Ecobiology

Genetic structure of natural populations: Concept of natural population. Elements of demography and population growth models. The gene pool and genetic diversity. Allele and genotype frequencies. Measuring genetic diversity at different levels of resolution. The nuclear and extranuclear genome. Genetic systems with uniparental and biparental inheritance. Models of allele frequency evolution: Random mating and Hardy–Weinberg (H–W) equilibrium. Attainment of equilibrium for X-linked alleles. Use of the H–W model to estimate allele frequencies. Testing H–W equilibrium using the chi-square test. Models of evolution for linked polymorphic loci (linkage disequilibrium). Stochastic variation in allele frequencies: The genetic drift model and the effect of population size on allele frequencies. Loss of allelic diversity, founder effect, and bottleneck model. Unequal number of males and females. Concept of effective population size. Probability of fixation of a mutant allele. Coalescent theory. Mating among related individuals: Wright’s inbreeding model and decrease in heterozygosity. Inbreeding depression and its consequences for species conservation. Concepts of autozygosity and allozygosity; estimation of the inbreeding coefficient in natural and captive populations. Use of inbreeding to manage heterozygosity levels within populations. Genomic estimation of autozygosity through runs of homozygosity (ROH). Strategies for maintaining heterozygosity and genetic health. Pedigrees: Analysis of the inheritance of simple Mendelian traits for conservation in captivity. From traditional pedigrees to genomic reconstructions of relatedness. Use of molecular markers for reproductive management and the preservation of genetic lineages. Natural selection: Unit of selection. Qualitative and quantitative concepts of fitness. Classical models of selection at a single biallelic locus. Frequency-dependent selection. The fundamental theorem of natural selection. Units of selection and the concept of genomic fitness. Detection of genomic regions under selection through molecular tests, adaptive GWAS, and selection scans (iHS, XP-EHH). Neutral theory and balancing selection on a genomic scale. Functional analyses and annotation of variants associated with adaptation. Population subdivision: Gene flow among populations; continent–island and archipelago models. The Wahlund principle. Genetic distances among natural populations. Wright’s F-statistics. Cytoplasmic and sex-linked genes. Population subdivision and conservation. Hybridization and the concept of genetic introgression. The continent–island model and the concept of metapopulation. Genetic variability: Models of unidirectional and bidirectional mutation; the concept of neutral mutation; the infinite alleles model. Models of mutation and genomic diversity: neutral, selective, and structural mutations. Effects of deleterious mutations and mutation load. Genomic differentiation between natural and captive populations. Models of interaction among major evolutionary forces: Selection–mutation balance, selection–migration balance, selection–drift interaction, and combined selection–drift–migration models. Dynamic equilibria in complex evolutionary scenarios. Shifting-balance models in fragmented environments and under anthropogenic pressure. Molecular aspects: Genome architecture and annotation. Genomic sequencing and resequencing techniques. Genomic markers and bioinformatic methods for conservation genomics. Multi-omic analyses (genomics, epigenomics, transcriptomics) and their role in population resilience. Gene flow and genomic structure. Wright’s F-statistics and their genomic extensions (Fst, Dxy, IBD). PCA, ADMIXTURE, and fineSTRUCTURE analyses to infer migration, isolation, and introgression. Implications for management and conservation. Conservation: Goals of conservation genomics—what and how to conserve. The “sixth extinction” and the genomic challenges of biodiversity. IUCN categories and genomic data for extinction risk assessment. eDNA approaches for species monitoring. Ethics and management of genomic data. Management units in conservation: Resolving taxonomic ambiguities using genomic data. Species delimitation, phylogenomics, and identification of Evolutionarily Significant Units (ESUs). Analysis of introgression, hybridization, and speciation using reference genomes and modern phylogenetic methods (e.g., ABBA–BABA test). Management of the genomic heritage of wild and captive populations. Polyploidy (autopolyploidy, allopolyploidy, and haplo-diploidy). Use of genetic analyses for species delimitation. Altering biodiversity: Transgene escape, domestication, and introgressive hybridization. Invasive species and their genomic evolution. Application of genomic models for population management and reintroduction. Risks and opportunities of modern biotechnologies.

The Conservation Genetics course requires prior knowledge of: Genetics (as covered in a bachelor’s degree course) Basic concepts of probability and algebra Fundamental knowledge of chemistry

Conservation and the genetics of populations di F.W. Allendorf e G. Luikart, Blackwell publishing Frankham, Ballou & Briscoe, Introduction to Conservation Genetics (Cambridge University Press) Hohenlohe & Rajora (Eds.), Conservation Genomics (Springer, 2020) Funk, Lovich & Shaffer, Population Genomics: Wildlife (Springer, 2021) Notes from the professor

Attendance is recommended but not mandatory.

The exam aims to verify the level of knowledge of the topics. The evaluation is expressed in thirtieths (minimum grade 18/30, maximum mark 30/30 with honors).

The course consists of 48 hours of theoretical lectures (6 ECTS). Classes are held twice a week in the classroom, and lectures are delivered with the support of the blackboard.