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Sunday, August 7, 2022

French and Indian War

From Wikipedia, the free encyclopedia
French and Indian War
Part of the Seven Years' War
French and indian war map.svg
The war theater
DateMay 28, 1754 – February 10, 1763
Location
North America
Result

British victory

Territorial
changes
France cedes New France east of the Mississippi River to Great Britain, retaining Saint Pierre and Miquelon, and transfers Louisiana to Spain
Belligerents
Commanders and leaders
Captain Jacobs 
Killbuck
Shingas
Pontiac
Strength
42,000 regulars and militia (peak strength, 1758) 10,000 regulars (troupes de la terre and troupes de la marine, peak strength, 1757)
Casualties and losses
  • 1,512 killed in action
  • 1,500 died of wounds
  • 10,400 died of disease
Unknown

The French and Indian War (1754–1763) was a theater of the Seven Years' War, which pitted the North American colonies of the British Empire against those of the French, each side being supported by various Native American tribes. At the start of the war, the French colonies had a population of roughly 60,000 settlers, compared with 2 million in the British colonies. The outnumbered French particularly depended on the natives.

Two years into the French and Indian War, in 1756, Great Britain declared war on France, beginning the worldwide Seven Years' War. Many view the French and Indian War as being merely the American theater of this conflict; however, in the United States the French and Indian War is viewed as a singular conflict which was not associated with any European war. French Canadians call it the guerre de la Conquête ('War of the Conquest').

The British colonists were supported at various times by the Iroquois, Catawba, and Cherokee tribes, and the French colonists were supported by Wabanaki Confederacy member tribes Abenaki and Mi'kmaq, and the Algonquin, Lenape, Ojibwa, Ottawa, Shawnee, and Wyandot (Huron) tribes. Fighting took place primarily along the frontiers between New France and the British colonies, from the Province of Virginia in the south to Newfoundland in the north. It began with a dispute over control of the confluence of the Allegheny River and Monongahela River called the Forks of the Ohio, and the site of the French Fort Duquesne at the location that later became Pittsburgh, Pennsylvania. The dispute erupted into violence in the Battle of Jumonville Glen in May 1754, during which Virginia militiamen under the command of 22-year-old George Washington ambushed a French patrol.

In 1755, six colonial governors met with General Edward Braddock, the newly arrived British Army commander, and planned a four-way attack on the French. None succeeded, and the main effort by Braddock proved a disaster; he lost the Battle of the Monongahela on July 9, 1755, and died a few days later. British operations failed in the frontier areas of the Province of Pennsylvania and the Province of New York during 1755–57 due to a combination of poor management, internal divisions, effective Canadian scouts, French regular forces, and Native warrior allies. In 1755, the British captured Fort Beauséjour on the border separating Nova Scotia from Acadia, and they ordered the expulsion of the Acadians (1755–64) soon afterwards. Orders for the deportation were given by Commander-in-Chief William Shirley without direction from Great Britain. The Acadians were expelled, both those captured in arms and those who had sworn the loyalty oath to the King. Natives likewise were driven off the land to make way for settlers from New England.

The British colonial government fell in the region of Nova Scotia after several disastrous campaigns in 1757, including a failed expedition against Louisbourg and the Siege of Fort William Henry; this last was followed by the Natives torturing and massacring their colonial victims. William Pitt came to power and significantly increased British military resources in the colonies at a time when France was unwilling to risk large convoys to aid the limited forces that they had in New France, preferring to concentrate their forces against Prussia and its allies who were now engaged in the Seven Years' War in Europe. The conflict in Ohio ended in 1758 with the British–American victory in the Ohio Country. Between 1758 and 1760, the British military launched a campaign to capture French Canada. They succeeded in capturing territory in surrounding colonies and ultimately the city of Quebec (1759). The following year the British were victorious in the Montreal Campaign in which the French ceded Canada in accordance with the Treaty of Paris (1763).

France also ceded its territory east of the Mississippi to Great Britain, as well as French Louisiana west of the Mississippi River to its ally Spain in compensation for Spain's loss to Britain of Spanish Florida. (Spain had ceded Florida to Britain in exchange for the return of Havana, Cuba.) France's colonial presence north of the Caribbean was reduced to the islands of Saint Pierre and Miquelon, confirming Great Britain's position as the dominant colonial power in northern America.

Nomenclature

In British America, wars were often named after the sitting British monarch, such as King William's War or Queen Anne's War. There had already been a King George's War in the 1740s during the reign of King George II, so British colonists named this conflict after their opponents, and it became known as the French and Indian War. This continues as the standard name for the war in the United States, although Indians fought on both sides of the conflict. It also led into the Seven Years' War overseas, a much larger conflict between France and Great Britain that did not involve the American colonies; some historians make a connection between the French and Indian War and the Seven Years' War overseas, but most residents of the United States consider them as two separate conflicts—only one of which involved the American colonies, and American historians generally use the traditional name. Less frequently used names for the war include the Fourth Intercolonial War and the Great War for the Empire.

Belligerents during the Seven Years' War. Canadians and Europeans view the French and Indian War as a theater of the Seven Years' War, while Americans view it a separate conflict.

In Europe, the French and Indian War is conflated into the Seven Years' War and not given a separate name. "Seven Years" refers to events in Europe, from the official declaration of war in 1756—two years after the French and Indian War had started—to the signing of the peace treaty in 1763. The French and Indian War in America, by contrast, was largely concluded in six years from the Battle of Jumonville Glen in 1754 to the capture of Montreal in 1760.

Canadians conflate both the European and American conflicts into the Seven Years' War (Guerre de Sept Ans). French Canadians also use the term "War of Conquest" (Guerre de la Conquête), since it is the war in which New France was conquered by the British and became part of the British Empire. In Quebec, this term was promoted by popular historians Jacques Lacoursière and Denis Vaugeois, who borrowed from the ideas of Maurice Séguin in considering this war as a dramatic tipping point of French Canadian identity and nationhood.

Background

The coureurs des bois were French Canadian fur traders, who did business with natives throughout the Mississippi and St. Lawrence watershed.

At this time, North America east of the Mississippi River was largely claimed by either Great Britain or France. Large areas had no colonial settlements. The French population numbered about 75,000 and was heavily concentrated along the St. Lawrence River valley, with some also in Acadia (present-day New Brunswick and parts of Nova Scotia), including Île Royale (Cape Breton Island). Fewer lived in New Orleans; Biloxi, Mississippi; Mobile, Alabama; and small settlements in the Illinois Country, hugging the east side of the Mississippi River and its tributaries. French fur traders and trappers traveled throughout the St. Lawrence and Mississippi watersheds, did business with local Indian tribes, and often married Indian women. Traders married daughters of chiefs, creating high-ranking unions.

British settlers outnumbered the French 20 to 1 with a population of about 1.5 million ranged along the Atlantic coast of the continent from Nova Scotia and the Colony of Newfoundland in the north to the Province of Georgia in the south. Many of the older colonies' land claims extended arbitrarily far to the west, as the extent of the continent was unknown at the time when their provincial charters were granted. Their population centers were along the coast, but the settlements were growing into the interior. The British captured Nova Scotia from France in 1713, which still had a significant French-speaking population. Britain also claimed Rupert's Land where the Hudson's Bay Company traded for furs with local Indian tribes.

Map of Iroquois expansion, 1711. By the mid-18th century, the Iroquois Confederacy had expanded from Upstate New York to the Ohio Country.

Between the French and British colonists, large areas were dominated by Indian tribes. To the north, the Mi'kmaq and the Abenakis were engaged in Father Le Loutre's War and still held sway in parts of Nova Scotia, Acadia, and the eastern portions of the province of Canada, as well as much of Maine. The Iroquois Confederation dominated much of upstate New York and the Ohio Country, although Ohio also included Algonquian-speaking populations of Delaware and Shawnee, as well as Iroquoian-speaking Mingos. These tribes were formally under Iroquois rule and were limited by them in their authority to make agreements. The Iroquois Confederation initially held a stance of neutrality to ensure continued trade with both French and British. Though maintaining this stance proved difficult as the Iroquois Confederation tribes sided and supported French or British causes depending on which side provided the most beneficial trade.

The Southeast interior was dominated by Siouan-speaking Catawbas, Muskogee-speaking Creeks and Choctaw, and the Iroquoian-speaking Cherokee tribes. When war broke out, the French colonists used their trading connections to recruit fighters from tribes in western portions of the Great Lakes region, which was not directly subject to the conflict between the French and British; these included the Hurons, Mississaugas, Ojibwas, Winnebagos, and Potawatomi.

The British colonists were supported in the war by the Iroquois Six Nations and also by the Cherokees, until differences sparked the Anglo-Cherokee War in 1758. In 1758, the Province of Pennsylvania successfully negotiated the Treaty of Easton in which a number of tribes in the Ohio Country promised neutrality in exchange for land concessions and other considerations. Most of the other northern tribes sided with the French, their primary trading partner and supplier of arms. The Creeks and Cherokees were subject to diplomatic efforts by both the French and British to gain either their support or neutrality in the conflict.

