Phylogeography of Daphnia magna Straus (Crustacea: Cladocera) in Northern Eurasia: Evidence for a deep longitudinal split between mitochondrial lineages

Spatiotemporal control of transgene expression using an infrared laser in the crustacean Daphnia magna

The crustacean Daphnia magna is an emerging model for ecological and toxicological genomics. However, the lack of methods for spatial and temporal control of gene expression has impaired the elucidation of molecular mechanisms underlying responses to environments in vivo. Here we report local activation of the hsp70 promoter-driven gene cassette in D. magna by the infrared laser-evoked gene operator (IR-LEGO), a method for heating the target cells with infrared irradiation. We identified the heat-inducible promoter upstream of the D. magna hsp70-A gene. Using this promoter, we generated a transgenic Daphnia harboring the heat-shock responsive GFP reporter gene and confirmed that the GFP gene responds to heat treatment not only in juveniles and adults but also in embryos. We collected embryos from the reporter line and irradiated four different regions of interest in the embryos: a proximal region of the third thoracic segment, a part of the midline, a second maxilla, and a distal region of the endopodite of the second antenna, all of which increased GFP fluorescence with an infrared laser. Our results suggest that the IR-LEGO method is useful for spatial and temporal control of gene expression and would advance the functional genomics in D. magna.

Cryptic Species in Ecotoxicology

The advent of genetic methods has led to the discovery of an increasing number of species that previously could not be distinguished from each other on the basis of morphological characteristics. Even though there has been an exponential growth of publications on cryptic species, such species are rarely considered in ecotoxicology. Thus, the particular question of ecological differentiation and the sensitivity of closely related cryptic species is rarely addressed. Tackling this question, however, is of key importance for evolutionary ecology, conservation biology, and, in particular, regulatory ecotoxicology. At the same time, the use of species with (known or unknown) cryptic diversity might be a reason for the lack of reproducibility of ecotoxicological experiments and implies a false extrapolation of the findings. Our critical review includes a database and literature search through which we investigated how many of the species most frequently used in ecotoxicological assessments show evidence of cryptic diversity. We found a high proportion of reports indicating overlooked species diversity, especially in invertebrates. In terrestrial and aquatic realms, at least 67% and 54% of commonly used species, respectively, were identified as cryptic species complexes. The issue is less prominent in vertebrates, in which we found evidence for cryptic species complexes in 27% of aquatic and 6.7% of terrestrial vertebrates. We further exemplified why different evolutionary histories may significantly determine cryptic species' ecology and sensitivity to pollutants. This in turn may have a major impact on the results of ecotoxicological tests and, consequently, the outcome of environmental risk assessments. Finally, we provide a brief guideline on how to deal practically with cryptic diversity in ecotoxicological studies in general and its implementation in risk assessment procedures in particular. Environ Toxicol Chem 2023;42:1889-1914. © 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

A new species of the genus Ceriodaphnia Dana, 1853 (Cladocera: Daphnidae) from Eastern Siberia (Russia) that combines morphological features of two species groups

Taxa of the genus Ceriodaphnia Dana, 1853 (Cladocera: Daphniidae) are ubiquitous in temperate and tropical lakes, and the taxonomy of the genus is confused. Moreover, present keys are often regional and insufficient for the taxonomic assignment of species at a global scale. This communication is aimed at improving our understanding of the C. dubia s.l. species group. We redescribe C. dubia s.l. from Northern Eurasia and describe a new species from Central Yakutia (Eastern Siberia, Russia). In contrast to typical members of the C. dubia group, C. nikolaii sp.nov. has the postabdomen of the parthenogenetic female with preanal margin slightly or strongly projecting and angulated. Moreover, adult males have a pronounced preanal angle and sensory seta of antenna I which is shorter than the longest easthetasc. Our finding challenges current definitions of species groups in Ceriodaphnia. Indeed, a postabdomen shape with a strongly projected preanal angle is characterstic of another group of this genus, namely the C. laticaudata-group. We found a taxon that combines the diagnostic morphological characters of two species groups. Further development of the genus taxonomy must be accompanied by redescriptions of all well-accepted and dubious taxa from their type localities and revisions of populations from other localities of the world.

