Rosie Drinkwater

Objective: This study aimed to investigate morphometric and plumage-colour variation among native chickens from Wallacea and Java, Indonesia, and to evaluate the contributions of geographic and production-system factors to phenotypic diversity. Methods: Native chickens were sampled from 259 households across eight provinces in Indonesia. Household-level information on production systems and farmer selection practices was collected through structured surveys. Morphometric traits and HSV-derived plumage-colour variables were analysed using principal component analysis (PCA), permutational multivariate analysis of variance (PERMANOVA), and hierarchical variance partitioning to assess phenotypic variation across locations, provinces, and islands. Results: Substantial phenotypic variation was observed among sampled populations, with significant province- and island-level differences detected for several morphometric traits. However, extensive overlap among locations was evident in both morphometric and plumage-colour space, indicating diffuse rather than discrete structuring. Within-location variation accounted for the largest proportion of total phenotypic variance across most traits, consistent with decentralised smallholder management and continued human-mediated exchange. Conclusion: Geographic fragmentation and agroecological heterogeneity alone appear insufficient to generate strongly differentiated phenotypic groups when connectivity among populations is maintained. Whether this phenotypic connectivity corresponds to contemporary gene flow, retained ancestral variation, or convergent environmental responses remains to be tested using genomic data.

Given the high levels of endemism, diversity, and increasing anthropogenic impacts in tropical regions, studies on species interactions and ecological networks are urgently needed to understand community responses to environmental change. Increasingly, molecular methods are used to monitor biodiversity and identify species interactions. In this study, we developed an optimised DNA metabarcoding protocol to construct quantitative dung beetle‐vertebrate trophic networks in a heterogenous tropical forest. We show that while the highest probability of detection is within 3 h of feeding, vertebrate DNA can still be detected in most beetles after 24 h, including around 50% of beetles with visually empty guts. Using the vertebrate taxa detected from DNA in the gut contents, we constructed dung beetle‐vertebrate networks across 50 forest sites. Our networks displayed high trophic generalism and nestedness. By using group‐specific primers, we documented interactions between dung beetles and multiple vertebrate species, including amphibians, birds, and rare mammals, such as the Sunda slow loris and Sunda pangolin. Our optimised molecular techniques contribute towards the development of new methods for comprehensive biodiversity assessments and ecological network studies that are urgently needed to monitor biodiversity in the hyper‐diverse tropics.

Sexual reproduction is ancient and ubiquitous despite its obvious disadvantages¹. Theory predicts that the reassortment of alleles that results from sex is necessary for natural selection to act effectively on individual loci; therefore, a purely clonal organism should rapidly accumulate deleterious mutations and go extinct^2,3,4. Nevertheless, many asexual species have existed for longer than theory predicts is possible^5,6,7, such as the Amazon molly (Poecilia formosa), a clonally reproducing fish arising from a single hybridization event more than 100,000 years ago^8,9,10. Here we show that although the Amazon molly has accumulated mutations faster than its sexual progenitor species, this has not led to functional mutational decay, defying theoretical expectations. Instead, gene conversion facilitates both adaptive and purifying selection by generating new clonal lineages in which previous mutations are either reverted or fixed, and by resolving hybrid incompatibilities between the ancestral haplotypes. The transition to clonality altered chromatin structure, but the asexual haplotypes of the Amazon molly nonetheless maintain the divergent mutational landscapes of their progenitor species. Together, these results provide new insights into long-standing questions about the trade-offs involved in asexual reproduction.

Several millennia of human-mediated translocation of non-native pig species (genus Sus ) to the islands of Wallacea and Oceania have considerably altered local ecosystems. To investigate the timing and trajectory of these introductions, we conducted both genomic analyses of 576 pig nuclear genomes and a geometric morphometric analysis of 708 modern and ancient dental remains. Our analyses demonstrate that free-living and domestic pigs in Wallacea and Oceania have diverse ancestries resulting from the introduction of multiple sequential pig populations followed by gene flow. Despite the variability in their genomic ancestry, these pigs all have a distinct tooth morphology as well as a genetic link to the Chinese domestic pig populations that accompanied the dispersal of Austronesian language speakers ~4000 to 3000 years ago via Taiwan and the Philippines.

