Journal of Biogeography

Aimto characterize the evolution of climatic niches during the diversification of the Phyllotis darwini species group, in order to assess the extent to which divergences involved in radiation were associated with patterns of conservatism or divergence of climatic niches, and whether the differentiation found among climatic niches correlated with species phylogenetic relationships. Locationsouth-central Andes, surrounding lowlands, and Patagonia, South America. Methodsspecies climatic niches were characterized by sampling contemporaneous precipitation and temperature conditions across occurrence locations and entire distributional ranges. Climatic niches were analyzed and modeled using multivariate statistics (PCA, PERMANOVA), a maximum entropy-based algorithm, and novel methods developed to explore levels of differentiation (niche overlap test) and divergence (niche divergence test) between realized and fundamental niches. Comparative phylogenetic methods were applied using a time-calibrated phylogeny and integrating climate niche data to estimate ancestral environmental niches within geographic and environmental spaces. Resultscomparisons revealed low levels of climatic niche overlap, both among species realized niches and among their fundamental niches, suggesting high levels of niche differentiation during the diversification of Phyllotis species. Quantifications of niche overlap further showed that observed differences among species lay primarily in the multidimensional nature of climatic niches, as unidimensional quantifications exhibited higher levels of overlap. Evolved differences among species climatic niches were better fitted to a Brownian motion model of evolution, but lacked phylogenetic signal and showed no significant association with species phylogenetic distances. Main conclusionslow levels of differentiation between ancestral climatic niches suggest that the early radiation of species in the Phyllotis darwini species group was promoted by geographic isolation, whereas the more recent diversification of extant species was accompanied by climatic niche differentiation, possibly involving local adaptation to regional ecoclimatic changes associated with Quaternary glacial cycles. The spatial separation of sister species, the complete divergence of their climatic niches, and the lack of phylogenetic signal in niche differences suggest a scenario of diversification in which divergences were prompted by the spatial isolation, but also by the divergent selection exerted by regional climatic differences.

As climate changes, habitat suitability for multiple taxa are also expected to change. In recent years, mangrove latitudinal range expansion has been linked to increasing temperatures and reduced freezing in temperate regions, happening mainly through encroachment into saltmarshes. The range limit of mangrove forests in Eastern South America has not seen drastic changes in the last four decades, despite trends of increased temperature and the seemingly favorable direction of the Brazilian Current. Here, we investigate if and how the distribution of South-Atlantic mangrove forests may respond to different scenarios of climate change. To do this, we combine ecological niche modelling with propagule dispersal simulations to understand the roles of climate and ocean currents in defining the austral limits of South-Atlantic American mangroves. Our results indicate that minimum sea surface temperature strongly constrains habitat suitability beyond the current distribution of mangroves (28{degrees}2868" S), while dispersal processes heavily limit propagule stranding beyond 35{degrees} S. The Brazil-Malvinas currents confluence zone creates steep temperature gradients and an oceanographic barrier that makes the latitudinal expansion of mangroves unlikely in this region, even in future scenarios of heating climate. We found no evidence of current nor future poleward expansion of mangroves, but total mangrove area has increased in Brazil over the last decades, likely due to landward migration, but anthropogenic interference and urban expansion may restrict this process, leading to coastal squeeze. Under scenarios where both landward and poleward migration are limited, South American mangroves may face increasing vulnerability, with potential impacts on the several ecological, biogeochemical and social cycles they support. Our results contribute to leading hypotheses of climate restriction and shed light on the role of ocean currents in South America, helping to explain why the poleward expansion reported in other regions has not yet been observed in the South-Atlantic mangrove range limit.

