A comparison of antibiotic resistance genes and mobile genetic elements in wild and captive Himalayan vultures.

As the most widely distributed scavenger birds on the Qinghai-Tibetan Plateau, Himalayan vultures (Gyps himalayensis) feed on the carcasses of various wild and domestic animals, facing the dual selection pressure of pathogens and antibiotics and are suitable biological sentinel species for monitoring antibiotic resistance genes (ARGs). This study used metagenomic sequencing to comparatively investigate the ARGs and mobile genetic elements (MGEs) of wild and captive Himalayan vultures. Overall, the resistome of Himalayan vultures contained 414 ARG subtypes resistant to 20 ARG types, with abundances ranging from 0.01 to 1,493.60 ppm. The most abundant resistance type was beta-lactam (175 subtypes), followed by multidrug resistance genes with 68 subtypes. Decreases in the abundance of macrolide-lincosamide-streptogramin (MLS) resistance genes were observed in the wild group compared with the zoo group. A total of 75 genera (five phyla) of bacteria were predicted to be the hosts of ARGs in Himalayan vultures, and the clinical (102 ARGs) and high-risk ARGs (35 Rank I and 56 Rank II ARGs) were also analyzed. Among these ARGs, twenty-two clinical ARGs, nine Rank I ARG subtypes, sixteen Rank II ARG subtypes were found to differ significantly between the two groups. Five types of MGEs (128 subtypes) were found in Himalayan vultures. Plasmids (62 subtypes) and transposases (44 subtypes) were found to be the main MGE types. Efflux pump and antibiotic deactivation were the main resistance mechanisms of ARGs in Himalayan vultures. Decreases in the abundance of cellular protection were identified in wild Himalayan vultures compared with the captive Himalayan vultures. Procrustes analysis and the co-occurrence networks analysis revealed different patterns of correlations among gut microbes, ARGs, and MGEs in wild and captive Himalayan vultures. This study is the first step in describing the characterization of the ARGs in the gut of Himalayan vultures and highlights the need to pay more attention to scavenging birds.

Comprehensive genome assembly reveals genetic diversity and carcass consumption insights in critically endangered Asian king vultures.

The Asian king vulture (AKV), a vital forest scavenger, is facing globally critical endangerment. This study aimed to construct a reference genome to unveil the mechanisms underlying its scavenger abilities and to assess the genetic relatedness of the captive population in Thailand. A reference genome of a female AKV was assembled from sequencing reads obtained from both PacBio long-read and MGI short-read sequencing platforms. Comparative genomics with New World vultures (NWVs) and other birds in the Family Accipitridae revealed unique gene families in AKV associated with retroviral genome integration and feather keratin, contrasting with NWVs' genes related to olfactory reception. Expanded gene families in AKV were linked to inflammatory response, iron regulation and spermatogenesis. Positively selected genes included those associated with anti-apoptosis, immune response and muscle cell development, shedding light on adaptations for carcass consumption and high-altitude soaring. Using restriction site-associated DNA sequencing (RADseq)-based genome-wide single nucleotide polymorphisms (SNPs), genetic relatedness and inbreeding status of five captive AKVs were determined, revealing high genomic inbreeding in two females. In conclusion, the AKV reference genome was established, providing insights into its unique characteristics. Additionally, the potential of RADseq-based genome-wide SNPs for selecting AKV breeders was demonstrated.

Blood transcriptome analysis of common kestrel nestlings living in urban and non-urban environments.

Urbanisation is one of the main anthropogenic forms of land cover affecting an ever-increasing number of wild animals and their habitats. Physiological plasticity represents an important process through which animals can adjust to the novel conditions of anthropogenic environments. Relying on the analysis of gene expression, it is possible to identify the molecular responses to the habitat conditions and infer possible environmental factors that affect the organismal physiology. We have quantified for the first time the blood transcriptome of common kestrel (Falco tinnunculus) nestlings living in urban sites and compared it to the transcriptome of kestrel nestlings inhabiting rural and natural environments. We found mild differences in the expression of genes among sites, indicating adaptability or acclimation of the birds to the urban habitat. We identified 58 differentially expressed genes between urban and natural kestrels, and 12 differentially expressed genes between urban and rural kestrels. The most striking differences among sites involved inflammatory-immunological, metabolic, apoptosis, DNA repair and development genes. In particular, we found that (i) urban kestrel nestlings had higher expression of genes linked to inflammation, repair of DNA damage, or apoptosis than natural kestrel nestlings, and (ii) natural and rural kestrel nestlings had higher expression of genes linked to the development and activation of immune cells, type I interferon response, or major histocompatibility complex than urban kestrel nestlings. Finally, the KEGG enrichment analysis identified the insulin signalling as the main pathway that differed between natural and urban kestrel nestlings. This is one of a limited number of studies on vertebrates that revealed habitat-associated differences in the transcriptome. It paves the way for further in-depth studies on the links between physiological variation and habitat structure at different spatial and temporal scales.

