Speciation in ancient cryptic species complexes: evidence from the molecular phylogeny of Brachionus plicatilis (Rotifera)

Ice-inhabiting species of Bdelloidea Rotifera reveal a pre-Quaternary ancestry in the Arctic cryosphere

Historical climate data indicate that the Earth has passed through multiple geological periods with much warmer-than-present climates, including epochs of the Miocene (23-5.3 mya BP) with temperatures 3-4°C above present, and more recent interglacial stages of the Quaternary, for example, Marine Isotope Stage 11c (approx. 425-395 ka BP) and Middle Holocene thermal maximum (7.5-4.2 ka BP), during which continental glaciers may have melted entirely. Such warm periods would have severe consequences for ice-obligate fauna in terms of their distribution, biodiversity and population structure. To determine the impacts of these climatic events in the Nordic cryosphere, we surveyed ice habitats throughout mainland Norway and Svalbard ranging from maritime glaciers to continental ice patches (i.e. non-flowing, inland ice subjected to deep freezing overwinter), finding particularly widespread populations of ice-inhabiting bdelloid rotifers. Combined mitochondrial and nuclear DNA sequencing identified approx. 16 undescribed, species-level rotifer lineages that revealed an ancestry predating the Quaternary (> 2.58 mya). These rotifers also displayed robust freeze/thaw tolerance in laboratory experiments. Collectively, these data suggest that extensive ice refugia, comparable with stable ice patches across the contemporary Norwegian landscape, persisted in the cryosphere over geological time, and may have facilitated the long-term survival of ice-obligate Metazoa before and throughout the Quaternary.

Maternal age effects on offspring lifespan and reproduction vary within a species

Across diverse taxa, offspring from older mothers have decreased lifespan and fitness. Little is known about the extent to which maternal age effects vary among genotypes for a given species, however, except for studies of a few arthropod species. To investigate the presence and degree of intraspecific variability in maternal age effects, we compared lifespan, reproductive schedule, and lifetime reproductive output of offspring produced by young, middle-aged, and old mothers in four strains of rotifers in the Brachionus plicatilis species complex. We found significant variability among strains in the magnitude and direction of maternal age effects on offspring life history traits. In one strain, offspring of young mothers lived 20% longer than offspring of old mothers, whereas there were no significant effects of maternal age on lifespan for other strains. Depending on strain, advanced maternal age had positive effects, negative effects, or no effect on lifetime reproductive output. Across strains, older mothers produced offspring that had higher maximum daily reproduction early in life. The effects of maternal age on offspring vital rates could not be explained by changes in trade-offs between lifespan and reproduction. This study documents intraspecific variability in maternal age effects in an additional clade. Investigating intraspecific variability is critical for understanding the ubiquity of maternal age effects and their role in the evolution of life history and aging.

Maternal age effects on offspring lifespan and reproduction vary within a species

Across diverse taxa, offspring from older mothers have decreased lifespan and fitness. Little is known about whether such maternal age effects vary among genotypes for a given species, however. We compared maternal age effects among four strains of rotifers in the Brachionus plicatilis species complex. For each strain, we measured lifespan, reproductive schedule, and lifetime reproductive output of offspring produced by young, middle-aged, and old mothers. We found unexpected variability among strains in the magnitude and direction of maternal age effects on offspring life history traits. In one strain, offspring of young mothers lived 20% longer than offspring of old mothers, whereas there were no significant effects of maternal age on lifespan for the other strains. Across strains, advanced maternal age had positive effects, negative effects, or no effect on lifetime reproductive output. For all but one strain, older mothers produced offspring that had higher maximum daily reproduction early in life. Maternal age effects appear to be genetically determined traits, not features of life history strategy or due to accumulation of age-related damage in the germline. Investigating intraspecific variability is critical for understanding the ubiquity of maternal age effects and their role in the evolution of life history and aging.

Spatial and temporal variation of genetic diversity and genetic differentiation in Daphnia galeata populations in four large reservoirs in southern China

Daphnia galeata is a common and dominant species in warmer waters, and has a strong top-down effect on both phytoplankton and bacteria. The knowledge of its temporal and spatial patterns of genetic diversity is fundamental in understanding its population dynamics and potential ecological function in ecosystems. Its population genetics have been investigated at regional scales but few within regions or at smaller spatial scales. Here, we examined the fine-scale spatial genetic variation of D. galeata within four large, deep reservoirs in wet and dry seasons and the six-year variation of genetic diversity in one of the reservoirs by using cytochrome c oxidase subunit I and microsatellites (simple sequence repeat). Our study shows that fine-scale spatial genetic variation commonly occurred within the reservoirs, indicating strong environmental selection at least in the two of reservoirs with strong longitudinal gradients. Since the environmental gradients established in the dry season was largely reduced in the wet season, the fine-scale spatial genetic variation was much higher in the dry season. The dynamics of local genetic diversity did not follow the theoretical pattern of rapid erosion but peaked in mid or mid-late growth season. The local genetic diversity of D. galeata appears to be shaped and maintained not only by recruitment from resting egg banks but also by gene flow within reservoirs. The temporal and fine-scale genetic variation within a water body suggests that it is necessary to pay attention to sampling periods and locations of a given water body in regional studies.

Morphology, molecular characterization and phylogeny of Bolbosoma nipponicum Yamaguti, 1939 (Acanthocephala: Polymorphidae), a potential zoonotic parasite of human acanthocephaliasis

Human acanthocephaliasis is a rare parasitic zoonosis mainly caused by acanthocephalans belonging to the genera Acanthocephalus, Bolbosoma, Corynosoma, Macracanthorhynchus, and Moniliformis. In the present paper, the juveniles of Bolbosoma nipponicum Yamaguti, 1939 collected from the northern fur seal Callorhinus ursinus (Linnaeus) (Mammalia: Carnivora) in Alaska, USA were precisely identified based on morphological characters and genetic data. Their detailed morphology was studied using light and, for the first time, scanning electron microscopy. The molecular characterization of the nuclear genes [small ribosomal subunit (18S) and large ribosomal subunit (28S)] and the mitochondrial cytochrome c oxidase subunit 1 (cox1) sequence data of B. nipponicum are provided for the first time. Moreover, in order to clarify the phylogenetic relationships of the genus Bolbosoma and the other genera in the family Polymorphidae, phylogenetic analyses were performed integrating different nuclear (18S + ITS+28S) and mitochondrial (cox1) sequence data using maximum likelihood (ML) and Bayesian inference (BI). The phylogenetic results showed that Bolbosoma has a sister relationship with Corynosoma, and also revealed that Southwellina is sister to Ibirhynchus + Hexaglandula. Our molecular phylogeny also indicated a possible host-switch pattern during the evolution of the polymorphid acanthocephalans. The ancestors of polymorphid acanthocephalans seem to have originally parasitized fish-eating waterfowl in continental habitats, then extended to fish-eating marine birds in brackish water and marine habitats, and finally, opportunistically infected the marine mammals.

