Conservation Genetics
○ Springer Science and Business Media LLC
Preprints posted in the last 30 days, ranked by how well they match Conservation Genetics's content profile, based on 15 papers previously published here. The average preprint has a 0.01% match score for this journal, so anything above that is already an above-average fit.
Lamarins, A.; Waples, R. S.; Piironen, J.; Primmer, C. R.
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1Effective population size (Ne) is a critical parameter for evaluating the evolutionary and persistence potential of endangered populations and for designing sustainable conservation strategies. Captive breeding and release programs are widely used across taxa to reduce risk of extinction when natural reproduction is insufficient or no longer possible, making it essential to assess their consequences. We used the case study of the landlocked Saimaa salmon (Salmo salar), one of the most critically en-dangered salmonid populations in Europe, with unique evolutionary significance due to its isolation from other populations since the last glaciation. Using long-term demographic data (1969-2024) from wild-caught founders of a captive breeding and release program, we estimated the effective population size under multiple scenarios of variance in reproductive success. Across scenarios, Ne ranged from 33 to 81 individuals, representing 32%-75% of the census size. Captive breeding practices aimed at equalizing parental contributions during fertilization and early life stages increased Ne by 12% compared to natural reproductive conditions. However, variation in survival after early developmental stages, typically beyond direct management control, remained a key determinant of Ne. Despite recent increases in the number of founders, the population remains genetically vulnerable due to historical bottlenecks. These results highlight that while captive breeding programs can partially mitigate genetic risks, their effectiveness depends critically on both controlled and uncontrolled sources of variance in reproductive success. Strengthening such programs may require combining breeding management with habitat restoration and, where appropriate, genetic rescue to ensure the long-term evolutionary potential of such unique and endangered populations.
Shukla, M.; Bohra, D. L.; Rao, B.; Narayan, L.; Kiran, S.; Thakur, V.
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Genomic erosion as a manifestation of small effective population size (Ne) and consanguinity subverts long-term perpetuation of threatened species by compromising their adaptive potential; however, the integration of genomics remains limited in applied conservation efforts to guide priorities. This study combines non-invasive sampling, double-digest Restriction site-associated DNA sequencing (ddRAD), and population-genomic analyses to assess genetic health in two vulture assemblages-mixed wild enclosure and captive breeding cohorts. Both the geographical locations exhibit signs of populations in distress: low genetic diversity and abundant intermediate-length runs of homozygosity (RoH), consistent with long-term reduced Ne plus recent demographic isolation. Our demographic model runs favoured ancient migration (AM) topology characterised by an ephemeral window of gene flow, taken over by a prolonged population separation period. The mutation quantification results from approximately 59,000 outgroup-polarised SNPs reveal higher additive burden and more homozygous-derived sites in BKN. However, this was later traced to low-impact and non-coding variants rather than a surge in the loss-of-function (LoF) alleles. The data support a genomic profile that carries an elevated risk from polygenic/aggregate deleterious burden in BKN despite a scarcity of high-impact mutations. By highlighting the disconnect between genetic resilience and demographic recovery, our results accentuate the need to incorporate genomics-informed inbreeding and monitoring programs, while also focusing on reducing anthropogenic mortality with genetic augmentation.
Luna-Ortiz, A.; Barbanti, A.; Pegueroles, C.; Abreu-Grobois, F. A.; Casale, P.; Freggi, D.; Giralt, S.; Labastida-Estrada, E.; Llera-Herrera, R.; Machkour-M'Rabet, S.; Marco, A.; Margaritoulis, D.; Turkozan, O.; Pascual Berniola, M.; Carreras, C.