The Cherokee, c. 1762. The Cherokee were subject to diplomatic efforts from the British and French in order to gain their support or neutrality in the event of a conflict.

At this time, Spain claimed only the province of Florida in eastern America. It controlled Cuba and other territories in the West Indies that became military objectives in the Seven Years' War. Florida's European population was a few hundred, concentrated in St. Augustine.

There were no French regular army troops stationed in America at the onset of war. New France was defended by about 3,000 troupes de la marine, companies of colonial regulars (some of whom had significant woodland combat experience). The colonial government recruited militia support when needed. The British had few troops. Most of the British colonies mustered local militia companies to deal with Indian threats, generally ill trained and available only for short periods, but they did not have any standing forces. Virginia, by contrast, had a large frontier with several companies of British regulars.

When hostilities began, the British colonial governments preferred operating independently of one another and of the government in London. This situation complicated negotiations with Indian tribes, whose territories often encompassed land claimed by multiple colonies. As the war progressed, the leaders of the British Army establishment tried to impose constraints and demands on the colonial administrations.

Céloron's expedition

New France's Governor-General Roland-Michel Barrin de La Galissonière was concerned about the incursion and expanding influence in the Ohio Country of British colonial traders such as George Croghan. In June 1747, he ordered Pierre-Joseph Céloron to lead a military expedition through the area. Its objectives were:

Roland-Michel Barrin de La Galissonière, the Governor of New France sent an expedition in 1749 into the Ohio Country in an attempt to assert French sovereignty.
  • to reaffirm to New France's Indian allies that their trading arrangements with colonists were exclusive to those authorized by New France
  • to confirm Indian assistance in asserting and maintaining the French claim to the territories which French explorers had claimed
  • to discourage any alliances between Britain and local Indian tribes
  • to impress the Indians with a French show of force against British colonial settler incursion, unauthorized trading expeditions, and general trespass against French claims

Céloron's expedition force consisted of about 200 Troupes de la marine and 30 Indians, and they covered about 3,000 miles (4,800 km) between June and November 1749. They went up the St. Lawrence, continued along the northern shore of Lake Ontario, crossed the portage at Niagara, and followed the southern shore of Lake Erie. At the Chautauqua Portage near Barcelona, New York, the expedition moved inland to the Allegheny River, which it followed to the site of Pittsburgh. There Céloron buried lead plates engraved with the French claim to the Ohio Country. Whenever he encountered British colonial merchants or fur-traders, he informed them of the French claims on the territory and told them to leave.

Céloron's expedition arrived at Logstown where the Indians in the area informed him that they owned the Ohio Country and that they would trade with the British colonists regardless of the French. He continued south until his expedition reached the confluence of the Ohio and the Miami rivers, which lay just south of the village of Pickawillany, the home of the Miami chief known as "Old Briton". Céloron threatened Old Briton with severe consequences if he continued to trade with British colonists, but Old Briton ignored the warning. Céloron returned disappointedly to Montreal in November 1749.

Céloron wrote an extensively detailed report. "All I can say is that the Natives of these localities are very badly disposed towards the French," he wrote, "and are entirely devoted to the English. I don't know in what way they could be brought back." Even before his return to Montreal, reports on the situation in the Ohio Country were making their way to London and Paris, each side proposing that action be taken. Massachusetts governor William Shirley was particularly forceful, stating that British colonists would not be safe as long as the French were present.

Negotiations

Map of European colonies in North America, c. 1750. Disputes over territorial claims persisted after the end of King George's War in 1748.

The War of the Austrian Succession ended in 1748 with the signing of the Treaty of Aix-la-Chapelle, which was primarily focused on resolving issues in Europe. The issues of conflicting territorial claims between British and French colonies were turned over to a commission, but it reached no decision. Frontier areas were claimed by both sides, from Nova Scotia and Acadia in the north to the Ohio Country in the south. The disputes also extended into the Atlantic Ocean, where both powers wanted access to the rich fisheries of the Grand Banks off Newfoundland.

In 1749, the British government gave land to the Ohio Company of Virginia for the purpose of developing trade and settlements in the Ohio Country. The grant required that it settle 100 families in the territory and construct a fort for their protection. But the territory was also claimed by Pennsylvania, and both colonies began pushing for action to improve their respective claims. In 1750, Christopher Gist explored the Ohio territory, acting on behalf of both Virginia and the company, and he opened negotiations with the Indian tribes at Logstown. He completed the 1752 Treaty of Logstown in which the local Indians agreed to terms through their "Half-King" Tanacharison and an Iroquois representative. These terms included permission to build a strong house at the mouth of the Monongahela River on the modern site of Pittsburgh, Pennsylvania.

Escalation in Ohio Country

Governor-General of New France Marquis de la Jonquière died on March 17, 1752, and he was temporarily replaced by Charles le Moyne de Longueuil. His permanent replacement was to be the Marquis Duquesne, but he did not arrive in New France until 1752 to take over the post. The continuing British activity in the Ohio territories prompted Longueuil to dispatch another expedition to the area under the command of Charles Michel de Langlade, an officer in the Troupes de la Marine. Langlade was given 300 men, including French-Canadians and warriors of the Ottawa tribe. His objective was to punish the Miami people of Pickawillany for not following Céloron's orders to cease trading with the British. On June 21, the French war party attacked the trading center at Pickawillany, capturing three traders and killing 14 Miami Indians, including Old Briton. He was reportedly ritually cannibalized by some Indians in the expedition party.

Construction of French fortifications

Fort Le Boeuf in 1754. In the spring of 1753, the French began to build a series of forts in the Ohio Country.

In the spring of 1753, Paul Marin de la Malgue was given command of a 2,000-man force of Troupes de la Marine and Indians. His orders were to protect the King's land in the Ohio Valley from the British. Marin followed the route that Céloron had mapped out four years earlier. Céloron, however, had limited the record of French claims to the burial of lead plates, whereas Marin constructed and garrisoned forts. He first constructed Fort Presque Isle on Lake Erie's south shore near Erie, Pennsylvania, and he had a road built to the headwaters of LeBoeuf Creek. He then constructed a second fort at Fort Le Boeuf in Waterford, Pennsylvania, designed to guard the headwaters of LeBoeuf Creek. As he moved south, he drove off or captured British traders, alarming both the British and the Iroquois. Tanaghrisson was a chief of the Mingo Indians, who were remnants of Iroquois and other tribes who had been driven west by colonial expansion. He intensely disliked the French whom he accused of killing and eating his father. He traveled to Fort Le Boeuf and threatened the French with military action, which Marin contemptuously dismissed.

The Iroquois sent runners to the manor of William Johnson in upstate New York, who was the British Superintendent for Indian Affairs in the New York region and beyond. Johnson was known to the Iroquois as Warraghiggey, meaning "he who does great things." He spoke their languages and had become a respected honorary member of the Iroquois Confederacy in the area, and he was made a colonel of the Iroquois in 1746; he was later commissioned as a colonel of the Western New York Militia.

The Indian representatives and Johnson met with Governor George Clinton and officials from some of the other American colonies at Albany, New York. Mohawk Chief Hendrick was the speaker of their tribal council, and he insisted that the British abide by their obligations and block French expansion. Clinton did not respond to his satisfaction, and Hendrick said that the "Covenant Chain" was broken, a long-standing friendly relationship between the Iroquois Confederacy and the British Crown.

Virginia's response

In 1754, George Washington, of the Virginia Regiment, was dispatched to warn the French to leave Virginian territory.

Governor Robert Dinwiddie of Virginia was an investor in the Ohio Company, which stood to lose money if the French held their claim. He ordered 21-year-old Major George Washington (whose brother was another Ohio Company investor) of the Virginia Regiment to warn the French to leave Virginia territory in October 1753. Washington left with a small party, picking up Jacob Van Braam as an interpreter, Christopher Gist (a company surveyor working in the area), and a few Mingos led by Tanaghrisson. On December 12, Washington and his men reached Fort Le Boeuf.

Jacques Legardeur de Saint-Pierre succeeded Marin as commander of the French forces after Marin died on October 29, and he invited Washington to dine with him. Over dinner, Washington presented Saint-Pierre with the letter from Dinwiddie demanding an immediate French withdrawal from the Ohio Country. Saint-Pierre said, "As to the Summons you send me to retire, I do not think myself obliged to obey it." He told Washington that France's claim to the region was superior to that of the British, since René-Robert Cavelier, Sieur de La Salle had explored the Ohio Country nearly a century earlier.

Washington's party left Fort Le Boeuf early on December 16 and arrived in Williamsburg on January 16, 1754. He stated in his report, "The French had swept south", detailing the steps which they had taken to fortify the area, and their intention to fortify the confluence of the Allegheny and Monongahela rivers.

