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Recent studies on the genetics of adaptive coat-color variation in pocket mice are reviewed in the context of several on-going debates about the genetics of adaptation. Association mapping with candidate genes was used to identify mutations responsible for melanism in four different populations of . Here, I review four main results (i) a single gene, the melanocortin- l-receptor , appears to be responsible for most of the phenotypic variation in color in one population, the Pinacate site; (ii) four or fewer nucleotide changes at appear to be responsible for the difference in receptor function; (iii) studies of migration-selection balance suggest that the selection coefficient associated with the dark allele at the Pinacate site is large; and (iv) different (unknown) genes underlie the evolution of melanism on three other lava flows. These findings are discussed in light of the evolution of convergent phenotypes, the average size of phenotypic effects underlying adaptation, the evolution of dominance, and the distinction between adaptations caused by changes in gene dosage versus gene structure.

is an island endemic of the Seychelles. After its geographic isolation on these islands, evolved into a host specialist on the fruit of — a fruit often noxious and repulsive to . Specialization on required the evolution of a suite of adaptations, including resistance to and preference for some of the toxins found in this fruit. Several of these adaptive traits have been studied genetically. Here, I summarize what is known about the genetics of these traits and briefly describe the ecological and geographical context that shaped the evolution of these characters. The data from suggest that adaptations are not as genetically complex as historically thought, although almost all of the adaptations of involve several genes.

Genetic correlations can affect the course of phenotypic evolution. Although genetic correlations among traits are a common feature of quantitative genetic analyses, they have played a very minor role in recent linkage-map based analyses of the genetic architecture of quantitative traits. Here, we use our work on host-associated races in pea aphids to illustrate how quantitative trait locus (QTL) mapping can be used to test specific hypotheses about how genetic correlations may facilitate ecological specialization and speciation.

Until recently, parallel genotypic adaptation was considered unlikely because phenotypic differences were thought to be controlled by many genes. There is increasing evidence, however, that phenotypic variation sometimes has a simple genetic basis and that parallel adaptation at the genotypic level may be more frequent than previously believed. Here, we review evidence for parallel genotypic adaptation derived from a survey of the experimental evolution, phylogenetic, and quantitative genetic literature. The most convincing evidence of parallel genotypic adaptation comes from artificial selection experiments involving microbial populations. In some experiments, up to half of the nucleotide substitutions found in independent lineages under uniform selection are the same. Phylogenetic studies provide a means for studying parallel genotypic adaptation in non-experimental systems, but conclusive evidence may be difficult to obtain because homoplasy can arise for other reasons. Nonetheless, phylogenetic approaches have provided evidence of parallel genotypic adaptation across all taxonomic levels, not just microbes. Quantitative genetic approaches also suggest parallel genotypic evolution across both closely and distantly related taxa, but it is important to note that this approach cannot distinguish between parallel changes at homologous loci versus convergent changes at closely linked non-homologous loci. The finding that parallel genotypic adaptation appears to be frequent and occurs at all taxonomic levels has important implications for phylogenetic and evolutionary studies. With respect to phylogenetic analyses, parallel genotypic changes, if common, may result in faulty estimates of phylogenetic relationships. From an evolutionary perspective, the occurrence of parallel genotypic adaptation provides increasing support for determinism in evolution and may provide a partial explanation for how species with low levels of gene flow are held together.

Hybridization is increasingly recognized as a significant creative force in evolution. Interbreeding among species can lead to the creation of novel genotypes and morphologies that lead to adaptation. On the Hawaiian island of O’ahu, populations of two species of plants in the endemic genus grow at similar elevations in the northern Wai’anae Mountains. These two species represent extremes of the phenotypic distribution of leaf shape: the leaves of individuals are compound and highly dissected while leaves of are simple. Based primarily on leaf shape morphology, a putative hybrid population of located at Pu’u Kawiwi was identified. Individuals in this population exhibit a range of leaf shapes intermediate in varying degrees between the leaf shapes of the putative parental species. We analyzed individuals from pure populations of and the putative hybrids using 133 AFLP markers. Genetic analysis of these neutral markers provided support for the hybrid origin of this population. The correlation between genetic background and leaf morphology in the hybrids suggested that the genome of the parental species with simple leaves might have significantly contributed to the evolution of a novel, compound leaf morphology.

Insect resistance in soybean has been an objective in numerous breeding programs, but efforts to develop high yielding cultivars with insect resistance have been unsuccessful. Three Japanese plant introductions, PIs 171451, 227687 and 229358, have been the primary sources of insect resistance alleles, but a combination of quantitative inheritance of resistance and poor agronomic performance has hindered progress. Linkage drag caused by co-introgression of undesirable agronomic trait alleles linked to the resistance quantitative trait loci (QTLs) is a persistent problem. Molecular marker studies have helped to elucidate the numbers, effects and interactions of insect resistance QTLs in the Japanese PIs, and markers are now being used in breeding programs to facilitate transfer of resistance alleles while minimizing linkage drag. Molecular markers also make it possible to evaluate QTLs independently and together in different genetic backgrounds, and in combination with transgenes from .

The finding that even the smallest of plant genomes has incurred multiple genome-wide chromatin duplication events, some of which may predate the origins of the angiosperms and therefore shape all of flowering plant biology, adds new importance to the molecular analysis of polyploidization/diploidization cycles and their phenotypic consequences. Early clues as to the possible phenotypic consequences of polyploidy derive from recent QTL mapping efforts in a number of diverse crop plants of recent and well-defined polyploid origins. A small sampling examples of the role(s) of polyploidy in conferring crop adaptation from human needs include examples of (1) dosage effects of multiple alleles in autopolyploids, and (2) ‘intergenomic heterosis’ conferring novel traits or transgressive levels of existing traits, associated with merging divergent genomes in a common allopolyploid nucleus. A particularly interesting manifestation of #2 is the evolution of complementary alleles at corresponding (‘homoeologous’) loci in divergent polyploid taxa derived from a common ancestor. Burgeoning genomic data for both botanical models and major crops offer new avenues for investigation of the molecular and phenotypic consequences of polyploidy, promising new insights into the role of this important process in the evolution of botanical diversity.

Plant domestication ranks as one of the most important developments in human history, giving human populations the potential to harness unprecedented quantities of the earth’s resources. But domestication has also played a more subtle historical role as the foundation of the modern study of evolution and adaptation. Until recently, however, researchers interested in domestication were limited to studying phenotypic changes or the genetics of simple Mendelian traits, when often the characters of most interest — fruit size, yield, height, flowering time, etc. — are quantitative in nature. The goals of this paper are to review some of the recent work on the quantitative genetics of plant domestication, identify some of the common trends found in this literature, and offer some novel interpretations of the data that is currently available.

Ecologists study the rules that govern processes influencing the distribution and abundance of organisms, particularly with respect to the interactions of organisms with their biotic and abiotic environments. Over the past decades, using a combination of sophisticated mathematical models and rigorous experiments, ecologists have made considerable progress in understanding the complex web of interactions that constitute an ecosystem. The field of genomics runs on a path parallel to ecology. Like ecology, genomicists seek to understand how each gene in the genome interacts with every other gene and how each gene interacts with multiple, environmental factors. Gene networks connect genes as complex as the ‘webs’ that connect the species in an ecosystem. In fact, genes exist in an ecosystem we call the genome. The genome as ecosystem is more than a metaphor — it serves as the conceptual foundation for an interdisciplinary approach to the study of complex systems characteristic of both genomics and ecology. Through the infusion of genomics into ecology and ecology into genomics both fields will gain fresh insight into the outstanding major questions of their disciplines.