Biology subjects

Rahbek, C.

Publications and source records attributed to Rahbek, C..

12 recordsLinked to original sources

bioRxiv2026

Human development and inequality shape global threat patterns for terrestrial biodiversity

Biodiversity loss is driven by unsustainable human activities, yet the contextual conditions and underlying drivers of threats remain poorly understood. We assessed how protected areas, socioeconomic conditions, and biophysical factors explain global patterns of threat probabilities across six major threat types and four vertebrate taxa. We identified key explanatory variables and their associations with threats using Extreme Gradient Boosting (XGBoost) and SHapley Additive exPlanations (SHAP). Socioeconomic conditions, specifically human development and income inequality, were the strongest predictors. Their associations were complex and non-linear: notably, high human development index (HDI) was associated with both higher and lower threat probabilities, depending on inequality and regional context. Second, land cover and biophysical variables, such as shrubland cover, tree cover, and elevation range, explained additional, but taxon-specific variation. Finally, protected areas showed limited ability to explain threat patterns. By linking threat probabilities to their contextual and socioecological conditions, we aim to build a better understanding of the systemic drivers of biodiversity loss.

ecology↗

bioRxiv2026

Global vertebrate hotspots

Effective biodiversity conservation requires tools that can identify priority areas under growing human pressures. Building on the concept of global biodiversity hotspots, we present a transparent and repeatable approach to mapping conservation priorities using data for 33,604 species of terrestrial vertebrates from the IUCN Red List. This framework expands the taxonomic scope of previous efforts and integrates updated information on key human-driven threats to biodiversity. We identify that around 13% of Earths terrestrial surface qualifies as vertebrate conservation hotspots, often shaped by distinct combinations of species groups and threats. These results highlight the need for tailored, context-specific conservation strategies. By providing a robust method to guide spatial prioritization, our work supports more effective implementation of conservation targets in a rapidly changing world.

ecology↗

bioRxiv2026

Palaeogenomics-informed inferences of European dog admixture enables scalable dingo conservation

Dingoes, mainland Australias sole terrestrial apex mammal for over 3,000 years, are important components of many ecosystems and Indigenous cultural heritage. Yet conflicts with farmers over livestock predation following European colonisation led to widespread lethal control. These measures are further reinforced by perceptions of hybrid ancestry with European dogs. Accurate estimation of European dog ancestry is therefore essential for effective conservation, but existing tests yield highly conflicting results. Leveraging pre-colonial dingo palaeogenomes and a robust ancestry modelling framework, we reassess the genetic ancestry of contemporary populations. Our approach corrects limitations and biases in existing methods, producing consistent estimates even with as few as 10,000 genome-wide transversion genetic markers. Accounting for admixture uncovers population structure that has persisted for over two millennia and reveals patterns of genetic admixture coinciding with human activity during the colonial era. This study underscores the value of palaeogenomes as a vital conservation tool, offering insights unattainable from modern DNA alone. By clarifying ancestry and population structure, our study offers a robust foundation for effective regionally informed dingo management across Australia.

genomics↗

bioRxiv2026

A time-calibrated phylogeny of hummingbirds supports stepwise diversification in the Andes

Hummingbirds (Trochilidae) represent the second largest avian family, with [~]356 species occupying diverse habitats across the Neotropical and Nearctic regions. Their extensive diversification includes notable adaptations to extreme environments, with nearly one-third of extant taxa belonging to the predominantly high-altitude Coquettes and Brilliants. Although recent work proposed a monophyletic Andean clade uniting these groups, consistent with rapid radiation during Andean orogeny, we find no support for this relationship. Using 2,949 nuclear loci sampled from 47 species spanning all nine major hummingbird clades, we recover a different evolutionary pattern: a stepwise sequence of diversification in which Brilliants are sister to a broader assemblage comprising Coquettes, the genus Patagona, Emeralds, Mountain Gems, and the recently diverged Bees. By assembling complete mitochondrial genomes, we additionally detect significant discordance between nuclear topologies and those derived from the mitogenome and Z chromosome. Analyses of gene-tree heterogeneity show that incomplete lineage sorting is pervasive across the phylogeny, with particularly strong impacts on branches associated with Andean diversification. Divergence-time estimation further indicates that the major Andean radiation--including Brilliants, Coquettes, Emeralds, Bees, and Mountain Gems--originated around [~]14 Ma, with the three younger clades diversifying [~]12 Ma, coinciding with both the mid-Miocene Andean uplift and the mid-Miocene Climate Transition that increased habitat heterogeneity and likely promoted rapid speciation. To support future phylogenomic efforts, we identify a reduced set of highly informative, independent protein-coding loci and present a near-complete species-level phylogeny constrained by our autosomal backbone. Our findings highlight the importance of integrating loci with distinct inheritance modes to detect and interpret phylogenetic incongruence in rapid radiations.

