BMC Ecology and Evolution

Despite their currently scarce taxonomic diversity, rhinocerotoids were among the most evolutionarily successful clades of large herbivorous mammals throughout the Caenozoic. Within an array of morphological adaptations, the cranial horn represents the clades most remarkable and name-giving feature, imposing significant morpho-functional demands on the skull. In this paper, patterns and drivers of the rhinos cranial evolution were investigated for the first time by compiling a three-dimensional geometric morphometric dataset of living and extinct species. Multiple aspects of morphological evolution were explored using phylogenetic comparative methods, including craniofacial evolutionary allometry (CREA - tendency of larger species to have longer faces), phylogenetic constraints, and tempo of evolution. Cranial shape variation linked to horn presence and size evolved under a phylogenetically constrained framework, with a notable transition from hornless to horned species. Rhinos significantly deviated from CREA, likely due to diversity of cranial forms and proportions that evolved independently across the clade in response to varying horn morphologies and dietary habits. Hornless and horned rhinos exhibited similar rates of cranial evolution, and shape variation was obtained through multiple episodes of accelerated evolution. This highlights the role of morphological innovations and Caenozoic global cooling events in the emergence of phenotypic diversity.

Karsts of Southeast Asia cover ~400,000 km2, with tropical limestone karsts possessing highly biodiverse flora in many, varied microhabitats that are unique from lowland- and hill forests. Begonia L. is a pantropical mega-genus with ~1,550 described species to date, ideal for studying evolutionary patterns and factors driving tropical population- diversity and speciation. Begonias grow on multiple substrates including limestone and granite, sandstone, quartzite, on steep earth slopes and near streams in primary forests. Niche partitioning is commonly observed, resulting in many single-site endemic Begonia species especially on limestone karsts. Molecular phylogenetic analyses were performed on combined chloroplast ndhF-rpl32 and nuclear internal transcribed spacer ITS sequences that included 30 selected Begonia species representing all sections from Peninsular Malaysia (Pen. Msia; ten limestone-, thirteen forest- and seven granite species). Results of Bayesian inference and molecular dating showed evolution of Begonia from continental Asia into Pen. Msia during the mid-late Miocene period of ~ 10.65 mya (9.7 - 12.12 mya), with at least two independent dispersal events observed by the early splitting of the ancestral lineage into two major clades i.e. clades A- and B at 9.85 mya (HPD 9.7-10.36 mya) and 8.85 mya (HPD 7.7-11.23 mya) respectively; followed by multiple speciation events colonizing limestone- as well as non-limestone (forest, granite) habitats. Begonia speciation into limestone habitats occurred three times, with climate indicated as more important factor than substrate in diversification - clade A contained the Indian/Continental Asia (monsoon climate) species, i.e. Sect. Platycentrum and Parvibegonia, resolved slightly older than clade B where Sect. Petermannia, Jackia and Ridleyella formed a Sunda Shelf (equatorial climate) centred group. Strong population structuring by locality, common in Begonias, was also observed (e.g. B. kingiana, B. foxworthyi, B. nurii, B. sinuata), regardless of distribution. However, for widespread species (B. kingiana, B. sinuata) behavioural (physiological) inertia on niche evolution, and/or genome size variation and dynamics (genome evolution) may potentially explain species cohesion. Phylogenetics relationships are mostly concordant with current sectional classifications excepting Sect. Parvibegonia, Sect. Diploclinium and two paraphyletic species complexes. Conservation of Begonias and biodiverse limestone karsts in Malaysia remains concerning due to ongoing threats (large-scale quarrying/mining, human encroachment), and most are still without any legal protection.

