A fossil-calibrated phylogenomic analysis of Daphnia and the Daphniidae

In the post-genomic era, much of phylogenetic analyses still relies on mitochondrial DNA, either alone or in combination with few nuclear genes. Although this approach often makes it possible to construct well-supported trees, it is limited because mtDNA describes the history of a single locus, and nuclear phylogenies based on a few loci may be biased, leading to inaccurate tree topologies and biased estimations of species divergence time. In this study, we perform a phylogenomic analysis of the Daphniidae family (Crustacea: Branchiopoda: Anomopoda) including some of the most frequently studied model organisms (Daphnia magna and D. pulex) whose phylogenetic relationships have been based primarily on an assessment of a few mtDNA genes. Using high-throughput sequencing, we were able to assemble 38 whole mitochondrial genomes and draft nuclear genomes for 18 species, including at least one species for each known genus of the family Daphniidae. Here we present phylogenies based on 636 nuclear single-copy genes shared among all sampled taxa and based on whole mtDNA genomes. The phylogenies we obtained were highly supported and showed some discrepancies between nuclear and mtDNA based trees at deeper nodes. We also identified a new candidate sister lineage of Daphnia magna. Our time-calibrated genomic trees, which we constructed using both fossil records and substitution rates, yielded very different estimates of branching event times compared to those based on mtDNA. By providing multi-locus, fossil-calibrated trees of the Daphniidae, our study contributes to an improved phylogenetic framework for ecological and evolutionary studies that use water fleas as a model system.Peer reviewe

Non-Indigenous Cladocera (Crustacea: Branchiopoda): From a Few Notorious Cases to a Potential Global Faunal Mixing in Aquatic Ecosystems

Non-indigenous species may pose a threat to native ecosystems worldwide. In aquatic environments, invasives may have a negative impact on human food security and livelihoods. Several water fleas (Crustacea: Branchiopoda: Cladocera) are notorious invasive alien species influencing large freshwater lake systems and even inland seas. In the current review, we discuss the state of knowledge regarding non-indigenous species in the Cladocera and their invasiveness potential in different continents. We argue that the potential impacts and occurrence of cladoceran exotics may be higher than generally assumed. We critically review 79 cases from literature sources, involving 61 cladoceran taxa where records outside of their natural distribution ranges were previously interpreted as invasions. We assessed the probability of natural range expansions versus human-mediated introductions and we discuss several major corridors of invasion. We estimate human-mediated transportations for at least 43 taxa (out of 61; ca 70%), while other cases can be seen as natural expansions of their distribution ranges (not necessarily/not likely human-mediated) and/or taxonomical confusion. We confirm non-indigenous presence in recipient regions for at least 41 cladoceran taxa, of which several are true invasives (i.e., with negative impacts on native ecosystems). The majority are zooplankters with effects on pelagic freshwater ecosystems, yet we also report on introductions by littoral taxa. We argue that cryptic introductions of cladocerans are taking place on a global scale, yet they remain under the radar. We highlight several striking case studies, such as the Ponto-Caspian onychopods that have invaded the Baltic Sea and the Laurentian Great Lakes, and several clones of the anomopod genera Daphnia and Bosmina that have successfully colonised new environments, causing equilibria shifts in native aquatic worlds. At the same time, we dispel some myths about taxa that were misconstrued as invasive in certain localities. Based on our review, the first of its kind for freshwater zooplankton, future environmental monitoring tools including molecular techniques and detailed surveys with rigorous and critical taxonomical assessments may help to provide a clearer picture on the extent of invasiveness of cladocerans.O

Whole-Genome Phylogenetic Reconstruction as a Powerful Tool to Reveal Homoplasy and Ancient Rapid Radiation in Waterflea Evolution

Although phylogeny estimation is notoriously difficult in radiations that occurred several hundred million years ago, phylogenomic approaches offer new ways to examine relationships among ancient lineages and evaluate hypotheses that are key to evolutionary biology. Here, we reconstruct the deep-rooted relationships of one of the oldest living arthropod clades, the branchiopod crustaceans, using a kaleidoscopic approach. We use concatenation and coalescent tree-building methods to analyze a large multigene data set at the nucleotide and amino acid level and examine gene tree versus species tree discordance. We unequivocally resolve long-debated relationships among extant orders of the Cladocera, the waterfleas, an ecologically relevant zooplankton group in global aquatic and marine ecosystems that is famous for its model systems in ecology and evolution. To build the data set, we assembled eight de novo genomes of key taxa including representatives of all extant cladoceran orders and suborders. Our phylogenetic analysis focused on a BUSCO-based set of 823 conserved single-copy orthologs shared among 23 representative taxa spanning all living branchiopod orders, including 11 cladoceran families. Our analysis supports the monophyly of the Cladocera and reveals remarkable homoplasy in their body plans. We found large phylogenetic distances between lineages with similar ecological specializations, indicating independent evolution in major body plans, such as in the pelagic predatory orders Haplopoda and Onychopoda (the "Gymnomera"). In addition, we assessed rapid cladogenesis by estimating relative timings of divergence in major lineages using reliable fossil-calibrated priors on eight nodes in the branchiopod tree, suggesting a Paleozoic origin around 325 Ma for the cladoceran ancestor and an ancient rapid radiation around 252 Ma at the Perm/Triassic boundary. These findings raise new questions about the roles of homoplasy and rapid radiation in the diversification of the cladocerans and help examine trait evolution from a genomic perspective in a functionally well understood, ancient arthropod group. [Cladocera; Daphnia; evolution; homoplasy; molecular clock; phylogenomics; systematics; waterfleas.]Peer reviewe

