Are all Mexican odonate species documented? An assessment of species richness

With the aim of protecting Mexican diversity, one current governmental task is to complete national biological inventories. In the case of odonate insects, several researchers have hypothesized that species richness is complete (205 dragonflies and 151 damselflies), but there has not been any formal exercise to test this. Thus, we have investigated whether odonate species richness (for Mexican endemics, dragonflies (suborder Anisoptera), damselflies (suborder Zygoptera) and total species) is complete using sample-based and coverage-based rarefaction curves. Along with this, we also showed how good distribution data are in the country. The rarefaction curves have indicated 100% completeness for all groups suggesting that the inventory is complete. However, species' distribution data is highly patchy regarding areas either well (e.g. central Mexico) or badly (e.g. coast of Guerrero and Oaxaca) collected. We encourage researchers to continue odonate sampling in order to support at least three conservation actions: (i) conservation assessment of endangered species; (ii) knowledge of range shifts given rising global temperatures; and (iii) increase public interest and awareness in protected, touristic areas.     

Diatom teratologies as biomarkers of contamination: Are all deformities ecologically meaningful?

Contaminant-related stress on aquatic biota is difficult to assess when lethal impacts are not observed. Diatoms, by displaying deformities (teratologies) in their valves, have the potential to reflect sub-lethal responses to environmental stressors such as metals and organic compounds. For this reason, there is great interest in using diatom morphological aberrations in biomonitoring. However, the detection and mostly the quantification of teratologies is still a challenge; not all studies have succeeded in showing a relationship between the proportion of abnormal valves and contamination level along a gradient of exposure. This limitation in part reflects the loss of ecological information from diatom teratologies during analyses when all deformities are considered. The type of deformity, the severity of aberration, species proneness to deformity formation, and propagation of deformities throughout the population are key components and constraints in quantifying teratologies. Before a metric based on diatom deformities can be used as an indicator of contamination, it is important to better understand the “ecological signal” provided by this biomarker. Using the overall abundance of teratologies has proved to be an excellent tool for identifying contaminated and non-contaminated environments (presence/absence), but refining this biomonitoring approach may bring additional insights allowing for a better assessment of contamination level along a gradient. The dilemma: are all teratologies significant, equal and/or meaningful in assessing changing levels of contamination? This viewpoint article examines numerous interrogatives relative to the use of diatom teratologies in water quality monitoring, provides selected examples of differential responses to contamination, and proposes solutions that may refine our understanding and quantification of the stress. This paper highlights the logistical problems associated with accurately evaluating and interpreting teratologies and stimulates more discussion and research on the subject to enhance the sensitivity of this metric in bioassessments.     

Are vocal characteristics related to leadership patterns in mixed‐species bird flocks?

What structures the organization of mixed‐species bird flocks, so that some ‘nuclear’ species lead the flocks, and others follow? Previous research has shown that species actively listen to each other, and that leaders are gregarious; such gregarious species tend to make contact calls and hence may be vocally conspicuous. Here we investigated whether vocal characteristics are associated with leadership, using a global dataset of mixed‐species flock studies and recordings from sound archives. We first asked whether leaders are different from following or occasional species in flocks in the proportion of the recordings that contain calls (n = 58 flock studies, 145 species), and especially alarm calls (n = 111 species). We found that leaders tended to have a higher proportion of their vocalizations that were classified as calls than occasional species, and both leaders and following species had a significantly higher proportion of their calls rated as alarms compared to occasional species. Next, we investigated the acoustic characteristics of flock participants’ calls, hypothesizing that leaders would make more calls, and have less silence on the recordings. We also hypothesized that leaders’ calls would be simple acoustically, as contact calls tend to be, and thus similar to each other, as well as being detectable, in being low frequency and with high frequence bandwidth. The analysis (n = 45 species, 169 recordings) found that only one of these predictions was supported: leading species were less often silent than following or occasional species. Unexpectedly, leaders’ calls were less similar to each other than occasional species. The greater amount of information available and the greater variety of that information support the hypothesis that leadership in flocks is related to vocal communication. We highlight the use of sound archives to ask questions about behavioral and community ecology, while acknowledging some limitations of such studies.     

Is geographic variation within species related to macroevolutionary patterns between species?

