The following passage is adapted from Ricki Lewis, "Did Donkeys Arise from an Inverted Chromosome?", originally published 2018 in PLOSOne Blogs.

In the world of genome sequencing, donkeys haven’t received nearly as much attention as horses. But now a report on a new-and-improved genome sequence of Willy, a donkey (Equus asinus) jack 5 born at the Copenhagen Zoo in 1997, appears in the new issue of Science Advances, from Gabriel Renaud, of the Centre for GeoGenetics, Natural History Museum of Denmark. (A female is a jenny or jennet.) The new view provides clues to how donkeys may have branched from horses along the tree of evolution.

Horses and their relatives, past and present, are genetically peculiar in that their chromosomes are rearranged, with respect to each other. That should  prevent them from producing viable hybrids – yet they do. Donkeys have 62 chromosomes and horses have 64. A mule comes from the mating of a male donkey and a female horse, and has 63 chromosomes. Mules are known for their  intelligence, calm, stamina, and persistence. Their horse-like bodies perched on donkey-like limbs make them ideal for hauling tourists around the Grand Canyon and schlepping supplies in combat situations. The ears are large like those of the horse mom, and mules make a sound that begins as a whinny and becomes a bray.

The complementary couple, a female donkey and a male horse, produces a hinny, smaller than a mule. Hinnies are the flip side of the mule, with a donkey’s physique atop horsey limbs, and short donkey ears. They’re rarer than mules, but also have 63 chromosomes. It’s easy to mix them up.

Comparing Willy’s genome to a horse genome revealed their close evolutionary relationship. Only about 15% of horse genes aren’t also in the donkey genome, and only about 10% of a donkey’s genes don’t have counterparts in the horse. Most of the genes that they share provide basic “housekeeping” functions like dismantling proteins, repairing DNA, enabling embryonic development, and controlling cell division. So that’s why a copy of each genome can smush together to yield mules and hinnies.

A second form of information encoded in genomes, in addition to the A, C, T, G sequence, is the pattern of whether the two variants of individual genes are different (heterozygous) or the same (homozygous). Many contiguous homozygous genes form a “run of homozygosity” (ROH).

An ROH indicates a chromosome chunk, perhaps as long as millions of DNA bases, that’s the same from each of an individual’s parents, who in turn inherited it from a shared ancestor, like a grandparent that cousins share. The longer the ROH, the more recent the shared ancestor, because it takes time for mutations to accrue that would break the sameness of the sequence.

Scrutinizing ROHs can reveal recent inbreeding and domestication, help to reconstruct possible branching patterns of evolution, and, more practically, help ancestry companies assign the DNA in spit samples to geographic areas where people’s ancestors might have come from. The new study compared ROHs for the three zebra and three ass species, confirming that Willy’s most recent ancestors were Somali wild asses.

The researchers used Chicago HiRise assembly technology to up the quality of Willy’s genome sequence. “This new assembly allowed us to identify fine chromosomal rearrangements between the horse and the donkey that likely played an active role in their divergence and, ultimately, speciation,” they write.

The bigger pieces enabled them to zero in on DNA sequences where chromosomes contort, such as inversions (where a sequence flips) or translocations (where different chromosome types exchange parts). These events could have fueled the reproductive isolation of small populations that can expand into speciation.

If eventually sperm with one inverted chromosome fertilized eggs with the same inversion, animals would have been conceived in which both copies of the chromosome are inverted – and they’d be fertile with each other, but not with horses. Once a subpopulation with the inversion became established, further genetic changes would separate them further from the ancestral horse.

This passage is adapted from “Flagship Species and Their Role in the Conservation Movement” (2020)

Until recently, two schools of thought have dominated the field of establishing “flagship” endangered species for marketing and awareness campaigns. These flagship species make up the subset of endangered species conservation experts utilize to elicit public support - both financial and legal - for fauna conservation as a whole. 

The first concerns how recognizable the general public, the audience of most large-scale funding campaigns, finds a particular species, commonly termed its “public awareness.” This school of thought was built on the foundation that if an individual recognizes a species from prior knowledge, cultural context, or previous conservational and educational encounters (in a zoo environment or classroom setting, for instance) that individual would be more likely to note and respond to the severity of its endangered status. However, recently emerging flagship species such as the pangolin have challenged the singularity of this factor. 

Alongside public awareness, conservation experts have long considered a factor they refer to as a “keystone species” designation in the flagstone selection process. Keystone species are those species that play an especially vital role in their respective habitats or ecosystems. While this metric is invaluable to the environmentalists in charge of designating funds received, recent data has expressed the more minor role a keystone species designation seems to play in the motivations of the public. 

