Patterns of Rarity in the Birds of the Atlantic Forest of Brazil

Patterns of rarity in species are generally explained by several factors: evolutionary history, spatial distribution, and genetic structure of each taxon. Human intervention also leads to or increases rarity in species. The discernment of causes of rarity is essential to the understanding of extinction patterns, and thus to devising conservation strategies. I examine patterns of rarity among bird species in the Atlantic forest region in Brazil, one of the most threatened ecosystems in the world. I assigned bird species to one of eight possible categories that differ in degree of vulnerability and that are based on three parameters of rarity: geographic distribution, habitat specificity, and population size. The Atlantic forest avifauna is a highly endangered group; 68% of the species are rare. Patterns of rarity among the birds in the region likely result from their specific ecologies or evolutionary histories. In addition, human alteration of natural habitats and hunting pressures have undoubtedly influenced rarity for a number of species.     

Rarity in Neotropical Forest Mammals Revisited

The identification of rare species is an important goal in conservation biology. Recent attempts to classify rare species have emphasized dichotomies in such characteristics as local population density, area of distribution, and degree of ecological specialization. In particular, Arita et al. (1990) dichotomized 100 Neotropical forest mammals according to local population density and area of distribution. Among these species of mammals, mean body mass was significantly associated with local population density and area of distribution. We argue that the effects of body mass should be removed before species are classified with respect to rarity. We re-evaluated the data on Neotropical mammal species, using regression analyses to remove the effects of body mass on population density and area of distribution, followed by analysis of residuals. This new method resulted in substantial changes in the dichotomous classification of rare species. We combined the analysis of regression residuals with a ranking procedure that assumed that local population density and area of distribution were equally important in their effects on rarity. The new ranking technique produced another different classification of the rarity of the Neotropical forest mammal species. A graphical analysis showed that ranked species differed substantially in their degree of rarity, and in the importance of local population density, area of distribution, or both, to their degree of rarity. The ranking method allows the species of greatest concern to be singled out, it can be modified to include additional variables such as niche breadth, and it should be helpful for making conservation decisions.     

Relations between Species Rarity,Vulnerability, and Range Contraction for a Beetle Group in a Densely Populated Region in the Mediterranean Biodiversity Hotspot

Rarity is often considered an indication of species extinction risk, and it is frequently used to obtain measures of species vulnerability. However, there is no strong evidence of a correlation between species vulnerability and threat. Moreover, there is no consensus about how rarity should be measured. I used a multidimensional characterization of species rarity to calculate a vulnerability index for tenebrionid beetles inhabiting an Italian region in the Mediterranean biodiversity hotspot. I used different metrics to examine 3 dimensions of rarity: species range, ecology, and population. Species with rarity values below the median were scored as rare for each dimension. I combined rarity scores into a vulnerability index. I then correlated species vulnerability with range trends (expanded vs. contracted). Different measures of the same rarity dimension were strongly correlated and produced similar vulnerability scores. This result indicates rarity‐based vulnerability estimates are slightly affected by the way a certain rarity dimension is measured. Vulnerability was correlated with range trends; species with the highest vulnerability had the strongest range contraction. However, a large number of common species also underwent range contraction in the last 50 years, and there was no clear relation between range contraction and their ecology. This indicates that in general human‐induced environmental changes affected species irrespective of their assumed vulnerability and that focusing only on rare species may severely bias perceptions of the extent of species decline. Relaciones entre Rareza de Especies, Vulnerabilidad y Contracción de Distribución Geográfica para un Grupo de Escarabajos en una Región Densamente Poblada en el Hotspot de Biodiversidad del Mediterráneo     

Incorporating geographical and evolutionary rarity into conservation prioritization

