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# The resolution property for schemes and stacks

## 1 Introduction

Roughly speaking, an algebraic stack is an object which looks locally like the quotient of an algebraic variety by a group action . Thus it is a fundamental question whether a given stack is globally the quotient of a variety by a group action. We show that a strong version of this property is equivalent to another fundamental property of stacks: having “enough” vector bundles for geometric purposes. The equivalence turns out to be interesting even in the special case where the stack is a scheme. Moreover, we prove the existence of enough vector bundles in the important case of orbifolds whose associated algebraic space is a scheme. In more detail, the two main results of the paper are:

###### Theorem 1.1

Let $`X`$ be a normal noetherian algebraic stack (over Z) whose stabilizer groups at closed points of $`X`$ are affine. The following are equivalent.

(1) $`X`$ has the resolution property: every coherent sheaf on $`X`$ is a quotient of a vector bundle on $`X`$.

(2) $`X`$ is isomorphic to the quotient stack of some quasi-affine scheme by an action of the group $`GL(n)`$ for some $`n`$.

For $`X`$ of finite type over a field $`k`$, these are also equivalent to:

(3) $`X`$ is isomorphic to the quotient stack of some affine scheme over $`k`$ by an action of an affine group scheme of finite type over $`k`$.

###### Theorem 1.2

Let $`X`$ be a smooth Deligne-Mumford stack over a field $`k`$. Suppose that $`X`$ has finite stabilizer group and that the stabilizer group is generically trivial. Let $`B`$ be the Keel-Mori coarse moduli space of $`X`$ . If the algebraic space $`B`$ is a scheme with affine diagonal (for example a separated scheme), then the stack $`X`$ has the resolution property.

Informally, Theorem 1.2 says that any “orbifold coherent sheaf” on a scheme with quotient singularities admits a resolution by “orbifold vector bundles.” For example, Theorem 1.2 implies that the moduli stacks of curves, $`\overline{M}_{g,n}`$ with $`g3`$ (so that the generic stabilizer is trivial), have the resolution property. This was proved earlier by Mumford  by showing that these particular stacks admit a Cohen-Macaulay global cover. The more general Theorem 1.2 has often been wished for, even in the special case where $`B`$ is quasi-projective. It allows the hard-to-verify assumption of a Cohen-Macaulay global cover to be removed from various papers, such as Kawamata’s paper on flips and derived categories .

In Theorem 1.1, the fact that quotient stacks $`W/GL(n)`$ with $`W`$ a noetherian quasi-affine scheme (an open subset of an affine scheme) have the resolution property is an easy special case of Thomason’s results on the resolution property , listed in Theorem 2.1 below. So the new implication is the opposite one, which says that stacks with the resolution property are quotient stacks of a very special kind. Edidin, Hassett, Kresch, and Vistoli proved a step in the direction of Theorem 1.1: they showed that a stack with quasi-finite stabilizer group which has the resolution property is a quotient stack $`W/GL(n)`$ with $`W`$ an algebraic space, that is, a stack with trivial stabilizer group (, Theorem 2.7 and Theorem 2.14). Algebraic spaces (and even schemes) do not all have the resolution property, as explained below, and so we need to strengthen the conclusion as in Theorem 1.1 in order to have an equivalence.

Remarks. (1) The restriction to stacks with affine stabilizer groups in Theorem 1.1 seems reasonable. In fact, I would argue that the resolution property is not meaningful for a stack whose stabilizer groups are not affine. The simplest example of such a stack is the classifying stack $`BE`$ of an elliptic curve $`E`$. Because every linear representation of an elliptic curve is trivial, coherent sheaves and vector bundles on $`BE`$ are both simply vector spaces. Thus, the resolution property for $`BE`$ holds, but this has no real geometric significance. In particular, the $`K`$-groups of $`BE`$ defined using either vector bundles or perfect complexes (cf. section 2) are simply the $`K`$-groups of a point.

(2) Theorem 1.1 cannot be strengthened to say that a stack $`X`$ with the resolution property (and affine stabilizer groups) is a quotient stack $`W/GL(n)`$ with $`W`$ an affine scheme. Indeed, quotient stacks of the latter form are very special. For example, by geometric invariant theory, any algebraic space which is the quotient of an affine scheme by a reductive group such as $`GL(n)`$ (as a stack, which means that the group action is free) is in fact an affine scheme (, Amplification 1.3).

Theorem 1.1 implies:

###### Proposition 1.3

Let $`X`$ be a noetherian algebraic stack whose stabilizer groups at closed points of $`X`$ are affine. If $`X`$ has the resolution property, then the diagonal morphism $`XX\times _\text{Z}X`$ is affine.

For example, a scheme $`X`$ has affine diagonal morphism if and only if the intersection of any two affine open subsets is affine. The property of having affine diagonal is a natural weakening of separatedness: the smooth non-separated scheme $`A^n_{A^n0}A^n`$ has affine diagonal for $`n=1`$ but not for $`n2`$. Thus Proposition 1.3 immediately implies Thomason’s observation that the scheme $`A^n_{A^n0}A^n`$ does not have the resolution property for $`n2`$ (, Exercise 8.6). Most other known counterexamples to the resolution property have non-affine diagonal and so are explained by Proposition 1.3. Unfortunately, not all stacks with affine diagonal have the resolution property. By Grothendieck, there is a normal (affine or projective) complex surface $`Y`$ which has a non-torsion element of $`H_{\text{et}}^2(Y,G_m)`$ (, II.1.11(b)). As Edidin, Hassett, Kresch, and Vistoli observed, the corresponding $`G_m`$-gerbe $`X`$ over $`Y`$ (a stack with stabilizer group $`G_m`$ at every point) is a stack with affine diagonal which is not a quotient of an algebraic space by $`GL(n)`$ (, Example 3.12). Therefore, Theorem 1.1 says that $`X`$ fails to have the resolution property. Despite this counterexample, we can ask the following optimistic questions about the resolution property:

Question 1. Let $`X`$ be a noetherian stack with quasi-finite stabilizer group (for example, an algebraic space or a scheme). Suppose that $`X`$ has affine diagonal (for example, $`X`$ separated). Does $`X`$ have the resolution property?

This would be very useful. I do not know how likely it is. At the moment, the resolution property is not known even for such concrete objects as normal toric varieties or smooth separated algebraic spaces over a field.

Question 2. Let $`X`$ be a smooth stack over a field such that $`X`$ has affine diagonal. Does $`X`$ have the resolution property?

Question 3. Let $`X`$ be a stack which has the resolution property. Suppose that $`X`$ has an action of a flat affine group scheme $`G`$ of finite type over a field or over Z. Does $`X/G`$ have the resolution property?

The converse to Question 3 is true and sometimes useful: if $`G`$ acts on a stack $`X`$ (for example, a scheme) such that the quotient stack $`X/G`$ has the resolution property, then so does $`X`$ (Corollary 5.2).

Thomason proved several cases of Question 3, listed in Theorem 2.1 below. One case where his methods do not immediately apply is the quotient stack $`Q`$ of the nodal cubic curve by the multiplicative group, which has several pathological properties described in section 9. Nonetheless, in that section we use some ideas from the proof of Theorem 1.1 to prove the resolution property for $`Q`$. In general, the proof of Theorem 1.1 often shows how to construct a coherent sheaf $`C`$ on a given stack $`X`$ such that $`X`$ has the resolution property if and only if the single sheaf $`C`$ is a quotient of a vector bundle. I expect that this method should help to prove the resolution property in other situations as well.

Finally, section 8 considers the question of whether surjectivity of the natural map from the Grothendieck group $`K_0^{\text{naive}}X`$ of vector bundles on $`X`$ to the group $`K_0X`$ of perfect complexes is enough to imply the resolution property. The answer is yes for smooth schemes, but not for smooth algebraic spaces or Deligne-Mumford stacks, as we will show in two examples.

I would like to thank Yujiro Kawamata and Gabriele Vezzosi for useful discussions on Theorem 1.2. In particular, the proof given here of Theorem 1.2 has been simplified by an idea of Vezzosi’s.

## 2 History of the resolution property

One important reason to consider the resolution property is its role in $`K`$-theory. For any scheme $`X`$, it is natural to consider the Grothendieck group of vector bundles $`K_0^{\text{naive}}X`$. Quillen extended this group to a sequence of groups $`K_{}^{\text{naive}}X`$ built from the category of vector bundles on $`X`$. We use the name “naive” because these groups do not satisfy the important properties such as Mayer-Vietoris for open coverings of arbitrary schemes. Thomason showed how to define the right $`K`$-groups $`K_{}X`$ for arbitrary schemes ; more generally, it seems that the same definition works for a stack $`X`$. Instead of vector bundles, he used perfect complexes, that is, complexes of sheaves which are locally quasi-isomorphic to bounded complexes of finite-dimensional vector bundles. The same idea comes up in topology. In simple situations such as compact Hausdorff spaces, one can define topological $`K`$-groups using only finite-dimensional vector bundles. In more complex situations, in order to get the right $`K`$-groups (satisfying Mayer-Vietoris), one has to consider Fredholm complexes, that is, complexes of infinite-dimensional vector bundles with finite-dimensional cohomology sheaves. An example where infinite-dimensional bundles are needed is the twisted $`K`$-theory recently considered by Freed, Hopkins, Teleman, and others, which can be viewed as the $`K`$-theory of a “topological stack,” the $`S^1`$-gerbe $`X`$ over a space $`Y`$ associated to an element of $`H^2(Y,S_{\text{cont}}^1)=H^3(Y,\text{Z})`$; when this element is not torsion, there are not enough finite-dimensional vector bundles on the stack $`X`$ (, ).

It is natural to ask for criteria to ensure that the natural map from $`K_{}^{\text{naive}}X`$ to $`K_{}X`$ is an isomorphism, because this means that Thomason’s $`K`$-groups give information about vector bundles on $`X`$, which are geometrically appealing. Thomason gave a satisfactory answer: if $`X`$ has the resolution property, then the map from $`K_{}^{\text{naive}}X`$ to $`K_{}X`$ is an isomorphism.

For clarity, perhaps I should add that the $`G`$-theory (or $`K^{}`$-theory) of coherent sheaves, also defined by Quillen, has good properties in general and has not had to be modified. In particular, for any regular scheme $`X`$, the natural map $`K_{}XG_{}X`$ is an isomorphism, whereas these groups may differ from $`K_{}^{\text{naive}}X`$ when the resolution property fails, for example for the regular scheme $`X=A^n_{A^n0}A^n`$ with $`n2`$ (, Exercise 8.6).

The resolution property is known to hold for a vast class of schemes and stacks. In particular, it holds for any noetherian scheme with an ample family of line bundles, by Kleiman and independently Illusie. Kleiman’s proof is given in Borelli , 3.3, and Illusie’s is in , 2.2.3 and 2.2.4. A convenient summary of the results on ample families of line bundles is given in Thomason-Trobaugh , 2.1. By definition, a scheme $`X`$ has an ample family of line bundles if $`X`$ is the union of open affine subsets of the form $`\{f0\}`$ with $`f`$ a section of a line bundle on $`X`$. Borelli and Illusie also showed that every regular (or, more generally, factorial) separated noetherian scheme has an ample family of line bundles (, 4.2 and , 2.2.7). (In fact, the same proof works a little more generally, as observed recently by Brenner and Schröer: every Q-factorial noetherian scheme with affine diagonal has an ample family of line bundles (, 1.3).) Also, an ample family of line bundles passes to locally closed subschemes, and so the resolution property holds for all quasi-projective schemes over an affine scheme. Finally, Thomason proved the resolution property for the most naturally occurring stacks, quotient stacks of the following types among others (, 2.4, 2.6, 2.10, 2.14):

###### Theorem 2.1

Let $`X`$ be a noetherian scheme over a regular noetherian ring $`R`$ of dimension at most 1. Let $`G`$ be a flat affine group scheme of finite type over $`R`$ together with an action of $`G`$ on $`X`$.

(1) If $`X`$ has an ample family of $`G`$-equivariant line bundles, then the stack $`X/G`$ has the resolution property.

(2) Suppose that $`G`$ is an extension of a finite flat group scheme by a smooth group scheme with connected fibers over $`R`$. (This is automatic if $`R`$ is a field.) If $`X`$ is normal and has an ample family of line bundles, then the stack $`X/G`$ has the resolution property.