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O_LIEffective conservation of highly migratory species requires understanding genetic structure across breeding populations and access high{square}resolution markers capable of assigning individuals from mixed aggregates (e.g. bycatch or new nesting sites) to their natal origins. Genomic approaches provide unprecedented resolution but add methodological challenges; thus, it is essential to first build a genomic baseline from known breeding areas and then evaluate strategies for assigning unknown individuals. C_LIO_LITo address this, we used 2b-RAD sequencing, a genomic reduction technique useful for degraded DNA, and loggerhead turtles as a case study. This species shows philopatric breeding, while juveniles and adults form mixed aggregations in foraging grounds. C_LIO_LIOur results highlight the importance of building baselines that include all potential source populations contributing to mixed aggregations. We detected hierarchical genetic differentiation and high resolution and successfully assigned the natal origin of 124 unknown individuals from four Mediterranean foraging grounds. These grounds showed distinct source contributions, and comparisons with previous studies suggest possible temporal shifts in stock composition. C_LIO_LIWe provide a comprehensive genomic baseline for individual assignment of Altanto-Mediterranean loggerhead turtles of unknown natal origin and a general framework for identifying population-specific threats in highly migratory species. C_LI
Summers, J.; Cosgrove, E. J.; Bakley, T.; Barve, S.; Bowman, R.; Fitzpatrick, J. W.; Chen, N.
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The fitness of immigrants and their descendants determines the effectiveness of gene flow. Genetic incompatibilities or outbreeding depression can limit the spread of novel alleles, while highly fit immigrant lineages can hasten introgression. These fitness effects of gene flow can also differ between generations as immigrant and resident haplotypes recombine. Understanding the genetic factors that shape immigrant fitness over multiple generations is increasingly important as habitat fragmentation threatens populations by reducing genetic variation and leading to increased levels of inbreeding. Few studies have measured the multigenerational fitness of immigrant lineages, especially within populations that had histories of high gene flow. We used 33 years of life history and pedigree data on a population of Florida scrub-jays (Aphelocoma coerulescens) with historically high immigration to quantify the fitness of immigrants and their descendants. We compared the fitness of immigrants and residents as well as their resulting descendants (F1, F2, etc.) to determine the composite genetic effects responsible for fitness differences. We found evidence of additive benefits of immigrant ancestry and heterosis driven by non-additive effects that persists for multiple generations. These results are promising for conservation efforts aiming to increase connectivity and illustrate the complex dynamics that determine the rates of introgression in natural populations.
Calderon, A. M.; Salis, A. T.; Toews, D. P. L.; Szpiech, Z. A.
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Strong population contractions can leave a persistent genomic legacy that can influence populations long after their demographic recovery. While bottlenecks facilitate the removal of strongly deleterious mutations, the effectiveness of purging may be limited in historically small populations. The Kirtlands warbler (Setophaga kirtlandii) is a rare North American songbird with an ancestrally small population. After narrowly evading extinction, they are one of few species that have been delisted from federal protections in the USA. Despite their recovery, a previous study showed evidence for recent inbreeding and a high burden of deleterious mutations that may have not been purged despite strong bottlenecks. Historical DNA offers a unique opportunity to understand the consequences of recent demographic declines on genetic diversity. Here, we use DNA from over 100-year-old museum specimens to estimate changes in genetic load in the Kirtlands warblers pre- and post-bottleneck. We validate our results with forward-in-time genetic simulations and explore how sample size and missing data can affect estimates. Both empirical data and simulations suggest a reduced ability to purge deleterious mutations in this historically small population. Our simulations also highlight that limited sampling design and data quality can constrain the ability to detect changes.
Ortego, J.; Lopez-Luque, R.; Backstrom, N.; Green, A. J.
