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When she sank in 1545, the Mary Rose took with her not just her crew but their dress, food, equipment and everything on board. Now, 35 years after the excavation of the ship began, the conserved finds are being published. Michael J Allen, Brendan Derham, Jeremy Montagu and Ann Stirland describe some of the astonishing things retrieved. Julie Gardiner, Mary Rose series editor, introduces this special feature.

Launched in 1511 and one of the first craft with guns on more than one deck, the Mary Rose was the flagship of Henry VIII's burgeoning navy. She sank on July 19 1545 in battle with the French off Spithead, Portsmouth, by keeling over as she turned to deliver a broadside. Lying at an angle on the bottom of the Solent, partly buried in sediment, she did not respond to immediate attempts to lift her. Over the centuries her position was lost.

She was found and partly salvaged in 1836 and 1840, and rediscovered by historian, journalist and amateur diver Alexander McKee in 1971. By then her exposed parts had eroded, leaving less than half of the hull to be recovered so memorably in 1982, after years of painstaking excavation.

She sank suddenly and unexpectedly, and the ship went down with most of her contents and nearly all her 400 plus crew. Agreat many items were trapped by rapidly accumulated silts. Unusually, therefore, we can be certain that the majority of finds from the "site" were associated in use at a specific date – July 1545. This is of immense importance, as the ship lies on the cusp between the late medieval and early post-medieval periods. The finds have implications for the interpretation of all archaeological assemblages of the time (and many historical records) from southern England and beyond.

The wreck has produced an unprecedented collection of objects. Everything in this feature, with much more, is described in Before the Mast (reviewed Jul/Aug), one of five volumes on the ship's archaeology.The exceptional preservation of organic materials has provided unparalleled opportunities for the study of many classes of wooden, leather and textile objects that are normally rare survivals on archaeological sites. It has also enabled us to gain valuable insights into the provisioning of the vessel and some idea of the general conditions experienced by the men on board. We have learnt much about the crew themselves, both from their physical remains and from their many personal possessions.

The sheer quantity and variety of objects and materials have resulted in huge programmes of conservation and analysis. Hundreds of specialists based all over the world have been involved, and it has taken more than 20 years for these major publications to appear.

The publication project has been managed for the Mary Rose Trust by Wessex Archaeology (Julie Gardiner series editor, Charlotte Matthews financial manager). The final preparation and production of the series has been enabled by a major grant from the Heritage Lottery Fund.

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When it comes to artefacts from the ship, says Julie Gardiner, many individual assemblages can be called biggest and best, let alone the whole collection

Many thousands of everyday objects were recovered from the Mary Rose. Personal items and over 200 woodworking tools belonging to the ship's carpenters were stored in more than 50 surviving sea chests. The range of these objects is breathtaking: jewellery, coinage, books, purses, pocket sundials, silk buttons, paternosters (rosaries), sewing kits, knives, combs, swords and daggers, tankards and even a private supply of peppercorns, to name but a few. Shoes and woolly hats were also stored away, but many of over 300 items of clothing, including leather and cloth jerkins and over 250 shoes and boots, were, unsurprisingly, in use at the time of the sinking.

The galley (kitchen) area produced several hundred wooden and pewter dishes, platters, bowls and drinking vessels as well as cooking and storage vessels. A pair of bellows, ash boxes and cut logs accompanied the two great cooking cauldrons. Officers' tableware included a monogrammed set (a "garnish") belonging to Vice Admiral Sir George Carew, who died on board.

Several exquisite leather and wood book covers were found – some originally contained fragments of paper and visible writing but these were sadly too fragile to preserve. These were prayer or psalm books. One, elaborately decorated, is dated to 1545 and is by a known London bookmaker (Martin Doture). Another, adorned with a spread eagle, bears a Latin motto that translates as The Word of the Lord Endureth for Ever.

Two covers very similar to this were adapted for other purposes: one to hold a coin balance and the other a sundial. The sundial is one of nine examples from the ship (only three are known elsewhere), similar in size to a man's wristwatch. Each is made of boxwood with a brass "gnomon" and has a decorated, sometimes painted, face. They were most likely made in Nuremburg and, as they would have been aligned for that latitude, were probably more status symbols than useful timepieces.