The relationship between microevolution and macroevolution is a central topic in evolutionary biology. An aspect of this relationship that remains very poorly studied in modern evolutionary biology is the relationship between within‐species geographic variation and among‐species patterns of trait variation. Here, we tested the relationship between climate and morphology among and within species in the salamander genus Plethodon. We focus on a discrete colour polymorphism (presence and absence of a red dorsal stripe) that appears to be related to climatic distributions in a common, wide‐ranging species (Plethodon cinereus). We find that this trait has been variable among (and possibly within) species for >40 million years. Furthermore, we find a strong relationship among species between climatic variation and within‐species morph frequencies. These between‐species patterns are similar (but not identical) to those in the broadly distributed Plethodon cinereus. Surprisingly, there are no significant climate–morphology relationships within most other polymorphic species, despite the strong between‐species patterns. Overall, our study provides an initial exploration of how within‐species geographic variation and large‐scale macroevolutionary patterns of trait variation may be related.     

How to describe species richness patterns for bryophyte conservation?

A large amount of data for inconspicuous taxa is stored in natural history collections; however, this information is often neglected for biodiversity patterns studies. Here, we evaluate the performance of direct interpolation of museum collections data, equivalent to the traditional approach used in bryophyte conservation planning, and stacked species distribution models (S‐SDMs) to produce reliable reconstructions of species richness patterns, given that differences between these methods have been insufficiently evaluated for inconspicuous taxa. Our objective was to contrast if species distribution models produce better inferences of diversity richness than simply selecting areas with the higher species numbers. As model species, we selected Iberian species of the genus Grimmia (Bryophyta), and we used four well‐collected areas to compare and validate the following models: 1) four Maxent richness models, each generated without the data from one of the four areas, and a reference model created using all of the data and 2) four richness models obtained through direct spatial interpolation, each generated without the data from one area, and a reference model created with all of the data. The correlations between the partial and reference Maxent models were higher in all cases (0.45 to 0.99), whereas the correlations between the spatial interpolation models were negative and weak (−0.3 to −0.06). Our results demonstrate for the first time that S‐SDMs offer a useful tool for identifying detailed richness patterns for inconspicuous taxa such as bryophytes and improving incomplete distributions by assessing the potential richness of under‐surveyed areas, filling major gaps in the available data. In addition, the proposed strategy would enhance the value of the vast number of specimens housed in biological collections.     

Is stress really all that important?

There is growing concern in many parts of the world that fertility of dairy cattle is reducing as milk yields increase. Stress could be one important cause. As an example, fertility is lower after caesarian operations. Delayed uterine involution after dystocia is associated with abnormal ovarian cyclicity and prolonged intervals to the next pregnancy. There is a greater reduction in fertility as the clinical conditions of lameness, milk fever or mastitis worsen. Changes in social groupings greatly increase the number of inseminations required per pregnancy. Transport reduces the number of CL after superovulation, and can interfere with pregnancy rates after estrous synchronization. Embryos collected from heat-stressed donors are less viable and have delayed trophoblast function. Human-animal interactions influence stress-responses in cattle--the behavior of stockman and embryo transfer personnel could affect success. Putting aside financial aspects, exposure of an animal to avoidable stress compromises welfare, whether application of biotechnology is involved or not. The fact that stressors can be deleterious to such an important function as reproduction, emphasizes that stress is very important and should be minimized whenever possible.     

Are all species of Pseudorhabdosynochus strictly host specific? — A molecular study

Species of the diplectanid monogenean genus Pseudorhabdosynochus are strictly host-specific (specialist), with the exception of P. cyanopodus, which was reported in New Caledonia, South Pacific, from two host species, Epinephelus cyanopodus and E. chlorostigma. We sequenced the COI gene of both host fish species and of their monogeneans. Morphological identification and pairwise distances showed that the two fish species were distinct (difference 6.1-6.6%), but that their monogeneans were not (difference 0-1.5%). A morphological study of sclerotised parts showed that specimens of P. cyanopodus are similar in both fish. Most species of groupers and their associated Pseudorhabdosynochus species are from warm surface waters, but the two groupers E. cyanopodus and E. chlorostigma are usually caught in deep-sea on the outer slope of the coral reef. This suggests that acquisition of a less strict host specificity is an adaptation of P. cyanopodus to deep-sea hosts.     

Do phytogeographic patterns reveal biomes or biotic regions?

We present the largest comparative biogeographical analysis that has complete coverage of Australia's geography (20 phytogeographical subregions), using the most complete published molecular phylogenies to date of large Australian plant clades (Acacia, Banksia and the eucalypts). Two distinct sets of areas within the Australian flora were recovered, using distributional data from the Australasian Virtual Herbarium (AVH) and the Atlas of Living Australia (ALA): younger Temperate, Eremaean and Monsoonal biomes, and older southwest + west, southeast and northern historical biogeographical regions. The analyses showed that by partitioning the data into two sets, using either a Majority or a Frequency method to select taxon distributions, two equally valid results were found. The dataset that used a Frequency method discovered general area cladograms that resolved patterns of the Australian biomes, whereas if widespread taxa (Majority method, with >50% of occurrences outside a single subregion) were removed the analysis then recovered historical biogeographical regions. The study highlights the need for caution when processing taxon distributions prior to analysis as, in the case of the history of Australian phytogeography, the validity of both biomes and historical areas have been called into question.     

