A robust nonparametric method for quantifying undetected extinctions.

Extinction in the Anthropocene.

The evolutionary history of large carnivorous mammals through the Ice Age have been investigated for the Italian peninsula. No endemisms are recorded in the mainland of Italy and large carnivore species composition reflected the similar fauna of European continent. Morpho-ecological adaptation of extinct Plio-Pleistocene species have been investigated throughout temporal PaleoCommunities (9 PCOMs – spanning 3.2 to 0.3 Ma) with statistical accuracy. Trophic apparatus of extant and extinct species was investigated with a geometric morphometric analysis of mandible shape while locomotory habits were assessed using long bone indices. The mandible shape analysis performed on extant Carnivora taxa confirms their morphological differences due principally to taxonomic affiliation (family). Although, when phylogenetic history is controlled with comparative methods, significant differences still to occur among taxa with different diets and between small and large forms (threshold posed at 7 kilograms). Interestingly, both mandibular regions (corpus and ascending ramus) are informative of Carnivora ecological adaptations and they result integrated at a macroevolutionary scale. This survey allows to consider geometric morphometric as a reliable technique to apply on fossil mandibles. Feeding habits have been predicted with a good degree of accuracy in several PlioPleistocene large carnivores on the basis of mandible shape data. The latter data –selecting only the corpus regionhave been considered also to perform a morphospace comparison between large carnivore guilds of Italian PCOMs and extant guilds representative of five mainland ecosystems worldwide. Disparity values computed for mandibular corpus shape of Plio-Pleistocene guilds did not differ significantly from extant guilds. Morphological variability in mandible shape is negatively influenced by number of species in each guild as well as number of prey confirming that ecomorph specialization does not occur at the extreme region of morphospace. Long bone proportions of Plio-Pleistocene large carnivores are grouped in the variability of extant species. Although some phenomena of morphological convergences occur among extinct and extant taxa because of similar locomotor adaptation (e.g. cursorial) and same body size constraint. These morphoecological data were also used to predict the relative adaptability of Plio-Pleistocene species to certain habitats (grassland and tropical). The macroecological analysis of presence/absence data confirms the striking relationship between the abundances of both predators and their prey thought Ice Age. On the other hand no morphoecological coordinate changes occurs between predators and their prey. It is noteworthy that large carnivores are overrepresented in the Italian fossil record and became rarer from Galerian to the Aurelian (also because of a possible interaction with human activities). A GIS model was then computed to compare large mammal communities toward Plio-Pleistocene in Italy. Structural changes occurred in large herbivore communities from Villafranchian through the Aurelian because of climate changes. On the other hand, the spatial structure of large carnivore communities was more affected by their prey during the Villafranchian, while in the Galerian and Aurelian there was a greater influence of uncontrolled factors like climate and human activity as well.

Plant-diversity hotspots on a global scale are well established, but smaller local hotspots within these must be identified for effective conservation of plants at the global and local scales. We used the distributions of endemic and endemic-threatened species of Myrtaceae to indicate areas of plant diversity and conservation importance within the Atlantic coastal forests (Mata Atlântica) of Brazil. We applied 3 simple, inexpensive geographic information system (GIS) techniques to a herbarium specimen database: predictive species-distribution modeling (Maxent); complementarity analysis (DIVA-GIS); and mapping of herbarium specimen collection locations. We also considered collecting intensity, which is an inherent limitation of use of natural history records for biodiversity studies. Two separate areas of endemism were evident: the Serra do Mar mountain range from Paraná to Rio de Janeiro and the coastal forests of northern Espírito Santo and southern Bahia. We identified 12 areas of approximately 35 km(2) each as priority areas for conservation. These areas had the highest species richness and were highly threatened by urban and agricultural expansion. Observed species occurrences, species occurrences predicted from the model, and results of our complementarity analysis were congruent in identifying those areas with the most endemic species. These areas were then prioritized for conservation importance by comparing ecological data for each.