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Detailed morphology of the juveniles of B. nipponicum was described for the first time.

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Molecular characterization of the 18S, 28S and cox1 genes of B. nipponicum was provided for the first time.

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Molecular phylogenetic analyses showed that Bolbosoma has a sister relationship with Corynosoma.

Genetic differentiation and phylogeography of rotifer Polyarthra dolichoptera and P. vulgaris populations between Southeastern China and eastern North America: High intercontinental differences

Genetic differentiations and phylogeographical patterns of small organisms may be shaped by spatial isolation, environmental gradients, and gene flow. However, knowledge about genetic differentiation of rotifers at the intercontinental scale is still limited. Polyarthra dolichoptera and P. vulgaris are cosmopolitan rotifers that are tolerant to environmental changes, offering an excellent model to address the research gap. Here, we investigated the populations in Southeastern China and eastern North America and evaluated the phylogeographical patterns from their geographical range sizes, geographic–genetic distance relationships and their responses to spatial‐environmental factors. Using the mitochondrial cytochrome c oxidase subunit I gene as the DNA marker, we analyzed a total of 170 individuals. Our results showed that some putative cryptic species, also known as entities were widely distributed, but most of them were limited to single areas. The divergence of P. dolichoptera and P. vulgaris indicated that gene flow between continents was limited while that within each continent was stronger. Oceanographic barriers do affect the phylogeographic pattern of rotifers in continental waters and serve to maintain genetic diversity in nature. The genetic distance of P. dolichoptera and P. vulgaris populations showed significant positive correlation with geographic distance. This might be due to the combined effects of habitat heterogeneity, long‐distance colonization, and oceanographic barriers. Furthermore, at the intercontinental scale, spatial distance had a stronger influence than environmental variables on the genetic differentiations of both populations. Wind‐ and animal‐mediated transport and even historical events of continental plate tectonics are potential factors for phylogeography of cosmopolitan rotifers.

Body size variability across habitats in the Brachionus plicatilis cryptic species complex

The body size response to temperature is one of the most recognizable but still poorly understood ecological phenomena. Other covarying environmental factors are frequently invoked as either affecting the strength of that response or even driving this pattern. We tested the body size response in five species representing the Brachionus plicatilis cryptic species complex, inhabiting 10 brackish ponds with different environmental characteristics. Principal Component Analysis selected salinity and oxygen concentration as the most important factors, while temperature and pH were less influential in explaining variation of limnological parameters. Path analysis showed a positive interclonal effect of pH on body size. At the interspecific level, the size response was species- and factor-dependent. Under the lack of a natural thermo-oxygenic relationship, the negative response of size to temperature, expected according to 'size-to-temperature response' rules, disappeared, but a positive response of size to oxygen, expected according to predictions selecting oxygen as a factor actually driving these rules, remained. Our results confirm the crucial role of oxygen in determining the size-to-temperature patterns observed in the field.

Genetic Variability of the Mating Recognition Gene in Populations of Brachionus plicatilis

The development of reproductive barriers promotes within-species divergence and is a requisite for speciation to occur. Mate recognition in the rotifer B. plicatilis is mediated through a surface glycoprotein called Mating Recognition Protein (MRP). Here we investigate the genetic variation of the mmr-b, MRP coding, gene in different natural populations of B. plicatilis from the Iberian Peninsula, that present different degree of population differentiation, with known adaptive divergence in some cases. The MRP gene consists of several nearly identical tandem repeats. We found a relatively high diversity within and among populations both in the number of repeats, as well as in the nucleotide sequence. Despite that most changes are neutral, variation that can potentially affect the protein function was found in two polymorphic sites within a repeat in some of these populations. Although being mostly subject to stabilizing selection, we have found a noticeable pattern of increasing mmr-b gene diversification correlated to increasing differences in environmental factors. The interplay between genetic differentiation, local adaptation and differentiation of the mating recognition system can lead to speciation events in nearly sympatric populations.

New insights on Pomphorhynchus sphaericus Gil de Pertierra, Spatz et Doma, 1996 (Acanthocephala: Pomphorhynchidae)

The finding of Pomphorhynchus sphaericus in new localities from La Plata River allowed the reevaluation of the species using a taxonomic integrative approach. The newly found specimens in Pimelodus maculatus from Samborombon Bay differ from P. sphaericus by the roots of hooks 1-6 which not form a wide sheet split into 2 apophysis, the slender, separated and equatorial testicles, the position of the cement glands, the shape of the proboscis, the shape and length of lemnisci, and the eggs size. Despite the notorious observed morphological differences, the COI mtDNA analysis confirmed that Pomphorhynchus individuals are the same conspecific, and showed that there is a high phenotypical plasticity in this species. Pomphorhynchus sphaericus is the first South American species analyzed to a DNA level (COI mtDNA, ITS, and 18S rDNA genes). The molecular analysis relates P. sphaericus to P. bulbocolli and P. purhepechus.

Genomics and transcriptomics of epizoic Seisonidea (Rotifera, syn. Syndermata) reveal strain formation and gradual gene loss with growing ties to the host

Background

Seisonidea (also Seisonacea or Seisonidae) is a group of small animals living on marine crustaceans (Nebalia spec.) with only four species described so far. Its monophyletic origin with mostly free-living wheel animals (Monogononta, Bdelloidea) and endoparasitic thorny-headed worms (Acanthocephala) is widely accepted. However, the phylogenetic relationships inside the Rotifera-Acanthocephala clade (Rotifera sensulato or Syndermata) are subject to ongoing debate, with consequences for our understanding of how genomes and lifestyles might have evolved. To gain new insights, we analyzed first drafts of the genome and transcriptome of the key taxon Seisonidea.