Understanding how dispersal and vicariance shape species distributions is a central goal in biogeography, yet the role of islands as sources of continental diversity remains poorly resolved. While multiple dispersal routes from the Eurasian continent to the Japanese Archipelago have been proposed, back dispersal from islands to the mainland is rarely documented, particularly in primary freshwater taxa constrained by marine barriers. Here, we investigated the population genetic structure and phylogeographic history of the Japanese stone loach Barbatula oreas, distributed in Hokkaido and Sakhalin, using mtDNA, nDNA, and genome-wide SNP data. We identified two differentiated Northern and Southern lineages within Hokkaido that diverged during the Pleistocene, indicating that geological events such as paleo-catchment reorganization, mountain uplift, and volcanic activity have shaped the present population structure. Ancestral area reconstruction based on mtDNA phylogeny identified Hokkaido as the origin of B. oreas and revealed dispersal from Hokkaido to Sakhalin, indicating back dispersal from islands toward the mainland. This pattern contrasts with the prevailing hypothesis of southward colonization from the continent via Sakhalin to Hokkaido. Additionally, low genetic differentiation between Hokkaido and Sakhalin suggested genetic exchange across the strait, consistent with paleo-catchment reconstruction indicating past catchment connectivity between the regions. These results highlight the combined roles of geological dynamics and sea-level fluctuations in shaping genetic structure, challenge the conventional continent-to-island dispersal paradigm. Moreover, our study demonstrates that island systems can act as biodiversity sources--not merely sinks--and provides a rare empirical example of back dispersal in primary freshwater species.

O_LIRapid climate warming threatens mountain biodiversity, particularly species with narrow climatic niches and limited dispersal capacity. Mountain ecosystems are especially vulnerable because steep environmental gradients restrict opportunities for species redistribution. The Kashmir Himalaya, a globally important biodiversity hotspot experiencing accelerated warming, has already undergone an increase of approximately 0.8 {degrees}C during the 20th century and is projected to warm by 2.5-2.8 {degrees}C by the 2050s. Despite climatic changes, future persistence of many threatened plants remains poorly understood. C_LIO_LIHere, we evaluate present and future habitat suitability for two Himalayan taxa, Gentiana cachemirica, an endemic species, and Gentiana kurroo, a critically endangered species. Specifically, we quantify how climate change and topographic variability influence species distribution and persistence under multiple emission scenarios. C_LIO_LIWe applied species distribution models (SDMs) to presence data of both species and forecasted habitat suitability under four Shared Socioeconomic Pathways (SSP126, SSP245, SSP370, and SSP585). We hypothesized that G. cachemirica, a narrow-niche, low-dispersal species, is expected to lose habitat due to thermal sensitivity, while G. kurroo may persist or expand under favorable scenarios because of broader tolerance and higher dispersal. We also expected microclimatic refuges to buffer populations, whereas extreme warming would accelerate habitat decline. C_LIO_LIThe predictions of our SDMs under current conditions indicate a highly restricted and fragmented habitat for G. cachemirica, covering 651 km{superscript 2}, but a broader suitable area (2,452 km{superscript 2}) for G. kurroo. In agreement with our hypotheses, our forecasts indicate severe habitat contraction (55-70%) for G. cachemirica across all SSPs, but scenario-dependent responses for G. kurroo, including modest expansion under low-emission scenarios and severe declines under high-emission scenarios. Centroid analyses suggest pronounced climate-driven range shifts, with G. kurroo projected to migrate up to 33 km toward the east-southeast by 2100, while G. cachemirica is projected to display limited dispersal capacity. C_LIO_LISynthesis. Our findings suggest that climatic niche breadth, dispersal limitation, and topographic buffering strongly mediate species responses to warming in mountain ecosystems. Endemic specialists are projected to experience disproportionate habitat fragmentation and range restriction, highlighting the importance of conserving climatic refugia and elevational connectivity under rapid environmental change. C_LI

