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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.

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Socotra Cormorants in the Arabian Gulf represent a large, but isolated population with low genetic diversity

Almansoori, N. M.; Razali, H.; Muzaffar, S. B.; Chabanne, D. B. H.; Natoli, A.; Almusallami, M.; Naser, H.; Khamis, A.; Al Harthi, F.; Aldhaheri, L. S. R.; Alaleeli, M. M. B.; Al Diwani, F. M.; Manlik, O.

2026-04-03 ecology 10.64898/2026.04.01.712451 medRxiv
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The Socotra Cormorant (Phalacrocorax nigrogularis) is a threatened seabird endemic to the coastal areas of the Arabian Gulf and the Arabian Sea, two regions separated by the Strait of Hormuz. Conserving threatened species requires clear delineation of population boundaries and the evaluation of genetic diversity. However, information on population structure and genetic variation, necessary for such an assessment, is lacking for the Socotra Cormorants. In this study, we assessed population structure and genetic diversity of Socotra Cormorants using two contrasting genetic markers: (1) maternally inherited mtDNA cytochrome oxidase 1 (COI) and (2) a nuclear non-coding region, {beta}-fibrinogen intron 7 (FIB7). A total of 279 individuals were sampled from four colonies in the Arabian Gulf and one colony on Hasikiyah Island in the Arabian Sea. Findings based on COI-variation suggest that the Arabian Gulf colonies represent one large population with extensive gene flow between Gulf colonies--except for the most distant pair of colonies--but isolated from Hasikiyah in the Arabian Sea. COI-variation indicated significant differentiation between the colonies inside the Gulf and the Hasikiyah colony. This is consistent with the reported distribution patterns, and may reflect phylogeographic processes of the region. The Gulf population showed substantially lower COI-diversity, with significantly lower nucleotide and haplotype diversity compared to Hasikiyah. In contrast, FIB7 results indicated extensive connectivity among colonies, with no detectable population structure or significant differences between the Gulf population and Hasikiyah. This study presents the first characterization of population structure and genetic diversity of Socotra Cormorants. The low genetic diversity coupled with relative isolation of the Gulf Socotra Cormorants raises conservation concerns regarding their long-term viability by potentially reducing fitness and eroding their evolutionary capacity to adapt to environmental change. LAY SUMMARYO_LIThe Socotra Cormorant is a threatened seabird found in the Arabian Gulf and Arabian Sea, but little was previously known about its population structure and genetic diversity. C_LIO_LIWe analyzed 279 birds from five nesting colonies (4 in the Gulf and 1 in the Arabian Sea), using two genetic markers to assess population connectivity and variation. C_LIO_LIWe found that the Socotra cormorants inside the Gulf appear to form a large, genetically isolated population with relatively low genetic diversity. C_LIO_LIThis is the first study that evaluates population structure and genetic diversity of this endangered seabird. C_LIO_LIThis is important information for the conservation of the Gulf Socotra cormorants because low genetic diversity, coupled with relative isolation, is associated with reduced fitness, and suggests that they may have a lower chance to adapt to environmental changes. C_LI

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Cryptic diversity in Astyanax (Characiformes: Acestrorhamphidae) from the Magdalena basin, Colombia: Insights from molecular and morphometric evidence

Marquez, E. J.; Garcia-Castro, K. L.; Alvarez, D. R.; DoNascimiento, C.

2026-03-31 genetics 10.64898/2026.03.28.714954 medRxiv
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Astyanax Baird & Girard, 1854 is a widely distributed and species-rich genus of Acestrorhamphidae, whose abundant populations in Neotropical basins play a crucial ecological role at the trophic level. Taxonomic uncertainties persist within the genus, as seen in Astyanax sp. (formerly designated as A. fasciatus) from the Magdalena basin in Colombia. Concerns about its genetic status are heightened due to ecological threats posed by hydroelectric dams, from habitat loss to river connectivity. We isolated and characterized 17 microsatellite loci to assess the population genetics of this species in a broad sample from the middle and lower sections of the Cauca River, now interrupted by the Ituango dam. Furthermore, a multidisciplinary approach integrating phylogenetic analyses of mitochondrial (COI) and nuclear (rag2) markers with geometric morphometric analyses was employed to evaluate potential cryptic diversity within Astyanax sp. Microsatellites revealed two genetic groups in the studied area, strongly supported as distinct lineages by phylogenetic analyses. Unexpectedly, one of these lineages of Astyanax sp. was recovered in an unresolved clade with samples of A. microlepis and allopatric samples of A. viejita from the Maracaibo Lake basin. Each genetic group showed high genetic diversity, but also evidence of recent bottleneck events and significant-high values of inbreeding. Morphometric analyses provided evidence of significant phenotypic differentiation among A. microlepis, Astyanax sp. 1 (Asp1), and Astyanax sp. 2 (Asp2). Morphological patterns ranged from the robust profile of A. microlepis to the streamlined shape of Astyanax sp. 2 (Asp2), with Astyanax sp. 1 (Asp1) displaying intermediate traits and localized differences in head length and fin placement. Statistical support from permutation tests and a high overall classification accuracy (95.65%) underscore the existence of distinct morphospecies, suggesting that phenotypic differentiation is well-established, despite the complex evolutionary history of the group. This study suggests the presence of cryptic diversity within Astyanax sp. and provides valuable genetic information for the conservation and management of their populations in the Magdalena basin.

