Low but highly geographically structured genomic diversity of East Asian Eurasian otters and its conservation implications

Populations of Eurasian otters Lutra lutra, one of the most widely distributed apex predators in Eurasia, have been depleted mainly since the 1950s. However, a lack of information about their genomic diversity and how they are organized geographically in East Asia severely impedes our ability to monitor and conserve them in particular management units. Here, we re-sequenced and analyzed 20 otter genomes spanning continental East Asia, including a population at Kinmen, a small island off the Fujian coast, China. The otters form three genetic clusters (one of L. l. lutra in the north and two of L. l. chinensis in the south), which have diverged in the Holocene. These three clusters should be recognized as three conservation management units to monitor and manage independently. The heterozygosity of the East Asian otters is as low as that of the threatened carnivores sequenced. Historical effective population size trajectories inferred from genomic variations suggest that their low genomic diversity could be partially attributed to changes in the climate since the mid-Pleistocene and anthropogenic intervention since the Holocene. However, no evidence of genetic erosion, mutation load, or high level of inbreeding was detected in the presumably isolated Kinmen Island population. Any future in situ conservation efforts should consider this information for the conservation management units.

Genomics Reveals Complex Population History and Unexpected Diversity of Eurasian Otters (Lutra lutra) in Britain Relative to Genetic Methods

Conservation genetic analyses of many endangered species have been based on genotyping of microsatellite loci and sequencing of short fragments of mtDNA. The increase in power and resolution afforded by whole genome approaches may challenge conclusions made on limited numbers of loci and maternally inherited haploid markers. Here, we provide a matched comparison of whole genome sequencing versus microsatellite and control region (CR) genotyping for Eurasian otters (Lutra lutra). Previous work identified four genetically differentiated "stronghold" populations of otter in Britain, derived from regional populations that survived the population crash of the 1950s-1980s. Using whole genome resequencing data from 45 samples from across the British stronghold populations, we confirmed some aspects of population structure derived from previous marker-driven studies. Importantly, we showed that genomic signals of the population crash bottlenecks matched evidence from otter population surveys. Unexpectedly, two strongly divergent mitochondrial lineages were identified that were undetectable using CR fragments, and otters in the east of England were genetically distinct and surprisingly variable. We hypothesize that this previously unsuspected variability may derive from past releases of Eurasian otters from other, non-British source populations in England around the time of the population bottleneck. Our work highlights that even reasonably well-studied species may harbor genetic surprises, if studied using modern high-throughput sequencing methods.

Bayesian Prediction of Multivariate Ecology from Phenotypic Data Yields New Insights into the Diets of Extant and Extinct Taxa

AbstractMorphology often reflects ecology, enabling the prediction of ecological roles for taxa that lack direct observations, such as fossils. In comparative analyses, ecological traits, like diet, are often treated as categorical, which may aid prediction and simplify analyses but ignores the multivariate nature of ecological niches. Furthermore, methods for quantifying and predicting multivariate ecology remain rare. Here, we ranked the relative importance of 13 food items for a sample of 88 extant carnivoran mammals and then used Bayesian multilevel modeling to assess whether those rankings could be predicted from dental morphology and body size. Traditional diet categories fail to capture the true multivariate nature of carnivoran diets, but Bayesian regression models derived from living taxa have good predictive accuracy for importance ranks. Using our models to predict the importance of individual food items, the multivariate dietary niche, and the nearest extant analogs for a set of data-deficient extant and extinct carnivoran species confirms long-standing ideas for some taxa but yields new insights into the fundamental dietary niches of others. Our approach provides a promising alternative to traditional dietary classifications. Importantly, this approach need not be limited to diet but serves as a general framework for predicting multivariate ecology from phenotypic traits.

The Different Fate of the Pyrenean Desman (Galemys pyrenaicus) and the Eurasian Otter (Lutra lutra) under Climate and Land Use Changes

Climate and land use change can affect biodiversity in different ways, e.g., determining habitat loss, altering reproduction periods or disrupting biotic interactions. Here, we investigate the effects of climate and land use change on the spatial distribution of two semi-aquatic mammals, the Pyrenean desman (Galemys pyrenaicus) and the Eurasian otter (Lutra lutra). We first modeled the current potential distribution of the desman and the otter in the Iberian Peninsula, considering topographic, climatic and land use variables. Second, we predicted their potential distribution in 2050 under climate and land use change scenarios. We calculated the percentage of range gain/loss and shift predicted for the two species under such scenarios and quantified the present and future spatial overlap between the two species distribution. Irrespective of the scenario, desman models show loss of suitable habitat, whereas the otter will undergo an opposite trend. Aside from a preponderant habitat loss, the desman is predicted to increase its spatial overlap with otter range under the optimistic scenarios, potentially meaning it will face an exacerbated predation by otters. The potential increase of both habitat loss and otters' predation might represent a major threat for the desman, which may affect the long-term persistence of this endemic species in the Iberian Peninsula.

