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The fossil record of wetlands documents unique and long-persistent floras and faunas with wetland habitats spawning or at least preserving novel evolutionary characteristics and, at other times, acting as refugia. In addition, there has been an evolution of wetland types since their appearance in the Paleozoic. The first land plants, beginning in the Late Ordovician or Early Silurian, were obligate dwellers of wet substrates. As land plants evolved and diversified, different wetland types began to appear. The first marshes developed in the mid-Devonian, and forest swamps originated in the Late Devonian. Adaptations to low-oxygen, low-nutrient conditions allowed for the evolution of fens (peat marshes) and forest mires (peat forests) in the Late Devonian. The differentiation of wetland habitats created varied niches that influenced the terrestrialization of arthropods in the Silurian and the terrestrialization of tetrapods in the Devonian (and later), and dramatically altered the way sedimentological, hydrological, and various biogeochemical cycles operated globally.

Widespread peatlands evolved in the Carboniferous, with the earliest ombrotrophic tropical mires arising by the early Late Carboniferous. Carboniferous wetland-plant communities were complex, and although the taxonomic composition of these wetlands was vastly different from those of the Mesozoic and Cenozoic, these communities were essentially structurally, and probably dynamically, modern. By the Late Permian, the spread of the Glossopteris flora and its adaptations to more temperate or cooler climates allowed the development of mires at higher latitudes, where peats are most common today. Although widespread at the end of the Paleozoic, peat-forming wetlands virtually disappeared following the end-Permian extinction.

The initial associations of crocodylomorphs, mammals, and birds with wetlands are well recorded in the Mesozoic. The radiation of Isoetales in the Early Triassic may have included a submerged lifestyle and hence, the expansion of aquatic wetlands. The evolution of heterosporous ferns introduced a floating vascular habit to aquatic wetlands. The evolution of angiosperms in the Cretaceous led to further expansion of aquatic species and the first true mangroves. Increasing diversification of angiosperms in the Tertiary led to increased floral partitioning in wetlands and a wide variety of specialized wetland subcommunities. During the Tertiary, the spread of grasses, rushes, and sedges into wetlands allowed for the evolution of freshwater and salt-water reed marshes. Additionally, the spread of Sphagnum sp. in the Cenozoic allowed bryophytes, an ancient wetland clade, to dominate high-latitude mires, creating some of the most widespread mires of all time. Recognition of the evolution of wetland types and inherent framework positions and niches of both the flora and fauna is critical to understanding both the evolution of wetland functions and food webs and the paleoecology of surrounding ecotones, and is necessary if meaningful analogues are to be made with extant wetland habitats.

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