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Body size, dental pathology and maternal genetic diversity of ancient horses in the eastern Baltic Sea region and western Russia

Honka, J.; Salazar, D.; Askeyev, A. O.; Askeyev, I. V.; Askeyev, O. V.; Aspi, J.; Asylgaraeva, G. S.; Niskanen, M.; Mannermaa, K.; Olli, S.; Piipponen, N.; Piliciauskiene, G.; Shaymuratova, D. N.; Valiev, R. R.; Kvist, L.

2026-03-19 genetics 10.64898/2026.03.17.712305 medRxiv
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The early evolutionary history of modern domestic horses (Equus caballus/E. ferus caballus), known as the DOM2 lineage, is well documented due to numerous archaeological and ancient DNA (aDNA) studies. Although many uncertainties remain in the domestication timeline, current evidence suggests that the domestication of modern horses began in the Pontic-Caspian steppe at least [~]2700 BCE (before common era), or even earlier. However, it is not known how long remnant wild horse populations survived or when domestic horses were introduced into Northern Europe. In this study, we review the current knowledge of horse domestication, focusing on Northern Europe. We analysed prehistoric horses from western Russia to assess the body sizes of wild horses from the Ivanovskaya site (5900-3800 BCE) in the Pontic-Caspian steppe, and the body weight of one Lithuanian wild horse (4000-3800 BCE). Additionally, we analysed body sizes of Late Bronze Age-Early Roman Age horses (1100 BCE-300 CE; common era) and re-analysed body sizes and estimated rider weights of historic domestic horses from Lithuania (100-1400 CE). We searched for pathological changes and signs of bit wear indicative of bridling. Furthermore, we investigated maternal genetic diversity by sequencing ancient mitochondrial DNA. We found that wild horses from Ivanovskaya were intermediate in body size between earlier and more recent horses of the Eurasian Steppe, and that the Lithuanian wild horse weighed only [~]270 kg and Late Bronze Age-Early Roman Age horses 200-300 kg. Lithuanian domestic horses were pony-sized (< 130 cm on average). Bit wear was confirmed on one tooth, the oldest domestic horse in Lithuania (799-570 cal BCE). Another tooth showed signs of the Equine Odontoclastic Tooth Resorption and Hypercementosis (EOTRH) condition. Mitochondrial DNA was successfully amplified from one Ivanovskaya wild horse along with 25 other ancient samples, including Lithuanias oldest domestic horse. mtDNA diversity was high, revealing several maternal lineages.

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Domestic dog introgression in Australian dingoes: environmental drivers and evolutionary consequences

Osuna-Mascaro, C.; Cairns, K.; Doan, K.; Flores-Manzanero, A.; Nesbitt, B. J.; Newsome, T. M.; Pilot, M.

2026-03-24 evolutionary biology 10.64898/2026.03.22.713106 medRxiv
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Introgressive hybridization between wild and domestic animals is a widespread phenomenon with important implications for genetic diversity, local adaptation, and conservation management. The causes and consequences of this process are poorly understood. In Australia, hybridization between dingoes and domestic dogs presents a dual conservation challenge, threatening the genetic integrity of dingoes while allowing potential adaptive introgression. To investigate the environmental drivers of this process, we analyzed high-density SNP array data in 390 dingoes and 396 domestic dogs. Dingo populations showed regional genetic structure and were clearly differentiated from domestic dogs. Using local ancestry inference and genome-environment association analyses, we found low levels of dog introgression in dingoes from remote areas in Central and Western Australia, and moderate levels in Eastern and Southern populations. Climatic variables (maximum temperature of the warmest month, mean temperature of the driest quarter) and the Human Footprint Index (reflecting density of human populations and environmental modifications) were significant predictors of introgression. We identified four genomic regions with overrepresented dog ancestry, including a large introgressed block on chromosome 27, which contained an olfactory receptor gene showing signatures of positive selection, suggesting adaptive introgression. In addition, a chromosomal inversion previously described in dogs and absent in dingoes was initially identified as an introgressed block. We also detected eight genomic regions nearly free of dog ancestry, suggesting purifying selection against maladaptive variants. Together, these results highlight the complex interplay between introgression, human influence, and local adaptation in dingoes, offering valuable insights for conserving the evolutionary potential of this apex predator in increasingly modified landscapes.

