes a backbone for future evolutionary, comparative, and taxonomic studies of Bombycoidea. We postulate that the rate shifts identified are due to the well-documented bat-moth “arms race”. Our research highlights the flexibility of AHE to generate genomic data from a wide range of museum specimens, both age and preservation method, and will allow researchers to tap into the wealth of biological data residing in natural history collections around the globe.
Contributors:Salomies, Lotta, Eymann, Julia, Khan, Imran, Di-Poï, Nicolas
Deep understanding of lifelong tooth replacement is hampered by the lack of polyphyodonty or oral dentition in conventional models. Here, we show that the bearded dragon, one of the rare vertebrate species with both polyphyodont and monophyodont teeth, constitutes a key model for filling this gap, allowing direct comparison of extreme dentition types. Our developmental and high-throughput transcriptomic data of microdissected dental cells unveils the critical importance of successional dental lamina patterning, in addition to maintenance, for vertebrate tooth renewal. This patterning process happens at various levels, including directional growth but also gene expression levels, dynamics, and regionalization, and involves a large number of yet uncharacterized dental genes. Furthermore, the alternative renewal mechanism of bearded dragon dentition, with dual location of slow-cycling cells, demonstrates the importance of cell migration and functional specialization of putative epithelial stem/progenitor niches in tissue regeneration, while expanding the diversity of dental replacement strategies in vertebrates.
Contributors:Carlson K.M., Hodgson J.A., Heilmayr R., Lucey J.M., Hill J.K., McClean C.J., Scriven S.A.
1. Habitat connectivity is important for tropical biodiversity
conservation. Expansion of commodity crops, such as oil palm, fragments
natural habitat areas, and strategies are needed to improve habitat
connectivity in agricultural landscapes. The Roundtable on Sustainable Palm
Oil (RSPO) voluntary certification system requires that growers identify
and conserve forest patches identified as High Conservation Value Areas
(HCVAs) before oil palm plantations can be certified as sustainable. We
assessed the potential benefits of these conservation set-asides for forest
2. We mapped HCVAs and quantified their forest cover in 2015. To assess
their contribution to forest connectivity, we modelled range expansion of
forest-dependent populations with five dispersal abilities spanning those
representative of poor dispersers (e.g., flightless insects) to more mobile
species (e.g., large birds or bats) across 70 plantation landscapes in
3. Because only 21% of HCVA area was forested in 2015, these conservation
set-asides currently provide few connectivity benefits. Compared to a
scenario where HCVAs contain no forest (i.e., a no-RSPO scenario), current
HCVAs improved connectivity by ~3% across all dispersal abilities. However,
if HCVAs were fully reforested, then overall landscape connectivity could
improve by ~16%. Reforestation of HCVAs had the greatest benefit for poor
to intermediate dispersers (0.5-3 km per generation), generating landscapes
that were up to 2.7 times better connected than landscapes without HCVAs.
By contrast, connectivity benefits of HCVAs were low for highly mobile
populations under current and reforestation scenarios, because range
expansion of these populations was generally successful regardless of the
amount of forest cover.
4.Synthesis and applications. The RSPO requires that HCVAs be set
aside to conserve biodiversity, but HCVAs currently provide few
connectivity benefits because they contain relatively little forest.
However, reforested HCVAs have the potential to improve landscape
connectivity for some forest species (e.g., winged insects), and we
recommend active management by plantation companies to improve forest
quality of degraded HCVAs (e.g., by enrichment planting). Future revisions
to the RSPO’s Principles and Criteria (P&C) should also ensure that large
(i.e., with a core area >2 km2) HCVAs are reconnected to continuous tracts
of forest to maximise their connectivity benefits.