Population genetic analysis of the microsporidium Ordospora colligata reveals the role of natural selection and phylogeography on its extremely compact and reduced genome

The determinants of variation in a species' genome-wide nucleotide diversity include historical, environmental, and stochastic aspects. This diversity can inform us about the species' past and present evolutionary dynamics. In parasites, the mode of transmission and the interactions with the host might supersede the effects of these aspects in shaping parasite genomic diversity. We used genomic samples from 10 populations of the microsporidian parasite Ordospora colligata to investigate present genomic diversity and how it was shaped by evolutionary processes, specifically, the role of phylogeography, co-phylogeography (with the host), natural selection, and transmission mode. Although very closely related microsporidia cause diseases in humans, O. colligata is specific to the freshwater crustacean Daphnia magna and has one of the smallest known eukaryotic genomes. We found an overlapping phylogeography between O. colligata and its host highlighting the long-term, intimate relationship between them. The observed geographic distribution reflects previous findings that O. colligata exhibits adaptations to colder habitats, which differentiates it from other microsporidian gut parasites of D. magna predominantly found in warmer areas. The co-phylogeography allowed us to calibrate the O. colligata phylogeny and thus estimate its mutation rate. We identified several genetic regions under potential selection. Our whole-genome study provides insights into the evolution of one of the most reduced eukaryotic genomes and shows how different processes shape genomic diversity of an obligate parasite.

Gene expression study alerted to possible impairment in Daphnia magna individuals as a consequence of exposure to sublethal concentrations of prochloraz

In the present study, Daphnia magna individuals were exposed for 21 days to 87, 130, 170, 230 and 380 μg/L of prochloraz. The expression of genes related to lipid metabolism (fabd), oxidative stress (cat and gst), heat shock proteins synthesis (hsp70 and hsp90), haemoglobin synthesis (hgb1 and hgb2), metallothioneins synthesis (mt-a, mt-b and mt-c), and vitellogenin synthesis (vgt1 y vgt2) were analyzed. Results showed that some gene expression in D. magna was altered as a consequence of the individual exposure to the fungicide. The genes fabd, vtg1 and vtg2, cat and gst resulted unaltered by the exposure of the daphnids to different fungicide concentrations. However, daphnid exposure to 380 μg/L of prochloraz resulted in an overexpression (p < 0.05) of hsp70 gene which indicated an alteration of the normal protein synthesis and its integrity maintenance. On the other hand, mt-b gene resulted significantly underexpressed (p < 0.05) in daphnids exposed to the lowest fungicide concentrations (87, 130 and 170 μg/L, respectively). In addition, hgb1 and hgb2 genes which are related with the haemoglobin synthesis weresignificantly overexpressed (p < 0.05). Results showed that hgb1 gene was overexpressed almost 100 times more in daphnids exposed for 21 days to 170, 230 and 380 μg/L than control values. However, many authors advocate for an association of these gene expression changes with the presence of contaminants in the medium, in fact they could be used as a good indicator of early contamination at low concentrations of toxicants.

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.

Mitochondrial Lineage Diversity and Phylogeography of Daphnia (Daphnia) (Crustacea: Cladocera) in North-East Russia

