BMC Ecology and Evolution

Understanding morphological variation is crucial for the study of speciation and for conservation as it helps in assessing biodiversity and predicting responses to environmental changes. These approaches are broadly applicable but are especially valuable in marine environments, where species are often elusive, difficult to study, and face heightened threats from rapid environmental shifts. The marine snail Littorina saxatilis is notable for its extensive polymorphism in shell shape, size, and colour, with ecotypes that evolve in response to environmental forces including wave exposure and crab predation. Morphometric tools have been central to investigating the mechanisms driving this phenotypic divergence; yet, a direct comparison of their methodological efficacy is lacking. Here, we took advantage of L. saxatilis ecotypes to contrast three morphometric approaches: elliptical Fourier analysis (EFA), landmarks-based geometric morphometrics (GM), and the growth-based model implemented in the ShellShaper software (SS). We assessed their clustering power, biological interpretability, robustness to measurement error and transferability among datasets. Our findings provide insights to guide method selection in studies aimed at exploring morphological variation: EFA is better suited for high-throughput screening and describing intermediate shapes; SS offers superior clustering power with highly interpretable growth parameters; and GM is best for detailed anatomical studies but is less efficient for large datasets. We provide guidelines to align method selection with specific research goals, balancing analytical efficiency with the required morphological and biological insight. By following this framework, researchers can ensure that robust morphological analysis is achieved, which is essential not only for elucidating mechanisms of adaptation and speciation but also for effective management and conservation of marine biodiversity.

Conspicuous coloration in animals is generally thought to evolve and be maintained through inter- or intraspecific interactions such as mate choice, but this might not always be the case. The sight-line hypothesis proposes that conspicuous light-dark contrast in front of the eyes (hereafter, eyeline) evolves and is maintained due to viability selection, enhancing an individual visual acuity and thus evolutionarily associated with a particular foraging behavior that requires accurate aiming. However, empirical evidence that supports the sight-line hypothesis is virtually absent, with no studies demonstrating the key prediction that the direction of eyelines matters. Here, I tested the sight-line hypothesis using macroevolutionary analyses in terns and allies, which are a suitable study system, because they have variation in facial color patterns, including presence/absence and, if any, various angles of eyelines. They also have a large variation in foraging behavior, including picking, plunge diving, and skimming. As predicted by the sight-line hypothesis, tern lineages that require accurate aiming at foraging (e.g., plunge diving) are more likely to have eyelines. In addition, the evolutionary transition to the state with eyelines and these foraging behaviors was more likely to occur than the reverse transition. Furthermore, as expected by the fact that the direction of travel is upwardly deviated from the direction of the bills during skimming, the eyeline angle from bills was evolutionarily positively associated with the occurrence of skimming behavior. To my knowledge, the current study is the first to demonstrate that the direction of the eyeline matters, thereby strongly supporting the sight-line hypothesis.

The evolution of visual traits in closely-related species living in sympatry is highly influenced by their ecological interactions: while sexual selection tends to promote the divergence of visual cues involved in mate choice, natural selection via predation may promote the convergence of dissuasive signals between prey species, especially in unpalatable or evasive prey. Here, we investigate the impact of sympatry on the evolution of the blue structural colouration in the wings of two closely-related Morpho butterfly species across several localities throughout Central and South America. Dorsal iridescence might affect mate choice and species recognition, which should promote its local divergence among species. However, the bright flashes and dynamic colour patterns produced by iridescence during flight might also increase survival by confusing predators and favouring escape. Such an effect might in turn lead to convergence in wing iridescence between evasive species occurring in sympatry, a phenomenon dubbed evasive mimicry. To test the effect of these putative antagonistic selective forces on visual cues evolution, we quantified the variation of the structural blue colour displayed at 13 different combinations of illumination/observation angles, on the wings of two closely-related Morpho species. We contrasted 10 sympatric and 11 allopatric locations and specifically compared the phenotypic distances between individuals from different species. Phenotypic distances between heterospecific pairs of individuals were significantly smaller in sympatry, consistent with the hypothesis of a local convergence of iridescence due to evasive mimicry. Interestingly, sexual dimorphism was found between males and females, suggesting that the trade-off between natural and sexual selection on the evolution of iridescence might differ between sexes. Our results suggest that local predation pressures may promote repeated evolutionary convergence of structural colouration between evasive prey species living in sympatry.

