From AI/AN ATS
As a follow up to my previous post on the tribal form of social organization, here’s a quick demonstration of how the Federal Government has systematically destroyed our Native American clans across the continent. The reason they did this should be clear: our decentralized clan system of tribal governance was one that could not be controlled by our oppressors, and therefore had to be eliminated and replaced with hierarchical “tribal” governments that could be easily controlled.
This was a court case in 1955 brought by the late leader of my own clan, William Paul of the Teeyhíttaan, against the United States in response to logging activity in Teeyhíttaan territory. William Paul had an idea that might seem revolutionary even among the Tlingit of today; that a clan is a sovereign entity. Put another way (and these are my interpretation of his ideas) your clan is your tribe and the Tlingit tribe as a whole is really a common cultural and social identity shared by dozens upon dozens of independent clans.
The state doesn’t particularly like clans, though, and in this court case they refused to acknowledge the Teeyhíttaan’s sovereignty and right to ownership of land. It would be a threat to state and federal power if kin groups controlled their own immediate surroundings, so their rights were simply ignored. The dismissal of this case was a part of what set the stage for the Alaska Native Claims Settlement Act, also pursued by Paul. Ultimately this further eroded clan sovereignty by organizing property ownership under village and regional corporations, though the sovereignty of clans may have already been extinguished anyway, making ANCSA a net gain from the perspective of landless Indians. Still, the overall trend was a move away from clan sovereignty.
The Various Navajo Clans vs. The U.S
In the traditional Navajo culture, local leadership was organized around clans, which are matrilineal kinship groups. The clan leadership roles have served as a de facto government on the local level of the Navajo reservation. In 1927, agents of the U.S. Federal government initiated a new form of local government entities called Chapters, modeled after government forms more familiar to the Federal agents, such as counties or townships. Each Chapter elected officers and followed parliamentary procedures. By 1933, more than 100 Chapters operated across the reservation. The chapters served as liaisons between the Navajo people and the federal government, and also acted as precincts for the elections of tribal council delegates. They also served as forums for local tribal leaders. But, the chapters had no authority within the structure of the Navajo Nation government. 
In 1998, the Council passed the “Local Governance Act,” which extended the political roles of the existing 110 chapters, giving them authority to make decisions on behalf of the Chapter members and take over certain roles previously delegated to the Council and Executive branches. This included entering into intergovernmental agreements with federal, state and tribal entities, subject to approval by the Intergovernmental Relations Committee of the Council.
Starting to see a common thread, here? Much like the Tlingit, the Navajo are a cultural and social identity under which multiple de-facto clan governments organized themselves. Again, the U.S. cannot tolerate such a decentralized system of governance and little by little moved the Navajo people from their traditional system of governance toward a hierarchical one, a form that the U.S. understood and could easily control.
I personally cannot speak to the state of Navajo clans today. Hopefully a reader could enlighten me, though?
The Spanish vs. the clans of Taos Pueblo
Taos Pueblo still has very intact clans that fulfill an important role in the community. Still, they have faced the same reorganization efforts as the aforementioned Tlingit and Navajo clans. The Spanish, much like the U.S, moved to set up a hierarchical tribal government in a Western context with a tribal governor and officers. While these days the clans still fulfill a role in picking said governor, it ought to be noted that the tribe never needed such a position or leader. This was a role created by an Imperial power that didn’t understand or felt threatened by indigenous tribal structures.
Virtually every Native American tribe on the continent underwent a similar process of moving our dominant form of governance from a decentralized clan system to one of an overarching, hierarchical tribal government. Many Indians today advocate for our tribal government’s to press our rights in Washington D.C, but the end result of this is more land and resources under the control of a form of government that is alien to Indian people. To advocate for true tribal sovereignty one must advocate for clan sovereignty and the dismantling of tribal governments as organized by our oppressors.