8.2: Emotional Development and Socioemotional Learning in Middle Childhood
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Learning Objectives
By the end of this section, you will be able to:
- Discuss the developing social skills of children in middle childhood
- Describe developmental achievements in emotional regulation
- Describe developmental achievements in social cognition and moral reasoning
Chandra’s parents need to meet with her teacher again. This time, it’s about an emotional outburst that happened during class. When she was supposed to be writing the names of state capitals on a test, she became frustrated.  When her pencils and water bottle hit the floor, she let out a scream and stormed off to the corner of the room to calm down.
 But lately she’s been having strong feelings, sometimes so strong that she becomes easily frustrated and overwhelmed. And even though her stepmom says it was Chandra’s responsibility to prepare for the test, she doesn’t feel the same way. Inside, Chandra feels frustrated that her teacher, her school, and the world seem to be making unrealistic demands.
Developing Socially in Middle Childhood
Middle childhood is often called the school-aged years because children in the United States commonly attend elementary grades one through six between the ages of six and twelve years. A typical week of school is about thirty-three hours, and on average, children attend 180 days per year (National Center for Education Statistics [NCES], 2017). Elementary school affords many new social opportunities but also makes emotional demands.  There’s not much chance to take a break or stay away from others. These new social experiences affect the way they manage their emotions and develop social skills. In this section, you’ll learn about emotional development in middle childhood, along with coping strategies of self-regulation and the social cognition skills that grow during this age.
Emotional Intelligence and Regulation
As you’ve learned 6.1 Social and Emotional Development in Early Childhood, emotional intelligence is the ability to monitor and manage your own emotions and respond to the emotions of others (Salovey & Mayer, 1990). Children with higher emotional intelligence have better attention skills, school engagement, and social relationships (Pauletto et al., 2021).
Emotional regulation, or self-regulation , describes the way we respond to events happening in our environment and manage our reactions. For example, Rafi is getting ready to give a short presentation in school. He recognizes that the funny feeling in his stomach mean he is nervous, and he thinks to himself, “I know I can do this!” and “I’m sure that other kids are feeling nervous too!” To distract himself from his nerves, he also takes a few deep breaths to calm himself and thinks about what he will do after school with friends. Rafi is showing that he recognizes his emotions (emotional intelligence) and has skills for managing his response (emotional regulation) to a meaningful challenge in his life.
Useful skills that allow children to have increased emotional intelligence and regulation continue to develop during middle childhood. For example, metacognitive skill, the awareness of their individual thought processes, allows them to understand their emotions and develop strategies to help them control their reactions. These skills continue to grow in early and middle childhood (Gascoine et al., 2017). However, regulating emotions is complex and requires a lot of skill and practice (Pennequin et al., 2020). So, during middle childhood, children may still struggle to handle their emotions, particularly when they are stressed or feeling overwhelmed by expectations (Moltrecht et al., 2021). For example, although a nine- or ten-year-old may still whine, sulk, or seek their family’s help when they are tired and stressed, more often they are practicing how to calm down and breathe deeply (Figure 8.4).
Researcher Michael Lewis (2022) discussed the development of secondary emotions that first appear during early childhood. These include other-evaluative emotion s like jealousy and compassion, which depend on the development of self-awareness, and self-conscious emotions like pride, guilt, and embarrassment, which are based on our understanding of social rules and conventions (Camras, 2022). In the elementary years, children may begin to feel these emotions more deeply as their cognitive capacity to understand and comprehend social situations increases. For instance, parents can often remedy a five-year-old’s jealousy of a younger sibling by giving attention, cuddles, or a distraction. By age nine years, a child who feels jealousy because their best friend is playing with another may experience a persistent, intense emotion sustained over hours, days, or weeks. They may reflect on this jealousy even when they are in other environments, so distraction does not help. Parents continue to play an important role in helping children process and regulate their emotions in middle childhood (De Raeymaecker & Dhar, 2022).
Increasingly, children begin to consider how they express their emotions. As they reflect, ruminate, and communicate their emotions in a more mature way, they also begin to self-regulate more independently (Lane & Smith, 2021).
Emotional Awareness
A valuable element of self-regulation is emotional awareness , being able to name and identify emotions (Lane & Smith, 2021). Emotional awareness depends on our ability to understand internal sensations and connect them to an emotion based on the current situation as well as past experiences (Satpute & Lindquist, 2019). Being upset, irritable, or grumpy without knowing why you feel that way can be a bewildering and overwhelming experience, but naming and identifying emotions allows children to better understand their internal state and decide how best to manage their emotional responses. Emotional awareness and coping techniques develop substantially in childhood, but our ability to understand our emotions and cope with our emotions continues to develop and influences our well-being across the lifespan (De France & Hollenstein, 2019).
Coping Techniques
Children develop several coping strategies as a set of techniques for overcoming stress, a major step in achieving self-regulation. Stressors that affect any social group regardless of culture or gender are transcultural stressors (Kim et al., 2018), such as family economic stress and lack of family cohesion. People of color or the children of immigrants may experience culture-specific stressors, such as learning a new language or facing discrimination. These may require unique coping strategies such as developing a new cultural identity that combines elements of multiple cultural groups (Nguyen & Benet–Martínez, 2013). In middle childhood, children’s coping techniques are shaped by their caregivers and culture.
Coping strategies vary in effectiveness, and some are healthier than others (Table 8.1). The most commonly used coping strategies in middle childhood are problem-solving , distraction , and support seeking (Skinner & Zimmer–Gembeck, 2016). Often, optimal coping strategies differ based on the situation. As children develop improved emotional regulation and coping strategies, they learn to use a varied approach and may improve in their ability to problem solve and take action to cope effectively (Eschenbeck et al., 2018). For example, if a child had a recent conflict with a close friend when they couldn’t agree on what to play at recess, they may benefit from a combination of strategies. They might start by telling their teacher they are upset (support seeking), then ask for advice on what to do (information seeking), and then return to their friend with a proposed compromise (problem-solving).
| Coping Strategy | Description |
|---|---|
| Problem-solving | Identifying and using a solution to a problem to resolve the issue |
| Behavioral and cognitive distraction | Shifting attention away from stress-causing situation |
| Support seeking | Relying on adults or peers for help with coping |
| Escape/avoidance | Leaving the stressful environment or avoiding the problem |
| Cognitive reframing | Trying to think of the problem differently such as focusing on the positive |
| Self-reliance | Accepting responsibility or otherwise regulating emotions alone |
| Opposition | Blaming others for problems |
| Rumination | Thinking about the problem over and over |
Negative coping techniques escalate a situation and make it worse, or they are maladaptive and become harmful in the long term. Positive coping techniques are adaptive, helpful, and healthful strategies that will de-escalate a situation. For example, when a sibling takes something without asking, a positive coping technique may be to breathe deeply to calm down, then calmly ask them to give it back or ask a parent for assistance. A child struggling to complete a task in school may try again, try another strategy, ask for help, or take a temporary break. Using positive coping techniques is a lifelong skill and one that helps us develop other positive skills such as communication, conflict resolution, and problem-solving. In middle childhood, children are likely to shift from heavily using their caregivers for coping (support seeking) to using their own improved emotional regulation skills (e.g., self-reliance) and other internal coping techniques (Perry et al., 2020; Skinner & Zimmer–Gembeck, 2007).
