Permian reef ecosystems suffered a protracted demise from the Lake Maokouan crisis through the end-Permian extinction (e.g., [32]). Reefs from Middle and Late Permian time are known primarily from the margin of Tethys, Tethyan and Panthalassic terranes, and epeiric basins. These reefs vary in composition geographically. Reefs that formed in the Tethyan realm were dominated by carbonate mud and contained algae, corals, brachiopods, and sponges [80]. The Panthalassic marginal basin reefs consisted of microbial-rich reefs and cold-water bryozoan, phylloid algae and stromatolitic reefs at higher latitudes [80]. The epeiric basins were truly unique and contained diverse sponge assemblages with abundant marine cements, microbialites, and problematic fossils [80] (Fig. 3A). The Capitan Reef of the Delaware Basin is one such reef that formed on the margin of an epeiric basin (e.g., [1], [51] and [67]). The Capitan reef is exposed primarily in West Texas and New Mexico and has been widely studied (e.g., [1], [40], [51] and [67]). This reef system is characterized by abundant early marine cements as well as a distinct, diverse biota (e.g. [15] and [30]). The reef ecosystem does not necessarily typify Permian reefs in that it formed in an intracratonic basin; however, the Capitan reef ecosystem is an example of a Late Paleozoic complex that contained abundant metazoans millions of years before their demise at the Permian–Triassic boundary.

Calcified sponges play a prominent role in the formation of the Capitan reef complex, as do unusual organisms such as Archaeolithoporella and Tubiphytes (Shamovella) that have putative origins including algae (e.g., [1], [40] and [51]) and calcimicrobes (e.g., [21]). Sphinctozoan sponges are volumetrically dominant in the reef and can also act as framework builders [39]. There are 34 species of sponges known from the top of the Capitan succession [63], but sponges are more dominant in the lower and middle sections. The occurrence of the large platy sponge Gigantospongia represents the optimum growth for this reef community [80] (Fig. 3B) and is common below the reef–outer shelf break [62]. Other organisms that are locally important, although volumetrically less significant, include fenestrate bryozoans, phylloid algae, microbes, brachiopods, mollusks, and foraminifera (e.g., [1], [39], [55], [70] and [80]). Because of the diverse biota that helped form a framework for the Capitan reef, dwelled within its cavities, and lived on its surface, this reef system stands in stark contrast to the microbial build-ups that dominated throughout the Early Triassic.

The Upper Permian reef complexes of South China and Skyros, Greece provide an ecological snapshot of reef systems that existed until the end-Permian extinction event. In Upper Permian deposits of Hubei and Sichuan Provinces of South China, large reef complexes have been described [16], [17] and [59]. This Late Permian reef complex formed a barrier reef belt around the Sichuan-Hubei Platform [17]. On Skyros Island of Greece, Uppermost Permian build-ups crop out in the central part of the island [23]. Both reef complexes show a high diversity of reef faunas that were decimated by the end-Permian mass extinction [23] and [82].

At Laolongdong in the Sichuan province, intra-platform patch reefs are well-exposed and can be as large as 140 m wide and 70 m thick [82]. The reef faunas are diverse and are comprised of sphinctozoan and inozoan sponges, tabulozoans, hydrozoans, bryozoans and green and red algae [82]. There is also high diversity gleaned from the inter-reef limestones, suggesting that foraminifera, brachiopods, and some echinoderms were diverse and abundant up to ~60 cm below the boundary [82]. The Upper Permian Tudiya build-up in Sichuan, China exhibits similar diversity, with sphinctozoan sponges being important reef builders (Fig. 3C). In addition to sphinctozoan sponges, inozoans, calcareous sponges and algae, Tubiphytes, and Archaeolithoporella dominate these reefs with other reef-dwellers such as crinoids and brachiopods playing a more minor role [23]. Metazoan reef development terminated in all areas of South China following the end-Permian mass extinction and did not become re-established until Early Anisian time (e.g., [44]).