Genetic distinctiveness of an endangered falcon: Implications for conservation in Europe.

In the Falconidae, the genus Falco comprises species of large birds of prey with wide distribution worldwide. However, the European lanner falcon Falco biarmicus feldeggii is rapidly heading for global extinction following a dramatic decline caused by anthropogenic interference. Conservation projects are currently underway with the main purpose of increasing its population size in the Mediterranean basin through captive breeding and release of birds into the wild. To support the projects, and strengthen the legitimacy of conservation efforts consistently with the Evolutionary Significant Unit concept, we explored the possibility of characterising the gene pool of the European lanner and reliably distinguishing it from other falcon taxa inhabiting the Mediterranean area, which show morphological and genetic similarities. To address the issue, we examined genetic variability at the nuclear level through the analysis of 12 neutral Short Tandem Repeat loci, and, for the first time in these taxa, two single-copy functional genes, coding for the brain-derived neurotrophic factor precursor and the oocyte maturation factor, respectively. The second exon of the major histocompatibility complex class II B gene was also investigated. Additionally, to frame our data with previously published data, we assess variation at the mitochondrial level by sequencing portions of the cytochrome b, 12S rRNA gene, and the control region. Our results showed that the European lanner is highly distinct from other falcon taxa, as revealed by nuclear, but not by mitochondrial DNA. We discuss our findings focusing on their implications for the preservation of this highly endangered European bird, and highlighted the critical role of genetic information in planning and monitoring concrete interventions.

Phylogenomic insights into the polyphyletic nature of Altai falcons within eastern sakers (Falco cherrug) and the origins of gyrfalcons (Falco rusticolus).

The Altai falcon from Central Asia always attracted the attention of humans. Long considered a totemic bird in its native area, modern falconers still much appreciated this large-bodied and mighty bird of prey due to its rarity and unique look. The peculiar body characteristics halfway between the saker falcon (Falco cherrug) and the gyrfalcon (F. rusticolus) triggered debates about its contentious taxonomy. The weak phylogenetic signal associated with traditional genetic methods could not resolve this uncertainty. Here, we address the controversial evolutionary origin of Altai falcons by means of a genome-wide approach, Restriction-site Associated DNA sequencing, using sympatric eastern sakers falcons, allopatric western saker falcons and gyrfalcons as outgroup. This approach provided an unprecedented insight into the phylogenetic relationships of the studied populations by delivering 17,095 unlinked SNPs shedding light on the polyphyletic nature of Altai falcons within eastern sakers. Thus we concluded that the former must correspond to a low taxonomic rank, probably an ecotype or form of the latter. Also, we found that eastern sakers are paraphyletic without gyrfalcons, thus, these latter birds are best regarded as the direct sister lineage of the eastern sakers. This evolutionary relationship, corroborated also by re-analyzing the dataset with the inclusion of outgroup samples (F. biarmicus and F. peregrinus), put eastern sakers into a new light as the potential ancestral genetic source of high latitude and altitude adaptation in descendent populations. Finally, conservation genomic values hint at the stable genetic background of the studied saker populations.

Sex ratio and relatedness in the Griffon vulture (Gyps fulvus) population of Serbia.

