Human activity is causing climates to change more rapidly than at any time in the last 10,000 years. If populations of organisms are unable to effectively respond to changing environments, they will be at risk of extinction. In plants, two of the most important mechanisms of response to environmental change are phenotypic plasticity, where the same genotype expresses different phenotypes in different environments, and adaptation, which requires changes in allele frequency in populations as exposed individuals show variable survival and reproduction. Although most researchers accept the importance of both of these mechanisms, they are most commonly considered in isolation in models of response and persistence to climate change. Here, I use the model species Arabidopsis thaliana to investigate the interaction of plasticity and selection in fitness and phenology response to simulated climate warming, the effect of artificial selection on variation for plastic response and cross-generational effects of environmentally induced variation in flowering time. I also study the effects of varying rates of environmental fluctuation on evolvability on populations of self-replicating computer programs using the artificial life platform Avida. I find that a small increase in ambient temperature, in line with predictions for the next few decades, is able to elicit significant plastic responses and that these responses have the potential to alter population genetic structure and affect future evolution. I also find that selection on flowering time can reduce variation for plastic response and that non-genetic effects on flowering time can significantly alter germination in the next generation. Lastly, I find that rapidly changing environments in the long term can select for more evolvable populations and genotypes. These results highlight the importance of considering plasticity and evolution together if we are going to make accurate predictions of climate change response.

Os padrões de covariância genética entre caracteres, expressos pela matriz de covariância aditiva G, desempenham um papel importante na evolução de morfologias complexas, visto que esta matriz influencia a direção e magnitude da resposta à seleção em uma população. Assumindo-se a estabilidade da matriz G ao longo do tempo, pode-se testar explicitamente hipóteses acerca da influência de processos evolutivos sobre a diversificação. Espera-se que esta matriz influencie os padrões expressos por sua equivalente fenotípica P, devido a contingências funcionais e ontogenéticas na relação entre genótipo e fenótipo, que levam à estruturação de modularidade nesta relação, de modo a otimizar a evolvabilidade. No presente trabalho, investiguei a estrutura da covariância genética no crânio e mandíbula de uma população do roedor sigmodontíneo Calomys expulsus, com o objetivo de estimar a similaridade entre covariâncias fenotípicas e genéticas; também avaliei a influência de padrões de modularidade sobre ambos os níveis de organização da variação morfológica. As matrizes P e G que obtive para o crânio e para a mandíbula se mostraram bastante similares no que diz respeito à sua estrutura de covariação e se relacionam parcialmente às hipótese de modularidade estabelecidas. Os resultados que obtive aqui são bastante similares àqueles obtidos para os mamíferos como um todo, portanto suportando a hipótese de estabilidade no padrão de covariâncias genéticas e fenotípicas na evolução do grupo. / Patterns of genetic covariance between characters (represented by the additive covariance matrix G) play an important role in the evolution of morphological complexes, since they influence the direction and norm of the response to selection in a population. Therefore, the assumption that G-matrices are stable through evolutionary timescales allows evolutionary biologists to infer the influence of evolutionary processes that operate over biological diversification. These matrices are also expected to influence the patterns expressed in their phenotypic counterparts (P-matrix), because of the imposition of multiple developmental and functional contingencies over the genotype/phenotype map, that leads to its modular organization in order to increase evolvability. Here, I have investigated patterns of genetic covariance structure in the skull and mandible of a population of the vesper mouse Calomys expulsus in order to estimate the level of similarity between additive and phenotypic covariances; I have also evaluated the influence of expected patterns of modularity over both levels of morphological variation. For either skull and mandible, I have obtained P- and G-matrices that are strongly similar in their structure; these matrices also support the modularity hypotheses for developmental and functional constrains, akin to the overall results obtained for mammals, thus supporting the hypothesis of stability in genetic and phenotypic covariance structure in mammalian evolution.