Recent scholarship has questioned both the singularity and the extent to which the above classifications impact the decision making of the general public. Though more complicated to measure, a third designation, known as a species’ “charisma,” is now the yardstick by which most flagship species are formally classified. Addressing the charisma of a species involves establishing and collecting data concerning its ecological (interactions with humans/the environments of humans),  aesthetic (appealing to human emotions through physical appearance and immediately related behaviors), and corporeal (affection and socialization with humans over the short- and long-terms) characteristics. This process has been understandably criticized by some for its costs and failure to incorporate the severity of an endangered species’ status into designation, but its impact on the public has been irrefutable. While keystone and public awareness designations are still often applied in the field because of their practicality and comparative simplicity, charisma is now commonly accepted as the most accurate metric with which to judge a species’ flagship potential.

The author of the passage uses the word “yardstick” in paragraph four in order to

This passage is adapted from “Flagship Species and Their Role in the Conservation Movement” (2020)

Until recently, two schools of thought have dominated the field of establishing “flagship” endangered species for marketing and awareness campaigns. These flagship species make up the subset of endangered species conservation experts utilize to elicit public support - both financial and legal - for fauna conservation as a whole. 

The first concerns how recognizable the general public, the audience of most large-scale funding campaigns, finds a particular species, commonly termed its “public awareness.” This school of thought was built on the foundation that if an individual recognizes a species from prior knowledge, cultural context, or previous conservational and educational encounters (in a zoo environment or classroom setting, for instance) that individual would be more likely to note and respond to the severity of its endangered status. However, recently emerging flagship species such as the pangolin have challenged the singularity of this factor. 

Alongside public awareness, conservation experts have long considered a factor they refer to as a “keystone species” designation in the flagstone selection process. Keystone species are those species that play an especially vital role in their respective habitats or ecosystems. While this metric is invaluable to the environmentalists in charge of designating funds received, recent data has expressed the more minor role a keystone species designation seems to play in the motivations of the public. 

Recent scholarship has questioned both the singularity and the extent to which the above classifications impact the decision making of the general public. Though more complicated to measure, a third designation, known as a species’ “charisma,” is now the yardstick by which most flagship species are formally classified. Addressing the charisma of a species involves establishing and collecting data concerning its ecological (interactions with humans/the environments of humans),  aesthetic (appealing to human emotions through physical appearance and immediately related behaviors), and corporeal (affection and socialization with humans over the short- and long-terms) characteristics. This process has been understandably criticized by some for its costs and failure to incorporate the severity of an endangered species’ status into designation, but its impact on the public has been irrefutable. While keystone and public awareness designations are still often applied in the field because of their practicality and comparative simplicity, charisma is now commonly accepted as the most accurate metric with which to judge a species’ flagship potential.

The author of the passage uses the word “understandably” in paragraph four in order to

The following passage is adapted from a speech delivered by Susan B. Anthony in 1873. The speech was delivered after Anthony was tried and fined $100 for voting in the 1872 presidential election.

Friends and fellow citizens: I stand before you tonight under indictment for the alleged crime of having voted at the last Presidential election, without having a lawful right to vote. It shall be my work this evening to prove to you that in thus voting, I not only committed no crime, but, instead, simply exercised my citizen’s rights, guaranteed to me and all United States citizens by the National Constitution, beyond the power of any State to deny.

The preamble of the Federal Constitution says: “We, the people of the United States, in order to form a more perfect union, establish justice, insure domestic tranquillity, provide for the common defense, promote the general welfare, and secure the blessings of liberty to ourselves and our posterity, do ordain and establish this Constitution for the United States of America.”

It was we, the people; not we, the white male citizens; nor yet we, the male citizens; but we, the whole people, who formed the Union. And we formed it, not to give the blessings of liberty, but to secure them; not to the half of ourselves and the half of our posterity, but to the whole people— women as well as men. And it is a downright mockery to talk to women of their enjoyment of the blessings of liberty while they are denied the use of the only means of securing them provided by this democratic-republican government—the ballot.

For any State to make sex a qualification that must ever result in the disfranchisement of one entire half of the people is a violation of the supreme law of the land. By it the blessings of liberty are forever withheld from women and their female posterity. To them this government had no just powers derived from the consent of the governed. To them this government is not a democracy. It is not a republic. It is an odious aristocracy; a hateful oligarchy of sex; the most hateful aristocracy ever established on the face of the globe; an oligarchy of wealth, where the right govern the poor. An oligarchy of learning, where the educated govern the ignorant, or even an oligarchy of race, where the Saxon rules the African, might be endured, but this oligarchy of sex, which makes father, brothers, husband, sons, the oligarchs over the mother and sisters, the wife and daughters of every household—which ordains all men sovereigns, all women subjects, carries dissension, discord and rebellion into every home of the nation. 

