Mammalogy Lecture 16 Conservation Genetics (with a side emphasis on Marine Mammals) Initial definition: Allele An allele is a viable DNA coding that occupies a given locus (position) on a chromosome (plural of locus is loci. A locus with more than one allele is said to be polymorphic. Genetic diversity is most commonly indexed by Heterozygosity. 1. Definition - Individual HI- average number of loci at which an individual is heterozygous. - Population HP - average heterozygosity of an individual in that population. Second definition is the value of interest in rare and endangered species because it is an index of the genetic diversity within that group. 2. Factors that determine levels of genetic diversity a) Genetic drift - random loss of low frequency alleles (will occur faster in small pops). b) Mutation stochastic creation of novel alleles c) Gene flow transfer of alleles between populations A. Genetic diversity is of fundamental interest in mammalogy because it is correlated to fitness. There are two primary ways in which genetic diversity and fitness are thought to be correlated: 1. Inbreeding and Inbreeding Depression Inbreeding is the non-random mating of close relatives, and a consequent elevated likelihood that unrelated organisms will carry alleles that are identical by descent (IBD). Inbreeding depression is a lowering in population fitness because of inbreeding depression. For example, the northern elephant seal (Mirounga angustirostris) had been reduced to ca. 15 individuals. Although the species has evidenced remarkable recovery, assays have revealed little or no genetic diversity, even at the hyper-variable major histocompatability complex. Interestingly, M. angustitostris populations show no signs of deleterious impacts, and thus show no signs of inbreeding depression (yet), even though clearly an example of extreme inbreeding. In contrast, the Northern Right Whale (Eubalaena glacialis) suffered similar population reductions, and has failed to recover regardless of 60 years of protection. A study by Schaeff et al suggests that this population is suffering from reduced fertility, fecundity, and juvenile survivorship. These parameters seem to be correlated to low diversity (compared to other right whale stocks).. 2. Loss of adaptive potential
Genetic diversity lends a species or population its capacity for coping with change in its environment: these changes could range from climatic fluctuation to the impact of novel diseases. A good review of the viability significance of diversity can be found in: Hansson & Westberg. 2002. Molecular Ecology, 11:2467. Download at Molecular Ecology B. MAMMALIAN GENETICS, SOME BROAD TOPICS There are a number of related areas of inquiry that are linked to the basic analysis of genetic diversity. Each of these is an enormously complex topic, and would merit its own class. Examples include: 1. Hybridization Example: Dusky dolphins (Lagenorhynchus obscurus) and southern right whale dolphin (Lissodelphis peronii) 2. Gene Flow and large scale population structure Example: Short beaked common dolphin (Delphinus delphis) 3. Social structure and mating systems Example: Humpback whales (Megaptera novaeangliae) 4. -Defining taxonomic units of management (species, evolutionarily significant units, distinct population segments, etc.) Example: Orcinus orca 5. Viability of Small Populations Baiji (Neophocaena phocaenoides asiaeorientalis) 5. Forensics Multiple cetaceans (e.g. Minkes whales, Balaenoptera bonaerensis) C. POPULATION ASSESSMENT Genetic diversity also has broad application in the study of marine mammals (and other mammalian taxa) in that populations that are small or cryptic can be studied using Non-invasive Genetic Sampling. The Polymerase Chain Reaction (PCR) can be used to amplify alleles from secondhand materials like bone, urine and hair, or even sloughed skin (Valsecchi et al 1998) or biopsy darting in the case of cetaceans. Any of the areas of inquiry that we just outlined can be researched using DNA amplified using this methodology. In addition, these methods have become extremely important in population census. Amplification of multiple alleles from an unknown sample allows for the derivation of a genotype, which can serve as a molecular tag in population minimum counts or Mark-recapture studies. Example: Gray seals (Halichoerus grypus) were censued by Reed et al using scat collected on rookery sites (1997). Numerous other species have been put forward as candidates.