Whole-Genome Phylogenetic Reconstruction as a Powerful Tool to Reveal Homoplasy and Ancient Rapid Radiation in Waterflea Evolution

Although phylogeny estimation is notoriously difficult in radiations that occurred several hundred million years ago, phylogenomic approaches offer new ways to examine relationships among ancient lineages and evaluate hypotheses that are key to evolutionary biology. Here, we reconstruct the deep-rooted relationships of one of the oldest living arthropod clades, the branchiopod crustaceans, using a kaleidoscopic approach. We use concatenation and coalescent tree-building methods to analyze a large multigene data set at the nucleotide and amino acid level and examine gene tree versus species tree discordance. We unequivocally resolve long-debated relationships among extant orders of the Cladocera, the waterfleas, an ecologically relevant zooplankton group in global aquatic and marine ecosystems that is famous for its model systems in ecology and evolution. To build the data set, we assembled eight de novo genomes of key taxa including representatives of all extant cladoceran orders and suborders. Our phylogenetic analysis focused on a BUSCO-based set of 823 conserved single-copy orthologs shared among 23 representative taxa spanning all living branchiopod orders, including 11 cladoceran families. Our analysis supports the monophyly of the Cladocera and reveals remarkable homoplasy in their body plans. We found large phylogenetic distances between lineages with similar ecological specializations, indicating independent evolution in major body plans, such as in the pelagic predatory orders Haplopoda and Onychopoda (the "Gymnomera"). In addition, we assessed rapid cladogenesis by estimating relative timings of divergence in major lineages using reliable fossil-calibrated priors on eight nodes in the branchiopod tree, suggesting a Paleozoic origin around 325 Ma for the cladoceran ancestor and an ancient rapid radiation around 252 Ma at the Perm/Triassic boundary. These findings raise new questions about the roles of homoplasy and rapid radiation in the diversification of the cladocerans and help examine trait evolution from a genomic perspective in a functionally well understood, ancient arthropod group. [Cladocera; Daphnia; evolution; homoplasy; molecular clock; phylogenomics; systematics; waterfleas.]Peer reviewe

Climate change effects on the potential distribution of the endemic Commiphora species (Burseraceae) on the island of Socotra

The Socotra Archipelago (Yemen) is an interesting biodiversity hotspot, with a significant proportion of endemic species that have evolved to survive in an arid subtropical environment, inscribed as a World Heritage Site by UNESCO. The terrestrial ecosystems of Socotra face several threats, including climate change, overgrazing and soil degradation. Socotra Island has four endemic species of the genus Commiphora (Burseraceae). Little is known about their local distribution and ecology, yet these trees could be useful indicator species. Our study focuses on the distribution and niche characterisation of the four endemic Commiphora species of Socotra and how climate change may affect them. The aim is to improve insights into their habitats and to provide an essential basis for future local management plans and ecological restoration. We compared the current distribution with the forecasted potential distribution under a CMIP6 (Coupled Model Intercomparison Project) climate scenario, allowing us to define target conservation areas and assess potential local extinction risks. To achieve this, we collected distribution data in the field throughout Socotra Island, covering the current distribution ranges of the four species. To assess the potential distribution of these species, we applied three models (GAM, MaxEnt, RandomForest) using bioclimatic, topographic and soil variables. Forecasts under a climate change scenario were made using bioclimatic variables from the CMCC-CESM2 climate model for two different socioeconomic pathways. The distribution of three endemic Socotran Commiphora is mainly correlated to clay content in the soil and winter precipitation, while C. socotrana is affected by seasonal precipitation and temperature. Under different potential future climate scenarios, the distribution of C. ornifolia is predicted to remain stable or increase, while C. parvifolia distribution could increase, yet C. planifrons and C. socotrana are predicted to undergo a strong reduction of suitable areas and an upward shift in the mountains. Our results highlight that it is essential to conserve the unique terrestrial ecosystems in Socotra and to preserve these endemic trees which have a wide range of ecosystem services. Updates on the predicted extinction risk assessment are fundamental to understand conservation priorities and strategize future actions to ensure the persistence of Socotran myrrh trees and other endangered endemic tree taxa on the island

Approaches to Assess the Suitability of Zooplankton for Bioregenerative Life Support Systems

