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Population Genetics and a Study of Speciation Using Next-Generation

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Population Genetics and a Study of Speciation Using Next-Generation PRIMER Population Genetics and a Study of Speciation Using Next-Generation Sequencing: An Educational Primer for Use with “Patterns of Transcriptome Divergence in the Male Accessory Gland of Two Closely Related Species of Field Crickets” Patricia J. Wittkopp1 Department of Ecology and Evolutionary Biology, and Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 SUMMARY Understanding evidence for the genetic basis of reproductive isolation is imperative for supporting students’ understand- ing of mechanisms of speciation in courses such as Genetics and Evolutionary Biology. An article by Andrés et al. in the February 2013 issue of GENETICS illustrates how advances in DNA sequencing are accelerating studies of population genetics in species with limited genetic and genomic resources. Andrés et al. use the latest sequencing technologies to systematically identify and characterize sites in the DNA that vary within, and have diverged between, species to explore speciation in crickets. This primer, coupled with that article, will help instructors introduce and reinforce important concepts in genetics and evolution while simultaneously introducing modern methodology in the undergraduate classroom. Related article in GENETICS: Andrés, J. A., E. L. Larson, S. M. Bogdanowicz, and R. G. Harrison, 2013 Patterns of transcriptome divergence in the male accessory gland of two closely related species of field crickets. Genetics 193: 501–513. Background Study system: Gryllus firmus and Gryllus pennsylvanicus ome of the fastest evolving proteins in insect genomes The senior author of the Andrés et al. (2013) study, Richard Sare transferred from males to females in their seminal G. Harrison, began investigating speciation in crickets in fluid (Findlay and Swanson 2010). Amino acid sequence di- the mid-1970s using protein electrophoresis techniques. vergence in these proteins can contribute to speciation by Since then, he and his colleagues have examined properties creating incompatibilities between sperm and eggs when of cricket mitochondrial DNA (Harrison et al. 1985; Rand two distantly related genotypes mate. Based on these obser- and Harrison 1986, 1989), studied hybrid zones where vations, it has been proposed that divergent seminal fluid different species of crickets meet (Willett et al. 1997; Ross proteins might contribute to the early stages of speciation and Harrison 2002; Maroja et al. 2009), and investigated in closely related species of field crickets Andrés et al. whether the bacterial parasite Wolbachia (Mandel et al. (2006). Andrés et al. (2013) explore this hypothesis by char- 2001; Maroja et al. 2008) and divergent reproductive pro- acterizing DNA sequence variation in the coding regions of teins (Andrés et al. 2006, 2008) contribute to speciation proteins expressed in accessory glands where seminal pro- in crickets. Most recently, their studies have focused on teins are found. G. firmus and G. pennsylvanicus, a pair of closely related spe- cies of field cricket found in the eastern region of North America. G. firmus is found on sandy soils along the east coast, and G. pennsylvanicus is found on firmer inland loam Copyright © 2013 by the Genetics Society of America soils. Hybrids resulting from mating between these two spe- doi: 10.1534/genetics.112.148171 1Address for correspondence: 1061 Natural Science Bldg., 830 N. University Ave., cies are found along the eastern edge of the Appalachian University of Michigan, Ann Arbor, MI 48109-1048. E-mail: [email protected] Mountains (Figure 1). When G. pennsylvanicus females mate Genetics, Vol. 193, 671–675 March 2013 671 that they would see greater sequence divergence between G. firmus and G. pennsylvanicus in genes encoding seminal fluid proteins than in genes encoding other proteins expressed inthesametissue(theaccessorygland). Sequencing targeted regions of the genome using the transcriptome Virtually all cells within an organism contain the same set of genes, but different subsets of genes are expressed (i.e., transcribed) in each cell type. These differences in gene ex- pression make one cell type different from another. Because Andrés et al. (2013) are interested in the evolution of genes that can disrupt interactions between sperm and eggs, they examined genes expressed in the male accessory gland. That is, they sequenced the accessory gland transcriptome, the subset of sequences in the genome that are transcribed to “ Gryllus pennsylvanicus produce RNA in accessory glands. Note that the word tran- Figure 1 Collection sites (black circles) for and ” Gryllus firmus are shown along with the approximate location of the scriptome has also been used by other