Emotional Display Rules
A culture- and context-specific social rule for outwardly showing emotion is known as an emotional display rule . The understanding of display rules emerges during middle childhood as children begin to understand that the emotion a person is experiencing is not necessarily the one they are expressing. By the age of seven years, children can use the emotional expressions of others to determine what these others want and/or believe (Wu & Schulz, 2019). They are also learning to control their own emotional expressions in certain situations. For instance, when children are playing with friends outside, the rules may allow them to squeal, giggle, and exhibit high-energy excitement. At school, however, the rules may require them to be calm, quiet, and attentive. Suppressing strong emotions such as sadness, embarrassment, and fear takes intense focus and self-regulation (Savina, 2021). Children in middle childhood often need to practice these skills to adhere to social display rules in a given setting.
Display rules vary by gender and culture. For example, in some cultures, there are different expectations for the emotions expressed by boys and girls (Chaplin & Aldao, 2013). This can lead to gender differences in emotional expression as children enter middle childhood, such as girls expressing more sadness and boys expressing more anger. In other words, these differences are not seen in infancy, meaning they are likely learned from the cultural environment (Chaplin & Aldao, 2013). Gender differences in emotional expressions are also much more present when children are with peers than when they are with their caregivers (Chaplin & Aldao, 2013). It also shows us that children are still seeking support from their caregivers and may feel more comfortable showing a wider range of emotions when they are in their home environment with parents who provide emotion coaching. For example, a child who has secure attachment with caregivers that use emotion coaching may contain their sadness over a bad test grade until they get home from school.
Social Cognition
Children often base their coping strategies on their level of social cognition , the ability to understand and think about what others are thinking and to engage in prosocial behaviors. Social cognition emerges during childhood and continues to develop in adolescence. Infants and younger children begin to understand that others have intentions, wants, and beliefs that may vary from their own. Skills necessary for social cognition include the ability to do the following:
- identify the emotions of others through facial expressions and body posture
- understand the mental states and perspectives of others, composed of theory of mind and perspective-taking skills
- show empathy, the ability to relate to the feelings of others (Arango–Tobón et al., 2023)
Theoretical Perspectives on Social Cognition
Many theories have considered the way social cognition develops during childhood. One of the most popular is the stage theory of cognitive development , which states that during infancy and early childhood, children are very egocentric and unable to see the world from someone else’s perspective (Piaget, 1954). As they move into middle childhood, Piaget believed, children get better at thinking about how others think and why they behave as they do. In other words, children become less egocentric and more capable of considering the perspective of others.
Another element of social cognition is theory of mind . Recall that when children acquire theory of mind, they can consider how the thoughts, feelings, and intentions of others influence their behaviors and differ from their own individual perspective. In other words, having theory of mind allows a child to explain why people do the things that they do. In particular, the development of empathy and of imitation , observing and repeating the behavior of others, supports theory of mind. Theory of mind and perspective-taking skills support better peer relationships and improve children’s ability to use reasoning to understand others (Lecce & Devine, 2022). As children develop improved social cognitive skills, such as perspective taking, and improve their use of emotional regulation and positive coping techniques, they are better able to have healthy relationships with friends and family (Figure 8.5). Theory of mind continues to develop into middle childhood and is shaped by our social experiences just as it shapes our social interactions and understanding (Devine & Lecce, 2021).
Interpreting and Responding to Social Situations
Imagine you are in second grade and on the playground during recess. You see your best friend walking toward you. You wave and say hello, but they walk right past without making eye contact or acknowledging you. Researchers have used scenarios such as this to understand social cognition in children (Dodge et al., 2015). Specifically, scenarios like this help us understand more about how children interpret social situations and the behaviors of others. Children with a negative bias, or hostile attributional error, are more likely to interpret the friend’s behavior as an aggressive or purposefully unkind act (Dodge et al., 2015; Gardner et al., 2017). They may judge their best friend as committing an offense and in response would aggressively confront them, blame them, raise their voice, push, or say mean things. This hostile reaction increases a child’s risk of unhealthy relationships and conflicts with peers. However, teaching children to have kinder attributions or use perspective taking may help them respond better in similar situations (Bengtsson & Arvidsson, 2011).
Finally, children who have developed positive coping strategies and emotional regulation skills tend to react with better emotional competence and have healthier relationships (Raine et al., 2023). For example, they are more likely to use cognitive reappraisal to cope and consider other factors, such as whether their friend wasn’t feeling well, was busy or late, or had just received bad news. When asked for their response, these children are more likely to reach out to their friend in a calm, friendly way to make sure everything is all right. Of course, a child’s personality and temperament will also play a role in how children respond to social situations. For example, a quieter, shyer child may be less likely to reach out, whereas an exuberant, outgoing child may be more likely to feel comfortable taking the first step.
It Depends: Should Adults Intervene with Shy Children?
When caregivers notice that their child is shy, they may worry that it will make it difficult for their child to interact with other children and adults. So, should adults intervene? Do children who are shy need help to develop social skills with peers?
Western parents tend to react to their children’s shyness with disappointment and worry, which is not generally the case among Chinese or other Asian parents. Xu and Krieg (2014) 2 point out distinct differences between being anxious and shy, which may be part of their temperament, and learning to display shyness based on the cultural values or context, which may be an adaptive strategy. In their empirical study with fourth and fifth graders, some children of Asian immigrants were adaptively shy and others anxious shy. The outcomes for these children were different in terms of their reported feelings of loneliness, even though their solitary behavior was not that different. Anxious-shy children were also more often socially excluded and experienced more anxious behavior. The less acculturated into U.S. values Asian American parents were, the more they accepted and encouraged regulated shyness in their children.
As this study and many others indicate, shyness might be considered a temperamental condition in the United States, and one that is not valued or encouraged. Even if a child has a shy temperament, it is not necessarily a concern. Many children are shy with adults, but it is less common for children to be shy around children their own age. However, if a child is so shy that they don’t interact with their peers, it may be helpful to intervene. Caregivers can schedule play dates and encourage their child to take part in extracurricular activities. They can also give their child helpful hints for ways to interact with other children and then offer positive feedback when they see their child do so. In addition, many schools offer social skills support groups for children. If the shyness persists and seems to be causing the child a great deal of social anxiety, a therapist can help.
Resilience and Positive Coping
Positive coping strategies support resilience, which further aids children in coping with stress and trauma (Twum–Antwi et al., 2020). The ability to successfully adapt and respond to stressful events is resilience (Masten, 2019). So, how do we help develop resilience in children?
Positive attachment relationships between a child and at least one caregiver is one critical factor supporting this goal (Thompson et al., 2021). As discussed in 4.4 Social Development in Infants and Toddlers, when attachment security is present, caregivers are responsive and nurturing and focus on the child’s protection, emotional regulation, and cognitive stimulation (Berástegui & Pitillas, 2023). Children with a history of a positive child-caregiver relationship are able to express their emotions and have strong emotional regulation (Kural & Kovacs, 2021), both key aspects of positive coping and resilience.
Healthy social relationships and adaptive responses to social interactions are also predictors of resilience. Strong social cognitive skills are essential for developing healthy relationships with others, which in turn matters for making friends, bonding with teachers at school, and spending enjoyable time with family. In middle childhood, children also show improved use of empathy and altruism to facilitate prosocial behaviors (Glen et al., 2020). Cognitively, empathy requires understanding the perspective and emotional states of others. Affectively, we need to vicariously feel what others are feeling and mirror their emotion. The awareness of what another might be feeling and the motivation to do something for them is sympathy . For instance, saying you are sorry to a friend who lost their toy requires sympathy. But feeling sad along with the friend requires empathy. Empathy and sympathy help to facilitate relationships because they let us take others’ perspectives and treat them as we would like to be treated, respond to their emotional needs, and strive to play fair.