Os Xenarthra representam um clado de mamíferos eutérios. Pouco se sabe sobre a evolução morfológica craniana do grupo. Esta tese iniciou os estudos relativos a esta questão com base na genética quantitativa, na morfometria e na sistemática, e teve por objetivos específicos: 1) avaliar empiricamente se as matrizes de variância e covariância fenotípica (matriz-P) dos diversos gêneros de Xenarthra estudados podem ser utilizadas como substitutas das respectivas matrizes de variância e covariância genética aditiva (matriz-G), uma vez que não existem matrizes-G estimadas para os Xenarthra, e também se elas podem ser utilizadas em estudos macroevolutivos; 2) testar se a diversificação morfológica craniana no grupo ocorreu somente através de deriva genética; e 3) compreender como a relação entre os caracteres morfológicos (módulos) e a magnitude geral de integração podem influir na evolução morfológica craniana. Além destes objetivos focados na evolução do grupo, também foi escopo desta tese inferir o hábito alimentar de taxa fósseis do final do Pleistoceno/início do Holoceno para melhorar o conhecimento sobre a ecologia de alguns grupos fósseis. O banco de dados utilizado foi composto por medidas lineares de aproximadamente 1150 espécimes adultos, representando 12 dos 14 gêneros atuais e sete dos diversos gêneros extintos de Xenarthra. Com base nesses dados, matrizes-P de variância e covariância e de correlação foram estimadas para cada gênero. Essas matrizes foram posteriormente comparadas par a par para avaliar a semelhança na estrutura das diferentes matrizes. Também a partir dessas matrizes, foram obtidas as variâncias entre e intra populações para testar se a diversificação morfológica ocorreu de acordo com a expectativa teórica de diversificação sob a ação exclusiva de deriva genética. As mesmas matrizes-P foram comparadas a diferentes matrizes teóricas de hipóteses de modularidade craniana. As matrizes teóricas expressaram a relação entre os caracteres com base no desenvolvimento e/ou desempenho de função compartilhado pelas partes do crânio. Para cada matriz-P de correlação calculou-se a magnitude geral de integração. Além disto, a dieta dos grupos extintos foi inferida através de análises de funções discriminantes a partir da relação entre forma e função dos animais atuais. Os resultados obtidos indicam que as matrizes-P dos diversos gêneros são similares entre si, o que sugere que matrizes-P podem ser utilizadas tanto como substitutas das matrizes-G quanto no contexto macroevolutivo. Os resultados obtidos refutaram a hipótese nula da diversificação morfológica craniana ocorrendo somente por deriva genética, ao menos nos níveis mais inclusivos da filogenia dos Xenarthra. Consequentemente, a seleção natural provavelmente atuou neste processo de diversificação. Os resultados também sugeriram que o crânio desse grupo está organizado em módulos, sendo os módulos mais conspícuos os relacionados à face. Além disso, foi detectada grande variação na magnitude geral de integração entre gêneros. A variação no padrão modular, mas principalmente na magnitude geral de integração, faz com que os gêneros apresentem diferenças nas possíveis capacidades de responder de forma alinhada às pressões seletivas. Por último, as análises morfofuncionais indicaram elevada diversidade de hábitos alimentares entre os Xenarthra extintos / Xenarthra are an eutherian mammal clade and little is known about their cranial morphological evolution. This thesis has initiated studies related to this topic and, based on quantitative genetics, morphometrics and systematics, aimed to: 1) empirically assess if the phenotypic variance and covariance matrices (P-matrix) of several genera can be used as surrogates for their respective additive genetic variance and covariance matrices (G-matrix), since G-matrices for Xenarthra are not available, and also if P-matrices can be used in macroevolutionary studies; 2) test whether the skull morphological diversification within the group occurred only through genetic drift; and 3) understand how the relationship between the traits (modules) and overall magnitude of integration may influence cranial morphological evolution. Besides these objectives focused on the evolution of the group, it was also within the scope of this thesis to infer the feeding habits of late Pleistocene/early Holocene fossil taxa to better understand the ecology of some fossil groups. The database used consist of linear measurements of approximately 1150 adult specimens, representing 12 of the 14 extant genera and seven of the several extinct genera of Xenarthra. The data gathered were used to estimate variance/covariance and correlation P-matrices for every genus. These matrices were compared between pairs of genera to evaluate the matrices\' structural similarities. Based on these matrices, within and between population variances were obtained and it was tested whether morphological diversification was in accordance to the theoretical expectation of diversification under genetic drift alone. The same matrices were compared to theoretical matrices expressing modularity hypotheses. These theoretical matrices represent the relationship among traits in reference to the shared development and/or function of different skull\'s anatomical regions (modules). For every correlation P-matrix the overall magnitude of integration was calculated. Moreover, the extinct groups\' diet was inferred through discriminant function analysis relying on the relationship between form and function of extant animals. Results indicate that P-matrices from several genera were structurally similar. This suggests that P-matrices can be used as surrogates of their G-matrices and in the macroevolutionary context. Results refuted the null hypothesis of cranial morphological diversification occurring only due to genetic drift, at least in more inclusive levels of Xenarthran phylogeny. Consequently, natural selection probably acted on this diversification process. The results also suggested that the Xenarthran skull is organized in modules, and the most conspicuous modules are in the face region. A large variation in the overall magnitude of integration among genera was detected. The variation in the modular pattern, but especially in the overall magnitude of integration, allows genera to differ in their potential capacity to respond aligned with selective pressures. Finally, morphofunctional analyses indicate a high diversity of feeding habits among extinct Xenarthra