Equivalently, under these assumptions, every $`G`$-equivariant coherent sheaf on $`X`$ is a quotient of a $`G`$-equivariant vector bundle on $`X`$. For example, it follows that the resolution property holds for one of Hironaka’s examples of a smooth proper algebraic space $`X`$ of dimension 3 which is not a scheme: $`X`$ is the quotient of a smooth separated scheme (hence a normal scheme with an ample family of line bundles) by a free action of the group $`\text{Z}/2`$ (, pp. 15–17). Hironaka’s paper , Example 2, gives closely related examples for which the resolution property seems to be unknown.

Hausen showed recently that a scheme (assumed to be reduced and of finite type over an algebraically closed field, although that should be unnecessary) has an ample family of line bundles if and only if it is a quotient $`W/(G_m)^n`$ for some free action of the torus $`(G_m)^n`$ on a quasi-affine scheme $`W`$ (, 1.1). This is a satisfying analogue to Theorem 1.1, though the situation is simpler in that only schemes are involved.

We can ask whether the resolution property holds in cases not covered by the above results, but here progress has been slow. As mentioned in the introduction, the resolution property is still an open problem even for such concrete objects as normal toric varieties or smooth separated algebraic spaces. For example, Fulton found a 3-dimensional normal proper toric variety $`X`$ over C which has zero Picard group (, p. 65); such a variety cannot have an ample family of line bundles, and it is unknown whether the resolution property holds. One encouraging result is the recent proof by Schröer and Vezzosi of the resolution property for all normal separated surfaces (, 2.1). There is a normal proper surface over C that has zero Picard group. Thus, Schröer and Vezzosi were able to construct enough vector bundles to prove the resolution property on such a variety, even though it does not have an ample family of line bundles.

As indicated in the introduction, all known examples of stacks without the resolution property are non-separated. The situation is very different in the complex analytic category, where Voisin has recently proved that the resolution property can fail even for compact Kähler manifolds of dimension 3 (, Appendix).

## 3 Proof of Theorem 1.1, first implications

We begin by proving the easier parts of Theorem 1.1: that (2) implies (1) and that (2) and (3) are equivalent.

First, (2) implies (1). Let $`X`$ be the quotient stack $`W/GL(n)`$ for some action of the group $`GL(n)`$ (over Z) on a noetherian quasi-affine scheme $`W`$. A noetherian scheme $`W`$ is quasi-affine if and only if the trivial line bundle $`O_W`$ is ample (, Proposition II.5.1.2). Given an action of $`GL(n)`$ on $`W`$, the trivial line bundle $`O_W`$ has the structure of a $`GL(n)`$-equivariant line bundle in a natural way, so $`O_W`$ is a $`GL(n)`$-equivariant ample line bundle on $`W`$. By Theorem 2.1, due to Thomason, it follows that every $`GL(n)`$-equivariant coherent sheaf on $`W`$ is a quotient of some $`GL(n)`$-equivariant vector bundle. Equivalently, the stack $`W/GL(n)`$ has the resolution property.

Next, let us show that (2) implies (3) in Theorem 1.1. Here we only consider stacks of finite type over a field $`k`$. The proof is an equivariant version of Jouanolou’s trick, which we will prove directly (, 1.5). Let $`X`$ be a quotient stack $`W/GL(n)`$ for some action of $`GL(n)`$ over $`k`$ on a quasi-affine scheme $`W`$ of finite type over $`k`$. By EGA II.5.1.9 , $`W`$ embeds as an open subset of an affine scheme $`Y`$ of finite type over $`k`$; we can also arrange for this embedding to be $`GL(n)`$-equivariant, simply by taking Spec of a bigger finitely generated subalgebra of $`O(W)`$. Here we are using that the $`GL(n)`$-module $`O(W)`$ over $`k`$ is a union of finite-dimensional representations of $`GL(n)`$; a direct proof is given in GIT , p. 25, although it is also a special case of the fact that a quasi-coherent sheaf on a noetherian stack (here $`BGL(n)`$ over $`k`$) is a filtered direct limit of its coherent subsheaves (, 15.4). Let the closed subset $`YW`$ be defined by the vanishing of regular functions $`f_1,\mathrm{},f_r`$ on the affine scheme $`Y`$; we can assume that the linear span of the functions $`f_1,\mathrm{},f_r`$ is preserved by the action of $`GL(n)`$, defining a representation $`GL(n)GL(r)`$ over $`k`$. Then we have a $`GL(n)`$-equivariant morphism $`\alpha :WA_k^r0`$ defined by

$$w(f_1(w),\mathrm{},f_r(w)).$$

The subsets $`\{f_i0\}`$ of $`W`$ are affine, and so $`\alpha `$ is an affine morphism.

Define the affine group $`\text{Aff}_{r1}`$ as the semidirect product $`(G_a)^{r1}GL(r1)`$. Then we can identify $`A^r0`$ with the homogeneous space $`GL(r)/\text{Aff}_{r1}`$. Define $`A`$ as the pullback scheme:

$$\begin{array}{ccc}A& & GL(r)\\ & & & & \\ W& & A^r0\end{array}$$

Since $`W`$ is affine over $`A^r0`$, $`A`$ is affine over $`GL(r)`$, and hence $`A`$ is an affine scheme. The group $`GL(n)\times \text{Aff}_{r1}`$ acts on $`W`$ and $`A^r0`$, with $`\text{Aff}_{r1}`$ acting trivially, and it acts on $`GL(r)`$ via left multiplication by $`GL(n)`$ (using the representation $`GL(n)GL(r)`$) and right multiplication by $`\text{Aff}_{r1}`$. It follows that the pullback scheme $`A`$ also has an action of $`GL(n)\times \text{Aff}_{r1}`$. We see from the diagram that we have an isomorphism of quotient stacks:

$$A/(GL(n)\times \text{Aff}_{r1})W/GL(n).$$

So the given stack $`X=W/GL(n)`$ is the quotient of the affine scheme $`A`$ by the affine group scheme $`GL(n)\times \text{Aff}_{r1}`$. Thus (2) implies (3) in Theorem 1.1.

To prove that (3) implies (2), we need the following well-known fact.

###### Lemma 3.1

Every affine group scheme $`G`$ of finite type over a field $`k`$ has a faithful representation $`GGL(n)`$ such that $`GL(n)/G`$ is a quasi-affine scheme.

Proof. To begin, let $`GGL(n)`$ be any faithful representation of $`G`$. By Chow, the homogeneous space $`GL(n)/G`$ is always a quasi-projective scheme over $`k`$. More precisely, there is a representation $`V`$ of $`GL(n)`$ and a $`k`$-point $`x`$ in the projective space $`P(V^{})`$ of lines in $`V`$ whose stabilizer is $`G`$ (, p. 483).

Let the group $`GL(n)\times G_m`$ act on $`V`$ by the given representation of $`GL(n)`$ and by the action of $`G_m`$ by scalar multiplication. Then the stabilizer in $`GL(n)\times G_m`$ of a point $`yV`$ lifting $`x`$ is isomorphic to $`G`$. That is, $`(GL(n)\times G_m)/G`$ is a quasi-affine scheme. Using the obvious inclusion $`GL(n)\times G_mGL(n+1)`$, the quotient $`GL(n+1)/(GL(n)\times G_m)`$ is an affine scheme, the “Stiefel manifold” of $`(n+1)\times (n+1)`$ matrices which are projections of rank 1. So $`GL(n+1)/G`$ maps to the affine scheme $`GL(n+1)/(GL(n)\times G_m)`$ with fibers the quasi-affine scheme $`(GL(n)\times G_m)/G`$. More precisely, the fiber embeds $`(GL(n)\times G_m)`$-equivariantly as a subscheme of the representation $`V`$, by its construction. It follows that $`GL(n+1)/G`$ is a quasi-affine scheme. QED

We can now prove that (3) implies (2) in Theorem 1.1. Let $`X`$ be the quotient stack of an affine scheme $`A`$ of finite type over a field $`k`$ by the action of an affine group scheme $`G`$ of finite type over $`k`$. By Lemma 3.1, there is a faithful representation $`GGL(n)`$ with $`GL(n)/G`$ a quasi-affine scheme. Let $`W`$ be the $`GL(n)`$-bundle over $`X`$ associated to the $`G`$-bundle $`AX`$, $`W=(A\times GL(n))/G`$. Then $`W`$ is an $`A`$-bundle over the quasi-affine scheme $`GL(n)/G`$. Since $`A`$ is affine, it follows that $`W`$ is a quasi-affine scheme.

## 4 From a stack to an algebraic space

We now begin the proof of the main part of Theorem 1.1, that (1) implies (2). Thus, let $`X`$ be a normal noetherian stack whose stabilizer groups at closed points of $`X`$ are affine. Suppose that $`X`$ has the resolution property. We will show that $`X`$ is isomorphic to the quotient stack $`W/GL(n)`$ for some quasi-affine scheme $`W`$ with an action of $`GL(n)`$. (In Theorem 1.1, we only need $`X`$ to be normal for this part, the proof that (1) implies (2). Normality will be used in section 5.) The following is a first step.

###### Lemma 4.1

Let $`X`$ be a noetherian stack (over Z) whose stabilizer groups at closed points of $`X`$ are affine. Suppose that $`X`$ has the resolution property. Then $`X`$ is isomorphic to the quotient stack of some algebraic space $`Z_1`$ over Z by an action of the group $`GL(n_1)`$ for some $`n_1`$.

Proof. Equivalently, we have to find a vector bundle $`E_1`$ on $`X`$ such that the total space $`Z_1`$ of the corresponding $`GL(n_1)`$-bundle over $`X`$ is an algebraic space. As Edidin, Hassett, Kresch, and Vistoli observed, it is equivalent to require that at every geometric point $`x`$ of $`X`$, the action of the stabilizer group $`G_x`$ of $`X`$ on the fiber $`(E_1)_x`$ is faithful (, Lemma 2.12).

By definition of a noetherian stack, there is a smooth surjective morphism from a noetherian affine scheme $`U`$ to $`X`$ . We can think of the stack $`X`$ as the quotient $`U/R`$ of $`U`$ by the groupoid $`R:=U\times _XU`$. In these terms, the defining properties of a noetherian stack over Z are that $`R`$ is a separated algebraic space over Z and that both projections $`RU`$ are smooth morphisms of finite type (, Proposition 4.3.1). Let $`G_UU`$ be the stabilizer group of $`X`$, that is, $`G_U=R\times _{U\times U}U`$. Here $`G_U`$ is a group in the category of algebraic spaces over $`U`$; it is pulled back from the stabilizer group $`G:=X\times _{X\times X}X`$ over $`X`$. Since $`G_U`$ is a closed subspace of $`R`$, it is separated of finite type over $`U`$.

A point of a stack $`X`$ is defined in such a way that a point of $`X`$ is equivalent to an $`R`$-orbit in the underlying topological space of the scheme $`U`$. Another way to think of a point is as an isomorphism class of substacks $`𝒢`$ of $`X`$ such that $`𝒢`$ is a gerbe over some field $`k`$ (, Corollary 11.4); explicitly, $`𝒢`$ is the quotient of the corresponding $`R`$-orbit by the restriction of the groupoid $`R`$. To say that $`𝒢`$ is a gerbe means that there is a field extension $`F`$ over $`k`$ such that $`𝒢\times _kF`$ is isomorphic to the classifying stack of some group over $`F`$. The set $`|X|`$ of points of $`X`$ is given the quotient topology from $`U`$; in particular, a closed point of $`X`$ can be identified with a closed $`R`$-orbit in $`U`$ (, Corollary 5.6.1).

For any vector bundle $`E`$ on the stack $`X`$, the kernel of the $`G`$-action on $`E`$ is a closed subgroup $`HG`$ over $`X`$, which pulls back to a closed subgroup $`H_UG_U`$ over $`U`$. Given a finite sequence of vector bundles $`E_1,\mathrm{},E_n`$ on $`X`$ with kernel subgroups $`H_1,\mathrm{},H_nG`$, the kernel subgroup of the direct sum $`E_1\mathrm{}E_n`$ is the intersection $`H_1\mathrm{}H_n`$. In this way, we can repeatedly cut down the kernel subgroup by finding one vector bundle on $`X`$ after another, and Lemma 4.1 is proved if this subgroup eventually becomes the trivial group over $`X`$.