The variability of the 12S gene fragment of the mtDNA for taxa belonging to subgenus Daphnia (Daphnia) O.F. Müller, 1776 (Crustacea: Cladocera) in NE Russia is studied, and their phylogenetic analysis performed. We identified (based both on morphological and molecular data) nine species belonging to four species complexes, namely: (A) D. longispina s.l.: (1) D. longispina O.F. Müller, 1776; (2) D. dentifera Forbes, 1893; (3) D. galeata Sars, 1864; (4) D. umbra Taylor, Hebert et Colbourne, 1996; (B) D. cristata s.l.: (5) D. cristata Sars, 1862; (6) D. longiremis Sars, 1862; (C) D. curvirostris s.l.: (7) D. curvirostris Eylmann, 1887; (D) D. pulex s.l.: (8) D. pulex Leydig, 1860; (9) D. middendorffiana Fischer, 1851. Rare arcto-mountainous taxon D. umbra was found in the mountains of the Sakha (Yakutia) Republic for the first time. Species diversity in NE Asia is relatively low, and the most revealed taxa are trans-Beringian. We also performed a phylogeographic analysis of D. dentifera and D. pulex s.l., the two most common species in NE Russia. Our new data allow us to assume that the daphniids of NE Asia have undergone various evolutionary scenarios during the Pleistocene period: survival is within some local refugia, and re-colonization from these areas and from North America through the Beringian land bridge, etc. We agree with previous authors who revealed that the patterns in the studied species groups are relatively recent (of Late Pleistocene or even Holocene age), although the main phylogenetic daphniid lineages (mainly congruent with the biological species) are very old. Our results provide convincing evidence for the hypothesis that NE Russia is a very important source of modern haplotypic diversity for the cladocerans.

Past climate cooling promoted global dispersal of amphipods from Tian Shan montane lakes to circumboreal lakes

Climate changes have substantial impacts on the geographic distribution of montane lakes and evolutionary dynamics of cold-adapted species. Past climate cooling is hypothesized to have promoted the dispersal of cold-adapted species via montane lakes, while future climate warming is thought to constrain their distributions. We test this hypothesis by using phylogeographic analysis and niche modeling of the Holarctic crustacean Gammarus lacustris with global sampling comprised of 567 sequenced individuals and 3180 occurrence records. We found that the species arose in Tian Shan in Central Asia and dispersed into montane lakes along the Alps, Himalayas, Tibet, East Asia, and the North American Rocky Mountain ranges, with accelerated diversification rates outside Tian Shan. Climatically suitable regions for geographic lineages of G. lacustris were larger during cooling periods (LGM), but smaller during warming periods (Mid-Holocene). In the future (2070) scenario, potential distributions in the Himalayas, North Tibet, South Tibet and North America are predicted to expand, whereas ranges in East Asia, Europe and Tian Shan will decline. Our results suggest that Mid-Miocene-to-Pleistocene continuous cooling promoted multiple independent dispersal events out of Tian Shan due to increased availability of montane lakes via "budding" of lineages. Montane lakes are conduits through which cold-adapted amphipods globally dispersed, dominating circumboreal lakes. However, future climate warming is likely to force organisms to shift upward in altitude and northward in latitude, leading to a future change in local populations. These findings highlight the importance of conservation of montane lakes, especially in the context of climate change.

Development of transgenic Daphnia magna for visualizing homology-directed repair of DNA

In the crustacean Daphnia magna, studying homology-directed repair (HDR) is important to understand genome maintenance during parthenogenesis, effects of environmental toxicants on the genome, and improvement of HDR-mediated genome editing. Here we developed a transgenic D. magna that expresses green fluorescence protein (GFP) upon HDR occurrence. We utilized the previously established reporter plasmid named DR-GFP that has a mutated eGFP gene (SceGFP) and the tandemly located donor GFP gene fragment (iGFP). Upon double-strand break (DSB) introduction on SceGFP, the iGFP gene fragment acts as the HDR template and restores functional eGFP expression. We customized this reporter plasmid to allow bicistronic expression of the mCherry gene under the control of the D. magna EF1α-1 promoter/enhancer. By CRISPR/Cas-mediated knock-in of this plasmid via non-homologous joining, we generated the transgenic D. magna that expresses mCherry ubiquitously, suggesting that the DR-GFP reporter gene is expressed in most cells. Introducing DSB on the SceGFP resulted in eGFP expression and this HDR event could be detected by fluorescence, genomic PCR, and quantitative reverse-transcription PCR, suggesting this line could be used for evaluating HDR. The established reporter line might expand our understanding of the HDR mechanism and also improve the HDR-based gene-editing system in this species.