A type of prosocial behavior called altruism involves acts of kindness even when at a cost. Altruism requires empathy and is associated with theory of mind (Rose et al., 2024), but it takes those cognitive and emotional components and translates them into action. Children in middle childhood display altruism when they help others in a way that is a cost to themselves. Examples include stopping to help someone, inviting a lonely child to play, sharing, taking turns, and teaching others. Children benefit from acting altruistically because it can strengthen friendships and family relationships, make them feel like they belong and are included, and help them to develop new skills and abilities (Butovskaya et al., 2020). It is not selfish if despite these benefits it still comes at a cost, such as stopping a game, giving up a toy, or choosing to wait for others.
Children who develop strong prosocial skills are more likely to trust others, to feel confident in themselves, and to feel comfortable working with others. Caregivers can take several steps to promote the development of prosocial skills throughout childhood. In addition to forming the high-quality caregiver-child relationship, they can apply a technique called emotion coaching (Gus et al., 2015). This consists of recognizing a child’s emotion, responding to the child with empathy, validating their feelings, and helping them label their emotions (Lisitsa, 2013). Positive coping behaviors, social cognition, and healthy relationships are all adaptive strategies that can promote resilience in middle childhood and across the lifespan.
Moral Reasoning
Moral development is the process by which children learn about the difference between what is right and wrong. Jean Piaget was interested in what children believe about moral issues (Carpendale, 2000), in other words, their moral reasoning rather than moral behaviors. He felt that a child’s moral reasoning was very closely tied to their cognitive development, and that this reasoning could not become more sophisticated until children were cognitively mature enough to consider the perspectives of others.
Piaget used short stories, or vignettes, to learn more about how children think about what is right or wrong. For example, the stories might entail one child breaking a cup while sneaking a cookie while another child breaks multiple cups by accident. After telling the story, Piaget asked children whether they thought the child was right or wrong and why. Based on his research, Piaget (1932) described stages of moral reasoning. In the first stage, in children under age five years, they have not yet learned morals. In the second stage, demonstrated by children between the ages of five and ten years, their morality is forming, and children follow rules and authority without any flexibility (Helwig & Turiel, 2002). Thus, they might believe the child who broke the cup was wrong regardless of if it was an accident or not. In Piaget’s third stage of moral development, starting around age eleven years, children become more adult in their moral perspective. They are more likely to be flexible in their thinking, considering the moral situation and the perspectives of others. They are now capable of understanding why rules might be beneficial to everyone and begin to value cooperation and mutual respect (Helwig & Turiel, 2002). They also understand that rules are flexible and are quick to tell you if they think a rule is unfair. For example, they may say a child who broke multiple cups should not be punished if it was an accident.
Lawrence Kohlberg developed Piaget’s theory of moral reasoning into a more comprehensive theory (Carpendale, 2000). He also presented vignettes to children of different ages to see how they reasoned whether someone’s actions were right or wrong. Consider the following, one of the most famous scenarios Kohlberg used in his research:
In Europe, a woman was near death from a very bad disease, a special kind of cancer. There was one drug that the doctors thought might save her. It was a form of radium that a druggist in the same town had recently discovered. The drug was expensive to make, but the druggist was charging ten times what the drug cost him to make. He paid $200 for the radium and charged $2,000 for a small dose of the drug. The sick woman’s husband, Heinz, went to everyone he knew to borrow the money, but he could only get together $1,000, which is half of what it cost. He told the druggist that his wife was dying and asked him to sell it cheaper or let him pay later. But the druggist said, “No, I discovered the drug, and I’m going to make money from it.” So, Heinz got desperate and broke into the man’s store to steal the drug for his wife. (Kohlberg & Kramer, 1969)
When Kohlberg asked children to tell him whether they believed Heinz was right or wrong, he was primarily interested in why the children gave the answer they gave. Based on his interviews with children, Kohlberg identified three levels of moral reasoning: preconventional, conventional, and postconventional.
In the preconventional level of moral development, typical of children under ten years of age, we make decisions based on what will happen to the individual as a result of their actions. For example, children might say Heinz was wrong to steal the drug because he will be punished or that he was right because his spouse will be so grateful and will reward him. Ultimately, moral decisions are made to avoid punishment, to be obedient, or to get some type of reward.
A child at the conventional level of moral development will judge an action based on what others might think of the individual taking it. They might therefore say that Heinz should not steal the drug because it is illegal, and others would think he was a criminal. Conversely, a child might say he should steal the drug because other people will think he is a good spouse. In both cases, the judgment is based on what others will think of Heinz.
The third and final level of moral development is the postconventional level . At this level, children internalize a moral code and principles based on abstract ideas like justice and compassion and ideas about what is best for humanity. For example, Heinz should steal the drug even though it is against the law, because his wife’s life is more important than the law or the potential consequences he might face because he broke it. However, a child could also focus on their interpretation of the value of justice and decide that Heinz is wrong to steal the drug because stealing is morally wrong and may harm others in society. This level is called postconventional because it goes beyond what other individuals may think is right or wrong (conventional) and is based on more universal ethical principles. However, critics of Kohlberg have pointed out that his theory is not universal and may not apply well when researching the moral development across multiple religions and cultures (Moheghi et al., 2020).
Kohlberg’s research was also done almost entirely with males. Researcher Carol Gilligan , who initially was a research assistant of Kohlberg’s, argued that his theory was biased against women by failing to consider various moral perspectives (Gilligan, 1982). To better assess moral reasoning in ways that were more gender inclusive, Gilligan developed a theory of moral development based on ideas about caring and interpersonal relationships. Ultimately, she argued that individuals have different moral perspectives, focusing either on their own personal needs, the needs of others, or both their needs and the needs of others, but that none of these moral reasons were better or worse.
More recent research on moral development and prosocial behaviors shows that there are many individual and contextual factors that can shape moral development and beliefs. For example, in one study, children in China were found to lie more than children in Canada about prosocial acts (Fu et al., 2016). This was based in part on the cultural values that were most important. Chinese children were more like to believe lying was acceptable if it helps promote group harmony, whereas Canadian children were more likely to focus on whether the lie helped or harmed the individual (Fu et al., 2007, 2016). Findings like these show the way children’s moral beliefs and choices are in part based on their understanding of cultural values.
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Pennequin, V., Questel, F., Delaville, E., Delugre, M., & Maintenant, C. (2020). Metacognition and emotional regulation in children from 8 to 12 years old. British Journal of Educational Psychology , 90 (1), 1–16. doi.org/10.1111/bjep.12305
Perry, N. B., Dollar, J. M., Calkins, S. D., Keane, S. P., & Shanahan, L. (2020). Maternal socialization of child emotion and adolescent adjustment: Indirect effects through emotion regulation. Developmental Psychology , 56 (3), 541–552. doi.org/10.1037/dev0000815
Piaget, J. (1954). The construction of reality in the child. New York: Basic Books.