Are aquatic insect species sensitive to banana plant cultivation?

Ephemeroptera, Plecoptera, Trichoptera and Coleoptera (EPTC) insect fauna were collected in ten streams located in the southeastern state of São Paulo (five located in areas with banana cultivation and five located in preserved areas). Specimens were collected during October and November 2005, using a Surber sampler and network D (0.25 mm mesh size) in areas of rapids and backwaters. The organisms collected were identified to genus level, except for some small or damaged specimens that remained at the family level. In total, 1812 individuals of EPTC were identified, in which 1105 organisms were from streams in areas of banana cultivation and 706 from streams in preserved areas. Heterelmis (Elmidae) was dominant in both sets of streams. In preserved streams, Hexacylloepus (Elmidae), Tupiperla and Paragrypopteryx (Gripopterygidae) and Nectopsyche (Leptoceridae) also had high participation. Leptonema (Hydropsychidae) and Xenelmis (Elmidae) were dominant in streams located in areas of banana cultivation. The analyses of indicator species point out to five taxa on preserved streams and two taxa in the banana streams. The forested streams had higher richness and diversity of EPTC than banana plantation streams. Correspondence analysis point for two groups, one gathered in the streams near the banana plantation and the other in the preserved streams. The similarity test (ANOSIM) pointed to significant differences (P < 0.05) between these groups. This agricultural activity seems to influence the EPTC community structure in low order streams in the Atlantic Forest region. The identification of groups at the EPTC genus level was important to point out the differences between the fauna of streams impacted by banana cultivation and to establish indicator species.     

Are genetic databases sufficiently populated to detect non-indigenous species?

Correct species identifications are of tremendous importance for invasion ecology, as mistakes could lead to misdirecting limited resources against harmless species or inaction against problematic ones. DNA barcoding is becoming a promising and reliable tool for species identifications, however the efficacy of such molecular taxonomy depends on gene region(s) that provide a unique sequence to differentiate among species and on availability of reference sequences in existing genetic databases. Here, we assembled a list of aquatic and terrestrial non-indigenous species (NIS) and checked two leading genetic databases for corresponding sequences of six genome regions used for DNA barcoding. The genetic databases were checked in 2010, 2012, and 2016. All four aquatic kingdoms (Animalia, Chromista, Plantae and Protozoa) were initially equally represented in the genetic databases, with 64, 65, 69, and 61 % of NIS included, respectively. Sequences for terrestrial NIS were present at rates of 58 and 78 % for Animalia and Plantae, respectively. Six years later, the number of sequences for aquatic NIS increased to 75, 75, 74, and 63 % respectively, while those for terrestrial NIS increased to 74 and 88 % respectively. Genetic databases are marginally better populated with sequences of terrestrial NIS of plants compared to aquatic NIS and terrestrial NIS of animals. The rate at which sequences are added to databases is not equal among taxa. Though some groups of NIS are not detectable at all based on available data—mostly aquatic ones—encouragingly, current availability of sequences of taxa with environmental and/or economic impact is relatively good and continues to increase with time.     

Can species distribution models be used to describe plant abundance patterns?

In recent years, there has been increasing interest in modelling of species abundance data in addition to presence data. In this study, we assessed the similarities and differences between presence‐absence distributions and abundance distributions along similar environmental gradients, derived, respectively, from presence‐absence and abundance data. Moreover, we examined the possibility of using presence‐absence distribution models to derive abundance distributions. For this purpose, we used Braun‐Blanquet abundance scores for 243 vascular species at 10 996 French forest sites. Species distribution models were used to analyse the link between the patterns of occurrence, low abundance and high abundance for each species with regard to mean annual temperature, June water balance, and soil pH. For each species, differences in the modelled distributions were characterised by the ecological optimum and ecological amplitude. A comparison of the presence‐absence and abundance distributions for all species revealed similar optima and different amplitudes along the three ecological factors. An abundant‐centre distribution was observed in environmental space, with species abundance being greatest at the optimal conditions and lower at less favourable conditions of the species occurrence response. Geographical habitat mapping also shows centred, high‐abundance suitability within the presence habitat of each species. We conclude that species distribution models derived from presence‐absence data provide useful information about the ecological optima of abundance distributions but overestimate the range of habitats suitable for high species abundance. This study demonstrates the utility of presence‐absence data for ecologist and conservation biologist when they are interested in the optimal conditions of high species abundance.     