Background: Once a widespread species across the region of Southeast Europe, the Griffon vulture is now confined to small and isolated populations across the Balkan Peninsula. The population from Serbia represents its biggest and most viable population that can serve as an important reservoir of genetic diversity from which the birds can be used for the region's reintroduction programmes. The available genetic data for this valuable population are scarce and as a protected species that belongs to the highly endangered vulture group, it needs to be well described so that it can be properly managed and used as a restocking population. Considering the serious recent bottleneck event that the Griffon vulture population from Serbia experienced we estimated the overall relatedness among the birds from this population. Sex ratio, another important parameter that shows the vitality and strength of the population was evaluated as well. Methods: During the annual monitoring that was performed in the period from 2013-2021, we collected blood samples from individual birds that were marked in the nests. In total, 169 samples were collected and each was used for molecular sexing while 58 presumably unrelated birds from different nests were used for inbreeding and relatedness analyses. The relatedness was estimated using both biparentally (10 microsatellite loci) and uniparentally (Cytb and D-loop I of mitochondrial DNA) inherited markers. Results: The level of inbreeding was relatively high and on average it was 8.3% while the mean number of relatives for each bird was close to three. The sex ratio was close to 1:1 and for the analysed period of 9 years, it didn't demonstrate a statistically significant deviation from the expected ratio of 1:1, suggesting that this is a stable and healthy population. Our data suggest that, even though a relatively high level of inbreeding can be detected among the individual birds, the Griffon vulture population from Serbia can be used as a source population for restocking and reintroduction programmes in the region. These data combined with previously observed genetic differentiation between the populations from the Iberian and Balkan Peninsulas suggest that the introduction of foreign birds should be avoided and that local birds should be used instead.

Evaluation of the Impact of the Peregrine Falcon (Falco peregrinus peregrinus) Reintroduction Process on Captive-Bred Population.

The main objective of this study was to determine the impact of increased demand for peregrine falcons via breeding (mainly Polish, Czech, German and Slovak) on the genetic structure of the birds. In the analysis, 374 specimens from six countries were sampled in 2008-2019 (omitting 2009), and all the birds analyzed were released into the wild as part of the Polish reintroduction program. The assessment of genetic variation was based on a well-known panel of 10 microsatellite markers described for the species. We calculated a fixation index for the samples from each year, and based on this, we determined the level of inbreeding. We also performed an analysis using the Bayesian cluster method, assuming that 1-19 hypothetical populations would define the division that best fit the samples. The most probable division was into two groups; in the first group, the samples from individuals delivered in 2013 were most often segregated; moreover, in this year, a jump in inbreeding, expressed by the fixation index, was observed.

Clock-linked genes underlie seasonal migratory timing in a diurnal raptor.

Seasonal migration is a dynamic natural phenomenon that allows organisms to exploit favourable habitats across the annual cycle. While the morphological, physiological and behavioural changes associated with migratory behaviour are well characterized, the genetic basis of migration and its link to endogenous biological time-keeping pathways are poorly understood. Historically, genome-wide research has focused on genes of large effect, whereas many genes of small effect may work together to regulate complex traits like migratory behaviour. Here, we explicitly relax stringent outlier detection thresholds and, as a result, discover how multiple biological time-keeping genes are important to migratory timing in an iconic raptor species, the American kestrel (Falco sparverius). To validate the role of candidate loci in migratory timing, we genotyped kestrels captured across autumn migration and found significant associations between migratory timing and genetic variation in metabolic and light-input pathway genes that modulate biological clocks (top1, phlpp1, cpne4 and peak1). Further, we demonstrate that migrating individuals originated from a single panmictic source population, suggesting the existence of distinct early and late migratory genotypes (i.e. chronotypes). Overall, our results provide empirical support for the existence of a within-population-level polymorphism in genes underlying migratory timing in a diurnally migrating raptor.

Vulture Genomes Reveal Molecular Adaptations Underlying Obligate Scavenging and Low Levels of Genetic Diversity.

Obligate scavenging on the dead and decaying animal matter is a rare dietary specialization that in extant vertebrates is restricted to vultures. These birds perform essential ecological services, yet many vulture species have undergone recent steep population declines and are now endangered. To test for molecular adaptations underlying obligate scavenging in vultures, and to assess whether genomic features might have contributed to their population declines, we generated high-quality genomes of the Himalayan and bearded vultures, representing both independent origins of scavenging within the Accipitridae, alongside a sister taxon, the upland buzzard. By comparing our data to published sequences from other birds, we show that the evolution of obligate scavenging in vultures has been accompanied by widespread positive selection acting on genes underlying gastric acid production, and immunity. Moreover, we find evidence of parallel molecular evolution, with amino acid replacements shared among divergent lineages of these scavengers. Our genome-wide screens also reveal that both the Himalayan and bearded vultures exhibit low levels of genetic diversity, equating to around a half of the mean genetic diversity of other bird genomes examined. However, demographic reconstructions indicate that population declines began at around the Last Glacial Maximum, predating the well-documented dramatic declines of the past three decades. Taken together, our genomic analyses imply that vultures harbor unique adaptations for processing carrion, but that modern populations are genetically depauperate and thus especially vulnerable to further genetic erosion through anthropogenic activities.