evolutionary biology↗

bioRxiv2024

Are protected areas tracking threats to terrestrial biodiversity?

1Protected areas (PAs) are vital for nature conservation, yet evidence shows that pressure on biodiversity is increasing despite their global expansion. Using threat probability maps based on the IUCN Red List and PA data, we analyzed the relationship between PA coverage and the major threats--agriculture, hunting, logging, pollution, invasive species, and urbanization--affecting amphibians, birds, mammals, and reptiles. Our analysis includes data on 33,379 species and 255,848 protected sites. Our results reveal a potential disconnect between global PAs and threat tracking, often leaving high-threat areas insufficiently protected. Over half of the mapped area for amphibians and mammals faces high threat impact probability and insufficient PA cover. Amphibians face the highest proportion of high-simultaneous threats and lack sufficient cover. Areas facing a high probability of impact lacking sufficient PA cover also harbor the highest proportion of threatened species across all taxonomic groups. Our research provides crucial insights into the current state of terrestrial PAs concerning threats, highlighting areas requiring immediate attention and guiding strategic conservation planning.

ecology↗

bioRxiv2023

The threats to reptiles at global and regional scales

At least 20% of reptiles are currently threatened with extinction. Due to the lack of comprehensive global assessments of the group, they have been omitted from spatial studies, especially the ones addressing conservation or spatial prioritization. With the recent release of global assessments for reptiles, in this study, we calculate the probability of seven biodiversity threats - logging, pollution, agriculture, invasive species, hunting, climate change and urbanization occurring at a global scale on a 50x50km grid and their impact measured as the probability of finding a threatened species. Despite the global nature of our approach, we compartmented the terrestrial land into 12 regions and conducted separate analyses on each region. We find that despite globally low levels of intensity, climate change and invasive species have the highest impact on reptiles. But when looked at the regional level, various threats have a high impact on biodiversity, even surpassing climate change and invasives. Our study highlights the importance of going beyond measuring the intensity of threats to measure impact and also the importance of subdividing the world into smaller units and testing the impacts separately.

zoology↗

bioRxiv2022

Species-specific traits mediate avian demographic responses under past climate change

Anticipating species responses to environmental change is a pressing mission in biodiversity conservation. Despite decades of research investigating how climate change may affect population sizes, historical context is lacking and the traits which mediate demographic sensitivity to changing climate remain elusive. We use whole-genome sequence data to reconstruct the demographic histories of 263 bird species over the past million years and identify networks of interacting morphological and life-history traits associated with changes in effective population size (Ne) in response to climate warming and cooling. Our results identify direct and indirect effects of key traits representing dispersal, reproduction, and survival on long-term demographic responses to climate change, thereby highlighting traits most likely to influence population responses to on-going climate warming. One-Sentence SummaryInteracting traits influence sensitivity of bird population sizes to climate warming and cooling over the past million years.