Gliding has evolved repeatedly across vertebrates and is often regarded as a classic example of convergent evolution associated with arboreal habitats. However, it remains unclear whether convergent locomotion corresponds to shared ecological responses across taxa. In this study, we investigated the distribution patterns and environmental drivers of gliding vertebrates in Southeast Asia using occurrence records and environmental variables representing climate and forest structure. We analyzed five major groups, including flying lemurs, flying squirrels, gliding lizards, gliding snakes, and gliding frogs, using presence-background logistic regression models. Across taxa, temperature seasonality showed consistently negative effects, while canopy height showed positive effects, indicating a shared association with climatically stable environments and well-developed vertical forest structure. In contrast, other environmental variables exhibited substantial taxon-specific variation. For example, elevation showed a strong negative effect only in gliding snakes, suggesting a tendency toward lowland habitats, whereas precipitation variables had limited explanatory power for gliding frogs. These results demonstrate that, despite the convergent evolution of gliding locomotion, ecological responses to environmental factors are not uniform across vertebrate taxa. Instead, species distributions are shaped by a combination of shared functional constraints and lineage-specific ecological traits. Our findings highlight the importance of vertical forest structure and suggest that habitat alteration affecting canopy structure may disproportionately impact certain taxa.

AimThe overarching aim of this study is to reconstruct the spatiotemporal evolutionary history of Australian Dysphania, including testing the littoral connection hypothesis, assessing the role of reticulation, and identifying the major drivers of diversification within the lineage. LocationAustralia and New Zealand TaxonDysphania, Chenopodioideae, Amaranthaceae, Caryophyllales, Angiosperms MethodsUsing a DNA sequence dataset based on a target enrichment approach with custom baits designed for Chenopodioideae, we compared alternative biogeographic and ancestral habitat models to infer the spatiotemporal evolutionary history of Australian Dysphania. In addition, we applied several complementary analyses to assess concordance and conflict within our phylogenomic datasets, estimate ploidy levels, and compare ecological niches among closely related species. Results and Main conclusionsOur results reveal a close evolutionary relationship between Sub-Saharan African and Australian desert ephemerals and indicate that Australian Dysphania originated through an ancestral reticulation event. The last common ancestor reached northwestern Australia during the Miocene, occupied riverine desert habitats, and migrated eastward with their expansion, potentially undergoing ecological speciation. Four major Australian clades subsequently diversified across Miocene to Pleistocene landscapes, from riverine deserts to salt lake mosaics, with divergence likely driven by salinity gradients, flood regimes, and microhabitat partitioning rather than polyploidisation or geographic isolation.

Background and AimsGroundwater-dependent ecosystems support disproportionate biodiversity in arid regions, yet the population genetics of spring-specialist plants remains poorly understood. Here, we present the first species-wide genetic dataset for crimson monkeyflower ( Mimulus verbenaceus, Phrymaceae), a spring-specialist plant distributed in seeps, springs, and associated riparian areas across desert regions of North America. MethodsUsing genome-wide reduced representation sequencing data consisting of 10,760 SNPs from 175 individuals across 17 populations, we characterized the patterns of genetic diversity using FST and Neis D. Population structure was assessed using ADMIXTURE and PCA. We examined the contributions of climate to range-wide genetic variation in crimson monkeyflower using redundancy analysis. Key ResultsPatterns of genetic differentiation were more consistent with those of spring-specialist animal taxa than those of upland plants or generalist riparian plants. We found strong population structure at both broad regional scales and at fine local scales. While riparian connectivity influenced local patterns of diversity, adaptation to local climatic variation was more influential at regional scales, with temperature, relative humidity, and a monsoon-driven climate gradient structuring genetic differentiation. ConclusionsOur findings highlight the distinctive influence of isolated perennial groundwater sources, as well as adaptation to climate, in shaping genetic variation in this spring-specialist plant. These findings suggest that spring-specialist plants deserve special consideration in ecological theory, management, and conservation.