Contributors:Rennison, Diana Jessie, Delmore, Kira E, Samuk, Kieran M, Owens, Gregory L, Miller, Sara E
Closely related populations often display similar patterns of genomic differentiation, yet it remains an open question which ecological and evolutionary forces generate these patterns. The leading hypothesis is that this similarity in divergence is driven by parallel natural selection. However, several recent studies have suggested that these patterns may instead be a product of the depletion of genetic variation that occurs as result of background selection (i.e. linked negative selection). To date, there have been few direct tests of these competing hypotheses. To determine the relative contributions of background selection and parallel selection to patterns of repeated differentiation, we examined 24 independently derived populations of freshwater stickleback occupying a variety of niches and estimated genomic patterns of differentiation in each relative to their common marine ancestor. Patterns of genetic differentiation were strongly correlated across pairs of freshwater populations adapting to the same ecological niche, supporting a role for parallel natural selection. In contrast to other recent work, by examining populations adapting to the same niche we did not find evidence that similar patterns of genomic differentiation are generated by background selection. We also found that overall patterns of genetic differentiation were considerably more similar for populations found in closer geographic proximity. In fact, the effect of geography on the repeatability of differentiation was greater than that of parallel selection. Our results suggest that shared selective landscapes and ancestral variation are the key drivers of repeated patterns of differentiation in systems that have recently colonized novel environments.
Background: Geographic speciation is a major force in generating biodiversity. However, how genomes diverge over time after geographic isolation has halted gene flow has remained unclear. We examine genome-wide divergence of putatively single-copy orthologous genes (POGs) from transcriptomes in 20 allopatric species/variety pairs from diverse angiosperm clades. Sixteen of these pairs reflect the well-known eastern Asia – eastern North America floristic disjunction; these species have been isolated for different lengths of time, from the Miocene to Pleistocene. Results: Molecular evolutionary analyses revealed that >90% of the genes examined are under purifying selection and <10% are under positive selection, and this pattern was observed for all taxon pairs, despite differences in divergence time. The divergence level at synonymous sites shared by most POGs in each taxon pair predicts the divergence time between the species/varieties. Divergence time estimates were positively correlated with abundance of genes under moderate purifying selection, but negatively correlated with abundance of genes under strong purifying selection. We identified 200 genes under strong positive selection across the species pairs, with 14 shared by 10-15 pairs and one shared by all taxon pairs. An additional 15 loci annotated to biological processes responding to various stimuli were present in 1-3 pairs.Conclusions: Our results suggest a common “most genes conserved–few genes adaptive” genomic architecture for the taxon pairs, which may be a key for maintaining a balance between the ability to conserve ancestral functions and the ability to evolve new features beneficial for new adaptations. As geographic isolation proceeds through time, the evolutionary trajectory of some genes changed from strong purifying selection to more relaxed selection. The allopatric divergence of these taxon pairs involved both neutral and adaptive evolution of functional genes.
Contributors:Haponski A.E., Foighil D.O.
The genus Corbicula consists of estuarine or freshwater clams native to temperate/tropical regions of Asia, Africa, and Australia that collectively encompass both sexual species and clonal (androgenetic) lineages. The latter have become globally invasive in freshwater systems and they represent some of the most successful aquatic invasive lineages. Previous studies have documented four invasive clonal lineages, Forms A, B, C, and Rlc, with varying known distributions. Form A (R in Europe) occurs globally, Form B is found solely in North America, mainly the western United States, Form C (S in Europe) occurs both in European watersheds and in South America, and Rlc is known from Europe. A putative fifth invasive morph, Form D, was recently described in the New World from the Illinois River (Great Lakes watershed), where it occurs in sympatry with Forms A and B. An initial study showed Form D to be conchologically distinct: possessing rust-colored rays and white nacre with purple teeth. However, its genetic distinctiveness using standard molecular markers (mitochondrial cytochrome c oxidase subunit I and nuclear ribosomal 28S RNA) was ambiguous. To resolve this issue, we performed a phylogenomic analysis using 1,699-30,027 nuclear genomic loci collected via the next generation double digested restriction-site associated DNA sequencing method. Our results confirmed Form D to be a distinct invasive New World lineage with a population genomic profile consistent with clonality. A majority (7/9) of the phylogenomic analyses recovered the four New World invasive Corbicula lineages (Forms A, B, C, and D) as members of a clonal clade, sister to the non-clonal Lake Biwa (Japan) endemic, C. sandai. The age of the clonal clade was estimated at 1.49 million years (my; ± 0.401– 2.955 my) whereas the estimated ages of the four invasive lineage crown clades ranged from 0.27-0.44 my. We recovered no evidence of nuclear genomic admixture among the four invasive lineages in our study populations. In contrast, 2/6 C. sandai individuals displayed partial nuclear genomic Structure assignments with multiple invasive clonal lineages. These results provide new insights into the origin and maintenance of clonality in this complex system.