evolutionary biology↗

bioRxiv2021

Climate and genetic diversity change in mammals during the Late Quaternary

Conservation decisions and future scenarios are in need of past baselines on climate change impacts in biodiversity. Although we know that climate change has contributed to diversity shifts in some mammals1,2,3,4,5,6,7, previous research often assumed that climate change is invariable across species ranges. We are therefore still ignorant of the true rates of climate change experienced by species assemblages over the last millennia, their impacts on intraspecific diversity, and how they compare to future climate change projections. Here, we use more than 9,000 Late Quaternary records, including fossils and ancient and modern DNA sequences, millennial-scale paleoclimatic reconstructions over the last 50,000 years and future climate change projections to document rates of climate change velocity and dynamics in genetic diversity experienced by an assemblage of 16 extinct and extant Holarctic mammal species. Extinct megafauna experienced velocities more than 15 times faster than the extant species, up to 15.2 km per decade. Notably, extant large-bodied grazers lost almost a 65% of their pool of genetic diversity since the Late Pleistocene, which indicates reduced ability to adapt to on-going global change. Additionally, mammal species experienced overall climate change velocities slower than that projected for the end of the 21st century but punctuated by comparable fast climate change episodes. Our results provide baselines on the impacts of ongoing and future climate change on the diversity of mammal species.

ecology↗

bioRxiv2021

Humans hastened the range collapse and extinction of woolly mammoth

Pathways to extinction start long before the death of the last individual. However, causes of early-stage population declines and the susceptibility of small residual populations to extirpation are typically studied in isolation. Using validated process-explicit models, we disentangle the ecological mechanisms and threats that were integral in the initial decline and later extinction of the woolly mammoth. We show that reconciling ancient DNA data on woolly mammoth population decline with fossil evidence of location and timing of extinction requires process-explicit models with specific demographic and niche constraints, and a constrained synergy of climatic change and human impacts. Validated models needed humans to hasten climate-driven population declines by many millennia, and to allow woolly mammoths to persist in mainland Arctic refugia until the mid-Holocene. Our results show that the role of humans in the extinction dynamics of woolly mammoth began well before the Holocene, exerting lasting effects on the spatial pattern and timing of its range-wide extinction.

ecology↗

bioRxiv2018

The population history of northeastern Siberia since the Pleistocene

Far northeastern Siberia has been occupied by humans for more than 40 thousand years. Yet, owing to a scarcity of early archaeological sites and human remains, its population history and relationship to ancient and modern populations across Eurasia and the Americas are poorly understood. Here, we analyze 34 ancient genome sequences, including two from fragmented milk teeth found at the ~31.6 thousand-year-old (kya) Yana RHS site, the earliest and northernmost Pleistocene human remains found. These genomes reveal complex patterns of past population admixture and replacement events throughout northeastern Siberia, with evidence for at least three large-scale human migrations into the region. The first inhabitants, a previously unknown population of \"Ancient North Siberians\" (ANS), represented by Yana RHS, diverged ~38 kya from Western Eurasians, soon after the latter split from East Asians. Between 20 and 11 kya, the ANS population was largely replaced by peoples with ancestry related to present-day East Asians, giving rise to ancestral Native Americans and \"Ancient Paleosiberians\" (AP), represented by a 9.8 kya skeleton from Kolyma River. AP are closely related to the Siberian ancestors of Native Americans, and ancestral to contemporary communities such as Koryaks and Itelmen. Paleoclimatic modelling shows evidence for a refuge during the last glacial maximum (LGM) in southeastern Beringia, suggesting Beringia as a possible location for the admixture forming both ancestral Native Americans and AP. Between 11 and 4 kya, AP were in turn largely replaced by another group of peoples with ancestry from East Asia, the \"Neosiberians\" from which many contemporary Siberians derive. We detect gene flow events in both directions across the Bering Strait during this time, influencing the genetic composition of Inuit, as well as Na Dene-speaking Northern Native Americans, whose Siberian-related ancestry components is closely related to AP. Our analyses reveal that the population history of northeastern Siberia was highly dynamic throughout the Late Pleistocene and Holocene. The pattern observed in northeastern Siberia, with earlier, once widespread populations being replaced by distinct peoples, seems to have taken place across northern Eurasia, as far west as Scandinavia.