Results

Analyses of gDNA-Seq and mRNA-Seq data uncovered two genetically distinct lineages in Seison nebaliae Grube, 1861 off the French Channel coast. Their mitochondrial haplotypes shared only 82% sequence identity despite identical gene order. In the nuclear genome, distinct linages were reflected in different gene compactness, GC content and codon usage. The haploid nuclear genome spans ca. 46 Mb, of which 96% were reconstructed. According to ~ 23,000 SuperTranscripts, gene number in S. nebaliae should be within the range published for other members of Rotifera-Acanthocephala. Consistent with this, numbers of metazoan core orthologues and ANTP-type transcriptional regulatory genes in the S. nebaliae genome assembly were between the corresponding numbers in the other assemblies analyzed. We additionally provide evidence that a basal branching of Seisonidea within Rotifera-Acanthocephala could reflect attraction to the outgroup. Accordingly, rooting via a reconstructed ancestral sequence led to monophyletic Pararotatoria (Seisonidea+Acanthocephala) within Hemirotifera (Bdelloidea+Pararotatoria).

Conclusion

Matching genome/transcriptome metrics with the above phylogenetic hypothesis suggests that a haploid nuclear genome of about 50 Mb represents the plesiomorphic state for Rotifera-Acanthocephala. Smaller genome size in S. nebaliae probably results from subsequent reduction. In contrast, genome size should have increased independently in monogononts as well as bdelloid and acanthocephalan stem lines. The present data additionally indicate a decrease in gene repertoire from free-living to epizoic and endoparasitic lifestyles. Potentially, this reflects corresponding steps from the root of Rotifera-Acanthocephala via the last common ancestors of Hemirotifera and Pararotatoria to the one of Acanthocephala. Lastly, rooting via a reconstructed ancestral sequence may prove useful in phylogenetic analyses of other deep splits.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07857-y.

An integrative taxonomic review of the Natal mountain catfish, Amphilius natalensis Boulenger 1917 (Siluriformes, Amphiliidae), with description of four new species

An integrative taxonomic analysis combining mitochondrial cytochrome oxidase subunit I sequences, morphology, colour pattern and two species delimitation approaches revealed the existence of five lineages within the Natal mountain catfish, Amphilius natalensis, in southern Africa. These lineages are separated by substantial genetic divergences (1.6%-9.46%), and they can be consistently distinguished from one another based on a combination of morphology and colour pattern differences. Additionally, the lineages are allopatrically distributed and confined to isolated river systems draining discrete mountain ranges, which makes gene flow among them unlikely. One of these lineages is A. natalensis s.s., which is confined to the uMngeni and Tukela river systems in KwaZulu Natal (KZN) Province in South Africa. The other four lineages represent new species to science which are described as Amphilius zuluorum sp. nov., endemic to the uMkhomazi River system in KZN, Amphilius engelbrechti sp. nov., endemic to the Inkomati River system in Mpumalanga Province in South Africa, Amphilius marshalli sp. nov., endemic to the Pungwe and Lower Zambezi river systems in Zimbabwe and Mozambique, and Amphilius leopardus sp. nov., endemic to the Ruo River in Malawi. The results show that Amphilius laticaudatus which is endemic to the Buzi River system in Zimbabwe and Mozambique, belongs to the A. natalensis s.l. complex. A redescription of A. laticaudatus is presented and an updated identification key for the mountain catfishes of southern Africa is provided.

Long-term stasis in acariform mites provides evidence for morphologically stable evolution: Molecular vs. morphological differentiation in Linopodes (Acariformes; Prostigmata)

Molecular species delimitation, usually by COI DNA barcoding, shows that cryptic speciation is a common phenomenon observed in most animal phyla. Cryptic species have frequently been observed among all major taxa of mites. The mites of the eupodoid genus Linopodes are cosmopolitan in distribution and are most often found in soil-related habitats. Currently, the genus consists of 22 morphologically similar species, which, in practice, are indistinguishable on the basis of their morphological features. The diagnostic issue of the Linopodes species may be caused by the poor delineation of the species, which need taxonomic revision, or the low morphological variability among cryptic species. In this paper, we present the results of molecular species delimitation carried out using sampled Linopodes populations and the level of morphological inter/intraspecific variation within defined groups. We compared COI, 18S and 28S sequence data together with morphological characters. The molecular delimitation revealed seven well-defined species of Linopodes based on DNA sequences. A well-supported phylogenetic tree revealed the same seven species, while morphological analysis showed negligible phenotypic differentiation among the species revealed. We demonstrate that mites can undergo changes in their DNA accompanied by morphological stasis lasting at least 80 MY.

Rotifers of Bahia State, Brazil: News records and limitations to studies

A first checklist of Rotifera species in freshwater environments in Bahia State, in northeastern Brazil, is provided. The list includes sampling data from 26 aquatic environments (lotic and lentic) undertaken from 2010 to 2016. One hundred and fifty-five species were recorded, with 68 new records for the state. The family Brachionidae and Lecanidae were the most representative (54.8%). The greatest richness was recorded in the Colônia River (57 species). Those results reflect the low numbers of studies previously undertaken in the region, indicating more research needs to be focused on Rotifera biodiversity in Bahia, the fifth largest state in Brazil (567,295 km2) with large numbers of freshwater bodies.

The genome of the euryhaline rotifer Brachionus paranguensis: Potential use in molecular ecotoxicology

Brachionus spp. rotifers have been proposed as model organisms for ecotoxicological studies. We analyzed the whole-genome sequence of B. paranguensis through NextDenovo, resulting in a total length of 106.2 Mb and 71 contigs. The N50 and the GC content were 4.13 Mb and 28%, respectively. A total of 18,501 genes were predicted within the genome of B. paranguensis. Prominent detoxification-related gene families of phase I and II detoxifications have been investigated. In parallel with other Brachionus rotifers, high gene expansion was observed in CYP clan 3 and GST sigma class in B. paranguensis. Moreover, species-specific expansion of sulfotransferase (SULTs) and gain of UDP-glucuronosyltransferases (UGTs) through horizontal gene transfer has been specifically found within B. plicatilis complex. This whole-genome analysis of B. paranguensis provides a basis for molecular ecotoxicological studies and provides useful information for comparative studies of the evolution of detoxification mechanisms in Brachionus spp.

