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1. Seeking compromise across competing goals in conservation translocations: The case of the ‘extinct’ Floreana Island Galapagos giant tortoise

   https://doi.org/10.1111/1365-2664.13516  

   Hunter, Elizabeth A. ; Gibbs, James P. ; Cayot, Linda J. ; Tapia, Washington ; Quinzin, Maud C. ; Miller, Joshua M. ; Caccone, Adalgisa ; Shoemaker, Kevin T. ; Rhodes, ed., Jonathan ( October 2019 , Journal of Applied Ecology)

   Conservation translocation projects must carefully balance multiple, potentially competing objectives (e.g. population viability, retention of genetic diversity, delivery of key ecological services) against conflicting stakeholder values and severe time and cost constraints. Advanced decision support tools would facilitate identifying practical solutions.

   We examined how to achieve compromise across competing objectives in conservation translocations via an examination of giant tortoises in the Galapagos Islands with ancestry from the extinct Floreana Island species (Chelonoidis niger). Efforts have begun to populate Floreana Island with tortoises genetically similar to its historical inhabitants while balancing three potentially competing objectives – restoring ecosystem services (sustaining a high tortoise population size), maximizing genome representation of the extinctC. nigerspecies and maintaining a genetically diverse population – under realistic cost constraints.

   We developed a novel approach to this conservation decision problem by coupling an individual‐based simulation model with generalized additive models and global optimization. We identified several incompatibilities among programme objectives, with quasi‐optimal single‐objective solutions (sets of management actions) differing substantially in programme duration, translocation age, incubation temperature (determinant of sex ratio) and the number of individuals directly translocated from the source population.

   Quasi‐optimal single‐objective solutions were able to produce outcomes (i.e. population size and measures of genetic diversity andC. nigergenome representation) to within 75% of their highest simulated outcomes (e.g. highest population size achieved across all simulations) within a cost constraint ofc. $2m USD, but these solutions resulted in severe declines (up to 74% reduction) in outcomes for non‐focal objectives. However, when all programme objectives were equally weighted to produce a multi‐objective solution, all objectives were met to within 90% of the highest achievable mean values across all cost constraints.

   Synthesis and applications. Multi‐objective conservation translocations are likely to encounter complex trade‐offs and conflicts among programme objectives. Here, we developed a novel combination of modelling approaches to identify optimal management strategies. We found that solutions that simultaneously addressed multiple, competing objectives performed better than single‐objective solutions. Our model‐based decision support tool demonstrates that timely, cost‐effective solutions can be identified in cases where management objectives appear to be incompatible.

    

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2. An island ‘endemic’ born out of hybridization between introduced lineages

   https://doi.org/10.1111/mec.16990  

   Salter, Jessie F. ; Brumfield, Robb T. ; Faircloth, Brant C. ( May 2023 , Molecular Ecology)

   Humans have profoundly impacted the distribution of plant and animal species over thousands of years. The most direct example of these effects is human‐mediated movement of individuals, either through translocation of individuals within their range or through the introduction of species to new habitats. While human involvement may be suspected in species with obvious range disjunctions, it can be difficult to detect natural versus human‐mediated dispersal events for populations at the edge of a species' range, and this uncertainty muddles how we understand the evolutionary history of populations and broad biogeographical patterns. Studies combining genetic data with archaeological, linguistic and historical evidence have confirmed prehistoric examples of human‐mediated dispersal; however, it is unclear whether these methods can disentangle recent dispersal events, such as species translocated by European colonizers during the past 500 years. We use genomic DNA from historical museum specimens and historical records to evaluate three hypotheses regarding the timing and origin of Northern Bobwhites (Colinus virginianus) in Cuba, whose status as an endemic or introduced population has long been debated. We discovered that bobwhites from southern Mexico arrived in Cuba between the 12th and 16th centuries, followed by the subsequent introduction of bobwhites from the southeastern USA to Cuba between the 18th and 20th centuries. These dates suggest the introduction of bobwhites to Cuba was human‐mediated and concomitant with Spanish colonial shipping routes between Veracruz, Mexico and Havana, Cuba during this period. Our results identify endemic Cuban bobwhites as a genetically distinct population born of hybridization between divergent, introduced lineages.

    

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3. The contribution of historical processes to contemporary extinction risk in placental mammals

   https://doi.org/10.1126/science.abn5856  

   Wilder, Aryn P. ; Supple, Megan A. ; Subramanian, Ayshwarya ; Mudide, Anish ; Swofford, Ross ; Serres-Armero, Aitor ; Steiner, Cynthia ; Koepfli, Klaus-Peter ; Genereux, Diane P. ; Karlsson, Elinor K. ; et al ( April 2023 , Science)