Oculocutaneous albinism—characterized by absent or decreased melanin in the skin, eyes and hair—often co-occurs with sensory, skin and immunity disorders. The genetic basis of albinism in humans is complex, with many loci implicated in multiple forms of the disorder. Less is known about the underlying genetic causes of albinism and leucism in other species, and cross-species studies of the molecular correlates of hypopigmentation could highlight common and conserved pathways underlying mammalian pigmentation disorders. We characterize the putative causal loci of reduced pigmentation in an Egyptian fruit bat (Rousettus aegyptiacus) that displayed features indicative of albinism. Despite albino or leucistic individuals having been reported in >100 bat species, the associated genetic backgrounds have not previously been studied. We used a digital gene expression panel to quantify mRNA levels in wing membrane samples of four candidate pigmentation genes in the focal albino fruit bat and control individuals. Significantly reduced SLC45A2 mRNA expression was found in the albino compared to five bats with typical coloration. Additionally, intraspecific sequence analyses of the albino bat SLC45A2 coding sequence identified two missense mutations, E18A and Q298R, the former of which was private to the albino bat. Position 18 of SLC45A2 was otherwise found to be highly conserved across 60 bat species and has not been previously linked to human albinism. By identifying SLC45A2 as the likely contributing locus, our results also indicate further support for the necessity of genetic testing for the reliable categorization of hypopigmented animals as either albino or leucistic.

Aculeate wasps are apex predators and play an important role in regulating arthropod populations. Determining what they hunt and how their diet varies with species ecology, geography and demography is essential to value their contributions as pest controllers in natural and human-modified ecosystems. There are many practical advantages in the study of social wasp diets. As central place foragers, hundreds of foragers bring prey back to the same location (the nest) every day; this means wasp diets can be explored by identifying taxa in prey balls collected directly from foragers arriving at the nest. A second advantage is that the colonies tend to contain large numbers of brood: prey can be identified from the gut contents of larvae or from the faeces that remain after metamorphosis. Morphological identification of insect remnants found in prey balls has provided insights into wasp diets but this approach is time-consuming and requires expert taxonomists. Metabarcoding is a more efficient method for describing insect diets; it has been used to identify prey of social wasps by sequencing prey balls, larvae guts and larval faeces. However, because of the ecological impact, data on social wasp diets are currently heavily skewed towards invasive populations. We lack comprehensive studies documenting what social wasps hunt in their native habitats. We use DNA metabarcoding to analyse the prey in over 500 wasp larvae guts from 14 nests of Vespula spp, sampled in their native range, across southern England. We describe the diverse diets of these insects, with the detection of 12 arthropod Orders in the guts of 554 larvae, and explore how diet varies across different locations. These data demonstrate the highly generalist predator role provided by Vespula , highlighting the key ecological roles they play as regulators of a broad range of arthropod taxa in native ecosystems and provide an important baseline for further exploring their ecological and economic value.

Human mediated translocation of non-native pig species (genus Sus ) to the islands of Wallacea and Oceania has significantly altered local ecosystems. To investigate the timing and trajectory of these introductions, we conducted both genomic analyses of 576 pig nuclear genomes and a geometric morphometric analysis of 714 modern and ancient dental remains. Our analyses demonstrate that feral and domestic pigs in Wallacea and Oceania possess diverse ancestries resulting from the introduction of multiple, sequential pig populations followed by gene flow. Despite the variability in their genomic ancestry these pigs all possess a distinct tooth morphology, and a genetic link to the Chinese domestic pig populations that accompanied the dispersal of Austronesian language speakers ∼4,000-3,000 years ago via Taiwan and the Philippines.