Assessment of the Genetic Potential of the Peregrine Falcon (Falco peregrinus peregrinus) Population Used in the Reintroduction Program in Poland.

Microsatellite DNA analysis is a powerful tool for assessing population genetics. The main aim of this study was to assess the genetic potential of the peregrine falcon population covered by the restitution program. We characterized individuals from breeders that set their birds for release into the wild and birds that have been reintroduced in previous years. This was done using a well-known microsatellite panel designed for the peregrine falcon containing 10 markers. We calculated the genetic distance between individuals and populations using the UPGMA (unweighted pair group method with arithmetic mean) method and then performed a Principal Coordinates Analysis (PCoA) and constructed phylogenetic trees, to visualize the results. In addition, we used the Bayesian clustering method, assuming 1-15 hypothetical populations, to find the model that best fit the data. Units were segregated into groups regardless of the country of origin, and the number of alleles and observed heterozygosity were different in different breeding groups. The wild and captive populations were grouped independent of the original population.

Genome-wide diversity in the California condor tracks its prehistoric abundance and decline.

Due to their small population sizes, threatened and endangered species frequently suffer from a lack of genetic diversity, potentially leading to inbreeding depression and reduced adaptability.1 During the latter half of the twentieth century, North America's largest soaring bird,2 the California condor (Gymnogyps californianus; Critically Endangered3), briefly went extinct in the wild. Though condors once ranged throughout North America, by 1982 only 22 individuals remained. Following decades of captive breeding and release efforts, there are now >300 free-flying wild condors and ∼200 in captivity. The condor's recent near-extinction from lead poisoning, poaching, and loss of habitat is well documented,4 but much about its history remains obscure. To fill this gap and aid future management of the species, we produced a high-quality chromosome-length genome assembly for the California condor and analyzed its genome-wide diversity. For comparison, we also examined the genomes of two close relatives: the Andean condor (Vultur gryphus; Vulnerable3) and the turkey vulture (Cathartes aura; Least Concern3). The genomes of all three species show evidence of historic population declines. Interestingly, the California condor genome retains a high degree of variation, which our analyses reveal is a legacy of its historically high abundance. Correlations between genome-wide diversity and recombination rate further suggest a history of purifying selection against linked deleterious alleles, boding well for future restoration. We show how both long-term evolutionary forces and recent inbreeding have shaped the genome of the California condor, and provide crucial genomic resources to enable future research and conservation.

Climate-driven flyway changes and memory-based long-distance migration.

Millions of migratory birds occupy seasonally favourable breeding grounds in the Arctic1, but we know little about the formation, maintenance and future of the migration routes of Arctic birds and the genetic determinants of migratory distance. Here we established a continental-scale migration system that used satellite tracking to follow 56 peregrine falcons (Falco peregrinus) from 6 populations that breed in the Eurasian Arctic, and resequenced 35 genomes from 4 of these populations. The breeding populations used five migration routes across Eurasia, which were probably formed by longitudinal and latitudinal shifts in their breeding grounds during the transition from the Last Glacial Maximum to the Holocene epoch. Contemporary environmental divergence between the routes appears to maintain their distinctiveness. We found that the gene ADCY8 is associated with population-level differences in migratory distance. We investigated the regulatory mechanism of this gene, and found that long-term memory was the most likely selective agent for divergence in ADCY8 among the peregrine populations. Global warming is predicted to influence migration strategies and diminish the breeding ranges of peregrine populations of the Eurasian Arctic. Harnessing ecological interactions and evolutionary processes to study climate-driven changes in migration can facilitate the conservation of migratory birds.

Genetic diversity of the Griffon vulture population in Serbia and its importance for conservation efforts in the Balkans.

The Griffon vulture was once a widespread species across the region of Southeast Europe, but it is now endangered and in some parts is completely extinct. In the Balkan Peninsula the largest Griffon vulture inland population inhabits the territory of Serbia. We present, for the first time, the genetic data of this valuable population that could be a source for future reintroduction programs planned in South-eastern Europe. To characterize the genetic structure of this population we used microsatellite markers from ten loci. Blood samples were collected from 57 chicks directly in the nests during the ongoing monitoring program. We performed a comparative analysis of the obtained data with the existing data from three native populations from French Pyrenees, Croatia, and Israel. We have assessed the genetic differentiation between different native populations and determined the existence of two genetic clusters that differentiate the populations from the Balkan and Iberian Peninsulas. Furthermore, we analysed whether the recent bottleneck events influenced the genetic structure of the populations studied, and we found that all native populations experienced a recent bottleneck event, and that the population of Israel was the least affected. Nevertheless, the parameters of genetic diversity suggest that all analysed populations have retained a similar level of genetic diversity and that the Griffon vulture population from Serbia exhibits the highest value for private alleles. The results of this study suggest that the Griffon vulture populations of the Balkan Peninsula are genetically differentiated from the populations of the Iberian Peninsula, which is an important information for future reintroduction strategies.