authors to refer to the hybrid zone (dotted line) between these two species. Reproduced with collection of RNAs produced from all transcribed sequences. permission from Willett et al. (1997). To isolate DNA sequences coding for proteins found in the accessory gland, Andrés et al. (2013) dissected acces- fi with G. firmus males, viable and fertile offspring are pro- sory glands from G. rmus and G. pennsylvanicus males, duced; however, when G. pennsylvanicus males mate with extracted RNA from each tissue sample, and used reverse G. firmus females, no hybrid offspring are observed (Harrison transcriptase to synthesize DNA complementary to the RNA “ ” 1985). (termed cDNA ). Consequently, the cDNA samples contained only DNA sequences from genes that were transcribed into Using sequence variation to identify genes contributing RNA. But sequences from each expressed gene are not repre- to speciation sented equally in cDNA: some genes are expressed at higher G. firmus and G. pennsylvanicus are thought to have become levels (i.e., transcribed more times into RNA molecules) than different species via allopatric speciation (Willett et al. others, and these differences in RNA abundance are reflected 1997). This is a mode of speciation in which populations in the population of cDNA. If the researchers had directly of the same species are geographically isolated from each sequenced this cDNA, they would have recovered sequences other and thereby evolve genetic differences over time that from highly expressed genes many times before observing reduce their ability to produce fully fertile offspring when sequences from genes with lower expression. their ranges overlap. When the isolation initially occurs, the To make the representation of all expressed genes more two populations share alleles throughout the genome. Over similar in the cDNA sample, a technique called “normaliza- generations, mutation, drift, and selection cause genetic dif- tion” was used. After using a DNA polymerase to turn the ferences to accumulate between the two populations. Most single-stranded cDNA molecules synthesized by reverse tran- of these genetic differences will have no effect on morphol- scriptase into double-stranded DNA, heat is used to separate ogy, physiology, or the ability of individuals from one pop- the complementary strands. As the sample is cooled, comple- ulation to interbreed with individuals from the other mentary DNA sequences find each other again and anneal, re- population—but some will affect one or more of these traits. creating fragments of double-stranded DNA. Transcripts that When hybridization between two species occurs and are the most abundant in the sample are most likely to find fertile offspring are produced, alleles are moved between a complementary sequence quickly and form double-stranded species. This mixing of genetic information, or gene flow, cDNA first. By treating the sample with an enzyme that spe- causes introgression that reduces the genetic divergence cifically degrades double-stranded DNA, sequences from the between species. Regions of the genome contributing to high-abundance transcripts are selectively eliminated. This reproductive isolation, however, cannot be exchanged since creates a cDNA sample in which transcribed sequences from reproductively incompatible individuals cannot mate. This all expressed genes are present at similar frequencies. leads to the “mosaic of different evolutionary histories” across the genome described by the authors. Gene flow Unpacking the Difficult Bits through a hybrid zone accentuates regions of the genome Combining results from multiple contributing to reproductive isolation by decreasing differ- sequencing technologies ences in DNA sequence elsewhere in the genome. Based on the idea that divergent seminal fluid proteins have played an During the past decade, advances in DNA sequencing have important role in speciation, Andrés et al. (2013) hypothesized revolutionized the way biological research is performed. 672 P. J. Wittkopp Table 1 Samples and sequencing used by Andrés et al. (2013). Biological sample(s) Sequencing technology Purpose Accessory gland RNA from 10 G. firmus males Sanger Assemble transcriptome Accessory gland RNA from a single G. firmus male 454/Roche Assemble transcriptome Accessory gland RNA from 15 G. firmus males Illumina Find SNPs; quantify allele frequencies Accessory gland RNA from 15 G. pennsylvanicus males Illumina Find SNPs; quantify allele frequencies 16 genomic DNA samples from individual G. firmus Sanger Verify allele frequencies; infer gene genealogies 16 genomic DNA samples from individual G. pennsylvanicus Sanger Verify allele frequencies; infer gene genealogies Instead of sequencing only one DNA fragment at a time, of RNA from 15 G. firmus or 15 G. pennsylvanicus male methods are now available to sequence billions
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