Raine, K. E., Zimmer–Gembeck, M. J., & Skinner, E. A. (2023). The role of coping in processes of resilience: The sample case of academic coping during late childhood and early adolescence. Development and Psychopathology, 35 (5), 2499–2515. https://doi.org/10.1017/S095457942300072X
Rose, L., Kovarski, K., Caetta, F., Makowski, D., & Chokron, S. (2024). Beyond empathy: Cognitive capabilities increase or curb altruism in middle childhood. Journal of Experimental Child Psychology , 239 , Article 105810. https://doi.org/10.1016/j.jecp.2023.105810
Salovey, P., & Mayer, J. D. (1990). Emotional intelligence. Imagination, Cognition and Personality , 9 (3), 185–211. doi.org/10.2190/DUGG-P24E-52WK-6CDG
Satpute A. B., Lindquist K. A. (2019). The default mode network’s role in discrete emotion. Trends in Cognitive Sciences . https://doi.org/10.1016/j.tics.2019.07.003
Savina, E. (2021). Self-regulation in preschool and early elementary classrooms: Why it is important and how to promote it. Early Childhood Education Journal , 49 (3), 493–501. https://doi.org/10.1007/s10643-020-01094-w
Skinner, E. A., & Zimmer–Gembeck, M. J. (2007). The development of coping. Annual Review of Psychology , 58 (1), 119–144. doi.org/10.1146/annurev.psyc....110405.085705
Skinner, E. A., Zimmer–Gembeck, M. J., (2016). Age differences and changes in ways of coping across childhood and adolescence. In E. A. Skinner, & M.J. Zimmer–Gembeck (Eds.), The development of coping (pp. 53–62). Springer. https://doi.org/10.1007/978-3-319-41740-0_3
Thompson, R. A., Simpson, J. A., & Berlin, L. J. (Eds.). (2021). Attachment: The fundamental questions . Guilford Publications.
Twum–Antwi, A., Jefferies, P., & Ungar, M. (2020). Promoting child and youth resilience by strengthening home and school environments: A literature review. International Journal of School & Educational Psychology , 8 (2), 78–89.
Wu, Y., & Schulz, L. E. (2019). Understanding social display rules: Using one person’s emotional expressions to infer the desires of another. Child Development , 91 (5), 1786–1799. doi.org/10.1111/cdev.13346
Xu, Y., & Krieg, A. (2014). Shyness in Asian American children and the relation to temperament, parents’ acculturation, and psychosocial functioning. Infant and Child Development , 23 (3), 333–342. doi.org/10.1002/icd.1860


Skip to main content
-
What factors contribute to a growing interest in entrepreneurship?
-
Unemployment levels
-
Low job turnover rates
-
Increasing levels of creativity
-
Decreasing rates of discrimination
-
Angel investors contribute to the entrepreneurial world by ________.
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Outpacing venture capitalists in access to startup funds
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Directly investing in entrepreneurial startups
-
Holding seminars to teach people how to become an entrepreneur
-
Forming groups of other investors to supply greater quantities of investment funds to entrepreneurs.
-
An entrepreneur is someone who ________.
-
Creates a small business based on other existing businesses
-
Creates a home-based business that sells products available through other retailers
-
Creates a business around the idea of solving a problem
-
Is highly creative
-
Roxanne Quimby of Burt’s Bees is an example of an entrepreneur primarily for which of the following reasons?
-
She saw available resources and recognized the resources could be used to create a business.
-
She acted on her passions.
-
She solved a significant societal problem.
-
She had the time and energy to dedicate to starting a business.
-
In the early stages of developing an entrepreneurial venture, the entrepreneur might seek funding from which group?
-
Venture capitalists
-
The local bank
-
Friends and family
-
Shark tank
-
The acronym SMART for goal setting stands for ________.
-
Short-term, measurable, accurate, relevant, and timely
-
Specific, measurable, accurate, relevant, and timely
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Specific, measurable, achievable, realistic, and time-oriented
-
Specific, measurable, achievable, results, and time-oriented
-
A vision statement does not include ________.
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A picture of the future described in words
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Concepts and ideas that inspire and focus people’s actions toward a united outcome
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Both creative and exploratory processes in creating the vision
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The scope of the venture
-
Which one of the following is not a quantifiable result?
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5 percent annual growth in sales
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Increase market share by 2 percent
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Decrease collection of accounts receivable by $5,000.00
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Increase creativity throughout the venture
-
Which of the following is not a creativity building technique or tool?
-
Conducting a case study
-
Brainstorming activities
-
Mind map creation
-
Brainwriting
-
Disruptive technologies include all but which of the following?
-
New methods or approaches that make established methods obsolete
-
Self-booking of air travel
-
Restaurant food delivery services
-
A change from ownership of resources to the ability to have access to resources
-
The entrepreneurial mindset includes ________.
-
A willingness to develop ideas that are not always initially popular
-
A willingness to wait for an idea to become popular before moving forward with that idea
-
An ability to focus on past successes
-
A belief in following tradition and established patterns


27.20: Nature-Men
Naturalism is a literary movement that arose in the late-ninteenth century and was prominent throughout the 20th century. Naturalism depicts people in their base, physiologically dependent states. These stories heavily suggest Darwinian ideals. Published in the mid-nineteenth century, the novellas Benito Cereno and The Heroic Slave , written by Herman Melville and Frederick Douglass respectively, arguably featured thematic that can be described as naturalist. Their depictions of race, slavery, and purpose in life seem to follow naturalist ideals, however different they are from one another.
Benito Cereno suggests conflict rather than outright narrating it. It isn’t clear to the reader that black rebellion has taken place, but Delano’s rhetoric shows that he is untrustworthy of his peers. We soon come to learn that the ship is under the influence of the black slaves, and that a number of white sailors were killed by them. To comment on the flu outbreak, the narrative states that more of the white sailors died from it than the slaves. This indicates that the black’s willpower to prevail under harsh circumstances is stronger than white mens’. Returning to the naturalist theme of this analysis, Melville continuously alludes to the idea of people being “born” to specific modes of living. “Most negroes are natural valet and hair-dressers” (Melville 212). And again, he generalizes race here, too: “But as a nation–continued he in his reveries–these Spaniards are all an odd set; the very word Spaniard has a curious, Guy-Fawkish twang to it” (206). Melville explicitly comments on naturalism in this final quote: “The whites , too, by nature, were the shrewder race” (201). Melville’s depiction of slave rebellion lies more in sub-text. He reinvents the white-black power dynamic by exploring naturalist themes, and in a way, shows the men as irrational-thinking animals by doing so.
The Heroic Slave is much more upfront about its themes than Melville is with his story. Within the first few pages, we come to see that Washington views black slaves as less than animals. “Those birds, perched on the swinging boughs… They live free, though they may die slaves… I am a slave–, born a slave… But here am I, a man–yes, a man!–with thoughts and wishes, with powers and faculties as far as angel’s flight above that hated reptile–yet he is my superior… I am galled with irons; yet even these are more tolerable than the consciousness” (Douglass, 5-6). Washington expresses than men are slaves to each other and to themselves. Consciousness is a prison in itself. His slavery is all the more suffering because he is aware that he is one. Douglass shows that slavery is unique among of humans in the animal kingdom, because we have a word for it. Humans have concepts of freedom and liberty, power and happiness. This is absent in the animal kingdom; wild animals are only slaves to their physiology, yet to them that is just life. Circumstances are much more important to humans than they are to animals. To Douglass, there is a certain humility and embarrassment to being a slave, because it appears to unnatural, and therefore irrational.
Melville and Douglass commentate on naturalism in there own unique ways. Their works are perhaps pre-cursors to the naturalism literary movement.


18.7.0: Review Questions
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- Last updated
- Save as PDF
Review Questions
1 .
What laboratory result is indicative of hypercapnia?
-
PaO 2 68 mm Hg
-
PaCO 2 24 mm Hg
-
HCO 3 24 mEq/L
-
PaCO 2 50 mm Hg
2 .
Diffusion works by which method of molecular movement?
-
Molecules move from the intravascular space to the surrounding tissue.
