The understanding of diatom evolution has progressed greatly over the last two decades. Existing data sets have been reanalyzed, new data sets have been generated, and new tools have been employed. Hindering progress is the seemingly endless number of diatom species remaining to be described and relative small number of investigators active in the field. This problem is further confounded by the dramatic reorganization of generic level classification in the group. Despite these problems, many conclusions can be made about prior hypotheses concerning the group's development. Most notably, the origin of the diatoms can be bracketed between the Late Triassic and Early Jurassic using fossil record and molecular clock estimates. This combination of techniques has also provided consensus and clarification to the origin and duration of specific lineages enhancing our understanding of the group's diversification, early ecology, and evolutionary relationships.

Applications of commonly used numerical techniques in diatom-based paleoecology are reviewed including: approaches used to model diatom taxa to important limnological variables; ordination and other commonly used multivariate approaches; and the myriad of approaches that are now being explored to infer environmental variables based on diatom assemblages.

Modelling the response of individual diatom taxa to limnologically important variables is consistent with ecological theory and has been largely accomplished using approaches based on generalized linear models. These techniques have established that strong and significant relationships exist between the numerically dominant diatom taxa and important limnological variables (e.g., pH, nutrients, salinity). Null modelling approaches have also been used. However, inclusion of rare taxa in null models results in high rates of type-II errors, and consequently spurious claims that only a minority of diatoms have significant relationships to important limnological variables such as lakewater pH and nutrients.

A variety of ordination techniques are widely used in diatom-based paleolimnological studies to aid in summarizing the main directions of variation in diatom assemblages, and to identify limnological variables that are strongly correlated to the diatom assemblages, both in time and space. More advanced ordination techniques, such as partial ordinations, are increasingly being used to assess the shared and unique variance attributable to groups of important limnological variables. Further, diatom-based approaches based on experimental designs with control lakes and appropriate multivariate statistics are now becoming increasingly common to assess, for example, the impact of forestry on water quality.

A number of different diatom-based inference models based on the present-day relationships between diatom assemblages and limnological variables are now available for inferring important limnological variables. These approaches vary from simple approaches such as weighted-averaging to more complex approaches involving curve fitting and maximum likelihood, neural networks, and Bayesian statistics. All of these approaches have been shown to result in strong inference models, each using aspects of ecological information available from the diatom assemblages.

New information and discussions regarding Mesozoic diatoms presented over the last decade advanced our knowledge of their origin and early history. The oldest confirmed centric diatom fossils are presented here from the earliest Cretaceous, and araphid and raphid pennate diatoms now date from the Late Cretaceous; all from terrestrial sediments. Molecular sequencing helped clarify relationships between diatom lineages, and verify the position of diatoms within the heterokontophytes. Molecular clock approaches estimate a diatom origin near ~135 Ma, but not before 240 Ma. Biomarkers in marine sediments are able to trace a diatom presence back to the mid-Cretaceous, even when siliceous fossils are absent. Seasonal growth and encystment cycles in Late Cretaceous planktonic marine diatoms are now well documented. A biostratigraphic framework for the Late Cretaceous Arctic will aid regional and global biostratigraphic correlations. The systematic position of many new taxonomic groups is now included within a more natural classification scheme that better reflects phylogenetic relationships evident in molecular data and affirmed by biostratigraphic micropaleontology. Discussions regarding the impact of diatoms on several global systems are maturing, as more information becomes available. Four stages in diatom evolution are proposed to explain the history of radiation, extinction, and expansion into new environments and habitats during the Mesozoic.

Diatoms provide the chief Cenozoic biostratigraphic tool in marine sediments beneath high primary productivity zones, especially where calcareous fossils are rare or poorly preserved. Diatom biostratigraphy, which is based on originations and extinctions of unique taxa, is especially useful in circum-Antarctic, equatorial Pacific, and high latitude North Pacific marine successions, which are available largely from ocean drilling. Oligocene to Holocene diatom biostratigraphic zonations are correlated with the geopaleomagnetic timescale, resulting in age control of million-year to as little as hundred-thousand year resolution. Paleocene and Eocene zonations are less well developed and have lower chronostratigraphic control, but are more widely applicable, because planktonic diatom assemblages of the globally warm early Paleogene were less provincial. We review the principals and methods of biostratigraphy and the application of diatoms to age control in stratigraphic successions worldwide. Distinct biostratigraphic zonations defined for the low latitudes, the North Pacific and the Antarctic, are reviewed, and Atlantic records and Antarctic coastal records are discussed. New biostratigraphic tools are introduced, including multidimensional graphic correlation of published diatom ranges.

Diatoms from estuarine and marsh sediments can be used to evaluate a number of geological processes. Information on salinity, elevation, and substrate derived from modern assemblages have been used to determine local and regional Holocene sea level history, identify seismic and tsunami events, and aid in the recognition of regional variations in precipitation. In order to apply diatoms to these questions, it is necessary to have a detailed knowledge of the ecology of marine, brackish, and freshwater taxa, as well as an understanding of the taphonomic processes that determine the final diatom assemblage. The potential for studies of pre-Holocene estuarine depositional systems is largely limited by the availability of study sites.