Key goals of conservation are to protect both species and the functional and genetic diversity they represent. A strictly species-based approach may underrepresent rare, threatened, or genetically distinct species and overrepresent widespread species. Although reserves are created for a number of reasons, including economic, cultural, and ecological reasons, their efficacy has been measured primarily in terms of how well species richness is protected, and it is useful to compare how well they protect other measures of diversity. We used Proteaceae species-occurrence data in the Cape Floristic Region of South Africa to illustrate differences in the spatial distribution of species and evolutionary diversity estimated from a new maximum-likelihood molecular phylogeny. We calculated species richness, phylogenetic diversity (i.e., summed phylogenetic branch lengths in a site), and a site-aggregated measure of biogeographically weighted evolutionary distinctiveness (i.e., an abundance weighted measure that captures the unique proportion of the phylogenetic tree a species represents) for sites throughout the Cape Floristic Region. Species richness and phylogenetic diversity values were highly correlated for sites in the region, but species richness was concentrated at a few sites that underrepresented the much more spatially extensive distribution of phylogenetic diversity. Biogeographically weighted evolutionary diversity produced a scheme of prioritization distinct from the other 2 metrics and highlighted southern sites as conservation priorities. In these sites, the high values of biogeographically weighted evolutionary distinctiveness were the result of a nonrandom relation between evolutionary distinctiveness and geographical rarity, where rare species also tended to have high levels of evolutionary distinctiveness. Such distinct and rare species are of particular concern, but are not captured by conservation schemes that focus on species richness or phylogenetic diversity alone.     

The influence of spatial and size scale on phylogenetic relatedness in tropical forest communities

The relative importance of biotic, abiotic, and stochastic processes in structuring ecological communities continues to be a central focus in community ecology. In order to assess the role of phylogenetic relatedness on the nature of biodiversity we first quantified the degree of phylogenetic niche conservatism of several plant traits linked to plant form and function. Next we quantified the degree of phylogenetic relatedness across two fundamental scaling dimensions: plant size and neighborhood size. The results show that phylogenetic niche conservatism is likely widespread, indicating that closely related species are more functionally similar than distantly related species. Utilizing this information we show that three of five tropical forest dynamics plots (FDPs) exhibit similar scale-dependent patterns of phylogenetic structuring using only a spatial scaling axis. When spatial- and size-scaling axes were analyzed in concert, phylogenetic overdispersion of co-occurring species was most important at small spatial scales and in four of five FDPs for the largest size class. These results suggest that phylogenetic relatedness is increasingly important: (1) at small spatial scales, where phylogenetic overdispersion is more common, and (2) in large size classes, where phylogenetic overdispersion becomes more common throughout ontogeny. Collectively, our results highlight the critical spatial and size scales at which the degree of phylogenetic relatedness between constituent species influences the structuring of tropical forest diversity.     

High genetic diversities and complex genetic structure in an Indo-Pacific tropical reef fish (Chlorurus sordidus): evidence of an unstable evolutionary past?

Historical sea level fluctuations have influenced the genetic structure and evolutionary history of marine species and examining widespread species across their species ranges may elucidate some of these effects. Chlorurus sordidus is a common and widespread parrotfish found on coral reefs throughout the Indo-central Pacific. We used phylogenetic, phylogeographic, and cladistic analyses to examine the genetic composition and population structure of this species across most of its latitudinal range limits. We sequenced 354 bp of the mitochondrial control region I in 185 individuals from nine populations. Populations of C. sordidus displayed high levels of genetic diversity, similar to those recorded for widespread pelagic fish species, but much greater nucleotide diversity values than those previously recorded for other demersal reef fishes. Both phylogenetic and phylogeographic analyses detected strong genetic subdivision at the largest spatial scale (i.e. among oceans). The Pacific Ocean was characterised by weak population genetic structure. Separation of the Hawaiian location from other Pacific and West Indian Ocean sites was evident in phylogenetic analyses, but not from analysis of molecular variance. NCA and isolation-by-distance tests suggested that the genetic structure of this species was the result of multiple contemporary and historical processes, including long-distance colonisation and range expansion arising from fluctuating sea levels, limited current gene flow, and isolation by distance. This pattern is to be expected when historically fragmented populations come into secondary contact. We suggest the patterns of population genetic structure recorded in C. sordidus are caused by large local population sizes, high gene flow, and a recent history of repeated fragmentation and remixing of populations resulting from fluctuating sea levels.Communicated by M.S. Johnson, Crawley     

