Indicator taxa revisited: useful for conservation planning?

Aim Indicators for biodiversity are needed to facilitate the identification of complementary reserve networks for biodiversity conservation. One widely adopted approach is to use indicator taxa, i.e. a single taxon such as birds or butterflies, despite the ongoing debate regarding their usefulness as indicators of broader biodiversity. Here we assess several aspects, such as influence of species number, of indicator taxa for three extensive data sets to improve our insight into the effectiveness of indicator taxa. Location Denmark, sub‐Saharan Africa and Uganda. Methods First, we investigate to what extent variation in species number between indicator taxa (e.g. 488 mammal spp. vs. 210 snake spp.) is causing the differences in effectiveness between indicator taxa. Second, we investigate whether indicator taxa are capable of outperforming indicator groups composed of random sets of species chosen among all taxa. Finally, we assess the correlation of specific properties such as mean range size of the indicator taxa to their effectiveness. We investigate these aspects of the effectiveness of indicator taxa through the separate analysis of three distinct distributional species data sets: sub‐Saharan Africa (4,039 spp.), Denmark (847 spp.) and Uganda (2,822 spp.). Results We overall found that indicator taxa comprising a greater number of species tend to perform better than indicator taxa with fewer species (e.g. 488 mammal spp. outperform 210 snake spp.), although there are some exceptions. Second, we found most indicator taxa to perform worse than indicator groups consisting of a comparable number of species selected among all taxa. Finally, the effectiveness of indicator taxa was seen to correlate poorly with selected distributional properties such as mean range size of the indicator taxa, suggesting that it is difficult to predict which taxa are efficient biodiversity indicators. Main conclusions Overall, these findings might suggest that focus should simply be on increasing the number of species among all taxa as basis for priority setting, rather than striving to obtain the ‘perfect’ indicator taxa.     

Identifying areas of high importance for orchid conservation in east Macedonia (NE Greece)

The establishment of a network of reserves is of fundamental importance to the loss of biodiversity. Seven different area selection methods for the establishment of a reserve network were applied in the present study: (a) 5% cut-off value of the grid cells with the highest species richness or conservation value, (b) complementarity analysis using as criteria species richness or conservation value or rarest species richness, and (c) mixed complementarity analysis using as criteria species richness or conservation value. These methods were applied in the orchid taxa of east Macedonia. The conservation values of taxa were estimated on the basis of regional rarity, broad-scale rarity, and species specialization. The spatial overlap between the resulting networks and the Natura 2000 network of the study area was assessed. Furthermore, the efficiency of the latter network to protect the orchid taxa of the study area was examined. Our results suggest that: (a) a multiscale estimation of rarity is necessary for the unbiased estimation of species conservation values; (b) species specialization adds valuable ecological information to the assessment of taxa conservation values; (c) complementarity and mixed complementarity analyses on species richness or conservation value safeguard all the taxa of the region; (d) complementarity analysis on the basis of the richness of the rarest species safeguards all the rarest taxa, but not the total number of the remaining taxa; (e) the 5% cut-off value on species richness or conservation value fails to protect all the taxa of the region, including a large number of the rarest taxa; and (f) the Natura 2000 network, despite its large coverage in the study area, fails to safeguard all the taxa, including some of the rarest.     

Species concepts and species reality: salvaging a Linnaean rank

The validity of the species category (rank) as a distinct level of biological organization has been questioned. Phenetic, cohesion and monophyletic species concepts do not delimit species-level taxa that are qualitatively distinct from lower or higher taxa: all organisms throughout the tree of life exhibit varying degrees of similarity, cohesion, and monophyly. In contrast, interbreeding concepts delimit species-level taxa characterized by a phenomenon (regular gene flow) not found in higher taxa, making the species category a distinct level of biological organization. Only interbreeding concepts delimit species-level taxa that are all comparable according to a biologically meaningful criterion and qualitatively distinct from entities assigned to other taxonomic categories. Consistent application of interbreeding concepts can result in counterintuitive taxonomies--e.g. many wide polytypic species in plants and narrow cryptic species in animals. However, far from being problematic, such differences are biologically illuminating--reflecting differing barriers to gene flow in different clades. Empirical problems with interbreeding concepts exist, but many of these also apply to other species concepts, whereas others are not as severe as some have argued. A monistic view of species using interbreeding concepts will encounter strong historical inertia, but can save the species category from redundancy with other categories, and thus justify continued recognition of the species category.     