Understanding how global biodiversity patterns arise is a central theme of biogeography, with contemporary theory recognising the roles of both dispersal and vicariance. Genera that are broadly distributed can provide important systems for disentangling the relative influence of these processes across evolutionary timescales. However, many lesser-studied groups, particularly those in the tropics, lack a densely sampled phylogeny which hinders robust inference of their evolutionary and biogeographic history. This study investigates the global diversification and systematics of the putative pantropical moth genus Parasa Moore (Lepidoptera: Limacodidae), with the aim of assessing the relative importance of dispersal and vicariance in shaping its distribution. Medium-coverage whole genome sequencing of specimens predominantly from museum collections were used to generate a globally sampled time-calibrated phylogeny of Parasa and associated genera (the Parasa-complex). Ancestral range estimation analyses were employed to infer geographical origins and possible dispersal times between bioregions. The Parasa-complex originated in Africa in the late Oligocene ([~]24 Ma) and, through a series of long-distance dispersal events during the early-mid Miocene, expanded into Asia ([~]23 Ma) and the Americas ([~]21 Ma). Across all regions, dispersal was the dominant process shaping present-day distributions, with a limited role of vicariance in some subregions. Phylogenetic analyses further demonstrated that Parasa is not monophyletic, with multiple independent lineages contributing to its apparent pantropical distribution. These findings highlight a central role of long-distance dispersal in generating certain global distributions. The results support a dynamic model of range evolution involving rapid Miocene dispersal and subsequent regional diversification. In addition, the non-monophyly of Parasa requires substantial taxonomic revision, underscoring the importance of robust phylogenetic frameworks for interpreting global biodiversity patterns.

Among Neotropical cichlids the tribe Heroini exhibits substantial ecological diversity and is one of the dominant fish groups across northern Neotropical riverscapes. The majority of studies on heroine cichlids have focused on macroevolutionary patterns but the role of geological and ecological factors shaping lineage diversification within the tribe remains poorly understood. Here we used ultraconserved elements (UCEs) to infer a taxonomically complete and geographically comprehensive phylogenomic framework of the early-diverging herichthyine sister genera Thorichthys and Trichromis and to comparatively investigate their evolutionary and biogeographic histories. All our phylogenomic hypotheses support the monophyly of both genera and two species subgroups within Thorichthys. Our results provide evidence of a) unrecognized diversity within Trichromis salvini, b) uncertainty in species boundaries in Thorichthys, and c) the first report of ghost introgression in fishes of the northern Neotropics. Additionally, our results demonstrate the importance of the Papaloapan and Coatzacoalcos watersheds for fish diversification in the region. Finally, we show patterns consistent with ecological divergence during the evolution of this group, particularly among sympatric species. Altogether, these patterns suggest that lineage diversification in northern Neotropical cichlids has been driven by the interaction of geological restructuring, climatic and sea-level oscillations, and heterogeneous ecological pressures.

Land-bridge islands are former mainland areas isolated by post-glacial sea-level rise (<15,000 years) and the most common island type. Because of their recurrent connectivity with continents, it is unclear whether species on land-bridge islands can undergo evolutionary changes associated with the more isolated oceanic islands ( island syndrome). Here, we test the hypothesis that the selective environment on land-bridge islands exerts predictable and consistent evolutionary shifts in morphological traits of songbirds. We apply Bayesian hierarchical models to a morphological dataset of 6,917 individuals comprising 185 species of songbirds from four land-bridge islands (Bioko, Sri Lanka, Taiwan and Trinidad) and adjacent continents. Across all 185 species, we find that occurrence on a land-bridge island has clear directional effects on five morphological traits related to beak, wing, and tarsus, as well as a general increase in body size. At the species level, 57 out of 90 tested species exhibit significant morphological divergence between land-bridge island and mainland, yet for only 20 of these are the land-bridge island populations recognised as distinct endemic subspecies. Our results show that occurrence on land-bridge islands has a detectable effect on passerine morphology consistent with the island syndrome, and suggest these islands harbour previously unrecognized unique biodiversity.

