How many species of host-specific insects feed on a species of tropical tree?

The assumptions on the host specificity of beetles that led Terry Erwin to suggest that there may be over 30 million arthropod species were tested for 10 species of trees and their insect associates at a rainforest site in Papua New Guinea. The data included 391 species and 4696 individuals of herbivorous beetles collected during a one year period using hand collecting, beating, branch clipping, intercept flight traps and pyrethrum knockdown. Insect host specificity was assessed by feeding trials in captivity. The data suggest that between 23 and 37 monophagous leaf-feeding species are most likely to be present in this system, whereas Erwin's method yields an estimate of 138 monophagous species. The major factors responsible for the discrepancy between our observations and Erwin's assumptions appears to be (a) the importance of transient species; (b) the insect fauna that is shared among tree species; (c) some generalist wood-eating species may inflate the apparent species richness of leaf-feeding beetles; and (d) the proportion of specialist species varies significantly among tree species. We conclude that studies reporting the proportion of specialist insect herbivores associated with particular tropical tree species will yield only a portion of the information needed to estimate global arthropod species richness, but may be useful for elucidating certain aspects of food-web ecology in tropical rain forests.     

How many species of Isothecium (Lembophyllaceae,Bryophyta) are there in Macaronesia? A survey using integrative taxonomy

Species boundaries are sometimes difficult to assess, especially when molecular data do not neatly match morphologically defined units. This study investigates the moss genus Isothecium, with special emphasis on Macaronesian populations. Morphological studies are combined with the analysis of three rapidly evolving markers: nuclear internal transcribed spacer and plastid trnG and trnL‐trnF. The results of the morphological studies suggest that Isothecium is represented by five species in Macaronesia, including a new endemic species from Madeira, I sothecium montanum sp. nov. , which is described here. The molecular results are less conclusive than the morphology results in delimiting species of this genus, even when indels are included as informative. Once possible methodological shortcomings have been discarded, the results can be interpreted as having been caused by incomplete lineage sorting, probably as a consequence of recent speciation. The molecular results also suggest that the origin of the Macaronesian endemics may be explained by at least two independent colonization events. Finally, the delimitation of a new endemic species of Isothecium in Macaronesia indicates that current knowledge on the taxonomy of spore‐producing plants may be far from complete in this hotspot of biodiversity. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 00 , 000–000.     

How many species of cichlid fishes are there in African lakes?

The endemic cichlid fishes of Lakes Malawi, Tanganyika and Victoria are textbook examples of explosive speciation and adaptive radiation, and their study promises to yield important insights into these processes. Accurate estimates of species richness of lineages in these lakes, and elsewhere, will be a necessary prerequisite for a thorough comparative analysis of the intrinsic and extrinsic factors influencing rates of diversification. This review presents recent findings on the discoveries of new species and species flocks and critically appraises the relevant evidence on species richness from recent studies of polymorphism and assortative mating, generally using behavioural and molecular methods. Within the haplochromines, the most species-rich lineage, there are few reported cases of postzygotic isolation, and these are generally among allopatric taxa that are likely to have diverged a relatively long time in the past. However, many taxa, including many which occur sympatrically and do not interbreed in nature, produce viable, fertile hybrids. Prezygotic barriers are more important, and persist in laboratory conditions in which environmental factors have been controlled, indicating the primary importance of direct mate preferences. Studies to date indicate that estimates of alpha (within-site) diversity appear to be robust. Although within-species colour polymorphisms are common, these have been taken into account in previous estimates of species richness. However, overall estimates of species richness in Lakes Malawi and Victoria are heavily dependent on the assignation of species status to allopatric populations differing in male colour. Appropriate methods for testing the specific status of allopatric cichlid taxa are reviewed and preliminary results presented.     