Selectivity in Mammalian Extinction Risk and Threat Types: a New Measure of Phylogenetic Signal Strength in Binary Traits

Abstract: The strength of phylogenetic signal in extinction risk can give insight into the mechanisms behind species’ declines. Nevertheless, no existing measure of phylogenetic pattern in a binary trait, such as extinction‐risk status, measures signal strength in a way that can be compared among data sets. We developed a new measure for phylogenetic signal of binary traits, D, which simulations show gives robust results with data sets of more than 50 species, even when the proportion of threatened species is low. We applied D to the red‐list status of British birds and the world's mammals and found that the threat status for both groups exhibited moderately strong phylogenetic clumping. We also tested the hypothesis that the phylogenetic pattern of species threatened by harvesting will be more strongly clumped than for those species threatened by either habitat loss or invasive species because the life‐history traits mediating the effects of harvesting show strong evolutionary pattern. For mammals, our results supported our hypothesis; there was significant but weaker phylogenetic signal in the risk caused by the other two drivers (habitat loss and invasive species). We conclude that D is likely to be a useful measure of the strength of phylogenetic pattern in many binary traits.     

Effects of rarity form on species’ responses to land use

Anthropogenic land-use change causes substantial changes in local and global biodiversity. Rare and common species can differ in sensitivity to land-use change; rare species are expected to be affected more negatively. Rarity may be defined in terms of geographic range size, population density, or breadth of habitat requirements. How these 3 forms of rarity interact in determining global responses to land use is yet to be assessed. Using global data representing 912 vertebrate species, we tested for differences in responses to land use of species characterized by different types of rarity. Land-use responses were fitted using generalized linear mixed-effects models, allowing responses to vary among groups of species with different forms of rarity. Species considered rare with respect to all 3 forms of rarity showed particularly strong declines in disturbed land uses (>40% of species and 30% of individuals in the most disturbed land uses). In contrast, species common both geographically and numerically and with broad habitat requirements showed strong increases (up to 90% increase in species and 40% in abundance in some land uses). Our results suggest that efforts to understand the vulnerability of species to environmental changes should account for different types of rarity where possible. Our results also have potentially important implications for ecosystem functioning, given that rare species may play unique roles within ecosystems.     

Phylogenetic Comparative Methods Strengthen Evidence for Reduced Genetic Diversity among Endangered Tetrapods

Abstract: The fitness of species with little genetic diversity is expected to be affected by inbreeding and an inability to respond to environmental change. Conservation theory suggests that endangered species will generally demonstrate lower genetic diversity than taxa that are not threatened. This hypothesis has been challenged because the time frame of anthropogenic extinction may be too fast to expect genetic factors to significantly contribute. I conducted a meta‐analysis to examine how genetic diversity in 894 tetrapods correlates with extinction threat level. Because species are not evolutionarily independent, I used a phylogenetic regression framework to address this issue. Mean genetic diversity of tetrapods, as assessed by protein heterozygosity, was 29.7–31.5% lower on average in threatened species than in their nonthreatened relatives, a highly significant reduction. Within amphibians as diversity decreased extinction risk increased in phylogenetic models, but not in nonphylogenetic regressions. The effects of threatened status on diversity also remained significant after accounting for body size in mammals. These results support the hypothesis that genetic effects on population fitness are important in the extinction process.     

Rarity of Organisms in the Sand Pine Scrub Habitat of Florida

Naturalists conceive of "rare" organisms as those narrow in geographic range, restricted to few habitats, or small in population sizes. Because rare organisms may be rare in a variety of ways, a particular conservation strategy that purports to protect them may not do so effectively in all cases; therefore, categorization of rarity in advance could help ensure that the chosen strategy has a reasonable chance of success in a particular case. We placed plants, amphibians, and reptiles resident in the Sand Pine scrub habitat of Florida into categories of rarity. Determining if and in what way a particular organism is rare proved difficult, because the process requires exact specification of what is meant by "narrow,""restricted," and "small." Furthermore, the process requires choice of a scale for judging rarity and relies upon data that are likely to be of variable availability and reliability. We categorized rarity by several schemes, and they produced distributions of taxa among categories of rarity that largely were similar to one another but that diverged in telling ways. The distributions of taxa among categories of rarity produced by any scheme were different for scrub plants than for scrub amphibians and reptiles. Likewise, these distributions were different than those produced by previously published studies of rarity. We found that the results of our categorization schemes did not match particularly well with the official listing of scrub organisms as endangered or potentially endangered.     

