Coexisting Cyclic Parthenogens Comprise a Holocene Species Flock in Eubosmina

Background

Mixed breeding systems with extended clonal phases and weak sexual recruitment are widespread in nature but often thought to impede the formation of discrete evolutionary clusters. Thus, cyclic parthenogens, such as cladocerans and rotifers, could be predisposed to “species problems” and a lack of discrete species. However, species flocks have been proposed for one cladoceran group, Eubosmina, where putative species are sympatric, and there is a detailed paleolimnological record indicating a Holocene age. These factors make the Eubosmina system suitable for testing the hypotheses that extended clonal phases and weak sexual recruitment inhibit speciation. Although common garden experiments have revealed a genetic component to the morphotypic variation, the evolutionary significance of the morphotypes remains controversial.

Methodology/Principal Findings

In the present study, we tested the hypothesis of a single polymorphic species (i.e., mixing occurs but selection maintains genes for morphology) in four northern European lakes where the morphotypes coexist. Our evidence is based on nuclear DNA sequence, mitochondrial DNA sequence, and morphometric analysis of coexisting morphotypes. We found significant genetic differentiation, genealogical exclusivity, and morphometric differentiation for coexisting morphotypes.

Conclusions

We conclude that the studied morphotypes represent a group of young species undergoing speciation with apparent reproductive barriers despite coexistence in the freshwater pelagic zone.     

Genome Size and Species Diversification

Theoretically, there are reasons to believe that large genome size should favour speciation. Several major factors contributing to genome size, such as duplications and transposable element activity have been proposed to facilitate the formation of new species. However, it is also possible that small genome size promotes speciation. For example, selection for genome reduction may be resolved in different ways in incipient species, leading to incompatibilities. Mutations and chromosomal rearrangements may also be more stably inherited in smaller genomes. Here I review the following lines of empirical evidence bearing on this question: (i) Correlations between genome size and species richness of taxa are often negative. (ii) Fossil evidence in lungfish shows that the accumulation of DNA in the genomes of this group coincided with a reduction in species diversity. (iii) Estimates of speciation interval in mammals correlate positively with genome size. (iv) Genome reductions are inferred at the base of particular species radiations and genome expansions at the base of others. (v) Insect clades that have been increasing in diversity up to the present have smaller genomes than clades that have remained stable or have decreased in diversity. The general pattern emerging from these observations is that higher diversification rates are generally found in small-genome taxa. Since diversification rates are the net effect of speciation and extinction, large genomes may thus either constrain speciation rate, increase extinction rate, or both. I argue that some of the cited examples are unlikely to be explained by extinction alone.     

Predatory Mites in Tropical Australia: Local Species Richness complementarity1

Although little supporting data is available, mites (Acari) are often considered to be one of the ‘hyperdiverse’ taxa in tropical ecosystems. To test this assumption, we sampled single guilds of predatory mites (Hydracarina and Mesostigmata) in three different habitats (fresh water, rotting fungi, and forest foliage) across a range of sites in monsoonal, wet-tropical, and subtropical Australia. Most species (61%) were collected at a single site; as a result, all seven collector's curves rose steeply with little indication of reaching asymptotes. Regional faunas ranged from 87–94 percent distinct and of the 247 species identified, 114 (46%) were previously unknown in Australia and appear to be new. Even within taxonomically well-studied groups, such as the Hydracarina and Phytoseiidae, we found many new species (32% and 60%, respectively). Our results suggest that the diversity of tropical mites is very high and comparable to that of many insect taxa. We propose a simple model to explain our results, i.e. that in the tropics, high levels of complementarity between sites amplify local mite species richness. We tested this model by additional sampling, comparing within-site to between-site complementarity, and contrasting temperate with tropical foliar Mesostigmata. As predicted by the model, collecting at new sites continued to accumulate new species, complementarity was significantly greater between-sites than within-sites (72 vs. 25%), and temperate collections were more homogeneous and less diverse than tropical collections.     

Predatory Efficiency of Crayfish: Comparison Between Indigenous and Non-Indigenous Species

The invasive crayfish Procambarus clarkii is highly dispersed within lentic waters in northern and central Italy. It is a polytrophic predator, exerting a strong influence on animal communities, including amphibians, fish, gastropods, and insect larvae. The indigenous species Austropotamobius italicus, inhabiting lotic waters, behaves as a generalist – but not opportunistic – species. The object of this study was to compare the predatory pressure exercised by the two species on potential prey, i.e., anuran tadpoles, urodelan larvae, fish fry, larvae of insects, and gastropods. Three main conclusions were drawn: (1) both species are skilled predators, adopting a sit-and-wait strategy, (2) the two crayfish seemed to form a `search image' of familiar prey, as the result of either visual or chemical perceptual changes, and (3) at least in the laboratory, P. clarkii readily switched to naive prey for it (tadpoles of Rana italica and larvae of Limnephilidae), unlike the less opportunistic A. italicus. These results furnish suggestions on the trophic preferences of the two crayfish species and provide a partial understanding of the effects that the invasive species have on the community dynamics. This revised version was published online in July 2006 with corrections to the Cover Date.     