Laboratory environments can induce rapid phenotypic changes, but the earliest responses of natural populations to laboratory conditions remain poorly understood. Using geometric morphometrics, we investigated changes in wing size and wing shape in the Neotropical drosophilid Drosophila sturtevanti. We compared field-collected males (G0) with descendants from 12 lines each established from a single female from the same native population in the first (F1) and tenth (F10) laboratory generations. Wing size showed heterogeneous responses in F1, followed by a consistent reduction by F10, possibly reflecting differences among founder females and larval density. Wing shape changed significantly in every line between G0 and F1 and between F1 and F10. Total shape variance increased significantly between G0 and F1. Within-line shape variation was not significantly lower in F1 or F10 than the variation observed in G0, while between-line variation increased as the lines diverged. These patterns are consistent with previously cryptic variation becoming expressed following environmental change, together with founder effects, drift and increasing homozygosity. Our results show that substantial morphological changes can arise within a single laboratory generation, challenging the assumption that F1 individuals provide an unaltered representation of natural populations.

Abstract 1. Comparative studies can reach different conclusions when genomic-diversity metrics use different denominators. 2. We analysed standardized ddRAD-seq data from 759 individuals, 149 species-by-site population records and 26 saproxylic beetle species across eight Polish forest complexes. 3. Species identity and sampling hierarchy explained most population-level variation. Deciduous-associated species had higher variant-site expected heterozygosity than conifer-associated species. 4. All-position nucleotide diversity showed stable phylogenetic signal, whereas occurrence tier and exploratory forest-management and protection contrasts showed no consistent associations. 5. Genomic-diversity metrics are not interchangeable; comparative assessments should report their denominator and test lineage sensitivity.

Ecogeographic rules predict that endotherms inhabiting colder environments exhibit larger body sizes and shorter appendages to reduce heat loss. However, these hypotheses have largely been tested using size-based traits, leaving it unclear whether climatic adaptation also alters body proportions that more directly influence surface-area-to-volume ratio. Here, I examined ecogeographic variation in body shape, body size, and relative limb lengths across climatic gradients in three western North American mustelids: American ermine (Mustela richardsonii), American mink (Neogale vison), and Pacific marten (Martes caurina). I then modeled how variation in body shape and size affected surface-area-to-volume ratio. Body size increased in colder climates in all three species, consistently supporting Bergmanns rule. In contrast, only ermines became stouter in colder climates, whereas body shape remained unchanged in minks and martens. Patterns of appendage variation also differed: ermines and martens exhibited relatively longer limbs in colder climates, contrary to Allens rule, whereas only minks exhibited relatively shorter hindlimbs. Modeling showed that increased body size reduced surface-area-to- volume ratio in all species, whereas body shape contributed only in ermines. These findings demonstrate that body shape, body size, and appendage lengths respond independently to climatic gradients, with species-specific ecological and functional constraints shaping thermoregulatory adaptation.

Specialized suction discs are functional innovations that enable fishes to attach to diverse surfaces and resist hydrodynamic forces. The adhesive discs of clingfishes (Gobiesocidae) vary in size and shape, but it is unclear how ecological factors have influenced their morphological evolution. Here we analyzed the disc and skull shape of 74 clingfish species using micro-CT scanning and 3D geometric morphometrics to investigate the role of habitat and substrate use on patterns of diversification. We also present novel comparisons of adhesive performance for 10 clingfish species. Clingfish interface directly with their environment using their adhesive discs, but we found that the disc and skulls are evolutionary integrated and share similar responses to habitat. Transitions from coastal habitats to coral reefs promoted elevated rates of evolution and morphological disparity across the body, whereas transitions to freshwater did not. Concurrently, repeated shifts from living on hard substrates to softer substrates (i.e., macroalgae and seagrass) were associated with more constrained disc shapes, convergent morphologies, and differences in adhesive performance. We propose that habitat and substrate use make complementary contributions to skeletal diversification in clingfishes, but the adhesive system requires further investigation to disentangle the complex interactions between form and function.

