Studying beta diversity: ecological variation partitioning by multiple regression and canonical analysis

Aims: Beta diversity is the variation in species composition amongsites in a geographic region. Beta diversity is a key conceptfor understanding the functioning of ecosystems, for the conservationof biodiversity and for ecosystem management. The present reportdescribes how to analyse beta diversity from community compositionand associated environmental and spatial data tables. Methods: Beta diversity can be studied by computing diversity indicesfor each site and testing hypotheses about the factors thatmay explain the variation among sites. Alternatively, one cancarry out a direct analysis of the community composition datatable over the study sites, as a function of sets of environmentaland spatial variables. These analyses are carried out by thestatistical method of partitioning the variation of the diversityindices or the community composition data table with respectto environmental and spatial variables. Variation partitioningis briefly described herein. Important findings: Variation partitioning is a method of choice for the interpretationof beta diversity using tables of environmental and spatialvariables. Beta diversity is an interesting ‘currency’for ecologists to compare either different sampling areas ordifferent ecological communities co-occurring in an area. Partitioningmust be based upon unbiased estimates of the variation of thecommunity composition data table that is explained by the varioustables of explanatory variables. The adjusted coefficient ofdetermination provides such an unbiased estimate in both multipleregression and canonical redundancy analysis. After partitioning,one can test the significance of the fractions of interest andplot maps of the fitted values corresponding to these fractions.     

Tetraphyllidean plerocercoids from Western Mediterranean cetaceans and other marine mammals around the world: a comprehensive morphological analysis

Tetraphyllidean plerocercoids have occasionally been reported in marine mammals, but they have rarely been described in detail, and the ecological significance of these infections is unclear. We described plerocercoids collected from the mucosa of the terminal colon and rectum, the anal crypts, and the hepatopancreatic ducts of 7 striped dolphins Stenella coeruleoalba, 1 Cuvier's beaked whale Ziphius cavirostris, and 3 Risso's dolphins Grampus griseus from the Spanish Mediterranean. We also examined undescribed plerocercoids from 3 cetacean species from the Atlantic and the Pacific. All plerocercoids had a lanceolate body, and a scolex with an apical sucker and 4 sessile monolocular bothridia. The bothridia had free posterior edges and an accessory sucker at their anterior end. Under light microscopy, the bothridia of some Mediterranean specimens looked bilocular without accessory suckers, but a true accessory sucker was observed in histological sections. A principal component analysis revealed 2 stable clusters of specimens along the first principal component regardless of host species. These "large" and "small" morphotypes are thought to represent early migratory stages of Phyllobothrium delphini and Monorygma grimaldii. The similarity in scolex morphology, the observation of plerocercoids buried in intestinal regions close to the sites where M. grimaldii and P. delphini occur, and the coexistence of all larval forms in the same individual hosts would support this hypothesis. Future molecular analysis may confirm it.     

Examining residual spatial correlation in variation partitioning of beta diversity in a subtropical forest

AimsThe relative roles of ecological processes in structuring beta diversity are usually quantified by variation partitioning of beta diversity with respect to environmental and spatial variables or gamma diversity. However, if important environmental or spatial factors are omitted, or a scale mismatch occurs in the analysis, unaccounted spatial correlation will appear in the residual errors and lead to residual spatial correlation and problematic inferences.     

Conservation biogeography of large Mediterranean islands. Butterfly impoverishment, conservation priorities and inferences for an ecologica "island paradigm"

Conservation biogeography is considered the Cinderella of biological conservation. Nevertheless biogeography provides the basis for establishing species distributions over space and time, therefore conservation priorities among areas and individual species. We demonstrate that there is no need to simplify analyses by using subsets of species (rare species, endemics) as surrogates. In doing so, we apply strict biogeographical techniques to determine butterfly impoverishment on three of the west Mediterranean's largest islands (Sardinia, Corsica and Sicily). The analyses performed on species, both collectively and individually, reveal that regional species richness in the Mediterranean zone can be largely predicted by latitude, altitude and latitudinal range (maximum minus minimum latitude), but that Sardinia and Corsica have clearly impoverished faunas. Logistic regression at individual species level demonstrates that several species, predicted to be present in these islands on the basis of their continental distributions, are actually absent. When compared with species that are present in these islands, such missing species are disclosed as having ecological traits which reduce their colonization capability. Probabilities of occurrence are calculated for each species on each island; they reflect the potential for each butterfly species to migrate to and colonise each island, and can be considered as a measure of conservation value. As such, species present on islands but having low immigration probabilities are predicted to represent isolated populations from the mainland that are unlikely to re-colonize the islands in the case of extinction. Island endemic species and races are shown to have lower occurrence probabilities compared to widespread species occurring on islands and illustrate the usefulness of occurrence probabilities for identifying isolated populations in need of conservation attention.     