Course of war

Even before Washington returned, Dinwiddie had sent a company of 40 men under William Trent to that point where they began construction of a small stockaded fort in the early months of 1754. Governor Duquesne sent additional French forces under Claude-Pierre Pécaudy de Contrecœur to relieve Saint-Pierre during the same period, and Contrecœur led 500 men south from Fort Venango on April 5, 1754. These forces arrived at the fort on April 16, but Contrecœur generously allowed Trent's small company to withdraw. He purchased their construction tools to continue building what became Fort Duquesne.

Early engagements

Dinwiddie had ordered Washington to lead a larger force to assist Trent in his work, and Washington learned of Trent's retreat while he was en route. Mingo sachem Tanaghrisson had promised support to the British, so Washington continued toward Fort Duquesne and met with him. He then learned of a French scouting party in the area from a warrior sent by Tanaghrisson, so he added Tanaghrisson's dozen Mingo warriors to his own party. Washington's combined force of 52 ambushed 40 Canadiens (French colonists of New France) on the morning of May 28 in what became known as the Battle of Jumonville Glen. They killed many of the Canadiens, including their commanding officer Joseph Coulon de Jumonville, whose head was reportedly split open by Tanaghrisson with a tomahawk. Historian Fred Anderson suggests that Tanaghrisson was acting to gain the support of the British and to regain authority over his own people. They had been inclined to support the French, with whom they had long trading relationships. One of Tanaghrisson's men told Contrecoeur that Jumonville had been killed by British musket fire. Historians generally consider the Battle of Jumonville Glen as the opening battle of the French and Indian War in North America, and the start of hostilities in the Ohio valley.

Washington with his war council during the Battle of Fort Necessity. After deliberations, it was decided to withdraw, and surrender the fort.

Following the battle, Washington pulled back several miles and established Fort Necessity, which the Canadians attacked under the command of Jumonville's brother at the Battle of Fort Necessity on July 3. Washington surrendered and negotiated a withdrawal under arms. One of his men reported that the Canadian force was accompanied by Shawnee, Delaware, and Mingo warriors—just those whom Tanaghrisson was seeking to influence.

News of the two battles reached England in August. After several months of negotiations, the government of the Duke of Newcastle decided to send an army expedition the following year to dislodge the French. They chose Major General Edward Braddock to lead the expedition. Word of the British military plans leaked to France well before Braddock's departure for North America. In response, King Louis XV dispatched six regiments to New France under the command of Baron Dieskau in 1755. The British sent out their fleet in February 1755, intending to blockade French ports, but the French fleet had already sailed. Admiral Edward Hawke detached a fast squadron to North America in an attempt to intercept them.

In June 1755, the British captured French naval ships sent to provide war matériel to the Acadian and Mi'kmaw militias in Nova Scotia.

In a second British action, Admiral Edward Boscawen fired on the French ship Alcide on June 8, 1755, capturing her and two troop ships. The British harassed French shipping throughout 1755, seizing ships and capturing seamen. These actions contributed to the eventual formal declarations of war in spring 1756.

An early important political response to the opening of hostilities was the convening of the Albany Congress in June and July, 1754. The goal of the congress was to formalize a unified front in trade and negotiations with the Indians, since the allegiance of the various tribes and nations was seen to be pivotal in the war that was unfolding. The plan that the delegates agreed to was neither ratified by the colonial legislatures nor approved by the Crown. Nevertheless, the format of the congress and many specifics of the plan became the prototype for confederation during the War of Independence.

British campaigns, 1755

The British formed an aggressive plan of operations for 1755. General Braddock was to lead the expedition to Fort Duquesne, while Massachusetts governor William Shirley was given the task of fortifying Fort Oswego and attacking Fort Niagara. Sir William Johnson was to capture Fort St. Frédéric at Crown Point, New York, and Lieutenant Colonel Robert Monckton was to capture Fort Beauséjour to the east on the frontier between Nova Scotia and Acadia.

British forces under fire from the French and Indian forces at Monongahela, when the Braddock expedition failed to take Fort Duquesne.

Braddock led about 1,500 army troops and provincial militia on the Braddock expedition in June 1755 to take Fort Duquesne, with George Washington as one of his aides. The expedition was a disaster. It was attacked by French regulars, Canadian Militiamen, and Indian warriors ambushing them from hiding places up in trees and behind logs, and Braddock called for a retreat. He was killed and approximately 1,000 British soldiers were killed or injured. The remaining 500 British troops retreated to Virginia, led by Washington. Washington and Thomas Gage played key roles in organizing the retreat—two future opponents in the American Revolutionary War.

The British government initiated a plan to increase their military capability in preparation for war following news of Braddock's defeat and the start of parliament's session in November 1755. Among the early legislative measures were the Recruiting Act 1756, the Commissions to Foreign Protestants Act 1756 for the Royal American Regiment, the Navigation Act 1756, and the Continuance of Acts 1756. England passed the Naval Prize Act 1756 following the proclamation of war on May 17 to allow the capture of ships and establish privateering.

The French acquired a copy of the British war plans, including the activities of Shirley and Johnson. Shirley's efforts to fortify Oswego were bogged down in logistical difficulties, exacerbated by his inexperience in managing large expeditions. In conjunction, he was made aware that the French were massing for an attack on Fort Oswego in his absence when he planned to attack Fort Niagara. As a response, he left garrisons at Oswego, Fort Bull, and Fort Williams, the last two located on the Oneida Carry between the Mohawk River and Wood Creek at Rome, New York. Supplies were cached at Fort Bull for use in the projected attack on Niagara.

Johnson's expedition was better organized than Shirley's, which was noticed by New France's governor the Marquis de Vaudreuil. Vaudreuil had been concerned about the extended supply line to the forts on the Ohio, and he had sent Baron Dieskau to lead the defenses at Frontenac against Shirley's expected attack. Vaudreuil saw Johnson as the larger threat and sent Dieskau to Fort St. Frédéric to meet that threat. Dieskau planned to attack the British encampment at Fort Edward at the upper end of navigation on the Hudson River, but Johnson had strongly fortified it, and Dieskau's Indian support was reluctant to attack. The two forces finally met in the bloody Battle of Lake George between Fort Edward and Fort William Henry. The battle ended inconclusively, with both sides withdrawing from the field. Johnson's advance stopped at Fort William Henry, and the French withdrew to Ticonderoga Point, where they began the construction of Fort Carillon (later renamed Fort Ticonderoga after the British captured it in 1759).

British raid on the Acadian settlement of Grimross. Efforts to undermine the French Fortress of Louisbourg resulted in the forcible removal of the Acadians.

Colonel Monckton captured Fort Beauséjour in June 1755 in the sole British success that year, cutting off the French Fortress Louisbourg from land-based reinforcements. To cut vital supplies to Louisbourg, Nova Scotia's Governor Charles Lawrence ordered the deportation of the French-speaking Acadian population from the area. Monckton's forces, including companies of Rogers' Rangers, forcibly removed thousands of Acadians, chasing down many who resisted and sometimes committing atrocities. Cutting off supplies to Louisbourg led to its demise. The Acadian resistance was sometimes quite stiff, in concert with Indian allies including the Mi'kmaq, with ongoing frontier raids against Dartmouth and Lunenburg, among others. The only clashes of any size were at Petitcodiac in 1755 and at Bloody Creek near Annapolis Royal in 1757, other than the campaigns to expel the Acadians ranging around the Bay of Fundy, on the Petitcodiac and St. John rivers, and Île Saint-Jean.

French victories, 1756–1757

Following the death of Braddock, William Shirley assumed command of British forces in North America, and he laid out his plans for 1756 at a meeting in Albany in December 1755. He proposed renewing the efforts to capture Niagara, Crown Point, and Duquesne, with attacks on Fort Frontenac on the north shore of Lake Ontario and an expedition through the wilderness of the Maine district and down the Chaudière River to attack the city of Quebec. His plan, however, got bogged down by disagreements and disputes with others, including William Johnson and New York's Governor Sir Charles Hardy, and consequently gained little support.

In January 1756, John Campbell was named as the new British Commander-in-Chief, North America.

Newcastle replaced him in January 1756 with Lord Loudoun, with Major General James Abercrombie as his second in command. Neither of these men had as much campaign experience as the trio of officers whom France sent to North America. French regular army reinforcements arrived in New France in May 1756, led by Major General Louis-Joseph de Montcalm and seconded by the Chevalier de Lévis and Colonel François-Charles de Bourlamaque, all experienced veterans from the War of the Austrian Succession. On May 18, 1756, Britain formally declared war on France, which expanded the war into Europe and came to be known as the Seven Years' War.

Governor Vaudreuil had ambitions to become the French commander in chief, in addition to his role as governor, and he acted during the winter of 1756 before those reinforcements arrived. Scouts had reported the weakness of the British supply chain, so he ordered an attack against the forts which Shirley had erected at the Oneida Carry. In the Battle of Fort Bull, French forces destroyed the fort and large quantities of supplies, including 45,000 pounds of gunpowder. They set back any British hopes for campaigns on Lake Ontario and endangered the Oswego garrison, already short on supplies. French forces in the Ohio valley also continued to intrigue with Indians throughout the area, encouraging them to raid frontier settlements. This led to ongoing alarms along the western frontiers, with streams of refugees returning east to get away from the action.