Plant Reproductive Traits as a Function of Local, Regional, and Global Abundance

Most ecological generalizations stem from the study of common organisms, but most species are rare. There are a number of reasons to expect that rare and common species may differ consistently in their characteristics, with possible implications for conservation. Past analyses of this issue, however, have generally considered only a single measure of rarity and have not corrected analyses for the lack of independence in the traits of related species. We compared several reproductive characteristics of Mediterranean annual crucifers as a function of their global range, regional abundance, and local population density in Israel, making use of independent contrast methods to correct for the phylogenetic relationships of the species involved. We found plants growing at low local density to be disproportionately likely to be self-compatible. Petal length and floral depth (sepal length) were correlated with breeding system but showed significant interaction effects between breeding system and abundance. Floral longevity was inversely related to abundance and also showed significant interaction effects between breeding system and abundance. Overall, rare species tended to display more extreme values for floral traits than did common plants with the same breeding systems; they had unusually large and deep flowers if self-incompatible and unusually small, shallow ones if self-compatible.     

A systematic study of some Black Corals species (Antipatharia,Hexacorallia) based on rDNA internal transcribed spacers sequences

A phylogenetic analysis based on rDNA internal transcribed spacers (ITS) sequences was performed on 15 species of black corals assigned to the genera Antipathes, Stichopathes, Cirrhipathes, Rhipidipathes, Antipathella, Myriopathes and Cupressopathes recorded from the Messina Strait (Mediterranean Sea) and the Bunaken Marine Park (Celebes Sea, Indonesia). The phylogenetic analysis shows that the examined species are grouped in two main branches corresponding to the families Antipathidae-Aphanipathidae and Myriopathidae. While among the Myriopathidae species there is a very small genetic distance, the Antipathidae-Aphanipathidae clade shows a high degree of divergence between different genera. According to this study, the taxon Antipathes? sp. 3 characterised by a bush-like corallum without a well-defined axis, probably belongs to a new undescribed genus of the family Antipathidae.     

Quantitative Determination of Rarity of Freshwater Fishes and Implications for Imperiled‐Species Designations

Abstract: Conserving rare species and protecting biodiversity and ecosystem functioning depends on sound information on the nature of rarity. Rarity is multidimensional and has a variety of definitions, which presents the need for a quantitative classification scheme with which to categorize species as rare or common. We constructed such a classification for North American freshwater fishes to better describe rarity in fishes and provide researchers and managers with a tool to streamline conservation efforts. We used data on range extents, habitat specificities, and local population sizes of North American freshwater fishes and a variety of quantitative methods and statistical decision criteria, including quantile regression and a cost‐function algorithm to determine thresholds for categorizing a species as rare or common. Species fell into eight groups that conform to an established framework for rarity. Fishes listed by the American Fisheries Society (AFS) as endangered, threatened, or vulnerable were most often rare because their local population sizes were low, ranges were small, and they had specific habitat needs, in that order, whereas unlisted species were most often considered common on the basis of these three factors. Species with large ranges generally had few specific habitat needs, whereas those with small ranges tended to have narrow habitat specificities. We identified 30 species not designated as imperiled by AFS that were rare along all dimensions of rarity and may warrant further study or protection, and we found three designated species that were common along all dimensions and may require a review of their imperilment status. Our approach could be applied to other taxa to aid conservation decisions and serve as a useful tool for future revisions of listings of fish species.     