###### Lemma 4.2

Let $`X`$ be a noetherian stack (over Z) which satisfies the resolution property. Let $`x`$ be a point of $`X`$ such that the stabilizer group $`G`$ of $`X`$ is affine at $`x`$. Then there is a vector bundle $`E`$ on $`X`$ whose kernel subgroup is trivial at $`x`$.

Proof. As explained above, $`x`$ corresponds to a substack $`𝒢`$ of $`X`$ which is a gerbe over some field $`k`$. Since $`X`$ is locally noetherian, there is a finite extension $`F`$ of $`k`$ such that $`𝒢\times _kF`$ is isomorphic to the classifying stack of a group $`G_s`$ over $`F`$, by , 11.2.1 and Theorem 11.3. The assumption means that $`G_s`$ is affine over $`F`$. Moreover, $`G_s`$ is of finite type over $`F`$, since $`GX`$ is of finite type. Therefore $`G_s`$ has a faithful representation over $`F`$. We can view such a representation as a vector bundle on the gerbe $`𝒢\times _kF`$. Its direct image to $`𝒢`$ is a vector bundle $`C_0`$ on $`𝒢`$ whose pullback to $`𝒢\times _kF`$ is a faithful representation of the group $`G_s`$. So the kernel subgroup of $`C_0`$ over $`𝒢`$ is trivial.

Let $`i:𝒢X`$ denote the inclusion. The direct image $`i_{}C_0`$ is a quasi-coherent sheaf on $`X`$, and therefore a direct limit of coherent sheaves on $`X`$ (, Proposition 13.2.6 and Proposition 15.4). Since $`X`$ has the resolution property, each of these coherent sheaves is a quotient of a vector bundle on $`X`$. Since $`C_0=i^{}i_{}C_0`$ and $`C_0`$ is coherent, one of these vector bundles $`E`$ on $`X`$ must restrict to a vector bundle on $`𝒢`$ which maps onto $`C_0`$. It follows that the kernel subgroup of $`E`$ over $`𝒢`$ is trivial. QED

We return to the proof of Lemma 4.1. We are given that the stabilizer group of $`X`$ at each closed point of $`X`$ is affine. By Lemma 4.2, it follows that for each closed point $`x`$ of $`X`$, there is a vector bundle $`E`$ on $`X`$ whose kernel subgroup $`HX`$ is trivial at $`x`$. This does not imply that the kernel subgroup of $`E`$ is trivial in a neighborhood of $`E`$. Nonetheless, since the morphism $`HX`$ has finite type, the dimensions of fibers make sense and are upper semicontinuous. (Indeed, it suffices to check this for the pulled-back group $`H_UU`$, and to consider an etale covering of the algebraic space $`H_U`$ by a scheme; then we can refer to EGA IV.13.1.3 .) Therefore the group $`HX`$ is quasi-finite (that is, of finite type and with finite fibers) over some neighborhood of the point $`x`$. The space $`|X|`$ of points of $`X`$ is a “sober” noetherian topological space (every irreducible closed subset of $`|X|`$ has a unique generic point) by , Corollary 5.7.2. It follows that every open subset of $`|X|`$ which contains all the closed points must be the whole space. Since $`|X|`$ is also quasi-compact, there are finitely many vector bundles $`E_1,\mathrm{},E_n`$ on $`X`$ such that the direct sum $`E_1\mathrm{}E_n`$ has kernel group which is quasi-finite over all of $`X`$. Let $`E`$ now denote this direct sum. In particular, the kernel subgroup $`HX`$ of $`E`$ is affine over every point of $`X`$.

Since the kernel group $`H_UU`$ is quasi-finite, it is finite over a dense open subset $`V`$ of $`U`$ (, exercise II.3.7). By Lemma 4.2, for every point $`xV`$, there is a vector bundle $`F`$ on $`X`$ whose kernel subgroup is trivial at $`x`$. Since $`H_{EF}`$ is a closed subgroup scheme of $`H_E`$, it is finite over $`V`$, while also being trivial at $`x`$. Therefore $`H_{EF}`$ is trivial over some neighborhood of $`x`$. By quasi-compactness of $`V`$, there is a vector bundle on $`X`$ (again to be called $`E`$) whose kernel subgroup is quasi-finite over $`U`$ and trivial over $`V`$. Then this kernel subgroup will be finite over a larger open subset of $`U`$, containing a dense open subset of $`UV`$, and so we can repeat the process. By noetherian induction, we end up with a vector bundle on $`X=U/R`$ with trivial kernel subgroup over all of $`U`$. QED

## 5 From an algebraic space to a scheme

In this section, we will complete the proof of Theorem 1.1.

Let $`X`$ be a normal noetherian stack $`X`$ with affine stabilizer groups at closed points of $`X`$. Suppose that $`X`$ satisfies the resolution property. We will show that $`X=W/GL(n)`$ for some quasi-affine scheme $`W`$ and some $`n`$. By Lemma 4.1, we know that there is a $`GL(n_1)`$-bundle $`Z_1`$ over $`X`$ for some $`n_1`$ which is at least an algebraic space. Since $`X`$ is normal, $`Z_1`$ is normal. We use the name $`E_1`$ for the vector bundle on $`X`$ that corresponds to the $`GL(n_1)`$-bundle $`Z_1`$.

By Artin, since $`Z_1`$ is a normal noetherian algebraic space, it is the coarse geometric quotient of some normal scheme $`A`$ by the action of a finite group $`G`$ (, 2.8; , 16.6.2). Moreover, the morphism $`\pi :AZ_1`$ is finite. (In general, the quotient morphism even of an affine noetherian scheme by a finite group need not be a finite morphism, by Nagata , but the situation here is better because we know $`Z_1`$ is noetherian to start with.) Let $`\pi :AZ_1`$ be the corresponding morphism. Let $`U_1,\mathrm{},U_r`$ be an open affine covering of the scheme $`A`$. Let $`S_i`$ be the closed subset $`AU_i`$, which we give the reduced subscheme structure. Let $`I_{S_i}`$ be the corresponding ideal sheaf (the kernel of $`O_AO_{S_i}`$), and let $`C`$ be the coherent sheaf $`C=_{i=1}^rI_{S_i}`$ on $`A`$. Then $`D:=\pi _{}C`$ is a coherent sheaf on $`Z_1`$ because $`\pi :AZ`$ is proper.

In order to use the resolution property for $`X`$ again, we need a suitable coherent sheaf on $`X=Z_1/GL(n)`$. That will be supplied by the following lemma.

###### Lemma 5.1

Let $`Z_1`$ be a noetherian algebraic space (over Z). Let $`G`$ be a flat affine group scheme over Z or over a field which acts on $`Z_1`$. Then any coherent sheaf on $`Z_1`$ is a quotient of some $`G`$-equivariant coherent sheaf on $`Z_1`$.

Proof. The morphism $`\alpha `$ from $`Z_1`$ to the quotient stack $`Z_1/G`$ is affine. So, for every coherent sheaf $`D`$ on $`Z_1`$, the natural map

$$\alpha ^{}\alpha _{}DD$$

is surjective. Here $`\alpha _{}D`$ is a quasi-coherent sheaf on $`Z_1/G`$. Thus, we have exhibited the coherent sheaf $`D`$ as the quotient of a $`G`$-equivariant quasi-coherent sheaf on $`Z_1`$. By Laumon and Moret-Bailly, every quasi-coherent sheaf on a noetherian stack is the filtered direct limit of its coherent subsheaves (, Proposition 15.4). So $`D`$ is in fact the quotient of some $`G`$-equivariant coherent sheaf on $`Z_1`$. QED

Before continuing with the proof of Theorem 1.1, note the following corollary which could be useful in checking the resolution property in examples. For example, to prove the resolution property for all coherent sheaves on a toric variety, it suffices to prove it for the equivariant coherent sheaves. Klyachko’s algebraic description of the equivariant vector bundles on a toric variety should be useful for the latter problem .

###### Corollary 5.2

Let $`Z_1`$ be a noetherian algebraic space (over Z). Let $`G`$ be a flat affine group scheme of finite type over Z or over a field which acts on $`Z_1`$. If the resolution property holds for the stack $`Z_1/G`$, then it holds for $`Z_1`$.

Proof of Corollary 5.2. Every coherent sheaf on $`Z_1`$ is a quotient of a $`G`$-equivariant coherent sheaf by Lemma 5.1, which in turn is a quotient of a $`G`$-equivariant vector bundle on $`Z_1`$ by the resolution property for $`Z_1/G`$. QED

We now return to the proof of Theorem 1.1. We apply Lemma 5.1 to the algebraic space $`Z_1`$ with $`X=Z_1/GL(n_1)`$ and the coherent sheaf $`D=\pi _{}C`$ on $`Z_1`$ defined above. It follows that $`\pi _{}C`$ is the quotient of some $`GL(n_1)`$-equivariant coherent sheaf $`D_1`$ on $`Z_1`$. Since the stack $`X`$ has the resolution property, there is a vector bundle $`E_2`$ on $`X`$ which maps onto $`D_1`$, viewed as a coherent sheaf on $`X`$. Thus, writing $`\alpha `$ for the $`GL(n_1)`$-bundle $`Z_1X`$, we have surjections

$$\alpha ^{}E_2D_1\pi _{}C$$

on $`Z`$. Since the morphism $`\pi :AZ_1`$ is finite, it is affine. So the natural map $`\pi ^{}\pi _{}CC`$ of sheaves over $`A`$ is surjective. Thus, we have found a vector bundle $`E_2`$ on $`X`$ whose pullback $`\pi ^{}\alpha ^{}E_2`$ to the scheme $`A`$ maps onto the coherent sheaf $`C=_{i=1}^nI_{S_i}`$.

Let $`Z_2`$ be the $`GL(n_2)`$-bundle over $`X`$ associated to the vector bundle $`E_2`$. Define $`W`$ and $`Y`$ as the indicated pullbacks:

$$\begin{array}{ccc}W& \underset{GL(n_2)}{\overset{\beta }{}}& A\\ & & \pi & & \\ Y& \underset{GL(n_2)}{}& Z_1\\ & & \alpha GL\left(n_1\right)& & \\ Z_2& \underset{GL(n_2)}{}& X\end{array}$$

Thus $`W`$ is the $`GL(n_2)`$-bundle over the scheme $`A`$ associated to the vector bundle $`\pi ^{}\alpha ^{}E_2`$, which we know maps onto the coherent sheaf $`C=_{i=1}^nI_{S_i}`$. It follows that the scheme $`W`$ is quasi-affine, by the following argument. By construction of $`W`$, the vector bundle $`\pi ^{}\alpha ^{}E_2`$ on $`A`$ pulls back to the trivial bundle on $`W`$. Let $`\beta :WA`$ denote this $`GL(n_2)`$-bundle. Then the coherent sheaf $`\beta ^{}(_{i=1}^nI_{S_i})=_{i=1}^nI_{\beta ^1(S_i)}`$ on $`W`$ is spanned by its global sections. This means that for each $`1in`$, the open subset $`W\beta ^1(S_i)`$ is the union of its open subsets of the form $`\{f_{ij}0\}`$, for certain regular functions $`f_{i1},\mathrm{},f_{ir}`$ on $`W`$ which vanish on $`\beta ^1(S_i)`$. Moreover, each subset $`S_i`$ was chosen so that $`AS_i`$ is an affine scheme. Since $`\beta :WA`$ is an affine morphism, $`W\beta ^1(S_i)`$ is also an affine scheme. It follows that the open subsets $`\{f_{ij}0\}`$ of $`W\beta ^1(S_i)`$ are affine. Thus, using all $`i`$ and $`j`$, $`W`$ is the union of open affine subschemes of the form $`\{f0\}`$ for regular functions $`f`$ on $`W`$. This means that the scheme $`W`$ is quasi-affine (, Proposition II.5.1.2).

By the pullback diagram above, $`Y`$ is a $`GL(n_1)\times GL(n_2)`$-bundle over $`X`$. Because $`Y`$ is a $`GL(n_2)`$-bundle over the algebraic space $`Z_1`$, $`Y`$ is an algebraic space. Moreover, as the pullback diagram shows, we have a finite surjective morphism from the quasi-affine scheme $`W`$ to $`Y`$. In general, this does not imply that $`Y`$ is a quasi-affine scheme, as Grothendieck observed (, Remark II.6.6.13); for example, there is a non-quasi-affine scheme whose normalization is quasi-affine.