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Accurate estimation of canine inbreeding using ultra low-coverage whole genomesequencing

Pellegrini, M.; Kim, R.; Rubbi, L.; Kislik, G.; Smith, D.

2026-04-07 bioinformatics 10.64898/2026.04.04.716453 medRxiv
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The measurement of inbreeding has gained significance across diverse fields, including population and conservation genetics, agricultural genetics, breeding programs for animals and plants, and wildlife management. This is due to the fact that inbreeding leads to increased homozygosity and results in lower genetic diversity, rendering populations more vulnerable to environmental changes, diseases, and other stressors. High or mid-coverage whole genome sequencing (WGS) has been widely used for inbreeding estimation, but it is resource-intensive. We aimed to investigate the use of ultra low-coverage whole genome sequencing (ulcWGS) as a cost-effective alternative for inbreeding analysis. Domestic dogs were used for our study as their extensive breeding histories lead to populations with a wide range of inbreeding levels. We constructed a multi-breed reference panel from high-coverage WGS samples. Inbreeding in independent ulcWGS samples was then estimated using runs of homozygosity (RoH) and inbreeding coefficients (F). We modeled the relationship between these measures and sequencing depth using nonlinear regression, to generate inbreeding estimates relative to sequencing depth. Resulting relative RoH and F measurements were significantly correlated, with purebred dogs exhibiting more runs of homozygosity and higher inbreeding coefficients compared to mixed-breed dogs. Our findings demonstrate that ulcWGS can provide reliable and economical estimations of inbreeding, expanding accessibility to genetic monitoring.

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Female site fidelity and repeated pairings across years in bull sharks (Carcharhinus leucas) inhabiting Fiji waters

Glaus, K.; Benestan, L. M.; Brunnschweiler, J.; Devloo-Delva, F.; Appleyard, S.; Rico, C.

2026-03-25 ecology 10.64898/2026.03.23.713736 medRxiv
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Understanding relatedness in sharks is challenging due to uncertainty in distributions, low population densities and difficulties in sampling across life stages. In Fiji, bull sharks (Carcharhinus leucas), with an effective population size estimate of [~]258, aggregate at the Shark Reef Marine Reserve (SRMR), but gravid females disperse at the end of the year to give birth in adjacent rivers. Questions remain regarding reproductive connectivity, female returns across years, and kinship structure. Using population genomics on 296 bull sharks across age classes (neonates, young-of-the-year, juveniles, and adults) collected over a decade at the SRMR and in three adjacent rivers, we assessed familial connections. Direct genetic links, including first- and second-degree relationships, connected SRMR adults with young age classes in the Navua and Rewa rivers, providing evidence of reproductive connectivity. Within rivers, genetic similarities across cohorts revealed reproductive philopatry. Remarkably, several individuals sampled years apart were assigned to the same sire-dam pairs, indicating repeated pairings across breeding seasons. However, the few related links detected between the SRMR and the rivers may reflect incomplete sampling. Altogether, bull shark reproduction in Fiji seems influenced by reproductive philopatry and repeated pairings, suggesting added complexity in their reproductive behaviour.

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Ghostbusting the national bird checklist: integrative evidence shows that Pionus fuscus does not occur in Colombia

Carrillo-Restrepo, J. C.; Velasquez-Tibata, J.