Are howler monkey species ecologically equivalent? Trophic niche overlap in syntopic Alouatta guariba clamitans and Alouatta caraya

According to the principle of competitive exclusion, niche differentiation allows the stable coexistence of closely related species. We analyzed dietary profile and diversity, and dietary overlap between syntopic brown howlers (BR; Alouatta guariba clamitans) and black and gold howlers (BLG; A. caraya) in the Atlantic Forest of NE Argentina, with the objective of evaluating the degree of trophic niche overlap and potential interspecific competition for food. During 12 months, we collected data on feeding behavior of two groups of each howler species using the scan sampling method, together with data on food availability. Both at the group‐ and species‐level, we analyzed feeding behavior in terms of monthly percentages of time spent feeding on each food type and specific food item, dietary diversity (Shannon index H′), and we estimated dietary overlap using the percentage index and the Morisita–Horn index (C_H). Across months, both howlers showed species‐specific preferences for certain food items, and BLG had a more diverse diet (mean±SE, H′=2.77±0.08) than BR (H′=2.39±0.09). However, diets of both species overlapped extensively (percentage index=45.64±2.97%; C_H=0.6±0.05) and diets of conspecific groups did not overlap more than diets of groups of different species. Given their high degree of trophic overlap, syntopic BR and BLG meet one of the conditions necessary for interspecific food competition to occur. Although at present we lack direct evidence for interspecific competition in these howler species, we conclude that high levels of niche overlap may have an important role in maintaining the essentially parapatric distribution of howler species throughout the Neotropics. Am. J. Primatol. 72:173–186, 2010. © 2009 Wiley‐Liss, Inc.     

Are all fishes ancient polyploids?

Euteleost fishes seem to have more copies of many genes than their tetrapod relatives. Three different mechanisms could explain the origin of these 'extra' fish genes. The duplicates may have been produced during a fish-specific genome duplication event. A second explanation is an increased rate of independent gene duplications in fish. A third possibility is that after gene or genome duplication events in the common ancestor of fish and tetrapods, the latter lost more genes. These three hypotheses have been tested by phylogenetic tree reconstruction. Phylogenetic analyses of sequences from human, mouse, chicken, frog (Xenopus laevis), zebrafish (Danio rerio) and pufferfish (Takifugu rubripes) suggest that ray-finned fishes are likely to have undergone a whole genome duplication event between 200 and 450 million years ago. We also comment here on the evolutionary consequences of this ancient genome duplication.     

Are all genes regulatory genes?

Although much has been learned about hereditary mechanisms since Gregor Mendel’s famous experiments, gene concepts have always remained vague, notwithstanding their central role in biology. During over hundred years of genetic research, gene concepts have often and dynamically changed to accommodate novel experimental findings, without ever providing a generally accepted definition of the ‘gene.’ Yet, the distinction between ‘regulatory genes’ and ‘structural genes’ has remained a common theme in modern gene concepts since the definition of the operon-model. This distinction is now challenged by recent findings which suggest that, at least in eukaryotes, structural genes may in many situations have a regulatory function that is independent of the function of the gene product (protein or non-coding RNA molecule). This brief paper discusses these new findings and some possible implications for the notion of the ‘regulatory gene.’     

Are all MRSA made equal?

The health and economic burden of methicillin-resistant Staphylococcus aureus (MRSA) in the medical realm is considerable. Although there is ample clinical and laboratory evidence indicating that methicillin-susceptible S. aureus (MSSA) is heterogeneous in disease causation, the same heterogeneity has not been well documented for MRSA. Data from animal models and human studies suggest that MRSA is at least as pathogenic as MSSA. Many comparative clinical studies, mainly retrospective, have assessed the virulence of MSSA and MRSA. Whereas the majority of these studies may be deficient in some aspects of clinical design, there has been a definite trend towards implicating MRSA as the more aggressive pathogen. Such an observation, however, must be tempered with the fact that few such studies have attempted to establish clonality among MRSA isolates. Thus, it is conceivable that hypervirulent clones may represent an important proportion of MRSA from hospital studies where patient-patient spread is likely and, accordingly, comparative studies may be biased. Future clinical studies should be prospective and should use well-defined and homogeneous patient groups. As well, for comparison of MRSA and MSSA, an understanding of clonality is essential.