We know, however, that $`Y`$ is normal, and that $`Y`$ is the coarse geometric quotient of the quasi-affine scheme $`W`$ by a finite group $`G`$. It follows by the usual construction of quotients by finite group actions that $`Y`$ is a quasi-affine scheme. Namely, since $`W`$ is quasi-affine, every finite subset of $`W`$ is contained in an affine open subset of the form $`\{f0\}`$ for some regular function $`f`$ on $`W`$. In particular, each $`G`$-orbit in $`W`$ is contained in an affine open subset. This subset can be taken to be of the form $`\{f0\}`$ for some $`G`$-invariant function $`f`$, by taking the product of the translates of a given function on $`W`$. Then we can define the geometric quotient $`Y`$ of $`W`$ by $`G`$ as a scheme, the union of open subsets $`\text{Spec }O(U)^G`$ corresponding to these affine open subsets $`U`$ of $`W`$; a reference that works in this generality is SGA 3 (, Theorem 4.1). Finally, the scheme $`Y`$ thus defined is quasi-affine because it is an open subset of the affine scheme $`\text{Spec }O(W)^G`$. (The rings $`O(W)`$ and $`O(W)^G`$ may not be noetherian, but that does not matter for the purpose of proving that $`Y`$ is quasi-affine.)

We can then consider the $`GL(n_1+n_2)`$-bundle over $`X`$ associated to the vector bundle $`E_1E_2`$. Its total space is a bundle over $`Y`$ with fiber the affine scheme $`GL(n_1+n_2)/(GL(n_1)\times GL(n_2))`$ (a Stiefel manifold as in section 3), and hence is a quasi-affine scheme. Theorem 1.1 is proved. QED

## 6 Proof of Proposition 1.3

We now prove Proposition 1.3. That is, let $`X`$ be a noetherian stack (over Z) with affine stabilizer groups at closed points of $`X`$. Suppose that $`X`$ has the resolution property. We will show that the diagonal morphism $`XX\times _\text{Z}X`$ is affine. In this section, I will write $`X\times Y`$ to mean $`X\times _\text{Z}Y`$.

Suppose first that $`X`$ is normal. By Theorem 1.1, $`X`$ is isomorphic to the quotient of some quasi-affine scheme $`W`$ by an action of $`GL(n)`$. A quasi-affine scheme $`W`$ is separated (that is, the diagonal morphism $`WW\times W`$ is a closed embedding). In particular, $`W`$ has affine diagonal. Since $`GL(n)`$ is an affine group scheme over Z, it follows that $`X=W/GL(n)`$ has affine diagonal. This is an easy formal argument, as follows. For brevity, let us write $`G`$ for $`GL(n)`$. Since $`WW/G`$ is faithfully flat, to show that $`W/GW/G\times W/G`$ is affine is equivalent to showing that the pulled-back map over $`W\times W`$ is affine, that is, that $`G\times WW\times W`$, $`(g,w)(w,gw)`$, is affine. But that map is the composition of the map $`G\times WG\times W\times W`$ by $`(g,w)(g,w,gw)`$, which is a pullback of the diagonal map of $`W`$ and hence is affine, with the projection map $`G\times W\times WW\times W`$ which is affine since $`G`$ is affine.

For an arbitrary noetherian stack $`X`$ with affine stabilizer groups at closed points, the proof of Theorem 1.1 works until the last step. We find that $`X`$ is isomorphic to $`Y/GL(n)`$ for some noetherian algebraic space $`Y`$ which admits a finite surjective morphism $`WY`$ from a quasi-affine scheme $`W`$. The point now is that $`Y`$ is separated since $`W`$ is, by the following lemma. In particular, $`Y`$ has affine diagonal, and so the stack $`X=Y/GL(n)`$ has affine diagonal. Proposition 1.3 is proved. QED

###### Lemma 6.1

Let $`f:XY`$ be a proper surjective morphism of noetherian algebraic spaces. If $`X`$ is separated, then $`Y`$ is separated.

Proof. We have the commutative diagram

$$\begin{array}{ccc}X& & X\times X\\ f& & & & \\ Y& \stackrel{g}{}& Y\times Y\end{array}$$

The map $`XX\times X`$ is proper since $`X`$ is separated, and $`X\times XY\times Y`$ is proper, so the composition $`XY\times Y`$ is proper. By the defining properties of a noetherian stack over Z (as in section 4 or ), the diagonal morphism $`g:YY\times Y`$ is separated and of finite type. We would like to conclude that $`g:YY\times Y`$ is proper, that is, $`Y`$ is separated, by EGA II.5.4.3 : “Let $`f:AB`$, $`g:BC`$ be morphisms of schemes such that $`gf`$ is proper. If $`g`$ is separated of finite type and $`f`$ is surjective, then $`g`$ is proper.” We have algebraic spaces rather than schemes here, but the same proof works, as follows. By definition of properness for a map of algebraic spaces (, Definition II.7.1), since we know that $`g`$ is separated of finite type, we only have to show that $`g`$ is universally closed. The hypotheses pull back under arbitrary morphisms of algebraic spaces, so it suffices to show that the morphism $`g`$ is closed, that is, that the images of closed sets are closed. But this is clear from surjectivity of $`f`$ together with the fact that the morphism $`gf`$ is closed. QED

## 7 Varieties with quotient singularities: proof of Theorem 1.2

We now prove Theorem 1.2. Thus, let $`X`$ be a smooth Deligne-Mumford stack over a field $`k`$. Suppose that $`X`$ has finite stabilizer group and that the stabilizer group is generically trivial. Let $`B`$ be the Keel-Mori coarse moduli space of $`X`$ . Finally, suppose that the algebraic space $`B`$ is a scheme with affine diagonal (for example a separated scheme). We will show that the stack $`X`$ has the resolution property.

We need the following important property of the Keel-Mori space, which I have stated in the full generality in which that space is defined.

###### Lemma 7.1

Let $`X`$ be a stack of finite type over a locally noetherian base scheme $`S`$. Suppose that $`X`$ has finite stabilizer group, so that there is a Keel-Mori quotient space $`B`$. Then the map $`XB`$ is proper.

This is a more general version of Keel and Mori , 6.4, which in turn is modeled on Kollár , 2.9.

Proof. Here properness for a map of stacks is defined in , Chapter 7. In the case at hand, there is a finite surjective morphism from a scheme to $`X`$ (, Theorem 2.7). As a result, there is a valuative criterion for properness using only discrete valuation rings (, Proposition 7.12), in which we ask for a lift after a suitable ramified extension of DVRs.

The problem is local over $`S`$, so we can assume that $`S`$ is noetherian. So $`X`$ is noetherian. Therefore we can find a smooth surjective morphism from an affine scheme $`U`$ to $`X`$. As in section 4, $`X`$ is the quotient stack of $`U`$ by the groupoid $`R:=U\times _XU`$. By property 1.8US of the Keel-Mori quotient, the map $`UB`$ is a universal submersion (as defined in EGA IV.15.7.8 ). Therefore, as Kollár explains, if $`T`$ is the spectrum of a DVR and $`u:TB`$ is a morphism then there is a dominant morphism, which we can assume to be finite, from another DVR $`T^{}`$ to $`T`$, such that the composition $`T^{}TB`$ lifts to a map $`\overline{u}:T^{}U`$. In the valuative criterion for properness of $`XB`$, we are also given a lift $`v`$ of $`u`$ restricted to the general point $`t_g`$ of $`T`$, $`v:t_gU`$. By property 1.8G of the Keel-Mori quotient, $`U(\xi )/R(\xi )B(\xi )`$ is a bijection for every geometric point $`\xi `$, and so $`\overline{u}|_{t_g^{}}`$ and $`v`$ become equivalent under the groupoid $`R`$ after base extension to another DVR $`T^{\prime \prime }`$ which is finite over $`T^{}`$. Since $`\overline{u}`$ is defined on all of $`T^{\prime \prime }`$, this checks the valuative criterion: the morphism $`XB`$ is proper. QED

We return to the proof of Theorem 1.2. Since $`X`$ is a smooth Deligne-Mumford stack with trivial generic stabilizer, it is the quotient of some algebraic space $`Z_1`$ by an action of $`GL(n_1)`$ over $`k`$, by Edidin, Hassett, Kresch, and Vistoli (, Theorem 2.18). (In characteristic zero, this is essentially Satake’s classical observation that an orbifold with trivial generic stabilizer is a quotient of a manifold by a compact Lie group, using the frame bundle corresponding to the tangent bundle (, p. 475).)

By Laumon and Moret-Bailly (generalized by Edidin, Hassett, Kresch, and Vistoli, as used in the above proof), there is a finite surjective morphism from a scheme $`A`$ to the Deligne-Mumford stack $`X`$ (, Theorem 16.6). Some special cases of this result were known before, by Seshadri , 6.1, and Vistoli , 2.6. By Lemma 7.1, the morphism $`XB`$ is proper, and so the composition $`AB`$ is proper. It is clearly also a quasi-finite morphism of algebraic spaces, and so it is finite, in particular affine. Define $`Z_A`$ by the following pullback diagram.

$$\begin{array}{ccc}Z_A& & Z_1\\ & & GL\left(n_1\right)& & \\ A& & X\\ & & & & \\ & & B\end{array}$$

Since $`Z_AA`$ is a $`GL(n_1)`$-bundle and $`AB`$ is finite, both morphisms are affine, and so the composition $`Z_AB`$ is affine. Since $`Z_AZ_1`$ is a finite surjective morphism of algebraic spaces over $`B`$, it follows from Chevalley’s theorem for algebraic spaces (, III.4.1) that the morphism $`Z_1B`$ is affine.

Since $`B`$ is a scheme and the morphism $`Z_1B`$ is affine, the smooth algebraic space $`Z_1`$ is a scheme. Likewise, since $`B`$ has affine diagonal and $`Z_1B`$ is affine, $`Z_1`$ has affine diagonal. To see this, write the diagonal morphism $`Z_1Z_1\times _kZ_1`$ as the composition of two maps. The first is $`Z_1Z_1\times _BZ_1`$, which is a closed embedding and hence affine since $`Z_1B`$ is affine and hence separated. Next is $`Z_1\times _BZ_1Z_1\times _kZ_1`$, which is a pullback of the affine morphism $`BB\times _kB`$ and hence is affine.

Thus, $`Z_1`$ is a smooth scheme with affine diagonal. So $`Z_1`$ has an ample family of line bundles, by Brenner and Schröer (or Kleiman and Illusie, in the separated case), as mentioned in section 2. Then, by Theorem 2.1, due to Thomason, the quotient stack $`X=Z_1/GL(n)`$ has the resolution property. QED

## 8 The resolution property and $`K`$-theory

As mentioned in section 2, if a stack $`X`$ has the resolution property, then the natural map $`K_0^{\text{naive}}XK_0X`$ is an isomorphism. In particular, every perfect complex on $`X`$ is equivalent in the Grothendieck group $`K_0X`$ of perfect complexes to a difference of vector bundles. We will present two examples to show that the converses to these statements are false. First, we state a positive result for smooth schemes.

###### Proposition 8.1

Let $`X`$ be a smooth scheme of finite type over a field. The following are equivalent.

(1) $`X`$ has affine diagonal. For a scheme, as here, it is equivalent to say that the intersection of any two affine open subsets of $`X`$ is affine.

(2) $`X`$ is a scheme with an ample family of line bundles.

(3) $`X`$ has the resolution property.

(4) The natural map from $`K_0^{\text{naive}}X`$ to $`K_0X=G_0X`$ is surjective. Equivalently, every coherent sheaf on $`X`$ is equivalent in the Grothendieck group $`G_0X`$ to a difference of vector bundles.

This is fairly easy, but perhaps suggestive. From my point of view, the interesting equivalence here is between (1) and (3), because one would often like to know whether the resolution property holds, and it is usually easy to check whether a scheme or stack has affine diagonal. We can hope that the equivalence between (1) and (3) holds in much greater generality; see Questions 1 and 2 in the introduction. In more general situations, property (2) will imply the resolution property but will definitely not be equivalent to it, as can be seen from several examples in section 2. Finally, the end of this section will present two examples showing that property (4) does not imply the resolution property in more general situations, for example for smooth algebraic spaces.