On Skyros Island of Greece, patch reefs have been described and form a less extensive system than the reefs of South China. The reefs of Skyros are exposed at two stratigraphic horizons and are 15-m and 12-m thick, respectively [23]. The first reef horizon, exposed about ~75 m below the Permian–Triassic boundary, consists of sphinctozoan, inozoan and other calcareous sponges as well as small solitary corals (Fig. 3D) [23]. Approximately 30 m below the Permian–Triassic boundary, the second reef horizon is dominated by various calcareous sponges as well as Tubiphytes and Archaeolithoporella [23]. Although the patch reefs of Skyros, Greece are less extensive than the barrier and patch reefs of South China, both systems are composed of relatively diverse reef communities that differ greatly from the microbial build-ups of the Early Triassic.

The largest extinction in the history of life occurred ~250 Myr ago and brought about a reorganization of almost every marine ecosystem; the reefs were no exception to this. A variety of mechanisms have been put forth as a possible cause of this extinction including, but not limited to, widespread volcanism and subsequent global warming which caused a catastrophic methane release (e.g., [65]), global anoxia [35], [36] and [83], a runaway greenhouse effect [11], and a bolide impact [2] and [5]. None of these have been universally accepted as the mechanism for the end-Permian mass extinction.

Many reef building-metazoans became extinct during the end-Permian mass extinction and caused a reduction in carbonate skeletal production in reefs by >99% [81]. Rugose and tabulate corals were so devastated that it marks their total extinction (e.g., [18]). The disappearance of rugose corals was initially thought to be a gradual decrease throughout the Late Permian [18], but later work showed that rugose corals thrived until the end of the Permian [14]. Tabulates underwent a decline during the Late Permian, and only a few survived until the end of the Changxingian [18]. Corals did not recover until the Middle Triassic when scleractinians emerged. Bryozoans suffered major extinctions at the generic level, but only one order, the fenestrates, disappeared entirely [79]. Diversity is low for bryozoans throughout the Early Triassic; a radiation follows in the Middle and Late Triassic [66]. In addition to the dominant reef-building organisms discussed above, many ancillary members of reef ecosystems were also devastated by the end-Permian mass extinction. These include crinoids, brachiopods, and foraminifers, which contributed significantly to Permian reef diversity [16] and [17], and in some cases were the dominant reef builders. The pattern of the extinction of reef builders has caused some researchers to attribute the demise of metazoan reefs to a drop in oxygen levels, and this may have not only caused the extinction but acted as a long-term source of stress [81].

Another area of growing interest is the delayed recovery from the end-Permian extinction event (e.g., [10]). It has long been recognized that marine ecosystems did not attain pre-extinction diversity levels until the Middle Triassic (e.g., [10], [31] and [32]); however, this too has to date been unsatisfactorily explained. Reef-building metazoans exhibit the same trend as many other metazoans; reef metazoans begin to increase in diversity at a variety of locations globally, after an absence from the world's oceans for 5–6 Myr [50] and [52]. The Early Triassic experiences a brief resurgence of microbial reefs that have been documented from many locations, and the replacement of microbial reefs by metazoan reefs in the Middle Triassic has been attributed to the dissipation of environmental stress (e.g., [56] and [69]).

Early Triassic microbial reefs have now been described from many regions including eastern Panthalassa, eastern, central, and western Tethys, and the Boreal ocean (Fig. 4). These reefs occur primarily as reef mounds that attained a relief of about 2 m above the seafloor. These are generally described as patch reef systems and are not as thick as Permian reefs though individual microbial reef-bearing deposits, like those in South China, are extensive over 10 000 km² [46]. The microbial reefs tend to crop out as individual mounds, and exhibit both stromatolitic and thrombolitic features. Some microbial build-ups contain the preserved remains of microbes such as Renalcis [43], and others contain only preserved microbial laminations [56].