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The marbled teal (Marmaronetta angustirostris) is a widely distributed but declining waterfowl species, classified as Near Threatened globally and Critically Endangered in Spain. Despite ongoing conservation actions, including ex situ management and population reinforcement programmes, the genomic consequences of long-term captivity, inbreeding, and patterns of functional genetic variation remain unknown due to the absence of a species-specific reference genome. Here, we present the first chromosome-level genome assembly for this species. The genome was generated using PacBio HiFi long reads and Omni-C data, yielding a 1.15Gb assembly with a scaffold N50 of 76.95Mb. A total of 97.16% of the assembly was anchored into 36 chromosome-scale scaffolds, including the Z and W sex chromosomes. BUSCO analysis recovered 99.2% of conserved avian genes. Gene prediction was performed using both ab initio and homology-based strategies, resulting in 16,048 protein-coding genes. This resource provides a foundation for genomewide analyses of inbreeding, demographic history, and adaptive variation, and will support evidencebased in situ and ex situ conservation strategies for this threatened species.
Moriguchi, Y.; Kimura, S. S.; Kume, M.; Takagi, J.; Uno, Y.; Kanoh, J.; Mitamura, H.
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Telomere length (TL) is increasingly used in ecology as a biomarker of individual quality and environmental stress, yet research on non-model species with complex life histories remains limited. Because TL varies among tissues and across ages in a species-specific manner, identifying non-lethal tissues that reliably reflect whole-organism telomere dynamics is essential for longitudinal telomere studies in the field. This study aimed to evaluate tissue-specific TL in Japanese eel (Anguilla japonica), an endangered catadromous fish. We first mapped the chromosomal distribution of telomeric sequences using fluorescent in situ hybridization (FISH), the first application of this method in this species. We then tested whether muscle and caudal fin, which can be sampled easily and non-lethally, can serve as suitable proxy tissues for TL measurements in wild individuals. Relative telomere length (RTL) was quantified by qPCR in blood, brain, caudal fin, gonads, heart, liver, and muscle. FISH analysis confirmed telomeric repeats at all chromosomal ends, with only weak interstitial signals on three chromosomal pairs unlikely to affect qPCR-based estimates. A generalized additive mixed model and Wilcoxons signed-rank tests revealed significant inter-tissue differences: RTL was shortest in the brain and muscle and longest in liver, blood and caudal fin. Muscle and caudal fin RTL were significantly correlated with RTL in many other tissues, supporting their use as proxy tissues for longitudinal TL monitoring, including responses to environmental variation. Both total length and age were tested as explanatory variables for RTL, and the model including total length showed a better fit than the age-based model. Non-linear relationships between RTL and total length observed in several tissues suggest physiological shifts associated with growth and sexual differentiation. Overall, these findings advance understanding of telomere dynamics in eels and establish muscle and caudal fin as suitable tissues for repeated, non-lethal TL assessment in ecological and conservation contexts.
Bugaud, N.; Anile, S.; Moraru, A.; Devillard, S.
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AimHome range size is a fundamental aspect of animal spatial ecology, and understanding the factors that shape it is important for conservation purposes. Several hypotheses, based on energy needs or competition, assume that home range size negatively correlates with population density. However, this pattern has been little investigated on a global scale, and it remains unclear whether it would stand at both intra- and interspecific levels. To fill this gap, we conducted a global exploration of this relationship at the level of an animal family. Location: Global. Time period: Contemporary. Major taxa studied: Wild Felidae. MethodsIndividual home range size records (n = 1022) and population density estimates (n = 1061) were retrieved from the literature for 23 felid species across the world. We first investigated the interspecific relationship by modelling the median home range size of a species as a function of its median population density. To study the intraspecific relationship, we spatially merged data points based on their spatial or temporal proximity. We then applied a mixed-effects linear model using species as a random factor. ResultsWe found that home range size was negatively associated with population density, at both interspecific (-1.323 {+/-} 0.180, p < 0.001) and intraspecific levels (-0.569 {+/-} 0.201 to - 0.537 {+/-} 0.201 depending on the merging approach, p < 0.01). Landscape features were also predictors of home range size, without confounding the effect of population density. Main conclusionsSeveral processes likely govern the relationship between home range size and population density: differences in body mass between species may drive the interspecific relationship, whereas the intraspecific pattern is probably explained by conspecific competition. Although more research is needed to quantify their relative contribution, our study highlights a worldwide ecological pattern that exists at multiple biological levels in the wild.