Proof. The implications $`(1)(2)(3)(4)`$ are discussed in section 2. First, Brenner and Schröer observed that (1) implies (2), that is, that a smooth scheme with affine diagonal has an ample family of line bundles. The proof is the same as in the case of a smooth separated scheme, due to Borelli and Illusie. Next, Kleiman and Illusie proved that (2) implies (3). Finally, Thomason proved that $`K_{}^{\text{naive}}XK_{}X`$ is an isomorphism when $`X`$ has the resolution property. The special case that (3) implies (4) is particularly simple: using the resolution property, every coherent sheaf has a resolution by vector bundles, which can be stopped after finitely many steps because the scheme $`X`$ is regular.

It remains to show that (4) implies (1). That is, if $`X`$ is a smooth scheme that does not have affine diagonal, we will find a coherent sheaf $`C`$ on $`X`$ whose class in $`K_0X=G_0X`$ is not a difference of vector bundles. The following proof extends an argument by Schröer and Vezzosi (, Proposition 4.2).

The assumption that $`X`$ does not have affine diagonal means that $`X`$ has open affine subsets $`U`$ and $`V`$ such that $`UV`$ is not affine. As is well known, the complement of an irreducible divisor $`D`$ in a smooth affine variety $`U`$ is affine. Indeed, $`D`$ is Cartier because $`U`$ is smooth, and so the inclusion from $`UD`$ into $`U`$ is an affine morphism, which implies that $`UD`$ is affine since $`U`$ is. As a result, if $`U(UV)`$ contains any irreducible divisor, we can remove it from $`U`$ without changing the properties we have stated for $`U`$, and likewise for $`V`$. Thus we can assume that $`U(UV)`$ and $`V(UV)`$ have codimension at least 2.

Since $`U`$ and $`V`$ are smooth, in particular normal, it follows that the restriction maps from $`O(U)`$ or $`O(V)`$ to $`O(UV)`$ are isomorphisms. Since $`U`$ and $`V`$ are affine, this means that both $`U`$ and $`V`$ are isomorphic to $`\text{Spec }O(UV)`$. Let $`S`$ be the closure in $`X`$ of $`U(UV)`$, and let $`T`$ be the closure in $`X`$ of $`V(UV)`$. We give these closed subsets the reduced scheme structure. Suppose that the coherent sheaf $`O_S`$ on $`X`$ is a difference of vector bundles $`EF`$ in the Grothendieck group $`G_0X`$; we will derive a contradiction.

After shrinking $`U`$ to a smaller affine open neighborhood of the generic point of an irreducible component of $`S`$, and shrinking $`V`$ to the corresponding neighborhood of the generic point of a component of $`T`$, we can assume that the vector bundles $`E`$ and $`F`$ are trivial on both $`U`$ and $`V`$. So each of these vector bundles is described up to isomorphism on $`UV`$ by an attaching map $`UVGL(n)`$. Since $`U(UV)`$ has codimension at least 2, every such map extends to $`U`$. It follows that $`E`$ and $`F`$ are in fact trivial on $`UV`$. Thus, our assumption implies that the class of $`O_S`$ in $`G_0X`$ restricts to zero in $`G_0(UV)`$.

Let $`S_U=SU=U(UV)`$ and $`T_V=TV=V(UV)`$; these are disjoint nonempty closed subsets of $`UV`$, and they are isomorphic. Consider the localization sequences in $`G`$-theory, due to Quillen :

$$\begin{array}{ccccccccc}G_1(UV)& & G_0S_U& & G_0U& & G_0(UV)& & 0\\ G_1(UV)& & G_0T_V& & G_0V& & G_0(UV)& & 0\\ G_1(UV)& & G_0(S_UT_V)& & G_0(UV)& & G_0(UV)& & 0\end{array}$$

Since the inclusions of $`UV`$ into $`U`$ and into $`V`$ are isomorphic, any element of $`G_1(UV)`$ has the same image in $`G_0S_U`$ as in $`G_0T_V`$, with respect to the isomorphism of $`S_U`$ with $`T_V`$. Furthermore, the class of $`O_S`$ in $`G_0S_U`$ is not zero. So the class of $`O_S`$ in $`G_0(S_UT_V)=G_0S_UG_0T_V`$ is not in the image of $`G_1(UV)`$. Thus the class of $`O_S`$ in $`G_0(UV)`$ is not zero, contradicting the previous paragraph. So in fact the class of the coherent sheaf $`O_S`$ in $`G_0X`$ is not a difference of vector bundles. We have proved that (4) implies (1). QED

Example 1. There is a smooth algebraic space $`Z`$ such that $`K_0^{\text{naive}}ZK_0Z`$ is surjective, that is, every perfect complex on $`Z`$ is equivalent in $`K_0Z`$ to a difference of vector bundles, but $`Z`$ does not have the resolution property.

In conformity with Question 1 in the introduction, the space we construct will not have affine diagonal. Let $`Y_r`$ be the smooth non-separated scheme $`Y=A^r_{A^r0}A^r`$, $`r2`$, over some field $`k`$ of characteristic not 2. The algebraic space $`Z_r`$ will be the quotient of $`Y_r`$ by a free action of the group $`\text{Z}/2`$, acting by $`1`$ on $`A^r`$ and switching the two origins. The algebraic space $`Z_r`$ is a well known example, described and illustrated by Artin  and named by Kollár a bug-eyed cover . Its best known property is that it is not locally separated at the image of the origin, and therefore not a scheme.

For $`r=1`$, the algebraic space $`Z_1`$ has the resolution property. Indeed, $`Y_1`$ is a smooth scheme with affine diagonal, and so it has an ample family of line bundles by the result of Brenner and Schröer mentioned in section 2. By Theorem 2.1, it follows that $`Z_1=Y_1/(\text{Z}/2)`$ has the resolution property. One gets a more direct proof by observing that the scheme $`Y_1=A^1_{A^10}A^1`$ is the quotient of $`A^20`$ by the diagonal torus $`G_mSL(2)`$. Likewise, the algebraic space $`Z_1`$ is the quotient of the quasi-affine scheme $`A^20`$ by the normalizer of $`G_m`$ in $`SL(2)`$. (This normalizer is a non-split extension of $`\text{Z}/2`$ by $`G_m`$.) Then it is immediate from Theorem 2.1 that $`Y_1`$ and $`Z_1`$ have the resolution property.

We now consider $`r2`$. Since $`Z_r`$ does not have affine diagonal, we know by Proposition 1.3 that $`Z_r`$ does not have the resolution property, as we will see more explicitly below. To compute the group $`K_0^{\text{naive}}Z_r`$, we need to describe the vector bundles on $`Z_r`$. Let $`\sigma :A^r0A^r0`$ be multiplication by $`1`$. A vector bundle $`E`$ on $`Z_r`$ is a vector bundle $`E`$ on $`A^r`$ together with an isomorphism

$$f:E\stackrel{}{}\sigma ^{}E$$

over $`A^r0`$, such that the composition

$$E\stackrel{𝑓}{}\sigma ^{}E\stackrel{\sigma ^{}f}{}\sigma ^{}\sigma ^{}E=E$$

is the identity on $`A^r0`$. Since $`r2`$, $`f`$ extends uniquely to a map $`f:E\sigma ^{}E`$ over all of $`A^r`$, and the above composition is the identity over $`A^r`$ because this is true over $`A^r0`$. Thus the category of vector bundles over $`Z_r`$ is equivalent to that of $`\text{Z}/2`$-equivariant vector bundles over $`A^r`$, with $`\text{Z}/2`$ acting on $`A^r`$ by multiplication by $`1`$. So

$`K_0^{\text{naive}}Z_r`$ $`K_0^{\text{naive}}(A^r/\text{Z}/2)`$
$`K_0(A^r/\text{Z}/2)`$
$`\text{Rep}(\text{Z}/2)`$
$`\text{Z}^2.`$
Here $`A^r/\text{Z}/2`$ denotes the quotient stack of $`A^r`$ by $`\text{Z}/2`$. Its naive $`K`$-theory coincides with its true $`K`$-theory because it has the resolution property, by Theorem 2.1. The calculation that $`K_0(A^r/\text{Z}/2)`$ is isomorphic to the representation ring of $`\text{Z}/2`$ follows from the homotopy invariance of equivariant algebraic $`K`$-theory, also proved by Thomason (, 4.1).

Next, we compute the true $`K`$-theory $`K_0Z_r`$, which is isomorphic to the Grothendieck group $`G_0Z_r`$ of coherent sheaves because the algebraic space $`Z_r`$ is smooth over $`k`$. By the previous paragraph, we can identify the map $`K_0^{\text{naive}}Z_rK_0Z_r`$ with the pullback map $`G_0(A^r/\text{Z}/2)G_0Z_r`$ associated to the obvious flat morphism from $`Z_r`$ to the quotient stack $`A^r/\text{Z}/2`$. We have exact localization sequences, by Thomason’s paper on equivariant $`K`$-theory (, 2.7):

$$\begin{array}{ccccccc}G_0(\text{point}/\text{Z}/2)& & G_0(A^r/\text{Z}/2)& & G_0((A^r0)/\text{Z}/2)& & 0.\\ & & & & & & \\ G_0((\text{2 points})/\text{Z}/2)& & G_0Z_r& & G_0((A^r0)/\text{Z}/2)& & 0.\end{array}$$

The left vertical map sends $`\text{Rep}(\text{Z}/2)\text{Z}^2`$ to $`G_0(\text{point})=\text{Z}`$ by the rank; in particular, it is surjective. The right vertical map is an isomorphism, and so the center vertical map is surjective. This means that $`K_0^{\text{naive}}Z_rK_0Z_r`$ is surjective, as we want.

We can also compute $`K_0Z_r`$ ($`=G_0Z_r`$) explicitly, using the above diagram. By a Koszul resolution, the pushforward map

$$\text{Rep}(\text{Z}/2)=G_0(\text{point}/\text{Z}/2)G_0(A^r/\text{Z}/2)=\text{Rep}(\text{Z}/2)$$

is multiplication by $`\lambda _1V:=(1)^i\mathrm{\Lambda }^iV`$, where $`V`$ denotes the representation of $`\text{Z}/2`$ on $`A^r`$. Therefore $`K_0Z_r`$ is the quotient of $`\text{Rep}(\text{Z}/2)`$ by the relation

$$W\lambda _1V=(\text{dim }W)\lambda _1V$$

for all $`W\text{Rep}(\text{Z}/2)`$. We thereby compute that $`K_0Z_r`$ is the quotient of $`K_0^{\text{naive}}Z_r=\text{Rep}(\text{Z}/2)=\text{Z}\text{Z}u`$, where $`u`$ is the nontrivial 1-dimensional representation of $`\text{Z}/2`$, by the relation $`2^r(1u)=0`$, so that $`K_0Z_r`$ is isomorphic to $`\text{Z}\text{Z}/2^r`$. In particular, we see again that the resolution property fails for $`Z_r`$, because the map $`K_0^{\text{naive}}Z_rK_0Z_r`$ is not an isomorphism. Explicitly, let $`O_{A^r}`$ and $`L`$ denote the $`\text{Z}/2`$-equivariant line bundles on $`A^r`$ associated to the trivial and the nontrivial 1-dimensional representations of $`\text{Z}/2`$. Let $`K`$ be the coherent sheaf

$$K=\mathrm{ker}(O_{A^r}LO_0),$$

where both $`O_{A^r}`$ and $`L`$ map onto $`O_0`$. Then $`K`$ is not a $`\text{Z}/2`$-equivariant coherent sheaf on $`A^r`$, but it is $`\text{Z}/2`$-equivariant outside the origin, and so it corresponds to a coherent sheaf on $`X_r`$. The sheaf $`K`$ is not a quotient of a vector bundle on $`X_r`$.