The generalized replication principle and the partitioning of functional diversity into independent alpha and beta components

The replication principle was first proposed by Hill (1973, Ecology 54: 247– 432) as an advantageous property of his family of diversity indices. Later Jost (2007, Ecology 88: 2427– 2439) discovered that diversity measures satisfying this principle allow partitioning of gamma diversity into independent alpha and beta components by simple multiplicative partitioning. Despite the emerging agreement on measuring taxonomic beta‐diversity by multiplicative partitioning of Hill diversity, there is no consensus on how to measure functional beta diversity. Two different generalizations of Hill numbers for measuring functional diversity were proposed by Leinster and Cobbold (2011, Ecology 93: 477– 489) and Chiu and Chao (2014, PLoS One 9: e1000014). Both generalizations attempted to satisfy the generalized replication principle, but they formulate it in different ways. The aims of this paper are 1) to review approaches for measuring functional diversity in units of equivalent numbers without explicit reference to replication principle; 2) to compare the two proposed replication principle and to point out some important differences in the behavior of diversity families derived from the two principles; 3) to explore the conditions necessary for partitioning functional diversity of Leinster and Cobbold into meaningful alpha and beta components; 4) and, finally, to explore how transformation of among‐species distances into similarities influences the sensitivity of functional diversity to the scale parameter.     

Character-based DNA barcoding allows discrimination of genera, species and populations in Odonata

DNA barcoding has become a promising means for identifying organisms of all life stages. Currently, phenetic approaches and tree-building methods have been used to define species boundaries and discover 'cryptic species'. However, a universal threshold of genetic distance values to distinguish taxonomic groups cannot be determined. As an alternative, DNA barcoding approaches can be 'character based', whereby species are identified through the presence or absence of discrete nucleotide substitutions (character states) within a DNA sequence. We demonstrate the potential of character-based DNA barcodes by analysing 833 odonate specimens from 103 localities belonging to 64 species. A total of 54 species and 22 genera could be discriminated reliably through unique combinations of character states within only one mitochondrial gene region (NADH dehydrogenase 1). Character-based DNA barcodes were further successfully established at a population level discriminating seven population-specific entities out of a total of 19 populations belonging to three species. Thus, for the first time, DNA barcodes have been found to identify entities below the species level that may constitute separate conservation units or even species units. Our findings suggest that character-based DNA barcoding can be a rapid and reliable means for (i) the assignment of unknown specimens to a taxonomic group, (ii) the exploration of diagnosability of conservation units, and (iii) complementing taxonomic identification systems.     

Biological diversification in a complex region: a spatial analysis of faunistic diversity and biogeography of the Andes of Colombia