Renn, C.; Ciotti, B. J.; Sims, D. W.; Edwards, A.; Turner, R. A.; Hosegood, P.; Sheehan, E. V.
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Designing effective spatial management for chondrichthyans (sharks, skates, rays and chimaeras) requires incorporating critical areas, sites essential for population maintenance, such as reproductive and feeding areas. Yet most area-based measures have been developed without consideration of chondrichthyan habitat use. The Important Shark and Ray Area (ISRA) initiative has been pivotal in designating priority areas through a rigorous, consultative process. To complement this, our study offers researchers a testable definition for generating robust evidence to strengthen future critical area delineations and related management decisions. We define critical areas using three criteria: 1) relative frequency of use, (2) extended within-year occupancy and (3) repeated use across years. This framework enables objective comparison among candidate sites and is generalisable across different critical area types. The definition builds upon established early-life-stage habitat concepts and applies these to broader life-history functions. The utility of this framework is then demonstrated through a systematic review of contemporary peer-reviewed literature of critical chondrichthyan areas in the European Atlantic. The review highlighted 62 critical areas with Strong evidence and 41 areas of Moderate strength evidence, which informed the European Atlantic ISRA selection process. Research effort was concentrated in inshore areas, particularly around the British Isles and Portugal, with biases towards large, threatened and commercially valuable species, whilst chimaeras were notably underrepresented. Early-life stage areas were most frequently identified, whereas resting areas were rarely documented. Evidence patterns and biases are examined in the context of evolving critical area concepts to advance their development and improve the quality and breadth of future research. By outlining a testable definition, identifying key knowledge gaps, and proposing research and reporting guidelines, this work enhances the consistency, comparability, and spatial coverage of future chondrichthyan habitat research to support its application to conservation planning.
Fabbri, G.; Battilani, D.; Mattucci, F.; Galaverni, M.; Stronen, A. V.; Musiani, M.; Godinho, R.; Lobo, D.; Scandura, M.; Randi, E.; Fabbri, E.; Caniglia, R.
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Hybridisation between wild and domestic taxa can favour the spread of domestic alleles into wild populations through backcrossing. The complex interplay of random genetic drift, recombination, and selection can shape the fate of introgressed alleles. Maladaptive domestic variants are likely to be purged by natural selection, but others may persist across generations. It has long been known that the Apennine Italian wolf population, exposed to large numbers of free-ranging dogs, has experienced extensive introgression. The unusually high frequency of black wolves observed in Italy, compared to other European populations, may parallel patterns documented in North American wolves, where the melanistic KB allele at the CBD103 gene, of domestic origin, has spread over thousands of years of introgression. We tested whether the KB mutation entered the peninsular Italian wolf population via hybridisation and spread through adaptive introgression. Genome-wide analyses of black and wild-type (grey-coated) Apennine wolves showed no clear signatures of recent dog ancestry in most melanistic animals. Our ancestry reconstruction approaches identified two distinct KB haplogroups of domestic origin, suggesting multiple introgression events. Notably, we found molecular evidence consistent with balancing selection on the KB haplotypes, whose functional role, nonetheless, warrants further research. Therefore, the microevolutionary genomic and ecological consequences of wolf-dog hybridisation in Italy should be carefully investigated to inform appropriate science-based conservation management strategies.
Osipova, E.; Dutton, P. H.; Bentley, B. P.; Alvarez-Costes, S.; Phillips, K. F.; Adkins, J.; Agyekumhene, A.; Allman, P.; Barragan Rocha, A. R.; Chacon-Chaverri, D.; Duffy, D. J.; Formia, A.; Frey, A.; Gaos, A.; Hamilton, R.; Horne, J. B.; Honarvar, S.; LaCasella, E. L.; Lontoh, D.; Nel, R.; Ortega, A.; Pakiding, F.; Prasetyo, A. P.; Sarti Martinez, A. L.; Piedra-Chacon, R.; Tiwari, M.; Stewart, K. R.; Thome, J. C. A.; Velez-Carballo, E.; Martin, S. L.; Alexander, A.; Wallace, B. P.; Komoroske, L. M.