2026-03-26 ecology 10.64898/2026.03.23.713821 medRxiv
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Natural history collections underpin our understanding of species distributions, yet some historical records remain embedded in modern avifaunal checklists despite limited documentation and no independent verification. One such case concerns the Dusky Parrot Pionus fuscus in Colombia: although reported from specimens collected by Melbourne A. Carriker Jr. in 1942 in the Serrania de Perija, the species has not been observed in the country for nearly eight decades yet continues to be included in national checklists and conservation assessments. We reassessed the validity of this record by applying a multi-evidence framework integrating historic archival reconstruction, specimen-based morphological comparisons, climatic niche analyses, biogeographic limit assessment and contemporary survey-effort data. Historical documentation and morphological evidence based on high-resolution specimen images and associated curatorial records demonstrate that the Carriker specimens correspond to Pionus chalcopterus, not P. fuscus. Climatic niche analyses reveal minimal environmental overlap between P. chalcopterus and P. fuscus, and place the Perija locality within the climatic niche of P. chalcopterus, while regional biogeography and extensive modern birdwatching coverage provide no support for the occurrence of P. fuscus in Perija. Together, these concordant lines of evidence demonstrate that P. fuscus does not occur in Colombia. Our findings support its removal from national bird lists and conservation assessments and highlight how integrated, multi-evidence reassessments of historical records strengthen ornithological baselines, improve biogeographic inference and ensure that conservation priorities rest on verifiable evidence.

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Climate cycles drive demographic history and genomic divergence in cactus wrens (Campylorhynchus brunneicapillus) across North American warm deserts

Rodriguez-Rojas, P. C.; Oceguera-Figueroa, A. F.; Navarro-Siguenza, A. G.; Vazquez Miranda, H.

2026-03-26 evolutionary biology 10.64898/2026.03.24.714001 medRxiv
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Text AbstractIn this study, we characterized the genetic structure and reconstructed the demographic history of cactus wrens (Campylorhynchus brunneicapillus), an endemic species of desert regions of North America, that shows a clear phenotypic and genotypic variation. We evaluated the effects of historical climate change on the structure and population dynamics of desert species using genomic data through genotyping by sequencing (GBS) and applied a population structure analysis (FST and ADMIXTURE), revealing two genetically differentiated groups: one continental and another peninsular in Baja California. Subsequently, we implemented the MSMC2 coalescent model on data divided into autosomal regions and the Z sex chromosome to estimate changes in effective population size (Ne) through evolutionary time. Additionally, we developed ecological niche models (ENMs) projected to the Last Glacial Maximum (LGM), Last Interglacial (LIG), Present times, and Future (2060 - 2080). Results indicate that both populations maintained moderated Nes before the LGM, experienced severe bottlenecks (Ne [~] 102-103), followed by a sustained expansion. However, recovery was limited to the Z chromosome of the peninsular population. These findings reveal how glaciations and interglacials shaped the evolutionary history of desert species and provide genomic evidence of the splitting of C. affinis from C. brunneicapillus. Article summaryThis research examines how climate changes shaped genetic diversity of cactus wrens across North American warm deserts. Using coalescent methods, researchers tracked effective population size changes over 100,000 years, using ecological niche modeling they predicted habitat suitability across climate periods. Results showed that continental and peninsular populations experienced bottlenecks during the Last Glacial Maximum, followed by demographic recovery on warm periods. However, the sex chromosome (Z) revealed male-biased demographic patterns in peninsular populations. Future projections indicated habitat suitability reductions for peninsular populations, highlighting conservation concerns. These findings demonstrate that past climate shaped genetic diversity of cactus wrens.

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Reassessing display behavior from Bels et al. (2025) given the complexity of anthropogenic hybridization and intraspecific diversity in Iguana iguana

van den Burg, M. P.; Thibaudier, J.

2026-03-23 zoology 10.64898/2026.03.19.713079 medRxiv
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Understanding behavioral differences between non-native and closely related endangered species could be important to aid conservation management. In volume 169 of Zoology, Bels et al. (2025) reported on their comparison of display-action-patterns (DAP) between native Iguana delicatissima and non-native iguanas present on islands of the Guadeloupe Archipelago in the Caribbean Lesser Antilles. Here, we address conceptual and methodological concerns about their work and reanalyze their data given our proposed corrections, primarily a literature-informed adjustment of their "species" category. We additionally utilize online videos from South American mainland I. iguana populations, from where the non-native iguanas in the Guadeloupe Archipelago originate, to better understand the different DAPs between native and non-native iguanas in the Guadeloupe Archipelago. Significant differences in DAP characteristics among "species" categories (native I. delicatissima, non-native iguanas, and hybrids) show that Bels et al. (2025) oversimplified their data analyses by merging all non-native populations into one group. This result indicates the presence of behavioral variation among subpopulations within widely hybridizing iguanid populations, which has been poorly studied. Additionally, videos from mainland populations across two major mitochondrial clades of Iguana iguana show that non-native iguanas on Guadeloupe retained DAP characteristics of those populations from which they originate. We discuss these findings in light of the proposed hypotheses put forward by Bels et al. (2025), of which two can be excluded. Overall, our reanalysis shows that studies focusing on characteristics within settings of complex hybridization in diverse species should acknowledge this complexity.