In Lower Triassic strata of South China, microbial build-ups occur as calcimicrobial mounds and biostromes [43]. The Smithian-Spathian calcimicrobial mounds attained the most significant relief of all the microbialites described from the Great Bank of Guizhou. These formed as domal or inverted conical mounds, and range in size from 0.1 to 1.5 m [43]. Because of their topographic relief, rigid organic framework, and presence of microorganisms such as Renalcis, these have been interpreted to represent microbial patch reefs [43].

Other examples of microbial reefs have been described from Lower Triassic strata of southern Turkey [3] and [4] (Fig. 5A). A variety of microbialites have been described including, but not limited to, columnar, domal, and conical stromatolites, and thrombolites [4]. The giant domal stromatolites attained a relief of ~2 m above the seafloor. Some examples of these giant stromatolites extend laterally for 10 m. Thrombolites consisting of massive mounds of clotted micrite measure up to 2 m in height and 10–20 m laterally [4].

Stromatolitic bioherms have been documented from Lower Triassic strata of Greenland [86]. These occur in Lower Griesbachian strata and consist of small, laterally extensive build-ups (< 1 m) that formed within laminated silty shales [86]. These build-ups formed on a thin bed of broken stromatolite and thick-shelled bivalve debris (Promyalina). In thin-section, the bioherms consist of alternating dark and light laminae of micrite. These carbonate build-ups are noticeable features surrounded by siliciclastics (P.B. Wignall, pers. commun., 2004).

Early Triassic microbial build-ups have been described from the western United States. Schubert and Bottjer [69] first noted that these stromatolites represent disaster forms that were able to flourish in the aftermath of the end-Permian mass extinction. Subsequent work on these microbial build-ups has suggested that they attained significant relief above the seafloor and therefore formed patch reefs [56] (Fig. 5B). The build-ups occur in one bed in which they are laterally extensive. Thin limestone beds lap out against the sides of the individual mounds suggesting a topographic relief of 1 m or more. In outcrop and on cut slabs, stromatolitic and thrombolitic fabrics are obvious features (Fig. 5C and D). In thin-section, microbial laminations, clotted fabrics, open framework crypts with bladed cements, and disarticulated metazoan debris are common features [56].

In addition to the various reports of microbial build-ups, other microbialites and possible microbial crusts have been noted from various sections around the world. Microbialites from Japan [68], Iran [33], and South China [38] and [39] have been described from Lowermost Triassic sections. These occurrences reflect an expansion of microbial fabrics immediately following the end-Permian mass extinction, and the distribution of microbialites throughout the Early Triassic indicates that microbialite formation was sustained for millions of years.

The diversification of metazoan reef-dwelling organisms took place in the Anisian (e.g., [22]). In addition to the diversification of reef-building metazoans (Fig. 6A and B), reef abundance also increased during this time. The oldest Tethyan reefs have been reported from the Pelsonian Dont Formation in the Dolomites of Italy (e.g., [25]). These reefs exhibit abundant Tubiphytes, although the Tubiphytes are considered to represent different forms than those of the Permian [25]. The Peri-Tethyan region of Silesia contains a reef system of a similar age to the Dont Formation. An increase in Tubiphytes-bearing reefs occurs in Middle Triassic strata of the Nanpanjiang Basin of South China (J.-L. Payne, pers. commun., 2003). Middle Triassic reef occurrences represent the recovery of metazoan reefs, a facies that had been absent from the rock record for ~7 Myr [15] and [21].

The metazoan reefs that re-appeared during the Anisian are composed of microbes and possible calcimicrobes (Tubiphytes), calcareous and siliceous sponges, bryozoans, and corals, with other organisms being locally important [21] and [25]. Low-diversity communities dominate many reefs of this time; however, a few examples of high diversity sponge-coral reefs have been described from southern Spain, the Dolomites of Italy, and Austria (e.g., [21] and references therein). The initial radiation of scleractinian corals occurred during the Middle Triassic, with the earliest ancestors reported from allochthonous deposits of platform carbonate blocks transported into offshore settings [58] and [77]. Scleractinians do not take over as dominant reef builders until later in the Triassic (e.g., [77]). Reef proliferation that began in the Anisian continued into the Ladinian and Early Carnian, and many of those reefs share characteristics with their Anisian predecessors.

