Ancient mitochondrial genomes recovered from small vertebrate bones through minimally destructive DNA extraction: phylogeography of the New Zealand gecko genus Hoplodactylus.

Methodological and technological improvements are continually revolutionizing the field of ancient DNA. Most ancient DNA extraction methods require the partial (or complete) destruction of finite museum specimens, which disproportionately impacts small or fragmentary subfossil remains, and future analyses. We present a minimally destructive ancient DNA extraction method optimized for small vertebrate remains. We applied these methods to detect lost mainland genetic diversity in the large New Zealand diplodactylid gecko genus Hoplodactylus, which is presently restricted to predator-free island sanctuaries. We present the first mitochondrial genomes for New Zealand diplodactylid geckos, recovered from 19 modern, six historic/archival (1898 to 2011) and 16 Holocene Hoplodactylus duvaucelii sensu latu specimens, and one modern Woodworthia sp. specimen. No obvious damage was observed in post-extraction micro-CT reconstructions. All ‘large gecko’ specimens examined from extinct populations were found to be conspecific with extant Hoplodactylus species, suggesting their large relative size evolved only once in the New Zealand diplodactylid radiation. Phylogenetic analyses of Hoplodactylus samples recovered two genetically (and morphologically) distinct North and South Island clades, probably corresponding to distinct species. Finer phylogeographic structuring within Hoplodactylus spp. highlighted the impacts of Late-Cenozoic biogeographic barriers, including the opening and closure of Pliocene marine straits, fluctuations in size and suitability of glacial refugia, and eustatic sea-level change. Recent mainland extinction obscured these signals from the modern tissue derived data. These results highlight the utility of minimally destructive DNA extraction in genomic analyses of less well studied small vertebrate taxa, and the conservation of natural history collections.

Small herbivores and abiotic heterogeneity promote trait variation of a saltmarsh plant in local communities

Intraspecific trait variation (ITV) enables plants to respond to global changes. However, causes for ITV, especially from biotic components such as herbivory, are not well understood. We explored whether small vertebrate herbivores (hares and geese) impact ITV of a dominant clonal plant (Elytrigia atherica) in local communities. Moreover, we looked at the relative importance of their direct (e.g., selective grazing) and indirect effects (altering genotypic richness/diversity and abiotic environment) on ITV. We used exclosures at two successional stages in a Dutch saltmarsh, where grazing pressure at the early successional stage was ca. 1.5 times higher than that of the intermediate successional stage. We measured key functional traits of E. atherica including height, aboveground biomass, flowering (flower or not), specific leaf area, and leaf dry matter content in local communities (1 m × 1 m plots) inside and outside the exclosures. We determined genotypic richness and diversity of each plant using molecular markers. We further measured abiotic variations in topography and clay thickness (a proxy for soil total nitrogen). Structural equation models revealed that small herbivores significantly promoted ITV in height and flowering at the early successional stage, while they marginally promoted ITV in height at the intermediate successional stage. Moreover, the direct effects of herbivores played a major role in promoting ITV. Small herbivores decreased genotypic diversity at the intermediate successional stage, but genotypic richness and diversity did not impact ITV. Small herbivores did not alter topographic variation and variation in clay thickness, but these variations increased ITV in all traits at the early successional stage. Small herbivores may not only impact trait means in plants as studies have shown but also their ITV.

Bizarre morphology in extinct Eocene bugs (Heteroptera: Pentatomidae)

Newly discovered fossil bugs (Insecta: Hemiptera: Heteroptera: Pentatomidae) from the Eocene of Messel (Germany) and Green River (North America) exhibit an exaggerated morphology including prominent spiny humeral and anterolateral angles of the pronotum and a spiny lateral abdominal margin. Especially the humeral angles are unique; they consist of expansive, rounded projections with strong spines, which is a rare trait among pentatomids. A hypothesis for the function of this extreme morphology is defence against small vertebrate predators, such as birds or reptiles. The same protuberances also produce a disruptive effect camouflaging the specimen in its environment and provide additional protection. Therefore, the extreme morphology provides primary as well as secondary anti-predator defence. The morphology of Eospinosus peterkulkai gen. et sp. nov. and E. greenriverensis sp. nov. resembles that of Triplatygini, which today occur exclusively in Madagascar, as well as that of Discocephalinae or Cyrtocorinae, which today occur in the Neotropics. Due to a lack of conclusive characters, it cannot be excluded that the fossil species may represent a case of remarkable convergence and are not related to either taxon. Phylogenetic analyses using parsimony as well as Bayesian algorithms confirmed that the new genus is a member of Pentatomidae, but could not solve its phylogenetic relationships within Pentatomidae.

Effect of food source availability in the salivary gland transcriptome of the unique burying beetle Nicrophorus pustulatus (Coleoptera: Silphidae)

Nicrophorus is a genus of beetles that bury and transform small vertebrate carcasses into a brood ball coated with their oral and anal secretions to prevent decay and that will serve as a food source for their young. Nicrophorus pustulatus is an unusual species with the ability to overtake brood of other burying beetles and whose secretions, unlike other Nicrophorus species, has been reported not to exhibit antimicrobial properties. This work aims to better understand how the presence or absence of a food source influences the expression of genes involved in the feeding process of N. pustulatus. To achieve that, total RNA was extracted from pooled samples of salivary gland tissue from N. pustulatus and sequenced using an Illumina platform. The resulting reads were used to assemble a de novo transcriptome using Trinity. Duplicates with more than 95% similarity were removed to obtain a “unigene” set. Annotation of the unigene set was done using the Trinotate pipeline. Transcript abundance was determined using Kallisto and differential gene expression analysis was performed using edgeR. A total of 651 genes were found to be differentially expressed, including 390 upregulated and 261 downregulated genes in fed insects compared to starved. Several genes upregulated in fed beetles are associated with the insect immune response and detoxification processes with only one transcript encoding for the antimicrobial peptide (AMP) defensin. These results confirm that N. pustulatus does not upregulate the production of genes encoding AMPs during feeding. This study provides a snapshot of the changes in gene expression in the salivary glands of N. pustulatus following feeding while providing a well described transcriptome for the further analysis of this unique burying beetle.

Does Communal Breeding Promote an Increase in Social Immunity in Burying Beetles? A Test Case with Nicrophorus Defodiens

Communal breeding is a reproductive system in which more than a single pair of individuals share parental care duties. Burying beetles (genus Nicrophorus) breed on small vertebrate carcasses, which is used as a food source for their young. On larger carcasses, burying beetles will breed communally, forming multiple male-female associations. A significant and costly component of parental investment by burying beetles is the preservation of the carcass with secretions containing immune molecules. Because this immune investment is for the benefit of the offspring, the behavior is a form of social immunity. We test the hypothesis that communal breeding in burying beetles evolved as a mechanism to increase the social immune investment on larger carcasses, which are more difficult to preserve. We used N. defodiens, a communal breeding burying beetle species to test the hypothesis. There were two experimental treatments wherein, the females either bred communally or non-communally. Our results show that the combined immune activity in the secretions were higher in communally breeding pairs than in the immune contribution of single male-female pairs. However, subordinate females were rarely observed on the carcass, and the level of social immune activity of dominant females was lower than females breeding singly. These data suggest that communal breeding in N. defodiens decreases the level of investment in social immunity. Our results demonstrate that the presence of multiple females, which is common under natural conditions, can greatly complicate patterns of social immunity investment in burying beetles.