In August 1756, French soldiers and native warriors led by Louis-Joseph de Montcalm successfully attacked Fort Oswego.

The new British command was not in place until July. Abercrombie arrived in Albany but refused to take any significant actions until Loudoun approved them, and Montcalm took bold action against his inertia. He built on Vaudreuil's work harassing the Oswego garrison and executed a strategic feint by moving his headquarters to Ticonderoga, as if to presage another attack along Lake George. With Abercrombie pinned down at Albany, Montcalm slipped away and led the successful attack on Oswego in August. In the aftermath, Montcalm and the Indians under his command disagreed about the disposition of prisoners' personal effects. The Europeans did not consider them prizes and prevented the Indians from stripping the prisoners of their valuables, which angered the Indians.

Loudoun was a capable administrator but a cautious field commander, and he planned one major operation for 1757: an attack on New France's capital of Quebec. He left a sizable force at Fort William Henry to distract Montcalm and began organizing for the expedition to Quebec. He was then ordered to attack Louisbourg first by William Pitt, the Secretary of State responsible for the colonies. The expedition was beset by delays of all kinds but was finally ready to sail from Halifax, Nova Scotia, in early August. In the meantime, French ships had escaped the British blockade of the French coast, and a fleet awaited Loudoun at Louisbourg which outnumbered the British fleet. Faced with this strength, Loudoun returned to New York amid news that a massacre had occurred at Fort William Henry.

Montcalm attempts to stop native warriors from attacking the British. A number of British soldiers were killed after the Siege of Fort William Henry.

French irregular forces (Canadian scouts and Indians) harassed Fort William Henry throughout the first half of 1757. In January, they ambushed British rangers near Ticonderoga. In February, they launched a raid against the position across the frozen Lake George, destroying storehouses and buildings outside the main fortification. In early August, Montcalm and 7,000 troops besieged the fort, which capitulated with an agreement to withdraw under parole. When the withdrawal began, some of Montcalm's Indian allies attacked the British column because they were angry about the lost opportunity for loot, killing and capturing several hundred men, women, children, and slaves. The aftermath of the siege may have contributed to the transmission of smallpox into remote Indian populations, as some Indians were reported to have traveled from beyond the Mississippi to participate in the campaign and returned afterward. Modern writer William Nester believes that the Indians might have been exposed to European carriers, although no proof exists.

British conquest, 1758–1760

Vaudreuil and Montcalm were minimally resupplied in 1758, as the British blockade of the French coastline limited French shipping. The situation in New France was further exacerbated by a poor harvest in 1757, a difficult winter, and the allegedly corrupt machinations of François Bigot, the intendant of the territory. His schemes to supply the colony inflated prices and were believed by Montcalm to line his pockets and those of his associates. A massive outbreak of smallpox among western Indian tribes led many of them to stay away from trading in 1758. The disease probably spread through the crowded conditions at William Henry after the battle; yet the Indians blamed the French for bringing "bad medicine" as well as denying them prizes at Fort William Henry.

Montcalm focused his meager resources on the defense of the St. Lawrence, with primary defenses at Carillon, Quebec, and Louisbourg, while Vaudreuil argued unsuccessfully for a continuation of the raiding tactics that had worked quite effectively in previous years. The British failures in North America combined with other failures in the European theater and led to Newcastle's fall from power along with the Duke of Cumberland, his principal military advisor.

British forces besieging the Fortress of Louisbourg. The French fortress fell in July 1758 after a 48-day siege.

Newcastle and Pitt joined in an uneasy coalition in which Pitt dominated the military planning. He embarked on a plan for the 1758 campaign that was largely developed by Loudoun. He had been replaced by Abercrombie as commander in chief after the failures of 1757. Pitt's plan called for three major offensive actions involving large numbers of regular troops supported by the provincial militias, aimed at capturing the heartlands of New France. Two of the expeditions were successful, with Fort Duquesne and Louisbourg falling to sizable British forces.

1758

The Forbes Expedition was a British campaign in September–October 1758, with 6,000 troops led by General John Forbes sent to drive out the French from the contested Ohio Country. The French withdrew from Fort Duquesne and left the British in control of the Ohio River Valley. The great French fortress at Louisbourg in Nova Scotia was captured after a siege.

A British expedition sent to invade Canada was repulsed by the French at the Battle of Carillon in July 1758.

The third invasion was stopped with the improbable French victory in the Battle of Carillon, in which 3,600 Frenchmen defeated Abercrombie's force of 18,000 regulars, militia, and Indian allies outside the fort which the French called Carillon and the British called Ticonderoga. Abercrombie saved something from the disaster when he sent John Bradstreet on an expedition that successfully destroyed Fort Frontenac, including caches of supplies destined for New France's western forts and furs destined for Europe. Abercrombie was recalled and replaced by Jeffery Amherst, victor at Louisbourg.

The French had generally poor results in 1758 in most theaters of the war. The new foreign minister was the duc de Choiseul, and he decided to focus on an invasion of Britain to draw British resources away from North America and the European mainland. The invasion failed both militarily and politically, as Pitt again planned significant campaigns against New France and sent funds to Britain's mainland ally of Prussia, while the French Navy failed in the 1759 naval battles at Lagos and Quiberon Bay. In one piece of good fortune, some French supply ships did manage to depart France and elude the British blockade of the French coast.

1759–1760

After a three-month siege of Quebec City, British forces captured the city at the Plains of Abraham.

The British proceeded to wage a campaign in the northwest frontier of Canada in an effort to cut off the French frontier forts to the west and south. They captured Ticonderoga and Fort Niagara, and they defeated the French at the Thousand Islands in the summer of 1759. In September 1759, James Wolfe defeated Montcalm in the Battle of the Plains of Abraham which claimed the lives of both commanders. After the battle, the French capitulated the city to the British.

In April 1760, François Gaston de Lévis led French forces to launch an attack to retake Quebec. Although he won the Battle of Sainte-Foy, Lévis' subsequent siege of Quebec ended in defeat when British ships arrived to relieve the garrison. After Lévis had retreated he was given another blow when a British naval victory at Restigouche brought the loss of French ships meant to resupply his army. In July Jeffrey Amherst then led British forces numbering around 18,000 men in a three pronged attack on Montreal. After eliminating French positions along the way all three forces met up and surrounded Montreal in September. Many Canadians deserted or surrendered their arms to British forces while the Native allies of the French sought peace and neutrality. De Lévis and the Marquis de Vaudreuil reluctantly signed the Articles of Capitulation of Montreal on September 8 which effectively completed the British conquest of New France.

Sporadic engagements, 1760–1763

Most of the fighting ended in America in 1760, although it continued in Europe between France and Britain. The notable exception was the French seizure of St. John's, Newfoundland. General Amherst heard of this surprise action and immediately dispatched troops under his nephew William Amherst, who regained control of Newfoundland after the Battle of Signal Hill in September 1762. Many of the British troops who were stationed in America were reassigned to participate in further British actions in the West Indies, including the capture of Spanish Havana when Spain belatedly entered the conflict on the side of France, and a British expedition against French Martinique in 1762 led by Major General Robert Monckton.

Peace

French authorities surrendering Montreal to British forces in 1760.

Governor Vaudreuil in Montreal negotiated a capitulation with General Amherst in September 1760. Amherst granted his requests that any French residents who chose to remain in the colony would be given freedom to continue worshiping in their Roman Catholic tradition, to own property, and to remain undisturbed in their homes. The British provided medical treatment for the sick and wounded French soldiers, and French regular troops were returned to France aboard British ships with an agreement that they were not to serve again in the present war.

General Amherst also oversaw the transfer of French fortifications to British control on the western frontier. The policies which he introduced in those lands disturbed large numbers of Indians and contributed to the outbreak of Pontiac's War in 1763. A series of Indian attacks on frontier forts and settlements required the continued deployment of British forces, and the conflict was not fully concluded until 1766.

Beginning from the 1750's and lasting until the 1760's, a smallpox outbreak devastated several Indian communities throughout the American Midwest. The outbreak was brought on in part by victorious Indian warriors who had fought on the side of the French bringing home prizes of war which had been infected with the disease; the Ojibwe, Odawa and Potawatomi peoples were most affected by the outbreak. An oral account from Odawa tribal leader and historian Andrew Blackbird claimed that the outbreak had "entirely depopulated and laid waste" to Waganagisi, a large Odawa settlement.

The war in North America, along with the global Seven Years War, officially ended with the signing of the Treaty of Paris on 10 February 1763, by the kingdoms of Great Britain, France and Spain, with Portugal in agreement. The British offered France the choice of surrendering either its continental North American possessions east of the Mississippi or the Caribbean islands of Guadeloupe and Martinique, which had been occupied by the British. France chose to cede the former but was able to negotiate the retention of Saint Pierre and Miquelon, two small islands in the Gulf of St. Lawrence, along with fishing rights in the area. They viewed the economic value of the Caribbean islands' sugar cane to be greater and easier to defend than the furs from the continent. French philosopher Voltaire referred to Canada disparagingly as nothing more than a few acres of snow. The British, however, were happy to take New France, as defence of their North American colonies would no longer be an issue (though the absence of that threat caused many colonists to conclude they no longer needed British protection). Britain also had ample places from which to obtain sugar. Spain traded Florida to Britain in order to regain Cuba, but they also gained Louisiana from France, including New Orleans, in compensation for their losses. Great Britain and Spain also agreed that navigation on the Mississippi River was to be open to vessels of all nations.