Isolation and characterization of microsatellite loci in merlins (Falco columbarius) and cross-species amplification in gyrfalcons (F. rusticolus) and peregrine falcons (F. peregrinus).

Merlins, Falco columbarius, breed throughout temperate and high latitude habitats in Asia, Europe, and North America. Like peregrine falcons, F. peregrinus, merlins underwent population declines during the mid-to-late twentieth century, due to organochlorine-based contamination, and have subsequently recovered, at least in North American populations. To better understand levels of genetic diversity and population structuring in contemporary populations and to assess the impact of the twentieth century decline, we used genomic data archived in public databases and constructed genomic libraries to isolate and characterize a suite of 17 microsatellite markers for use in merlins. We also conducted cross-amplification experiments to determine the markers' utility in peregrine falcons and gyrfalcons, F. rusticolus. These markers provide a valuable addition to marker suites that can be used to determine individual identity and conduct genetic analyses on merlins and congeners.

Genetic Structure and Diversity of Two Populations of the Eastern Buzzard (Buteo japonicus japonicus and B. j. toyoshimai) in Japan.

The nominotypical subspecies of the Eastern buzzard (Buteo japonicus japonicus; BJJ) is a common raptor inhabiting East Asia and Japan. Another subspecies, B. j. toyoshimai (BJT), inhabits only the Bonin Islands of the Ogasawara Islands, where there are only an estimated 85 breeding pairs. Because of this low population size, this subspecies is classified as endangered (class IB) in Japan. The aims of the present study were to examine genetic differences between BJJ and BJT, determine the genetic structure of the Eastern Buzzard, and assess genetic diversity within each subspecies. We sequenced 1526 bp within the control region of the mtDNA of 10 BJJ individuals during the breeding season in four sites; similarly, we sequenced 23 BJJ individuals during winter in three sites. We detected 24 haplotypes among the 33 individuals. In a similar analysis performed with 12 BJT individuals, three haplotypes were detected. The phylogenetic analysis showed that BJJ and BJT have diverged into distinct clades, supporting the genetic differentiation between the subspecies. Network and mismatch distribution analyses indicated that BJJ may have experienced population expansion. In addition, comparisons with other raptors revealed a high degree of genetic diversity in the BJJ population. In contrast, the genetic diversity of the BJT population is lower than that in other raptors. Our results indicated that it is necessary to protect BJT to prevent the reduction in its genetic diversity.

Ancient DNA from a 2,500-year-old Caribbean fossil places an extinct bird (Caracara creightoni) in a phylogenetic context.

Since the late Pleistocene humans have caused the extinction of species across our planet. Placing these extinct species in the tree of life with genetic data is essential to understanding the ecological and evolutionary implications of these losses. While ancient DNA (aDNA) techniques have advanced rapidly in recent decades, aDNA from tropical species, especially birds, has been historically difficult to obtain, leaving a gap in our knowledge of the extinction processes that have influenced current distributions and biodiversity. Here we report the recovery of a nearly complete mitochondrial genome from a 2,500 year old (late Holocene) bone of an extinct species of bird, Caracara creightoni, recovered from the anoxic saltwater environment of a blue hole in the Bahamas. Our results suggest that this extinct species is sister (1.6% sequence divergence) to a clade containing the extant C. cheriway and C. plancus. Caracara creightoni shared a common ancestor with these extant species during the Pleistocene (1.2-0.4 MYA) and presumably survived on Cuba when the Bahamas was mostly underwater during Quaternary interglacial intervals (periods of high sea levels). Tropical blue holes have been collecting animals for thousands of years and will continue to improve our understanding of faunal extinctions and distributions. In particular, new aDNA techniques combined with radiocarbon dating from Holocene Bahamian fossils will allow us to place other extinct (species-level loss) and extirpated (population-level loss) vertebrate taxa in improved phylogenetic, evolutionary, biogeographic, and temporal contexts.

Telomere shortening rate predicts species life span.