How many damaged corals in Red Sea reef systems? A quantitative survey

Quantitative coral damage assessment by means of line transects was performed in several northern Red Sea coral reef sites in Israel (Eilat) and Egypt (Hurghada area). Reefs with high and low visitor frequency were compared. For both reef systems, breakage was found to be the most common damage category, being significantly higher on highly frequented reefs. Also, all observed damage (breakage, tissue loss, algal overgrowth) was most frequent within the first ten meters depth. A significant difference in the amount of corals overgrown by algae was found on the reefs near Hurghada as compared to all other reefs. Algal overgrowth was correlated with the occurrence of tissue loss and breakage, being considered as a consequence of pollution or the former damage types. In all cases of damage, Acropora was the most frequently affected genus, while Millepora dichotoma was the most affected species.     

How many species of Hipposideros have occurred on Madagascar since the Late Pleistocene?

Populations of the Malagasy Hipposideros commersoni (family Hipposideridae) are threatened by deforestation and hunting. Maximum likelihood and Bayesian analysis of 148 cytochrome b sequences found this species to be paraphyletic and composed of three well‐supported monophyletic clades. Clades B and C form a monophyletic lineage that can be referred to H. commersoni; these two clades are separated by 6% sequence variation. Clade A represents a distinct evolutionary lineage separate (9–11% average sequence divergence) from H. commersoni (clades B and C) and is named herein as a new species, H ipposideros cryptovalorona sp. nov. In the phylogeny presented herein, this species is strongly associated with the outgroup taxa Hipposideros gigas and Hipposideros vittatus, both restricted to Africa. External, cranial and dental measurements taken from the same individuals used in the molecular study indicate no clear distinction in morphology amongst these three clades; this includes noseleaf structure and craniodental characteristics. Principal component analyses showed limited separation of the three clades. Comparison to a Quaternary fossil species from north‐west Madagascar, Hipposideros besaoka, found little morphological overlap between any of the three clades and this extinct species. Hence, at least three species of Hipposideros have occurred on Madagascar since the Late Pleistocene, two extant (H. commersoni s.s. and H. cryptovalorona sp. nov.) and one extinct (H. besaoka). © 2015 The Linnean Society of London     

How many marmoset (Primates: Cebidae: Callitrichinae) genera are there? A phylogenetic analysis based on multiple morphological systems

The marmosets, tribe Callitrichini, are the most speciose clade in the subfamily Callitrichinae, containing 21 species. However, there is no consensus among molecular and morphological systematists as to how many genera should be recognized for the group. To test the morphological support for the alternative generic classifications, this study presents a comprehensive phylogenetic analysis. It is the first such analysis to include all 21 species and employ continuous and discrete osteological, pelage and tegument, karyological and vocal characters. This dataset was combined with nucleotide sequences from two mitochondrial and four nuclear regions. Separate analyses showed that, among morphological datasets, osteological characters were best at solving relationships at more inclusive levels, whilst pelage characters were most informative at the interspecific level. This suggests the presence of different transformation rates for the two character sets. When a single most parsimonious tree was obtained using the 83‐character matrix, three main clades were identified, supporting the division of the marmosets into three genera: Callithrix, Cebuella and Mico. The total evidence analysis that included an additional 3481 molecular characters corroborated most of the morphology‐based clades and also supported a three‐genus classification of the marmosets. This is the first morphological study to support an Amazonian marmoset clade (Cebuella + Mico), which is also strongly supported in exclusively molecular phylogenies, and to synonimize Callibella under Mico.     

How many species are in the genus Batrachuperus? A phylogeographical analysis of the stream salamanders (family Hynobiidae) from southwestern China