A new set of highly efficient primers for COI amplification in rotifers

Rotifers are a small-sized but key group of freshwater zooplankters with high species richness, linking primary producers to higher consumers in aquatic food webs. DNA barcoding has been widely used in exploring its biodiversity, cryptic speciation and phylogeny. However, the inefficiency of universal primers to amplify COI of rotifers hinders our understanding of their species richness and genetic diversity. Here, we develop a new pair of primers, 30 F and 885 R, to amplify the COI gene of rotifers. We used 22 species to test their PCR success rate and found that the new pair of primers was more efficient (86%) than two pairs of universal primers, namely, dgLCO and dgHCO (32%), and Folmer primers (59%). The new primers will allow the barcoding of groups that were so far difficult to sequence and will contribute to clarify species diversity and phylogeny of rotifers.

Brachionus rotifers as a model for investigating dietary and metabolic regulators of aging

Because every species has unique attributes relevant to understanding specific aspects of aging, using a diversity of study systems and a comparative biology approach for aging research has the potential to lead to novel discoveries applicable to human health. Monogonont rotifers, a standard model for studies of aquatic ecology, evolutionary biology, and ecotoxicology, have also been used to study lifespan and healthspan for nearly a century. However, because much of this work has been published in the ecology and evolutionary biology literature, it may not be known to the biomedical research community. In this review, we provide an overview of Brachionus rotifers as a model to investigate nutritional and metabolic regulators of aging, with a focus on recent studies of dietary and metabolic pathway manipulation. Rotifers are microscopic, aquatic invertebrates with many advantages as a system for studying aging, including a two-week lifespan, easy laboratory culture, direct development without a larval stage, sexual and asexual reproduction, easy delivery of pharmaceuticals in liquid culture, and transparency allowing imaging of cellular morphology and processes. Rotifers have greater gene homology with humans than do established invertebrate models for aging, and thus rotifers may be used to investigate novel genetic mechanisms relevant to human lifespan and healthspan. The research on caloric restriction; dietary, pharmaceutical, and genetic interventions; and transcriptomics of aging using rotifers provide insights into the metabolic regulators of lifespan and health and suggest future directions for aging research. Capitalizing on the unique biology of Brachionus rotifers, referencing the vast existing literature about the influence of diet and drugs on rotifer lifespan and health, continuing the development of genetic tools for rotifers, and growing the rotifer research community will lead to new discoveries a better understanding of the biology of aging.

Morphological and genetic characterisation of Centrorhynchus clitorideus (Meyer, 1931) (Acanthocephala: Centrorhynchidae) from the little owl Athene noctua (Scopoli) (Strigiformes: Strigidae) in Pakistan

Centrorhynchus Lühe, 1911 is a large genus of acanthocephalans mainly parasitic in various strigiform and falconiform birds. Some species of Centrorhynchus have not been adequately described. Here, the detailed morphology of C. clitorideus (Meyer, 1931) was studied using light and, for the first time, scanning electron microscopy, based on newly collected specimens from the little owl Athene noctua (Scopoli) (Strigiformes: Strigidae) in Pakistan. Partial sequences of the 18S and 28S nuclear ribosomal RNA genes and the mitochondrial cytochrome c oxidase subunit 1 (cox1) of C. clitorideus were generated for the first time. No nucleotide variation was detected for the partial 18S and 28S regions, but 3.30% of intraspecific nucleotide divergence was found for the cox1 gene. Phylogenetic analyses based on 28S and 18S sequence data showed that C. clitorideus formed a sister relationship with Centrorhynchus sp. MGV-2005 or Centrorhynchus sp. MGV-2005 + C. microcephalus (Bravo-Hollis, 1947), respectively.

Temperature-dependent life history and transcriptomic responses in heat-tolerant versus heat-sensitive Brachionus rotifers

Thermal stress response is an essential physiological trait that determines occurrence and temporal succession in nature, including response to climate change. We compared temperature-related demography in closely related heat-tolerant and heat-sensitive Brachionus rotifer species. We found significant differences in heat response, with the heat-sensitive species adopting a strategy of long survival and low population growth, while the heat-tolerant followed the opposite strategy. In both species, we examined the genetic basis of physiological variation by comparing gene expression across increasing temperatures. Comparative transcriptomic analyses identified shared and opposing responses to heat. Interestingly, expression of heat shock proteins (hsps) was strikingly different in the two species and mirrored differences in population growth rates, showing that hsp genes are likely a key component of a species' adaptation to different temperatures. Temperature induction caused opposing patterns of expression in further functional categories including energy, carbohydrate and lipid metabolism, and in genes related to ribosomal proteins. In the heat-sensitive species, elevated temperatures caused up-regulation of genes related to meiosis induction and post-translational histone modifications. This work demonstrates the sweeping reorganizations of biological functions that accompany temperature adaptation in these two species and reveals potential molecular mechanisms that might be activated for adaptation to global warming.

Molecular identification of Neoechinorhynchus rutili parasite diagnosed in some fish species caught in Menzelet dam lake in Kahramanmaras province (Turkey)

This study details the molecular identification of the parasite Neoechinorhynchus rutili diagnosed in fish (Capoeta barroisi, Cyprinus carpio, Barbus rajanorum) caught in Menzelet Dam Lake in Kahramanmaras Province, Turkey. Parasite samples were obtained from the intestines of fish caught from January to June of 2013. The collected parasites were stored in sample vials containing 70% alcohol. Using staining methods and based on morphology, 120 N. rutili specimens were identified. DNA isolation of N. rutili was accomplished using special tissue sets for parasites. Specific primers were utilized in the molecular identification of N. rutili using polymerase chain reaction (PCR) and it was possible to verify that all of the parasites contained N. rutili molecules. In conclusion, using multiple methods we successfully identified and confirmed the presence of N. rutili parasites in the fish caught in Kahramanmaras Province. The process of identification of N. rutili using morphology and staining methods is time-consuming; however, PCR was successfully performed in a short time to accomplish the same results. The success of this study may lead to more original and extensive work aimed at the efficient molecular identification of parasitic agents found in fish.