Future manned space exploration will send humans farther away from Earth than ever before (e.g., to Mars), leading to extended mission durations and thus to a higher demand for essentials such as food, water and oxygen. As resupplying these items from Earth is nearly impossible, aquatic bioregenerative life support systems (BLSS) appear to be a promising solution. Due to its central role in aquatic ecosystems, zooplankton could act as a key player in aquatic BLSS, linking oxygen liberating, autotrophic producers and higher trophic levels. However, prior to the utilization of BLSS in space, organisms proposed to inhabit these systems have to be studied thoroughly to evaluate any space-borne adverse traits, which may impede a proper function of the system. To investigate the impact of microgravity (μg), in particular, several platforms are available, providing μg periods ranging from seconds (Bremen drop tower and parabolic flights), to minutes (sounding rockets), up to even days and months (space flights and the International Space Station (ISS)). Furthermore, ground-based facilities, such as clinostats, enable the of candidate organisms to variable periods of simulated/functional μg. In this book chapter, research on zooplankton utilizing these methods is summarized

Male meiosis in Crustacea:synapsis, recombination, epigenetics and fertility in Daphnia magna

We present the first detailed cytological study of male meiosis in Daphnia (Crustacea: Branchiopoda: Cladocera)—an aquatic microcrustacean with a cyclical parthenogenetic life cycle. Using immunostaining of the testes in Daphnia magna for baseline knowledge, we characterized the different stages of meiotic division and spermiogenesis in relation to the distribution of proteins involved in synapsis, early recombination events and sister chromatid cohesion. We also studied post-translational histone modifications in male spermatocytes, in relation to the dynamic chromatin progression of meiosis. Finally, we applied a DNA fragmentation test to measure sperm quality of D. magna, with respect to levels of inbreeding. As a proxy for fertility, this technique may be used to assess the reproductive health of a sentinel species of aquatic ecosystems. Daphnia proves to be a model species for comparative studies of meiosis that is poised to improve our understanding of the cytological basis of sexual and asexual reproduction. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00412-015-0558-1) contains supplementary material, which is available to authorized users

A hidden species becoming visible : biogeography and ecology of Rhynchotalona latens (Cladocera, Anomopoda, Chydoridae)

A long hidden chydorid (Chydoridae, Cladocera) taxon, first found as fossil specimens and recently redefined as Rhynchotalona latens (Sarmaja-Korjonen et al., Hydrobiologia 436: 165-169, 2000) is investigated for its biogeography and ecology. Late Holocene sediment sequence from Lake Sylvilampi, NE Finnish Lapland, and R. latens spatial distribution in relation to limno-climatic attributes in Finland were examined. Principal component analyses of fossil cladoceran communities showed that R. latens is mostly affiliated with Alonella excisa-Alonopsis elongata-Alonella nana species pool. Generalized linear modeling of R. latens responses to limno-climatic variation indicated that it prefers acidic, mesotrophic, humic and shallow lakes with organic sediments in NE Lapland and has a north boreal-subarctic climatic affiliation. At the northern end of its geographical distribution (NE Lapland), it reproduces with abundant gamogenesis under environmental stress. The specialized taxon is a benthic detritivore and scraper and has a Holarctic northern-alpine distribution. It is a glacial relict associated with modern analogs of periglacial aquatic environments, and it occurs in semi-aquatic wetlands, lush lake littorals and clear and cold waters. Examination of chydorids as bioindicators, especially those with restricted niches, allow us to understand biodiversity responses of lake littorals under changing limno-climatic regimes.Peer reviewe

Seed Viability and Potential Germination Rate of Nine Endemic Boswellia Taxa (Burseraceae) from Socotra Island (Yemen)

The endemic Boswellia species (Burseraceae) on Socotra Island (Yemen) are of great local significance due to their various local ethnobotanical uses. However, despite the fact that these trees are endangered, little is known about their biology. We tested seed germination rates in controlled experiments (trials of 21 days) for two subsequent years and for nine endemic taxa of Boswellia occurring on Socotra Island. For this, seeds were collected island-wide from a wide range of localities and for several populations per species. We observed differences in germination among Boswellia species, among species and localities and among both years, which indicates that the development of seeds is strongly affected by external ecological factors. Although we noted a large variation in seed germination (relatively high in Boswellia socotrana), and half of the species showed relatively low mean daily germination, our study indicated that all endangered endemic Frankincense Tree taxa of Socotra harbor the potential for in situ conservation through recruitment, given that known impacts can be reduced in local replantation areas (e.g., grazing).O

Loss of susceptibility as a novel breeding strategy for durable and broad-spectrum resistance

Recent studies on plant immunity have suggested that a pathogen should suppress induced plant defense in order to infect a plant species, which otherwise would have been a nonhost to the pathogen. For this purpose, pathogens exploit effector molecules to interfere with different layers of plant defense responses. In this review, we summarize the latest findings on plant factors that are activated by pathogen effectors to suppress plant immunity. By looking from a different point of view into host and nonhost resistance, we propose a novel breeding strategy: disabling plant disease susceptibility genes (S-genes) to achieve durable and broad-spectrum resistance