Regional‐scale patterns and predictors of species richness and abundance across twelve major tropical inter‐reef taxa

Species richness and abundance are biodiversity metrics widely used to describe and estimate changes in biodiversity. Studies of marine species richness and abundance typically focus on one, or just a few, taxa. Consequently, it is currently not possible to understand the performance of predictors of species richness and abundance across marine taxa. Using a taxonomically comprehensive dataset of twelve major taxa of flora and fauna from eight phyla sampled from the inter‐reef seabed region of the Great Barrier Reef, Australia, we used boosted regression trees to test the performance of fourteen environmental and spatial predictors of species richness and abundance. Sediment composition predicted richness best for all taxa: gravel contributed up to 39% relative influence for one group and all taxa had low richness in muddy habitats. Sea surface temperature, seabed current shear stress, depth and latitude were also influential predictors for species richness for eight groups. Sediment was frequently an influential predictor for abundance also, while distance to domain (reef/coast) and longitude were relatively influential for six taxa. Within‐site richness was correlated between nearly all pairs of taxa, as was within‐site abundance, however ρ values were low. Overall, model performance was high, explaining up to 62% deviance of species richness, and 38% of abundance. Typically, deviance explained was greater for richness than abundance and may indicate that some drivers of species richness operate independently of any effects on species richness mediated by their effect on abundance. Deviance explained differed most between richness and abundance for bryozoans (23.3% difference) and soft corals (15.2% difference). While sediments were consistently the best predictors across all taxa, the inconsistent influence of all other predictors across taxonomic groups, as well as the low correlation of richness and abundance across taxonomic groups, cautions against predicting regional patterns of species richness and abundance from few taxa.     

Species monophyly

In biological systematics, as well as in the philosophy of biology, species and higher taxa are individuated through their unique evolutionary origin. This is taken by some authors to mean that monophyly is a (relational) property not only of higher taxa, but also of species. A species is said to originate through speciation, and to go extinct when it splits into two daughter species (or through terminal extinction). Its unique evolutionary origin is said to bestow identity on a species through time and change, and to render species names rigid designators. Species names are thus believed to function just like names of supraspecific taxa. However, large parts of the Web of Life are composed of species that do not have a unique evolutionary origin from a single population, lineage or stem-species. Further, monophyly is an ambiguous concept if it is defined simply in terms of 'unique evolutionary origin'. Disambiguating the concept by defining a monophyletic taxon as 'a taxon that includes the ancestor and all, and only, its descendant' renders monophyly inapplicable to species. At the heart of the problem lies a fundamental distinction between species and monophyletic taxa, where species form mutually exclusive reticulated systems, while higher taxa form inclusive hierarchical systems. Examples are given both at the species level and below to illustrate the problems that result from the application of the monophyly criterion to species. The conclusion is that the concepts of exclusivity and monophyly should be treated as non-overlapping: exclusivity marks out a species synchronistically, i.e. in the present time. Monophyly marks out clades (groups of species) diachronistically, i.e. within an historical dimension.     

Rewilding the tropics,and other conservation translocations strategies in the tropical Asia‐Pacific region