It is amusing to observe that, over the complex numbers, the non-separated scheme $`Y_r=A^r_{A^r0}A^r`$ is weak homotopy equivalent to the sphere $`S^{2r}`$, and the quotient algebraic space $`Z_r`$ is weak homotopy equivalent to real projective space $`\text{R}\text{P}^{2r}`$. The true $`K`$-group $`K_0Z_r=\text{Z}\text{Z}/2^r`$ maps isomorphically to the topological $`K`$-group $`K_{\text{top}}^0\text{R}\text{P}^{2r}`$, as computed by Atiyah (, p. 107). This suggests that the $`K`$-theory of any stack with affine stabilizer group should be closely related to its topological or etale $`K`$-theory. The relation will not always be visible on the level of $`K_0`$, but rather in the groups $`K_i`$ with $`i`$ large. Precisely, there should be an isomorphism

$$K_{}(X;\text{Z}/l^\nu )[\beta ^1]K_{\text{et}}^{}(X;\text{Z}/l^\nu ),$$

where $`\beta `$ denotes the Bott map. In fact, one problem here is to define the groups on the right. For $`X`$ a locally separated algebraic space of finite type over a reasonable base scheme, or more generally for quotient stacks $`X/G`$ of such an algebraic space by a linear algebraic group, Thomason proved analogous results in $`G`$-theory (, 3.17 and Theorem 5.9), which coincides with $`K`$-theory for regular stacks. Some of his results apply to the above example $`Z_r=Y_r/\text{Z}/2`$.

Example 2. There is a smooth Deligne-Mumford stack $`X`$ for which the natural map $`K_0^{\text{naive}}XK_0X`$ is an isomorphism, but $`X`$ does not have the resolution property.

As above, let $`Y_r`$ be the smooth non-separated scheme $`A^r_{A^r0}A^r`$ over a field $`k`$ of characteristic not 2. Let $`X_r`$ be the quotient stack of $`Y_r`$ by the action of $`\text{Z}/2`$ which is the identity outside the origin and which switches the two origins. We will show that $`X_r`$ has the desired properties for $`r2`$.

For $`r=1`$, $`X_1`$ does have the resolution property. Indeed, $`Y_1`$ is a smooth scheme with affine diagonal and hence has an ample family of line bundles by Brenner and Schröer, as mentioned in section 2. Therefore the quotient stack $`X_1=Y_1/\text{Z}/2`$ has the resolution property by Theorem 2.1. More explicitly, the stack $`X_1`$ has the resolution property, by Theorem 2.1, because it is the quotient of the quasi-affine scheme $`A^20`$ by the orthogonal group $`O(2)`$. (The orthogonal group $`O(2)`$ of the quadratic form $`x_1x_2`$ is a split extension of $`\text{Z}/2`$ by $`G_m`$.)

For $`r2`$, one checks (by arguments as in Example 1) that pulling back via the flat morphism $`X_rA^r/\text{Z}/2`$ induces an equivalence of categories of vector bundles. Here $`A^r/\text{Z}/2`$ denotes the quotient stack of $`A^r`$ by the trivial action of $`\text{Z}/2`$, and so a vector bundle on $`A^r/\text{Z}/2`$ is simply a direct sum of bundles $`E_0E_1`$ on $`A^r`$, where $`\text{Z}/2`$ acts trivially on $`E_0`$ and by $`1`$ on $`E_1`$. It follows that

$`K_0^{\text{naive}}X`$ $`=K_0^{\text{naive}}(A^r/\text{Z}/2)`$
$`=\text{Rep}(\text{Z}/2)`$
$`=\text{Z}^2.`$
The true $`K`$-group $`K_0X_r`$ maps isomorphically to $`G_0X_r`$ since $`X_r`$ is smooth over $`k`$. By the localization sequence as in Example 1, $`K_0X_r`$ is the quotient of $`K_0^{\text{naive}}X_r=\text{Rep}(\text{Z}/2)`$ by the relation that

$$W\lambda _1V=(\text{dim }W)\lambda _1V$$

for all $`W\text{Rep}(\text{Z}/2)`$, where $`V`$ is the representation of $`\text{Z}/2`$ on $`A^r`$. In this example, $`V`$ is the trivial representation, and so $`\lambda _1V=0`$. Therefore the map from $`K_0^{\text{naive}}X_r`$ to $`K_0X_r`$ is an isomorphism, as promised.

Finally, we know that $`X_r`$ does not have the resolution property by Proposition 1.3, since $`X_r`$ does not have affine diagonal, using that $`r2`$. One can define an explicit coherent sheaf $`K`$ on $`X_r`$ which is not a quotient of a vector bundle, by the same formula as in Example 1.

## 9 How to prove the resolution property in an example: the nodal cubic

Suppose that one wishes to prove the resolution property for a stack $`X`$. The proof of Theorem 1.1 gives an idea of how to proceed. In many cases, the proof indicates how to construct a coherent sheaf $`C`$ on $`X`$ such that $`X`$ has the resolution property if and only if the single sheaf $`C`$ is a quotient of a vector bundle. One statement of this type is formulated in Lemma 9.2, below. I hope that this will be a useful way to prove the resolution property in cases of interest.

In this section, we carry the procedure out in the following example.

###### Proposition 9.1

Let $`X`$ be the nodal cubic over a field $`k`$, that is, $`\text{P}^1`$ with the points 0 and $`\mathrm{}`$ identified. Let $`T:=G_m`$ act on $`X`$ in the natural way. Then the quotient stack $`X/T`$ has the resolution property.

Here $`X`$ is a projective variety and so the resolution property is well known for $`X`$, but the action of $`T`$ is “bad” in several ways. In particular, any $`T`$-equivariant line bundle on $`X`$ has degree 0 and so there is no $`T`$-equivariant embedding of $`X`$ into projective space; there is not even an ample family of $`T`$-equivariant line bundles on $`X`$. Thus Theorem 2.1, due to Thomason, does not immediately apply to show that $`X/T`$ has the resolution property. The phenomenon that $`X`$ has an ample family of line bundles but no ample family of $`T`$-equivariant line bundles can only occur for non-normal schemes such as this one, which is why it seemed worth finding out whether $`X/T`$ has the resolution property. (Since $`X`$ is not normal, Theorem 1.1 as stated does not apply to $`X`$, but the methods still work.) The fact that we will prove the resolution property in this “bad” case is encouraging for Question 3 in the introduction, proposing that the resolution property is always preserved upon taking the quotient by a linear algebraic group.

Proof of Proposition 9.1. It seems convenient to begin by considering an etale double covering $`Y`$ of $`X`$, the union of two copies $`A`$ and $`B`$ of $`\text{P}^1`$, with 0 in $`A`$ identified with $`\mathrm{}`$ in $`B`$ and $`\mathrm{}`$ in $`A`$ identified with $`0`$ in $`B`$. I will write $`p`$ for the point $`0`$ in $`AY`$ and $`q`$ for the point $`\mathrm{}`$ in $`AY`$. The $`T`$-action on $`X`$ lifts to a $`T`$-action on $`Y`$ which commutes with the $`\text{Z}/2`$-action (switching the two copies of $`\text{P}^1`$ in the natural way), and so we have an isomorphism of quotient stacks $`X/TY/(\text{Z}/2\times T)`$. The scheme $`Y`$ resembles $`X`$ in that it has no ample family of $`T`$-equivariant line bundles. What suggests that $`Y`$ should be easier to study than $`X`$ is that unlike $`X`$, $`Y`$ is at least a union of $`T`$-invariant affine open subsets, $`Yp`$ and $`Yq`$.

To show that the stack $`Y/T`$ has the resolution property, we will use the following lemma, which isolates part of the proof of Theorem 1.1.

###### Lemma 9.2

Let $`Y`$ be a noetherian scheme with an action of a flat affine group scheme $`T`$ of finite type over Z or over a field. Let $`S_1,\mathrm{},S_r`$ be closed $`T`$-invariant subschemes whose complements form an affine open covering of $`Y`$. Let $`C`$ be the direct sum of the ideal sheaves $`I_{S_1},\mathrm{},I_{S_r}`$. Then the stack $`Y/T`$ has the resolution property if and only if the $`T`$-equivariant coherent sheaf $`C`$ on $`Y`$ is a quotient of some $`T`$-equivariant vector bundle on $`Y`$.

Proof. To say that the stack $`Y/T`$ has the resolution property means that every $`T`$-equivariant coherent sheaf on $`Y`$ is a quotient of some $`T`$-equivariant vector bundle on $`Y`$. So suppose that $`C`$ is a quotient of some $`T`$-equivariant vector bundle $`E`$ on $`Y`$. Let $`W`$ be the $`GL(n)`$-bundle over $`Y`$ corresponding to $`E`$. Then the pullback of $`C`$ to $`W`$ is spanned by its global sections. By the choice of $`C`$, plus affineness of the morphism $`WY`$, it follows that the scheme $`W`$ is quasi-affine (this argument is given in more detail in the proof of Theorem 1.1). Therefore the stack $`W/(T\times GL(n))Y/T`$ has the resolution property by Theorem 2.1. QED

We return to the union $`Y`$ of two copies of $`\text{P}^1`$ with the action of $`T=G_m`$. Since $`Y`$ is the union of the $`T`$-invariant affine open subsets $`Yp`$ and $`Yq`$, Lemma 9.2 shows that $`Y`$ has the resolution property if the $`T`$-equivariant coherent sheaf $`I_{S_1}I_{S_2}`$ on $`Y`$ is a quotient of some $`T`$-equivariant vector bundle, for some $`T`$-invariant subschemes $`S_1`$ and $`S_2`$ with support equal to $`p`$ and $`q`$, respectively. By the $`\text{Z}/2`$-symmetry of $`Y`$, it suffices to show that $`I_S`$ is a quotient of a $`T`$-equivariant vector bundle on $`Y`$, for some $`T`$-invariant subscheme $`S`$ with support equal to $`p`$. Replacing the bundle by its dual, it is equivalent to find a $`T`$-equivariant vector bundle $``$ on $`Y`$ with a $`T`$-invariant section $`s:O_Y`$ which vanishes (to any order) at $`p`$ and nowhere else on $`Y`$.

To define a $`T`$-equivariant vector bundle $``$ on $`Y`$, we need to define $`T`$-equivariant vector bundles $`E`$ on $`A`$ and $`F`$ on $`B`$, together with $`T`$-equivariant isomorphisms $`E|_0F|_{\mathrm{}}`$ and $`E|_{\mathrm{}}F|_0`$. Take $`E=O(1)O(1)`$ and $`F=O(1)O(1)`$ as vector bundles on $`\text{P}^1`$. Define the action of $`T`$ on $`E`$ to be trivial on $`E|_{\mathrm{}}`$, with weight 1 on $`O(1)|_0E|_0`$, and weight $`1`$ on $`O(1)|_{\mathrm{}}E|_0`$. Define the action of $`T`$ on $`F`$ to be trivial on $`F|_0`$, with weight $`1`$ on $`O(1)|_{\mathrm{}}F|_{\mathrm{}}`$, and weight $`1`$ on $`O(1)|_{\mathrm{}}F|_{\mathrm{}}`$. Clearly there are isomorphisms of $`T`$-representations $`E|_0F|_{\mathrm{}}`$ and $`E|_{\mathrm{}}F|_0`$, which we can use to define a $`T`$-equivariant vector bundle $`=(E,F)`$ on $`Y`$. For our purpose, we need to choose the isomorphism between the trivial 2-dimensional representations $`E|_{\mathrm{}}`$ and $`F|_0`$ of $`T`$ so as to send the line $`O(1)|_{\mathrm{}}E|_{\mathrm{}}`$ to the line $`O(1)|_0F|_0`$. With this choice, the $`T`$-vector bundle $``$ on $`Y`$ is not a direct sum of two $`T`$-line bundles.

The vector bundle $``$ has a $`T`$-invariant section over $`Y`$ (contained in the subbundle $`O(1)E`$ over $`A`$ and in the subbundle $`O(1)F`$ over $`B`$) which vanishes at $`p`$ (the image of $`0A\text{P}^1`$ and of $`\mathrm{}B\text{P}^1`$) but nowhere else in $`Y`$. Thus, as we have explained, the dual $`T`$-vector bundle $`^{}`$ on $`Y`$ maps onto the $`T`$-coherent sheaf $`I_S`$ for some subscheme $`S`$ with support equal to $`p`$. By Lemma 9.2, the stack $`Y/T`$ has the resolution property.