Nee et al. (1994) presented likelihood equations for estimating speciation and extinction rates based on phylogenies of only extant species; in particular their method can infer extinction patterns without extinct species data. Meanwhile, even for the simplest model of speciation and extinction, namely, the constant rate birth–death process, a number of studies have been published using different likelihood equations (Thompson 1975; Rannala and Yang 1996; Yang and Rannala 1997; Gernhard 2008; Stadler 2009). The likelihood functions differ due to conditioning the likelihood on different quantities, like the age of the tree, survival of the tree, or the number of species in the tree. Which conditionings yield the most accurate speciation and extinction rate estimates? In order to answer this question, I present an overview of 7 likelihood functions (which have been published in previous articles), conditioning on different aspects of the tree. I investigate and discuss the impact of the different conditionings toward accuracy of the maximum-likelihood rate estimates by inferring rates based on simulated phylogenies. The second part of this article discusses a possible bias in speciation and extinction rate estimates when analyzing incomplete phylogenies, that is, phylogenies in which not all extant species are included. The analytic considerations reveal that we cannot estimate the fraction of nonsampled species, but have to know it, when estimating speciation and extinction rates. The conclusions reached in this article, assuming the simple constant rate birth–death model, will also apply when assuming the more realistic macroevolutionary models allowing for nonconstant rates (Rabosky 2007; Alfaro et al. 2009; FitzJohn et al. 2009; Morlon et al. 2011; Stadler 2011a; Silvestro et al. 2011; Etienne et al. 2012), as these general models all contain the constant rate birth– death model as a special case. This article ends with contrasting these different method implementations (Table 1) and providing some recommendations for end users in order to facilitate model comparison across packages. SEVEN TREE LIKELIHOOD FUNCTIONS

Species richness (the number of species) in an assemblage is a key metric in many research fields of ecology. Simple counts of species in samples typically underestimate the true species richness and strongly depend on sampling effort and sample completeness. Based on possibly unequal‐sampling effort and incomplete samples that miss many species, there are two approaches to infer species richness and make fair comparisons among multiple assemblages,: (1) An asymptotic approach via species richness estimation. This approach aims to compare species richness estimates across assemblages. We focus on the nonparametric estimators that are universally valid for all species abundance distributions. (2) A non‐asymptotic approach via the sample‐size‐ and coverage‐based rarefaction and extrapolation on the basis of standardised sample size or sample completeness (as measured by sample coverage). This approach aims to compare species richness estimates for equally large or equally complete samples. Two R packages (SpadeR and iNEXT) are applied to beetle data for illustration. Key Concepts Due to sampling limitation, there are undetected species in almost every biodiversity survey. Empirical species counts underestimate species richness and highly depend on sampling efforts and sample completeness. Based on incomplete samples, species richness (observed plus undetected) is statistically difficult to estimate accurately especially for highly diverse assemblages with many rare species. Abundant species (which are certain to be detected in samples) contain almost no information about the undetected species richness. Rare species (which are likely to be either undetected or infrequently detected) contain nearly all the information about the undetected species richness. Most nonparametric estimators of the number of undetected species are based on the frequency counts of the detected rare species, e.g. singletons and doubletons for abundance data. Nonparametric estimators of species richness are universally valid for all species abundance distributions and thus are more robust than parametric estimators that are based on specified parametric abundance models. Rarefaction and extrapolation methods allow for fair and meaningful comparison of species richness estimates for standardised samples on the basis of sample size or sample completeness. Sample‐size‐based rarefaction and extrapolation methods aim to compare species richness estimates for equally large samples determined by samplers. Coverage‐based rarefaction and extrapolation methods aim to compare species richness estimates for equally complete samples or equal fractions of population individuals reliably estimated from data.

Schildia Aldrich, 1923, a distinctive and rarely collected genus of Leptogastrinae (Diptera: Asilidae), is revised. Ten species are recognized, of which four are new to science. The nine extant species are Afrotropical, Neotropical and Oriental in distribution. The extant Neotropical species are Schildia alphus Martin, 1975, Schildia caliginosa sp.n. (Ecuador and Venezuela), Schildia fragilis (Carrera, 1944), Schildia guatemalae Martin, 1975, Schildia gracillima (Walker, 1855), Schildia jamaicensis Farr, 1963, and Schildia microthorax Aldrich, 1923. The only extant Afrotropical species, Schildia adina sp.n., is described from extant and subfossilized specimens (Malagasy copal) from south-western Madagascar. The extant Oriental species, Schildia malaya sp.n., is described from northern Malaysia. One extinct species, Schildia martini sp.n., is newly described from Dominican amber. Two new synonyms are proposed: Schildia ocellata Martin, 1975 is a junior synonym of Schildia gracillima and Schildia zonae Martin, 1975 is synonymized with Schildia fragilis. Redescriptions and descriptions of the genus and all extant and extinct species are provided. An identification key to the extant and extinct species is presented. Illustrations, photographs, and scanning electron micrographs are provided to support the descriptions and key. Distribution, biogeography, occurrence in biodiversity hotspots, seasonal incidence and biology are discussed.

