Publications

2012
Tong W, Hoekstra HE. Mus spicilegus. Current Biology 2012;20(2):858-859.Abstract

What or who is Mus spicilegus? Mus spicilegus, aka ‘the mound-building mouse’, is a rather nondescript, brown mouse that looks just like its close relative, the commensal house mouse (Mus musculus). In fact, they look so much like house mice that the first individuals described in 1840 from a garden in Odessa probably were house mice. Its epithet ‘spicilegus’ is derived from the Latin, spica meaning a spike of grain, and legere, to collect, which makes sense, since these mice do in fact gather grains.

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Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE. Double digest RADseq: An inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS One 2012;7:e37135.Abstract

The ability to efficiently and accurately determine genotypes is a keystone technology in modern genetics, crucial to studies ranging from clinical diagnostics, to genotype-phenotype association, to reconstruction of ancestry and the detection of selection. To date, high capacity, low cost genotyping has been largely achieved via "SNP chip" microarray-based platforms which require substantial prior knowledge of both genome sequence and variability, and once designed are suitable only for those targeted variable nucleotide sites. This method introduces substantial ascertainment bias and inherently precludes detection of rare or population-specific variants, a major source of information for both population history and genotype-phenotype association. Recent developments in reduced-representation genome sequencing experiments on massively parallel sequencers (commonly referred to as RAD-tag or RADseq) have brought direct sequencing to the problem of population genotyping, but increased cost and procedural and analytical complexity have limited their widespread adoption. Here, we describe a complete laboratory protocol, including a custom combinatorial indexing method, and accompanying software tools to facilitate genotyping across large numbers (hundreds or more) of individuals for a range of markers (hundreds to hundreds of thousands). Our method requires no prior genomic knowledge and achieves per-site and per-individual costs below that of current SNP chip technology, while requiring similar hands-on time investment, comparable amounts of input DNA, and downstream analysis times on the order of hours. Finally, we provide empirical results from the application of this method to both genotyping in a laboratory cross and in wild populations. Because of its flexibility, this modified RADseq approach promises to be applicable to a diversity of biological questions in a wide range of organisms.

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Domingues VS, Poh YP, Peterson BK, Pennings PS, Jensen JD, Hoekstra HE. Evidence of adaptation from ancestral variation in young populations of beach mice. Evolution 2012;66:3209-23.Abstract

To understand how organisms adapt to novel habitats, which involves both demographic and selective events, we require knowledge of the evolutionary history of populations and also selected alleles. There are still few cases in which the precise mutations (and hence, defined alleles) that contribute to adaptive change have been identified in nature; one exception is the genetic basis of camouflaging pigmentation of oldfield mice (Peromyscus polionotus) that have colonized the sandy dunes of Florida's Gulf Coast. To quantify the genomic impact of colonization as well as the signature of selection, we resequenced 5000 1.5-kb noncoding loci as well as a 160-kb genomic region surrounding the melanocortin-1 receptor (Mc1r), a gene that contributes to pigmentation differences, in beach and mainland populations. Using a genome-wide phylogenetic approach, we recovered a single monophyletic group comprised of beach mice, consistent with a single colonization event of the Gulf Coast. We also found evidence of a severe founder event, estimated to have occurred less than 3000 years ago. In this demographic context, we show that all beach subspecies share a single derived light Mc1r allele, which was likely selected from standing genetic variation that originated in the mainland. Surprisingly, we were unable to identify a clear signature of selection in the Mc1r region, despite independent evidence that this locus contributes to adaptive coloration. Nonetheless, these data allow us to reconstruct and compare the evolutionary history of populations and alleles to better understand how adaptive evolution, following the colonization of a novel habitat, proceeds in nature.