Ecological genomics of adaptation to unpredictability in experimental rotifer populations

Elucidating the genetic basis of phenotypic variation in response to different environments is key to understanding how populations evolve. Facultatively sexual rotifers can develop adaptive responses to fluctuating environments. In a previous evolution experiment, diapause-related traits changed rapidly in response to two selective regimes (predictable vs unpredictable) in laboratory populations of the rotifer Brachionus plicatilis. Here, we investigate the genomic basis of adaptation to environmental unpredictability in these experimental populations. We identified and genotyped genome-wide polymorphisms in 169 clones from both selective regimes after seven cycles of selection using genotyping by sequencing (GBS). Additionally, we used GBS data from the 270 field clones from which the laboratory populations were established. This GBS dataset was used to identify candidate SNPs under selection. A total of 76 SNPs showed divergent selection, three of which are candidates for being under selection in the particular unpredictable fluctuation pattern studied. Most of the remaining SNPs showed strong signals of adaptation to laboratory conditions. Furthermore, a genotype-phenotype association approach revealed five SNPs associated with two key life-history traits in the adaptation to unpredictability. Our results contribute to elucidating the genomic basis for adaptation to unpredictable environments and lay the groundwork for future evolution studies in rotifers.

Neutral and niche forces as drivers of species selection

The evolutionary and ecological processes behind the origin of species are among the most fundamental problems in biology. In fact, many theoretical hypothesis on different type of speciation have been proposed. In particular, models of sympatric speciation leading to the formation of new species without geographical isolation, are based on the niche hypothesis: the diversification of the population is induced by the competition for a limited set of available resources. Interestingly, neutral models of evolution have shown that stochastic forces are sufficient to generate coexistence of different species. In this work, we put forward this dichotomy within the context of species formation, studying how neutral and niche forces contribute to sympatric speciation in a model ecosystem. In particular, we study the evolution of a population of individuals with asexual reproduction whose inherited characters or phenotypes are specified by both niche-based and neutral traits. We analyze the stationary state of the dynamics, and study the distribution of individuals in the whole phenotypic space. We show, both numerically and analytically, that there is a non-trivial coupling between neutral and niche forces induced by stochastic effects in the evolution of the population allowing the formation of clusters, that is, species in the phenotypic space. Remarkably, our framework can be generalized also to sexual reproduction or other type of population dynamics.

From marine park to future genomic observatory? Enhancing marine biodiversity assessments using a biocode approach

Few tropical marine sites have been thoroughly characterised for their animal species, even though they constitute the largest proportion of multicellular diversity. A number of focused biodiversity sampling programmes have amassed immense collections to address this shortfall, but obstacles remain due to the lack of identification tools and large proportion of undescribed species globally. These problems can be partially addressed with DNA barcodes ("biocodes"), which have the potential to facilitate the estimation of species diversity and identify animals to named species via barcode databases. Here, we present the first results of what is intended to be a sustained, systematic study of the marine fauna of Singapore's first marine park, reporting more than 365 animal species, determined based on DNA barcodes and/or morphology represented by 931 specimens (367 zooplankton, 564 macrofauna including 36 fish). Due to the lack of morphological and molecular identification tools, only a small proportion could be identified to species solely based on either morphology (24.5%) or barcodes (24.6%). Estimation of species numbers for some taxa was difficult because of the lack of sufficiently clear barcoding gaps. The specimens were imaged and added to "Biodiversity of Singapore" (http://singapore.biodiversity.online), which now contains images for > 13,000 species occurring in the country.

Brachionus paranguensis sp. nov. (Rotifera, Monogononta), a member of the L group of the Brachionus plicatilis complex

The Brachionus plicatilis complex represents the most studied group of rotifers, although the systematics of the species complex has not been completely clarified. Many studies have been conducted trying to explore the diversity within the complex, leading to the recognition of three major morphotypes: large (L), small-medium (SM), and small (SS). Currently six species have been described and classified under these types and another nine taxa have been identified but not formally described. Within the L group, three species have been officially described [B. plicatilis s.s. (L1), B. manjavacas (L2), and B. asplanchnoidis (L3)], while a formal description of L4, unofficially known as B. 'Nevada', is still lacking. In the present study, a new species, Brachionus paranguensis sp. nov., is formally described and presented as a representative of the L4 clade. The species has been named after a high altitude saline crater lake from Central Mexico, where the specimens were collected. An integrated approach using DNA taxonomy through COI and ITS1 markers, morphology, and ecology was used to confirm the identity of the new species.

Facing Adversity: Dormant Embryos in Rotifers

An in-depth look at the basic aspects of dormancy in cyclic parthenogenetic organisms is now possible thanks to research efforts conducted over the past two decades with rotifer dormant embryos. In this review, we assemble and compose the current knowledge on four central themes: (1) distribution of dormancy in animals, with an overview on the phylogenetic distribution of embryo dormancy in metazoans, and (2) physiological and cellular processes involved in dormancy, with a strong emphasis on the dormant embryos of cyclically parthenogenetic monogonont rotifers; and discussions of (3) the selective pressures and (4) the evolutionary and population implications of dormancy in these animals. Dormancy in metazoans is a widespread phenomenon with taxon-specific features, and rotifers are among the animals in which dormancy is an intrinsic feature of their life cycle. Our review shows that embryo dormancy in rotifers shares common functional pathways with other taxa at the molecular and cellular level, despite the independent evolution of dormancy across phyla. These pathways include the arrest of similar metabolic routes and the usage of common metabolites for the stabilization of cellular structures and to confer stress resistance. We conclude that specific features of recurrent harsh environmental conditions are a powerful selective pressure for the fine-tuning of dormancy patterns in rotifers. We hypothesize that similar mechanisms at the organism level will lead to similar adaptive consequences at the population level across taxa, among which the formation of egg banks, the coexistence of species, and the possibility of differentiation among populations and local adaptation stand out. Our review shows how studies of rotifers have contributed to improved knowledge of all of these aspects.