Aim Understanding large‐scale patterns of beta diversity and endemism is essential for ecoregional conservation planning. We present a study of spatial patterns of faunal diversification and biogeographical relationships in the Andean region of Colombia. This region has a great geomorphological complexity, as it is formed by several mountain ranges with different geologic origins. We hypothesize that this complexity results in a high turnover in species composition among subregions. Location The Andean region of Colombia, including the Santa Marta and Macarena mountain ranges. Methods The region was divided into subregions, represented by the eastern and western slopes of each of the three Andean cordilleras, the Cauca and Magdalena valley bottoms, and the peripheral mountain ranges of Perijá, Macarena and Sierra Nevada de Santa Marta. Species lists for five animal taxa (rodents, bats, birds, frogs and butterflies) were compiled for each subregion and similarities in species composition were determined by cluster analysis. To explore biogeographical relationships, species were classified into one of four distributional categories: endemic, tropical Andean, Andean‐Central American and wide continental distribution. Results The highest species richness in the region was found in the Pacific and eastern versants of the Andes, and the lowest in the Cauca and Magdalena valley bottoms. Inter‐Andean slopes were intermediate in species richness. However, when species richness was calculated per unit area, the most diverse regions were the Santa Marta and Macarena ranges, the Cauca Valley watershed and the Pacific slope. Although each taxonomic group had a different branching pattern, dendrograms indicated five common subregional clusterings: (1) Perijá‐Sierra Nevada, (2) the Pacific slope, (3) the eastern Andean slope, (4) the Cauca and Magdalena valley bottoms, and (5) the inter‐Andean slopes. Clustering patterns of inter‐Andean slopes varied among taxa. In birds, bats and rodents, grouping was by opposite slopes of the same valley, whereas frogs were grouped by mountain ranges and butterflies by valleys and their respective slopes. Seventy‐five per cent of species in all taxa were found in less than five subregions. The fauna of the Magdalena and Cauca valley bottoms was composed mostly of lowland species with wide geographical distributions, whereas the cordilleran fauna was mostly restricted to the tropical Andes. Main conclusions The western and eastern versants of the Andes have the highest species richness, but are also the largest subregions. On a per unit area basis, the peripheral ranges (Santa Marta and Macarena) are the richest, followed by the western portion of the Andes (the Cauca Valley watershed and the Pacific versant). Clustering patterns in dendrograms suggest two major patterns of differentiation of the Andean fauna: one elevational (lowlands vs. highlands) and one horizontal (among ranges and/or slopes). Biogeographical affinities of the inter‐Andean valley bottoms are with the lowland faunas of tropical America. In contrast, Andean faunas diversified locally, resulting in the evolution of a large number of endemic species, particularly among the less vagile taxa. Three different main branches of Andean fauna can be recognized, one confined to the Pacific, another to the eastern (Amazonian‐Llanos) versant of the Andes, and the third one composed by the inter‐Andean slopes of the Cauca and Magdalena valleys. The identification of five main biogeographical units in the Andean region of Colombia has important implications for the conservation of the regional biota. Conservation initiatives that seek to preserve representative samples of the regional biodiversity should take into account the patterns of diversification described here, and the evolutionary processes that gave rise to these patterns.     

江苏蜻蜓区系及多样性

2005-2010年,在江苏一些比较适合蜻蜓生长的水域附近进行了蜻蜓采集,用静观和网捕法记录采集路线两侧各20m范围内的蜻蜓,鉴定统计后分析其区系成分及多样性.结果表明:江苏地区现有蜻蜓53种,隶属于11科35属;古北-东洋种类较多,有18种,占总数的33.96%;古北界种类相对较少,只有5种,约占总数的9.43%;江苏地区蜻蜓的多样性指数为3.108,均匀度指数为0.782,优势度指数为0.169,优势集中性指数为0.072;南京和连云港地区蜻蜓的物种丰富度、多样性指数和均匀度指数最高,优势集中性指数最低,这可能与这两地生境的多样性相对较高、适宜蜻蜓生存的生境多有关.     

Phylogenetic diversity and the conservation biogeography of African primates

Aim Phylogenetics has an important role in conservation biogeography. However, there are few data on the phylogenetic diversity of African primates. The phylogenetic diversity (PD) of a species is a measure of its taxonomic distinctness and can be estimated by looking at the phylogenetic relationships among taxa. Species‐specific metrics on PD can then be used to determine conservation priorities at various biogeographical scales. We used PD metrics to rank 55 African primate species according to their conservation priorities at the country level and within six African biogeographical regions. We also addressed the following question: are there differences in conservation rankings between the IUCN Red List and our PD metrics? Location Africa. Methods We created a consensus phylogeny for all African primate clades based on genetic studies. Analyses of species distributions were determined using presence/absence scores at two levels: country and biogeographical region. A node‐based method that standardizes for widespread taxa and endemicity was used to calculate PD indices. Hierarchical cluster analysis was used to convert one of the standardized, phylogenetic indices into three clusters that could be ranked and compared with the main IUCN conservation rankings of endangered, vulnerable, and lower risk. Results At the country and region levels, the top‐priority species in terms of PD are Pan paniscus, Macaca sylvanus, Arctocebus calabarensis, Gorilla beringei, Arctocebus aureus, Allenopithecus nigroviridis, Gorilla gorilla, Procolobus verus, Cercopithecus solatus, Cercocebus galeritus, Colobus angolensis, Theropithecus gelada, Galagoides zanzibaricus, Galagoides granti, and Procolobus (Piliocolobus) badius. Geographic rankings were highest for the Democratic Republic of the Congo (country level) and Central Africa (region level). Although there were no overall differences between IUCN conservation ranks and the PD rankings, there were significant differences between the two systems for vulnerable and endangered primate taxa. Main conclusions There are few ecological and behavioural data on populations of some of the African primates that represent the highest levels of phylogenetic diversity. Studies of primate taxa with high PD rankings should focus on identifying sites suitable for intensive studies of population densities, feeding ecology, and reproductive behaviour. We suggest that PD metrics can serve as an important, complementary data set in the IUCN ranking system for primates.     