Understanding the processes that underlie biodiversity requires insight into the evolutionary history of the taxa involved. Accurate estimation of speciation, extinction, and diversification rates is a prerequisite for gaining this insight. Here, we develop a stochastic birth-death model of speciation and extinction that predicts the probability distribution of both extinct and extant numbers of species in a clade. We present two estimation methods based on this model given data on the number of extinct species (from the fossil record) and extant species (from diversity assessments): a multivariate method of moments approach and a maximum-likelihood approach. We show that, except for some special cases, the two estimation methods produce very similar estimates. This is convenient, because the usually preferred maximum-likelihood approach is much more computationally demanding, so the method of moments can serve as a proxy. Furthermore, we introduce a correction for possible bias that can arise by the mere fact that we will normally only consider extant clades. We find that in some cases the bias correction affects the estimates profoundly. Finally, we show how our model can be extended to incorporate incomplete preservation. Preservation rates can, however, not be reliably estimated on the basis of numbers of extant and extinct species alone.

The genus Zelkova (Ulmaceae) has occurred in Europe and Southwest Asia since the Eocene represented mostly by the fossil species Z. zelkovifolia. Currently, relict populations of Z. abelicea, Z. sicula and Z. carpinifolia can be found in Crete, Sicily and the Euxino-Hyrcanian province, respectively. To reveal relationships between extinct and extant Zelkova species, we compared fossil Miocene leaves of Z. zelkovifolia and leaves of extant species using morphological leaf characteristics and statistical methods (Tukey’s test, discrimination analysis, principal component analysis, agglomeration). The fossil leaves of Z. zelkovifolia appeared more variable and generally intermediate between all three extant species. The lowest level of significant differences was found between Z. zelkovifolia and Z. abelicea in the leaves from fertile shoots and between Z. zelkovifolia and Z. sicula leaves from vegetative long shoots. The intermediate positions of fossil leaves of Z. zelkovifolia between leaves of Z. abelicea, Z. sicula and Z. carpinifolia could indicate that the extinct species was an ancestor of all three extant taxa. Consequently, this result suggests divergence between Z. abelicea, Z. sicula and Z. carpinifolia no earlier than the late Miocene and/or during the Pliocene.

Birth–death models and coalescent point processes: The shape and probability of reconstructed phylogenies

Determinants of orchid species diversity in world islands.

At present there are many animal phyla that contain only a few species. The existence of these small phyla can be used to test assumptions about speciation and extinction in multicellular animals.We first model the number of species in a monophyletic clade with a birth and death process that assumes rates of speciation and extinction are constant. If no new phyla have evolved since the Cambrian and speciation and extinction rates for minor phyla are similar to or greater than those estimated from fossils, then our model shows that the probabilities of minor phyla surviving to the present are small. Random variation in extinction and speciation rates does not improve the chances for persistence. If speciation rates exceed extinction rates at the initial radiation of the clade, but before the clade becomes large, speciation rates come to equal extinction rates and both are low, persistence from before the Ordovician up to the present becomes likely. These models show that if speciation and extinction rates are independent of the number of species in a clade, then conditions before the Ordovician strongly influence today's distribution of species among taxa.We also discuss a model in which speciation and extinction rates depend on the number of species in a clade. This alternative model can account for the persistence of phyla with few species to the present and predicts a short duration for phyla that did not exceed a threshold number of species.

Dictated by limited resource availability for land acquisition, a central question in conservation biology is the ability of areas of different size to maintain species diversity. The selected reserves should not only be species rich at the moment, but should also maintain species diversity in the long run. We used two sets of data on vascular plant species in boreal lakes collected in 1933/34 and 1996 to test the relationships between lake area and the extinction, immigration and turnover rates of the species. Moreover, we investigated, whether the number of species in 1933/34 or water connection between lakes was related to extinction, immigration and turnover rates of species. We found that lake area or shoreline length was not correlated with immigration or turnover rate. But extinction rate was slightly negatively correlated with shoreline length. The original number of species was positively related to the number of species extinctions and to the absolute turnover rate in the lakes, which indicates that species richness does not create stability in these communities. Species number was not correlated with immigration rate. Upstream water connections in the lakes did not affect immigration, extinction or turnover rates. We conclude that length of the shoreline is a better measure of suitable area for water plants than the lake area, and that because the correlation between shoreline length and extinction rate was slight, also small lakes can be valuable for conservation.