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Understanding the drivers of genomic health and their consequences for population viability is often overlooked but potentially important to effective conservation amidst the biodiversity crisis of the Anthropocene. Leatherback turtle (Dermochelys coriacea) populations have declined globally due to anthropogenic factors, with some populations losing over 90% of their abundance over the past 30-50 years. While conservation efforts have been successful in stabilizing some populations, others continue to decline, and the reasons for these differential trajectories remain unclear. To assess how recent demographic factors, such as population size and decline, influence population genomic health, we combined population monitoring information with medium depth whole-genome and reduced representation resequencing data from globally representative populations. We found that small-stable populations have lower genomic diversity and higher inbreeding than large declining populations, reflecting prolonged small population sizes and limited gene flow. Yet, small-stable populations also show evidence of deleterious allele purging, suggesting genetic resilience. This, combined with lack of detectable genomic erosion over the study period, provides hope for potential recovery of healthy leatherback populations provided that anthropogenic threats are effectively mitigated. However, potential time lags and possible recent increases in inbreeding among close relatives in recently declined populations warrant continued monitoring and assessment. Genomic and abundance-based metrics were less aligned following rapid population declines, emphasizing the different timescales of the evolutionary and demographic processes they reflect, respectively, and the strength in their complementary, integrative use for extinction risk assessments. This also supports that it is not too late to turn the tide for recently declined leatherback populations and that continued investment in conservation efforts and threat reductions are warranted. Collectively, our results highlight how recent and historical demography shapes current genomic health and recovery potential in leatherback turtles, aids understanding of current risks and informs future conservation and management strategies.
Kutt, A. S.; Fraser, H. S.
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The small mammals in the tropical savannas of northern Australia, have undergone a degree of change in recent decades, best documented in the Northern Territory. Data is limited from northern Queensland and though the same trends are assumed, the topographic and climatic features differ substantially. In this study we examined data systematically collected from 725 sites between 1998-2012 in three bioregions representing a climatic gradient: from semi-arid to monsoon tropical savannas. We investigated via information-theoretic models and model averaging, the relationship between five mammal groupings and three landscape variables (fractional cover green, elevation and vegetation diversity) to elucidate any consistent or different patterns in the mammal fauna. Key patterns included relationships with increasing elevation (critical weight range species richness positively associated with elevation, rodent species richness negatively associated), increasing rodent and dasyurid species richness with vegetation diversity, and lower macropod and dasyurids abundance with increasing fractional cover green. These relationships underscore a need to consider mammal conservation in Queensland with more nuance than in the more topographically inert Northern Territory. Management strategies need to be more attuned to taxonomic and regional differences, to prevent perverse outcomes.
Guilford-Pearce, B. J.; Staiger, M.; Stevens, G. M. W.; Doherty, P. D.; Ali, J.