genomics↗

bioRxiv2018

Abundance drives generalisation in hummingbird-plant pollination networks

Abundant pollinators are often more generalised than rare pollinators. This could be because abundance drives generalisation: neutral effects suggest that more abundant species will be more generalised simply because they have more chance encounters with potential interaction partners. On the other hand, generalisation could drive abundance, as generalised species could have a competitive advantage over specialists, being able to exploit a wider range of resources and gain a more balanced nutrient intake. Determining the direction of the abundance-generalisation relationship is therefore a chicken-and-egg dilemma. Here we determine the direction of the relationship between abundance and generalisation in plant-hummingbird pollination networks sampled from a variety of locations across the Americas. For the first time we resolve the direction of the abundance-generalisation relationship using independent data on animal abundance. We find evidence that hummingbird pollinators are generalised because they are abundant, and little evidence that hummingbirds are abundant because they are generalised. Additionally, a null model analysis suggests this pattern is due to neutral processes: most patterns of species-level abundance and generalisation were well explained by a null model that assumed interaction neutrality. These results suggest that neutral processes play a key role in driving broad patterns of generalisation in animal pollinators across large spatial scales.\n\nDeclarationsFunding - BIS is supported by the Natural Environment Research Council as part of the Cambridge Earth System Science NERC DTP [NE/L002507/1]. JVB was funded by CERL - Engineer Research and Development Center. PKM was funded by the Sao Paulo Research Foundation (FAPESP grant #2015/21457-4). PAC was funded by the David Lack studentship from the British Ornithologists Union and Wolfson College, University of Oxford. CL was funded by the ESDEPED-UAT grant. MAM acknowledges the Consejo Nacional para Investigaciones Cientificas y Tecnologicas (Costa Rica), German Academic Exchange Service and the research funding program LOEWE-Landes-Offensive zur Entwicklung Wissenschaftlicho konomischer Exzellenz of Hesses Ministry of Higher Education, Research, and the Arts (Germany). ROP was funded by CONACyT (project 258364). MAR was supported by the State of Sao Paulo Research Foundation (FAPESP) within the BIOTA/FAPESP, The Biodiversity Institute Program (www.biota.org.br) and the Parcelas Permanentes project, as well as by Coordenacao de Pessoal de Nivel Superior (CAPES), Fundo de Apoio ao Ensino e a Pesquisa (FAEP)/Funcamp/Unicamp and The Nature Conservancy (TNC) of Brazil. LCR was supported by CNPq and Capes. MS was funded by CNPq (grant #302781/2016-1). AMMG is supported through a Marie Skodowska-Curie Individual Fellowship (H2020-MSCA-IF-2016-704409). LVD was supported by the Natural Environment Research Council (grants NE/K015419/1 and NE/N014472/1). AMMG, JS, CR and BD thank the Danish National Research Foundation for its support of the Center for Macroecology, Evolution and Climate (grant no. DNRF96). WJS is funded by Arcadia.

ecology↗

bioRxiv2017

Can net diversification rates account for spatial patterns of species richness?

The diversification rate hypothesis (DRH) proposes that spatial patterns of species richness result from spatial variation in net diversification rates. We developed an approach using a time-calibrated phylogeny and distributional data to estimate the maximum explanatory power of the DRH, over a given time period, to current species richness in an area. We used this approach to study species richness patterns of a large family of suboscine birds across South America. The maximum explanatory power of the DRH increased with the duration of the time period considered and grain size; it ranged from 13 - 37 fold local increases in species richness for T = 33 Ma to less than 2-fold increases for T [≤] 10 Ma. For large grain sizes ([≤] 8{degrees} x 8{degrees}) diversification rate over the last 10 Ma could account for all the spatial variance in species richness, but for smaller grain sizes commonly used in biogeographical studies (1{degrees} x 1{degrees}), it could only explain < 16% of this variance. Thus, diversification since the Late Miocene, often thought to be a major determinant of Neotropical diversity, had a limited imprint on spatial richness patterns at small grain sizes. Further application of our approach will help determine the role of the DRH in explaining current spatial patterns of species richness.\n\nNote to readersThis manuscript has been seen by a few researchers, some of whom suggested that before publishing our work in a peer-reviewed journal we should conduct simulations to demonstrate that our methods properly estimate the contribution of variance in diversification rates to spatial variation in species richness. Although we believe that our approach derives logically from theory and statistics and is therefore valid, we understand that it is rather unique and see why some readers would think that an independent validation is necessary. Unable to complete such validation in the near future, however, we decided to make this manuscript available as a preprint to share our ideas and hopefully stimulate discussion on what we believe is a most interesting topic. We also hope to receive feedback that may enable us to improve our work for publication in a journal at a later date.

evolutionary biology↗