High and low tides occur twice a day (every [~]12.4 hours), with the largest tidal ranges during spring tides around new and full moons (every [~]14.765 days). While these lunar cycles are known to influence many animal phenotypes, particularly the reproduction of coastal animals, the genetic basis of lunar-related rhythms remains unclear. Since phenotypic variation is a valuable resource for elucidating such mechanisms, we examined geographic variation in the lunar-regulated mass spawning of the grass puffer (Takifugu alboplumbeus) along the Japanese coast. We found that western populations spawn during the first half of the spring tides, whereas eastern populations spawn during the second half. Furthermore, although spawning typically occurs a few hours before high tide, this timing is restricted to a specific time window that is earlier in the western populations than in the eastern ones. Behavioral analysis of larvae also revealed a shorter free-running circadian period ({tau}) in the western population than in the eastern ones. As differences in {tau} affect individual variation in the timing of physiological functions and behaviors, we hypothesized that differences in {tau} could account for the different time windows and consequently the observed difference in spawning days. Population genomics analysis identified proline-rich transmembrane protein 1-like (prrt1l) as a candidate gene. Expression of prrt1l was observed in the circadian pacemaker suprachiasmatic nucleus, and triple CRISPR F0 knockout of prrt1l shortened the free-running period in larvae. These findings suggest a potential mechanism underlying the geographic variation in lunar-synchronized spawning behavior. HighlightsO_LIThe geographic variation exists in the lunar-regulated spawning of the grass puffer, with differences in spawning dates and times between western and eastern Japan. C_LIO_LIThe free-running period of western populations is shorter than that of eastern populations, which is consistent with their earlier spawning timing. C_LIO_LIPopulation genomics analysis identified prrt1l as a candidate gene harboring population-specific missense mutations, the knockout of which shortens the free-running period. C_LI

A major challenge to investigating the proximate causes of ecological adaptation is the difficulty of studying the phenotypes of organisms in their natural environments. By necessity, many studies seeking to determine the genetic and cellular basis of adaptation therefore investigate potentially adaptive phenotypes under laboratory conditions where organisms are more easily experimentally manipulated. For laboratory models, it remains unclear if organisms maintained long term under laboratory conditions are representative of relatives in their natural environment. In recent years, Drosophila sechellia, a specialist species endemic to the Seychelles, has emerged as a (neuro)genetic model for studying the molecular basis of ecological adaptation. A multitude of studies have investigated the genetic and cellular basis of various aspects of this species specialization in a laboratory setting. However, the vast majority of these studies use laboratory strains of D. sechellia that were collected many decades ago, and have been maintained under conditions very different from their natural niche. Thus, it remains unclear if and how these strains resemble their wild counterparts. Here, we compare the phenotypes of these laboratory strains with recently-collected wild D. sechellia to ask if laboratory strains display a loss or degradation of phenotypes potentially involved in their specialization resulting from their long-term laboratory maintenance. Across several behavioral and anatomical phenotypes, we find a high degree of similarity between wild-caught and laboratory-maintained strains. Our results suggest that studies of the molecular mechanisms underlying D. sechellias phenotypes associated with specialization are likely representative of the evolution of these flies in the wild.

The extent to which phenotypic evolution can be constrained by genetic correlations is an important question in evolutionary biology. To address this question, biological invasions are opportune models where derived, invasive populations can be compared to their extant ancestors, allowing to track the evolution of genetic correlations from the ancestor, throughout the invasion process. In this paper, we focused on the worldwide invasion of Drosophila suzukii (Matsumara, 1931), and investigated the evolution of the genetic covariance matrix G of wing shape between ancestral native, and derived invasive populations. Leveraging demographic history resolved by population genetics approaches, we tested whether G remained stable during the invasion. Using a multivariate QST-FST approach, we further tested whether or not the observed phenotypic divergence in wing shape aligned with a neutral scenario of evolution. Our results show moderate yet significant quantitative genetic differentiation of wing shape among D. suzukii populations and a relative stability in the structure of G, presenting a roughly spherical shape but slightly different volumes. These characteristics likely reflect the demographic history of populations and suggest a low level of genetic constraint on wing shape evolution. The divergence between populations was greater than expected under a purely neutral model of evolution, compatible with an effect of divergent selection among them. Overall, our study suggests that selection and drift, but not ancestral genetic constraints, affected the early stages of wing shape evolution during D. suzukii invasion.