AO_SCPLOWBSTRACTC_SCPLOWMountain gradients facilitate our understanding of species range limits, competition dynamics, stress-resilience trade-offs, and determinants of vegetation zone boundaries. Forest compositional models often use altitude as the main predictor, a proxy for temperature that is defensible where floristic transitions are gradual and climate relationships are linear. However, mountains with distinct assemblages, representing tropical gradients or areas with complex biogeographic history, require a modeling framework that reflects non-linear dynamics or interactions between environmental factors, including outlier events (rather than mean conditions). Our study system encompasses both tropical and temperate forests along a broad ([~]3000 m) altitudinal gradient, positioned within a narrow latitudinal band (< 1{degrees}) and composed of mature, continuous forest in the Bhutan Himalaya. To represent the breadth of climatic conditions experienced over a trees lifetime, we used a Bayesian modeling paradigm and integrated multi-generational field knowledge to develop a priori hypotheses and informed priors, with consideration of monsoon seasonality and possible ecophysiological thresholds. Our approach followed three stages (the Pattern, the Mechanism, the Test). Specifically, we interpolated microclimate data and derived custom metrics based on thermodynamics, propagating uncertainty into subsequent models to test whether climate posteriors outperformed altitude in explaining growth form partitioning. For spatial patterns, we identified six distinct vegetation zones (encompassing 145 species from 57 families), with a mid-gradient peak in richness at the tropical-temperate transition zone, and convergence of deciduousness at either end of the gradient. For individual growth forms, abundance was tied to different ecological mechanisms, explained by adaptations to climatic stressors and competition trade-offs. For instance, evergreen broad-leaved dominance was linked to ephemeral cloud immersion, whereas tropical deciduous species were affiliated with higher vapor pressure deficit at lower altitudes. Most importantly, compositional (between-group) models showed that the interaction between frost events and fog probability (air saturation prior to the dry season) governed growth form partitioning more than any single factor; temperate deciduous species, confined to a narrow altitudinal band, exemplified this finding. Our methodological approach is transferable to other data-sparse mountain systems, and our results highlight the vulnerability of unique habitat types and montane endemics under climate change scenarios that alter the fog-frost dynamics. Second abstract in DzongkhaTo see the second abstract in Dzongkha, the official language of Bhutan, please visit our Zenodo site: https://doi.org/10.5281/zenodo.19081441.

True lemmings (genus Lemmus) underwent substantial range shifts during the Late Pleistocene and the Pleistocene-Holocene transition, but the impact of these events on present-day diversity remains poorly understood. Here, we used whole-genome sequencing data from modern and ancient samples across the Palearctic range to address this knowledge gap. Reconstruction of autosomal phylogeny revealed that Palearctic true lemmings exhibit relatively shallow genetic structure, contrasting with the deep divergence inferred from mitochondrial genomes. Genetic variation largely follows an isolation-by-distance pattern, and no elevated nuclear divergence was detected between the major mitochondrial lineages. Window-based phylogenetic analyses identified several peripheral populations with high concordance factors, including Norway and Amur lemmings. The high degree of phylogenetic concordance along the genome in these populations is likely a consequence of postglacial bottlenecks and isolation, as indicated by reduced heterozygosity and the presence of runs of homozygosity in them. Overall, our results indicate that the modern genomic structure of Palearctic lemmings was shaped primarily by range fragmentation and population isolation following the broad distribution of the genus during the Last Glacial Maximum. Thus, the current genetic structure appears to represent only a fraction of the Late Pleistocene true lemming diversity. This is illustrated by a genetically distinct ancient specimen ([~]40 ka BP) from the Indigirka River basin that does not cluster with any modern lineage. From a taxonomic perspective, these findings do not support strong species-level differentiation among the major Palearctic lineages and highlight the discrepancy between mitochondrial and nuclear patterns of diversity within the genus.