Island populations of large vertebrates have experienced higher extinction rates than mainland populations over long timescales due to demographic stochasticity, genetic drift, and inbreeding. While being more susceptible to extinction and as such potentially targeted for conservation interventions such as genetic rescue, small-island populations can experience relatively less anthropogenic habitat degradation than those on larger islands. Here, we determine the consequences and conservation implications of long-term isolation and recent human activities on genetic diversity of island populations of two forest-dependent mammals endemic to the Wallacea archipelago: the anoa ( Bubalus spp.) and babirusa ( Babyrousa spp.). Using genomic analyses and habitat suitability models, we show that, compared to closely related species, populations on mainland Sulawesi exhibit low heterozygosity, high inbreeding, a high proportion of deleterious alleles, and experience a high rate of anthropogenic disturbance. In contrast, populations on smaller islands occupy higher-quality habitats, possess fewer deleterious mutations despite exhibiting lower heterozygosity and higher inbreeding. Site frequency spectra indicate that these patterns reflect stronger, long-term purging in smaller-island populations. Our results thus suggest that conservation efforts should focus on protecting small-island high-quality habitats and avoiding translocations from mainland populations. This study highlights the crucial role of small offshore islands for the long-term survival of Wallacea’s iconic and indigenous mammals in the face of development on the mainland.

With biodiversity loss escalating globally, a step change is needed in our capacity to accurately monitor species populations across ecosystems. Robotic and autonomous systems (RAS) offer technological solutions that may substantially advance terrestrial biodiversity monitoring, but this potential is yet to be considered systematically. We used a modified Delphi technique to synthesize knowledge from 98 biodiversity experts and 31 RAS experts, who identified the major methodological barriers that currently hinder monitoring, and explored the opportunities and challenges that RAS offer in overcoming these barriers. Biodiversity experts identified four barrier categories: site access, species and individual identification, data handling and storage, and power and network availability. Robotics experts highlighted technologies that could overcome these barriers and identified the developments needed to facilitate RAS-based autonomous biodiversity monitoring. Some existing RAS could be optimized relatively easily to survey species but would require development to be suitable for monitoring of more ‘difficult’ taxa and robust enough to work under uncontrolled conditions within ecosystems. Other nascent technologies (for instance, new sensors and biodegradable robots) need accelerated research. Overall, it was felt that RAS could lead to major progress in monitoring of terrestrial biodiversity by supplementing rather than supplanting existing methods. Transdisciplinarity needs to be fostered between biodiversity and RAS experts so that future ideas and technologies can be codeveloped effectively.

Invertebrate‐derived DNA (iDNA) has been successfully utilized for surveying mammalian biodiversity in several ecosystems. Yet, as with all sampling methods, this approach suffers from potential biases, including those introduced by the choice of invertebrate sampler, as well as the stochasticity of DNA amplification during PCR. Occupancy modeling is a statistical framework that can help account for imperfect detections in sampling and can be used to improve iDNA surveys. Using a case study based on the DNA screened from the blood meals of leeches, we demonstrate how multiscale occupancy models can be applied to the molecular detection of vertebrates to reveal the nuances in iDNA detections. Leeches were collected across a habitat degradation gradient in Sabah, Malaysian Borneo, in 2015 and 2016. We estimated three probabilities describing the occupancy, availability, and detection of three abundant mammals (bearded pig, muntjac and sambar deer) and compared how these values were impacted by environmental and technical covariates. For 2015, we found that null models without covariates revealed no clear differences in each of the three probabilities across taxa. However, in 2016, although the taxa have comparable occupancy, deviations occurred in the other two probabilities, with the sambar deer showing the lowest availability and muntjac with the lowest detection probability. Univariate models constructed for each taxon and year revealed differential impacts of the covariates; for example, a strong positive effect of DNA concentration on the detection of sambar deer and bearded pig was seen in 2016 only. Finally, our estimation of the minimum numbers of biological and technical replicates highlights the important trade‐off between achieving high probabilities of availability and detection and realistic amounts of sampling. Our results showcase the use of occupancy models for leech‐iDNA biodiversity surveys but highlight the potential effects of sample type, methodological design, and sample size.