Better sturdy or slender? Eurasian otter skull plasticity in response to feeding ecology

Otters are semi-aquatic mammals specialized in feeding on aquatic prey. The Eurasian otter Lutra lutra is the most widely distributed otter species. Despite a low degree of genetic variation across its European range, the population from Great Britain exhibits distinct genetic structuring. We examined 43 skulls of adult Eurasian otters belonging to 18 sampling localities and three genetic clusters (Shetlands, Wales and Scotland). For each sample location, information regarding climate was described using bioclimatic variables from WorldClim, and information on otter diet was extracted from the literature. By using photogrammetry, 3D models were obtained for each skull. To explore any evidence of adaptive divergence within these areas we used a three dimensional geometric morphometric approach to test differences in skull size and shape between areas with genetically distinct populations, as well as the influence of diet, isolation by distance and climate. Males were significantly larger in skull size than females across all the three genetic clusters. Skull shape, but not size, appeared to differ significantly among genetic clusters, with otters from Shetland exhibiting wider zygomatic arches and longer snouts compared to otters from Wales, whereas otters from Scotland displayed intermediate traits. A significant relationship could also be found between skull shape variation, diet as well as climate. Specifically, otters feeding on freshwater fish had more slender and short-snouted skulls compared to otters feeding mostly on marine fish. Individuals living along the coast are characterised by a mixed feeding regime based on marine fish and crustaceans and their skull showed an intermediate shape. Coastal and island otters also had larger orbits and eyes more oriented toward the ground, a larger nasal cavity, and a larger distance between postorbital processes and zygomatic arch. These functional traits could also represent an adaptation to favour the duration and depth of diving, while the slender skull of freshwater feeding otters could improve the hydrodynamics.

Phylogenomics of the world's otters

Comparative whole-genome analyses hold great power to illuminate commonalities and differences in the evolution of related species that share similar ecologies. The mustelid subfamily Lutrinae includes 13 currently recognized extant species of otters,^1-5 a semiaquatic group whose evolutionary history is incompletely understood. We assembled a dataset comprising 24 genomes from all living otter species, 14 of which were newly sequenced. We used this dataset to infer phylogenetic relationships and divergence times, to characterize patterns of genome-wide genealogical discordance, and to investigate demographic history and current genomic diversity. We found that genera Lutra, Aonyx, Amblonyx, and Lutrogale form a coherent clade that should be synonymized under Lutra, simplifying the taxonomic structure of the subfamily. The poorly known tropical African Aonyx congicus and the more widespread Aonyx capensis were found to be reciprocally monophyletic (having diverged 440,000 years ago), supporting the validity of the former as a distinct species. We observed variable changes in effective population sizes over time among otters within and among continents, although several species showed similar trends of expansions and declines during the last 100,000 years. This has led to different levels of genomic diversity assessed by overall heterozygosity, genome-wide SNV density, and run of homozygosity burden. Interestingly, there were cases in which diversity metrics were consistent with the current threat status (mostly based on census size), highlighting the potential of genomic data for conservation assessment. Overall, our results shed light on otter evolutionary history and provide a framework for further in-depth comparative genomic studies targeting this group.

Evaluating otter reintroduction outcomes using genetic spatial capture-recapture modified for dendritic networks