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Reef manta rays (Mobula alfredi) are threatened by fishing and other anthropogenic threats. Which, when coupled with conservative life history traits, have made this species vulnerable to extinction. Spatiotemporal ecological knowledge, such as site fidelity and visitation patterns to key aggregation sites, are imperative for effective conservation management of M. alfredi. A novel method of environmental sensing, remote underwater photo systems (RUPs), was employed to understand drivers of M. alfredi habitat use and resighting patterns. RUPs were deployed at four cleaning sites around Laamu Atoll, Maldives. Between March 2021 and May 2023, 455,458 photos were analysed. Generalised linear models revealed increases in M. alfredi presence in response to high chlorophyll-a concentrations, low illumination moon states, the Southwest Monsoon, and in the morning, while human presence had no effect. Branchial spot patterns allowed for 81 M. alfredi individuals to be identified, from 629 sightings, representing 51.59% of Laamu Atolls previously identified population (n = 157). Cleaning stations are visited more intensively during periods of increased productivity of the Southwest Monsoon, likely in response to greater foraging opportunities near the study areas. Additionally, moon state, used as a proxy for tidal strength, was associated with increased visitation during new moon periods, suggesting that weaker tidal states may facilitate presence. These data support integrating RUPs with observational surveys to improve inferences about habitat use and our understanding of cleaning sites frequented by M. alfredi. This study aims to inform the implementation of Laamu Atolls first marine protected area management plan.
Wilde, J. A.; Ozsanlav-Harris, L.; Madden, J.
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The release of tens of millions of common pheasants (Phasianus colchicus) across the UK for shooting may pose an ecological risk to native species and sensitive habitats, particularly if the birds move into protected areas (PAs) such as Special Areas of Conservation (SAC), Special Protection Areas (SPA), and Sites of Special Scientific Interest (SSSI). The extent of this ecological risk depends on the abundance of pheasants in these sensitive sites, especially if they are attracted there after the shooting season when game management efforts to retain the birds cease. We used relative pheasant abundance measures derived from British Trust for Ornithology bird atlas data from 3793 2km tetrads across four English counties (Berkshire, Cornwall, Devon, and Hertfordshire) to determine if pheasants preferentially disperse into or reside in areas with greater PA coverage. We analysed relative abundance in both the winter shooting season and the breeding season using a Bayesian occupancy-abundance model, controlling for habitat type and diversity. Our results showed a strong influence of habitat on pheasant abundance, consistent with known habitat preferences. However, we found no evidence of a relationship between relative pheasant abundance and the proportion of ecologically relevant PA coverage in a tetrad. This lack of a relationship was consistent across all four counties and across both the winter and breeding seasons. Our finding suggests that common pheasants do not preferentially disperse into or reside in protected areas compared to surrounding, unprotected land, suggesting that the ecological impacts caused by released pheasants are no more likely to occur in protected areas than in non-protected areas.
Gibson, E.; Kantar, M. B.; Runck, B.
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Sky islands are high-elevation ecosystems surrounded by lowland habitats that create isolated environments with distinct climatic conditions. These factors have driven the evolution of many endemic species, separated from their larger, contiguous populations. An Individual-Based Model (IBM) was used to simulate population dynamics by modeling the behaviors and interactions of Tamiasciurus hudsonicus grahamensis (Mount Graham Red Squirrel) a subspecies of the American red squirrel (Tamiasciurus hudsonicus) that is endemic to the Pinaleno Mountains in southeastern Arizona. This approach can help predict future population trends based on historical species data leading to better conservation decisions. Using species-specific ecological preferences--including temperature, precipitation, and vegetation indices (NDVI)--an IBM was developed to simulate population dynamics and spatial distribution projections through 2100. Climate change projections, based on the best- and worst-case scenarios outlined in the 2014 National Climate Assessment, were incorporated to assess potential future population trends under changing environmental conditions. The population faces a 45-62% probability of extinction by 2100, with a significant risk of extinction within the next 50 years. A translocation experiment was conducted to evaluate the viability of relocating individuals to the Chiricahua Mountains, another sky island with a larger habitable area. However, the risk of extinction remains even higher (87-89%) due to environmental disturbances affecting both the Chiricahua and Pinaleno regions. This highlights the challenges of conservation efforts in the face of climate change and emphasizes the need for targeted management strategies to preserve this critically endangered subspecies.
Ellis, M. B.; Lewis, H. M.; Cameron, T. C.
