We present a broad comparative assessment of nested subsets in species composition among ecological communities. We assembled presence-absence data from a broad range of taxa, geographic regions, and spatial scales; and subjected this collection of datasets to common analyses, including a variety of metrics for measuring nestedness and null hypotheses against which to evaluate them. Here we identify ecological patterns in the prevalence and strength of nested subset structure, and assess differences and biases among the available methodologies. In all, we compiled 279 presence-absence matrices, of which 163 do not overlap in their coverage of species and sites. The survey includes studies on vertebrates, arthropods, mollusks, plants, and other taxa; from north temperate, tropical, and south temperate latitudes. Our results were as follows. Statistically significant nestedness was common. Assemblages from landbridge archipelagos were strongly nested, and immigration experiments were least nested. This adds further empirical support to the hypothesis that extinction plays a major role in producing nested structure. Nestedness was positively correlated with the ratio of the areas of the largest and smallest sites, suggesting that the range in area of sites affects nestedness. Taxonomic differences in nestedness were weak. Higher taxonomic levels showed stronger nesting than their constituent lower taxa. We observed no effect of distance of isolation on nestedness; nor any effects of latitude. With regard to methodology, the metrics Nc and Ut yielded similar results, although Nc proved slightly more flexible in use, and deals differently with tied sites. Similarities also exist in the behavior of N0 ("N") and Up, and between N1 and Ua. Standardized nestedness metrics were mostly insensitive to matrix size, and were useful in comparative analyses among presence-absence matrices. Most metrics were affected by the proportion of presences in the matrix. All analyses of nestedness, therefore, should test for bias due to matrix fill. We suggest that the factors controlling nested subset structure can be thought of as four filters that species pass to occur at a site: a sampling filter, a distance filter, a habitat filter, and an area filter - and three constraints on community homogeneity: evolutionary history, recent history, and spatial variation in the environment. The scale of examination can also have important effects on the degree of nestedness observed.

The faunas of habitat islands, such as those produced by fragmentation of formerly continuous habitats, are commonly made up of nonrandom subsets of the total available species pool. Faunas within an archipelago may form a nested series, with depauperate faunas made up of subsets of more species‐rich faunas. The pattern is seldom perfect: widespread species may be absent from otherwise rich faunas (holes), and uncommon species may occur in depauperate faunas (outliers). The “nestedness” of an assemblage of faunas (its fit to the “nested subset model”; Patterson & Atmar 1986) can be measured by summing the holes and outliers. The distributions of boreal mammals and birds among mountain ranges in the Great Basin of western North America were analyzed by this method Despite differences in their derivation (mammalian faunas are thought to be relicts, isolated since the Pleistocene; bird faunas have probably experienced recurrent colonization throughout their history] both groups show an approximately equal (and highly significant) fit to the nested subset model. They differ, however, in the relative numbers of holes and outliers in their patterns. The mammalian pattern is hole‐rich; the bird pattern is outlier‐rich. The present‐day composition of the mammalian faunas is the result of selective extinction of species of originally richer faunas. The existence of nested subsets in these faunas suggests that extinction is a highly deterministic process: extinctions occurred in approximately the same sequence throughout the region, despite wide variation in extinction rates Extinction sequence has, in fact, been less variable than extinction rates.

We examined the radiocarbon age, taphonomic condition and stratigraphic position of shells of the venerid bivalveChionespp. from the tidal flats of Bahia la Choya, Sonora, Mexico. Shells in Bahia la Choya are time-averaged. Thirty shells yielded radiocarbon dates from modern (A.D. 1950 or younger) to 3569 years before present. The median calendar age of inner flat shells is 483 years; the median age of tidal channel shells is 427 years. We interpret such long shell survival to be the result of frequent shallow burial. Such burial retards bioerosion of shells.The taphonomic condition of shells varied with environment. Shells from the surface of the inner flats were better preserved than shells from the tidal channel. Shells are more likely to be physically worn and biologically degraded in the waters of the channel than on the quieter and more frequently exposed inner tidal flat. Taphonomic condition is an unreliable indicator of a shell's time-since-death. Poorly-preserved shells on the inner flats tended to be old, but in general shell condition was much more variable than shell age. A shell's condition is more likely the result of its total residence time on the surface than its time-since-death (surface time plus burial time).Two composite short (44 cm and 50 cm) cores revealed varying degrees of stratigraphic disorder (the departure from perfect correlation between relative stratigraphic position and relative age). One of eight shells in the inner flats core was disordered; four of nine shells in the tidal channel were disordered. The actual age range of surface shells approximates the age range of shells in cores. Stratigraphic disorder is a consequence of both time-averaging and physical and biogenic mixing.Time-averaging controls the degree of precision possible in paleoecological studies. Environmental changes and ecological phenomena occurring within a span of 3500 years would not be recognized in deposits like those of Bahia la Choya. Time-averaging and stratigraphic disorder also constrain the temporal resolution possible in microstratigraphic studies of evolution. The extent of time-averaging and stratigraphic disorder will dictate an appropriate sample interval. In order to prevent temporal overlap between successive samples in deposits like Bahia la Choya, sample spacing should not be less than approximately 0.5 m.

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