Sexual interactions involve the exchange of information-including olfactory, auditory, and visual cues-that has been shaped by sexual selection to maximize fitness. While these courtship signals and behaviors are often characterized as stereotypical and species-specific, male courtship is plastic and can depend on the population identity of the courted female. The ability of a male to adjust his courtship behavior based on female identity has significant implications for how selection operates on courtship, potentially driving behavioral divergence between populations and the eventual emergence of new species. A major challenge is identifying the cues that males use to adjust their courtship strategy. We used Drosophila melanogaster to investigate the mechanisms facilitating courtship plasticity, focusing on male song production. Male song is often considered the paramount behavior performed by males and is stimulated by female pheromones. Previous observations have focused on cosmopolitan (non-African) genotypes, whereas the singing rate and singing plasticity is highly variable in African populations. In genotypes from Zimbabwe, females have a different major pheromone compound (5,9-HD) compared to non-African females and show strong behavioral preference for Zimbabwe males. We created a Zimbabwe genotype lacking 5,9-HD by disrupting the gene desat2 in the Zimbabwe Z53 strain. We tested the hypothesis that Zimbabwe male courtship plasticity depends on female pheromones by allowing males to court non-African, wild type Z53, and Z53 desat2 null mutant females. We found that males treated Z53 desat2 null females like wild type Z53 females, not using pheromone cues to determine singing and courtship plasticity. This suggests that other female behavioral feedback influences singing plasticity. This courtship plasticity could contribute to the asymmetrical reproductive isolation between these populations and could provide insight to the broad pattern of asymmetrical reproductive isolation across broad taxonomic groups.

The nautilus (Nautilus sp.) is an early-branching cephalopods. It retains several conchiferan synapomorphies, including an external planispiral biomineralized shell. The shells complex structure allows it to withstand hydrostatic pressure, control buoyancy, and protect against external hazards. In this study, we comprehensively examined shell microstructures across different shell components and regions representing various ontogenetic stages in two adult museum shell specimens. We found that the nautilus shell is composed of five microstructural types (spherulitic, prismatic, nacreous, semi-prismatic, and irregularly oriented prismatic structures) organized into layered architectures within individual shell components and coordinated across the shell as an integrated system. Our observations highlight transitions between distinct microstructures within and across shell components and local variation within individual components such as the dorsal and ventral shell walls, suggesting that these patterns may contribute to shell strength and overall mechanical performance. Variation in caecum morphology suggests that this structure may be developmentally plastic and subject to relatively relaxed structural constraints. These findings show that the Nautilus shell is an integrated biomineral system in which diverse microstructures are organized across shell components to meet functional demands and provide the mechanical strength needed for survival.

This research addresses a central question in Palaeolithic research: how hunter-gatherer mobility was structured across space and time in the Cantabrian Region (northern Iberia), which has human occupation evidence spanning from the Middle Pleistocene through the Holocene. A multidisciplinary framework integrating primarily {delta}3S isotope values, combined with {delta}{superscript 1}3C and {delta}{superscript 1}N, palaeoproteomics, Bayesian age modelling, palaeoclimatic reconstruction, isoscape mapping, and ecological diversity was developed. A total of 905 animal bone collagen samples, with evidence of anthropogenic modifications, from 16 key archaeological sites from the Mousterian to Mesolithic (Marine Isotopic Stage 5 to 1, between 100-7 ka BP) were analysed, permitting the reconstruction of spatial patterns of resource exploitation and human mobility. The {delta}3S isotope values show weak, inconsistent relationships with climatic proxies, suggesting that sulfur signatures are primarily driven by geographic and ecological factors rather than climate. Strong spatial trends are observed, with higher {delta}3S values in coastal zones and lower values inland. Diachronic trends reveal marked shifts in human mobility: smaller ranges during the Mousterian, increasing mobility through the Chatelperronian and especially the Aurignacian, followed by reduced mobility in the Gravettian and Solutrean, and renewed territorial expansion during the Magdalenian and, likely, the Azilian. In contrast, the Mesolithic is characterised by decreased mobility and thus increased territoriality in both coastal and inland contexts. Faunal isotope values and isoscape predictions reveal that some animals were acquired beyond local foraging ranges during the Palaeolithic, particularly in inland regions with lower {delta}3S values. Isotopic niche analyses indicate partial interspecific overlap consistent with ecological flexibility. Macromammal and micromammal diversity exhibit contrasting patterns, with a significant negative correlation in Simpson and Shannon indices. Macromammal diversity correlates negatively with {delta}3S values, linking increased hunting diversity to expanded catchment areas and longer-distance foraging, whereas micromammal diversity shows positive correlations with {delta}3S, {delta}{superscript 1}3C and {delta}{superscript 1}N reflecting stronger climatic influence. Overall, these results demonstrate that hunter-gatherer behaviour in northern Iberia during the Middle and Late Palaeolithic was highly dynamic, combining logistical and residential strategies that shifted in response to changing environmental conditions, resource distributions and cultural adaptations.