Monitoring the demographics and genetics of reintroduced populations is critical to evaluating reintroduction success, but species ecology and the landscapes that they inhabit often present challenges for accurate assessments. If suitable habitats are restricted to hierarchical dendritic networks, such as river systems, animal movements are typically constrained and may violate assumptions of methods commonly used to estimate demographic parameters. Using genetic detection data collected via fecal sampling at latrines, we demonstrate applicability of the spatial capture-recapture (SCR) network distance function for estimating the size and density of a recently reintroduced North American river otter (Lontra canadensis) population in the Upper Rio Grande River dendritic network in the southwestern United States, and we also evaluated the genetic outcomes of using a small founder group (n = 33 otters) for reintroduction. Estimated population density was 0.23-0.28 otter/km, or 1 otter/3.57-4.35 km, with weak evidence of density increasing with northerly latitude (β = 0.33). Estimated population size was 83-104 total otters in 359 km of riverine dendritic network, which corresponded to average annual exponential population growth of 1.12-1.15/year since reintroduction. Growth was ≥40% lower than most reintroduced river otter populations and strong evidence of a founder effect existed 8-10 years post-reintroduction, including 13-21% genetic diversity loss, 84%-87% genetic effective population size decline, and rapid divergence from the source population (F ST accumulation = 0.06/generation). Consequently, genetic restoration via translocation of additional otters from other populations may be necessary to mitigate deleterious genetic effects in this small, isolated population. Combined with non-invasive genetic sampling, the SCR network distance approach is likely widely applicable to demogenetic assessments of both reintroduced and established populations of multiple mustelid species that inhabit aquatic dendritic networks, many of which are regionally or globally imperiled and may warrant reintroduction or augmentation efforts.

Differing limb functions and their potential influence upon the diversification of the mustelid hindlimb skeleton

Though form-function relationships of the mammalian locomotor system have been investigated for over a century, recent models of trait evolution have hitherto been seldom used to identify likely evolutionary processes underlying the locomotor system’s morphological diversity. Using mustelids, an ecologically diverse carnivoran lineage, I investigated whether variation in hindlimb skeletal morphology functionally coincides with climbing, digging, swimming and generalized locomotor habits by using 15 linear traits of the femur, tibia, fibula, calcaneum and metatarsal III across 44 species in a principal component analysis. I subsequently fit different models of Brownian motion and adaptive trait diversification individually to each trait. Climbing, digging and swimming mustelids occupy distinct regions of phenotypic space characterized by differences in bone robustness. Models of adaptive and neutral evolution are, respectively, the best fits for long bone lengths and muscle in-levers, suggesting that different kinds of traits may be associated with different evolutionary processes. However, simulations based upon models of best fit reveal low statistical power to rank the models. Though differences in mustelid hindlimb skeletal morphology appear to coincide with locomotor habits, further study, with sampling expanded beyond the Mustelidae, is necessary to better understand to what degree adaptive evolution shapes morphological diversity of the locomotor system.

Assessment of ecotoxicological risks to river otters from ingestion of invasive red swamp crayfish in metal contaminated areas: Use of feces to estimate dietary exposure

The invasive red swamp crayfish (Procambarus clarkii) has become a major food resource for Eurasian otters (Lutra lutra) in the Iberian Peninsula. Crayfish accumulate large amounts of metals, and hence otters could be at risk of exposure and intoxication through crayfish consumption. We conducted a food safety risk assessment for otters inhabiting two historical mining areas in central Spain affected by lead (Pb) and mercury (Hg) pollution. Estimated daily intakes (EDI) of Pb and Hg were non-invasively calculated from the proportion of crayfish remains and metal levels in otter feces. We considered that the abdominal muscle and the carcass of crayfish differ significantly in relative weight, total metal content and bioavailability of metals to reduce the uncertainty of risk characterization. Fecal concentrations of Hg and Pb in the polluted areas were 1.878 and 6.554 μg/g d. w., respectively (13-fold and 7-fold higher compared to a non-polluted area). EDI of Hg and Pb in the polluted areas were 66.02 and 78.26 μg/kg-day, respectively (14- and 8-fold higher than in the reference area). EDI from the Hg area were above minimum levels susceptible to cause neurotoxicity in mustelids, and 6.3% were above levels susceptible to cause histopathological lessions. In the Pb area, 16.7% of EDI were consistent with levels causing reproductive effects. Metal exposure through crayfish consumption might prevent or slow the recovey of otters in these polluted environments, thus this factor should be considered in management strategies aimed to protect otter populations.