The genome of the marine monogonont rotifer Brachionus plicatilis: Genome-wide expression profiles of 28 cytochrome P450 genes in response to chlorpyrifos and 2-ethyl-phenanthrene

Brachionus spp. (Rotifera: Monogononta) are globally distributed in aquatic environments and play important roles in the aquatic ecosystem. The marine monogonont rotifer Brachionus plicatilis is considered a suitable model organism for ecology, evolution, and ecotoxicology. In this study, we assembled and characterized the B. plicatilis genome. The total length of the assembled genome was 106.9 Mb and the number of final scaffolds was 716 with an N50 value of 1.15 Mb and a GC content of 26.75%. A total of 20,154 genes were annotated after manual curation. To demonstrate the use of whole genome data, we targeted one of the main detoxifying enzyme of phase I detoxification system and identified in a total of 28 cytochrome P450 s (CYPs). Based on the phylogenetic analysis using the maximum likelihood, 28 B. plicatilis-CYPs were apparently separated into five different clans, namely, 2, 3, 4, mitochondrial (MT), and 46 clans. To better understand the CYPs-mediated xenobiotic detoxification, we measured the mRNA expression levels of 28 B. plicatilis CYPs in response to chlorpyrifos and 2-ethyl-phenanthrene. Most B. plicatilis CYPs were significantly modulated (P < 0.05) in response to chlorpyrifos and 2-ethyl-phenanthrene. In addition, xenobiotic-sensing nuclear receptor (XNR) response element sequences were identified in the 5 kb upstream of promoter regions of 28 CYPs from the genome of B. plicatilis, indicating that these XNR can be associated with detoxification of xenobiotics. Overall, the assembled B. plicatilis genome presented here will be a useful resource for a better understanding the molecular ecotoxicology in the view of molecular mechanisms underlying toxicological responses, particularly on xenobiotic detoxification in this species.

Evidence for a species complex in Indialona ganapati (Chydoridae)

Indialona ganapati (Petkovski 1966 ), is one of the three known cladoceran endemic species from India. It is also the only one of these species that is monotypic and endemic to central India. In this study we report on habitat shifts for this species as well as presence of parthenogenetic and ephippial females throughout the year, phenomena that are uncommon in most species of the family Chydoridae. These factors prompted us to undertake a study evaluating the taxonomic status of this species in collections from India using morphological and molecular methods. This included recognition of some degree of morphometric diversity based on sexual differentiation and reproductive patterns which were not correlated with speciation events. Analysis of our data does, however, suggest that I. ganapati can be split into two recent clades. Also, phylogenetic as well as haplotype network analysis of our data suggests the presence of a sibling species complex of I. ganapati in the river Godavari. This suggests that reconsideration of taxonomic status of this species may be appropriate. In addition, this study underscores the potential utility of using COI gene based 'barcode' DNA sequences for recognizing the existence of cryptic species among the cladocera.

Body size-dependent interspecific tolerance to cadmium and their molecular responses in the marine rotifer Brachionus spp

Although several studies have reported on different interspecific sensitivities in response to various toxicants, the response mechanisms are still poorly understood. Here, we investigate the interspecific toxicity of cadmium (Cd) and its mechanism using three marine rotifer Brachionus spp. that are distinguishable by body size, which is considered the most significant indicator of phenotypic difference. The body sizes of B. plicatilis, B. koreanus, and B. rotundiformis are significantly different throughout their life cycles (egg, neonate, and adult), with the smaller rotifer exhibiting higher sensitivity to Cd. To investigate the mechanisms that result in body size-dependent tolerance to Cd, metabolic and Cd bioaccumulation rates were investigated. Both rates have shown a significant correlation with body size, indicating that body size and its variables are important factors in determining Cd tolerance in Brachionus spp. In addition, similar patterns that further explain body size-dependent tolerance are shown in the phosphorylation status of mitogen-activated protein kinases, reactive oxygen species level, and antioxidant enzymatic activities. Our study provides valuable insight into size- and species-dependent toxicity mechanisms of species in the same genus.

Long-distance passive dispersal in microscopic aquatic animals

Given their dormancy capability (long-term resistant stages) and their ability to colonise and reproduce, microscopic aquatic animals have been suggested having cosmopolitan distribution. Their dormant stages may be continuously moved by mobile elements through the entire planet to any suitable habitat, preventing the formation of biogeographical patterns. In this review, I will go through the evidence we have on the most common microscopic aquatic animals, namely nematodes, rotifers, and tardigrades, for each of the assumptions allowing long-distance dispersal (dormancy, viability, and reproduction) and all the evidence we have for transportation, directly from surveys of dispersing stages, and indirectly from the outcome of successful dispersal in biogeographical and phylogeographical studies. The current knowledge reveals biogeographical patterns also for microscopic organisms, with species-specific differences in ecological features that make some taxa indeed cosmopolitan with the potential for long-distance dispersal, but others with restricted geographic distributions.

Congeneric variability in lifespan extension and onset of senescence suggest active regulation of aging in response to low temperature

Lifespan extension under low temperature is well conserved across both endothermic and exothermic taxa, but the mechanism underlying this change in aging is poorly understood. Low temperature is thought to decrease metabolic rate, thus slowing the accumulation of cellular damage from reactive oxygen species, although recent evidence suggests involvement of specific cold-sensing biochemical pathways. We tested the effect of low temperature on aging in 11 strains of Brachionus rotifers, with the hypothesis that if the mechanism of lifespan extension is purely thermodynamic, all strains should have a similar increase in lifespan. We found differences in change in median lifespan ranging from a 6% decrease to a 100% increase, as well as differences in maximum and relative lifespan extension and in mortality rate. Low temperature delays reproductive senescence in most strains, suggesting an extension of healthspan, even in strains with little to no change in lifespan. The combination of low temperature and caloric restriction in one strain resulted in an additive lifespan increase, indicating these interventions may work via non- or partially-overlapping pathways. The known low temperature sensor TRPA1 is present in the rotifer genome, but chemical TRPA1 agonists did not affect lifespan, suggesting that this gene may be involved in low temperature sensation but not in chemoreception in rotifers. The congeneric variability in response to low temperature suggests that the mechanism of low temperature lifespan extension is an active genetic process rather than a passive thermodynamic one and is dependent upon genotype.