Macroevolutionary Dynamics and Historical Biogeography of Primate Diversification Inferred from a Species Supermatrix

Phylogenetic relationships, divergence times, and patterns of biogeographic descent among primate species are both complex and contentious. Here, we generate a robust molecular phylogeny for 70 primate genera and 367 primate species based on a concatenation of 69 nuclear gene segments and ten mitochondrial gene sequences, most of which were extracted from GenBank. Relaxed clock analyses of divergence times with 14 fossil-calibrated nodes suggest that living Primates last shared a common ancestor 71–63 Ma, and that divergences within both Strepsirrhini and Haplorhini are entirely post-Cretaceous. These results are consistent with the hypothesis that the Cretaceous-Paleogene mass extinction of non-avian dinosaurs played an important role in the diversification of placental mammals. Previous queries into primate historical biogeography have suggested Africa, Asia, Europe, or North America as the ancestral area of crown primates, but were based on methods that were coopted from phylogeny reconstruction. By contrast, we analyzed our molecular phylogeny with two methods that were developed explicitly for ancestral area reconstruction, and find support for the hypothesis that the most recent common ancestor of living Primates resided in Asia. Analyses of primate macroevolutionary dynamics provide support for a diversification rate increase in the late Miocene, possibly in response to elevated global mean temperatures, and are consistent with the fossil record. By contrast, diversification analyses failed to detect evidence for rate-shift changes near the Eocene-Oligocene boundary even though the fossil record provides clear evidence for a major turnover event (“Grande Coupure”) at this time. Our results highlight the power and limitations of inferring diversification dynamics from molecular phylogenies, as well as the sensitivity of diversification analyses to different species concepts.     

两种瓢虫对刺槐蚜的捕食作用

在实验室条件下研究了龟纹瓢虫成虫和异色瓢虫成虫对不同密度刺槐蚜的捕食功能反应,符合HollingⅡ 型功能反应模型,其模型分别为:Na=0.4050/1+0.0073N和Na=0.4227N/1+0.0046N,x2值均小于X20. 05=9.49,最大捕食量分别为55.6头和90.9头.圆盘方程理论值与实测值相符.随着瓢虫密度的增加,单个瓢虫捕食率下降,龟纹瓢虫和异色瓢虫自身密度的干扰效应模型分别为:E=0.208P-0.235,E=0.236P-0.324.     

Evolutionary History and Functional Diversification of Phosphomannomutase Genes

Phosphomannomutases (PMMs) catalyze the interconversion of mannose-6-phosphate to mannose-1-phosphate. In humans, two PMM enzymes exist—PMM1 and PMM2; yet, they have different functional specificities. PMM2 presents PMM activity, and its deficiency causes a Congenital Disorder of Glycosylation (PMM2-CDG). On the other hand, PMM1 can also act as glucose-1,6-bisphosphatase in the brain after stimulation with inosine monophosphate and thus far has not been implicated in any human disease. This study aims to refine the evolutionary time frame at which gene duplication gave rise to PMM1 and PMM2, and to identify the most likely amino acid positions underlying the proteins’ different functions. The phylogenetic analysis using available protein sequences, allowed us to establish that duplication occurred early in vertebrate evolution. In order to understand the molecular basis underlying the functional divergence, conserved and most likely functional divergence-related sites were identified, through the analysis of site-specific evolutionary rates. This analysis indicates that most of the sites known to be important in the homodimer formation and in the catalytic activity are conserved in both proteins. Among those potentially related to functional divergence, two positions (183 and 186 in human PMM1) emerge as the most interesting ones. The residues at these positions have different side-chain conformations in the protein structure in the unbound and bound states, and are highly but differently conserved in PMM1 and in PMM2 proteins. Altogether, these results provide new data into the evolutionary history of PMM1 and PMM2 duplicates and highlight the most probable sites that evolved to distinct functional specificities.     

Extensive Functional Diversification of the Populus Glutathione S-Transferase Supergene Family

Identifying how genes and their functions evolve after duplication is central to understanding gene family radiation. In this study, we systematically examined the functional diversification of the glutathione S-transferase (GST) gene family in Populus trichocarpa by integrating phylogeny, expression, substrate specificity, and enzyme kinetic data. GSTs are ubiquitous proteins in plants that play important roles in stress tolerance and detoxification metabolism. Genome annotation identified 81 GST genes in Populus that were divided into eight classes with distinct divergence in their evolutionary rate, gene structure, expression responses to abiotic stressors, and enzymatic properties of encoded proteins. In addition, when all the functional parameters were examined, clear divergence was observed within tandem clusters and between paralogous gene pairs, suggesting that subfunctionalization has taken place among duplicate genes. The two domains of GST proteins appear to have evolved under differential selective pressures. The C-terminal domain seems to have been subject to more relaxed functional constraints or divergent directional selection, which may have allowed rapid changes in substrate specificity, affinity, and activity, while maintaining the primary function of the enzyme. Our findings shed light on mechanisms that facilitate the retention of duplicate genes, which can result in a large gene family with a broad substrate spectrum and a wide range of reactivity toward different substrates.     