Phylogeographical analysis of DNA sequence data has been routinely used to test species boundaries using the monophyly criterion; however, a complementary criterion, reproductive isolation, is often ignored. We used a combination of phylogenetic and population genetic approaches to determine species boundaries among stream salamanders in the genus Batrachuperus . First, cytochrome b sequence data from 174 Batrachuperus individuals, sampled from 78 populations, were used to reconstruct historical relationships within the genus. Second, allozyme data for 14 presumptive nuclear loci, from 463 individuals sampled from 60 populations, were collected and analysed to assess population similarity or disparity, as well as potential reproductive isolation. The DNA sequence data grouped all populations into seven major monophyletic groups, and the allozyme data provided evidence for reproductive isolation among four of the seven groups, thereby supporting the species status of these groups. The allozyme data suggested that two of the other groups share the same gene pool, and therefore belong to a single species. Finally, the allozyme data revealed two reproductively isolated units within the seventh group, which we suggest represents a case of 'budding speciation' based on the DNA gene tree. In total, seven species of the genus Batrachuperus were defined, two of which were previously unknown. The phylogeographical analysis also revealed that vicariance events might have dominated the evolutionary history of this group, but the speciation events might precede the formation of the existing mountain topology. This study demonstrates the importance of including frequency data from multiple nuclear gene loci in determining species boundaries.     

Nitrogen limitation on land and in the sea: How can it occur?

The widespread occurrence of nitrogen limitation to net primary production in terrestrial and marine ecosystems is something of a puzzle; it would seem that nitrogen fixers should have a substantial competitive advantage wherever nitrogen is limiting, and that their activity in turn should reverse limitation. Nevertheless, there is substantial evidence that nitrogen limits net primary production much of the time in most terrestrial biomes and many marine ecosystems. We examine both how the biogeochemistry of the nitrogen cycle could cause limitation to develop, and how nitrogen limitation could persist as a consequence of processes that prevent or reduce nitrogen fixation. Biogeochemical mechansism that favor nitrogen limitation include:

the substantial mobility of nitrogen across ecosystem boundaries, which favors nitogen limitation in the “source” ecosystem — especially where denitrification is important in sediments and soils, or in terrestrial ecosystems where fire is frequent;

differences in the biochemistry of nitrogen as opposed to phosphorus (with detrital N mostly carbon-bonded and detrital P mostly ester-bonded), which favor the development of nitrogen limitation where decomposition is slow, and allow the development of a positive feedback from nitrogen limitation to producers, to reduced decomposition of their detritus, and on to reduced nitrogen availability; and

other more specialized, but perhaps no less important, processes.

A number of mechanisms could keep nitrogen fixation from reversing nitrogen limitation. These include:

energetic constraints on the colonization or activity of nitrogen fixers;

limitation of nitrogen fixers or fixation by another nutrient (phosphorus, molybdenum, or iron) — which would then represent the ultimate factor limiting net primary production;

other physical and ecological mechanisms.

The possible importance of these and other processes is discussed for a wide range of terrestrial, freshwater, and marine ecosystems.     

How many species of Diacyclops? New taxonomic characters and species richness in a freshwater cyclopid genus (Copepoda,Cyclopoida)

The genus Diacyclops Kiefer, 1927 emend. Morton (1985) includes more than 100 species, widely distributed in all kinds of freshwater environments, and is the richest genus in the family Cyclopidae. Traditionally, Diacyclops species were defined according to differences in a few morphological characters; some characters (number of antennulary segments, segmentation pattern of swimming legs) are useful only in the separation of species groups, others (length of caudal rami and caudal setae) are highly variable even within the same population. During the study of the D. languidoides-group, minute morphological characters were used to differentiate between species (spinulation pattern and setation of antennary basis, setation and aesthetasc shape of male antennule, setation of mandibulary palp and maxilliped, shape of leg 4 basis) which allow to identify several valid species up to now concealed under the name `Diacyclops languidoides' (Lilljeborg, 1901). The coexistence of up to six congeneric species in the same sampling area: (a) supports the validity of the proposed taxonomic characters, (b) demonstrates that species richness may be highly underestimated in freshwater cyclopoid assemblages in absence of good taxonomic practice; and (c) requires an ecological explanation of species coexistence. The role of morphologically based taxonomy in order to solve general problems of distributional ecology and theoretical biology is explored.     