-
Movement of molecules is from interstitial to intravascular space.
-
Molecular movement is from high to low concentration along a gradient.
-
Molecules are moved across a filter by expenditure of ATP.
3 .
What substance is a powerful vasoconstrictor, synthesized by reactions of the kidneys and the lungs?
-
aldosterone
-
angiotensin II
-
renin
-
angiotensin I
4 .
What substance reduces alveolar surface tension, thereby preventing the collapse of alveoli?
-
surfactant
-
macrophage
-
bradykinin
-
prostaglandin
5 .
What patient’s respiratory status would a nurse in the emergency department be
most
concerned about?
-
68-year-old with fifty-pack-year smoking history
-
52-year-old with brainstem infarction
-
45-year-old with right lower lobe pneumonia
-
34-year-old with latent tuberculosis
6 .
A nursing student who is preparing to educate a patient on the use of the incentive spirometer practices by telling the preceptor the patient will be told to use what technique?
-
“Inhale through the mouthpiece like a thick milkshake through a straw.”
-
“Blow into the mouthpiece as hard as you can for as long as you can.”
-
“Breathe in and out through the mouthpiece quickly ten times in ten seconds.”
-
“Cough into the mouthpiece to see if the regulator rises to the goal.”
7 .
Norepinephrine enhances perfusion by what mechanism?
-
dilates blood vessels
-
produces hypotension
-
causes vasoconstriction
-
normalizes temperature
8 .
The combined processes of cellular respiration and gas exchange are referred to by what terminology?
-
ventilation
-
perfusion
-
internal respiration
-
Kreb cycle
9 .
The impulse of the normal cardiac electrical cycle travels from the SA node to the AV node, then to which structure?
-
Purkinje fibers
-
bundle of His
-
ventricular wall
-
interventricular septum
10 .
A nurse anticipates what symptom from a patient who has low CO?
-
clammy skin
-
clear mentation
-
bradycardia
-
robust pedal pulses
11 .
Metabolic syndrome is associated with what combination of diagnoses?
-
hyperglycemia, central obesity, hypertension
-
high triglycerides, high HDL, hyperglycemia
-
hypertension and severe obesity
-
high triglycerides, low HDL, hypoglycemia
12 .
Acid-base balance is reflected by what factor?
-
PaCO 2
-
pH
-
PaO 2
-
HCO 3
13 .
A nurse is educating a patient about lifestyle choices; what behavior is of most concern for respiratory implications?
-
sedentary activity level
-
high sodium intake
-
150 minutes of moderate walking
-
smoking
14 .
The amount and rate of inspiration and expiration of air are measured by what test?
-
oximetry
-
capnography
-
spirometry
-
PEFR
15 .
The telemetry nurse notices a patient’s HR has slowed to 45 beats/minute; upon reviewing the continuous ECG monitor, no P-waves are visible, but the QRS complexes are regular. The nurse prepares to call to inform the cardiologist of what suspected issue?
-
The patient is in HF.
-
An MI is occurring.
-
A-fib has developed.
-
The SA node is not firing.
16 .
A nurse reads a postintubation chest x-ray report that indicates a patient has subcutaneous emphysema in the anterior right chest, near the clavicle. What assessment finding should the nurse anticipate in this region?
-
no breath sounds
-
crepitus
-
alkalosis
-
wheezing
17 .
A patient is admitted for an acute-on-chronic exacerbation of emphysema. What powerful class of drugs does the nurse expect to be prescribed to treat the acute inflammatory process?
-
decongestant
-
expectorant
-
corticosteroid
-
antitussive
18 .
An unresponsive patient who is not breathing and whose cardiac rhythm is identified as VF is a candidate for what emergency intervention?
-
cardioversion
-
O 2 by CPAP
-
IV sedation
-
defibrillation
19 .
A patient with secretions in bilateral anterior upper lobes of the lungs has been taking guaifenesin, has undergone chest physiotherapy to include percussion of the upper anterior chest, and is now to be positioned for postural drainage. In what position will the nurse place the patient?
-
Trendelenburg
-
supine and flat
-
prone
-
high Fowler


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1: An Invisible World
Week 1
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1.4: Review Questions
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Week 1
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1.4: Review Questions
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5: The Population Genetics of Divergence and Molecular Substitution
“History is just one damn thing after another.” -sometimes attributed to Arnold Toynbee
There are over \(30\) million base pair substitutions between human and chimpanzees, sites where humans carry one allele and chimps another at orthologous locations. These changes have occurred in the seven million years or so since human and chimp last shared a common ancestor. Other substitutions are shared between the sister species human and chimp to the exclusion of gorilla, yet others are shared between human, chimps and Gorilla but not Orangs. Long-term evolution, from the molecular perspective, is just one damn substitution after another. These substitutions represent changes at just a small percentage of sites genome-wide as we share the majority of our genome, our evolutionary history, and our biology with the other great apes. Each of the substitutions must have arisen as a mutation in the population, spread through the population as a polymorphism before eventually reaching fixation. What forces drove the spread of these alleles through the population to become substitutions?
| Human |
accacagcatttgttagttactgccaagaagcctgtatctgtagggtaaaatcctcgctgaagtgggttg
|
| Chimp |
......................................g...........c...................
|
| Gorilla |
..................................................cc..................
|
| Orangutan |
.........c.........c..............................c...................
|
| Gibbon |
...................c..............................—.................
|
| Crab-eating macaque |
g.............gg...c..............................c..t.t..............
|
Many substitutions were driven by selection, as there has undoubtedly been plenty of adaptive phenotypic adaptive evolution in great apes. However, these adaptive changes may be a small minority of all the subsitutions, for a start many of these substitutions have occurred in non-coding DNA with no known functional effect. Thus it is reasonable initial position that the majority of substitutions genome-wide may well be neutral. How can we hope to identify regions undergoing adaptive divergence? How could we hope to address the claim that many amino-acid changing substitutions are also neutral, as posited by the Neutral theory of molecular evolution. One way forward is to understand what neutral theory predicts for the rate of molecular substition, and then develop ways to test these ideas.
The Neutral Substitution process.
So how then do neutral substitutions occur? It is very unlikely that a rare neutral allele accidentally drifts up to fixation; more likely, such an allele will be eventually lost from the population. However, populations experience a large and constant influx of rare alleles due to mutation, so even if it is very unlikely that an individual allele fixes within the population, some neutral alleles will fix by chance. So we’ll need to understand the probability that a neutral mutation fixes, and then how we can think about the rate of substitutions accumulate over time.
probability of the eventual fixation of a neutral allele
An allele which reaches fixation within a population is an ancestor to the entire population. In a particular generation there can only be a single allele that all other alleles at the locus in a later generation can claim as an ancestor (See Figure \(\PageIndex{2}\)). At a neutral locus, the actual allele does not affect the number of descendants that the allele has (this follows from the definition of neutrality: neutral alleles don’t leave more or less descendants on average than other neutral alleles). An equivalent way to state this is that the allele labels don’t affect anything; thus the alleles are exchangeable . As a consequence of being exchangeable, any allele is equally likely to be the ancestor of the entire population. In a diploid population of size \(N\) , there are \(2N\) alleles, all of which are equally likely to be the ancestor of the entire population at some later time point. So if our allele is present in a single copy, the chance that it is the ancestor to the entire population in some future generation is \(\frac{1}{(2N)}\) , i.e. the chance our neutral allele is eventually fixed is \(\frac{1}{(2N)}\) . In Figure \ref{fig:subs_simulation}, our orange allele in the first generation is one of 10 differently coloured alleles, and so has a \(1/10\) chance of being the ancestor of the entire population at some later time point (and in this simulation it does become the common ancestor, by the 9th generation).