MADS-box基因家族基因重复及其功能的多样性

基因的重复(duplication)及其功能的多样性(diversification)为生物体新的形态进化提供了原材料。MADS-box基因在植物(特别是被子植物)的进化过程中发生了大规模的基因重复事件而形成一个多基因家族。MADS-box基因家族的不同成员在植物生长发育过程中起着非常重要的作用,在调控开花时间、决定花分生组织和花器官特征以及调控根、叶、胚珠及果实的发育中起着广泛的作用。探讨MADS-box基因家族的进化历史有助于深入了解基因重复及随后其功能分化的过程和机制。本文综述了MADS-box基因家族基因重复及其功能分化式样的研究进展。     

Functional and Numerical Responses of Three Species of Predatory Phytoseiid Mites (Acari: Phytoseiidae) to Thrips flavidulus (Thysanoptera: Thripidae)

Phytoseiid mites are considered the most effective natural enemies of pest mites. They also have been shown to attack pest thrips. It is unknown, however, whether phytoseiid mites can reduce high densities of Thrips flavidulus (Bagnall). We addressed this question by the study of functional and numerical responses. The aim of this research was to evaluate the potential predation success of the adults of three predatory mites, Neoseiulus cucumeris (Oudemans), Neoseiulus barkeri (Hughes), and Euseius nicholsi (Ehara & Lee), against the first-instar of T. flavidulus in a climatic chamber at five different temperatures. The results showed that the functional responses of those predators reflected the Holling type II functional response and were density dependent and positively related to temperature. For the three predatory mites, predation and successful attack rates increased with increasing temperature up to 26°C, reducing afterward. Handling time had the opposite trend. Reproductive ability also increased with an increase in temperature and prey consumption.     

Adaptive Evolution of Defense Ability Leads to Diversification of Prey Species

In this paper, by using the adaptive dynamics approach, we investigate how the adaptive evolution of defense ability promotes the diversity of prey species in an initial one-prey–two-predator community. We assume that the prey species can evolve to a safer strategy such that it can reduce the predation risk, but a prey with a high defense ability for one predator may have a low defense ability for the other and vice versa. First, by using the method of critical function analysis, we find that if the trade-off is convex in the vicinity of the evolutionarily singular strategy, then this singular strategy is a continuously stable strategy. However, if the trade-off is weakly concave near the singular strategy and the competition between the two predators is relatively weak, then the singular strategy may be an evolutionary branching point. Second, we find that after the branching has occurred in the prey strategy, if the trade-off curve is globally concave, then the prey species might eventually evolve into two specialists, each caught by only one predator species. However, if the trade-off curve is convex–concave–convex, the prey species might eventually branch into two partial specialists, each being caught by both of the two predators and they can stably coexist on the much longer evolutionary timescale.     

C4 Photosynthesis Promoted Species Diversification during the Miocene Grassland Expansion

Identifying how organismal attributes and environmental change affect lineage diversification is essential to our understanding of biodiversity. With the largest phylogeny yet compiled for grasses, we present an example of a key physiological innovation that promoted high diversification rates. C₄ photosynthesis, a complex suite of traits that improves photosynthetic efficiency under conditions of drought, high temperatures, and low atmospheric CO₂, has evolved repeatedly in one lineage of grasses and was consistently associated with elevated diversification rates. In most cases there was a significant lag time between the origin of the pathway and subsequent radiations, suggesting that the ‘C₄ effect’ is complex and derives from the interplay of the C₄ syndrome with other factors. We also identified comparable radiations occurring during the same time period in C₃ Pooid grasses, a diverse, cold-adapted grassland lineage that has never evolved C₄ photosynthesis. The mid to late Miocene was an especially important period of both C₃ and C₄ grass diversification, coincident with the global development of extensive, open biomes in both warm and cool climates. As is likely true for most “key innovations”, the C₄ effect is context dependent and only relevant within a particular organismal background and when particular ecological opportunities became available.     

Fatal Systemic Cladosporiosis in a Merino Sheep Flock

Systemic cladosporiosis is described in 25 merino sheep from a flock consisting 250 animals. The fungal pneumonia appeared after an intensive antibiotic treatment, because of a respiratory system disorder. The pen of the flock was humid and crowded, and animals had signs of respiratory distress, coughing, fever and anorexia. All of the ill animals died, and necropsy was performed on 10 sheep. The lesions were characterized by a multifocal pyogranulomatous pneumonia and an abomasitis. Severe hemorrhages were observed in the lungs. At the histopathological examination, severe vasculitis with thrombosis was observed in various organs, especially in the lungs and abomasums, suggestive for a hematogenous dissemination of the infection in these organs. Numerous PAS-positive fungal elements were seen in the pyogranulomatous foci. Dark green fungal colonies were seen in the blood agar and Sabouraud dextrose agar that were identified as Cladosporium cladosporioides. This report highlights that phaeohyphomycosis can cause a severe systemic and fatal disease in merino sheep under insufficient management conditions.