A comprehensive description and evolutionary analysis of 9 Loliginidae mitochondrial genomes

Forty South American aquatic plant species were selected and categorised in four a priori status classes (alien naturalised, alien invasive, native and absent) according to expert opinion, for 16 South American regions (Argentina, Bolivia, Brazil, Chile, Colombia, Ecuador, Falklands Islands, French Guiana, Galapagos, Guyana, Paraguay, Peru, South Georgia and South Sandwich Islands, Suriname, Uruguay and Venezuela). The 40 aquatic plant species were assessed using the US Aquatic Weed Risk Assessment (USAqWRA) scheme for each of the 16 South American regions, for a total number of 644 assessments and for South America (153 assessments). The method was benchmarked against expert opinion (invasive, non-invasive). We ranked 17 of them as naturalised, and 15 as invasive species in at least one South American region. The USAqWRA distinguished between non-invaders and invaders with an overall accuracy of 84.9% in South America and 54.1% in the 16 regions, with areas under the curves equal to 0.893 and 0.853, at a threshold score of 51.5 and 43.5, respectively. The study highlights that the USAqWRA could represent a suitable screening protocol to prioritise aquatic species that have the potential to cause negative impacts, prevent attempts of introduction and to manage risky aquatic plants in South America.     

Land use modifies Odonata diversity in streams of the Brazilian Cerrado

The presence of riparian vegetation provides microclimatic regulation of stream conditions [e.g. luminosity (lux), air temperature (°C) and relative humidity (%)], which varies naturally throughout the day. These variables explain the diurnal behaviour patterns of ectotherms such as Odonata in natural areas. However, human land uses (e.g. pastures) modify the abiotic conditions of riparian environments, favouring the presence of disturbance-tolerant species. In this context, we assess relationships between riparian land use (control streams-natural areas and pasture), abiotic conditions habitat integrity index (in control and pastures streams), (air temperature, luminosity and humidity in control streams), and Odonata diversity (between pasture and control streams and throughout the time of day) in Brazilian savannah (Cerrado) streams. First, the control streams had higher habitat integrity index than pasture. Higher abundance and difference in composition of Odonata species were observed in streams surrounded by pasture relative to natural areas. The conversion of natural areas to pasture near streams was also accompanied by an increase in overall body size of Odonata species. Odonata species richness and abundance in natural areas varied throughout the day, but peaked around 12:00 h, coinciding with changes in air temperature and luminosity. Our study highlights that changes in the physical characteristics of streams through conversion of natural habitats to pasture will change environmental conditions and act as a filter on the distribution and persistence of Odonata species in Cerrado streams.     

Redefining the damselfly families: a comprehensive molecular phylogeny of Zygoptera (Odonata)