Evidence supporting cryptic species within two sessile microinvertebrates, Limnias melicerta and L. ceratophylli (Rotifera, Gnesiotrocha)

Microorganisms, including rotifers, are thought to be capable of long distance dispersal. Therefore, they should show little population genetic structure due to high gene flow. Nevertheless, substantial genetic structure has been reported among populations of many taxa. In rotifers, genetic studies have focused on planktonic taxa leaving sessile groups largely unexplored. Here, we used COI gene and ITS region sequences to study genetic structure and delimit cryptic species in two sessile species (Limnias melicerta [32 populations]; L. ceratophylli [21 populations]). Among populations, ITS region sequences were less variable as compared to those of the COI gene (ITS; L. melicerta: 0-3.1% and L. ceratophylli: 0-4.4%; COI; L. melicerta: 0-22.7% and L. ceratophylli: 0-21.7%). Moreover, L. melicerta and L. ceratophylli were not resolved in phylogenetic analyses based on ITS sequences. Thus, we used COI sequences for species delimitation. Bayesian Species Delimitation detected nine putative cryptic species within L. melicerta and four putative cryptic species for L. ceratophylli. The genetic distance in the COI gene was 0-15.4% within cryptic species of L. melicerta and 0.5-0.6% within cryptic species of L. ceratophylli. Among cryptic species, COI genetic distance ranged 8.1-21.9% for L. melicerta and 15.1-21.2% for L. ceratophylli. The correlation between geographic and genetic distance was weak or lacking; thus geographic isolation cannot be considered a strong driver of genetic variation. In addition, geometric morphometric analyses of trophi did not show significant variation among cryptic species. In this study we used a conservative approach for species delimitation, yet we were able to show that species diversity in these sessile rotifers is underestimated.

Remarkable morphological variation in the proboscis of Neorhadinorhynchus nudus (Harada, 1938) (Acanthocephala: Echinorhynchida)

The acanthocephalans are characterized by a retractible proboscis, armed with rows of recurved hooks, which serves as the primary organ for attachment of the adult worm to the intestinal wall of the vertebrate definitive host. Whilst there is a considerable variation in the size, shape and armature of the proboscis across the phylum, intraspecific variation is generally regarded to be minimal. Consequently, subtle differences in proboscis morphology are often used to delimit congeneric species. In this study, striking variability in proboscis morphology was observed among individuals of Neorhadinorhynchus nudus (Harada, 1938) collected from the frigate tuna Auxis thazard Lacépède (Perciformes: Scombridae) in the South China Sea. Based on the length of the proboscis, and number of hooks per longitudinal row, these specimens of N. nudus were readily grouped into three distinct morphotypes, which might be considered separate taxa under the morphospecies concept. However, analysis of nuclear and mitochondrial DNA sequences revealed a level of nucleotide divergence typical of an intraspecific comparison. Moreover, the three morphotypes do not represent three separate genetic lineages. The surprising, and previously undocumented level of intraspecific variation in proboscis morphology found in the present study, underscores the need to use molecular markers for delimiting acanthocephalan species.

Morphological and molecular study of Neorhadinorhynchus nudus (Harada, 1938) (Acanthocephala: Cavisomidae) from Auxis thazard Lacepede (Perciformes: Scombridae) in the South China Sea

In the present study, Neorhadinorhynchus nudus (Harada, 1938) is reported from the frigate tuna Auxis thazard (Lacepéde) (Perciformes: Scombridae), in the South China Sea for the first time. The detailed morphology of N. nudus was studied using light and scanning electron microscopy based on the newly collected material. The results showed some morphometric variability between our specimens and previous studies, including the number of hooks per longitudinal row and the size of copulatory bursa and eggs. Our SEM observations also revealed all proboscis hooks emerged from elevated round rims on proboscis surface. In addition, N. nudus was firstly characterised using molecular methods by sequencing and analysing the ribosomal ITS and mitochondrial cox1 regions. There is no nucleotide divergence found in the ITS sequences, but a low level of nucleotide variability detected in the cox1 regions (the level of intraspecific nucleotide variability being 0.75% to 2.54%). The DNA sequence data obtained herein will indeed be a useful reference for rapid and accurate species identification of Neorhadinorhynchus.

Reverse taxonomy applied to the Brachionus calyciflorus cryptic species complex: Morphometric analysis confirms species delimitations revealed by molecular phylogenetic analysis and allows the (re)description of four species

The discovery and exploration of cryptic species have been profoundly expedited thanks to developments in molecular biology and phylogenetics. In this study, we apply a reverse taxonomy approach to the Brachionus calyciflorus species complex, a commonly studied freshwater monogonont rotifer. By combining phylogenetic, morphometric and morphological analyses, we confirm the existence of four cryptic species that have been recently suggested by a molecular study. Based on these results and according to an exhaustive review of the taxonomic literature, we name each of these four species and provide their taxonomic description alongside a diagnostic key.

Hidden diversity in the genus Tethya: comparing molecular and morphological techniques for species identification

Correctly determining species' identity is critical for estimating biodiversity and effectively managing marine populations, but is difficult for species that have few morphological traits or are highly plastic. Sponges are considered a taxonomically difficult group because they lack multiple consistent diagnostic features, which coupled with their common phenotypic plasticity, makes the presence of species complexes likely, but difficult to detect. Here, we investigated the evolutionary relationship of Tethya spp. in central New Zealand using both molecular and morphological techniques to highlight the potential for cryptic speciation in sponges. Phylogenetic reconstructions based on two mitochondrial markers (rnl, COI-ext) and one nuclear marker (18S) revealed three genetic clades, with one clade representing Tethya bergquistae and two clades belonging to what was a priori thought to be a single species, Tethya burtoni. Eleven microsatellite markers were also used to further resolve the T. burtoni group, revealing a division consistent with the 18S and rnl data. Morphological analysis based on spicule characteristics allowed T. bergquistae to be distinguished from T. burtoni, but revealed no apparent differences between the T. burtoni clades. Here, we highlight hidden genetic diversity within T. burtoni, likely representing a group consisting of incipient species that have undergone speciation but have yet to express clear morphological differences. Our study supports the notion that cryptic speciation in sponges may go undetected and diversity underestimated when using only morphology-based taxonomy, which has broad scale implications for conservation and management of marine systems.