The ocean tides influence key Earth system processes at a range of spatial and temporal scales. It is known that the geometry of ocean basins is the leading controller of tidal energetics, so well-constrained palaeogeographic reconstructions and tidal properties for Earths past are imperative when investigating other Earth system processes. Here, we present a novel way to constrain both deep-time tidal model results and reconstructions, by combining palaeoecology with sedimentology. We compare new palaeo-tidal model simulations for the Cambrian period, significant for the early origin and radiation of major animal fauna, to tidal proxies. One of the most abundant soft-bodied organisms preserved during this time are cnidarian medusae (jellyfish). A total of 17 cnidarian medusae localities were obtained through the literature, which had an adequate global distribution and occurred at regular intervals throughout the period of study. In some locations there were also estimates of palaeo-tidal range. Our results show a good agreement between the simulations and proxy data. In the few locations where there is disagreement, it is proposed that the palaeogeographic reconstructions are missing details, e.g., island chains, and our results allow for the palaeogeographic reconstructions to be improved. The proxy method presented is promising and can be applied to other time-periods with different marine fossils, particularly at evolutionary and extinction periods where the marginal marine environment is of importance.

Genetic variation exists for many male reproductive traits despite apparent strong sexual selection in favor of particular males. Understanding how that variation is maintained is an unresolved problem in evolutionary biology. One proposed solution to this problem is genotype-by-environment interactions (GEIs), where no male genotype is universally superior across environments. Another proposed answer is variation in female preference, such that different females prefer different male genotypes. Additionally, male genotypes may differ in their reproductive output as they age. The house fly Musca domestica is a well-suited system to evaluate these explanations for genetic variation in male reproductive traits because two male genotypes (YM and IIIM) differ in mating performance. Specifically, IIIM males outcompete YM males in mating assays because IIIM males have a shorter copulation latency. To determine the relative importance of GEIs, female variation, and male age on the maintenance of genetic variation in male reproductive behaviors, we performed non-competitive (one male to one female) and competitive (one IIIM male and one YM male to one female) mating assays while considering multiple ages and different female strains. IIIM males attempted more matings regardless of competition level, female genotype or age, but mated faster than YM males only with females of their own strain and only performed more matings in non-competitive trials. However, female strain did not improve the mating success of YM males. We also did not observe evidence for genotype-by-age interactions on male mating success. Importantly, we did not identify any conditions where YM males outcompeted IIIM males, and therefore there was no evidence for interactions or trade-offs that could explain the maintenance of genetic variation for male mating success. To explain the maintenance of IIIM and YM males, other factors such as additional social environments or varying temperature should be investigated, as the genotypes are found in natural environments with contrasting temperatures.