Sclerotinia sclerotiorum causes white mold and severe yield losses of pea. 484 accessions from the Pisum core collection were screened for resistance using a mini-agar plug technique. 49, 41, and 13 accessions were identified with partial resistance based on lesion expansion inhibition (LEI), nodal transmission inhibition (NTI), and both traits combined, respectively. A genetic linkage map based on F2 DNA from the cross, Lifter/PI240515, was developed with 78 markers on 9 linkage groups (LG) spanning 734 cM. Two quantitative trait loci (QTL) were identified based on phenotypic data from F2:3 and F3:4 families. A single QTL on LGIII explained 34.1% of the phenotypic variation for LEI, while a second QTL on LGII(b) explained 2.5% of the phenotypic variation for NTI. This is the first report of QTL for S. sclerotiorum resistance in pea which will be useful in development of resistant pea varieties.

Objectives: This article presents estimates of narrow-sense heritability and bivariate genetic correlation for 14 tooth crown morphological variants scored on permanent premolars, first molars, and second molars. The objective is to inform data collection and analytical practices in dental biodistance and to provide insights on the development of molar crowns as integrated structures. Materials and Methods: African American dental casts from the Menegaz-Bock collection were recorded for the Arizona State University Dental Anthropology System. Estimates of narrow-sense heritability and genetic correlation were generated using SOLAR v.8.1.1, which included assessment of age, sex, and birth year as covariates. Both continuous scale and dichotomized estimates are provided. Results: Heritability estimates were nonsignificant for the majority of variables; however, for variables yielding significant estimates, values were moderate to high in magnitude and comparable to previous studies. Comparing left and right-side heritability estimates suggests directional asymmetry in the expression of environmental variance, something not seen in anterior tooth traits. Genetic correlations were moderate among antimeres and metameres and low for different traits scored on the same tooth crown. Although several negative correlations were noted, few reached statistical significance. Results affirm some of the current data cleaning and analytical practices in dental biodistance, but others are called into question. These include the pooling of males and females and combining left and right-side data into a single dataset. Conclusions: In comparison to anterior tooth crown traits, postcanine heritabilities were more often non-significant; however, those traits with significant heritability also tended to produce higher estimates. Genetic correlations were unremarkable, in part, because they were underpowered. However, M1 results may provide insight into the complex relationship between genes, environment, and development in determining ultimate crown form.

Presented in the session “Global Leadership in Dental Anthropological Research: A symposium in honor of G. Richard Scott." The Arizona State University Dental Anthropology System (ASUDAS) or Turner-Scott System revolutionized the use of dental morphology for reconstructing evolutionary processes in past populations. By providing globally-recognized data collection standards, the system has elevated the status of dental morphology to an indispensable line of evidence in biodistance research. The efficacy of morphological data rests upon foundational assumptions about underlying tooth crown biology; namely, that the traits are highly heritable and minimally sexually dimorphic. Scott and colleagues have also outlined best practices for the application of dental morphology to biodistance studies, most aimed at curtailing genetic redundancy in multivariate datasets (see Turner et al., 1991). Quantitative genetic approaches have the potential to validate these assumptions. Here, we present the first robust estimates of heritability and genetic correlation for ASUDAS crown characters. Data were collected from a casted sample of South Carolina Gullah individuals (N=469) and analyzed using maximum likelihood variance components analysis. While several postcanine traits yielded heritability estimates of 0.0, mean estimates across statistically significant models were moderate to high (anterior=0.34; postcanine=0.75). Results of covariate screening support the long-held assumption that ASUDAS traits are sexually monomorphic, with the exception of canine marginal/cingular ridge characters and certain molar accessory cusps. Additionally, patterns of heritability and genetic correlation groundtruth most prescribed biodistance practices: dichotomizing trait expression, collapsing bi-antimeric datasets, and prioritizing traits scored on key (sensu Scott et al., 2018) teeth. Notwithstanding, our results suggest that certain assumptions require reconsideration and underscore the importance of continued validation work in additional populations.