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There is an urgent need to gather data on harvest rates of waterbirds in Europe to assess the sustainability of hunting. Estimates of total waterbird harvest in the United Kingdom (UK) and the relative harvest of different huntable species come from two separate surveys, the Value of Shooting (PACEC 2014) and National Gamebag Census (NGC, Aebischer 2019), and these have been recently used to explore the likelihood of unsustainable harvests of wild waterbirds by UK hunters (Ellis and Cameron 2022; Madden et al., 2025). The reliability of these sustainability estimates depends on how representative the original surveys are of hunter behaviour and success. There are also 1-3 million released game-farm mallard (Anas platyrhynchos) that takes up considerable and unquantified proportions of the UK waterbird harvest. Here we explore uncertainties in the UK winter harvest of wild waterfowl by comparing estimates from the NGC dataset with those from the Crown Estate coastal hunting clubs, and a novel approach using analysis of social-media images (2019/20 to 2023/24). We explore the difference in species-specific harvest with and without the uncertainties in the number of released mallard and the total number of duck harvested in the UK. Waterbird harvest estimates differ markedly depending on the input dataset and whether released mallard are included in the analysis. Confidence intervals of each estimate are inflated by uncertainties in the number of released game-farm mallard contributing to, and the size of that national bag. Estimates extrapolated from social media suggest the national harvest of several species may be considerably larger than the corresponding NGC estimates (e.g. Teal *2.07 and gadwall *11.2), while mallard harvests away from formal shoots represented by NGC are significantly lower (*0.71). Excluding released mallard reduces the statistical estimate of total wild duck harvest by 56-63%, which would have biologically significant effects if realised.
Kauf, L.; Vila-Farre, M.; Ficze-Schmidt, F.; Bakula, E.; Rink, J.; Bilandzija, H.
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The Dinaric karst of Croatia encompasses a network of over 10,000 caves and represents one of the worlds most important subterranean biodiversity hotspots. It is inhabited by remarkably diverse and often endemic species, including planarian flatworms, which are among the rarest macroinvertebrates encountered in cave habitats. Although the presence of cave planarians has long been known, no integrative research on this group has been conducted to date, and the evolutionary relationships between these animals and their surface water counterparts are currently unresolved. To address these gaps, we combined field sampling, phylogenetic analysis based on COI and 18S genes, and phenotypic characterization. Our results show that cave planariids in Croatia belong to at least three genera and are more widespread and diverse across both Croatia, and the broader Dinaric karst, than previously assumed. We increased the number of cave records in the Dinaric karst from 26 to 37 and documented cf. Atrioplanaria and Phagocata in Croatian caves for the first time. Phylogenetic reconstructions suggest numerous independent cave colonization events, including multiple instances within the genera Crenobia and cf. Atrioplanaria. Variation in pigmentation and eye reduction, both within and between populations, further reveal heterogeneous evolutionary trajectories of cave-associated phenotypes. The biogeographical patterns and high genetic diversity we report here point to a complex evolutionary history of planariids in the Dinarides. Our newly generated molecular phylogenies and systematic documentation of trait variability establish Planariidae as a valuable model for studying mechanisms underlying convergent evolution of pigment loss and eye reduction in cave environments.
Bravington, M. V.; Baylis, S. M.; Eveson, P.; Feutry, P.
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AO_SCPLOWBSTRACTC_SCPLOWClose-Kin Mark-Recapture (CKMR) is a statistical framework for estimating demographic parameters of wild populations. Instead of recapturing individuals, it relies on the identification of closely-related pairs such as parents and offspring, or siblings. By measuring how often such close-kin are "recaptured" among sampled animals (whether alive or dead), scientists can estimate demographic parameters such as census size, mortality rates, and connectivity. CKMR is starting to change fisheries and wildlife management by giving more reliable demographic information, even for many species that resist conventional approaches. Here we introduce the kinference R package, which provides a set of tools for finding close-kin pairs among thousands of samples each genotyped at thousands of SNPs, and for associated quality control. The CKMR context implies different requirements and assumptions to many other kinship programs. In particular, kinference accounts empirically for linkage without requiring a genome assembly, is able to estimate and control false-negative and false-positive probabilities, and can cope with null alleles. The package has been developed and used in numerous CKMR projects since 2017. This paper documents the assumptions, statistical algorithms, and intended workflow for kinference.