The great abundance and diversity of diatoms in lacustrine sediments and their ability to adjust to rapid changes in physical, chemical, and biological conditions makes them ideal for the study of lake history. Continuous diatom records from long-lived lakes have the potential to answer questions of basin history, climate variability, ecological change, and evolution. Isolated Tertiary outcrops provide a more limited record of environmental conditions, but as the ability to correlate individual exposures improves through the use of techniques such as tephrochronology, it is becoming possible to evaluate the timing of environmental or evolutionary changes on a regional basis.

Fossil diatom assemblages are useful for reconstructing past environmental changes in riverine systems. However, few studies have attempted to utilize paleolimnological techniques in these settings. Analysis of sediments from riverine environments can provide key information predating the impact of human development, which cannot be acquired by other means. Paleolimnological techniques can be used to determine the natural variability in these systems and to estimate the magnitude and rates of change that the environment may have undergone as a result of anthropogenic or climatic factors, and to provide realistic goals for management of negatively-impacted systems.

Reconstructing past riverine settings requires an understanding of the factors that control the spatial distribution of diatoms in riverine settings; this paper discusses the impact of resources, stressors, and disturbance events, which are the primary controls on the distribution of benthic diatoms in modern riverine environments. A selection of case studies that utilize paleolimnological techniques to infer past stream hydrology are also discussed; these examples encompass the use of fossil diatom assemblages from sediments recovered from lowland floodplain and meandering river systems, estuarine environments, fluvial lakes, arctic deltaic environments, and terminal lakes.

Serious environmental issues, including acid rain, eutrophication, and decreasing water availability, require knowledge of the: 1) baseline conditions (i.e., what were conditions like before human disturbance); 2) natural variability; and 3) time or level of disturbance when the system responded to the environmental change. This type of knowledge can only be obtained from a historical perspective, which is best achieved through actual measurements of environmental variables. Such records, however, rarely extend more than a few decades, which is usually insufficiently long to determine baseline conditions and natural variability. Diatoms, single celled algae characterized by a cell wall composed of opaline silica, preserved in lake sediments are one of the most widely used paleoindicators, and provide robust estimates of lakewater pH, nutrient concentration and lake level change. A variety of approaches have been developed to infer environmental variables using diatom data, and robust inferences of many environmental variables are now possible. Using paleolimnological techniques, fossil diatoms have been used to track pH, nutrients and lake levels. These records have significantly contributed to our understanding of the causes and impacts of lakewater acidification, eutrophication and hydrologic change, and provide a basis for developing effective management strategies.

Average global temperatures are predicted to rise over the next century and changes in precipitation, humidity, and drought frequency will likely accompany this global warming. Understanding associated changes in continental precipitation and temperature patterns in response to global change is an important component of long-range environmental planning. For example, agricultural management plans that account for decreased precipitation over time will be less susceptible to the effects of drought through implementation of water conservation techniques.

A detailed understanding of environmental response to past climate change is key to understanding environmental changes associated with global climate change. To this end, diatoms are sensitive to a variety of limnologic parameters, including nutrient concentration, light availability, and the ionic concentration and composition of the waters that they live in (e.g. salinity). Diatoms from numerous environments have been used to reconstruct paleosalinity levels, which in turn have been used as a proxy records for regional and local paleoprecipitation. Long-term records of salinity or paleoprecipitation are valuable in reconstructing Quaternary paleoclimate, and are important in terms of developing mitigation strategies for future global climate change. High-resolution paleoclimate records are also important in groundtruthing global climate simulations, especially in regions where the consequences of global warming may be severe.

Paleolimnological techniques have been used successfully to reconstruct environmental change in the Arctic and Antarctic. Diatoms are powerful indicators of environmental change because their community composition responds to changes in environmental conditions. As more regional diatom calibrations throughout the high latitude regions are achieved, the autecology of diatom taxa can be quantified and transfer functions for the driving environmental variables developed. In most instances, environmental variables related to physical, chemical, and climate-related characteristics are the main drivers affecting diatom distribution across polar aquatic bodies. A decline in ice cover and increase in growing season length results in an increase in diatom diversity as well as increased productivity, and increased thermal stratification in lakes (vs. shallow ponds). Because the siliceous cell wall preserves well in sediments, diatoms are among the most commonly used organisms used in paleolimnological analyses. Polar latitudes are experiencing amplification of the current global warming trend and as such, analyses of diatoms from high latitude lake and pond sediments are revealing the timing and extent of these trends. Diatom-based paleolimnological analyses are also being used to track the environmental impact of excess nutrient additions to lakes. Similar findings have also been reported from marine ecosystems.

The application of diatom analysis in determining whether drowning was the cause of death has proved to be a valuable tool in forensic science. The basic principal of the “diatom test” in drowning is based on inference that diatoms are present in the medium where the possible drowning took place and that the inhalation of water causes penetration of diatoms into the alveolar system and blood stream, and thus, their deposition into the brain, kidneys, and other organs.

I provide an informal assessment of “reliability” of the “diatom test” through correlations between control samples and samples from organs and clothing in two case studies. In studies, all organ and clothing samples except one had matching analogues in the modern diatom dataset from the body recovery sites, reinforcing drowning as the cause of death. The analogue matching provides further information on the precise site of drowning, in particular differentiating between drowning in a bathtub versus a naturally occurring body of water.