Some of the most interesting and rarest items are the humblest. Every man probably carried a small, sharp knife and many seem to have made themselves a decorative knife-sheath. At least 24 of these otherwise unknown objects were found, each made of boxwood and decorated with a range of designs including crowns, eagles, geometric and foliate patterns, a fish and even a ship. We can picture the men whittling away at these in their idle hours while playing dice, dominoes, ninemen's morris or even "tabula" – an early form of backgammon, a table for which was found in the carpenters' cabin.

The ship's array of navigation instruments is of particular importance as it includes some of the earliest known ships' compasses, tide calculator, sounding lines and sandglasses as well as dividers and chart sticks indicative of the use of charts, some 50 years before they were thought to have been available for British waters.

The heart of any ship is its bell: the Mary Rose's does not bear a name, but, like the ship herself, it has survived.

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The band may not have been playing as the Mary Rose went down, but as Jeremy Montagu explains, the musical instruments recovered from the wreck have a significant story to tell

Apart from the five boatswain's calls (whistles used for transmitting orders on ships), at least nine instruments are represented from the Mary Rose: two whistles (one almost certainly a later intrusion, perhaps 19th century); part only of a tabor (a portable snare drum typically used to accompany dancing), its case and a beater (a fragmentary side-drum stick is also probably an intrusion); a shawm (a woodwind instrument, ancestral to the oboe); three tabor pipes (so named as they were played with one hand while the other drummed); two fiddles, and one bow.

The recovery of these items has been of the greatest importance, for each, with the exception of the whistles and the second long tabor pipe, is unique. One, the still (or quiet) shawm, has answered questions that plagued scholars for many years.

The shawm, tabor pipes and fiddles have confirmed the accuracy of iconography and texts long held to be doubtful. In the late 15th century, Tinctoris wrote a description of the instruments known to him, among them a douçaine, a quiet shawm with cylindrical bore and an incomplete range. No such instrument was known, though the term douçaine (and cognate words) also turned up elsewhere. The Mary Rose shawm fits Tinctoris's description precisely, save that due to the skills of its maker its range is not incomplete, as Charles Foster has discovered with his reconstructions. Thus the survival of this unique instrument has answered all the questions that Tinctoris's description raised and has shown that the douçaine had been improved, presumably in England, during the intervening decades.

Two of the tabor pipes are far longer than any other known example and match depictions from Britain and the Low Countries almost exactly contemporary with them. They require such a stretch of the arm that the depictions had never been taken seriously, but if real, as the Mary Rose instruments prove they were, they allow a musical compass less shrill and more suited to indoor and ensemble use than those of a more normal size. Together with those same depictions, they confirm contemporary evidence that pipe and tabor were used in ensemble with other instruments as well as by themselves. The third pipe is shorter but more finely made of better quality wood, and bears the double-plume or rabbit's foot mark of makers many of whose instruments survive. One of the other pipes bears the otherwise unknown name E Legros.

The two fiddles have back and sides carved from a block with a separate soundboard but, unlike the only other known contemporary fiddle, had an added neck and pegbox (alas lost to us), rather than being carved as a unit, thus again an improvement over continental contemporaries.

The Mary Rose instruments fill wide gaps in our knowledge. Even the surviving tabor beater, found inside the Legros pipe, thinner and lighter than any depicted, shows that playing techniques more elaborate than those notated in the period were available.

Jeremy Montagu is a percussionist who played with most of the major London and BBC orchestras, a collector of historic and contemporary musical instruments, and former curator of the Bate Collection of Musical Instruments and lecturer in the University of Oxford. He has written widely on musical instruments and their history.

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From pig DNA to hay stuffed into ill-fitting boots, says Michael J Allen, the Mary Rose is offering scientists an exceptional range of materials for study

Many wrecks have been studied, and samples of goo and mud taken for examination, but none has been subjected to wholesale environmental scrutiny like the Mary Rose. Opportunities are rare, as few wrecks contain a large quantity of the organic matter originally on board, such as food, flavourings, packing, insects and medicaments.

Unusually for the time, the Mary Rose recovery team included an environmental archaeologist (most significantly Ian Oxley), taking nearly 2,000 samples during the excavation. Many of these await processing as techniques improve. People and animal food were largely reduced to their bones, though astonishingly some human brain matter survived, as did animal fats. Some of the shrivelled, deformed but recognisable plant materials remained green and smelled of hay!