Consequences

The resulting peace dramatically changed the political landscape of North America, with New France ceded to the British and the Spanish.

The war changed economic, political, governmental, and social relations among the three European powers, their colonies, and the people who inhabited those territories. France and Britain both suffered financially because of the war, with significant long-term consequences.

Britain gained control of French Canada and Acadia, colonies containing approximately 80,000 primarily French-speaking Roman Catholic residents. The deportation of Acadians beginning in 1755 made land available to immigrants from Europe and migrants from the colonies to the south. The British resettled many Acadians throughout its American provinces, but many went to France and some went to New Orleans, which they expected to remain French. Some were sent to colonize places as diverse as French Guiana and the Falkland Islands, but these efforts were unsuccessful. The Louisiana population contributed to founding the Cajun population. (The French word "Acadien" changed to "Cadien" then to "Cajun".)

King George III issued the Royal Proclamation of 1763 on October 7, 1763, which outlined the division and administration of the newly conquered territory, and it continues to govern relations to some extent between the government of Canada and the First Nations. Included in its provisions was the reservation of lands west of the Appalachian Mountains to its Indian population, a demarcation that was only a temporary impediment to a rising tide of westward-bound settlers. The proclamation also contained provisions that prevented civic participation by the Roman Catholic Canadians.

A copy of the Quebec Act passed in 1774 which addressed a number of grievances held by French Canadians and Indians, although it angered American colonists

The Quebec Act of 1774 addressed issues brought forth by Roman Catholic French Canadians from the 1763 proclamation, and it transferred the Indian Reserve into the Province of Quebec. The Act maintained French Civil law, including the seigneurial system, a medieval code removed from France within a generation by the French Revolution. The Quebec Act was a major concern for the largely Protestant Thirteen Colonies over the advance of "popery". It is typically associated with other Intolerable Acts, legislation that eventually led to the American Revolutionary War. The Quebec Act served as the constitutional document for the Province of Quebec until it was superseded by the Constitutional Act 1791.

The Seven Years' War nearly doubled Great Britain's national debt. The Crown sought sources of revenue to pay it off and attempted to impose new taxes on its colonies. These attempts were met with increasingly stiff resistance, until troops were called in to enforce the Crown's authority, and they ultimately led to the start of the American Revolutionary War. France attached comparatively little value to its American possessions, apart from the highly profitable sugar-producing Antilles islands which it retained. Minister Choiseul considered that he had made a good deal at the Treaty of Paris, and Voltaire wrote that Louis XV had lost a few acres of snow.  However, the military defeat and the financial burden of the war weakened the French monarchy and contributed to the advent of the French Revolution in 1789.

The elimination of French power in America meant the disappearance of a strong ally for some Indian tribes. The Ohio Country was now more available to colonial settlement due to the construction of military roads by Braddock and Forbes. The Spanish takeover of the Louisiana territory was not completed until 1769, and it had modest repercussions. The British takeover of Spanish Florida resulted in the westward migration of Indian tribes who did not want to do business with them. This migration also caused a rise in tensions between the Choctaw and the Creek, historic enemies who were competing for land. The change of control in Florida also prompted most of its Spanish Catholic population to leave. Most went to Cuba, although some Christianized Yamasee were resettled to the coast of Mexico.

France returned to America in 1778 with the establishment of a Franco-American alliance against Great Britain in the American Revolutionary War, in what historian Alfred A. Cave describes as French "revenge for Montcalm's death".

Single-nucleotide polymorphism

From Wikipedia, the free encyclopedia

The upper DNA molecule differs from the lower DNA molecule at a single base-pair location (a G/A polymorphism)

In genetics, a single-nucleotide polymorphism (SNP /snɪp/; plural SNPs /snɪps/) is a germline substitution of a single nucleotide at a specific position in the genome. Although certain definitions require the substitution to be present in a sufficiently large fraction of the population (e.g. 1% or more), many publications do not apply such a frequency threshold.

For example, at a specific base position in the human genome, the G nucleotide may appear in most individuals, but in a minority of individuals, the position is occupied by an A. This means that there is a SNP at this specific position, and the two possible nucleotide variations – G or A – are said to be the alleles for this specific position.

SNPs pinpoint differences in our susceptibility to a wide range of diseases, for example age-related macular degeneration (a common SNP in the CFH gene is associated with increased risk of the disease) or nonalcoholic fatty liver disease (a SNP in the PNPLA3 gene is associated with increased risk of the disease). The severity of illness and the way the body responds to treatments are also manifestations of genetic variations caused by SNPs. For example, the APOE E4 allele that is determined by two common SNPs, rs429358 and rs7412, in the APOE gene is not only associated with increased risk for Alzheimer’s disease but also younger age at onset of the disease.

A single-nucleotide variant (SNV) is a general term for single nucleotide change in DNA sequence. So a SNV can be a common SNP or a rare mutation, and can be germline or somatic and can be caused by cancer, but a SNP has to segregate in a species' population of organisms. SNVs also commonly arise in molecular diagnostics such as designing PCR primers to detect viruses, in which the viral RNA or DNA sample may contain SNVs.

Types

Types of SNPs
Types of single-nucleotide polymorphism (SNPs)

Single-nucleotide polymorphisms may fall within coding sequences of genes, non-coding regions of genes, or in the intergenic regions (regions between genes). SNPs within a coding sequence do not necessarily change the amino acid sequence of the protein that is produced, due to degeneracy of the genetic code.

SNPs in the coding region are of two types: synonymous SNPs and nonsynonymous SNPs. Synonymous SNPs do not affect the protein sequence, while nonsynonymous SNPs change the amino acid sequence of protein.

  • SNPs in non-coding regions can manifest in a higher risk of cancer, and may affect mRNA structure and disease susceptibility. Non-coding SNPs can also alter the level of expression of a gene, as an eQTL (expression quantitative trait locus).
  • SNPs in coding regions:
    • synonymous substitutions by definition do not result in a change of amino acid in the protein, but still can affect its function in other ways. An example would be a seemingly silent mutation in the multidrug resistance gene 1 (MDR1), which codes for a cellular membrane pump that expels drugs from the cell, can slow down translation and allow the peptide chain to fold into an unusual conformation, causing the mutant pump to be less functional (in MDR1 protein e.g. C1236T polymorphism changes a GGC codon to GGT at amino acid position 412 of the polypeptide (both encode glycine) and the C3435T polymorphism changes ATC to ATT at position 1145 (both encode isoleucine)).
    • nonsynonymous substitutions:

SNPs that are not in protein-coding regions may still affect gene splicing, transcription factor binding, messenger RNA degradation, or the sequence of noncoding RNA. Gene expression affected by this type of SNP is referred to as an eSNP (expression SNP) and may be upstream or downstream from the gene.

Frequency

More than 335 million SNPs have been found across humans from multiple populations. A typical genome differs from the reference human genome at 4 to 5 million sites, most of which (more than 99.9%) consist of SNPs and short indels.

Within a genome

The genomic distribution of SNPs is not homogenous; SNPs occur in non-coding regions more frequently than in coding regions or, in general, where natural selection is acting and "fixing" the allele (eliminating other variants) of the SNP that constitutes the most favorable genetic adaptation. Other factors, like genetic recombination and mutation rate, can also determine SNP density.

SNP density can be predicted by the presence of microsatellites: AT microsatellites in particular are potent predictors of SNP density, with long (AT)(n) repeat tracts tending to be found in regions of significantly reduced SNP density and low GC content.

Within a population

There are variations between human populations, so a SNP allele that is common in one geographical or ethnic group may be much rarer in another. However, this pattern of variation is relatively rare; in a global sample of 67.3 million SNPs, the Human Genome Diversity Project "found no such private variants that are fixed in a given continent or major region. The highest frequencies are reached by a few tens of variants present at >70% (and a few thousands at >50%) in Africa, the Americas, and Oceania. By contrast, the highest frequency variants private to Europe, East Asia, the Middle East, or Central and South Asia reach just 10 to 30%."

Within a population, SNPs can be assigned a minor allele frequency—the lowest allele frequency at a locus that is observed in a particular population. This is simply the lesser of the two allele frequencies for single-nucleotide polymorphisms.

With this knowledge scientists have developed new methods in analyzing population structures in less studied species. By using pooling techniques the cost of the analysis is significantly lowered. These techniques are based on sequencing a population in a pooled sample instead of sequencing every individual within the population by itself. With new bioinformatics tools there is a possibility of investigating population structure, gene flow and gene migration by observing the allele frequencies within the entire population. With these protocols there is a possibility in combining the advantages of SNPs with micro satellite markers. However, there are information lost in the process such as linkage disequilibrium and zygosity information.