The climatic transition from Marine Isotope Stage 3 (MIS3) to the Last Glacial Maximum (LGM) had caused widespread vegetation change. Despite the dynamic equilibrium between vegetation and climate, the specific role of functional composition in vegetation response to climate change was inadequately understood. Here, we analyzed the long-term trajectories of palynological diversity, vegetation coverage and community-weighted-mean (CWM) functional traits based on EH22 pollen record (35-18 cal ka BP) from Erhai Lake, southwestern China. The results disclosed a vegetation transition from temperate deciduous broadleaf forest dominance in late MIS3 to cold coniferous and mixed broadleaved/coniferous forests in LGM. This vegetation dynamic involved functional composition shifts from competitive-driven functional convergence to partial recovery via niche differentiation during the late MIS3, and finally to a low-diversity but functional differentiation state through trait complementarity and diversification strategies during the cold LGM. Our results likely support a function-mediated climate filtering process whereby climate change regulated long-term vegetation dynamics during the MIS3 to LGM transition primarily through shifts in CWM functional composition. These findings underscore the potential of pollen-based trait approaches to reconstruct ecosystem properties and advance our understanding of ecosystem change over decadal to millennial time-scales.

Commonly shared patterns of introduction and spread into new environmental conditions are often poorly understood, even though a better understanding of invasion history and niche dynamics among closely related invasive species could give practitioners valuable information to prevent and mitigate the impact of biological invasions. For this study, we investigate the invasion history and niche patterns among congeneric invasive species. We synthesize public occurrence data for five invasive alien anurans (Eleutherodactylus coqui, E. planirostris, E. johnstonei, E. antillensis, and E. martinicensis) to reconstruct their historic introductions and evaluate evidence for climatic niche shifts between their native and established non-native ranges. By pairing these data with current and future climate projections, we compare patterns of range shifts under future climate scenarios. Our results highlight different temporal and geographic introduction histories in invasive Eleutherodactylus, but a strong signal of colonizing broader invasive climatic niches, specifically into colder environmental conditions. Under future climate scenarios, suitable habitats for most of the non-native regions are likely to increase, although this increase is restricted under scenarios with high greenhouse gas emissions. Our results reveal that despite different invasion histories, the ability to spread into colder regions may be a conserved trait among the most widespread Eleutherodactylus anurans. This study ultimately shows that commonalities among closely related invasive species can provide clues about their ability to expand into areas with particular abiotic conditions, a pattern likely to be widespread, offering a potentially valuable opportunity to deploy targeted prevention strategies.

Mitochondrial loci were for long considered as markers of choice to reconstruct phylogenies. The development of high-throughput sequencing over the past two decades fostered the sequencing of mitogenomes, allowing further macroevolutionary questions to be tested. Several biological traits of birds (e.g. body mass, migration distances) have been related to mitochondrial substitution rates. Environmental parameters in ectothermics vertebrates, and potentially in endotherms, have been further suggested to impact substitution rates for specific taxa or loci. Yet, the relative importance of biological traits versus bioclimatic variables is unknown because the former were not systematically controlled for in studies that underlined the effect of the bioclimatic variables. To assess the importance of bioclimatic variables on selection regimes, we analysed the thirteen mitochondrial protein-coding genes for 176 Piciformes (toucans, honeyguides, woodpeckers), a clade with homogeneous life-history traits that can be found in diverse bioclimatic environments. Our analyses highlighted a negative relationship between temperature annual range and the non synonymous to synonymous substitutions ratio. The higher purifying selection in temperate environments may be a result of the strong constraints on maintaining an optimal metabolism in broader climatic variations. Our results further highlight that care should be taken when applying general mitochondrial clocks to estimate divergence times among avian lineages distributed in different climatic conditions.