Alarm over the prospects for survival of species in a rapidly changing world has encouraged discussion of translocation conservation strategies that move beyond the focus of ‘at‐risk’ species. These approaches consider larger spatial and temporal scales than customary, with the aim of recreating functioning ecosystems through a combination of large‐scale ecological restoration and species introductions. The term ‘rewilding’ has come to apply to this large‐scale ecosystem restoration program. While reintroductions of species within their historical ranges have become standard conservation tools, introductions within known paleontological ranges—but outside historical ranges—are more controversial, as is the use of taxon substitutions for extinct species. Here, we consider possible conservation translocations for nine large‐bodied taxa in tropical Asia‐Pacific. We consider the entire spectrum of conservation translocation strategies as defined by the IUCN in addition to rewilding. The taxa considered are spread across diverse taxonomic and ecological spectra and all are listed as ‘endangered’ or ‘critically endangered’ by the IUCN in our region of study. They all have a written and fossil record that is sufficient to assess past changes in range, as well as ecological and environmental preferences, and the reasons for their decline, and they have all suffered massive range restrictions since the late Pleistocene. General principles, problems, and benefits of translocation strategies are reviewed as case studies. These allowed us to develop a conservation translocation matrix, with taxa scored for risk, benefit, and feasibility. Comparisons between taxa across this matrix indicated that orangutans, tapirs, Tasmanian devils, and perhaps tortoises are the most viable taxa for translocations. However, overall the case studies revealed a need for more data and research for all taxa, and their ecological and environmental needs. Rewilding the Asian‐Pacific tropics remains a controversial conservation strategy, and would be difficult in what is largely a highly fragmented area geographically.     

A meta-analysis of spatial relationships in species richness across taxa: Birds as indicators of wider biodiversity in temperate regions

AimIndicators are an important tool by which conservationists monitor biodiversity because resources and expertise needed to survey biodiversity in a more direct way are often lacking. We aim to examine the effectiveness of species richness in birds as an indicator of species richness in other taxa. Birds are perhaps the most widely monitored species group so it is important to understand whether they can act as surrogates for distribution and abundance of other taxa.MethodsWe use a meta-analytical approach to assess the effectiveness of birds as indicators of cross-taxonomic species richness on spatial data from terrestrial temperate studies.ResultsThe literature showed mixed results but, in general, species richness in birds only weakly reflected species richness in other taxa. On average 19% of the variation in total species richness in other taxa was explained by species richness in birds. This is marginally higher than results found in a previous meta-analysis of species richness correlations between all taxa. Birds were more effective at reflecting cross-taxa species richness in study areas that were dominated by agricultural mosaics or mixtures of habitat types; they were less effective in forests and grassland environments. Overall, birds were better at reflecting species richness in mammals than other taxa, and relationships were more effective at larger spatial scales.Main conclusionsSpecies richness in birds only weakly reflected that of other taxa. Birds might be most useful as indicators of spatial variation in wider biodiversity in relatively patchy environments and for taxa that have similar spatial requirements. Species richness is one of many potential metrics for measuring biodiversity. There is a need to assess whether temporal change in bird populations and assemblages, as opposed to spatial variation, reflects change in other taxa and to identify elements of biodiversity for which birds could be the most effective surrogates.     

Electrophoretic delineation of species boundaries within the short-necked freshwater turtles of Australia (Testudines: Ghelidae)

A total of 222 specimens from 55 populations of short-necked chelid turtle was collected from drainages in Australia and Papua New Guinea. Two populations were initially considered to belong to different diagnosable taxa if all individuals in one population could be distinguished from all individuals in the other by fixed allozyme differences. When two populations or diagnosable taxa shared allozymes at all presumptive loci, their profiles were combined into a single diagnosable taxon. Comparisons between populations and emerging diagnosable taxa were repeated until no further changes were possible. The species Elseya dentata comprised five clearly diagnosable taxa, differing by between 4 and 19 fixed allozyme differences. The currently recognized El. latisternum and El. novaeguineae were each a single diagnosable taxon, and there were three diagnosable taxa, including a sibling pair, that could not be assigned to a currendy described Elseya species. In contrast, all forms of Emydura were very closely related, with no two taxa differing by more than three fixed allozyme differences. There were three diagnosable taxa in the north (Em. victoriae, Em. subglobosa and one new form), though support for them was marginal. In the south, Em. macquarii, Em. krefflii and Em. signata formed only a single diagnosable taxon, even sharing rare alleles. If the phylogenetic species concept is adopted, there is support for recognition of 16 species of short-necked turtle in Australia, including Pseudemydura umbrina. Currendy only 10 are described. Our data also provide evidence of reproductive isolation in some cases (sympatric or parapatric), and comparative evidence (sensu Mayr) in others, than the traditional biological species concept applies also to these diagnosable taxa.     