Whether sexual selection facilitates or hinders adaptation to novel environments is a question of fundamental importance due to current rapid environmental change. Using phylogenetic comparative analysis in 42 Drosophila species, we found that sperm length - a sexually selected ornament - positively associates with the ability of males to survive high temperatures. However, the ability to remain fertile does not increase with sperm length to the same extent, meaning that longer sperm species experience a larger gap between temperatures that kill and temperatures that sterilize males. The findings are consistent with the idea that strong sexual selection on condition-dependent exaggerated traits may facilitate somatic resilience to environmental stressors, but that susceptibility to heat-induced infertility may be a cost of extreme sperm ornamentation. Overall, the data suggests multifaceted links between postcopulatory sexual selection and climate change.

Color polymorphisms offer a powerful lens for examining how selection shapes genetic and phenotypic variation. Genomic analyses of color variation provide deeper insight into how genetic differences and phenotypic plasticity contribute to trait variation. Here, we use the bluefin killifish (Lucania goodei) to study this relationship. Male fins can display either red or yellow coloration based on pigments (pterins) or blue structural coloration (iridophores) often induced in UV-depauperate environments. Female fins lack pigmentation. To characterize the molecular basis of this variation, we assembled a high-quality genome and examined gene expression in the anal fins of male and female bluefin killifish to identify the molecular mechanisms underlying color variation. Our gene expression analysis found sex differences driven by male-biased upregulation of melanin synthesis and canonical pigment pathway genes. We additionally identified that the progesterone sex receptor was upregulated in females. Among male color morphs, several genes involved in xanthophore and iridophore formation differed between blue and non-blue males, including the transcription factor tfec, and iridophore-patterning genes atic, pnp4a, and sox10. Extraocular opsins, which are involved in non-image-forming light perception, were expressed at low levels across all fins, but showed population- and morph-specific patterns; notably, rgrb (retinal G protein coupled receptor b) was upregulated in blue males. To the best of our knowledge, this is the first report of an extraocular opsin varying as a function of population and color morph. Together, these results identify the pigment pathways underlying male-limited color polymorphisms and reveal candidate genes likely involved in light-sensitive phenotypic plasticity.

Sexual dimorphism is a well-studied phenomenon in which males and females of a species exhibit different phenotypic characteristics. However, the degree of sexual dimorphism within a species may vary among populations and may be influenced by geographic factors such as seasonality, prey availability, and population density. In this study, we examined the effects of sexual dimorphism and geographic region on the craniomandibular morphology of bobcats (Lynx rufus) in Washington State. Using digital calipers, we measured 13 craniomandibular traits from 35 males and 42 females. We found that the degree of skull dimorphism does not differ between the eastern and western side of the Cascade Mountains. However, we found significant effects of sex and geographic region on craniomandibular morphology. Across the geographic regions, males were significantly larger than females in most craniomandibular traits, excluding postorbital constriction breadth (POC). After correcting for expected size differences, only condylobasal length (CBL) was disproportionately longer in males, indicating subtle shape dimorphism within this trait, that is largely unexplained by allometry. Mechanical advantage (MA) of the temporalis and masseter muscles did not differ between the sexes at the canine or the molar bite points. Comparisons between populations east and west of the Cascade Range revealed that while sex remains the primary indicator of overall size, there is a small regional effect on size as western bobcats are slightly larger than eastern bobcats. These regional differences highlight how environmental pressures including local prey availability and severe winter conditions may influence functional skull design. Future ecological and behavioral studies are needed to further clarify how these localized environmental drivers shape phenotypic variation across populations.