From here it is easy to deduce that the quotient stack of the nodal cubic $`X`$ by $`T`$ also has the resolution property, as we wanted. Namely, writing $`\sigma `$ for the generator of the $`\text{Z}/2`$-action on $`Y`$, $`^{}\sigma ^{}(^{})`$ is a $`\text{Z}/2\times T`$-equivariant vector bundle on $`Y`$ which maps onto the $`\text{Z}/2\times T`$-equivariant sheaf $`I_SI_{\sigma (S)}`$. So, by Lemma 9.2 again, the stack $`Y/(\text{Z}/2\times T)=X/T`$ has the resolution property. Proposition 9.1 is proved. QED

It is interesting to add that the proof of Theorem 1.1 works completely for $`X/T`$ even though the nodal cubic $`X`$ is not normal, because it is a scheme, not just an algebraic space. That proof shows that since $`X/T`$ has the resolution property, it is the quotient of a quasi-affine scheme by $`GL(n)`$ for some $`n`$. Thus this apparently bad example of a stack turns out to have some very good properties. As mentioned at the beginning of this section, this is encouraging for Question 3 in the introduction.

DPMMS, Wilberforce Road, Cambridge CB3 0WB, England.

b.totaro@dpmms.cam.ac.uk


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# Simplifying the mosaic description of DNA sequences

## I INTRODUCTION

One of the major goals in DNA sequence analysis is in gaining an understanding of the overall organization of the genome. Beyond identifying the manifestly functional regions such as genes, promoters, repeats, etc., it has also been of interest to analyse the properties of the DNA string itself. One set of studies has been directed towards examining the nature of correlations between the bases. There is some evidence for long-range correlations which give rise to 1/f spectra in genomic DNA ; this feature has been attributed to the presence of complex heterogeneities in nucleotide sequences . These result in hierarchical patterns in DNA, the mosaic or ‘domain within domain’ picture . This structure is most conveniently explored through segmentation analysis based on information theoretic measures , although other schemes to uncover the correlation structure over long scales, such as detrended fluctuation analysis of DNA walks  or wavelet tranform technique  have also been applied. There have been some attempts to decode the biological implications of such complexity , but these are incompletely understood as of now. On shorter length scales there is a prominent 3-base correlation in coding regions of DNA; this offers a means of locating and identifying genes . There are other short–range correlations as well  corresponding to structural constraints on the DNA double helix.

Segmentation analysis is a powerful means of examining the large–scale organization of DNA sequences . The most commonly used procedure  is based on maximization of the Jensen-Shannon (J-S) divergence through which a given DNA string is recursively separated into compostionallly homogeneous segments called domains (or patches). This results in a coarse-grained description of the DNA string as a sequence of distinct domains. The criterion for continuing the segmentation process is based on statistical significance (this is equivalent to hypothesis testing)  or, alternatively, within a model selection framework based on the Bayesian information criterion . This criterion can be extended and used to detect isochores , CpG islands, origin and terminus of replication in bacterial genomes, complex repeats in telomere sequences, etc.. Segmentation using a 12-symbol alphabet derived from codon usage has been shown recently to delineate the border between coding and noncoding regions in a DNA sequence .

In the present work, we analyse the segmentation structure of genomic DNA for a class of genomes ranging in (evolutionary) complexity from bacteria to human. Our motivation is to understand the complexity of genome organization in terms of the domains obtained. We further aim to correlate the domain picture with evolutonary biological processes.

By construction a given domain is heterogenous with respect to its neighbours, but it may nevertheless be compositionally similar to other domains. Based on this premise, we attempt to draw a larger domain picture by obtaining ‘domain sets’. These consist of a set of domains which are homogeneous when concatenated. A domain set may thus be interpreted as a larger homogeneous sequence, parts of which are scattered nonuniformly in a genomic sequence. The number of domain sets constructed thus is found to be much fewer than the domains obtained upon segmentation . We propose here an optimal procedure, starting from the domains found from one of the above segmentation methods, and building up a domain set by adding together all its components. We then use standard complexity measures to show that this gives a superior model in as much as the complexity is reduced.

This paper is organised as follows. In the next section, we briefly review the segmentation methods based on the J-S divergence. Section III contains our main results. We first segment a given genome to reveal the primary domain structure that derives from the J-S divergence. We then show how the domain sets are constructed, and analyse the attendant decrease in complexity. In Section IV, we speculate that such domain organization ocurred during genomic evolution when there was lateral gene and/or DNA transfer between species. To that end, we present the results of numerical experiments based on a host-parasite model, where we artificially insert fragments of one genome inside another, and demonstrate that this process can be uncovered via segmentation. Section V concludes the paper with a summary and discussion of our results.

## II Segmentation methods

In this section we briefly review the segmentation methodology that is used here in order to fragment a genome into homogeneous domains. Consider a sequence $`𝒮`$ as a concatenation of two subsequences $`𝒮^{(1)}`$ and $`𝒮^{(2)}`$. The Jensen–Shannon divergence  of the subsequences is

$`𝐃(^{(1)},^{(2)})`$ $`=`$ $`H(\pi ^{(1)}^{(1)}+\pi ^{(2)}^{(2)})[\pi ^{(1)}H(^{(1)})+\pi ^{(2)}H(^{(2)})],`$ (1)
where $`^{(i)}=\{f_1^{(i)},f_2^{(i)},\mathrm{},f_k^{(i)}\},i=1,2`$ are the relative frequency vectors, and $`\pi ^{(1)}`$ and $`\pi ^{(2)}`$ their weights. In Eq. (1), $`H`$ is the Shannon entropy (in unit of bits)

$$H()=\underset{i=1}{\overset{k}{}}f_i\mathrm{log}_2f_i,$$
(2)
although, as can be appreciated, a variety of other functions on the $`f_i`$’s can also be used as a criterion for estimating the divergence of two sequences.

The algorithm proposed by Bernaola-Galván $`etal.`$  proceeds as follows. A sequence is segmented in two domains such that the J-S divergence $`𝐃`$ is maximum over all possible partitions. Each resulting domain is then further segmented recursively.

The main issue with regard to continual segmentation is that unless the significance of a given segmentation step is properly assessed, it is possible to arrive at segments which have no great significance. This question is also related to a second issue, namely when one should stop the recursion. Since we consider finite DNA sequences, it is again possible to keep segmenting until the segments are very short. Both these questions can be answered through one of two possible approaches which we now describe.

### A Hypothesis testing framework

The statistical significance of the segmentation is determined by computing the maximum value of the J-S divergence for the two potential subsegments, $`𝐃_{max}`$, and estimating the probability of getting this value or less in a random sequence. This defines the significance level, $`s(x)`$, as

$$s(x)=Prob\{𝐃_{max}x\}.$$
(3)
The probablility distribution of $`𝐃_{max}`$ has an analytic approximation  and

$$s(x)=[F_\nu (\beta 2N\mathrm{ln}2x)]^{N_{eff}},$$
(4)
where $`F_\nu `$ is the chi–square distribution function with $`\nu `$ degrees of freedom, $`N`$ is the sequence length, $`\beta `$ is a scale factor which is essentially independent of $`N`$ and $`k`$ and for each $`k`$, $`N_{eff}=a\mathrm{ln}N+b.`$ The values of $`\beta `$ and $`N_{eff}`$ (and thus the constants $`a`$ and $`b`$) are found from Monte Carlo simulations by fitting the empirical distributions to the above expression .

Within the hypothesis testing framework, then, the segmentation is allowed if and only if $`s(x)`$ is greater than a preset level of statistical significance. It is possible to segment a given sequence initially at a (usually very high) significance level, and these domains are further segmented at lower levels of significance to detect the inner structure or other patterns .

### B Model selection framework

A different criterion can be evolved for stopping the recursive segmentation within the so-called model selection framework . This is based on the Bayesian information criterion , denoted $`𝐁`$ below,

$$𝐁=2\mathrm{log}(\widehat{L})+\mathrm{log}(N)K+O(1)+O(\frac{1}{\sqrt{N}})+O(\frac{1}{N}),$$
(5)
where $`\widehat{L}`$ is the maximum likelihood of the model, $`N`$ is the sample size and $`K`$ is the number of parameters in the model.

A potential segmentation based on the J-S divergence $`𝐃`$ is deemed acceptable if $`𝐁`$ is reduced after segmentation. From the above equation, this condition is

$$2N𝐃>(K_2K_1)\mathrm{log}(N),$$
(6)
where $`K_1`$ and $`K_2`$ are the number of free parameters of the models before and after the segmentation. This is the lower bound of the significance level; an upper bound can be preset by using a measure of segmentation strength ,

$$s=\frac{2N𝐃(K_2K_1)\mathrm{log}(N)}{(K_2K_1)\mathrm{log}(N)}.$$
(7)
Eq. (6) is equivalent to the condition $`s>0`$.

## III Applications and analysis

In the present work we consider DNA sequences as strings in a 4–letter alphabet ($`A,T,C,G`$). In the model selection framework discussed above, therefore, the relevant parameters are $`K_1=3`$ (since only 3 of the 4 nucleotides are independent) and $`K_2=7`$ (the 3 free parameters from each of the two subsegments, and in addition, the partition point which is another independent parameter) . The importance of this segmentation approach in detecting some of the structural and functional units in DNA sequences has been demonstrated recently . The results that follow have been obtained by the application of this approach.

### A Labeling the domains

The complete genome of a bacterium Ureaplasma urealyticum (751719 bp) and a contig of human chromosome 22 (gi $`10879979`$ ref $`NT\mathrm{\_}011521.1`$, 767357 bp) were segmented at the lower bound of the stopping criterion, namely Eq. (6). The number of segments obtained by this procedure is 86 for the bacterium and 248 for human chromosome 22 contig. Labeling each of these segments by a unique symbol gives a coarse–grained view of the entire sequence, say $`S_1S_2\mathrm{}S_N`$.

While each segment $`S_k`$ is heterogeneous with respect to its neighbours, $`S_{k\pm 1}`$, it need not be compositionally distinct from a non–neighbouring segment, $`S_j`$. Therefore, we now examine the inter se heterogeneity of all segments with respect to each other. Segments $`S_k`$ and $`S_j`$ are concatenated, and if this ‘supersegment’ cannot be segmented by the same criterion, then both $`S_k`$ and $`S_j`$ are assigned the same domain symbol. This is done recursively and exhaustively, so that within the model selection framework of segmentation, all domains that cannot be distinguished from one another are assigned the same symbol. This gives a reduced and further coarse–grained view of the domain structure of a DNA sequence.

To ensure that the above procedure is as complete and self–consistent as possible, we examine each segment $`S_k`$ by concatenating it with $`S_j`$ and all preceding distinct segments that share the same domain symbol as $`S_j`$, and examine whether this larger sequence can be segmented. Explicitly, if segments $`S_i`$ and $`S_j`$ have the same symbol (following the procedure given above) we examine the supersegment $`S_iS_jS_k`$ to determine whether segment $`S_k`$ should share the same domain symbol or not. It is further required to to consider all possible subsets ($`S_iS_k`$, $`S_jS_k`$, etc.) to ensure that all segments that are deemed to share a given domain symbol do indeed belong to one class, namely that such superdomains do not undergo further segmentation.