Webster, Worcester and Bouvier all define a citizen to be a person in the United States, entitled to vote and hold office. The one question left to be settled now is: Are women persons? And I hardly believe any of our opponents will have the hardihood to say they are not. Being persons, then, women are citizens; and no State has a right to make any law, or to enforce any old law, that shall abridge their privileges or immunities. Hence, every discrimination against women are citizenswomen in the constitutions and laws of the several States is today null and void, precisely as is every one against African Americans.

The author uses the word “alleged” in the first paragraph to:

The following passage is adapted from a speech delivered by Susan B. Anthony in 1873. The speech was delivered after Anthony was tried and fined $100 for voting in the 1872 presidential election.

Friends and fellow citizens: I stand before you tonight under indictment for the alleged crime of having voted at the last Presidential election, without having a lawful right to vote. It shall be my work this evening to prove to you that in thus voting, I not only committed no crime, but, instead, simply exercised my citizen’s rights, guaranteed to me and all United States citizens by the National Constitution, beyond the power of any State to deny.

The preamble of the Federal Constitution says: “We, the people of the United States, in order to form a more perfect union, establish justice, insure domestic tranquillity, provide for the common defense, promote the general welfare, and secure the blessings of liberty to ourselves and our posterity, do ordain and establish this Constitution for the United States of America.”

It was we, the people; not we, the white male citizens; nor yet we, the male citizens; but we, the whole people, who formed the Union. And we formed it, not to give the blessings of liberty, but to secure them; not to the half of ourselves and the half of our posterity, but to the whole people— women as well as men. And it is a downright mockery to talk to women of their enjoyment of the blessings of liberty while they are denied the use of the only means of securing them provided by this democratic-republican government—the ballot.

For any State to make sex a qualification that must ever result in the disfranchisement of one entire half of the people is a violation of the supreme law of the land. By it the blessings of liberty are forever withheld from women and their female posterity. To them this government had no just powers derived from the consent of the governed. To them this government is not a democracy. It is not a republic. It is an odious aristocracy; a hateful oligarchy of sex; the most hateful aristocracy ever established on the face of the globe; an oligarchy of wealth, where the right govern the poor. An oligarchy of learning, where the educated govern the ignorant, or even an oligarchy of race, where the Saxon rules the African, might be endured, but this oligarchy of sex, which makes father, brothers, husband, sons, the oligarchs over the mother and sisters, the wife and daughters of every household—which ordains all men sovereigns, all women subjects, carries dissension, discord and rebellion into every home of the nation. 

Webster, Worcester and Bouvier all define a citizen to be a person in the United States, entitled to vote and hold office. The one question left to be settled now is: Are women persons? And I hardly believe any of our opponents will have the hardihood to say they are not. Being persons, then, women are citizens; and no State has a right to make any law, or to enforce any old law, that shall abridge their privileges or immunities. Hence, every discrimination against women are citizenswomen in the constitutions and laws of the several States is today null and void, precisely as is every one against African Americans.

The author includes Webster, Worcester, and Bouvier’s definition of a citizen in paragraph 5 primarily in order to

The passage is excerpted from Ngonghala CN, et. al’s “Poverty, Disease, and the Ecology of Complex Systems” © 2014 Ngonghala et al.

The modern economics literature on poverty traps, however, is strikingly silent about the role of feedbacks from biophysical and biosocial processes. Two overwhelming characteristics of under-developed economies and the poorest, mostly rural, subpopulations in those countries are (i) the dominant role of resource-dependent primary production—from soils, fisheries, forests, and wildlife—as the root source of income and (ii) the high rates of morbidity and mortality due to parasitic and infectious diseases. For basic subsistence, the extremely poor rely on human capital that is directly generated from their ability to obtain resources, and thus critically influenced by climate and soil that determine the success of food production. These resources in turn influence the nutrition and health of individuals, but can also be influenced by a variety of other biophysical processes. For example, infectious and parasitic diseases effectively steal human resources for their own survival and transmission. Yet scientists rarely integrate even the most rudimentary frameworks for understanding these ecological processes into models of economic growth and poverty.

The author discusses parasitic and infectious diseases in order to:

The passage is excerpted from Ngonghala CN, et. al’s “Poverty, Disease, and the Ecology of Complex Systems” © 2014 Ngonghala et al.