The physiology of ectotherms can change substantially during acclimation to changing environmental temperature. The role of transcription in acclimation responses has been well-established, but it remains unclear whether transcriptional regulation generally reflects abrupt changes after surpassing temperature thresholds, or whether transcript abundance is a relatively monotonic, continuous function of acclimation temperature. In this study we exposed adult male Drosophila subobscura flies to four different 96-hour acclimation treatments at temperatures that were not acutely stressful but ranged from relatively cold (10{degrees}C) to relatively warm (27{degrees}C) with respect to standard rearing conditions. Transcriptome sequencing of whole-body homogenates (mRNAseq) revealed a massive, transcriptome-wide response across acclimation temperatures, with a marked overrepresentation of genes that were continuously and monotonically up- and down-regulated in response to increasing acclimation temperature. Though some genes showed more complex relationships consistent with putative threshold responses, a high percentage of the differentially expressed transcriptome (42%) showed continuous and strictly monotonic relationships. Functional enrichment suggested continuous up-regulation of spermatogenesis-related transcripts with increasing temperature and continuous up-regulation of oxidative phosphorylation-related transcripts with decreasing temperature, illustrating contrasting patterns consistent with previous studies of thermal sensitivity of male reproduction and metabolic compensation in the cold. Thus, continuous thermal sensitivity of transcription is a hallmark of acclimation in D. subobscura that likely underlies the continuous thermal sensitivity of downstream physiological processes. We also provide evidence for shared transcriptomic responses across short-term acclimation (this study) vs. published results for long-term, developmental acclimation.

To implement adequate nutritional landscapes to bumble bees and inform conservation efforts, we need a better understanding of how different pollen sources impact bumble reproductive performances and phenology. We assessed the impact of multiple native pollen on bees reproductive success by feeding 40 wild-caught Bombus impatiens and B. griseocollis queens with either commercially wildflower pollen mix commonly used to breed Bombus queens (control group) or 75% red maple pollen (Acer rubrum) and 25% pollen mix (RM group). In a second experiment, we monitored the reproductive success of 45 microcolonies of workers, harvested from B. impatiens colonies. Microcolonies were fed either: 1) pollen mix (N=15), 2) pollen mix and hawthorn (Crataegus canadensis, N=15), or 3) pollen mix and sumac (Rhus typhina, N=15). In experiment 1, RM significantly increased reproductive outputs for both species. RM-fed founding queens were twice more likely to produce workers, and produced them significantly earlier, though total number of workers did not vary between groups. However, RM-fed founding queens produced significantly more brood cells, males and gynes than control colonies, and produced them significantly earlier. In experiment 2, we found an interaction between initial colony diet and current microcolony diet. Overall, workers harvested from RM-fed colonies produced significantly more brood cells and males than workers harvested from control colonies. However, when fed hawthorn pollen during experiment 2, workers from control colonies performed as well as workers from RM-fed colonies. This suggests carry-over effects from early pollen sources provided to colonies on workers, which may be circumstantially offset by pollen sources with specific nutrient profile. Using detailed nutritional information of each pollen (including data on 32 nutrients), we provide nutritional requirements of pollen to support bumble bee reproduction, especially regarding vitamin B3 and vitamin C contents. This study will help inform land managers and captive breeding programs on the ideal pollen sources for bumble bees to ensure reproductively successful colonies.

Urbanisation imposes novel environmental conditions that can shape phenotypic traits including plumage, yet, its effects on characteristics beyond colouration remain poorly understood. Feather microstructure plays an important role in thermoregulation, protection from solar radiation and waterproofing, and its expression is sensitive to environmental conditions. Here, we quantified feather barbule density, a key component of feather microstructure, in great tits (Parus major) from five urban-rural paired populations across Europe to assess its association with urbanisation, temperature and elevation. We found no significant effects of the urban environment or temperature. However, feather microstructure significantly varied between the studied areas and was positively associated with elevation and ultraviolet B (UV-B) radiation, suggesting a potential adaptive response to variation in solar radiation.