缺失数据和贝叶斯系统发育分析精确度之探索

The effect of missing data on phylogenetic methods is a potentially important issue in our attempts to reconstruct the Tree of Life. If missing data are truly problematic, then it may be unwise to include species in an analysis that lack data for some characters (incomplete taxa) or to include characters that lack data for some species. Given the difficulty of obtaining data from all characters for all taxa (e.g., fossils), missing data might seriously impede efforts to reconstruct a comprehensive phylogeny that includes all species. Fortunately, recent simulations and empirical analyses suggest that missing data cells are not themselves problematic, and that incomplete taxa can be accurately placed as long as the overall number of characters in the analysis is large. However, these studies have so far only been conducted on parsimony, likelihood, and neighbor-joining methods. Although Bayesian phylogenetic methods have become widely used in recent years, the effects of missing data on Bayesian analysis have not been adequately studied. Here, we conduct simulations to test whether Bayesian analyses can accurately place incomplete taxa despite extensive missing data. In agreement with previous studies of other methods, we find that Bayesian analyses can accurately reconstruct the position of highly incomplete taxa (i.e., 95% missing data), as long as the overall number of characters in the analysis is large. These results suggest that highly incomplete taxa can be safely included in many Bayesian phylogenetic analyses.     

Supraspecific taxa as terminals in cladistic analysis: implicit assumptions of monophyly and a comparison of methods

The use of supraspecific terminal taxa to represent groups of species in phylogenetic analyses can result in changes to inferred relationships as compared to a complete species level analysis. These changes in topology result from interactions among (1) the cladistic status of the supraspecific taxa; (2) the method used to represent the taxa as single terminals, and (3) incongruence in the data set. We examine the effects of using supraspecific terminal taxa using a parallel analysis of hypothetical examples and an actual data matrix for the true seals (Mammalia: Phocidae). Incongruence among characters can produce changes in topology by shifting the ‘balance of power’ among groups of characters when supraspecific taxa are represented as single terminals. In the absence of homoplasy, the correct topology is maintained. Of the three methods for representing supraspecific taxa, the ‘ancestral’ method, which explicidy infers the common ancestor of the group corresponding to the taxon, performed the best, always maintaining the correct topology when monophyletic taxa were represented. This agrees with theoretical predictions. The ‘democratic’ and ‘exemplar’ methods, which represent the higher level taxon through a survey of all or one of its extant constituent species, respectively, were not as effective in maintaining the correct topology. Although both occasionally provided correct answers, their occurrences were largely unpredictable. The success of the exemplar method varies with the species selected. The simultaneous representation of two or more higher level taxa produced interactive effects where the resultant topology included different clades than when the taxa were collapsed individually. Interactive effects occurred with all three methods, albeit to a lesser degree for the ancestral method. Changes in topology were observed regardless of whether the higher group was monophyletic or not, but were more prevalent when it was paraphyletic. Unfortunately, there does not seem to be a reliable way to determine when a paraphyletic group has been included in the analysis (e.g. through bootstrap values or indices measuring homoplasy). The implications of these findings for phylogenetic analyses of molecular data are also discussed.     

An annotated checklist of dinoflagellates in the Black Sea

An annotated checklist of free-living dinoflagellates (Dinophyceae) of the Black Sea, based on literature records, is reported and compared to the Mediterranean Sea and world oceans. Toxic species and/or responsible of harmful algal blooms (HAB) are marked in the checklist. From the 267 species (54 genera) listed nearly all taxa can be considered as cosmopolitan and no species as endemic. Several typically Arctic-boreal species (non recorded from the Mediterranean Sea) are reported from the Black Sea. The taxonomy and the biogeography of the taxa are discussed.     