In the 1960s the new technique of gel electrophoresis revealed what was then considered to be an astonishing amount of molecular variation in natural populations, with about 30% of genetic loci being polymorphic. It was thought at the time that natural selection the dominant principle in evolutionary biology could not account for such high levels of variability the costs of selection would be too high. This prompted the proposal of the neutral theory of molecular evolution (Kimura 1968; King & Jukes 1969; Kimura 1983), which postulated that most molecular evolution did not involve natural selection at all: in this model, selectively neutral mutations arose and their frequencies simply fluctuated at random, as is inevitable in a finite population. Tropical forests pose a similar puzzle for ecologists. The enormous numbers of species seem to challenge our classical notions that coexistence requires that each species has its own unique niche: how can so many species construct unique niches from such a small number of requirements sun, water, a patch of ground? The same puzzle in a different context became known as the 'paradox of the plankton' (Hutchinson 1961). As in molecular evolution, so too in ecology a neutral theory has been proposed which may resolve our puzzle (Bell 2001; Hubbell 2001) and is attracting much attention. The theory's advocates have more in mind than tropical trees, but I will restrict myself to trees to make the discussion specific. This was the context in which the theory was first proposed (Hubbell 1979) and one of the main biological areas where we have a puzzle apparently requiring a radical solution. Hereafter I will refer to the neutral theory of biodiversity as NTB. The underlying stochastic theory is the same in the two areas, although it has been studied for much longer in population genetics, as neutral advocates point out (Hubbell 2001; Volkov et al. 2003). This means we can import many results from the population genetics literature, simply interpreting the biology in a different way. In this paper I will import an important result concerning the time-scale of the neutral process, which raises serious difficulties for the NTB as an explanation of tropical forest diversity. This difficulty has been noted before (Leigh 1999; Lande et al. 2003), but does not appear to be as widely known as it should. Nonetheless, as I will discuss, neutral theory can still provide useful null models for the interpretation of data. In the fir t section, I gather together some basic theoretical results that are common to both population genetics and NTB. This is for two reasons. First of all, it serves to emphasize that we really are talking about the same theory, giving us the confidence to bring into the body of NTB an important result from population genetics concerning the time-scale of the neutral process. This will be done in the third section. Secondly, people may find it useful to have these basic results gathered toget er in one place they are currently somewhat scattered about. Having emphasized the underlying identity of the theory, I then briefly explore the implications of the biological differences between the worlds of molecular evolution and biodiversity for the likely future development of the theory in the biodiversity context.

Eastern Africa is home to the largest terrestrial migrations on Earth. Though these migratory systems have been well studied for decades, little is known of their antiquity and evolutionary history. Serially sampled strontium stable isotopes (87Sr/86Sr) from tooth enamel can be used to track migration in mammals. Here we analyse 87Sr/86Sr for 79 bovid and equid individuals representing 18 species from four localities in Kenya to characterize prehistoric migratory systems during the Last Glacial Period (115-11.7 ka). Of the species analysed, 16 lack definitive evidence for migration, including blue wildebeest (Connochaetes taurinus), Thomson's gazelle (Eudorcas thomsonii) and plains zebra (Equus quagga), which are long-distance migrants today in the Greater Serengeti Ecosystem and historically in the Athi-Kapiti Plains. Only two species, the extinct wildebeests Rusingoryx atopocranion and Megalotragus sp., were migratory. These findings suggest a possible alternative narrative about ecosystem dynamics during the Last Glacial Period and shed light on the behaviour of both extant and extinct species at this time. In particular, these results indicate that migratory behaviour in extant species either emerged during the Holocene or was more spatiotemporally constrained in the past. Our results contribute to a growing body of evidence suggesting that the structure and function of geologically recent large mammal communities in eastern Africa differed considerably from those observed in the present day.

The Central Yangtze ecoregion in China includes a number of lakes, but these have been greatly affected by human activities over the past several decades, resulting in severe loss of biodiversity. In this paper, we document the present distribution of the major lakes and the changes in size that have taken place over the past 50 years, using remote sensing data and historical observations of land cover in the region. We also provide an overview of the changes in species richness, community composition, population size and age structure, and individual body size of aquatic plants, fishes, and waterfowl in these lakes. The overall species richness of aquatic plants found in eight major lakes has decreased substantially during the study period. Community composition has also been greatly altered, as have population size and age and individual body size in some species. These changes are largely attributed to the integrated effects of lake degradation, the construction of large hydroelectric dams, the establishment of nature reserves, and lake restoration practices.