More generally, if our neutral allele is present in \(i\) copies in the population, of \(2N\) alleles, the probability that this allele becomes fixed is \(\frac{i}{(2N)}\) , i.e. the probability that a neutral allele is eventually fixed is simply given by its frequency ( \(p\) ) in the population. (We can also derive this result by letting \(Ns \rightarrow 0\) in Equation \ref{eqn:prob_fixed}, a result we’ll encounter later.)
How long does it take on average for such an allele to fix within our population? In developing Equation \ref{TMRCA_neutral} we’ve seen that it takes on average \(4N\) generations for a large sample of alleles to all trace their ancestry back to a single most recent common ancestral allele. Any single-base pair change which arose as a single mutation at a locus, and fixed in the population, must have been present in the sequence transmitted by the most recent common ancestor of the population at that locus. Thus it must take roughly \(4N\) generations for a neutral allele present in a single copy within the population to fix. This argument can be made more precise, but in general we would still find that it takes \(\approx 4N\) generations for a neutral allele to go from its introduction to fixation with the population.
Rate of substitution of neutral alleles
A substitution between populations that do not exchange gene flow is simply a fixation event within one population. The rate of substitution is therefore the rate at which new alleles fix in the population, so that the long-term substitution rate is the rate at which mutations arise that will eventually become fixed within our population.
Let’s assume, based on our discussion of the neutral theory of molecular evolution, that there are only two classes of mutational changes that can occur with a region, highly deleterious mutations and neutral mutations. A fraction \(C\) of all mutational changes are highly deleterious, and cannot possibly contribute to substitution nor polymorphism. The other \(1-C\) fraction of mutations are neutral. If our total mutation rate is \(\mu\) per transmitted allele per generation, then a total of \(2N \mu (1-C)\) neutral mutations enter our population each generation.
Each of these neutral mutations has a \(\frac{1}{(2N)}\) probability chance of eventually becoming fixed in the population. Therefore, the rate at which neutral mutations arise that eventually become fixed within our population is
\[2N\mu(1-C)\frac{1}{2N} = \mu(1-C)\]
Thus the rate of substitution, under a model where newly arising alleles are either highly deleterious or neutral, is simply given by the mutation rate of neutral alleles, i.e. \(\mu(1-C)\) .
Consider a pair of species that have diverged for \(T\) generations, i.e. orthologous sequences shared between the species last shared a common ancestor \(T\) generations ago. If these species have maintained a constant \(\mu\) over that time, they will have accumulated an average of
\[2\mu(1-C)T \label{eqn:moleclock}\]
neutral substitutions. This assumes that \(T\) is a lot longer than the time it takes to fix a neutral allele, such that the total number of alleles introduced into the population that will eventually fix is the total number of substitutions.
This is a really pretty result as the population size has completely canceled out of the neutral substitution rate. However, there is another way to see this in a more straight forward way. If I look at a sequence in me compared to, say, a particular chimp, I’m looking at the mutations that have occurred in both of our germlines since they parted ways \(T\) generations ago. Since neutral alleles do not alter the probability of their transmission to the next generation, we are simply looking at the mutations that have occurred in \(2T\) generations worth of transmissions. Thus the average number of neutral mutational differences separating our pair of species is simply \(2\mu (1-C) T\) .
Implications for the Molecular Clock.
A number of observations follow under this model, from Equation \ref{eqn:moleclock}. The first is that a primary determinant of patterns of molecular evolution in a genomic region is the level of constraint ( \(C\) ). This pattern generally seems to hold empirically: non-coding regions often evolve more rapidly than coding regions, synonymous substitutions accumulate faster than nonsynonymous, and nonsynonymous substitutions accumulate faster in less vital proteins than ones that are absolutely necessary for early development. For example, fibrinopeptides evolve in a less constrained manner than the cytochrome c gene, see Figure \(\PageIndex{3}\). Note that this constraint prediction is not a unique prediction of the neutral model, e.g. less constrained regions may also be better able to evolve adaptively. However, it is a fantastically useful general insight, e.g. it allows us to spot putatively functional non-coding regions by looking for genomic regions that have very low levels of divergence among distantly related species.
The second important insight, and critical for the development of the neutral theory, is that Equation \ref{eqn:moleclock} is seemingly consistent with ’s hypothesis of a surprisingly constant, protein molecular clock. The protein molecular clock is the observation that for some proteins there’s a linear relationship between the number of non-synonymous (NS) substitutions and the time species last shared a common ancestor in the fossil record. provided an for early example of this observation (Figure \(\PageIndex{3}\)), by comparing various organisms whose molecular sequences were available to him. For example, he found that humans and rattlesnakes, who last share a common ancestor in the fossil record around 300 million years, are separated by roughly \(15\) NS substitutions per \(100\) sites in the cytochrome c protein. While, humans and dogfish, which diverged around 400 million years, are separated by \(19\) NS substitutions per \(100\) sites in this gene.
In Equation \ref{eqn:moleclock}, if we double the amount of time separating a pair of species \(T\) , we double the number of substitutions predicted. Note that for this to be true \(T\) must be measured in generations. To explain a protein molecular clock between species that clearly differed dramatically in generation time it was hypothesized that the mutation rate actually scaled with generation time, i.e. short-lived organisms introduced fewer mutations per generation, e.g. as they had fewer rounds of mitosis. This generation-time assumption meant that the mutation rate per year could be constant, such that \(\mu T\) would be a constant for pairs of species that had diverged for similar geological times, which are measured in years, even if the organisms differed in generation time. This assumption would allow neutral theory to be consistent with a protein molecular clock measured in years. We now know that this critical generation time assumption is false: organisms with shorter generation times have somewhat higher mutation rates per year so a strict neutral model is inconsistent with the protein molecular clock. We’ll return to these ideas when we discuss the fate of very weakly selected mutations in Chapter \ref{Selection_Stochasticity} and ’s Nearly Neutral theory. If you are still reading this send Graham a picture of Tomoko Ohta receiving the Crafoord Prize, an analog of the Nobel prize for biology, for her contributions to molecular evolution.
The contribution of ancestral polymorphism to divergence.
If we are considering \(T\) to represent the divergence between long-separated species, then we can think of \(T\) as the time that the species split. However, for more recently diverged populations and species, we need to include the fact that the sorting of ancestral polymorphism contributes to divergence among species. In Figure \ref{fig:split_anc_pop}, we see our two populations split \(T_s\) generations ago. However, the coalescence of our A and B lineage is necessarily deeper in time than \(T_s\) . The top mutation was polymorphic in the ancestral population but now contributes to the divergence between A and B. Assuming that our ancestral population had effective size \(N_A\) individuals, and that our populations split cleanly with no subsequent gene flow, then
\[T = T_s + 2N_A.\]
If our species split time is very large compared to \(2N\) then we can think of \(T\) as the split time.
[fig:split_anc_pop]
For this, and the next question, assume that humans and chimps split around 5.5 \(\times 10^6\) years ago, have a generation time 20 years, that the speciation occurred instantaneously in allopatry with no subsequent gene flow, and the ancestral effective population size of the human and chimp common ancestor population was 10,000 individuals.
Nachman and Crowell sequenced 12 pseudogenes in humans and chimps and found substitutions at 1.3% of sites.
- What is the mutation rate per site per generation at these genes?
- All of the pseudogenes they sequenced are on the autosomes. What would your prediction be for pseudogenes on the X and Y chromosomes, given that few mutations occur in the female germline than in the male germline per generation.