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Protocol for genotyping cephalopod sex using a skin swab and quantitative PCR

Montague, T. G.; Rubino, F. A.; Gibbons, C. J.; Mungioli, T. J.; Small, S. T.; Coffing, G. C.; Kern, A. D.

2026-04-02 molecular biology 10.64898/2026.03.31.715692 medRxiv
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The coleoid cephalopods (octopus, cuttlefish, and squid) are emerging model organisms for neuroscience, development, and evolutionary biology. Determining their sex early in life is critical for population management and controlled experiments. Here, we present a protocol to non-invasively determine the sex of multiple cephalopod species as young as 3 hours post-hatching using a skin swab and quantitative PCR (qPCR). We describe steps for designing qPCR primers, swabbing live animals, extracting DNA, running the qPCR, and analyzing the results. For complete details on the use and execution of this protocol, please refer to Rubino et al.1 HighlightsO_LISwab live cephalopods as early as 3 hours post-hatching C_LIO_LIExtract DNA from cephalopod skin swabs C_LIO_LIPerform qPCR-based sex determination C_LIO_LIDesign and validate qPCR primers for new species C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=190 SRC="FIGDIR/small/715692v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@3aa68dorg.highwire.dtl.DTLVardef@8c7e61org.highwire.dtl.DTLVardef@1bd45d9org.highwire.dtl.DTLVardef@134cc4d_HPS_FORMAT_FIGEXP M_FIG C_FIG

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The OS-Prey (Omnibus Study of Prey) database: A compilation of diet records for birds of prey.

Uiterwaal, S. F.; La Sorte, F. A.; Coblentz, K. E.; DeLong, J. P.

2026-03-31 ecology 10.64898/2026.03.28.714998 medRxiv
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MotivationThe diet composition of a predator is a direct reflection of its role in a food web, resulting from interactions with prey species. Raptors (including hawks, owls, and falcons) are ubiquitous predators with diverse diets, yet there is no comprehensive database of raptor diet composition. We present a database of over 3500 raw raptor diet records, compiled from more than 1000 studies and representing 173 raptor species from across the world. Our dataset complements existing qualitative summaries of species diets by compiling thousands of quantitative diet "samples" over time and space to present diet data at a uniquely fine resolution. Main types of variable containedThe database comprises published records of raptor diets from pellets, prey remains, direct or photographic observations, prey DNA, and raptor gut or gullet contents. For each diet, we present the taxonomic identity and amounts of consumed prey. We additionally present various metadata for each diet such as location, habitat, and season. Spatial location and grainThe study incorporates diet records collected worldwide, with each record assigned geographic coordinates corresponding to the location where the diet information was obtained. Time period and grainThe database includes diet records from 1893 to 2025. We report a year for each diet record. Major taxa and level of measurementWe recorded raptor diet at the species level, including raptors from three orders: Strigiformes, Falconiformes and Accipitriformes excluding vultures. Most prey are identified to species, but prey taxonomic level varies depending on the extent to which they could be identified. Software formatDiet records and metadata are provided in two files with comma-separated value (.csv) format.

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Bed and breakfast in the bush: Selection of resting sites and kill sites by leopards (Panthera pardus) on Namibian farmland

Sabeder, N.; Oliveira, T.; Portas, R.; Hocevar, L.; Flezar, U.; Wachter, B.; Melzheimer, J.; Krofel, M.

2026-03-20 ecology 10.64898/2026.03.18.712594 medRxiv
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Sleeping and feeding are crucial for survival of any animal. In case of large predators, knowing where these activities occur can help us understand their behavioural adaptations for coexisting with people and could help mitigating human-carnivore conflicts. Leopard (Panthera pardus) is an elusive and highly adaptable large felid that mostly lives outside protected areas and can survive also in close proximity to humans. However, most leopard research in Africa has been conducted in protected areas and we poorly understand leopards habitat selection while resting and hunting. To shed light on their coexistence with humans, we investigated habitat features influencing leopard selection of resting and kill sites on farmlands in central Namibia, using generalized linear mixed models (GLMM) under a use-availability study design and blinded field-sampling. Leopards primarily selected resting sites that were located in mountainous, steep, rugged terrain and sites with good concealment while kill sites were selected in mountainous habitats. Human infrastructure did not affect leopard resting and kill site selection. Thus, the capacity of leopards to perform essential life-supporting behaviours while coexisting with people appears to be primarily driven by their ability to remain concealed, rather than spatially avoiding humans.