Abstract/SummaryHere we untangle the systematics of the Asiatic white-eye complex (Zosterops spp.) to better understand the early stages of a recent island radiation. We adopt an integrative approach involving allelic data, genome-scale single nucleotide polymorphisms (SNPs), and museum-based morphometrics coupled with a comprehensive sampling to provide the most holistic understanding of the group to date. The island lineages of Asiatic white-eyes across Indonesia, the Philippines, East Asia, the adjacent oceanic islands of the Western Pacific underwent a deep split separating Zosterops everetti and Z. nigrorum in the Phillippines from a very rapid radiation including Z. japonicus, Z. meyeni, and Z. montanus in the Philippines, Japan, and Indonesia. Z. nigrorum catarmanensis on Camiguin South in the Philippines was found to be nested within Z. montanus and a species limit between Z. nigrorum populations on Panay and Luzon was strongly supported. Phylogenetic splits and population structure were detected within the clade containing Z. japonicus, Z. meyeni, and Z. montanus. A well-supported split separates a northern group including Northern Philippines Z. montanus subspecies, Z. meyeni, and Z. japonicus from the southerly Z. montanus taxa. This creates a paraphyletic Z. montanus. However, based on speciation rates within the broader Asiatic white-eye clade this break likely does not yet represent evolutionarily independent species lineages. Morphological evolution is taking place within the Asiatic white-eyes especially within the robust, large-billed subspecies of Z. japonicus on the oceanic islands of Japan and in the newly identified yellow-morph of Z. montanus on Camiguin South.

Natural environmental variations are normal occurrences, however human-driven climatic changes continue to exacerbate the magnitude of these variations. This pushes organisms to their physiological limits where they must adapt or face extinction. The potential for organisms to adapt is of concern; however, the presence of fluctuating regimes to incorporate natural environmental variation is occasionally considered. Here, we investigate the standing variation in thermal optima of ten Chlamydomonas reinhardtii strains along a latitudinal gradient and determine whether adaptation to its temperature extremes is possible via long-term evolution. Despite their broad geographic origins, C. reinhardtii strains exhibited a similar thermal optimum (31.2{degrees}C - 32.4{degrees}C). We then evolved one strain for [~]900 generations under cold, hot and fluctuating growth conditions. Those grown in constant environmental conditions became specialized to their environment of 20{degrees}C or 37{degrees}C, whereas those evolved in a fluctuating regime performed comparably to the specialists, suggesting no long-term cost of adaptation via a fluctuating regime. We also found no differences in the amount of variation between fluctuating and constant conditions, suggesting similar amounts of divergence between conditions. Overall, despite our predictions that a fluctuating regime would hinder adaptation, we found that these lineages were able to adapt to this variable environment.

The evolution of body shape reflects the interplay between functional constraints and habitat structure. In fishes, cave environments are well known for promoting regressive traits such as eye and pigment loss, yet their influence on overall body form remains poorly understood. Here, we examine patterns of body shape variation in cave- and surface-dwelling trichomycterid catfishes from northeastern Colombia to assess whether consistent associations exist between habitat type and morphology. Using geometric morphometric analyses, we quantified differences in body shape among species inhabiting subterranean and surface environments. Our results reveal significant habitat-associated differentiation in body shape along the main axes of morphological variation. Cave-dwelling species exhibit more elongated and fusiform body shapes, whereas surface-dwelling species tend to show deeper and more robust morphologies. In a functional context, these contrasting body patterns suggest associations with differing locomotor demands imposed by subterranean versus surface habitats. Although we do not explicitly test convergence or performance, the recurrence of similar body shapes among species from different clades occupying comparable habitats is consistent with repeated morphological responses to shared ecological constraints. Research HighligthsO_LIMultivariate shape analyses reveal significant habitat-associated variation in trichomycterid fishes. Recurrent morphological patterns suggest repeated responses potentially mediated by habitat constraints. C_LIO_LIBody shape differs consistently between cave- and surface-dwelling trichomycterids. Cave species exhibit more elongated and fusiform forms, whereas surface species display deeper body configurations. C_LI