Tests of molecular evolution
One of the great appeals of neutral models is they offer a simple null for us to test real data against.
Comparing the rates of non-synonymous to synonymous substitutions \(\frac{d_N}{d_S}\)
One common tool in molecular evolution is to compare the estimated number (or rates) of substitutions in different classes of genomic sites, for example the ratio of the rates of non-synonymous ( \(d_N\) ) to synonymous substitutions ( \(d_S\) ) in a given gene. The simplest way to think about calculating \(d_N\) is to count up the non-synonymous changes and divide by the total number of positions in the gene where a non-synonymous point mutation could occur and then divide by time. We can do likewise for synonymous changes \(d_S\) , and then take the ratio \(\frac{d_N}{d_S}\) .
For the vast majority of protein-coding genes in the genome we see that \(\frac{d_N}{d_S} < 1\) . This observation is consistent with the view that non-synonymous sites are much more constrained than synonymous sites, i.e. that most non-synonymous mutations are deleterious and quickly removed from the population. If we are willing to make the assumption that all synonymous changes are neutral, \(d_S= \mu\) , then we can estimate the degree of constraint on non-synonymous sites. (Note that synonymous changes can sometimes be subject to both positive and negative selection, but this neutral assumption is a useful starting place.)
Assume that a fraction \(C\) of non-synonymous changes are too deleterious to contribute to divergence, and that there are no beneficial mutations. Then, we expected rate of neutral non-synonymous substitutions is
\[d_N = (1-C) \mu\]
Dividing by \(d_S\) , we find
\[\frac{d_N}{d_S} = (1-C)\]
Therefore, if we assume that non-synonymous mutations can only be strongly deleterious or neutral, we estimate the fraction of mutational changes that are constrained by negative selection as \(C= 1- \frac{d_N}{d_S}\) . C has the interpretations of being the fraction of non-synonymous mutations that are quickly weeded out of the population by selection, and so do not contribute to divergence among species.
We can test whether our gene is evolving in a constrained way at the protein level by estimating \(\frac{d_N}{d_S}\) and testing whether this is significantly less that \(1\) . A \(\frac{d_N}{d_S}\) test can provide evolutionary evidence that a stretch of DNA proposed to be protein-coding is subject to selective constraint, and so likely does encode for a functional protein. We can also perform a \(\frac{d_N}{d_S}\) test on specific branches of a phylogeny for a gene, to test on which branches the gene is subject to constraint, or to test for changes in the level of constraint across the phylogeny.
Loss of constraint at pseudogenes.
While most protein genes evolve under constraint, we can find examples of genes that are evolving in a much less constrained manner. The simplest example of this is where the gene has lost function. Genes can lose function because of inactivating mutations that stop them being transcribed or translated into functional proteins. Such genes are called ‘pseudogenes’. When a gene completely loses function there is no longer selection against non-synonynous changes and so such mutations are just as free to accumulate as synonymous changes, and so \(\frac{d_N}{d_S}=1\) . Pseudogenes are a wonderful example of the extension of Darwin’s ideas about vestigial traits (‘Rudimentary organs’) to the DNA level; we can still recognize a once useful word (gene) whose spelling is slowly degrading. Our genomes are filled with old pseudogenes whose original meanings (functional protein coding sequences) are slowly being eroded through the accumulation of neutral substitutions. One nice example of a gene that has repeatedly lost function, i.e. become repeatedly psuedogenized, is the enamlin gene from the study of Meredith et al. (2009).
The protein enamlin is a key structural protein involved in the outer cap of enamel on teeth. Various mammals have secondarily evolved diets that do not require hard teeth, and so greatly reduced the selection pressure for hard enamel, or even teeth at all. For example, two-toed sloths ( Choloepus ), pygmy sperm whales ( Kogia ), and aardvark ( Orycteropus ) all lack enamel on teeth. Other mammals have lost their teeth entirely, e.g. giant anteaters ( Myrmecophaga ) and baleen whales. Due to this relaxation of constraint on the phenotype, the enamlin gene has accumulated pseudogenizing substitutions such as premature stop codons and frameshift mutations (see Figure \(\PageIndex{7}\) for examples). Meredith et al. (2009) sequenced enamlin across a range of species and found that none of the species with enamel have frameshift mutations in enamlin , while 17/20 of species that lack enamel or teeth have frameshifts in enamlin , and all of them carry premature stop codons.
Meredith et al. (2009) found that the branches of the enamlin phylogeny with a functional enamlin gene had an estimated \(\frac{d_N}{d_S}= 0.51\) , consistent with the protein evolving in a constrained manner. In contrast, the branches with a pseudogenized Enamlin had \(\frac{d_N}{d_S} = 1.02\) , consistent with the gene evolving a completely unconstrained way. The branches where the gene was likely transitioning from a functional to non-function state, i.e. pre-mutation and mixed, had intermediate values of \(\frac{d_N}{d_S}=0.83-0.98\) , consistent with a transition from a constrained to unconstrained mode of protein evolution somewhere along these branches of the phylogeny.
The enamlin gene was pseudogenized somewhere along the branch leading to Aardvarks ( Orycteropus afer ), see Figure \ref{fig:Aardvark_pseudogene}. estimated that this branch has a \(\frac{d_N}{d_S}=0.75\)
- Calculate the average constraint against amino-acid changes on this branch.
- Aardvarks last shared a common ancestor with Afrosoricida (golden moles, tenrecs) and Macroscelidea (elephant shrews) around \(\sim 75.1\) million years ago in the Cretaceous. Assume that for the portion of the branch while enamlin was functional \(\frac{d_N}{d_S} = 0.51\) and after it was pseudogenized there was no constaint (i.e. \(\frac{d_N}{d_S} = 1\) ). Based on the branch’s average \(\frac{d_N}{d_S}=0.75\) , can you estimate the time at which enamlin was pseudogenized? (I.e. when is the star in Figure \ref{fig:Aardvark_pseudogene}?)
Adaptive evolution and \(\frac{d_N}{d_S}\)
Clearly genes are not only subject to neutral and deleterious mutations; beneficial mutations must also arise and fix from from time to time. Let’s assume that a fraction \(B\) of non-synonymous mutations that arise are beneficial such that \(2 N \mu B\) beneficial mutations arise per generation. Newly arisen beneficial alleles are not destined to fix in the population, as they may be lost to genetic drift when they are rare in the population (we’ll discuss how to calculate the fixation probability for beneficial alleles in Chapter \ref{Selection_Stochasticity}). A newly arisen beneficial allele reaches fixation in the population with probability \(f_B\) from its initial frequency of \(\frac{1}{2N}\) . This fixation probability may be much higher than that of neutral mutations, but still much less than \(1\) . The expected total rate of non-synonymous substitutions is
\[dN= (1-C - B) \mu + (2 N \mu B) \times f_B.\]
Then
\[\frac{d_N}{d_S} = (1-C-B) + 2 N B f_B \label{eqn:dNDS_C_B}\]
assuming again that all synonymous mutations are neutral. Note that this means that our estimates of \(C\) using \(1-\frac{d_N}{d_S}\) will be a lower bound on the true constraint if even a small fraction of mutations are beneficial. Those cases where the gene is evolving more rapidly at the protein level than at synonymous sites, i.e. \(d_N/d_S > 1\) , are potentially strong candidates for positive selection rapidly driving change at the protein level. We can identify genes that have \(\frac{d_N}{d_S}\) significantly greater than one, either on the complete gene phylogeny, or on particular branches. Note that is a very conservative test that few genes in the genome meet, as many genes that are fixing adaptive non-synonymous substitutions will have \(\frac{d_N}{d_S}<1\) ; even if adaptive mutations are common, genes may still evolve in a constrained way (i.e. \(\frac{d_N}{d_S}<1\) ) if the rapid fixation of beneficial mutations due to positive selection is outweighed by the loss of non-synonymous mutations to negative selection.