How many species of Paradoxurus civets are there? New insights from India and Sri Lanka

Using molecular data and morphological features, we investigated the species limits and genetic diversity among populations of the Asian palm civets of the genus Paradoxurus. Our main objectives were to determine the number of species within Paradoxurus hermaphroditus and to test the validity of the newly proposed species within Paradoxurus zeylonensis. Fragments of two mitochondrial (Cytochrome b, Control Region) and one nuclear (intron 7 of the beta fibrinogen) markers were sequenced from 128 individuals of P. hermaphroditus, P. zeylonensis and Paradoxurus jerdoni. DNA sequences were analysed using phylogenetic and haplotype network methods. Our analyses confirmed that P. hermaphroditus comprises three major clades, which should be recognized as separate species: P. hermaphroditus (Indian and Indochinese regions), Paradoxurus musangus (mainland Southeast Asia, Sumatra, Java and other small Indonesian islands) and Paradoxurus philippinensis (Mentawai Islands, Borneo and the Philippines). Furthermore, we have proposed that there are two subspecies within both P. musangus and P. philippinensis, and there might be at least two or three subspecies within P. hermaphroditus. We found a very low genetic diversity and no geographical structure within P. zeylonensis and did not find any support for splitting P. zeylonensis into several species nor subspecies. Finally, we confirmed that P. jerdoni and P. zeylonensis are sister species.     

How do insect nuclear and mitochondrial gene substitution patterns differ? Insights from Bayesian analyses of combined datasets

We analyzed 12 combined mitochondrial and nuclear gene datasets in seven orders of insects using both equal weights parsimony (to evaluate phylogenetic utility) and Bayesian methods (to investigate substitution patterns). For the Bayesian analyses we used relatively complex models (e.g., general time reversible models with rate variation) that allowed us to quantitatively compare relative rates among genes and codon positions, patterns of rate variation among genes, and substitution patterns within genes. Our analyses indicate that nuclear and mitochondrial genes differ in a number of important ways, some of which are correlated with phylogenetic utility. First and most obviously, nuclear genes generally evolve more slowly than mitochondrial genes (except in one case), making them better markers for deep divergences. Second, nuclear genes showed universally high values of CI and (generally) contribute more to overall tree resolution than mitochondrial genes (as measured by partitioned Bremer support). Third, nuclear genes show more homogeneous patterns of among-site rate variation (higher values of alpha than mitochondrial genes). Finally, nuclear genes show more symmetrical transformation rate matrices than mitochondrial genes. The combination of low values of alpha and highly asymmetrical transformation rate matrices may explain the overall poor performance of mitochondrial genes when compared to nuclear genes in the same analysis. Our analyses indicate that some parameters are highly correlated. For example, A/T bias was positively and significantly associated with relative rate and CI was positively and significantly associated with alpha (the shape of the gamma distribution). These results provide important insights into the substitution patterns that might characterized high quality genes for phylogenetic analysis: high values of alpha, unbiased base composition, and symmetrical transformation rate matrices. We argue that insect molecular systematists should increasingly focus on nuclear rather than mitochondrial gene datasets because nuclear genes do not suffer from the same substitutional biases that characterize mitochondrial genes.     

Unraveling cryptic invasion of a freshwater snail in Chile based on molecular and morphological data

Cryptic species may cause biological invasions to be overlooked leading to underestimation of the potential impacts of invaders on the new ecosystems. Identification of freshwater snails is challenging because of the scarcity of discriminative morphological characters and the limited taxonomic knowledge of some taxa. Here, molecular and morphological analyses were performed to investigate the identity of viable populations of the genus Physa in aquatic ecosystems of different basins in northern and central Chile, including habitats where the native species Physa chilensis and Physa nodulosa have been traditionally recognized. Molecular analyses based on mitochondrial DNA sequences from the small subunit 16S rDNA and cytochrome c oxidase subunit 1 identified all specimens sequenced as belonging to the globally invasive species Physa acuta. Microscopic examination of the radula and morphological observations of the reproductive system were congruent with these findings. Highly divergent haplotypes found in El Salto suggest multiple introductions of different lineages of the invader in this locality. It is clear that for future management planning a more reliable assessment of the status of P. chilensis and P. nodulosa is required.     