Examples of Ladinian and Early Carnian reefs include bivalve build-ups in Germany, algal and microbial mounds in Spain, and microbial-calcareous sponge mounds in the Alps [21]. Ladinian and Early Carnian reefs are comprised of the same constructional reef types as Anisian reefs; however, the late Middle Triassic reefs are more widely distributed and abundant than those of the Anisian [21]. Additionally, the taxonomic composition of the Ladinian-Early Carnian reefs differs markedly from Anisian reefs; many Anisian sponges and corals became extinct prior to the Ladinian. The establishment of large reef complexes occurred later in the Triassic during the Norian–Rhaetian reef bloom, and at this time, scleractinian corals replaced calcareous sponges in many reef successions, illustrating the initial rise to dominance of scleractinian reefs (e.g., [74]). The Norian also marks the appearance of Lazarus taxa that had been absent since the Permian, suggesting a long-term existence in refugia [21].

During Anisian to Carnian time, reefs dominated the Tethyan realm, most especially western Tethys. Anisian reefs fall into a few broad categories based on their dominant faunas and these include thrombolite reefs, Tubiphytes reefs, calcareous sponge reefs, coral reefs, algal reefs and bivalve build-ups [21]. During Early Anisian time, reefs formed in the Yangtze Platform of South China, the Dont Formation of the Dolomites, and the Camorelli Platform of northern Italy [21]. Other small Anisian biostromes are known from deposits in British Columbia [89]. The descriptions of South China and the Northern Calcareous Alps provide two examples of regions that were dominated by reef systems for much of the Middle and Late Triassic, but by no means encompass all of the diversity of reef types and faunas captured in Middle and Upper Triassic strata.

Middle Triassic reefs initially occur without scleractinian corals acting as framework builders. Anisian reefs from South China formed along an east-west trending warm seaway in the Tethyan realm (e.g., [77]). In the Guizhou province of South China, initial build-ups lacked scleractinians acting as framework builders [58]. Instead, scleractinian corals made their first appearances in transported carbonate platform blocks that were deposited in offshore environments [9] and [58]. With the onset of major reef development during the Middle and Upper Anisian, major carbonate contributors included calcareous algae, sponges, mollusks, bryozoans, problematic organisms such as Tubiphytes, and microbialites [24]. During this time, there was a change in carbonate shelves to systems that were dominated by skeletal organisms after an absence of significant skeletal deposits for much of the Early Triassic. Although initially the main components of reefs in South China did not include scleractinians, they became extremely important in reef ecosystems later in the Triassic [77].

In the northern Calcareous Alps, major reef development began in the Late Anisian to Early Ladinian and persisted through the Late Triassic. Early Middle Triassic reefs of this region consist of small 10–100-m thick build-ups within the Steinalm Limestone [19]. Large-scale reefs, like the Wetterstein reefs, became established during the Ladinian and formed vast reef complexes in the Northern Calcareous Alps that were several tens to hundreds of square kilometers in size [19] and [21]. Calcareous sponges and problematic organisms such as Tubiphytes dominated these reefs [53] with lesser components being scleractinian corals, calcareous algae, and bivalves [21]. Although the reef facies is continuous through hundreds of meters, at any given time, individual reefs likely attained a relief of tens of meters [21].

Reefs of the northern Calcareous Alps that formed during Norian–Rhaetian time show a distinct change in reef faunas from those of the Ladinian–Carnian. These reefs, called the ‘Dachstein reefs’, developed along platform edges of Tethyan basins [21]. The Dachstein reefs contain calcareous sponges and corals as important framework builders, which differentiate them from Ladinian–Carnian reefs (see above) [19]. The Dachstein reefs of the Northern Calcareous Alps are composed of randomly situated patch reefs that persist through tens to hundreds of meters of strata.