Nonetheless, for the billion people who still languish in chronic extreme poverty, Malthus’s ideas about the importance of biophysical and biosocial feedback (e.g., interactions between human behavior and resource availability) to the dynamics of economic systems still ring true. Indeed, while they were based on observations of human populations, Malthus ideas had reverberations throughout the life sciences. His insights were based on important underlying processes that provided inspiration to both Darwin and Wallace as they independently derived the theory of evolution by natural selection. Likewise, these principles underlie standard models of population biology, including logistic population growth models, predator-prey models, and the epidemiology of host-pathogen dynamics.

The author uses the word “reverberations” in the highlighted sentence primarily in order to

This passage is adapted from “Flagship Species and Their Role in the Conservation Movement” (2020)

Until recently, two schools of thought have dominated the field of establishing “flagship” endangered species for marketing and awareness campaigns. These flagship species make up the subset of endangered species conservation experts utilize to elicit public support - both financial and legal - for fauna conservation as a whole. 

The first concerns how recognizable the general public, the audience of most large-scale funding campaigns, finds a particular species, commonly termed its “public awareness.” This school of thought was built on the foundation that if an individual recognizes a species from prior knowledge, cultural context, or previous conservational and educational encounters (in a zoo environment or classroom setting, for instance) that individual would be more likely to note and respond to the severity of its endangered status. However, recently emerging flagship species such as the pangolin have challenged the singularity of this factor. 

Alongside public awareness, conservation experts have long considered a factor they refer to as a “keystone species” designation in the flagstone selection process. Keystone species are those species that play an especially vital role in their respective habitats or ecosystems. While this metric is invaluable to the environmentalists in charge of designating funds received, recent data has expressed the more minor role a keystone species designation seems to play in the motivations of the public. 

Recent scholarship has questioned both the singularity and the extent to which the above classifications impact the decision making of the general public. Though more complicated to measure, a third designation, known as a species’ “charisma,” is now the yardstick by which most flagship species are formally classified. Addressing the charisma of a species involves establishing and collecting data concerning its ecological (interactions with humans/the environments of humans),  aesthetic (appealing to human emotions through physical appearance and immediately related behaviors), and corporeal (affection and socialization with humans over the short- and long-terms) characteristics. This process has been understandably criticized by some for its costs and failure to incorporate the severity of an endangered species’ status into designation, but its impact on the public has been irrefutable. While keystone and public awareness designations are still often applied in the field because of their practicality and comparative simplicity, charisma is now commonly accepted as the most accurate metric with which to judge a species’ flagship potential.

The author cites the example species of the pangolin in paragraph two primarily in order to:

The following is an excerpt from Night and Day, a novel by Virginia Woolf that was first published in 1919. The novel tells the story of two main female characters in London in the early 20th century.

It was a Sunday evening in October, and in common with many other young ladies of her class, Katharine Hilbery was pouring out tea. Perhaps a fifth part of her mind was thus occupied, and the remaining parts leapt over the little barrier of day which interposed between Monday morning and this rather subdued moment, and played with the things one does voluntarily and normally in the daylight. But although she was silent, she was evidently mistress of a situation which was familiar enough to her, and inclined to let it take its way for the six hundredth time, perhaps, without bringing into play any of her unoccupied faculties. A single glance was enough to show that Mrs. Hilbery was so rich in the gifts which make tea-parties of elderly distinguished people successful, that she scarcely needed any help from her daughter, provided that the tiresome business of teacups and bread and butter was discharged for her. 

Considering that the little party had been seated round the tea-table for less than twenty minutes, the animation observable on their faces, and the amount of sound they were producing collectively, were very creditable to the hostess. It suddenly came into Katharine’s mind that if some one opened the door at this moment he would think that they were enjoying themselves; he would think, “What an extremely nice house to come into!” and instinctively she laughed, and said something to increase the noise, for the credit of the house presumably, since she herself had not been feeling exhilarated. At the very same moment, rather to her amusement, the door was flung open, and a young man entered the room. Katharine, as she shook hands with him, asked him, in her own mind, “Now, do you think we’re enjoying ourselves enormously?”... “Mr. Denham, mother,” she said aloud, for she saw that her mother had forgotten his name. 

That fact was perceptible to Mr. Denham also, and increased the awkwardness which inevitably attends the entrance of a stranger into a room full of people much at their ease, and all launched upon sentences. At the same time, it seemed to Mr. Denham as if a thousand softly padded doors had closed between him and the street outside. A fine mist, the etherealized essence of the fog, hung visibly in the wide and rather empty space of the drawing-room, all silver where the candles were grouped on the tea-table, and ruddy again in the firelight. With the omnibuses and cabs still running in his head, and his body still tingling with his quick walk along the streets and in and out of traffic and foot-passengers, this drawing-room seemed very remote and still; and the faces of the elderly people were mellowed, at some distance from each other, and had a bloom on them owing to the fact that the air in the drawing-room was thickened by blue grains of mist. Mr. Denham had come in as Mr. Fortescue, the eminent novelist, reached the middle of a very long sentence. He kept this suspended while the newcomer sat down, and Mrs. Hilbery deftly joined the severed parts with several remarks. 