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Hoekstra HE. Genomics: Stickleback is the catch of the day. Nature 2012;484:46-7. PDF
Kronforst MR, Barsh GS, Kopp A, Mallet J, Monteiro A, Mullen SP, Protas M, Rosenblum EB, Schneider CJ, Hoekstra HE. Unraveling the thread of nature's tapestry: The genetics of diversity and convergence in animal pigmentation. Pigment Cell & Melanoma Research 2012;25:411-33.Abstract

Animals display incredibly diverse color patterns yet little is known about the underlying genetic basis of these phenotypes. However, emerging results are reshaping our view of how the process of phenotypic evolution occurs. Here, we outline recent research from three particularly active areas of investigation: melanin pigmentation in Drosophila, wing patterning in butterflies, and pigment variation in lizards. For each system, we highlight (i) the function and evolution of color variation, (ii) various approaches that have been used to explore the genetic basis of pigment variation, and (iii) conclusions regarding the genetic basis of convergent evolution which have emerged from comparative analyses. Results from these studies indicate that natural variation in pigmentation is a particularly powerful tool to examine the molecular basis of evolution, especially with regard to convergent or parallel evolution. Comparison of these systems also reveals that the molecular basis of convergent evolution is heterogeneous, sometimes involving conserved mechanisms and sometimes not. In the near future, additional work in other emerging systems will substantially expand the scope of available comparisons.

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2011
Goncalves G, Hoekstra HE, de Freitas. TRO. Striking coat colour variation in tuco-tucos (Rodentia: Ctenomyidae): A role for the melanocortin-1 receptor?. Biological Journal of the Linnean Society 2011;105:665-80.Abstract

South American tuco-tucos (Ctenomys) are characterized by striking variation in coat colour. A range of phenotypes, from pale blonde to dark black, is observed across species, with some of them matching their local substrate colour. Moreover, phenotypic convergence is evident in some taxa that occupy similar habitats. The present study investigated a role for the melanocortin-1 receptor (Mc1r) in determining coat-colour variation in a wide range of Ctenomys species. We sequenced 1250 bp, including the entire Mc1r coding region and a portion of the adjacent 5 and 3untranslated regions, in 21 species. In total, 20 amino acid replacements were identified in Mc1r. However, our findings suggest that these changes have not contributed to coat-colour differences among tuco-tucos because no amino acid replacement was associated with pigmentation phenotype in a simple way. Levels of Mc1r expression were measured in skin samples from dorsal, flank, and ventral body regions in pale, brown, and melanic individuals. We did not observe any significant difference in transcript abundance among phenotypes, although we identified a significant reduction of expression level from the dorsal to ventral region in both pale and brown morphs but not in the completely melanic form. Thus, a role for Mc1r regulation in tuco-tucos colour pattern cannot be completely ruled out, although further functional assays are needed. Finally, selection analysis suggests that Mc1r, in a majority of lineages, has evolved under purifying selection but with relaxation in functional constraint in some regions, especially in the fourth transmembrane domain. In summary, the results obtained in the present study suggest that this trait may have a complex basis, and that other pigmentation genes are involved in generating the dramatic diversity in coat-colour phenotypes observed among Ctenomys species. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105, 665–680.

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Manceau M, Domingues VS, Mallarino R, Hoekstra HE. The developmental role of Agouti in color pattern evolution. Science 2011;331:1062-5.Abstract

Animal color patterns can affect fitness in the wild; however, little is known about the mechanisms that control their formation and subsequent evolution. We took advantage of two locally camouflaged populations of Peromyscus mice to show that the negative regulator of adult pigmentation, Agouti, also plays a key developmental role in color pattern evolution. Genetic and functional analyses showed that ventral-specific embryonic expression of Agouti establishes a prepattern by delaying the terminal differentiation of ventral melanocytes. Moreover, a skin-specific increase in both the level and spatial domain of Agouti expression prevents melanocyte maturation in a regionalized manner, resulting in a novel and adaptive color pattern. Thus, natural selection favors late-acting, tissue-specific changes in embryonic Agouti expression to produce large changes in adult color pattern.