A classic example for looking at adaptive evolution using \(\frac{d_N}{d_S}\) is the evolution of the lysozyme gene in primates . The lysozyme protein is a key component for the breakdown of bacterial walls. The lysozyme gene shows very fast protein evolution (see the phylogeny in Figure \(\PageIndex{11}\)), notably on the lineages leading to apes (e.g. gibbons and humans) and Colobines (e.g. colobus and langur monkeys). Colobines have leaf-based diets. They digest these leaves by bacterial fermentation in their foregut, and then use lysozymes to break down the bacteria to extract energy from the leaves. In Colobines, the lysozyme protein has evolved to work well in the high-PH environment of the stomach. Remarkably, the Colobine lysozyme protein has convergently evolved this activity via very similar amino-acid changes at 5 key residuals in cows and Hoatzins
The McDonald-Kreitman test
As noted above, a big issue with using \(\frac{d_N}{d_S}\) to detect adaptation is that it is very conservative. For a more powerful test of rapid divergence, what we need to do is adjust for the level of constraint a gene experiences at non-synonymous sites. One way to do this is to use polymorphism data as an internal control. If we see little non-synonymous polymorphism at a gene, but a lot of synonymous polymorphism, we now know that there is likely strong constraint on the gene (i.e. high \(C\) ), thus we expect \(\frac{d_N}{d_S}\) to be low. devised a simple test of the neutral theory of molecular evolution at a gene based on this intuition . took the case where we have polymorphism data at a gene for one species and divergence to a closely related species. They partitioned polymorphism and fixed differences in their sample into the number of non-synonymous and synonymous changes:
| Poly. | Fixed | |
|---|---|---|
| Non-Syn. | \(P_N\) | \(D_N\) |
| Syn. | \(P_S\) | \(D_S\) |
| Ratio | \(P_N/P_S\) | \(D_N/D_S\) |
[fig:MK_tree]
Under neutral theory, we expect a smaller number of non-synonymous to synonymous fixed differences ( \(D_N/D_S < 1\) ) and exactly the same expectation holds for polymorphism ( \(P_N/P_S\) ). Let’s consider a gene with \(L_S\) and \(L_N\) sites where synonymous and non-synonymous mutations could arise respectively. We can think of the underlying gene genealogy at our gene, see Figure \ref{fig:MK_tree}, with the total time on the coalescent genealogy within the species as \(T_{tot}\) and the total time for fixed differences between our species as \(T_{div}'\) , note that \(T_{div}'\) is the total time where a an allele that would appear as a subsitution could arise. Then under neutrality we expect \(\mu L_N (1-C) T_{tot}\) non-synonymous polymorphisms (i.e. our number of segregating sites), and \(\mu L_N (1-C) T_{div}'\) non-synonymous fixed differences. We can then fill out the rest of our table as follows:
| Poly. | Fixed | |
|---|---|---|
| Non-Syn. | \(\mu L_N (1-C) T_{tot}\) | \(\mu L_N (1-C) T_{div}'\) |
| Syn. | \(\mu L_S T_{tot}\) | \(\mu L_S T_{div}'\) |
| Ratio | \(L_N(1-C)/( L_S)\) | \(L_N (1-C) / ( L_S)\) |
Therefore, we expect the ratio of non-synonymous to synonymous changes to be the same for polymorphism and divergence under a strict neutral model. We can test this expectation of equal ratios via the standard tests of a \(2 \times 2\) table. If the ratio of \(N/S\) is significantly higher for divergence than polymorphism we have evidence that non-synonymous substitutions are accumulating more rapidly than we would predict given levels of constraint alone.
As example of a Mcdonald-Kreitman (MK) table consider the work of on the molecular evolution of L photopigment opsin in admiral ( Limenitis ) butterflies, responsible for colour vision in the long-wavelength part of the visual spectrum. found that the sensitivity of this opsin had shifted towards blue in its sensitivity in L. archippus archippus (viceroy) compared to L. arthemis astyanax . To test whether this molecular evolution reflected positive selection they sequenced 24 L. arthemis astyanax individuals and one L. archippus archippus sequence. They identified 11 polymorphic sites in L. arthemis astyanax and 16 fixed differences, which break down as follows:
| Poly. | Fixed | |
|---|---|---|
| Non-Syn. | \(2\) | \(12\) |
| Syn. | \(9\) | \(4\) |
| Ratio | \(\frac{2}{9}\) | \(\frac{3}{1}\) |
Note the strong excess of non-synonymous to synonymous divergence compared to polymorphism (p-value of \(0.006\) , Fisher’s exact test), which is consistent with the gene evolving in an adaptive manner among the two species. We would expect roughly only \(3\) non-synonymous substitutions out of 16 substitutions if the gene was evolving neutrally ( \(16 \times \frac{2}{11}\) ).
Summary
- In a diploid population of size \(N\) , any of a set of \(2N\) selectively equivalent (ie neutral) alleles are equally likely to be the ancestor of the entire population at some future distant time point. Therefore, the probability that a new mutation eventually fixes in the population is \(\frac{1}{2N}\) .
- Under a model where a fraction \(C\) of new mutations are neutral and \(1-C\) mutations are strongly deleterious, \(2NC\mu\) mutations arise every generation that can possibly become substitutions. Therefore, the per-generation rate of neutral substitution is \(2N(1-C)\mu \times \frac{1}{2N} = (1-C)\mu\) . This is independent of the population size and just depends on levels of constraint and mutation rates.
- The constant rate of neutral substitution gives rise to a per-generation molecular clock, which can potentially be used to estimate constraint ( \(C\) ) and mutation rates.
- Many summaries and tests of molecular evolution, e.g. \(\frac{d_N}{d_S}\) , are based on comparing rates of substitution between functional classes of sites. These allow differing levels of constraint to be identified and signals of adaptive substitution to be detected.
- Tests of molecular evolution for adaptation that also incorporate both divergence and polymorphism, e.g. the Mcdonald-Kreitman test, are potentially powerful tools as polymorphism levels allow a somewhat independent measure of levels of constraint.
Assuming that the mutation rate is \(\mu\) /gamete/generation and the population size is N diploid individuals, what is the number of new mutations introduced into the population each generation?
What is the probability of fixation of a unique new, neutral mutation in a population of N haploid individuals?
Why is dN/dS much less than one for the majority of genes in our genome?
You sequence a gene in Drosophila melanogaster and D. simulans . You observe 5 non-synonymous substitutions out of 500 bases where non-synonymous substitutions could occur, and 15 synonymous substitutions out of 500 bases where synonymous substitutions could occur. What is the level of constraint at nonsynonymous sites?
Analyzing polymorphism and divergence data for a gene, you calculate the following McDonald-Kreitman table.
| Polymorp. | Fixed | |
|---|---|---|
| Synonymous | 40 | 80 |
| Non-synonymous | 20 | 80 |
- Based on the ratio of non-synonymous to synonymous polymorphisms, and given the 80 synonymous substitutions, how many nonsynymous substitutions would you expect if this gene were evolving neutrally?
- Is this table consistent with the gene evolving neutrally? If not what could explain the results?