Phylogenetic analyses of some genera in Oedipodidae （Orthoptera： Acridoidea） based on 16S mitochondrial partial gene sequences

Basedonthe 16S mitochondrial partial gene sequences of 29 genera, containing 26 from Oedipodidae and one each from Tanaoceridae, Pyrgomorphidae and Tetrigidae （as outgroups）, the homologus sequences were compared and phylogenetic analyses were performed. A phylogenetic tree was inferred by neighbor-joining （N J）. The results of sequences compared show that： （i） in a total of 574 bp of Oedipodidae, the number of substituted nucleotides was 265 bp and the average percentages ofT, C, A and G were 38.3%, 11.4%, 31.8% and 18.5%, respectively, and the content of A＋T （70.1%） was distinctly richer than that of C＋G （29.9%）; and （ii） the average nucleotide divergence of 16S rDNA sequences among genera of Oedipodidae were 9.0%, among families of Acridoidea were 17.0%, and between superfamilies （Tetrigoidea and Acridoidea） were 23.9%, respectively. The phylogenetic tree indicated： （i） the Oedipodidae was a monophyletic group, which suggested that the taxonomic status of this family was confirmed; （ii） the genus Heteropternis separated from the other Oedipodids first and had another unique sound-producing structure in morphology, which is the type-genus of subfamily Heteropterninae; and （iii） the relative intergeneric relationship within the same continent was closer than that of different continents, and between the Eurasian genera and the African genera, was closer than that between Eurasians and Americans.     

A morphological and molecular perspective of Trichoderma viride: is it one or two species?

Trichoderma (Ascomycetes, Hypocreales) strains that have warted conidia are traditionally identified as T. viride, the type species of Trichoderma. However, two morphologically distinct types of conidial warts (I and II) have been found. Because each type corresponds to a unique mitochondrial DNA pattern, it has been questioned whether T. viride comprises more than one species. Combined molecular data (sequences of the internal transcribed spacer 1 [ITS-1] and ITS-2 regions and of part of the 28S rRNA gene along with results of restriction fragment length polymorphism analysis of the endochitinase gene and PCR fingerprinting), morphology, physiology, and colony characteristics distinguish type I and type II as different species. Type I corresponds to "true" T. viride, the anamorph of Hypocrea rufa. Type II represents a new species, T. asperellum, which is, in terms of molecular characteristics, close to the neotype of T. hamatum.     

The importance of lake morphometry and catchment characteristics in limnology – ranking based on statistical analyses

This work introduces an interpretational key to quantify and understand how much of variations among lakes in fundamental ecosystem characteristics that may be related to lake morphometry, catchment area features, measurement uncertainties and other factors (mostly climate). The size and form of lakes regulate many general transport processes, such as sedimentation, internal loading and outflow, which in turn regulate many abiotic state variables, such as concentrations of phosphorus, colour, water chemical variables and water clarity, which regulate primary production, which regulate secondary production. This paper discusses relationships between key abiotic state variables, lake morphometry and catchment area characteristics using empirical/statistical analyses based on data from 95 lakes. It has been shown that of the studied variables Secchi depth depends most on morphometry (34%); 31% of the variations among the lakes in Secchi depth may be related to catchment area characteristics, 1% to uncertainties in empirical data and 34% to other (climatological) factors. The corresponding figures for alkalinity, which depends least on lake morphometry are, 0% related to morphometry, 34% to catchment conditions, 1% to empirical uncertainty and 58% to other causes. For all other studied variables, i.e., conductivity, hardness (CaMg), calcium, iron, colour, pH and phosphorus the corresponding figures vary between these values. The interpretational key helps to explain the mechanistic reasons for these statistical/empirical results.     

How many heteropteran species can live on alien goldenrods Solidago canadensis and S. gigantea in Europe?