O_LIAnimal-mediated seed dispersal is key for the maintenance and functioning of tropical ecosystems. Specifically, in the Cerrado, the largest Neotropical savanna and a global biodiversity hotspot, nearly 60% of plant species rely on animals for dispersal. C_LIO_LIClimate change threatens these interactions by affecting species distributions, reshaping communities, and potentially decoupling plants from their dispersers. Anticipating how such disruptions may alter seed dispersal networks is particularly relevant for understanding the resilience of future tropical ecosystems. C_LIO_LIHere, we combined empirical data on 139 pairwise plant-frugivore interactions with species distribution forecasts to build probabilistic interaction matrices under present and future climate scenarios, which were then used to construct 6,221 local seed dispersal networks. Using ecological niche modelling, we tested how climate change influences species range size and centroid displacement. Then, we evaluated whether such changes translate into losses of pairwise plant-frugivore co-occurrence. Finally, we investigated how these changes in occurrence overlap may affect key structural properties of future local seed dispersal networks. C_LIO_LIWe forecast that by the 2070s, under a business-as-usual climate scenario, species are likely to contract their ranges by 56 {+/-} 33% and shift their distribution centroids by 88 {+/-} 57 km within the Cerrado, leading to a 27 {+/-} 29% loss in plant-frugivore co-occurrence mainly driven by reductions in plant species distributions. At the community level, these losses will lead to smaller and more nested networks and specialized, indicating a structural simplification of seed dispersal systems in the Cerrado. C_LIO_LISynthesis: By combining empirical data on animal-mediated seed dispersal with forecasts of species distributions, we found that climate change may simplify frugivore-plant interaction networks in the Cerrado by decreasing species ranges and co-occurrence of partners. Our study demonstrates that future climate may pose a threat not only to species distributions but also to ecological interactions, such as seed dispersal, that are key to enabling climate-tracking by plants. Thus, preventing the simplification of interaction networks will be essential to conserve biodiversity in species-rich regions. C_LI

Species distribution forecasts commonly overlook intraspecific genetic variation, missing a potentially important mechanism of ecosystem change: climate-driven range shifts among lineages within a species native range. Here we integrate population genomic analysis of 495 individuals, multi-site common garden experiments, and species distribution modeling based on 837 occurrence records for three major genetic lineages of the foundation grass Phragmites australis in China. The octoploid FEAU lineage (haplotype P) exhibits superior heat tolerance (critical temperature Tcrit and T50) and produces significantly greater total biomass in three of four common gardens compared to the cold-adapted CN lineage (tetraploid, haplotypes O/M), which occupies a climatic niche with lower annual mean temperature (Bio1) and mean temperature of the wettest quarter (Bio8). Genomic analyses further reveal bidirectional but asymmetric introgression, with admixed individuals showing a systematic bias toward FEAU ancestry. Under the high-emission scenario (SSP5-8.5) by 2070, projected highly suitable habitat for the FEAU lineage expands by 18.6%, while the CN lineage shows a smaller relative increase. By contrast, the subtropical SW lineage (haplotypes U/I) exhibits limited and stable suitable habitat. These results demonstrate that climate change interacts with intraspecific variation rooted in polyploidy, thermal tolerance, and asymmetric gene flow to drive potential lineage replacement within a native range, a process already suggested by field observations of FEAU expansion in a plateau lake. Our findings argue for integrating evolutionary history and genetic identity into ecological forecasting to better anticipate ecosystem responses under ongoing climate warming.