Life-history strategies in zooplankton promote coexistence of competitors in extreme environments with high metal content

The toxicity of pollutants on aquatic communities is determined by the specific sensitivities and by the ecological relationships between species, although the role of ecological interactions on the specific sensitivity to pollutants is complex. We tested the effect of exposure to copper on the life-history strategies of two coexisting rotifer species of the genus Brachionus from Inca-Coya lagoon, an isolated water body located in Atacama Desert. The experiments looked at differences in the response to the stress by chemical pollution mimicking field conditions of copper exposure, levels of food, and salinity, between single-species cultures and coexisting species. Under single species cultures, B. ‘Nevada’ had lower densities, growth rates, and resting eggs production than B. quadridentatus; when in competition, B. ‘Nevada’ performed better than B. quadridentatus in most life-history traits. B. ‘Nevada’ was a copper-tolerant species, which outcompeted B. quadridentatus, more copper-sensitive, with higher levels of copper. Species-specific responses to environmental conditions and pollution, plus differential relationships between population density and production of resting eggs, resulted in reduced niche overlap between species, allowing stabilized coexistence. The extreme environmental conditions and the isolation of the Inca-Coya lagoon, make it an excellent model to understand the adaption of aquatic organisms to stressed environments.

First report on cystacanths of Sphaerirostris lanceoides (Petrochenko, 1949) (Acanthocephala: Centrorhynchidae) from the Asiatic toad Bufo gargarizans Cantor (Amphibia: Anura) in China

Everted cystacanths of Sphaerirostris lanceoides (Petrochenko, 1949) Golvan 1956 are reported from the Asiatic toad Bufo gargarizans Cantor (Amphibia: Anura) for the first time. The prevalence was 1.96% and the intensity ranged between 1.0-3.0 acanthocephalans. SEM observations revealed the morphology of the gonopore and the presence of a flat, bare region on the apical part of the proboscis. Moreover, S. lanceoides was characterised using molecular approaches by sequencing the ribosomal ITS1-5.8S-ITS2 region and the mitochondrial cox1 gene. The resulting ITS sequences were identical and the cox1 sequences showed a divergence of 0-0.75%. Sphaerirostris lanceoides is the first species of the genus for which the ITS1-5.8S-ITS2 and cox1 loci have been sequenced to aid species identification.

The genome of the freshwater monogonont rotifer Brachionus calyciflorus

Monogononta is the most speciose class of rotifers, with more than 2,000 species. The monogonont genus Brachionus is widely distributed at a global scale, and a few of its species are commonly used as ecological and evolutionary models to address questions related to aquatic ecology, cryptic speciation, evolutionary ecology, the evolution of sex and ecotoxicology. With the importance of Brachionus species in many areas of research, it is remarkable that the genome has not been characterized. This study aims to address this lacuna by presenting, for the first time, the whole-genome assembly of the freshwater species Brachionus calyciflorus. The total length of the assembled genome was 129.6 Mb, with 1,041 scaffolds. The N50 value was 786.6 kb, and the GC content was 24%. A total of 16,114 genes were annotated with repeat sequences, accounting for 21% of the assembled genome. This assembled genome may form a basis for future studies addressing key questions on the evolution of monogonont rotifers. It will also provide the necessary molecular resources to mechanistically investigate ecophysiological and ecotoxicological responses.

Indigenous species barcode database improves the identification of zooplankton

Incompleteness and inaccuracy of DNA barcode databases is considered an important hindrance to the use of metabarcoding in biodiversity analysis of zooplankton at the species-level. Species barcoding by Sanger sequencing is inefficient for organisms with small body sizes, such as zooplankton. Here mitochondrial cytochrome c oxidase I (COI) fragment barcodes from 910 freshwater zooplankton specimens (87 morphospecies) were recovered by a high-throughput sequencing platform, Ion Torrent PGM. Intraspecific divergence of most zooplanktons was < 5%, except Branchionus leydign (Rotifer, 14.3%), Trichocerca elongate (Rotifer, 11.5%), Lecane bulla (Rotifer, 15.9%), Synchaeta oblonga (Rotifer, 5.95%) and Schmackeria forbesi (Copepod, 6.5%). Metabarcoding data of 28 environmental samples from Lake Tai were annotated by both an indigenous database and NCBI Genbank database. The indigenous database improved the taxonomic assignment of metabarcoding of zooplankton. Most zooplankton (81%) with barcode sequences in the indigenous database were identified by metabarcoding monitoring. Furthermore, the frequency and distribution of zooplankton were also consistent between metabarcoding and morphology identification. Overall, the indigenous database improved the taxonomic assignment of zooplankton.

Novel in vivo experimental viability assays with high sensitivity and throughput capacity using a bdelloid rotifer

Rotifers have been used in biological research as well-characterized models of aging. Their multi-organ characters and their sensitivity for chemicals and environmental changes make them useful as in vivo toxicological and lifespan models. Our aim was to create a bdelloid rotifer model to use in high-throughput viability and non-invasive assays. In order to identify our species Philodina acuticornis odiosa (PA), 18S rDNA-based phylogenetic analysis was carried out and their species-specific morphological markers identified. To execute the rotifer-based experiments, we developed an oil-covered water-drop methodology adapted from human in vitro fertilization techniques. This enables toxicological observations of individual one-housed rotifers in a closed and controllable micro-environment for up to several weeks. Hydrogen peroxide (H₂O₂) and sodium azide (NaN₃) exposures were used as well-understood toxins. The toxicity and survival lifespan (TSL), the bright light disturbance (BLD) the mastax contraction frequency (MCF) and the cellular reduction capacity (CRC), indices were recorded. These newly developed assays were used to test the effects of lethal and sublethal doses of the toxins. The results showed the expected dose-dependent decrease in indices. These four different assays can either be used independently or as an integrated system for studying rotifers. These new indices render the PA invertebrate rotifer model a quantitative system for measuring viability, toxicity and lifespan (with TSL), systemic reaction capacity (with BLD), organic functionality (with MCF) and reductive capability of rotifers (with CRC), in vivo. This novel multi-level system is a reliable, sensitive and replicable screening tool with potential application in pharmaceutical science.