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Barrett RD, Hoekstra HE. Molecular spandrels: Tests of adaptation at the genetic level. Nature Reviews Genetics 2011;12:767-80.Abstract

Although much progress has been made in identifying the genes (and, in rare cases, mutations) that contribute to phenotypic variation, less is known about the effects that these genes have on fitness. Nonetheless, genes are commonly labelled as 'adaptive' if an allele has been shown to affect a phenotype with known or suspected functional importance or if patterns of nucleotide variation at the locus are consistent with positive selection. In these cases, the 'adaptive' designation may be premature and may lead to incorrect conclusions about the relationships between gene function and fitness. Experiments to test targets and agents of natural selection within a genomic context are necessary for identifying the adaptive consequences of individual alleles.

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2010
Robinson GE, Banks JA, Padilla DK, Burggren WW, Cohen CS, Delwiche CF, Funk V, Hoekstra HE, Jarvis ED, Johnson L, Martindale MQ, del Rio MC, Medina M, Salt DE, Sinha S, Specht C, Strange K, Strassmann JE, Swalla BJ, Tomanek L. Empowering 21st century biology. BioScience 2010;60:923-30.Abstract

Several lists of grand challenges in biology have been published recently, highlighting the strong need to answer fundamental questions about how life evolves and is governed, and how to apply this knowledge to solve the pressing problems of our times. To succeed in addressing the challenges of 21st century biology, scientists need to generate, have access to, interpret, and archive more information than ever before. But for many important questions in biology, progress is stymied by a lack of essential tools. Discovering and developing necessary tools requires new technologies, applications of existing technologies, software, model organisms, and social structures. Such new social structures will promote tool building, tool sharing, research collaboration, and interdisciplinary training. Here we identify examples of the some of the most important needs for addressing critical questions in biology and making important advances in the near future.

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Hoekstra HE. Evolutionary Biology: The Next 150 years. In: Bell MA, Futuyma DA, Eanes WF, Levinton JS Evolution Since Darwin: The First 150 Years. Sunderland, MA: Sinauer Press; 2010 PDF
Hoekstra HE. From Darwin to DNA: The genetic basis of color adaptation. In: Losos JB In the Light of Evolution: Essays from the Laboratory and Field. Greenwood Village, CO: Roberts and Co. Publishers; 2010 PDF
Hoekstra HE. In search of the elusive behavior gene. In: Grant P, Grant R Search for the Causes of Evolution: From Field Observations to Mechanisms. Princeton, NJ: Princeton University Press; 2010
Fisher HS, Hoekstra HE. Competition drives cooperation among closely related sperm of deer mice. Nature 2010;463:801-3.Abstract

Among the extraordinary adaptations driven by sperm competition is the cooperative behaviour of spermatozoa. By forming cooperative groups, sperm can increase their swimming velocity and thereby gain an advantage in intermale sperm competition. Accordingly, selection should favour cooperation of the most closely related sperm to maximize fitness. Here we show that sperm of deer mice (genus Peromyscus) form motile aggregations, then we use this system to test predictions of sperm cooperation. We find that sperm aggregate more often with conspecific than heterospecific sperm, suggesting that individual sperm can discriminate on the basis of genetic relatedness. Next, we provide evidence that the cooperative behaviour of closely related sperm is driven by sperm competition. In a monogamous species lacking sperm competition, Peromyscus polionotus, sperm indiscriminately group with unrelated conspecific sperm. In contrast, in the highly promiscuous deer mouse, Peromyscus maniculatus, sperm are significantly more likely to aggregate with those obtained from the same male than with sperm from an unrelated conspecific donor. Even when we test sperm from sibling males, we continue to see preferential aggregations of related sperm in P. maniculatus. These results suggest that sperm from promiscuous deer mice discriminate among relatives and thereby cooperate with the most closely related sperm, an adaptation likely to have been driven by sperm competition.