Scale Dependency of Rarity, Extinction Risk, and Conservation Priority

Abstract:   In developing red data books of threatened species, the World Conservation Union uses measures of rarity, rates of decline, and population fragmentation to categorize species according to their risk of extinction. However, most quantitative measures of these three concepts are sensitive to the scale at which they are made. In particular, definitions of rarity based on an area-of-occupancy threshold can nearly always be met if area of occupancy is calculated from a sufficiently fine-scale (high-resolution) grid. Recommendations for dealing with scale dependency include (1) choosing a standard scale of measurement, (2) using multiple scales of measurement, and (3) developing indices that combine information from multiple scales. As an example of the second and third approach, the construction of a species' scale-area curve represents a unifying method for quantifying all three indicators of extinction risk—rarity, rate of decline, and population fragmentation—as functions of area of occupancy and measurement scale. A multiscale analysis is also of practical importance because measurements made at different scales are relevant to different extinction processes. Coarse-scale measures of rarity are most appropriate when threat is assessed on the basis of spatially autocorrelated events of a large extent, such as global climate change, whereas fine-scale measures may best predict extinction risk due to local processes such as demographic stochasticity. We illustrate our arguments with a case study of the British distributions of two related plant species that show a 200-fold reversal in their relative rarity when measured at different scales.     

Seeing stars: a molecular and morphological investigation into the evolutionary history of Odontasteridae (Asteroidea) with description of a new species from the Galapagos Islands

Odontasteridae (Asteroidea: Echinodermata) (Verrill in Am J Sci, 1899) is placed within Valvatida, a derived assemblage of sea stars. Odontasterids are found in the Southern, Atlantic, and Pacific Oceans and are concentrated in high southern latitudes. To date, the phylogenetic and evolutionary history of Odontasteridae as a whole has not been rigorously examined. We conducted molecular and morphological phylogenetic analyses of Odontasteridae to assess the interrelationships among and within recognized genera. We used mitochondrial 16S and cytochrome c oxidase subunit I molecular markers and 29 external morphological characters in an attempt to reconstruct the evolutionary history of the group. Generally, our results indicate that traditionally used external skeletal characters are not representative of phylogenetic history of Odontasteridae. We can conclude that species present in high latitudes in the Southern Hemisphere (i.e., Southern Ocean) are the most derived taxa. Additionally, mtDNA data suggest unrecognized lineages of odontasterids are present in high southern latitudes. A new species Odontaster cynthiae sp. nov. is described from the Galapagos Islands.     

Trait space of rare plants in a fire‐dependent ecosystem

The causes of species rarity are of critical concern because of the high extinction risk associated with rarity. Studies examining individual rare species have limited generality, whereas trait‐based approaches offer a means to identify functional causes of rarity that can be applied to communities with disparate species pools. Differences in functional traits between rare and common species may be indicative of the functional causes of species rarity and may therefore be useful in crafting species conservation strategies. However, there is a conspicuous lack of studies comparing the functional traits of rare species and co‐occurring common species. We measured 18 important functional traits for 19 rare and 134 common understory plant species from North Carolina's Sandhills region and compared their trait distributions to determine whether there are significant functional differences that may explain species rarity. Flowering, fire, and tissue‐chemistry traits differed significantly between rare and common, co‐occurring species. Differences in specific traits suggest that fire suppression has driven rarity in this system and that changes to the timing and severity of prescribed fire may improve conservation success. Our method provides a useful tool to prioritize conservation efforts in other systems based on the likelihood that rare species are functionally capable of persisting.     

Implications of Phylogenetic Studies for Conservation of Genetic Diversity in Shiitake Mushrooms

We consider the impact of recent molecular phylogenetic analyses on conservation issues for shiitake mushrooms. Bused on mating compatibility, shiitake has been considered a single species, Lentinula edodes sensu lato . Phylogenetic analyses of ribosomal RNA internal transcribed spacers (Hibbett et al. 1995), however, suggest that shiitake is composed of four distinct lineages. Thus, under a phylogenetic species concept, four species of shiitake should be recognized. A classification of shiitake based on a phylogenetic species concept would convey information about evolutionary relationships and distribution of genetic variation, whereas a classification based on a biological species concept would lack such information. This is a clear case in which new insights into phylogenetic relationships can be used to target areas for conservation action and formulate international agricultural policies. At the heart of our argument is the belief that the basic units of both taxonomy and conservation should be unique evolutionary lineages of organisms identified through phylogenetic studies.     