Objectives: This article presents estimates of narrow-sense heritability and bivariate genetic correlation for a series of morphological crown variants of the anterior dentition. These results provide insight into the value of dental phenotypes as evolutionary proxies, as well as the development of tooth crowns as integrated or modular structures. Materials and Methods: African American dental casts from the Menegaz-Bock collection were scored for a standard set of dental morphological variables using the Arizona State Dental Anthropology System. Estimates of narrow-sense heritability and genetic correlations were generated using SOLAR v. 8.1.1, controlling for the covariates of age, sex, and birth year. Analyses were run using ordinal/continuous scale variables that were then dichotomized at various breakpoints, consistent with standard practices in dental anthropology. Results: Heritability estimates were low to moderate for most traits, and lower in magnitude than those reported for odontometric data from the same study sample. Only winging, canine shoveling, and canine double shoveling returned narrow-sense heritabilities that did not differ significantly from zero. Genetic correlations were high among antimeres and metameres and low for different traits scored on the same tooth crown. These results affirm standard data cleaning practices in dental biodistance. Double shoveling was atypical in returning strong negative correlations with other traits, shoveling in particular. Conclusions: Additive genetic variation contributes to dental morphological variation, although the estimates are uniformly lower than those observed for odontometrics. Patterns of genetic correlation affirm most standard practices in dental biodistance. Patterns of negative pleiotropy involving lingual and labial crown features suggest a genetic architecture and developmental complex that differentially constrain morphological variation of distinct surfaces of the same tooth crown. These patterns warrant greater consideration and cross-population validation.

Objectives: This article provides estimates of narrow-sense heritability and genetic pleiotropy for mesiodistal tooth dimensions for a sample of 20th century African American individuals. Results inform biological distance analysis and offer insights into patterns of integration in the human dentition. Materials and Methods: Maximum mesiodistal crown dimensions were measured using Hillson-FitzGerald calipers on 469 stone dental casts from the Menegaz-Bock Collection. Narrow-sense heritability estimates and genetic and phenotypic correlations were estimated using SOLAR 8.1.1 with covariate screening for age, sex, age*sex interaction, and birth year. Results: Heritability estimates were moderate (∼0.10 – 0.90; h2 mean = 0.51) for most measured variables with sex as the only significant covariate. Patterns of genetic correlation indicate strong integration across tooth classes, except molars. Comparison of these results to previously published work suggests lower overall heritability relative to other human populations and much stronger genetic integration across tooth classes than obtained from nonhuman primate genetic pleiotropy estimates. Conclusions: These results suggest that the high heritabilities previously published may reflect overestimates inherent in previous study designs; as such the standard estimate of 0.55 used in biodistance analyses may not be appropriate. For the Gullah, isolation and endogamy coupled with elevated levels of physiological and economic stress may suppress narrow-sense heritability estimates. Pleiotropy analyses suggest a more highly integrated dentition in humans than in other mammals.

Several studies examining the genetics of adaptation have identified single alleles, of large phenotypic e ect, contributing to divergence between populations. This empirical finding is consistent with predictions made by the geometric model of adaptation, where a small number of alleles of large e ect and many alleles of small e ect are fixed as the population adapts. However, these examples of single genes of large e ect may represent a biased sample of the alleles of adaptation with polygenic allele shifts having a greater contribution than currently understood. Increasing power to detect smaller e ect variants, due to falling sequencing costs and improved statistical methods, has made the contribution of small allele frequency shifts at many loci, or polygenic adaptation, more apparent. In contrast to models predicting single genes of large e ect with large allele frequency changes, polygenic adaptation allows for small allele frequency changes across many alleles of small e ect to contribute to phenotypic change. Using artificial selection, I demonstrate the alignment of genetic e ects contributing to wing shape variation within a developmental pathway but a lack of replication of these same genetic e ects in other wild-caught populations. Secondly, using advanced intercross QTL mapping between altitudinally diverged populations, I demonstrate a polygenic basis for wing shape and size variation. Finally, using comparative developmental biology I investigate how change to cell size and number in the wing may contribute to divergence between high and low altitude populations. Together, this work provides evidence for many alleles of small e ect rather than alleles of large e ect contributing to adaptive divergence of wing shape and size and provides context for identified alleles through replication in other populations and comparative developmental biology. / Thesis / Doctor of Philosophy (PhD)

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