   INTRODUCTION The Anthropocene is marked by an accelerated loss of biodiversity, widespread population declines, and a global conservation crisis. Given limited resources for conservation intervention, an approach is needed to identify threatened species from among the thousands lacking adequate information for status assessments. Such prioritization for intervention could come from genome sequence data, as genomes contain information about demography, diversity, fitness, and adaptive potential. However, the relevance of genomic data for identifying at-risk species is uncertain, in part because genetic variation may reflect past events and life histories better than contemporary conservation status. RATIONALE The Zoonomia multispecies alignment presents an opportunity to systematically compare neutral and functional genomic diversity and their relationships to contemporary extinction risk across a large sample of diverse mammalian taxa. We surveyed 240 species spanning from the “Least Concern” to “Critically Endangered” categories, as published in the International Union for Conservation of Nature’s Red List of Threatened Species. Using a single genome for each species, we estimated historical effective population sizes ( N e ) and distributions of genome-wide heterozygosity. To estimate genetic load, we identified substitutions relative to reconstructed ancestral sequences, assuming that mutations at evolutionarily conserved sites and in protein-coding sequences, especially in genes essential for viability in mice, are predominantly deleterious. We examined relationships between the conservation status of species and metrics of heterozygosity, demography, and genetic load and used these data to train and test models to distinguish threatened from nonthreatened species. RESULTS Species with smaller historical N e are more likely to be categorized as at risk of extinction, suggesting that demography, even from periods more than 10,000 years in the past, may be informative of contemporary resilience. Species with smaller historical N e also carry proportionally higher burdens of weakly and moderately deleterious alleles, consistent with theoretical expectations of the long-term accumulation and fixation of genetic load under strong genetic drift. We found weak support for a causative link between fixed drift load and extinction risk; however, other types of genetic load not captured in our data, such as rare, highly deleterious alleles, may also play a role. Although ecological (e.g., physiological, life-history, and behavioral) variables were the best predictors of extinction risk, genomic variables nonrandomly distinguished threatened from nonthreatened species in regression and machine learning models. These results suggest that information encoded within even a single genome can provide a risk assessment in the absence of adequate ecological or population census data. CONCLUSION Our analysis highlights the potential for genomic data to rapidly and inexpensively gauge extinction risk by leveraging relationships between contemporary conservation status and genetic variation shaped by the long-term demographic history of species. As more resequencing data and additional reference genomes become available, estimates of genetic load, estimates of recent demographic history, and accuracy of predictive models will improve. We therefore echo calls for including genomic information in assessments of the conservation status of species. Genomic information can help predict extinction risk in diverse mammalian species. Across 240 mammals, species with smaller historical N e had lower genetic diversity, higher genetic load, and were more likely to be threatened with extinction. Genomic data were used to train models that predict whether a species is threatened, which can be valuable for assessing extinction risk in species lacking ecological or census data. [Animal silhouettes are from PhyloPic] 

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4. Individual heterogeneity influences the effects of translocation on urban dispersal of an invasive reptile

   https://doi.org/10.1186/s40462-022-00300-1  

   Feuka, Abigail B. ; Nafus, Melia G. ; Yackel Adams, Amy A. ; Bailey, Larissa L. ; Hooten, Mevin B. ( January 2022 , Movement Ecology)

   Invasive reptiles pose a serious threat to global biodiversity, but early detection of individuals in an incipient population is often hindered by their cryptic nature, sporadic movements, and variation among individuals. Little is known about the mechanisms that affect the movement of these species, which limits our understanding of their dispersal. Our aim was to determine whether translocation or small-scale landscape features affect movement patterns of brown treesnakes (Boiga irregularis), a destructive invasive predator on the island of Guam.

   We conducted a field experiment to compare the movements of resident (control) snakes to those of snakes translocated from forests and urban areas into new urban habitats. We developed a Bayesian hierarchical model to analyze snake movement mechanisms and account for attributes unique to invasive reptiles by incorporating multiple behavioral states and individual heterogeneity in movement parameters.

   We did not observe strong differences in mechanistic movement parameters (turning angle or step length) among experimental treatment groups. We found some evidence that translocated snakes from both forests and urban areas made longer movements than resident snakes, but variation among individuals within treatment groups weakened this effect. Snakes translocated from forests moved more frequently from pavement than those translocated from urban areas. Snakes translocated from urban areas moved less frequently from buildings than resident snakes. Resident snakes had high individual heterogeneity in movement probability.

   Our approach to modeling movement improved our understanding of invasive reptile dispersal by allowing us to examine the mechanisms that influence their movement. We also demonstrated the importance of accounting for individual heterogeneity in population-level analyses, especially when management goals involve eradication of an invasive species.

    

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5. A critically endangered estuarine limpet’s only two populations are genomically and morphologically distinct

   https://doi.org/10.1002/aqc.3993  

   de Coito, Paula M. ; Emami‐Khoyi, Arsalan ; Hedderson, Terry A. ; Toonen, Robert J. ; Teske, Peter R. ; Branch, George M. ( July 2023 , Aquatic Conservation: Marine and Freshwater Ecosystems)

   Seagrass habitats are declining worldwide, placing several seagrass‐associated animals at risk of extinction. The Critically Endangered limpetSiphonaria compressais one of the rarest molluscs in Africa, and has been reported from only two disjunctive lagoons in South Africa. Being a highly specialized grazer that lives exclusively on the narrow blades of Cape eelgrass,Zostera capensis, which is itself listed as Endangered in the South African Red List and has decreased in abundance, conservation initiatives are urgently needed to ensure the long‐term survival ofS. compressa.

   Molecular data (sequence data from the mitochondrial genome and single nucleotide polymorphism data of the nuclear genome) and morphological data were analysed to determine whether the two populations are conspecific, with implications for whether translocation between localities could be a viable management strategy to restore either population in the event of a collapse, or to maintain the genetic diversity of each population.

   Strong evidence emerged for the distinctness of the two populations, including a lack of shared mtDNA haplotypes that indicate an absence of contemporary gene flow, a divergence time that dates to the late Pleistocene, and a number of morphological characters that distinguish their shells. These findings indicate that the two populations are distinct cryptic subspecies.

   As the two populations occur in different temperature‐defined marine biogeographical regions, they are probably adapted to different thermal environments. Translocations are not recommended, as this management strategy has considerable potential to result in outbreeding depression and exacerbate the extinction risk. Instead, each population should be managed separately, and several alternative conservation measures are discussed, including the protection and restoration of seagrass beds.

    

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