Avery recent programme of (ongoing) DNA analysis has isolated the genetic affinities of some of the crew. A pilot study of just nine mandibles has identified mitochondrial DNA of several haplogroups, indicating that the crew was of mixed, probably European ethnicity. Further analysis, complemented by isotope studies, will hopefully enable places of origin to be identified.

Without the Mary Rose, the science of DNA analysis from archaeological remains might not exist at all. In 1990 pig DNA was isolated from a pig bone from the ship: hardly startling in itself, but this was the first occasion on which the genuine survival of DNA from an archaeological specimen of known date had been proven, and was crucial in the development of forensic science.

Masses of animal and fish bone survived. Several casks contained salted beef and pork. The carcasses had been specifically butchered (on an industrial scale) to supply the navy, in a way not seen in any Tudor land-based assemblage.

Beef carcasses were strung up on hangers before being cleaved down the backbone, the limbs removed and the torso chopped up into pieces for salting and packing. Hams were hung below decks close to the galley. Salt cod, beheaded and filleted, was the other staple food, packed in casks and also found in a number of well-preserved wicker baskets.

Amonotonous diet of salt meat and fish would have been supplemented with butter, bread and peas and washed down with a daily ration of a gallon of "small" beer. None of these latter foodstuffs has survived.

Fresh fruits and seasoning were present in small quantities. Baskets of plums/greengages, a few cherries and nuts were usually found in the cabins where they may have been personal supplies. Flavourings included peppercorns which may also have had medicinal use.

A protective springy layer of twigs and broom "dunnage" was packed around goods stowed in the hold. Bracken and hay were used as stuffing for mattresses, and hay was also stuffed into ill-fitting shoes and boots.

MJ Allen is environmental manager for Wessex Archaeology.His research is focussed on the development of prehistoric landscapes, and has included coordinating recent specialist study of Stonehenge.

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In 1938 archaeologists in Wiltshire thought they had dug up a medieval barber-surgeon – a skeleton and a pair of scissors. From the hold of the Mary Rose, as Julie Gardiner describes, came the whole workshop

One of the most remarkable finds was in a cabin on the main deck, the chest that contained over 60 items belonging to the ship's barber-surgeon. The cabin also held other equipment, such as an angled bench for setting broken limbs. This is the most complete 16th century collection of medical equipment and surgical instruments yet known.

Though all iron components had disintegrated, it was possible to identify the wooden handles of trepans, saws, amputation knives, cautery irons and needles. Pewter, copper-alloy and wooden objects were well preserved and included dishes, a bleeding bowl, chafing dish, mortar, three urethral syringes, a wooden mallet, spoons (including one with an angled bowl for administering medicine), spatulae and a unique wooden feeding bottle. Medicine and ointment jars, flasks and bottles in wood, pewter, ceramic, leather and glass were also in the chest and cabin along with seven Raeren stoneware jugs, from which residues were extracted for chemical analysis. Several rolls of linen impregnated with a sticky resinous substance seem to be prepared bandages.

The shaving and grooming elements of the barber-surgeon's role (or more probably that of an assistant) are represented by 10 of the 13 razors found on the ship, a shaving bowl, whetstone, brushes, earscoops and combs. More personal items included the barbersurgeon's "badge of office" – his beautifully-preserved black velvet bonnet or coif – wooden tankards, a leather pouch containing silver coins, a sword hilt and several pewter dishes stamped with the letters WE and RWE.

Although the Mary Rose was probably never at sea for many days at a time, the barber-surgeon was clearly well-equipped to deal with most eventualities. On a simple, personal level, the men are likely to have suffered from a variety of parasites and pests reflecting the generally unhygienic conditions on board. Rats were inevitable, food was infected with weevils, and insect remains of latrine flies, human fleas and dung beetles have been found. The on-board barber "shop" probably experienced a steady flow of itchy customers!

Among the "everyday" illnesses that could have been presented to him were the "Spanish pox" (probably gonorrhoea – hence the urethral syringes), diarrhoea, respiratory diseases and fevers, and the possibility of more serious infectious conditions such as yellow fever, dysentery, typhoid and "ague". In the long, hot summer of 1545 it was recorded that many men of both the British and French fleets died of "plague": it is thought quite likely that this was actually an epidemic of food poisoning.