An extensive molecular phylogenetic reconstruction of the suborder Zygoptera of the Odonata is presented, based on mitochondrial (16S, COI) and nuclear (28S) data of 59% of the 310 genera recognized and all (suspected) families except the monotypic Hemiphlebiidae. A partial reclassification is proposed, incorporating morphological characters. Many traditional families are recovered as monophyletic, but reorganization of the superfamily Coenagrionoidea into three families is proposed: Isostictidae, Platycnemididae and Coenagrionidae. Archboldargia Lieftinck, Hylaeargia Lieftinck, Palaiargia Förster, Papuargia Lieftinck and Onychargia Selys are transferred from Coenagrionidae to Platycnemididae, and Leptocnemis Selys, Oreocnemis Pinhey and Thaumatagrion Lieftinck from Platycnemididae to Coenagrionidae. Each geographically well‐defined clade of Platycnemididae is recognized as a subfamily, and thus Disparoneurinae (i.e. Old World ‘Protoneuridae’) is incorporated, Calicnemiinae is restricted, and Allocnemidinae (type genus: Allocnemis Selys) subfam.n ., Idiocnemidinae (type genus: Idiocnemis Selys) subfam.n . and Onychargiinae (type genus: Onychargia Selys) subfam.n . and Coperini trib.n . (type genus: Copera Kirby) are described. Half of Coenagrionidae belongs to a well‐supported clade incorporating Coenagrion Kirby and the potential subfamilies Agriocnemidinae, Ischnurinae and Pseudagrioninae. The remainder is less well defined, but includes the Pseudostigmatidae and New World Protoneuridae that, with Argiinae and Teinobasinae, may prove valid subfamilies with further evidence. Ninety‐two per cent of the genera formerly included in the polyphyletic Amphipterygidae and Megapodagrionidae were studied. Pentaphlebiidae, Rimanellidae and Devadattidae fam.n . (type genus: Devadatta Kirby) are separated from Amphipterygidae, and Argiolestidae, Heteragrionidae, Hypolestidae, Philogeniidae, Philosinidae and Thaumatoneuridae from Megapodagrionidae. Eight further groups formerly placed in the latter are identified, but are retained as incertae sedis; the validity of Lestoideidae, Philogangidae and Pseudolestidae is confirmed. For some families (e.g. Calopterygidae, Chlorocyphidae) a further subdivision is possible; Protostictinae subfam.n . (type genus: Protosticta Selys) is introduced in Platystictidae. Numerous new combinations are proposed in the Supporting Information. Many long‐established families lack strong morphological apomorphies. In particular, venation is incongruent with molecular results, stressing the need to review fossil Odonata taxonomy: once defined by the reduction of the anal vein, Protoneuridae dissolves completely into six clades from five families.     

Determinants of alpha and beta vascular plant diversity in Mediterranean island systems: the Ionian islands,Greece

The Ionian archipelago is the second largest Greek archipelago after the Aegean, but the factors driving plant species diversity in the Ionian islands are still barely known. We used stepwise multiple regressions to investigate the factors affecting plant species diversity in 17 Ionian islands. Generalized dissimilarity modelling was applied to examine variation in the magnitude and rate of species turnover along environmental gradients, as well as to assess the relative importance of geographical and climatic factors in explaining species turnover. The values of the residuals from the ISAR log₁₀‐transfomed models of native and endemic taxa were used as a measure of island floristic diversity. Area was confirmed to be the most powerful single explanatory predictor of all diversity metrics. Mean annual precipitation and temperature, as well as shortest distance to the nearest island are also significant predictors of vascular plant diversity. The island of Kalamos constitutes an important plant diversity hotspot in the Ionian archipelago. The recent formation of the islands, the close proximity to the mainland source and the relatively low dispersal filtering of the Ionian archipelago has resulted in islands with a flora principally comprising common species and a low proportion of endemics. Small islands keep a key role in conservation of plant priority sites.     

Effects of land use on taxonomic and functional diversity: a cross-taxon analysis in a Mediterranean landscape

Land-use change is the major driver of biodiversity loss. However, taxonomic diversity (TD) and functional diversity (FD) might respond differently to land-use change, and this response might also vary depending on the biotic group being analysed. In this study, we compare the TD and FD of four biotic groups (ants, birds, herbaceous, woody vegetation) among four land-use types that represent a gradient of land-use intensity in a Mediterranean landscape (Mediterranean shrublands, dehesas, mixed-pine forests, olive groves). Analyses were performed separately at two different spatial scales: the sampling unit scale and the site scale. Land-use intensity effects on TD and FD were quite different and highly varied among the four biotic groups, with no single clear pattern emerging that could be considered general for all organisms. Additive partitioning of species diversity revealed clear contrasting patterns between TD and FD in the percentage of variability observed at each spatial scale. While most variability in TD was found at the larger scales, irregardless of organism group and land-use type, most variability in FD was found at the smallest scale, indicating that species turnover among communities is much greater than functional trait turnover. Finally, we found that TD and FD did not vary consistently, but rather followed different trajectories that largely depended on the biotic group and the intensity of land-use transformation. Our results highlight that the relationship of land use with TD and FD is highly complex and context-dependent.