Pozo, G.; Cisneros-Heredia, D. F.; Barragan-Orbe, D.; Sanchez-Nivicela, J. C.; Arbelaez, E.; Torres, M.
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Holcosus orcesi, the Orces Blue Whiptail, is a Critically Endangered lizard endemic to the upper Jubones River basin in southern Ecuador. Restricted to a narrow elevational range within semi-arid Andean shrublands, it represents one of the few montane members of a predominantly lowland lineage. Here we present the first high-quality reference genome for H. orcesi, generated using Oxford Nanopore Technologies long-read sequencing. The assembly spans 1.68 Gb across only 91 contigs, with an N50 of 76.2 Mb and a BUSCO completeness of 96.8%, making it among the most contiguous and complete squamate genomes to date. Structural annotation predicted 25,682 genes, of which 85% showed homology to known proteins and 45% were assigned Gene Ontology terms. Repetitive elements accounted for 46.3% of the genome, with LINEs representing the predominant class. This genome provides a foundational resource for future evolutionary, comparative and conservation-genomic research of H. orcesi and other mountain reptiles, enabling studies of population genomics, local adaptation, and genomic erosion in isolated populations. By expanding the genomic representation of tropical montane reptiles, this work helps address longstanding phylogenetic and geographic gaps in global biodiversity genomics and provides a foundation for evidence-based conservation of H. orcesi and related taxa.
Osvath, G.; Denes, A. L.; Kovacs, Z.; Birau, A. C.; Papp, E.; Jako, G. V.; Zeitz, R.
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Romania represents one of the few European Union member states in which all four Old World vulture species historically maintained breeding populations: the Griffon Vulture (Gyps fulvus), Cinereous Vulture (Aegypius monachus), Egyptian Vulture (Neophron percnopterus) and Bearded Vulture (Gypaetus barbatus). Until the 2026 reintroduction efforts initiated by Foundation Conservation Carpathia and Rewilding Romania, Romania remained the last EU country whose former vulture guild had not been targeted for active recovery. Despite this exceptional significance in a European conservation context, no comprehensive synthesis of the historical and contemporary distribution of these species in Romania has been undertaken. We conducted a comprehensive review to gather all available vulture occurrence data and present a fully georeferenced database of 1,170 occurrence records spanning 1818-2025. We systematically searched museum collections, historical ornithological literature, modern field surveys and citizen-science platforms. The database documents substantial breeding populations across the Carpathian arc and Dobrogea until the early twentieth century, followed by near-total breeding collapse between the 1920s and 1960s driven by persecution, secondary poisoning and agrarian transformation. In total, 149 confirmed or probable breeding records have been documented for the four species combined, with the most recent confirmed breeding records dating to 1929 (Gyps fulvus), 1929 (Gypaetus barbatus), 1942 (Aegypius monachus) and 1966 (Neophron percnopterus). Non-breeding occurrences increase markedly after 2010, consistent with dispersal from expanding Balkan source populations. The F[a]g[a]ra {square} and Retezat Mountains emerge as the historically most important breeding strongholds for all four species. Our dataset constitutes the most detailed historical baseline currently available for vulture conservation in Romania and is intended to identify key historical sites with high potential for future reintroduction and recovery. Our results show that Romania historically supported the full guild of European obligate scavengers, and that its collapse occurred within barely four decades (1920s-1960s). The dataset highlights the value of reconstructing historical baselines in regions where functional extinction preceded the onset of modern monitoring, and provides an empirical foundation for reassembling a keystone scavenger guild at a continental scale.