High intervality explained by phylogenetic constraints in host-parasite webs

The finding of invariant structures in species interaction webs is of central importance for ecology, with the greatest challenge remaining the elucidation of the processes governing these universal web patterns. Here we quantify the degree of intervality of seven fish-metazoan and 33 mammal-flea webs, i.e., the number of irreducible gaps in parasite diets along the host spectrum, and then challenge the idea that some invariant structures may emerge in host-parasite webs. Using a null model of random links between parasite and host species we find that empirical host-parasite webs exhibit a strong bias toward contiguity of parasite diet, i.e., toward intervality. Going one step further, we demonstrate that a null model with phylogenetic constraints on host-parasite links produced webs very similar to empirical ones, particularly when phylogenetic constraints occur at the family level, that is, when two hosts from the same family are more likely to be infected than two random hosts. In addition, we propose a new standardized measure of intervality which describes a novel "facet" of natural networks as it is independent of connectance or web size. We suggest using this measure as a surrogate of web maturity or saturation as phylogenetic constraints can drive webs toward intervality.     

Species phylogenetic relatedness, priority effects, and ecosystem functioning

Species immigration history can structure ecological communities through priority effects, which are often mediated by competition. As competition tends to be stronger between species with more similar niches, we hypothesize that species phylogenetic relatedness, under niche conservatism, may be a reasonable surrogate of niche similarity between species, and thus influence the strength of priority effects. We tested this hypothesis using a laboratory microcosm experiment in which we established bacterial species pools with different levels of phylogenetic relatedness and manipulated the immigration history of species from each pool into microcosms. Our results showed that strong priority effects, and hence multiple community states, only emerged for the species pool with the greatest phylogenetic relatedness. Community assembly also resulted in a significant positive relationship between bacterial phylogenetic diversity and ecosystem functions. Interestingly, these results emerged despite a lack of phylogenetic conservatism for most of the bacterial functional traits considered. Our results highlight the utility of phylogenetic information for understanding the structure and functioning of ecological communities, even when phylogenetically conserved functional traits are not identified or measured.     

Impacts of phylogenetic nomenclature on the efficacy of the U.S. Endangered Species Act

Cataloging biodiversity is critical to conservation efforts because accurate taxonomy is often a precondition for protection under laws designed for species conservation, such as the U.S. Endangered Species Act (ESA). Traditional nomenclatural codes governing the taxonomic process have recently come under scrutiny because taxon names are more closely linked to hierarchical ranks than to the taxa themselves. A new approach to naming biological groups, called phylogenetic nomenclature (PN), explicitly names taxa by defining their names in terms of ancestry and descent. PN has the potential to increase nomenclatural stability and decrease confusion induced by the rank‐based codes. But proponents of PN have struggled with whether species and infraspecific taxa should be governed by the same rules as other taxa or should have special rules. Some proponents advocate the wholesale abandonment of rank labels (including species); this could have consequences for the implementation of taxon‐based conservation legislation. I examined the principles of PN as embodied in the PhyloCode (an alternative to traditional rank‐based nomenclature that names biological groups based on the results of phylogenetic analyses and does not associate taxa with ranks) and assessed how this novel approach to naming taxa might affect the implementation of species‐based legislation by providing a case study of the ESA. The latest version of the PhyloCode relies on the traditional rank‐based codes to name species and infraspecific taxa; thus, little will change regarding the main targets of the ESA because they will retain rank labels. For this reason, and because knowledge of evolutionary relationships is of greater importance than nomenclatural procedures for initial protection of endangered taxa under the ESA, I conclude that PN under the PhyloCode will have little impact on implementation of the ESA. Impactos de la Nomenclatura Filogenética sobre la Eficiencia del Acta Estadunidense para las Especies en Peligro