Honeypot ants represent an example of convergent evolution, where a group of workers specialized in storing liquid food in their crops (i.e., stomach) has independently evolved multiple times across different ant genera. While seasonal resource scarcity and arid conditions are thought to drive the evolution of repletism, the role of environmental variables in this process has not been tested. With this is mind, species ensemble models were computed to assess suitability and richness areas, and the importance of predictors. Predictor importance was compared between genera and groups occupying a similar geographical area. Niche overlap and similarity between honeypot ant species were also evaluated to determine whether they occupy similar environmental spaces. Similarity was mainly found within genera, and Leptomyrmex and Myrmecocystus showed striking niche differences. Overall, Leptomyrmex distribution was mainly influenced by atmospheric bioclimatic variables like precipitation and temperature, while Myrmecocystus had soil bioclimatic variables as the most important predictors for their current distribution. Our results indicate that honeypot ants species currently do not occupy the same environmental space, and are not experiencing the same contemporary environmental stressors. While our results suggest that contemporary environmental factors cannot explain the convergence of honeypot ants, future research will examine past climatic conditions along with investigations into the ant genomes to understand more about the causes and consequences of the convergence.

Understanding the genetic basis of polygenic adaptation is challenging. Populations that undergo parallel evolution serve as experimental replications enabling the study of molecular mechanism. Apis cerana is widely-distributed in Asia and has repeatedly colonized the Qinghai-Tibet Plateau. The highland populations are derived from lowland colonies while showed not admixture with each other, representing independent events of colonization. We investigated resequencing genomes of five populations to study the genetic basis of highland adaptation in A. cerana. Using two complementary methods, we isolated genes with adaptive signals in each lineage. Although large proportion of adaptive loci are unique to each population, most potentially adaptive polymorphism shared with genetic variation in lowland populations, consistent with widespread signals of soft selection sweeps. Whereas parallelism was low at the level of adaptive loci, it was greater for functional pathways and greatest for phenotypes. Further enrichment analysis found the shared adaptive loci were overrepresented in pathways related to the development of sensory system and body morphogenesis. These highly connected pathways and loci could buffer different genetic paths and maintain developmental stability. Adaptive signals in the development-related loci suggest stabilizing selection further drive phenotypic convergence under similar stress. However, lineage-specific loci and pathways facilitated adaptive divergence in each lineage within the broadly similar highland environment. Our results demonstrate the genetic redundancy of highland adaptation and lineage-specific evolution via independent colonization in A. cerana. This underscores that predicting a populations adaptive potential requires understanding its full adaptive architecture within the ecological context--including abiotic and biotic interactions.

We examined how thermal shifts influence development time and adult body size in Drosophila melanogaster. Individual flies were exposed to alternating temperatures of 25{degrees}C (optimal) and 17{degrees}C (cold), with shifts introduced at key developmental transitions: larval hatching and pupariation. We found while larval-stage temperature is the biggest determinant of thermal plasticity of development time and adult size, the egg-stage temperature also influences the pace of development and growth throughout pre-adult duration. The effect of low-to-high and high-to-low temperature shifts on development and growth may not be symmetric. When eggs are reared at 25{degrees}C and then shifted to 17{degrees}C, larval and pupal durations undergo reduction compared to constant 17{degrees}C, but it produces slightly larger adults. A higher egg-stage temperature thus seem to exert a carryover effect that accelerates subsequent development and growth when later stages experience colder temperatures. Surprisingly, flies whose egg stage is exposed to 17{degrees}C followed by a shift to 25{degrees}C also have reduced larval duration and larger size, relative to those developing at constant 25{degrees}C. We speculate this could be either because 17{degrees}C to 25{degrees}C represents a low-to-high temperature shift or a sub-optimal-to-optimal thermal shift that results in metabolic and/or hormonal changes accelerating differentiation and growth. While pupal duration is sensitive to current and to some extent prior thermal environments, it does not contribute substantially to thermal plasticity of size. Development time is longer in males than in females, and this difference seems to start from larval stage while the pupal duration plays a bigger role in creating this sex-specific difference. Overall, employing individual fly rearing, this study helped to unravel the effect of thermal shifts on growth and development in D. melanogaster with great precision.