Following the above, the 86 domains obtained from the segmentation of U. urealyticum are reduced to a total of 17 distinct domain types:

$`\begin{array}{cccccccccccc}\underset{¯}{S_1}& S_2& S_3& S_4& S_5& S_3& \underset{¯}{S_1}& S_2& \underset{¯}{S_1}& S_6& S_4& \underset{¯}{S_1}\\ S_6& S_7& S_2& \underset{¯}{S_1}& S_6& S_4& S_8& S_9& S_4& S_9& S_{10}& S_4\\ S_9& S_4& S_{11}& S_{12}& S_6& S_4& S_{10}& S_6& S_{10}& S_6& S_{11}& S_6\\ S_7& S_6& S_{11}& S_7& S_3& S_{11}& S_3& S_{10}& S_6& S_3& S_9& S_{11}\\ S_{10}& S_4& S_{11}& S_{10}& S_{13}& S_4& S_{13}& S_9& S_{11}& S_4& S_6& S_4\\ S_{11}& S_4& S_{14}& S_6& S_8& S_6& S_{14}& S_4& S_6& S_{15}& \underset{¯}{S_1}& S_9\\ S_4& S_{16}& S_9& S_{17}& S_{15}& S_6& S_{17}& S_7& S_{17}& \underset{¯}{S_1}& S_{17}& S_8\\ S_{16}& S_{14}& & & & & & & & & & \end{array}`$

The 248 segments of human chromosome 22 also undergo simplification, to a total of 53 distinct domain types:

$`\begin{array}{cccccccccccc}S_1& S_2& S_3& S_4& S_5& S_4& S_3& S_6& S_4& S_6& S_7& S_4\\ S_8& S_4& S_9& S_{10}& S_6& S_4& S_7& S_1& S_4& S_7& S_6& S_4\\ S_7& S_{11}& S_4& S_{12}& \underset{¯}{S_{13}}& S_4& S_{14}& S_{12}& S_4& S_{15}& S_{16}& S_{14}\\ S_6& S_9& S_{10}& S_{17}& S_{16}& S_{10}& S_{16}& S_6& S_{12}& S_{18}& S_{12}& S_{10}\\ S_3& S_1& S_3& S_1& S_{10}& S_9& S_6& S_3& S_{12}& S_{16}& S_3& S_{12}\\ S_{14}& S_1& S_7& S_6& S_{12}& S_7& S_1& S_6& S_{19}& S_6& S_{20}& S_{17}\\ S_7& S_{21}& S_7& S_{22}& S_{21}& S_{22}& S_{23}& S_7& S_{23}& S_{24}& S_{17}& S_{21}\\ S_7& S_{21}& S_1& S_{21}& S_7& S_{21}& S_7& S_{16}& S_{25}& S_1& S_{16}& S_{15}\\ S_{26}& S_8& S_{15}& S_8& S_{21}& S_8& S_{21}& S_{27}& S_{16}& S_{12}& S_1& S_{28}\\ S_{21}& S_{28}& S_{21}& S_{12}& S_{21}& S_{16}& S_{12}& S_{16}& S_{12}& S_{28}& S_{16}& S_{19}\\ S_{17}& S_{27}& S_{28}& S_{16}& S_{20}& S_{21}& S_{29}& S_{25}& S_{30}& S_{25}& S_{31}& S_{25}\\ S_{28}& S_8& S_{25}& S_{29}& S_{32}& S_3& S_{25}& S_{31}& S_{33}& S_8& S_{31}& S_{34}\\ S_{31}& S_{29}& S_{30}& S_{31}& S_{35}& S_{36}& S_{21}& S_{36}& S_{37}& S_{36}& S_2& S_{36}\\ S_9& S_1& S_9& \underset{¯}{S_{13}}& S_{38}& \underset{¯}{S_{13}}& S_{39}& S_{29}& S_{34}& S_{37}& S_2& S_{29}\\ S_{40}& S_{41}& S_{31}& S_{37}& S_{31}& \underset{¯}{S_{13}}& S_{35}& S_{42}& S_9& S_5& S_9& S_{42}\\ S_7& S_{41}& S_1& S_{43}& S_{44}& S_{45}& S_{46}& S_{42}& S_{45}& S_{47}& S_{45}& S_{44}\\ S_{32}& S_{44}& S_{45}& S_{44}& S_{48}& S_{43}& S_{25}& S_{45}& S_{11}& S_{49}& \underset{¯}{S_{13}}& S_{49}\\ S_{11}& S_{49}& S_{47}& S_{50}& S_{47}& \underset{¯}{S_{13}}& S_{26}& \underset{¯}{S_{13}}& S_{44}& \underset{¯}{S_{13}}& S_{45}& \underset{¯}{S_{13}}\\ S_8& S_9& S_{45}& S_{50}& S_9& S_{51}& S_5& S_{52}& S_{32}& S_{51}& S_5& S_{51}\\ S_{45}& S_9& S_{21}& S_2& S_9& S_{21}& S_9& S_{39}& S_9& S_{43}& \underset{¯}{S_{13}}& S_{53}\\ S_{39}& \underset{¯}{S_{13}}& S_{43}& \underset{¯}{S_{13}}& S_{49}& \underset{¯}{S_{13}}& S_{47}& \underset{¯}{S_{13}}& & & & \end{array}`$

This gives a maximally coarse–grained view of the DNA squence, in terms of “domain sets”: these are the elements of a given domain type which may be scattered over the entire genome. Examples above are domains like $`S_1`$ in bacterium or $`S_{13}`$ in human which are widely dispersed (these are underlined for visual clarity above), suggesting that these fragments possibly had a common origin, or that they were inserted at the same time during evolution. Expansion–modification  and insertion–deletion  are thought to play major role in evolution: the former ensures duplication accompanied by point mutations in genomes and the latter results in insertion of a part of chromosome inside a nucleotide sequence or deletion of base pairs from a nucleotide sequence. An initial homogeneous sequence may thus become heterogeneous by insertions/deletions that consistently go on with the evolution. Insertions may cause the pieces of a homogeneous sequence to spread.

### B Insertion–deletion and heterogeneity

The process of insertion–deletion  has played an important role in increasing the complexity of genomes. Motivated by the simplification of domain description as above, we perform the following numerical experiment in order to examine the increase in complexity by such processes. Fragments of the U. urealyticum bacterial sequence of total length $`80`$ Kbp are inserted at $`N`$ random positions in the human chromosome 22 contig ($`gi|10879979|ref|NT\mathrm{\_}011521.1|`$). The heterogeneity will naturally increase because of such insertions.

Prior to the insertion of bacterial fragments, the total number of domains in the human chromosome 22 contig is 248; after inserting the fragments at random positions, in a typical realization, the number of segments obtained is 375. The results of such experiments can be quantified through the sequence compositional complexity , denoted $`𝐒`$,

$`𝐒`$ $`=`$ $`H(S){\displaystyle \underset{i=1}{\overset{n}{}}}{\displaystyle \frac{n_i}{N}}H(S_i)`$ (8)
$`=`$ $`{\displaystyle \underset{i=1}{\overset{n}{}}}{\displaystyle \frac{n_i}{N}}[H(S)H(S_i)],`$ (9)
where $`S`$ denotes the whole sequence of length $`N`$ and $`S_i`$ is the $`i`$th domain of length $`n_i`$. This measure, which is independent of the length of sequence quantifies the difference or dispersion among the compositions of the domains. The higher the $`𝐒`$, the more heterogeneous the DNA sequence.

When fragments of very different composition are inserted into a given DNA sequence, the complexity will necessarily increase. We compute $`\mathrm{\Delta }_S=𝐒^{}𝐒`$ for domains obtained after and before the insertion for the example as above and also for a number of genomes. In all cases $`\mathrm{\Delta }_S>0`$: the compositional complexity increases after insertion. If deletion is also introduced, say by removing a fragment of random length from a random position (the range of lengths being deleted is kept same as that of the ‘inserts’) in general $`\mathrm{\Delta }_S`$ increases further.

### C Measuring the complexity

We quantify the simplication of domain description of the two representative genomes by considering a complexity measure within the model selection framework, namely the Bayesian information criterion ($`𝐁`$). Within standard statistical analyisis, one model is superior in comparison with another if it has a lower $`𝐁`$. For the case of U. urealyticum , where the segmentation procedure gives 86 domains,

$`𝐁`$ $`=`$ $`2\mathrm{log}(\widehat{L})+343\mathrm{log}(N)`$ (10)
where $`K=343`$ parameters correspond to $`86\times 3`$ base compositions and $`85`$ borders. These are reorganized into 17 domain sets, and thus

$`𝐁^{}`$ $`=`$ $`2\mathrm{log}(\widehat{L^{}})+136\mathrm{log}(N)`$ (11)
($`136=17\times 3+85`$). The maximum likelihood can be expressed as

$$L(p_\alpha )=\underset{\alpha }{}p_\alpha ^{N_\alpha },$$
(12)
where $`\{p_\alpha \}`$ and $`\{N_\alpha \}`$ are the base composition parameter and the base counts respectively corresponding to alphabet $`\{\alpha =A,T,G,C\}`$ of a sequence. $`\mathrm{\Delta }_B=𝐁^{}𝐁`$ depends on the relative contribution of both terms; typically $`L>L^{}`$ since the first segmentation uses a more accurate measurement of base composition. The reduction in this measure comes from the second term through the drastic reduction in the number of domains which reduces the model complexity.

For U. urealyticum and human, $`\mathrm{\Delta }_B=1709`$ and $`4884`$ respectively which shows that the model representative of the domain set is better than the original one (we use the lower bound i.e. $`\mathrm{\Delta }_B<0`$ for determining the statistical significance ). As another example, we found $`\mathrm{\Delta }_B`$ for Thermoplasma acidophilum (archaeabacteria, $`1564906`$ bp) and another contig of human chromosome 22 (gi $`10880022`$ ref $`NT\mathrm{\_}011522.1`$, $`1528072`$ bp) to be $`2808`$ and $`10420`$ respectively. We repeated this procedure for different available genomes and found the above results to be consistent. Note that the simplication can also be quantified in terms of $`𝐒`$ and we observe $`\mathrm{\Delta }_S<0`$ in all cases.

## IV In silico experiments on domain insertion: a host–parasite perspective

It is tempting to speculate that the heterogeneity that is uncovered by the segmentation procedures discussed above is a reflection of the evolutionary history of the given sequence, and in particular, that the different domains arise from insertion processes acting at different evolutionary times. For instance, it is well–known that the human genome contains a small fraction of bacterial genome which have most likely arisen from processes such as viral insertion or lateral gene transfer.

To what extent can the segmentation process determine the exact pattern of insertions? Here we describe some simple experiments that are designed to explore this question. Starting with a homogeneous fragment of human DNA, we insert fragments from (a homogeneous segment of) bacterial genomes; this increases the heterogeneity. We then apply the segmentation algorithm followed by the labeling procedure and compare the results with the (known) control.

Experiments were done on a homogeneous domain set from the human genome, of total length 100139 bp. Into this, fragments from a homogeneous segment of length 17584 bp from the genome of U. urealyticum were inserted. In a representative case, we took 3 fragments (of lengths 5000, 7000 and 5584 bp respectively) and inserted them at locations 10000, 50000 and 92000 in the human genome domain.

Upon segmentation, all seven segments were identified, with the boundaries between the bacterial and human DNA sequences determined as follows: 9984 (10000), 15000 (15000), 49751, 50060 (50000), 56968 (57000), 91636 (92000) and 97575 (97584), (the exact values are given in brackets). There is thus one false positive, but otherwise all the boundaries are determined to fairly high precision. The domain sets can also be reconstructed, and the seven segments, $`𝒮_1𝒮_2𝒮_1𝒮_2𝒮_1𝒮_2𝒮_1`$ conform to two sets.

Shown in Fig. 1(a) is the insertion process for a case where fragments from two bacterial genomes, Ureaplasma urealyticum and Thermoplasma acidophilum are randomly inserted in the human genome segment. Carrying out segmentation at varying strength $`s`$ gives a greater number of segments compared to the correct value of 13. With $`s=0.2`$, one gets 18 segments (see Fig. 1(b)) which is the best reconstruction possible within the present framework. On obtaining domain sets, we find that up to about 85% of human and U. urealyticum genomes are properly identified, the errors affecting the reconstruction of T. acidophilum which is only 67% accurate.

To summarize, our results from several numerical experiments show that the reconstruction of the fragmentation process can be done to high accuracy so long as the inserted fragments are sufficiently long and widely separated.

## V Discussion and Summary

Segmentation offers a novel view of the compositional heterogeneity of a DNA sequence. In the present work we have applied the segmentation analysis to genomic sequences from several organisms.

Our main focus has been on understanding the organization and to this end we have applied a number of different analytical tools. Our main analysis has been directed towards obtaining a coarse–grained representation of DNA as a string of minimal domain labels. Complexity measures indicate that the reduced model in terms of domain sets is superior to a model where each domain is treated as independent.

Insofar as the different domains are considered, our main hypothesis is that these arise when fragments of one (possibly homogenous) DNA sequence get randomly inserted into another (also possibly homogenous) sequence. A controlled set of (numerical) experiments give support to this hypothesis: we are able to identify domain boundaries to high accuracy so long as inserted domains are not very short. The accuracy could be further increased by improving the segmentation process, for example, using 1 to 3 segmentation rather than the binary or 1 to 2 segmentation used here: binary segmentation is only one of several possible segmentation procedures (see Ref. ).

A consequence of this analysis, and one that we are currently exploring, is that different domains (or domain sets) in one genome can have arisen via insertion from another organism. Homology analysis (say by the use of standard tools such as BLAST or FASTA) can help to unravel the origins of the domains. Thus segmentation analysis can possibly help in reconstructing the evolutionary history of the genome.

## ACKNOWLEDGMENT:

RR is supported by a grant from the Department of BioTechnology, India.