Applications

  • Association studies can determine whether a genetic variant is associated with a disease or trait.
  • A tag SNP is a representative single-nucleotide polymorphism in a region of the genome with high linkage disequilibrium (the non-random association of alleles at two or more loci). Tag SNPs are useful in whole-genome SNP association studies, in which hundreds of thousands of SNPs across the entire genome are genotyped.
  • Haplotype mapping: sets of alleles or DNA sequences can be clustered so that a single SNP can identify many linked SNPs.
  • Linkage disequilibrium (LD), a term used in population genetics, indicates non-random association of alleles at two or more loci, not necessarily on the same chromosome. It refers to the phenomenon that SNP allele or DNA sequence that are close together in the genome tend to be inherited together. LD can be affected by two parameters (among other factors, such as population stratification): 1) The distance between the SNPs [the larger the distance, the lower the LD]. 2) Recombination rate [the lower the recombination rate, the higher the LD].
  • In genetic epidemiology SNPs are used to estimate transmission clusters.

Importance

Variations in the DNA sequences of humans can affect how humans develop diseases and respond to pathogens, chemicals, drugs, vaccines, and other agents. SNPs are also critical for personalized medicine. Examples include biomedical research, forensics, pharmacogenetics, and disease causation, as outlined below.

Clinical research

Genome-wide association study (GWAS)

One of main contributions of SNPs in clinical research is genome-wide association study (GWAS). Genome-wide genetic data can be generated by multiple technologies, including SNP array and whole genome sequencing. GWAS has been commonly used in identifying SNPs associated with diseases or clinical phenotypes or traits. Since GWAS is a genome-wide assessment, a large sample site is required to obtain sufficient statistical power to detect all possible associations. Some SNPs have relatively small effect on diseases or clinical phenotypes or traits. To estimate study power, the genetic model for disease needs to be considered, such as dominant, recessive, or additive effects. Due to genetic heterogeneity, GWAS analysis must be adjusted for race.

Candidate gene association study

Candidate gene association study is commonly used in genetic study before the invention of high throughput genotyping or sequencing technologies. Candidate gene association study is to investigate limited number of pre-specified SNPs for association with diseases or clinical phenotypes or traits. So this is a hypothesis driven approach. Since only a limited number of SNPs are tested, a relatively small sample size is sufficient to detect the association. Candidate gene association approach is also commonly used to confirm findings from GWAS in independent samples.

Homozygosity mapping in disease

Genome-wide SNP data can be used for homozygosity mapping. Homozygosity mapping is a method used to identify homozygous autosomal recessive loci, which can be a powerful tool to map genomic regions or genes that are involved in disease pathogenesis.

Forensics

SNPs have historically been used to match a forensic DNA sample to a suspect but has been made obsolete due to advancing STR-based DNA fingerprinting techniques. However, the development of next-generation-sequencing (NGS) technology may allow for more opportunities for the use of SNPs in phenotypic clues such as ethnicity, hair color, and eye color with a good probability of a match. This can additionally be applied to increase the accuracy of facial reconstructions by providing information that may otherwise be unknown, and this information can be used to help identify suspects even without a STR DNA profile match.

Some cons to using SNPs versus STRs is that SNPs yield less information than STRs, and therefore more SNPs are needed for analysis before a profile of a suspect is able to be created. Additionally, SNPs heavily rely on the presence of a database for comparative analysis of samples. However, in instances with degraded or small volume samples, SNP techniques are an excellent alternative to STR methods. SNPs (as opposed to STRs) have an abundance of potential markers, can be fully automated, and a possible reduction of required fragment length to less than 100bp.

Pharmacogenetics

Pharmacogenetics focuses on identifying genetic variations including SNPs associated with differential responses to treatment. Many drug metabolizing enzymes, drug targets, or target pathways can be influenced by SNPs. The SNPs involved in drug metabolizing enzyme activities can change drug pharmacokinetics, while the SNPs involved in drug target or its pathway can change drug pharmacodynamics. Therefore, SNPs are potential genetic markers that can be used to predict drug exposure or effectiveness of the treatment. Genome-wide pharmacogenetic study is called pharmacogenomics. Pharmacogenetics and pharmacogenomics are important in the development of precision medicine, especially for life threatening diseases such as cancers.

Disease

Only small amount of SNPs in the human genome may have impact on human diseases. Large scale GWAS has been done for the most important human diseases, including heart diseases, metabolic diseases, autoimmune diseases, and neurodegenerative and psychiatric disorders. Most of the SNPs with relatively large effects on these diseases have been identified. These findings have significantly improved understanding of disease pathogenesis and molecular pathways, and facilitated development of better treatment. Further GWAS with larger samples size will reveal the SNPs with relatively small effect on diseases. For common and complex diseases, such as type-2 diabetes, rheumatoid arthritis, and Alzheimer’s disease, multiple genetic factors are involved in disease etiology. In addition, gene-gene interaction and gene-environment interaction also play an important role in disease initiation and progression.

Examples

Databases

As there are for genes, bioinformatics databases exist for SNPs.

  • dbSNP is a SNP database from the National Center for Biotechnology Information (NCBI). As of June 8, 2015, dbSNP listed 149,735,377 SNPs in humans.
  • Kaviar is a compendium of SNPs from multiple data sources including dbSNP.
  • SNPedia is a wiki-style database supporting personal genome annotation, interpretation and analysis.
  • The OMIM database describes the association between polymorphisms and diseases (e.g., gives diseases in text form)
  • dbSAP – single amino-acid polymorphism database for protein variation detection
  • The Human Gene Mutation Database provides gene mutations causing or associated with human inherited diseases and functional SNPs
  • The International HapMap Project, where researchers are identifying Tag SNPs to be able to determine the collection of haplotypes present in each subject.
  • GWAS Central allows users to visually interrogate the actual summary-level association data in one or more genome-wide association studies.

The International SNP Map working group mapped the sequence flanking each SNP by alignment to the genomic sequence of large-insert clones in Genebank. These alignments were converted to chromosomal coordinates that is shown in Table 1. This list has greatly increased since, with, for instance, the Kaviar database now listing 162 million single nucleotide variants (SNVs).

Chromosome Length(bp) All SNPs
TSC SNPs


Total SNPs kb per SNP Total SNPs kb per SNP
1 214,066,000 129,931 1.65 75,166 2.85
2 222,889,000 103,664 2.15 76,985 2.90
3 186,938,000 93,140 2.01 63,669 2.94
4 169,035,000 84,426 2.00 65,719 2.57
5 170,954,000 117,882 1.45 63,545 2.69
6 165,022,000 96,317 1.71 53,797 3.07
7 149,414,000 71,752 2.08 42,327 3.53
8 125,148,000 57,834 2.16 42,653 2.93
9 107,440,000 62,013 1.73 43,020 2.50
10 127,894,000 61,298 2.09 42,466 3.01
11 129,193,000 84,663 1.53 47,621 2.71
12 125,198,000 59,245 2.11 38,136 3.28
13 93,711,000 53,093 1.77 35,745 2.62
14 89,344,000 44,112 2.03 29,746 3.00
15 73,467,000 37,814 1.94 26,524 2.77
16 74,037,000 38,735 1.91 23,328 3.17
17 73,367,000 34,621 2.12 19,396 3.78
18 73,078,000 45,135 1.62 27,028 2.70
19 56,044,000 25,676 2.18 11,185 5.01
20 63,317,000 29,478 2.15 17,051 3.71
21 33,824,000 20,916 1.62 9,103 3.72
22 33,786,000 28,410 1.19 11,056 3.06
X 131,245,000 34,842 3.77 20,400 6.43
Y 21,753,000 4,193 5.19 1,784 12.19
RefSeq 15,696,674 14,534 1.08
Totals 2,710,164,000 1,419,190 1.91 887,450 3.05

Nomenclature

The nomenclature for SNPs include several variations for an individual SNP, while lacking a common consensus.

The rs### standard is that which has been adopted by dbSNP and uses the prefix "rs", for "reference SNP", followed by a unique and arbitrary number. SNPs are frequently referred to by their dbSNP rs number, as in the examples above.

The Human Genome Variation Society (HGVS) uses a standard which conveys more information about the SNP. Examples are:

  • c.76A>T: "c." for coding region, followed by a number for the position of the nucleotide, followed by a one-letter abbreviation for the nucleotide (A, C, G, T or U), followed by a greater than sign (">") to indicate substitution, followed by the abbreviation of the nucleotide which replaces the former
  • p.Ser123Arg: "p." for protein, followed by a three-letter abbreviation for the amino acid, followed by a number for the position of the amino acid, followed by the abbreviation of the amino acid which replaces the former.