Habitat transitions are a major driver of morphological evolution. Teleost fishes have repeatedly transitioned from benthic to pelagic habitats, often evolving predictable changes in body shape that enhance hydrodynamic efficiency. While freshwater sculpins (Cottidae, Perciformes) are usually benthic, two genera in Lake Baikal, Comephorus and Cottocomephorus, have independently evolved into midwater niches. As sculpins lack a swim bladder, these lineages instead improved buoyancy through reduced skeletal density and increased lipid stores. Using micro-computed tomography and two-dimensional morphometrics, we characterized skeletal evolution across the Baikal sculpin radiation. We found that parallel changes in bone mineral density and microstructure independently evolved in the two pelagic clades. Density reductions occurred throughout the skull in pelagic species. The basibranchials and neurocranium exhibited the lowest overall bone density across all cranial elements. While the jaws maintained the highest absolute density values among the bones we measured, they also showed the greatest proportional reduction in density associated with pelagic habitat use, with a 56.86% decrease in percentage hydroxyapatite and a 21.39% increase in porosity. Morphometric analyses further identified convergence toward an elongate body shape, reduced and posteriorly shifted eyes, and elevated fin insertion in pelagic taxa. These results demonstrate a repeated skeletal lightening and body shape changes accompanying benthic-to-pelagic transitions. This pattern mirrors other benthic-to-pelagic transitions in teleosts that lack swim bladders, highlighting shared biomechanical and microstructural solutions to life in the open water.

Turtles and tortoises (Order Testudines) possess a unique bony shell that varies in shape across ecological niches. Previous studies have linked turtle shell abnormalities to the presence of environmental stress, leading to asymmetry in shell shape. Here we present the first large-scale geometric morphometric analysis of shell asymmetry in preserved museum specimens from 92 turtle species, using high-resolution 3D scans and (semi)landmark-based methods. We quantified fluctuating asymmetry (FA) and directional asymmetry (DA) in the whole shell, carapace, and plastron, and tested for ecological and phylogenetic influences on shell shape. Our results reveal significant ecological effects on both symmetric and asymmetric components of shell morphology, with aquatic and marine species exhibiting higher FA than their terrestrial counterparts. The carapace showed higher asymmetry and integration than the plastron, suggesting different developmental constraints. Phylogenetic signal was present but weak, indicating convergence in shell shape among ecologically similar but distantly related species. Partial least squares analysis revealed strong covariation between symmetric and asymmetric components, supporting the shell as an integrated morphological unit. These findings highlight the utility of FA as a non-invasive indicator of developmental instability, with implications for conservation monitoring using preserved and living specimens.

Landscape composition is central in shaping how pollinators utilise floral resources, yet its influence on foraging behaviour of co-occurring Asian honey bees remains underexplored. Resolving this gap is crucial to understand how closely-related, native and introduced species maintain foraging efficiency in rapidly changing environments. We investigated nectar preferences, sucrose responsiveness, and foraging task partitioning in three co-occurring honey bee species in India: Apis florea (native open-nesting), Apis cerana (native cavity-nesting), and Apis mellifera (introduced cavity-nesting), across forest, agricultural, and urban landscapes. Landscape type strongly influenced crop sugar concentrations of honey bees. While all species collected high-concentration nectar in forests, A. mellifera and A. cerana collected lower concentrations than A. florea in urban habitats. A. florea showed consistent preference for high-concentration nectar across landscapes. Complementing this, sucrose responsiveness assays revealed a lower responsiveness of A. florea compared to cavity-nesting species. Foraging task partitioning differed among species, but interestingly, also among landscapes. While A. cerana predominantly collected nectar, A. mellifera foraged equally for pollen, nectar and water, and A. florea shifted task allocation across landscapes. In conclusion, we provide the first comparative evidence that landscape composition and species characteristics jointly shape foraging preferences and organisation of foraging labour in Asian honey bees.