Objective: This study aimed to investigate morphometric and plumage-colour variation among native chickens from Wallacea and Java, Indonesia, and to evaluate the contributions of geographic and production-system factors to phenotypic diversity. Methods: Native chickens were sampled from 259 households across eight provinces in Indonesia. Household-level information on production systems and farmer selection practices was collected through structured surveys. Morphometric traits and HSV-derived plumage-colour variables were analysed using principal component analysis (PCA), permutational multivariate analysis of variance (PERMANOVA), and hierarchical variance partitioning to assess phenotypic variation across locations, provinces, and islands. Results: Substantial phenotypic variation was observed among sampled populations, with significant province- and island-level differences detected for several morphometric traits. However, extensive overlap among locations was evident in both morphometric and plumage-colour space, indicating diffuse rather than discrete structuring. Within-location variation accounted for the largest proportion of total phenotypic variance across most traits, consistent with decentralised smallholder management and continued human-mediated exchange. Conclusion: Geographic fragmentation and agroecological heterogeneity alone appear insufficient to generate strongly differentiated phenotypic groups when connectivity among populations is maintained. Whether this phenotypic connectivity corresponds to contemporary gene flow, retained ancestral variation, or convergent environmental responses remains to be tested using genomic data.

Diurnal ectotherms in hot and dry ecosystems face an acquisition trade-off between maximizing collective energy intake and minimizing individual exposure time. We employed optimal foraging and thermoregulation models to examine the surface foraging and thermoregulatory strategies of Pogonomyrmex barbatus foragers in response to habitat warming in a tropical deciduous forest. Foraging activity was evaluated using field-based thermal performance curves (fTPCs) for individual foraging speed and collective foraging success. Thermoregulation was assessed through indices of thermal unsuitability, as well as thermoregulatory effectiveness and exploitation. Our results show that afternoon conditions were significantly hotter and drier than those in the morning. Furthermore, the decoupling of fTPCs was dynamic; while the optimal temperature (Topt) for individual foraging speed remained stable at 44 degrees C, the Topt for collective foraging success shifted from 35 degrees C in the morning to 41 degrees C in the afternoon. This shift in foraging strategy, driven by stressful afternoon conditions, was reflected in a transition of the thermoregulatory strategy. Specifically, the probability of foraging activity decreased as thermal unsuitability increased, with a lower baseline in the afternoon. The thermoregulatory exploitation dropped from 94% in the morning to 63% in the afternoon. Based on thermoregulatory effectiveness, foragers transitioned from an active thermoregulatory strategy in the morning to a thermoconformist strategy in the afternoon while foraging on the surface. So, the observed colonies optimized the balance between individual foraging speed and collective foraging success through a thermoregulatory strategy that was primarily spatial in the morning and strictly temporal in the afternoon. A comparison with historical data from the same site reveals a 40% contraction in the total daily foraging window since 2013.

Aim To investigate how repeated historical connections between continental islands and the mainland have shaped the phylogeographic structure and genetic diversity of populations, using the widespread water strider Aquarius paludum as a model. Location Japan Taxon Water strider Aquarius paludum (Insecta: Hemiptera: Gerridae) Methods We analysed mitochondrial (COI and COII) and nuclear (ITS1) DNA sequences from populations across the Japanese archipelago and the Eurasian continent. Phylogenetic and population genetic analyses were used to reconstruct phylogeographic structure and infer demographic history. Results Western Japanese populations exhibited nucleotide diversity comparable to that of continental populations despite their insular distribution. Bayesian phylogenetic analyses identified two major mitochondrial haplogroups (A and B) that frequently co-occurred across the Japanese archipelago. Haplogroup A, which is rare on the Eurasian continent, occurred at high frequency in Japan and showed pronounced isolation by distance, whereas haplogroup B showed only weak but significant isolation by distance and was significantly more frequent in populations closer to the coast. These contrasting spatial patterns within species indicate distinct demographic histories for the two mitochondrial lineages. Main conclusion Repeated colonization from the Eurasian continent and the long-term coexistence of mitochondrial lineages with different demographic histories have shaped the pattern of genetic diversity of A. paludum in the Japanese archipelago. Our findings exemplify how continental islands can accumulate genetic diversity through lineage accumulation and secondary contact, which produces an intraspecific phylogeographic pattern comparable to those observed during an early phase of the taxon cycle between species.