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Complementary evidence from historical and contemporary gene dispersal reveals contrasting population dynamics in a tropical tree species

Bonnier, J.; Heuertz, M.; Traissac, S.; Brunaux, O.; Lepais, O.; Troispoux, V.; Chancerel, E.; Compagnie, Z.; Tysklind, N.

2026-03-25 ecology 10.64898/2026.03.23.713184 medRxiv
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Gene flow shapes the demographic stability and evolutionary potential of tropical forest trees, yet its dynamics may differ depending on the temporal scale at which it is assessed. We combined spatial genetic structure (SGS), parentage analyses, and reproductive success metrics to investigate historical and contemporary gene dispersal in four populations of Dicorynia guianensis across French Guiana, encompassing sites differing in environment and management history. A total of 1,528 individuals were genotyped using 66 nuclear and 23 plastid microsatellite markers, enabling high-resolution inference of biparental and maternal gene dispersal. Historical mating and dispersal parameters inferred from SGS revealed marked contrasts among populations. Some populations exhibited high historical gene dispersal distances and weak spatial genetic structure, whereas others showed stronger SGS and long-term aggregative dispersal patterns. Contemporary parentage analyses further highlighted differences in seed and pollen dispersal distances, parent assignment rates, and reproductive skew. In certain populations, pronounced reproductive inequality and reduced effective connectivity were observed, while others displayed more balanced reproductive contributions. By jointly evaluating long-term dispersal legacies and present-day reproductive patterns, our study demonstrates the value of combining indirect and direct genetic approaches to assess population dynamics and conservation status in tropical forest trees. This multi-temporal perspective provides a comprehensive basis for long-term monitoring and sustainable management in heterogeneous tropical landscapes.

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Patterns of host plant use by monarch butterflies revealed through annotation of more than 35,000 community science records

Freedman, M.

2026-04-08 ecology 10.64898/2026.04.06.716508 medRxiv
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Community science data are increasingly recognized as important resources for biodiversity research, in part because of the spatial and temporal resolution that they afford. While these data are useful for applications such as describing occurrence patterns, tracking movement of migratory animals, and recording phenological events, they can also be probed for "second-order" purposes, such as documenting species interactions. Here, I present a dataset of more than 35,000 annotated interactions between monarch butterfly (Danaus plexippus) larvae and their associated host plants from the community science platform iNaturalist. I document more than 70 unique species of milkweed hosts (Apocynaceae: Asclepiadoideae) used by monarch larvae, including a number of previously undocumented interactions. Monarchs show strong seasonal turnover in the species of host plants used across the migratory cycle, highlighting the importance of early season hosts like Asclepias viridis and A. asperula in eastern North America and A. californica and A. cordifolia in the west. I also demonstrate that non-native horticultural milkweed species have increased the spatial extent of monarch breeding during winter (November - February) by more than 60%, a pattern previously suggested from observational data but not formally quantified until now. To my knowledge, this represents the largest analysis to date of species interactions using unstructured community science data and highlights the value of platforms like iNaturalist for conducting fundamental research in ecology and conservation.

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Transcriptomes resolve phylogenetic relationships and reveal undescribed diversity in taildropper slugs (Genus Prophysaon)

Smith, M. L.; Moshier, S.; Shoobs, N. F.

2026-03-27 evolutionary biology 10.64898/2026.03.25.713997 medRxiv
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The temperate rainforests of the Pacific Northwest of North America harbor many endemic taxa whose evolutionary histories have been shaped by major climatic and geologic events. The enigmatic taildropper slugs (genus Prophysaon) are one example, notable for their ability to autonomize their tails to escape predators. Despite extensive work uncovering the evolutionary history of individual lineages, relationships among the nine recognized species of Prophysaon remain poorly understood due to insufficient molecular data. To address this, we collected transcriptomes for six of the nine currently accepted species of Prophysaon. Using these data, we were able to resolve species relationships, calling into question the existing subgeneric classification based on morphology. We also detected undescribed phenotypic diversity within the P. andersonii--P. foliolatum species complex, with molecular data supporting the distinctness of two phenotypically distinct populations from Washington. Finally, our transcriptomic data suggest a moderate role of introgression in shaping the evolutionary history of Prophysaon. Here, we synonymize the subgenus Mimetarion with nominotypical Prophysaon. Future work should further investigate whether the undescribed diversity detected here represents species level differentiation.