A common assumption in molecular evolution is the fixed selection nature of a mutation, for instance, a neutral mutation is selectively neutral for all individuals who carry the mutation, and so forth a deleterious or beneficial mutation. Our recent work challenged this presumption, postulating that individuals with a specific mutation exhibit a fluctuation in fitness, short for FSI (fluctuating selection among individuals). Moreover, an intriguing phenomenon called selection-duality emerges, that is, a slightly beneficial mutation could be a negative selection (the substitution rate less than the mutation rate). It appears that selection-duality is bounded: the low-bound is the generic neutrality where the mutation is neutral by the means of fitness on average, while the up-bound is the substitution neutrality where the substitution rate equals to the mutation rate. In this paper, we conducted a thorough theoretical analysis to evaluate how many generations needed for a selection-duality mutation to be fixed in a finite population. A striking finding is that the mean fixation time of a selection-duality mutant, including the generic neutrality and the substitution neutrality, is approximately identical, which is considerably shorter than the case of strict neutrality without FSI. One may further envisage that the fast-fixation nature of selection-duality mutations could result in a considerable genetic reduction at linked sites.

Sarita Lake, British Columbia houses a distinctive population of threespine stickleback (Gastrosteus aculeatus L.) with a phenotype characterized by unusually large individuals relative to nearby conspecifics. We tested the hypothesis that members of this population are not isometrically larger but rather exhibit variation in allometric trajectories that reflect changes in developmental timing impacting the developmental-genetic architecture of the phenotype. We used 3D geometric morphometrics to characterize the size and shape of skulls, pectoral girdles and pelvic girdles from a sample of individuals from nearby freshwater and marine populations and compare them to a sample from Sarita Lake. We showed that individuals from the Sarita Lake population are larger in each body region compared to most other populations examined. Further, these individuals have dorsally expanded skulls and relatively robust pelvic armour. We also showed that the relationship between size and shape is differently structured among body regions and is heavily influenced by non-uniform sexually-mediated variation across populations sampled. Our results reflect complex underlying developmental trajectories, and we suggest that the large phenotype observed may be driven by fecundity selection on female size in combination with a limnetic trophic niche and relatively increased predation pressure in Sarita Lake.

The olfactory system plays a critical role in mammalian environmental perception, with some clades relying on an expanded accessory olfactory (vomeronasal) system (VNS) to detect larger, non-volatile odorants. Mammals make extensive use of this system for social communication between conspecifics. Recent studies have begun to investigate how the VNS changes in response to or as part of ecological transitions. Several studies have identified trends of VNS-associated gene loss or regression in secondarily aquatic mammals. However, continuing discussion on genotype-phenotype correlation within the VNS means that greater effort should be made to investigate the morphology of the VNS in species where it remains poorly understood. Here, we use skeletal and soft-tissue data to demonstrate that the vomeronasal groove, an established osteological correlate for the VNO in bats and primates, is also a valid indicator for its presence in Caniformia. Additionally, we confirm the presence of the VNO in the secondarily aquatic North American river otter (Lontra canadensis) and compare its morphology with that of two close-related species, the semi-aquatic American mink (Neogale vison) and the terrestrial long-tailed weasel (Neogale frenata). This study expands the valid taxonomic scope of the vomeronasal grooves proxy as an osteological correlate, confirms the presence of the VNO in the previously undescribed system of the North American river otter, and highlights the complexity of the mammalian accessory olfactory system.

Multivariate phylogenetic comparative methods for modelling high-dimensional traits such as 3D shapes or gene expression proBiles have been recently developed. However, these approaches are impractical and almost impossible to use when the number of traits exceeds a few thousands, as they become computationally prohibitive. We overcome these limitations by proposing a new maximum likelihood approach based on the Empirical Bayes framework. This approach takes into account the information of the complete covariances (among species and traits) to infer parameters and compare models of trait evolution for high-dimensional datasets. Through simulations, we demonstrate that the proposed approach can accurately estimate parameters of various trait evolution models, even when the number of traits is ten times larger than the number of lineages; it requires less memory and is at least 10 times faster than currently available approaches. This fast, efBicient framework enabled us to extend the high-dimensional multivariate phylogenetic comparative toolkit by including an Ornstein-Uhlenbeck process with multiple optima to study adaptation to various selective regimes. Applying our approach to the evolution of jaw morphology in relation to dietary adaptation in mammals, we demonstrate morphological convergence in carnivorous and herbivorous lineages. The proposed Empirical Bayes framework, implemented in the R package mvMORPH, enables phylogenetic comparative methods to efBiciently handle high-dimensional datasets and complex models of trait evolution.

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