Fruit characters as a basis of fruit choice and seed dispersal in a tropical forest vertebrate community

Summary Interactions between a large community of vertebrate frugivore-granivores (including 7 species of large canopy birds, 19 species of rodents, 7 species of ruminants, and 6 species of monkeys), and 122 fruit species they consume, were studied for a year in a tropical rainforest in Gabon.The results show how morphological characters of fruits are involved in the choice and partitioning of the available fruit spectrum among consumer taxa. Despite an outstanding lack of specificity between fruit and consumer species, consideration of simple morphological traits of fruits reveals broad character syndromes associated with different consumer taxa. Competition between distantly related taxa that feed at the same height is far more important than has been previously supposed. The results also suggest how fruit characters could have evolved under consumer pressure as a result of consumer roles as dispersers or seed predators. Our analyses of dispersal syndromes show that fruit species partitioning occurs more between mammal taxa than between mammals and birds. There is thus a bird-monkey syndrome and a ruminant-rodent-elephant syndrome. The bird-monkey syndrome includes fruit species on which there is no pre-dispersal seed predation. These fruits (berries and drupes) are brightly colored, have a succulent pulp or arillate seeds, and no protective seed cover. The ruminant-rodent-elephant syndrome includes species for which there is pre-dispersal predation. These fruits (all drupes) are large, dull-colored, and have a dry fibrous flesh and well-protected seeds.     

Hot spots, indicator taxa, complementarity and optimal networks of taiga

If hot spots for different taxa coincide, priority-setting surveys in a region could be carried out more cheaply by focusing on indicator taxa. Several previous studies show that hot spots of different taxa rarely coincide. However, in tropical areas indicator taxa may be used in selecting complementary networks to represent biodiversity as a whole. We studied beetles (Coleoptera), Heteroptera, polypores or bracket fungi (Polyporaceae) and vascular plants of old growth boreal taiga forests. Optimal networks for Heteroptera maximized the high overall species richness of beetles and vascular plants, but these networks were least favourable options for polypores. Polypores are an important group indicating the conservation value of old growth taiga forests. Random selection provided a better option. Thus, certain groups may function as good indicators for maximizing the overall species richness of some taxonomic groups, but all taxa should be examined separately.     

Taxonomic complexity and breeding system transitions: conservation genetics of the Epipactis leptochila complex (Orchidaceae)

The genus Epipactis contains a problematical complex of autogamous taxa among which species limits are difficult to define. Different authors have treated these plants in different ways, some recognizing the different taxa as distinct species, others considering them as minor intraspecific variants. These contrasting treatments have a direct impact on the conservation resources and status such plants command; 'endemic orchid species' are perceived as having high conservation value, 'localized minor variants' are not. We used allozyme and chloroplast restriction fragment length polymorphism (RFLP) and sequencing analyses to investigate patterns of population genetic structure underlying the taxonomic complexity in this group. Populations of E. dunensis, E. leptochila and E. muelleri were homozygous and uniform for all loci studied here. There were, however, fixed genetic differences among these taxa. Comparisons with published data from the putative progenitor species for the autogamous taxa (the widespread, allogamous E. helleborine) suggest iterative origins of autogamy, rather than the self-pollinating taxa all being merely mutational variants of a single autogamous lineage.     

Discordance of species trees with their most likely gene trees: the case of five taxa

Under a coalescent model for within-species evolution, gene trees may differ from species trees to such an extent that the gene tree topology most likely to evolve along the branches of a species tree can disagree with the species tree topology. Gene tree topologies that are more likely to be produced than the topology that matches that of the species tree are termed anomalous, and the region of branch-length space that gives rise to anomalous gene trees (AGTs) is the anomaly zone. We examine the occurrence of anomalous gene trees for the case of five taxa, the smallest number of taxa for which every species tree topology has a nonempty anomaly zone. Considering all sets of branch lengths that give rise to anomalous gene trees, the largest value possible for the smallest branch length in the species tree is greater in the five-taxon case (0.1934 coalescent time units) than in the previously studied case of four taxa (0.1568). The five-taxon case demonstrates the existence of three phenomena that do not occur in the four-taxon case. First, anomalous gene trees can have the same unlabeled topology as the species tree. Second, the anomaly zone does not necessarily enclose a ball centered at the origin in branch-length space, in which all branches are short. Third, as a branch length increases, it is possible for the number of AGTs to increase rather than decrease or remain constant. These results, which help to describe how the properties of anomalous gene trees increase in complexity as the number of taxa increases, will be useful in formulating strategies for evading the problem of anomalous gene trees during species tree inference from multilocus data.     