SNP analysis

SNPs can be easily assayed due to only containing two possible alleles and three possible genotypes involving the two alleles: homozygous A, homozygous B and heterozygous AB, leading to many possible techniques for analysis. Some include: DNA sequencing; capillary electrophoresis; mass spectrometry; single-strand conformation polymorphism (SSCP); single base extension; electrochemical analysis; denaturating HPLC and gel electrophoresis; restriction fragment length polymorphism; and hybridization analysis.

Programs for prediction of SNP effects

An important group of SNPs are those that corresponds to missense mutations causing amino acid change on protein level. Point mutation of particular residue can have different effect on protein function (from no effect to complete disruption its function). Usually, change in amino acids with similar size and physico-chemical properties (e.g. substitution from leucine to valine) has mild effect, and opposite. Similarly, if SNP disrupts secondary structure elements (e.g. substitution to proline in alpha helix region) such mutation usually may affect whole protein structure and function. Using those simple and many other machine learning derived rules a group of programs for the prediction of SNP effect was developed:

  • SIFT This program provides insight into how a laboratory induced missense or nonsynonymous mutation will affect protein function based on physical properties of the amino acid and sequence homology.
  • LIST (Local Identity and Shared Taxa) estimates the potential deleteriousness of mutations resulted from altering their protein functions. It is based on the assumption that variations observed in closely related species are more significant when assessing conservation compared to those in distantly related species.
  • SNAP2
  • SuSPect
  • PolyPhen-2
  • PredictSNP
  • MutationTaster: official website
  • Variant Effect Predictor from the Ensembl project
  • SNPViz This program provides a 3D representation of the protein affected, highlighting the amino acid change so doctors can determine pathogenicity of the mutant protein.
  • PROVEAN
  • PhyreRisk is a database which maps variants to experimental and predicted protein structures.
  • Missense3D is a tool which provides a stereochemical report on the effect of missense variants on protein structure.

Ferromagnetism

From Wikipedia, the free encyclopedia

A magnet made of alnico, a ferromagnetic iron alloy, with its keeper

Ferromagnetism is the basic mechanism by which certain materials (such as iron) form permanent magnets, or are attracted to magnets. In physics, several different types of magnetism are distinguished. Ferromagnetism (along with the similar effect ferrimagnetism) is the strongest type and is responsible for the common phenomenon of magnetism in magnets encountered in everyday life. Substances respond weakly to magnetic fields with three other types of magnetism—paramagnetism, diamagnetism, and antiferromagnetism—but the forces are usually so weak that they can be detected only by sensitive instruments in a laboratory. An everyday example of ferromagnetism is a refrigerator magnet used to hold notes on a refrigerator door. The attraction between a magnet and ferromagnetic material is "the quality of magnetism first apparent to the ancient world, and to us today".

Permanent magnets (materials that can be magnetized by an external magnetic field and remain magnetized after the external field is removed) are either ferromagnetic or ferrimagnetic, as are the materials that are noticeably attracted to them. Only a few substances are ferromagnetic. The common ones are iron, cobalt, nickel and most of their alloys, and some compounds of rare-earth metals. Ferromagnetism is very important in industry and modern technology and is the basis for many electrical and electromechanical devices such as electromagnets, electric motors, generators, transformers, and magnetic storage such as tape recorders, and hard disks, and nondestructive testing of ferrous materials.

Ferromagnetic materials can be divided into magnetically "soft" materials like annealed iron, which can be magnetized but do not tend to stay magnetized, and magnetically "hard" materials, which do. Permanent magnets are made from "hard" ferromagnetic materials such as alnico and ferrimagnetic materials such as ferrite that are subjected to special processing in a strong magnetic field during manufacture to align their internal microcrystalline structure, making them very hard to demagnetize. To demagnetize a saturated magnet, a certain magnetic field must be applied, and this threshold depends on coercivity of the respective material. "Hard" materials have high coercivity, whereas "soft" materials have low coercivity. The overall strength of a magnet is measured by its magnetic moment or, alternatively, the total magnetic flux it produces. The local strength of magnetism in a material is measured by its magnetization.

History and distinction from ferrimagnetism

Ferromagnetic material: all the molecular magnetic dipoles are pointed in the same direction
 
Ferrimagnetic material: some of the dipoles point in the opposite direction, but their smaller contribution is overcome by the others

Historically, the term ferromagnetism was used for any material that could exhibit spontaneous magnetization: a net magnetic moment in the absence of an external magnetic field; that is any material that could become a magnet. This general definition is still in common use.

However, in a landmark paper in 1948, Louis Néel showed that there are two levels of magnetic alignment that result in this behavior. One is ferromagnetism in the strict sense, where all the magnetic moments are aligned. The other is ferrimagnetism, where some magnetic moments point in the opposite direction but have a smaller contribution, so there is still a spontaneous magnetization.

In the special case where the opposing moments balance completely, the alignment is known as antiferromagnetism. Therefore antiferromagnets do not have a spontaneous magnetization.

Ferromagnetic materials

Curie temperatures for some crystalline ferromagnetic materials
Material Curie
temp. (K)
Co 1388
Fe 1043
Fe2O3 948
NiOFe2O3 858
CuOFe2O3 728
MgOFe2O3 713
MnBi 630
Ni 627
Nd2Fe14 B 593
MnSb 587
MnOFe2O3 573
Y3Fe5O12 560
CrO2 386
MnAs 318
Gd 292
Tb 219
Dy 88
EuO 69


Ferromagnetism is an unusual property that occurs in only a few substances. The common ones are the transition metals iron, nickel, cobalt and their alloys, and alloys of rare-earth metals. It is a property not just of the chemical make-up of a material, but of its crystalline structure and microstructure. Their ferromagnetism results from having many unpaired electrons in their d-block in the case of iron and its relatives, or the f-block in the case of the rare-earth metals, a result of Hund's rule of maximum multiplicity. There are ferromagnetic metal alloys whose constituents are not themselves ferromagnetic, called Heusler alloys, named after Fritz Heusler. Conversely, there are non-magnetic alloys, such as types of stainless steel, composed almost exclusively of ferromagnetic metals.

Amorphous (non-crystalline) ferromagnetic metallic alloys can be made by very rapid quenching (cooling) of a liquid alloy. These have the advantage that their properties are nearly isotropic (not aligned along a crystal axis); this results in low coercivity, low hysteresis loss, high permeability, and high electrical resistivity. One such typical material is a transition metal-metalloid alloy, made from about 80% transition metal (usually Fe, Co, or Ni) and a metalloid component (B, C, Si, P, or Al) that lowers the melting point.

A relatively new class of exceptionally strong ferromagnetic materials are the rare-earth magnets. They contain lanthanide elements that are known for their ability to carry large magnetic moments in well-localized f-orbitals.

The table lists a selection of ferromagnetic and ferrimagnetic compounds, along with the temperature above which they cease to exhibit spontaneous magnetization (see Curie temperature).

Unusual materials

Most ferromagnetic materials are metals, since the conducting electrons are often responsible for mediating the ferromagnetic interactions. It is therefore a challenge to develop ferromagnetic insulators, especially multiferroic materials, which are both ferromagnetic and ferroelectric.

A number of actinide compounds are ferromagnets at room temperature or exhibit ferromagnetism upon cooling. PuP is a paramagnet with cubic symmetry at room temperature, but which undergoes a structural transition into a tetragonal state with ferromagnetic order when cooled below its TC = 125 K. In its ferromagnetic state, PuP's easy axis is in the ⟨100⟩ direction.

In NpFe2 the easy axis is ⟨111⟩. Above TC ≈ 500 K, NpFe2 is also paramagnetic and cubic. Cooling below the Curie temperature produces a rhombohedral distortion wherein the rhombohedral angle changes from 60° (cubic phase) to 60.53°. An alternate description of this distortion is to consider the length c along the unique trigonal axis (after the distortion has begun) and a as the distance in the plane perpendicular to c. In the cubic phase this reduces to c/a = 1.00. Below the Curie temperature

which is the largest strain in any actinide compound. NpNi2 undergoes a similar lattice distortion below TC = 32 K, with a strain of (43 ± 5) × 10−4. NpCo2 is a ferrimagnet below 15 K.

In 2009, a team of MIT physicists demonstrated that a lithium gas cooled to less than one kelvin can exhibit ferromagnetism. The team cooled fermionic lithium-6 to less than 150 nK (150 billionths of one kelvin) using infrared laser cooling. This demonstration is the first time that ferromagnetism has been demonstrated in a gas.

In 2018, a team of University of Minnesota physicists demonstrated that body-centered tetragonal ruthenium exhibits ferromagnetism at room temperature.

Electrically induced ferromagnetism

Recent research has shown evidence that ferromagnetism can be induced in some materials by an electric current or voltage. Antiferromagnetic LaMnO3 and SrCoO have been switched to ferromagnetic by a current. In July 2020 scientists reported inducing ferromagnetism in the abundant diamagnetic material iron pyrite ("fool's gold") by an applied voltage. In these experiments the ferromagnetism was limited to a thin surface layer.

