Contributors:Giles S., Friedman M., Dobson C., Johanson Z., Liston J.
Our understanding of the ecology and phylogenetic relationships of Pachycormiformes, a group of Mesozoic stem teleosts including the iconic Leedsichthys, has often been hindered by a lack of comprehensive morphological information. Micro‐CT scanning of an articulated, although flattened, cranium of the edentulous Martillichthys renwickae from the Middle Jurassic (Callovian) Oxford Clay of the UK reveals previously unknown internal details of the most complete suspension‐feeding pachycormiform skull known, including the palate, braincase and branchial skeleton. The latter preserves gill rakers with elongate, pointed projections similar to those of Asthenocormus, in contrast to the finer fimbriations associated with Leedsichthys. We also reinterpret some previously described features, including dermal bone patterns of the snout, skull roof and lower jaw, and the morphology of the ventral hyoid arch. These new anatomical data reinforce the phylogenetic placement of Martillichthys as part of the Jurassic clade of edentulous pachycormiforms. The elongate skull geometry of these Jurassic taxa is strikingly similar to that of Ohmdenia, the sister taxon to edentulous pachycormiforms, but contrasts sharply with the morphology of the Late Cretaceous edentulous pachycormiform Bonnerichthys, raising questions over the phylogenetic relationships among these taxa. Most significantly, Martillichthys shows specialized characters with a restricted phylogenetic distribution among suspension‐feeding pachycormiforms, including the distinctive gill rakers and a greatly extended occipital stalk. Our analysis of Martillichthys supports past interpretations of a close relationship with Asthenocormus, and provides a model for interpreting the less complete remains of other members of this enigmatic group of fishes.
Contributors:Kastally, Chedly, Trasoletti, Marta, Mardulyn, Patrick
Analysing genomic variation within and between sister species is a first step towards understanding species boundaries. We focused on two sister species of cold-resistant leaf beetles, Gonioctena quinquepunctata and G. intermedia, whose ranges overlap in the Alps. A previous study of DNA sequence variation had revealed multiple instances of mitochondrial genome introgression in this region, suggesting recent hybridizations between the two species. To evaluate the extent of gene exchange resulting from these hybridization events, we sampled individuals of both species inside and outside the hybrid zone and analysed genomic variation among them using RAD-seq markers. Individual levels of introgression in the nuclear genome were estimated first by defining species-specific SNPs (displaying a fixed difference between species) a priori, and second by using model-based methods. Both types of analyses indicated little gene exchange, if any, between species at the level of the nuclear genome. While the first method suggested slightly more gene flow, we argue that it has likely overestimated introgression in the phylogeographic context of this study. We conclude that strong intrinsic barriers prevent genetic exchange at the level of the nuclear genome between the two species. The apparent discrepancy observed between introgression occurring in the nuclear and mitochondrial genomes could be explained by selection acting in favour of the latter. Also, these results have consequences for the phylogeographic study of each species, since we can assume that genetic diversity in the overlapping portion of their ranges is not the product of introgression.
Information on how migratory populations are genetically structured during the overwintering season of the annual cycle can improve our understanding of the strength of migratory connectivity and help identify populations as units for management. Here, we use a genotype-by-sequencing approach to investigate whether population genetic structure exists among overwintering aggregations of the Pacific Dunlin subspecies (Calidris alpina pacifica) sampled at two spatial scales (i.e. within and among overwintering sites) in the eastern Pacific Flyway. Genome-wide analyses of 874 single nucleotide polymorphisms across 80 sampled individuals revealed no evidence for genetic differentiation among aggregations overwintering at three locations within the Fraser River Estuary (FRE) of British Columbia. Similarly, comparisons of aggregations in the FRE and those overwintering in southern sites in California and Mexico indicated no genetic segregation between northern and
southern overwintering areas. These results suggest that Pacific Dunlin residing within the FRE, Sacramento Valley (California) and Guerrero Negro (Mexico) are genetically homogeneous, with no evident genetic structure between sampled sites or regions across the overwintering range. Despite no evidence for differentiation among aggregations, we identified a significant effect of geographical distance between sites on the distribution of individual genotypes in a redundancy analysis; however, a small proportion of the total genotypic variance (R2 = 0.036, P = 0.011) was explained by the combined effect of latitude and longitude, suggesting weak genomic patterns of isolation-by-distance that are consistent with chain-like migratory connectivity between breeding and overwintering areas. Our study represents the first genome-scale investigation of population structure for a Dunlin subspecies and provides essential baseline estimates of genomic diversity and differentiation
within the Pacific Dunlin.
Contributors:Rohani P., King A.A., Magpantay F.M.G.
Mathematical models of childhood diseases date back to the early twentieth century. In several cases, models that make the simplifying assumption of homogeneous time-dependent transmission rates give good agreement with data in the absence of secular trends in population demography or transmission. The prime example is afforded by the dynamics of measles in industrialized countries in the pre-vaccine era. Accurate description of the transient dynamics following the introduction of routine vaccination has proved more challenging, however. This is true even in the case of measles which has a well-understood natural history and an effective vaccine that confers long-lasting protection against infection. Here, to shed light on the causes of this problem, we demonstrate that, while the dynamics of homogeneous and age-structured models can be qualitatively similar in the absence of vaccination, they diverge subsequent to vaccine roll-out. In particular, we show that immunization induces changes in transmission rates, which in turn reshapes the age distribution of infection prevalence, which effectively modulates the amplitude of seasonality in such systems. To examine this phenomenon empirically, we fit transmission models to measles notification data from London that span the introduction of the vaccine. We find that a simple age-structured model provides a much better fit to the data than does a homogeneous model, especially in the transition period from the pre-vaccine to the vaccine era. Thus, we propose that age structure and heterogeneities in contact rates are critical features needed to accurately capture transient dynamics in the presence of secular trends.
Contributors:Mathur S., Tomecek J.M., Heniff A., Luna R., DeWoody J.A.
Population extirpations are often precursors to species extinctions. Anthropogenic activities often lead to smaller populations that are more prone to extirpations and advocates for active conservation management have recently called for the preservation and monitoring of genetic diversity, particularly with regard to the adaptive potential of vulnerable populations. We used genomics and curated arrays of molecular markers, including those expected to impact key fitness traits, to quantify evidence of genomic erosion in core and peripheral populations of a gallinaceous bird. The Montezuma quail (Cyrtonyx montezumae) is a game species considered vulnerable to extirpation in Texas, but core populations in Arizona and New Mexico are robust and have the potential to serve as genetic reservoirs. We sequenced the Montezuma quail genome then developed a single nucleotide polymorphism (SNP) assay to quantify genetic variation, effective population sizes, signatures of natural selection, and population structure. We genotyped SNPs from gene deserts and from genes associated with fitness traits and found the isolated Texas population exhibits an extremely small effective population size, is genetically distinct from our Arizona and New Mexico samples, and has reduced heterozygosity at the fitness-related markers. Thus, our samples from Texas exhibit symptoms of genetic erosion that could exacerbate future risk of local extirpation. Management agencies must decide if active conservation efforts such as assisted gene flow or genetic rescue are now warranted. This decision may not be straightforward because the current conservation status of the Texas population reflects its isolated geographic locale on the periphery of the species’ range.
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.
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.
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.