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Manceau M, Domingues VS, Linnen CR, Rosenblum EB, Hoekstra HE. Convergence in pigmentation at multiple levels: mutations, genes and function. Philosophical Transactions of the Royal Society 2010;365:2439-50.Abstract

Convergence--the independent evolution of the same trait by two or more taxa--has long been of interest to evolutionary biologists, but only recently has the molecular basis of phenotypic convergence been identified. Here, we highlight studies of rapid evolution of cryptic coloration in vertebrates to demonstrate that phenotypic convergence can occur at multiple levels: mutations, genes and gene function. We first show that different genes can be responsible for convergent phenotypes even among closely related populations, for example, in the pale beach mice inhabiting Florida's Gulf and Atlantic coasts. By contrast, the exact same mutation can create similar phenotypes in distantly related species such as mice and mammoths. Next, we show that different mutations in the same gene need not be functionally equivalent to produce similar phenotypes. For example, separate mutations produce divergent protein function but convergent pale coloration in two lizard species. Similarly, mutations that alter the expression of a gene in different ways can, nevertheless, result in similar phenotypes, as demonstrated by sister species of deer mice. Together these studies underscore the importance of identifying not only the genes, but also the precise mutations and their effects on protein function, that contribute to adaptation and highlight how convergence can occur at different genetic levels.

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Weber JN, Peters MB, Tsyusko OV, Linnen CR, Hagen C, Schable NA, Tuberville TD, McKee AM, Lance SL, Jones KL, Fisher HS, Dewey MJ, Hoekstra HE, Glenn TC. Five hundred microsatellite loci for Peromyscus. Conservation Genetics 2010;11:1243-46.Abstract

Mice of the genus Peromyscus, including several endangered subspecies, occur throughout North America and have been important models for conservation research. We describe 526 primer pairs that amplify microsatellite DNA loci for P. maniculatus bairdii, 467 of which also amplify in P. polionotus subgriseus. For 12 of these loci, we report diversity data from a natural population. These markers will be an important resource for future genomic studies of Peromyscus evolution and mammalian conservation.

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Chuong EB, Tong W, Hoekstra HE. Maternal-fetal conflict: Rapidly evolving proteins in the rodent placenta. Molecular Biology and Evolution 2010;27:1221-5.Abstract

Conflicting evolutionary interests between mother and offspring are hypothesized to drive an evolutionary arms race during mammalian pregnancy, and thus, positive selection may cause the rapid divergence of placental proteins that affect maternal or fetal fitness. We investigated the genomic consequences of placental expression in rodents and report that a substantial proportion (20.5%) of genes specifically expressed in the mature placenta are rapidly evolving. Moreover, we found that most rapidly evolving genes belong to just three pregnancy-related gene families: placental cathepsins, prolactins, and placental carcinoembryonic antigens. We then sequenced the most rapidly evolving gene, trophoblast-specific protein alpha (Tpbpa), in nine different Mus species/subspecies and found evidence of positive selection within the Mus lineage, with an excess of nonsynonymous changes clustering near a functionally important interaction site. Together, these results suggest that placental proteins, which mediate interactions between mother and offspring, often may be the targets of evolutionary conflict.

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Linnen CR, Hoekstra HE. Measuring natural selection on genotypes and phenotypes in the wild. Cold Spring Harbor Symposia on Quantitative Biology 2010;74:155-68.Abstract

A complete understanding of the role of natural selection in driving evolutionary change requires accurate estimates of the strength of selection acting in the wild. Accordingly, several approaches using a variety of data-including patterns of DNA variability, spatial and temporal changes in allele frequencies, and fitness estimates-have been developed to identify and quantify selection on both genotypes and phenotypes. Here, we review these approaches, drawing on both recent and classic examples to illustrate their utility and limitations. We then argue that by combining estimates of selection at multiple levels-from individual mutations to phenotypes-and at multiple timescales-from ecological to evolutionary-with experiments that demonstrate why traits are under selection, we can gain a much more complete picture of the adaptive process.

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Rosenblum EB, Rompler H, Schoneberg T, Hoekstra HE. Molecular and functional basis of phenotypic convergence in white lizards at White Sands. PNAS 2010;107:2113-7.Abstract