Contributors:Graham R.T., Rhodes K.L., Baremore I.
Fish spawning aggregations (FSA) act as biological hotspots that concentrate food and nutrients across a broad trophic spectrum. In Pohnpei (Federated States of Micronesia), 20 female grey reef sharks (Carcharhinus amblyrhynchos) were acoustically tagged at two multi-species grouper (Epinephelidae) FSA to examine the likelihood that these mesopredators utilize FSA as a seasonal food source. Both FSA sites are within small-scale MPAs, thus providing a secondary opportunity to examine their conservation potential during these ephemeral events. Shark movement and residency was gauged against known spatial and temporal grouper reproductive patterns using an array of 15 and 50 acoustic receivers at Ant Atoll and Pohnpei (Island), respectively. Activity space was investigated using Kernel Density estimates of individual sharks, and residency indices (RI) were analyzed based on daily and monthly occurrence at the array. Three distinct residency patterns were identified: transient, semi-transient, or resident (Daily RI 0.400.80, respectively). Generalized linear mixed models (GLMMs) were used to identify biological and environmental factors influencing shark activity space, including month, temperature, shark size, spawning month, and residency pattern. Findings revealed significant changes in average monthly residency indices and kernel densities during spawning months in support of an opportunistic foraging strategy around FSA. Monthly residency was higher during spawning months among semi-resident and transient sharks, while average monthly activity space was concentrated around FSA. Best-fit models for the GLMM indicated that activity spaces were most influenced by month and grouper spawning month. Seven of 20 sharks demonstrated inter-island movement and wide variations in individual movement and spatial requirements were shown. The concentration of sharks and groupers at unprotected FSA sites increases their vulnerability to fishing and supports the need for combined area and non-area management measures to effectively protect these species.
Contributors:Wilken, Alec T, Middleton, Kevin M, Sellers, Kaleb C, Cost, Ian N, Holliday, Casey M
Many vertebrates exhibit cranial kinesis, or movement between bones of the skull other than at the jaw joint. Many kinetic species possess a particular suite of features to accomplish this movement, including flexible cranial joints and protractor musculature. Whereas the skeletal anatomy of these kinetic systems is well understood, how these joints are biomechanically loaded, how different soft tissues affect joint loading and kinetic capacity, and how the protractor musculature loads the skull remain poorly understood. Here we developed a Finite Element Model of the savannah monitor, Varanus exanthematicus, a modestly kinetic lizard, to better elucidate the roles of soft tissue in mobile joints and protractor musculature on cranial loading. We described the 3D resultants of jaw muscles and histology of palatobasal, otic and jaw joints. We tested the effects of joint tissue types, bite point, and muscle loads to evaluate the biomechanical role of muscles have on the palate and braincase. We found the jaw muscles have significant mediolateral components and resultants that can impart stability across palatocranial joints. We found articular tissues affect the magnitude of strains experienced across the palatobasal and otic joints. We found that without protractor muscle loading, the palate, quadrate and braincase experience higher strains suggesting this muscle helps insulate the braincase and palatoquadrate from high loads. Finally, we found the cross-sectional properties of the bones of Varanus exanthematicus is well suited for performing under torsional loads. These findings suggest that torsion may be a significant driver in the evolution of cranial kinesis in lepidosaurs.