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Species-specific versus community-wide assays in eDNA monitoring of European eel Anguilla anguilla: Trade-offs between detection sensitivity and the value of additional community data

Monaghan, A. I. T.; Sellers, G. S.; Griffiths, N. P.; Lawson Handley, L.; Hänfling, B.; Macarthur, J. A.; Wright, R. M.; Bolland, J. D.

2026-03-20 ecology 10.64898/2026.03.19.712641 medRxiv
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Effective monitoring of the critically endangered European eel (Anguilla anguilla) is essential for conservation planning and regulatory decision-making, particularly in heavily fragmented rivers. Environmental DNA (eDNA) methods offer sensitive alternatives to traditional surveys, but there is uncertainty around whether targeted assays or community-wide approaches are better suited to achieve monitoring objectives. We compared eDNA metabarcoding and species-specific quantitative PCR (qPCR) for detecting A. anguilla across 145 pumped catchments in the Fens, East Anglia, England. All sites were sampled once initially, and sites negative for A. anguilla were re-sampled based on metabarcoding results. This allowed comparison of detection rates from a single water sample and site-level retrospective identification of sites where qPCR could have identified A. anguilla in earlier samples. The findings were also set in the context of the wider biodiversity information generated by metabarcoding. From the initial (single) water sample, qPCR detected A. anguilla at seven more sites than metabarcoding (17 versus 10). With repeated sampling, metabarcoding detected A. anguilla at 43 sites, including all but one of the sites where qPCR detected A. anguilla, and ten sites where qPCR did not detect A. anguilla within the same number of samples. Indeed, the additional sampling effort required to detect A. anguilla with metabarcoding at sites also positive with qPCR was small relative to the overall sampling effort. Furthermore, metabarcoding additionally detected 28 non-target fish species alongside fish, amphibian and mammal species of conservation concern. Our results highlight trade-offs between target-species sensitivity and the broader ecological information provided by each method, and support metabarcoding as an effective tool for a holistic conservation approach, with the additional community data outweighing the marginally increased sensitivity of qPCR.

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How farming practices and livestock management affect Human-Wildlife Conflict intensity in Southern Ecuador: The case of the Spectacled Bear (Tremarctos ornatus) and feral dogs

Lopes, F.; Penaherrera-Aguirre, M.; Cisneros, R.

2026-03-30 ecology 10.64898/2026.03.29.715147 medRxiv
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BackgroundHuman-Wildlife Conflict is emerging as one of the most critical conservation and socio-economic challenges in the Ecuadorian Andes, where both rural livelihoods and native fauna are under increasing pressure. Small-scale livestock producers in the region depend almost entirely on a limited number of cattle, meaning that the loss of even a single animal can lead to severe economic hardship. In response, antagonistic actions against wildlife are frequent, further threatening vulnerable species. At the same time, the recent proliferation of feral dogs adds a new dimension to conflict, posing risks to both livestock and native fauna. Despite the growing severity of this conflict, little is known of its drivers, spatial patterns, and socio-ecological consequences. This study seeks to fill that gap by generating insights to inform targeted conservation strategies for community-based mitigation of conflict with spectacled bears and feral dogs. MethodsTo assess the drivers and dynamics of HWC in southern Ecuador, we conducted structured interviews with livestock owners, quantifying the frequency and intensity of conflicts across multiple species and evaluating whether farm composition and management practices predict conflict patterns. ResultsOur results reveal that large carnivores cause significantly higher economic losses than smaller predators; furthermore, feral dogs have emerged as the primary source of financial damage over the past five years. Farms with a greater proportion of forest edge were associated with a higher probability of severe conflict, particularly with large carnivores. ConclusionsThese findings underscore the urgent need for proactive strategies to promote coexistence. Identifying predictive variables of conflict risk is crucial for vulnerability assessments and the design of effective mitigation policies. Controlling feral dog populations is likely to be a critical step in safeguarding both rural human livelihoods and native biodiversity in the Andean landscape.

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Diet and breeding productivity in European Shag (Gulosus aristotelis): insights from two Portuguese colonies

Vieira, B.; Goncalves, D.; Oliveira, N.