Minor injuries and wounds were probably commonplace on board any ship, but the Mary Rose's crew faced the prospect of serious battle injuries including shattered limbs, missile wounds and burns. It is clear that several men had already survived horrific injuries. On July 19, 1545, the barber-surgeon may well have been in his cabin preparing to admit casualties. He was never called upon and went down with the ship.

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Brendan Derham analysed the barber-surgeon's medicines and ointments

The eminent surgeon William Clowes (1544–1604) listed 85 pharmaceutical items he considered to be essential. The question posed by the Mary Rose was whether residues associated with the barber-surgeon's chest could be successfully analysed, identified and interpreted to illuminate the reality rather than the theoretical ideal of 16th century naval medical care.

The residues had chemically changed in a wide variety of ways resulting from the particular environmental and degradative conditions of the site. Forty four samples were chemically analysed, mostly from containers in the barber-surgeon's cabin, using a range of techniques: elemental analysis for a general indication of the samples' nature, gas chromatography-mass spectrometry (GC-MS) to identify organic components, X-ray fluorescence spectrometry (XRF) for intractable inorganic material, and microscopy for any intact plant remains.

It was thus possible to identify seven major groups. Three are indeterminate: marine silt (nothing else surviving); inorganic concretions formed by metal corrosion; and samples too degraded to identify.

Many ointments were based on oleoresin or rosin oil, the viscous resin exuded by pine and spruce trees, diluted with beeswax or a range of minerals, oils or more exotic resins. Frankincense had been added in two of the preparations. In one case oleoresin had been heated to make a more mobile "rosin oil" which had then been blended with mercury.

By contrast, several samples are mainly animal fat, probably butter or tallow, in one case blended with a lead-based compound.

Some samples do not fall clearly into any other category – such a s a wooden canister containing peppercorns. Finally there are bandage rolls or magdaleones: linen bandages coated with pine oleoresins or coniferous tar that could be used to dress wounds. The spiral appearance of the structures was still visible under x-ray.

One normally associates medieval "medicine" with herbal preparations based on the use of plant or animal parts. However, only occasional botanical remains such as the peppercorns survived on the Mary Rose. The medicines that did survive consisted of processed and at least partially refined chemicals: beeswax, butter or tallow, frankincense, minerals based on copper, lead, mercury, sulphur and tin and organic resins derived from pine or spruce.

The limited range of medicines on board offered treatment mainly for wounds, burns and other skin complaints. Most were probably fairly effective, as they contained ingredients used in medicine until the start of the 20th century – and in one case, to the present day. One burns preparation consisted of zinc mixed in animal fat – similar to modern Calamine lotion whose active ingredient is zinc oxide. Another consisted of copper salt in animal fat, an ointment used until recently to treat necrotic skin ulcers. The chest contained large quantities of pine resin, an antibiotic dressing for wounds which prevents fluid loss and dehydration.

If the barber-surgeon had pursued a minimalist policy, of cleaning wounds and applying the antiseptic dressings recovered, then provided that no systemic infection took hold, such treatments may have contributed to successful therapeutic outcomes. The danger of systemic infection and the absence of effective systemic antibiotics remained the bane of all therapeutic practices until the mid 20th century.Awide range of anodynes or painkillers was available in the early 16th century to "aswage dolour and pain" (Gale 1563). It is unfortunate, particularly for the crew, that no evidence for narcotics was identified in any sample.

Brendan Derham worked in the chemical industry before researching archaeological evidence of plant extract use. Now a Wellcome Research Fellow in BioArchaeology at the University of Newcastle, he is seeking trace residues of natural narcotics, snuffs and hunting poisons in archaeological and ethnographic contexts.

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The Anthony Roll, compiled in 1546, recorded the Mary Rose crew as 415 men, of whom about three dozen survived. Ann Stirland examined the remains of many of those who did not

When the ship sank, men were trapped at all levels. Agreat deal of mixing of the remains then occurred, due to the wreck's angle on the sea bed, tides and predators, but the human bone was superbly preserved by the anaerobic conditions.

A probable total of 179 individuals out of a possible 380 deaths was derived from a count of skulls. The preservation allowed the matching of paired bones, and 92 fairly complete skeletons (FCS) were isolated. These were males, of whom 71 (80%) were less than 30 years old. They were mostly young adults (54) and adolescents (17), with a small number of older men and at least one boy. The average stature (using Trotter's formulae) was 5'7"±2" (c1.7m).