D. MATING AND SOCIAL SYSTEMS 1) Assessing social systems and mating patterns in mammals has traditionally been the province of observational studies. These studies have been limited, however, by the fact that it s nearly impossible to observe all interactions between individuals in a structured mammalian society. Mating events- particularly those initiated by subordinate individuals- may not be recorded. 2) Without genetic analysis, the success of any given mating event is uncertain. 3) There are a number of ways in which genetic diversity can be used to elucidate relationships within and between populations. We will ignore some broad topics, and focus on two a. Exclusion Analysis For any nuclear DNA locus (a locus contained within the DNA in the cellular nucleus) a given organism will carry 2 alleles: one inherited from its mother, and one from its father. Thus, an organism that carries neither of the alleles displayed by a potential parent at a given locus cannot be an offspring of that potential parent. Note, however, that there are a limited number of alleles at a given locus in any population. Thusan organism may display a paternal allele at a locus without actually being an offspring of that parent. Thus, you need to look at a large number of loci to be statistically confident that you ve exclude all non-parents. (The total number will hinge on the overall diversity in the population) This approach is one method used in Bill Amos s Where have all the fathers gone paper, which we will cover in class. b. Kinship analysis The concept of relatedness was formalized by Hamilton (1964) as part of his discussion of inclusive fitness. Relatedness or r can be calculated directly through tracing pedigrees. However, Queller and Goodnight (1989) have theoretically demonstrated that r can also be indirectly derived from genetic data. When two organisms carry the same allele (same evolutionary origin for the allele) the alleles are said to be identical by descent (IBD) This leads us to the statistic known as relatedness ( r ). For any pair of organisms, r is calculated based on the overall frequency of alleles in the study population, and on the level of allele sharing between the two individuals. Relatedness is defined as twice the probability that random alleles from each of two individuals are IBD. Thus, an organism, compared against itself, would have an r value of 1.0. (For two organisms with the same genetic makeup, such as twins the probability of drawing two
such alleles (IBD) from the same locus will be 50%). R values generally vary according to the closeness of a pedigree relationship. Some classic values include: Self ( r = 1.0), Parent-offspring ( r = 0.5 ), Full sibs ( r = 0.5 ), Half-sibs (r = 0.25 ), Cousins ( r = 0.120 ) and half cousins ( r = 0.065 ). Unrelated individuals, on the average, will display an r value of 0.0. Calculating relatedness for pairs of organisms generally requires that a large number of loci be assayed. These calculations are used in the Amos et al paper that we will review for class. Calculations of average within-group relatedness are also possible. A high population-level r value can correlate to patterns of inbreeding- or, at the least close patterns of kinship. This type of analysis was used by Sherman in his research on alarm calls in Spermophilus beldingi. F. Where have all the Fathers Gone? a) Overview Halichoerus grypus- the grey seal Classically (based on observation) thought to display a polygynous mating system, in which dominant males controlled access to reproductive opportunities. However- in a prior study (using a technique called DNA fingerprinting) only 20% of pups on North Rona, Scotland could be assigned a father from the cadre of dominant males. b) Methods Samples collected via biopsy darting on North Rona and Isle of May, 1991-1997. Primary DNA marker was the microsatellite. Bi-parentally inherited, nuclear DNA, non-coding (not subject to natural selection) High rates of mutation (many alleles within populations) Ubiquitious and common in all organisms assayed Predominant DNA marker used in contemporary population studies c) Analysis Parentage assigned using both the Exclusion and Relatedness methods (discussed earlier in lecture) All genetic results scrutinized for errors, such as null alleles Significance of parentage assignments assessed using bootstrap methods. (Creation of pseudomales ) d) Results Only 49% (North Rona) and 29% (Isle of May) of pups could be assigned paternity. Strongly suggests that more than one reproductive strategy is at play. Possible alternative
hypotheses include: Noctural matings Matings in other colonies Unexpected levels of aquatic mating D. FORENSICS Wildlifeforensics,toquotetheU.S.FishandWildlifeService,involvesproceduresusedto examine, identify,andcompareevidenceusingawiderangeofscientificproceduresandinstruments,in theattempttolinksuspect,victimandcrimescenewithphysicalevidence.. DNAcanbeusedtolinkaforensicspecimentoawildpopulation. Thereareseveralprimarytools: 1) Privatealleles Researchersmaytrytoidentifyallelesfoundonlyinonepopulation. Ifthisalleleisfoundinaforensicsample,thesamplemostlikelyderivesfrom thatpopulation. Theuseofprivateallelesassumesthatallpossiblesourcepopulationshave beenassayedthoroughly ThePalumbipaperthatwasassignedlooksatmitochondrialDNAlocispecific todifferentstocksofminkewhales(balaenopterabonaerensis),andanalyzes samplegroupsinadditiontoindividualsamples. 2) AssignmentTests Basedonallelefrequencies,aforensicsamplewillhavedifferingassignment probabilitiesindifferentpopulations Example Ifenoughlociareassayed,theseassignmentprobabilitieswillallowfor identifyingsourcepopulationswithstatisticalconfidence Assumesthatallpossiblesourcepopulationshavebeenassayed Canbeconfoundedbymigrationandintrogression(geneticexchange betweenpopulations)