Functional Morphology and Morphological Diversification of Hind Limb Cross-Sectional Traits in Mustelid Mammals

Locomotor habits in mammals are strongly tied to limb bones’ lengths, diameters, and proportions. By comparison, fewer studies have examined how limb bone cross-sectional traits relate to locomotor habit. Here, we tested whether climbing, digging, and swimming locomotor habits reflect biomechanically meaningful differences in three cross-sectional traits rendered dimensionless— cross-sectional area (CSA), second moments of area (SMA), and section modulus (MOD)—using femora, tibiae, and fibulae of 28 species of mustelid. CSA and SMA represent resistance to axial compression and bending, respectively, whereas MOD represents structural strength. Given the need to counteract buoyancy in aquatic environments and soil’s high density, we predicted that natatorial and fossorial mustelids have higher values of cross-sectional traits. For all three traits, we found that natatorial mustelids have the highest values, followed by fossorial mustelids, with both of these groups significantly differing from scansorial mustelids. However, phylogenetic relatedness strongly influences diversity in cross-sectional morphology, as locomotor habit strongly correlates with phylogeny. Testing whether hind limb bone cross-sectional traits have evolved adaptively, we fit Ornstein–Uhlenbeck (OU) and Brownian motion (BM) models of trait diversification to cross-sectional traits. The cross-sectional traits of the femur, tibia, and fibula appear to have, respectively, diversified under a multi-rate BM model, a single rate BM model, and a multi-optima OU model. In light of recent studies on mustelid body size and elongation, our findings suggest that the mustelid body plan—and perhaps that of other mammals—is likely the sum of a suite of traits evolving under different models of trait diversification.

Morphological diversification of biomechanical traits: mustelid locomotor specializations and the macroevolution of long bone cross-sectional morphology

BACKGROUND

Morphological diversity of limb bone lengths, diameters, and proportions in mammals is known to vary strongly with locomotor habit. It remains less well known how different locomotor habits are correlated with cross-sectional traits of the limb skeleton, such as cross-sectional area (CSA), second moments of area (SMA), and section modulus (MOD) and whether these traits have evolved adaptively. CSA and SMA represent the bone's resistance to axial compression and bending, respectively, whereas MOD represents bone structural strength related to shape. Sampling 28 species of mustelids, a carnivoran lineage with diverse locomotor habits, we tested for differences in humeral, radial, and ulnar cross-sectional traits among specialists for climbing, digging, and swimming, in addition to generalists. Given that the limbs of digging specialists function in the dense substance of soil, and that swimming specialists need to counteract buoyancy, we predicted that these mustelids with these specializations should have the greatest values of cross-sectional traits.

RESULTS

We analyzed cross-sectional traits (calculated via μCT scanning and rendered dimensionless) in 5% increments along a bone's length and found significant differences among locomotor habits, though differences in ulnar cross-sectional traits were fewer than those for the humerus and radius. Swimming specialists had the greatest values of cross-sectional traits, followed by digging specialists. Climbing specialists had the lowest values of cross-sectional traits. However, phylogenetic affinity underlies these results. Fitting models of trait evolution to CSA and SMA revealed that a multi-rate Brownian motion model and a multi-optima Ornstein-Uhlenbeck model are the best-fitting models of evolution for these traits. However, inspection of α-values uncovered that many of the OU models did not differ from a Brownian motion model.

CONCLUSIONS

Within Mustelidae, differences in limb function and locomotor habit influence cross-sectional traits in ways that produce patterns that may diverge from adaptive patterns exhibited by external traits (e.g., bone lengths) of the mammalian limb skeleton. These results suggest that not all the traits of a single organ evolve under a single evolutionary process and that models of trait evolution should be fit to a range of traits for a better understanding of the evolution of the mammalian locomotor system.

Feeding capability in the extinct giant Siamogale melilutra and comparative mandibular biomechanics of living Lutrinae

At 50 kg in estimated weight, the extinct Siamogale melilutra is larger than all living otters, and ranks among the largest fossil otters. The biomechanical capability of S. melilutra jaws as related to their large size is unknown but crucial to reconstructing the species' potentially unique ecological niche. Here we compare the mandibular biomechanics of S. melilutra using engineering-based performance measures against ten extant otter biomechanical models. Despite a wide range of feeding preferences from durophagy to piscivory, living otter species exhibit a linear relationship between mandible stiffness and volume, as expected in isometric model scaling. In contrast, S. melilutra models exhibit a six-fold increase in stiffness from expected stiffness-volume relationships calculated from extant species models. Unlike stiffness, mechanical efficiency of biting is conserved among living otters and in S. melilutra. These findings indicate that although similar to living bunodont otters in morphology and biting efficiency, jaw strength in S. melilutra far surpasses molluscivores such as sea otters and Cape clawless otters, even after accounting for size. Therefore, Siamogale represents a feeding ecomorphology with no living analog, and its giant size and high mandibular strength confer shell-crushing capability matched only by other extinct molluscivores such as the marine bear Kolponomos.