INTERSPECIFIC HYBRIDITY IN THE DESMID GENUS PLEUROTAENIUM1

Three desmid taxa, isolated from different parts of Australia, conform to the morphological taxa Pleurotaenium ehrenbergii, P. mamillatum, and P. coronatum. Use of successful zygospore formation between cells of mixed populations as an indication of ability to share a common gene pool shows that all 3 taxa are at least closely related and probably are members of the same biological species. Tentatively, we suggest synonymy of these taxa and urge the adoption of sexual criterion in delimiting desmid species.     

The adequacy of collecting techniques for estimating species richness of grassland invertebrates

1.  There is still considerable debate about the most effective methods of sampling invertebrates in monitoring and assessment programmes.
2.  The above-ground invertebrates of a limestone grassland in north-east England were compared between samples from pitfall traps and from a D-vac suction trap combined with a lightweight swish net (SW/DV).
3.  Over 14 000 individuals were captured, with similar numbers in the pitfall and SW/DV samples. A total of 480 species of Hemiptera, Coleoptera, Diptera and Araneae was identified and placed into 14 taxa for further analysis.
4.  The pitfall sample produced species/specimen curves from which it was possible to estimate species richness for all the Coleoptera and Araneae taxa and the calypterate Schizophora. The SW/DV sample was adequate to estimate the species richness of Hemiptera, most Diptera taxa, herbivorous Coleoptera and Linyphiidae.
5.  The proportion of Coleoptera and Araneae taxa that were method-unique was higher in the pitfall sample than the SW/DV sample and vice versa for the Hemiptera and Diptera taxa. Nevertheless, a relatively high proportion of method-unique species of most taxa was found in both sample types, indicating that they can each contribute to assessing species assemblages in grasslands.
6.  Both pitfall traps and SW/DV samples are needed to estimate species richness in grasslands for all taxa except Heteroptera, Homoptera and Lycosidae. Herbivorous Coleoptera and Linyphiidae were collected in numbers adequate for assessing richness in both sample types, but more specimens were required in one or other sample for the remaining taxa.     

Weak links: 'Rapoport's rule' and large-scale species richness patterns

Many hypotheses have been proposed to explain regional species richness patterns. Among these, ‘Rapoport's rule’ has sparked considerable controversy by stating that the latitudinal gradient in species richness can be explained indirectly as a function of narrower geographic ranges for species at low latitudes. Annual climatic variability, or deviation from mean climatic conditions, has been hypothesized to moderate this phenomenon. Furthermore, taxa that avoid much of this seasonality, such as temperate zone insects that enter diapause or species that migrate, were predicted to show reduced latitudinal gradients in richness. I test the suggested link between ‘Rapoport's rule’ and species richness for two higher level insect taxa as well as for the class Mammalia. Although these taxa exhibit the well-known latitudinal gradient in species richness, simple annual climatic variability and deviation from mean annual climatic conditions provide very poor predictions of species richness in each of them. Potential evapotranspiration, a measurement of ambient climatic energy, explains most of the observed variance in regional species richness patterns for all three taxa, consistent with the species richness-energy hypothesis. I find no support for an indirect link between ‘Rapoport's rule’ and terrestrial species richness patterns in North America.     

An integrative approach to species delimitation in Echinodorus (Alismataceae) and the description of two new species

Summary  Taxonomy of the genus Echinodorus is partially revisited in the light of current understanding of the phylogenetic relationships of the genus. As a result of new taxonomy, the species status of some previously synonymised taxa are restored, other names are synonymised, and some nomenclatural problems unnoticed by previous authors are resolved. Two new species, Echinodorus reptilis and E. emersus are described. The subgeneric divisions of the genus are not accepted, and all subspecific taxa are either rejected or established as species. As a result, 28 species based on a phylogenetic species concept are now recognised in Echinodorus and an identification key to these species is provided.