There are many striking examples of phenotypic convergence in nature, in some cases associated with changes in the same genes. But even mutations in the same gene may have different biochemical properties and thus different evolutionary consequences. Here we dissect the molecular mechanism of convergent evolution in three lizard species with blanched coloration on the gypsum dunes of White Sands, New Mexico. These White Sands forms have rapidly evolved cryptic coloration in the last few thousand years, presumably to avoid predation. We use cell-based assays to demonstrate that independent mutations in the same gene underlie the convergent blanched phenotypes in two of the three species. Although the same gene contributes to light phenotypes in these White Sands populations, the specific molecular mechanisms leading to reduced melanin production are different. In one case, mutations affect receptor signaling and in the other, the ability of the receptor to integrate into the melanocyte membrane. These functional differences have important ramifications at the organismal level. Derived alleles in the two species show opposite dominance patterns, which in turn affect their visibility to selection and the spatial distribution of alleles across habitats. Our results demonstrate that even when the same gene is responsible for phenotypic convergence, differences in molecular mechanism can have dramatic consequences on trait expression and ultimately the adaptive trajectory.

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Turner LM, Young AR, Rompler H, Schoneberg T, Phelps SM, Hoekstra HE. Monogamy evolves through multiple mechanisms: Evidence from V1aR in deer mice. Molecular Biology and Evolution 2010;27:1269-78.Abstract

Genetic variation in Avpr1a, the locus encoding the arginine vasopressin receptor 1A (V1aR), has been implicated in pair-bonding behavior in voles (genus Microtus) and humans, raising the possibility that this gene may contribute commonly to mating-system variation in mammals. In voles, differential expression of V1aR in the brain is associated with male partner-preference behavior in a comparison of a monogamous (Microtus ochrogaster) and promiscuous (Microtus montanus) species. This expression difference is correlated, in turn, with a difference in length of a 5' regulatory microsatellite in Avpr1a. Here, we use a combination of comparative sequencing of coding and regulatory regions, analysis of neural expression patterns, and signaling assays to test for differences in V1aR expression and function among eight species of deer mice (genus Peromyscus). Despite well-documented variation in Peromyscus social behavior, we find no association between mating system and length variation in the microsatellite locus linked to V1aR expression in voles. Further, there are no consistent differences in V1aR expression pattern between monogamous and promiscuous species in regions of the brain known to influence mating behavior. We do find statistical evidence for positive selection on the V1aR coding sequence including several derived amino acid substitutions in a monogamous Peromyscus lineage, yet these substitutions have no measurable effect on V1aR signaling activity. Together, these results suggest that mating-system variation in rodents is mediated by multiple genetic mechanisms.

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Hull JM, Mindell DP, Talbot SL, Kay EH, Hoekstra HE, Ernest HB. Population structure and plumage polymorphism: The intraspecific evolutionary relationships of a polymorphic raptor, Buteo jamaicensis harlani. BMC Evolutionary Biology 2010;10:224.Abstract

BACKGROUND: Phenotypic and molecular genetic data often provide conflicting patterns of intraspecific relationships confounding phylogenetic inference, particularly among birds where a variety of environmental factors may influence plumage characters. Among diurnal raptors, the taxonomic relationship of Buteo jamaicensis harlani to other B. jamaicensis subspecies has been long debated because of the polytypic nature of the plumage characteristics used in subspecies or species designations. RESULTS: To address the evolutionary relationships within this group, we used data from 17 nuclear microsatellite loci, 430 base pairs of the mitochondrial control region, and 829 base pairs of the melanocortin 1 receptor (Mc1r) to investigate molecular genetic differentiation among three B. jamaicensis subspecies (B. j. borealis, B. j. calurus, B. j. harlani). Bayesian clustering analyses of nuclear microsatellite loci showed no significant differences between B. j. harlani and B. j. borealis. Differences observed between B. j. harlani and B. j. borealis in mitochondrial and microsatellite data were equivalent to those found between morphologically similar subspecies, B. j. borealis and B. j. calurus, and estimates of migration rates among all three subspecies were high. No consistent differences were observed in Mc1r data between B. j. harlani and other B. jamaicensis subspecies or between light and dark color morphs within B. j. calurus, suggesting that Mc1r does not play a significant role in B. jamaicensis melanism. CONCLUSIONS: These data suggest recent interbreeding and gene flow between B. j. harlani and the other B. jamaicensis subspecies examined, providing no support for the historical designation of B. j. harlani as a distinct species.

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