The Neotropical genus Atelopus has experienced a drastic population decline in recent decades. Despite this, a knowledge gap remains regarding the conservation genetic status, phylogeography, and demographic history of most of its species, especially those endemic to areas with limited access like the Sierra Nevada de Santa Marta in Colombia. In this genomic study, we inferred phylogenetic relationships, demographic history, and gene flow among four endemic Atelopus morphospecies in the Sierra Nevada de Santa Marta-SNSM. Additionally, we compared the effective population size (Ne) estimates with the available population census data. NextRAD was used to obtain genomic data from 95 individuals collected at five sites in the SNSM and two in the Colombian Pacific (outgroup). The morphospecies recently diverged in a scenario without gene flow and were recovered as monophyletic. Their phylogenetic relationships were discordant, which is attributed to the presence of incomplete lineage sorting-ILS, which would also explain their shared ancestry among them. The lack of gene flow as well as the recent divergence times given by demography suggests a recent and rapid speciation. However, the reproductive isolation mechanisms that promote or maintain the species boundaries in this group remain unknown and require further investigation. We suggest that this process may have been influenced by the complex topography of the SNSM, traits such as high philopatry, low dispersal ability, and behavioral factors such as habitat preference or to factors related to genetic architecture that influenced the rapid formation of reproductive barriers among populations. Additionally, a pattern of population decline was observed around 200.000 years ago, with recent increases in three morphospecies. Despite the reduction in effective population size, no signs of inbreeding were detected. However, for A. laetissimus, the only species surveyed, the estimated value of Ne and its implications should be interpreted with caution. Ultimately, our findings reveal an evolutionary history shaped by a burst of diversification and abrupt reproductive isolation, highlighting how the resulting endemism and restricted genetic connectivity shape the unique evolutionary trajectory and vulnerability of this threatened montane species. Significance StatementThe mechanisms driving rapid speciation in montane ecosystems remain a central question in evolutionary biology. This study provides crucial genomic insights into the diversification of four endemic Atelopus species in an isolated Neotropical massif. We reveal a compelling evolutionary scenario where species diverge rapidly in absence of gene flow. This rapid speciation was likely facilitated by complex topography, environmental heterogeneity, and ecological and behavioral differences among species. Nevertheless, the evolutionary processes that limited gene flow among SNSM species have not yet been identified.

The ongoing decline in biodiversity highlights the need for understanding the causes of population changes. This study uses 25-year, large-scale monitoring dataset to investigate the influence of climate and landscape structure on the annual population growth rates of 84 bird species across Poland. Our methodological framework involves the spatiotemporal decomposition of these environmental drivers to decouple demographic effects of long-term carrying capacities from the short-term effects of environmental perturbations. Using species-specific demographic models followed by a community-wide meta-analysis, we evaluated how individual species responses scale up to shape community-level dynamics. The results reveal significant variation in species-specific responses to individual drivers. At the community level, our findings suggest that bird populations are mainly regulated by the long-term spatial constraints rather than short-term disturbances. Persistent environmental heterogeneity had the strongest positive demographic effect on birds, followed by temperature, forest dominance over croplands, and precipitation. In contrast, rapid temporal shifts in environmental heterogeneity and precipitation anomalies negatively affected population growth, whereas urbanisation consistently exerted a negative effect across both spatiotemporal dimensions. Our results highlight the significance of protecting existing heterogeneous and ecotonal habitats, as well as the need to incorporate features that enhance habitat heterogeneity into urban development. Article impact statementPreserving heterogeneous habitats is essential for the conservation of bird populations.

Understanding how habitat connectivity shapes biodiversity remains a major ecological challenge. In particular, the roles of connectivity and ecological heterogeneity on co-variation in plant species diversity and intraspecific genetic diversity is not understood. We combined species distribution modelling, resistance-to-movement mapping, landscape connectivity analysis and population genomics to investigate diversity patterns in three wet meadow herbs, Scorzonera humilis, Oenanthe peucedanifolia and Lychnis flos-cuculi, and their surrounding plant communities. Genetic diversity patterns differed strongly among co-occurring species. Connectivity metrics explained genetic diversity only in O. peucedanifolia, and environmental drivers of genetic diversity were highly species specific. Importantly, genetic diversity changed with the presence of some species in the community, but it was consistently unrelated to indicators of local plant community diversity. Overall, the processes shaping within-species biodiversity may differ fundamentally from those structuring habitat connectivity and plant species communities, with important implications for conservation.