There is a lot of evidence recorded in these remains. Dietary deficiencies, for example, may result from an imbalance, such as starvation, or from illness. It is clear from the records that famine was a persistent problem in early 16th century Europe when these men were young. There is evidence in the skeletons for childhood deficiency of vitamin D. This causes rickets, resulting in weakened and plastic bones which become bowed with weight bearing. This bowing can persist in the adult skeleton. There is also evidence for osteomalacia, the adult form of rickets.

There are some healed fractures, including a broken nose. Neither bone in an old spiral fracture of the right tibia and fibula had been reset, nor the leg immobilised, so the bones set in their fractured positions. This kind of break is caused when a twisting force is applied, as can happen when a boot is stuck in mud and the individual tries to stride on over rough ground. There are head wounds, some of them depressed fractures. Penetrating wounds occurred, one probably caused by a bodkin arrowhead on an arrow fired from above, perhaps during practice at the butts; this was healing when the man drowned.

Other fractures, known as avulsions, can happen at sites on the skeleton where ligaments attach, when the stronger ligament tears away a piece of bone. Certain fractures can affect the joint surfaces at the ends of bones, such as at the knee. An accident can cause a disruption of the blood supply to the joint, causing a piece of bone to die and fall off, leaving a characteristic scar. This usually occurs during adolescence and is fairly common today in young boys. Fracture-dislocations of the hip can occur when a force is applied to the shaft of the femur (upper leg) while the knee is bent. The force of the impact causes the femur head to travel backwards, carrying a piece of the rim of the hip joint with it. Evidence for all these traumatic events in the crew's bones suggests a hard and dangerous life.

The most exciting result from studying the skeletons is the opportunity to identify activity patterns. Two distinct possibilities for specialised movements emerged. First, there were changes in a relatively high number of shoulder blades. Second, a group of spines belonging to very young men exhibited changes usually associated with increasing age.

The affected shoulder blades (scapulae) had loose fragments of bone that had failed to unite with the rest of the skeleton at the appropriate time during adolescence. The occurrence is much higher than in modern populations, and is more prevalent on the left side. There is a strong possibility that this was caused by the persistent use from a young age of very heavy war bows. These had a predicted draw weight (the loading required to draw the bow with the string) of 45.5–78kg at a draw of 0.75m (30"). Drawing and shooting the bow uses the major muscles of the arms and shoulders. Other changes in young men, including evidence for twisting of the mid spine, may also be due to this activity. Every able-bodied male between the ages of seven and 60 had to be trained in bow use, but some would be better than others. The shoulder anomalies and the very heavy war bows recovered suggest the presence of specialist archers on the ship.

A large culverin (a long-barrelled cannon, two of which are recorded to have been on board) was found on the main deck in close association with a group of six skeletons. All the men were in their early to mid 20s and three of them have very stressed spines. These include huge joints, some of which are fused at the back, and one very young man with herniated intervertebral discs. These and other changes suggest that this was probably a gun crew.

The human remains from the Mary Rose represent largely young, strong and fit men. They had large bones and strongly developed muscle attachments. Many of them may have suffered from childhood diseases and some of them from diseases as adults. Starvation was probably prevalent, at least in England when they were children during the 1520s, and adult deficiency diseases seem to have been present later.

Many of the skeletal changes probably resulted from work on board the ship and suggest that some, at least, were professionals. Some of the pelvis, leg and foot bones suggest that certain men had worked in an unstable physical environment for some time, perhaps as mariners. A small number of professional mariners would have been needed at all times as ship-keepers and as officers. Good men are likely to have been kept on, especially as manpower was in such short supply.

The only information we have about the crew is that contained in their bones. Apart from the Vice Admiral, we do not know who they were or where they came from. It seems likely that some of them, at least, came from mainland Europe, but careful research has not revealed the identity of any other individuals.

Ann Stirland is a freelance consultant anthropologist and palaeopathologist with extensive experience of studying human skeletons, and cofounder of the Journal of Osteoarchaeology. See also AJ Stirland 2005 The Men of the Mary Rose: Raising the Dead (Sutton).

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