Katharine stirred her tea, and seemed to speculate, so Denham thought, upon the duty of filling somebody else’s cup, but she was really wondering how she was going to keep this strange young man in harmony with the rest. She observed that he was compressing his teacup, so that there was danger lest the thin china might cave inwards. She could see that he was nervous; one would expect a bony young man with his face slightly reddened by the wind, and his hair not altogether smooth, to be nervous in such a party. Further, he probably disliked this kind of thing, and had come out of curiosity, or because her father had invited him–anyhow, he would not be easily combined with the rest.

Katharine Hilbery uses the quote in the underlined sentence primarily in order to:

The following passage is adapted from Ricki Lewis, "Did Donkeys Arise from an Inverted Chromosome?", originally published 2018 in PLOSOne Blogs.

In the world of genome sequencing, donkeys haven’t received nearly as much attention as horses. But now a report on a new-and-improved genome sequence of Willy, a donkey (Equus asinus) jack 5 born at the Copenhagen Zoo in 1997, appears in the new issue of Science Advances, from Gabriel Renaud, of the Centre for GeoGenetics, Natural History Museum of Denmark. (A female is a jenny or jennet.) The new view provides clues to how donkeys may have branched from horses along the tree of evolution.

Horses and their relatives, past and present, are genetically peculiar in that their chromosomes are rearranged, with respect to each other. That should  prevent them from producing viable hybrids – yet they do. Donkeys have 62 chromosomes and horses have 64. A mule comes from the mating of a male donkey and a female horse, and has 63 chromosomes. Mules are known for their  intelligence, calm, stamina, and persistence. Their horse-like bodies perched on donkey-like limbs make them ideal for hauling tourists around the Grand Canyon and schlepping supplies in combat situations. The ears are large like those of the horse mom, and mules make a sound that begins as a whinny and becomes a bray.

The complementary couple, a female donkey and a male horse, produces a hinny, smaller than a mule. Hinnies are the flip side of the mule, with a donkey’s physique atop horsey limbs, and short donkey ears. They’re rarer than mules, but also have 63 chromosomes. It’s easy to mix them up.

Comparing Willy’s genome to a horse genome revealed their close evolutionary relationship. Only about 15% of horse genes aren’t also in the donkey genome, and only about 10% of a donkey’s genes don’t have counterparts in the horse. Most of the genes that they share provide basic “housekeeping” functions like dismantling proteins, repairing DNA, enabling embryonic development, and controlling cell division. So that’s why a copy of each genome can smush together to yield mules and hinnies.

A second form of information encoded in genomes, in addition to the A, C, T, G sequence, is the pattern of whether the two variants of individual genes are different (heterozygous) or the same (homozygous). Many contiguous homozygous genes form a “run of homozygosity” (ROH).

An ROH indicates a chromosome chunk, perhaps as long as millions of DNA bases, that’s the same from each of an individual’s parents, who in turn inherited it from a shared ancestor, like a grandparent that cousins share. The longer the ROH, the more recent the shared ancestor, because it takes time for mutations to accrue that would break the sameness of the sequence.

Scrutinizing ROHs can reveal recent inbreeding and domestication, help to reconstruct possible branching patterns of evolution, and, more practically, help ancestry companies assign the DNA in spit samples to geographic areas where people’s ancestors might have come from. The new study compared ROHs for the three zebra and three ass species, confirming that Willy’s most recent ancestors were Somali wild asses.

The researchers used Chicago HiRise assembly technology to up the quality of Willy’s genome sequence. “This new assembly allowed us to identify fine chromosomal rearrangements between the horse and the donkey that likely played an active role in their divergence and, ultimately, speciation,” they write.

The bigger pieces enabled them to zero in on DNA sequences where chromosomes contort, such as inversions (where a sequence flips) or translocations (where different chromosome types exchange parts). These events could have fueled the reproductive isolation of small populations that can expand into speciation.

If eventually sperm with one inverted chromosome fertilized eggs with the same inversion, animals would have been conceived in which both copies of the chromosome are inverted – and they’d be fertile with each other, but not with horses. Once a subpopulation with the inversion became established, further genetic changes would separate them further from the ancestral horse.

The passage suggests that an individual with a high level of homozygosity