Explanation

The Bohr–Van Leeuwen theorem, discovered in the 1910s, showed that classical physics theories are unable to account for any form of magnetism, including ferromagnetism. Magnetism is now regarded as a purely quantum mechanical effect. Ferromagnetism arises due to two effects from quantum mechanics: spin and the Pauli exclusion principle.

Origin of magnetism

One of the fundamental properties of an electron (besides that it carries charge) is that it has a magnetic dipole moment, i.e., it behaves like a tiny magnet, producing a magnetic field. This dipole moment comes from the more fundamental property of the electron that it has quantum mechanical spin. Due to its quantum nature, the spin of the electron can be in one of only two states; with the magnetic field either pointing "up" or "down" (for any choice of up and down). The spin of the electrons in atoms is the main source of ferromagnetism, although there is also a contribution from the orbital angular momentum of the electron about the nucleus. When these magnetic dipoles in a piece of matter are aligned, (point in the same direction) their individually tiny magnetic fields add together to create a much larger macroscopic field.

However, materials made of atoms with filled electron shells have a total dipole moment of zero: because the electrons all exist in pairs with opposite spin, every electron's magnetic moment is cancelled by the opposite moment of the second electron in the pair. Only atoms with partially filled shells (i.e., unpaired spins) can have a net magnetic moment, so ferromagnetism occurs only in materials with partially filled shells. Because of Hund's rules, the first few electrons in a shell tend to have the same spin, thereby increasing the total dipole moment.

These unpaired dipoles (often called simply "spins", even though they also generally include orbital angular momentum) tend to align in parallel to an external magnetic field – an effect called paramagnetism. Ferromagnetism involves an additional phenomenon, however: in a few substances the dipoles tend to align spontaneously, giving rise to a spontaneous magnetization, even when there is no applied field.

Exchange interaction

When two nearby atoms have unpaired electrons, whether the electron spins are parallel or antiparallel affects whether the electrons can share the same orbit as a result of the quantum mechanical effect called the exchange interaction. This in turn affects the electron location and the Coulomb (electrostatic) interaction and thus the energy difference between these states.

The exchange interaction is related to the Pauli exclusion principle, which says that two electrons with the same spin cannot also be in the same spatial state (orbital). This is a consequence of the spin–statistics theorem and that electrons are fermions. Therefore, under certain conditions, when the orbitals of the unpaired outer valence electrons from adjacent atoms overlap, the distributions of their electric charge in space are farther apart when the electrons have parallel spins than when they have opposite spins. This reduces the electrostatic energy of the electrons when their spins are parallel compared to their energy when the spins are antiparallel, so the parallel-spin state is more stable. This difference in energy is called the exchange energy. In simple terms, the outer electrons of adjacent atoms, which repel each other, can move further apart by aligning their spins in parallel, so the spins of these electrons tend to line up.

This energy difference can be orders of magnitude larger than the energy differences associated with the magnetic dipole–dipole interaction due to dipole orientation, which tends to align the dipoles antiparallel. In certain doped semiconductor oxides RKKY interactions have been shown to bring about periodic longer-range magnetic interactions, a phenomenon of significance in the study of spintronic materials.

The materials in which the exchange interaction is much stronger than the competing dipole–dipole interaction are frequently called magnetic materials. For instance, in iron (Fe) the exchange force is about 1000 times stronger than the dipole interaction. Therefore, below the Curie temperature virtually all of the dipoles in a ferromagnetic material will be aligned. In addition to ferromagnetism, the exchange interaction is also responsible for the other types of spontaneous ordering of atomic magnetic moments occurring in magnetic solids, antiferromagnetism and ferrimagnetism. There are different exchange interaction mechanisms which create the magnetism in different ferromagnetic, ferrimagnetic, and antiferromagnetic substances. These mechanisms include direct exchange, RKKY exchange, double exchange, and superexchange.

Magnetic anisotropy

Although the exchange interaction keeps spins aligned, it does not align them in a particular direction. Without magnetic anisotropy, the spins in a magnet randomly change direction in response to thermal fluctuations and the magnet is superparamagnetic. There are several kinds of magnetic anisotropy, the most common of which is magnetocrystalline anisotropy. This is a dependence of the energy on the direction of magnetization relative to the crystallographic lattice. Another common source of anisotropy, inverse magnetostriction, is induced by internal strains. Single-domain magnets also can have a shape anisotropy due to the magnetostatic effects of the particle shape. As the temperature of a magnet increases, the anisotropy tends to decrease, and there is often a blocking temperature at which a transition to superparamagnetism occurs.

Magnetic domains

Electromagnetic dynamic magnetic domain motion of grain-oriented electrical silicon steel
 
Kerr micrograph of metal surface showing magnetic domains, with red and green stripes denoting opposite magnetization directions
 

The above would seem to suggest that every piece of ferromagnetic material should have a strong magnetic field, since all the spins are aligned, yet iron and other ferromagnets are often found in an "unmagnetized" state. The reason for this is that a bulk piece of ferromagnetic material is divided into tiny regions called magnetic domains (also known as Weiss domains). Within each domain, the spins are aligned, but (if the bulk material is in its lowest energy configuration; i.e. unmagnetized), the spins of separate domains point in different directions and their magnetic fields cancel out, so the object has no net large scale magnetic field.

Ferromagnetic materials spontaneously divide into magnetic domains because the exchange interaction is a short-range force, so over long distances of many atoms the tendency of the magnetic dipoles to reduce their energy by orienting in opposite directions wins out. If all the dipoles in a piece of ferromagnetic material are aligned parallel, it creates a large magnetic field extending into the space around it. This contains a lot of magnetostatic energy. The material can reduce this energy by splitting into many domains pointing in different directions, so the magnetic field is confined to small local fields in the material, reducing the volume of the field. The domains are separated by thin domain walls a number of molecules thick, in which the direction of magnetization of the dipoles rotates smoothly from one domain's direction to the other.

Magnetized materials

Moving domain walls in a grain of silicon steel caused by an increasing external magnetic field in the "downward" direction, observed in a Kerr microscope. White areas are domains with magnetization directed up, dark areas are domains with magnetization directed down.

Thus, a piece of iron in its lowest energy state ("unmagnetized") generally has little or no net magnetic field. However, the magnetic domains in a material are not fixed in place; they are simply regions where the spins of the electrons have aligned spontaneously due to their magnetic fields, and thus can be altered by an external magnetic field. If a strong enough external magnetic field is applied to the material, the domain walls will move by the process of the spins of the electrons in atoms near the wall in one domain turning under the influence of the external field to face in the same direction as the electrons in the other domain, thus reorienting the domains so more of the dipoles are aligned with the external field. The domains will remain aligned when the external field is removed, creating a magnetic field of their own extending into the space around the material, thus creating a "permanent" magnet. The domains do not go back to their original minimum energy configuration when the field is removed because the domain walls tend to become 'pinned' or 'snagged' on defects in the crystal lattice, preserving their parallel orientation. This is shown by the Barkhausen effect: as the magnetizing field is changed, the magnetization changes in thousands of tiny discontinuous jumps as the domain walls suddenly "snap" past defects.

This magnetization as a function of the external field is described by a hysteresis curve. Although this state of aligned domains found in a piece of magnetized ferromagnetic material is not a minimal-energy configuration, it is metastable, and can persist for long periods, as shown by samples of magnetite from the sea floor which have maintained their magnetization for millions of years.

Heating and then cooling (annealing) a magnetized material, subjecting it to vibration by hammering it, or applying a rapidly oscillating magnetic field from a degaussing coil tends to release the domain walls from their pinned state, and the domain boundaries tend to move back to a lower energy configuration with less external magnetic field, thus demagnetizing the material.

Commercial magnets are made of "hard" ferromagnetic or ferrimagnetic materials with very large magnetic anisotropy such as alnico and ferrites, which have a very strong tendency for the magnetization to be pointed along one axis of the crystal, the "easy axis". During manufacture the materials are subjected to various metallurgical processes in a powerful magnetic field, which aligns the crystal grains so their "easy" axes of magnetization all point in the same direction. Thus the magnetization, and the resulting magnetic field, is "built in" to the crystal structure of the material, making it very difficult to demagnetize.

Curie temperature

As the temperature increases, thermal motion, or entropy, competes with the ferromagnetic tendency for dipoles to align. When the temperature rises beyond a certain point, called the Curie temperature, there is a second-order phase transition and the system can no longer maintain a spontaneous magnetization, so its ability to be magnetized or attracted to a magnet disappears, although it still responds paramagnetically to an external field. Below that temperature, there is a spontaneous symmetry breaking and magnetic moments become aligned with their neighbors. The Curie temperature itself is a critical point, where the magnetic susceptibility is theoretically infinite and, although there is no net magnetization, domain-like spin correlations fluctuate at all length scales.

The study of ferromagnetic phase transitions, especially via the simplified Ising spin model, had an important impact on the development of statistical physics. There, it was first clearly shown that mean field theory approaches failed to predict the correct behavior at the critical point (which was found to fall under a universality class that includes many other systems, such as liquid-gas transitions), and had to be replaced by renormalization group theory.

Female infanticide

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