During the vegetation periods of 2001–2003 Heteroptera associated with the invasive alien tall goldenrods Solidago canadensis and S. gigantea were studied in seven model habitats in the north-eastern part of the Czech Republic. Heteropterans associated with adjacent growths were also studied in 2002–2003. A set of 3,042 specimens of 127 samples was analyzed with the aim of estimating average species richness, abundance and trophic structure of the heteropteran assemblages of the studied plant stand. On alien Solidago, 68 heteropteran species were recorded and 71 species were collected in the stands adjacent to the tall goldenrods with 48 shared species. Despite the nearly indentical species richness and similar abundances in Solidago and adjacent stands, there are differences in the trophic structure. The majority of the shared species and species found on Solidago canadensis only are polyphagous contrary to the majority of stenophagous species found on Solidago free stands only. Only a small proportion of heteropteran species that were recorded on alien Solidago stands are specialized to Asteraceae and their abundance was mostly low. Only the lygaeid Nysius senecionis, an Asteraceae specialist, occured in masses on S. canadensis in sunny and warm habitats. Similarly, predatory Orius minutus and O. niger reached high abundance values in Solidago stands compared to adjacent stands.     

Are adaptive loci transferable across genomes of related species? Outlier and environmental association analyses in Alpine Brassicaceae species

Local adaptation is one possible response of organisms to survive in a changing environment. However, the genetic basis of adaptation is not well understood, especially in nonmodel species. To infer recurrent patterns of local adaptation, we investigated whether the same putative adaptive loci reoccur in related species. We performed genome scans using amplified fragment length polymorphism (AFLP) markers on populations of five Alpine Brassicaceae species sampled across a wide range of environmental conditions. To identify markers potentially under directional selection, we performed outlier and environmental association analyses using a set of topo‐climatic variables available as GIS layers. Several AFLP loci showed signatures of adaptation, of which one, found in Cardamine resedifolia (Cre_P1_212.5), was associated with precipitation. We sequence‐characterized this candidate locus and genotyped single nucleotide polymorphisms (SNPs) found within this locus for all species. Testing for environmental associations of SNPs revealed the same association of this locus in Arabis alpina but not in other study species. Cumulative statistical evidence indicates that locus Cre_P1_212.5 is environmentally relevant or is linked to a gene under selection in our study range. Furthermore, the locus shows an association to the same potentially selective factor in at least one other related species. These findings help to identify trends in plant adaptation in Alpine ecosystems in response to particular environmental parameters.     

How are tree species distributed in climatic space? A simple and general pattern

Aim Although many factors undoubtedly affect species geographic distributions, can a single, simple model nonetheless capture most of the spatial variation in the probability of presence/absence in a large set of species? For 482 North American tree species that occur east of the Rocky Mountains, we investigated the shape(s) of the relationship between the probability of occupancy of a given location and macroclimate, and its consistency among species and regions. Location North America. Methods Using Little's tree range maps, we tested four hypothetical shapes of response relating occupancy to climate: (1) high occupancy of all suitable climates; (2) threshold response (i.e. unsuitable climates exclude species, but within the thresholds, species presence is independent of climate); (3) occupancy is a bivariate normal function of annual temperature and precipitation; and (4) asymmetric limitation (i.e. abiotic factors set abrupt range limits in stressful climates only). Finally, we compared observed climatic niches with the occupancy of similar climates on off‐shore islands as well as west of the Rockies. Results (a) Species' distributions in climatic space do not have strong thresholds, nor are they systematically skewed towards less stressful climates. (b) Occupancy can generally be described by a bivariate normal function of temperature and precipitation, with little or no interaction between the two variables. This model, averaged over all species, accounts for 82% of the spatial variation in the probability of occupancy of a given area. (c) Occupied geographic ranges are typically ringed by unoccupied, but climatically suitable areas. (d) Observed climatic niche positions are largely conserved between regions. Main conclusions We conclude that, despite the complexities of species histories and biologies, to a first approximation most of the variation in their geographic distributions relates to climate, in similar ways for nearly all species.