2026-03-30 ecology 10.64898/2026.03.29.715095 medRxiv
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Climate change and anthropogenic pressures are reshaping marine food webs, altering prey availability and affecting top predators. The European Shag (Gulosus aristotelis), a coastal demersal seabird, provides a valuable model for examining environmentally mediated dietary variation, given its trophic plasticity and capacity to adjust prey use according to local availability, while also allowing assessment of potential demographic consequences. This study investigated spatial and temporal variation in diet at two Portuguese colonies (Berlengas and Arrabida) between 2016 and 2024 and assessed long-term reproductive productivity at Berlengas. A total of 468 regurgitated pellets were analysed, and diet composition was quantified using the Index of Relative Importance (IRI). Generalised additive models were applied to assess environmental, spatial, and period-specific effects on diet composition, while reproductive productivity was modelled in relation to prey biomass. Diet variation was primarily explained by environmental predictors, including sea surface temperature, chlorophyll-a concentration, and zooplankton, whereas year per se had no significant effect, indicating environmentally mediated bottom-up effects. Spatial differences between colonies reflected contrasting prey field structures, and period-specific patterns suggested increased specialisation during breeding. Higher biomass of sandeels (Ammodytidae) was positively associated with reproductive output, whereas shifts toward lower-energy prey were associated with reduced productivity. These findings demonstrate that environmentally driven dietary change has measurable demographic consequences, underscoring the importance of bottom-up processes in shaping seabird population dynamics and informing conservation strategies under ongoing climate change.

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Twenty-five years of monitoring reveals that uninterrupted rodent control is the fundamental driver of breeding success in the Galapagos Petrel Pterodroma phaeopygia

Lopes, F.; Gibbs, J. P.; Carrion, J.

2026-03-30 ecology 10.64898/2026.03.29.715149 medRxiv
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The long-standing misconception that the Galapagos petrel (Pterodroma phaeopygia) and the Hawaiian petrel (Pterodroma sandwichensis) were conspecific masked the severe vulnerability of the Galapagos population. By the time its distinct status was recognized, the Galapagos petrel was already in marked decline, primarily due to invasive predators. Consequently, sustained rodent control programs have been implemented on Santa Cruz Island. An unintentional one-year failure in rodent control provided a rare quasi-experimental opportunity to quantify the demographic consequences of the invasive black rat predator. During this year, hatching success declined by [~]35% and breeding success by [~]40% relative to long-term means (66% and 62%, respectively), representing a substantial reproductive collapse. Fledging success exhibited a comparatively modest decline (from a long-term mean of 94% to 86% in 2017), suggesting stage-specific vulnerability. These results support the hypothesis that invasive black rats primarily affect early reproductive stages through egg predation and predation on small chicks, while older chicks surpass a critical size threshold that reduces susceptibility. Across the remaining managed years, reproductive metrics exhibited great stability, demonstrating the petrels resilience against other environmental or climatic stressors. Our findings provide robust empirical evidence that invasive rodent control is the dominant driver of reproductive success in this endangered seabird. The quasi-experimental failure underscored both the effectiveness and the necessity of continuous predator management, highlighting the severe and immediate consequences of even short-term lapses.

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The role and origins of human attitudes in Human-Wildlife Conflict responses: Insights from Spectacled Bears (Tremarctos ornatus) and other wild carnivores in Southern Ecuador

Lopes, F.; Penaherrera-Aguirre, M.; Cisneros, R.

2026-03-30 ecology 10.64898/2026.03.29.715142 medRxiv
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BackgroundHuman-wildlife conflict, which motivates retaliatory killings, is a major driver of species decline globally. Addressing an open question in human-wildlife conflict, we test whether evolutionary-rooted human attitudes, independent of economic losses, better predict retaliatory responses. MethodsWe examined human attitudes toward spectacled bears (Tremarctos ornatus) and other wild carnivores in a wildlife conflict-zone in southern Ecuador by conducting interviews in rural communities. We measured both established variables - such as education levels, age, and gender - and novel psychometric variables to identify predictors of human-wildlife conflict responses. ResultsPerceptions of animals emerged as the strongest predictor of conflict responses. Communities exhibiting high levels of vengefulness, particularly within an animal-directed Culture of Honor, where individuals, especially men, are expected to respond strongly or violently to perceived threats, were more likely to support lethal interventions. Conversely, individuals with strong environmental education backgrounds demonstrated more positive perceptions of wildlife, highlighting educations potential role in conflict mitigation. ConclusionEvolutionary-derived attitudes, rather than economic factors, primarily drive human responses to wildlife conflict. Effective strategies to reduce violence against wildlife should incorporate human perceptions and culturally rooted values to address the underlying social and psychological drivers of conflict.