Telomere shortening to a critical length can trigger aging and shorter life spans in mice and humans by a mechanism that involves induction of a persistent DNA damage response at chromosome ends and loss of cellular viability. However, whether telomere length is a universal determinant of species longevity is not known. To determine whether telomere shortening can be a single parameter to predict species longevities, here we measured in parallel the telomere length of a wide variety of species (birds and mammals) with very different life spans and body sizes, including mouse (Mus musculus), goat (Capra hircus), Audouin's gull (Larus audouinii), reindeer (Rangifer tarandus), griffon vulture (Gyps fulvus), bottlenose dolphin (Tursiops truncatus), American flamingo (Phoenicopterus ruber), and Sumatran elephant (Elephas maximus sumatranus). We found that the telomere shortening rate, but not the initial telomere length alone, is a powerful predictor of species life span. These results support the notion that critical telomere shortening and the consequent onset of telomeric DNA damage and cellular senescence are a general determinant of species life span.

Analysis of the Genetic Diversity and Structure of the Grey-Faced Buzzard (Butastur indicus) in Japan, Based on mtDNA.

The grey-faced buzzard (Butastur indicus) is a raptor that inhabits East Asia, including Japan. Because the number of individuals has decreased by 75% over the last 40 years, this species is classified as vulnerable (VU) in Japan. In the present study, wesought to reveal the genetic structure of the Japanese grey-faced buzzard population at several breeding sites, and to assess the levels of genetic diversity within the Japanese population. We sequenced 555 bp of the mitochondrial DNA of 96 individuals sampled during the breeding season at 18 sites, and 11 individuals sampled during the winter season at one site. In total, 21 variable sites were found in the control region, and we detected 26 haplotypes among the 107 individuals. Fukuoka represented the core breeding area for grey-faced buzzards, as half of all haplotypes were detected there. Four unique haplotypes were detected in the overwintering area. The results of the network and mismatch distribution analyses indicated that the grey-faced buzzard has not experienced a genetic bottleneck in the past, but did experience recent population expansion. In addition, comparisons with other raptors revealed rich genetic diversity in the grey-faced buzzard population. Our results indicate that conservation of both breeding and wintering areas is important for the protection of the grey-faced buzzard.

Low genetic diversity and shallow population structure in the endangered vulture, Gyps coprotheres.

Globally, vulture species are experiencing major population declines. The southern African Cape vulture (Gyps coprotheres) has undergone severe population collapse which has led to a listing of Endangered by the IUCN. Here, a comprehensive genetic survey of G. coprotheres is conducted using microsatellite markers. Analyses revealed an overall reduction in heterozygosity compared to other vulture species that occur in South Africa (Gypaetus barbatus, Necrosyrtes monachus, and Gyps africanus). Bayesian clustering analysis and principal coordinate analysis identified shallow, subtle population structuring across South Africa. This provides some support for regional natal philopatry in this species. Despite recent reductions in population size, a genetic bottleneck was not detected by the genetic data. The G. coprotheres, however, did show a significant deficiency of overall heterozygosity. This, coupled with the elevated levels of inbreeding and reduced effective population size, suggests that G. coprotheres is genetically depauperate. Given that genetic variation is considered a prerequisite for adaptation and population health, the low genetic diversity within G. coprotheres populations is of concern and has implications for the future management and conservation of this species.

Stage-Structured Evolutionary Demography: Linking Life Histories, Population Genetics, and Ecological Dynamics.

Demographic processes and ecological interactions are central to understanding evolution and vice versa. We present a novel framework that combines basic Mendelian genetics with the powerful demographic approach of matrix population models. The ecological components of the model may be stage classified or age classified, linear or nonlinear, time invariant or time varying, and deterministic or stochastic. Genotypes may affect, in fully pleiotropic fashion, any mixture of demographic traits (viability, fertility, development) at any points in the life cycle. The dynamics of the stage × genotype structure of the population are given by a nonlinear population projection matrix. We show how to construct this matrix and use it to derive sufficient conditions for a protected genetic polymorphism for the case of linear, time-independent demography. These conditions demonstrate that genotype-specific population growth rates (λ) do not determine the outcome of selection. Except in restrictive special cases, heterozygote superiority in λ is neither necessary nor sufficient for a genetic polymorphism. As a consequence, the population growth rate does not always increase, and populations can be driven to extinction due to evolutionary suicide. We demonstrate the construction and analysis of the model using data on a color polymorphism in the common buzzard (Buteo buteo). The model exhibits a stable genetic polymorphism and declining growth rate, consistent with field data and previous models.