Multiple Recent Colonizations of the Australian Region by the Chydorus sphaericus Group (Crustacea: Cladocera)

Biotic introductions are an ongoing disruption for many ecosystems. For passively dispersed freshwater zooplankton, transcontinental introductions have been common but are poorly studied in the southern hemisphere. Here we assess the hypothesis of recent introduction for populations of the Chydorus sphaericus group (Crustacea: Cladocera) in Australia. We analyzed 254 sequences (63 original sequences) from the cytochrome oxidase I region of mitochondrial DNA of Chydorus sp., which included global representation. Three Australian populations were connected with separate clades in the northern hemisphere, suggesting multiple colonization events for Australia. The timescale of the divergences was consistent with recent (Quaternary) dispersal. As Australian populations are exposed to migrating birds from the northern hemisphere, both avian and anthropogenic sources are candidates for dispersal vectors. We concluded that recent cross-hemisphere dispersal in the Chydorus sphaericus group is more common than previously believed.

Potential differences in chitin synthesis ability cause different sensitivities to diflubenzuron among three strains of Daphnia magna

Ecotoxicity testing of crustaceans using Daphnia magna has been implemented in the chemical management systems of various countries. While the chemical sensitivity of D. magna varies depending on genetically different clonal lineages, the strain used in ecotoxicity tests, including the acute immobilization test (OECD TG202), has not been specified. We hypothesized that comprehensive gene expression profiles could provide useful information on phenotypic differences among strains, including chemical sensitivity. To test this hypothesis, we performed mRNA sequencing on three different strains (NIES, England, and Clone 5) of D. magna under culture conditions. The resulting expression profile of the NIES strain was clearly different compared to the profiles of the other two strains. Gene ontology (GO) enrichment analysis suggested that chitin metabolism was significantly enriched in the NIES strain compared to that in the England strain. Consistent with the GO analysis, evidence of high levels of chitin metabolism in the NIES strain were observed across multiple levels of biological organization, such as expression of chitin synthase genes, chitin content, and chitinase activity, which suggested that the different strains would exhibit different sensitivities to chemicals used to inhibit chitin synthesis. We found that among all strains, the NIES strain was more tolerant to diflubenzuron, a chitin synthesis inhibitor, with a 14-fold difference in the 48 h-EC₅₀ value for the acute immobilization test compared to the England strain. The present study demonstrates that the differences among strains in chitin metabolism may lead to sensitivity difference to diflubenzuron, and serves as a case study of the usefulness of comprehensive gene expression profiles in finding sensitivity differences.

Genetic Signature of a Past Anthropogenic Transportation of a Far-Eastern Endemic Cladoceran (Crustacea: Daphniidae) to the Volga Basin

Most studies of water flea (Crustacea: Cladocera) invasions are concentrated on a few taxa with an obvious harmful influence on native ecosystems, while our knowledge of cases of anthropogenic introduction with not-so-obvious consequences, in most other taxa, is poor. We found in the Volga basin (European Russia) a population that contained D. curvirostris Eylmann, 1887 and its hybrids with D. korovchinskyi Kotov et al. 2021. The latter taxon is endemic to the Far East and it has appeared in the Volga basin as a result of past human-mediated transportation. The population from Bakhilovo is represented by two strongly different groups of the COI haplotypes belonging, respectively, to (1) D. curvirostris and (2) D. korovchinskyi. We detected SNPs in the position 60 of the HSP-90ex3 locus and in the 195 positions of 28S rRNA locus, which differentiate two species. Part of the specimens from Bakhilovo belonged to D. curvirostris s.str., demonstrating homozygote SNP sites in two loci, but two specimens had heterozygote SNP sites in both nuclear loci. They belong to D. curvirostris x korovchinskyi hybrids. Most morphological traits of the females were characteristic of D. curvirostris. We found in some specimens some characters which could suggest their hybrid status, but this opinion is a hypothesis only, which needs to be checked on more ample material. The exact hybrid system in this pond is not known. Moreover, we have no evidences of sexual reproduction of the hybrids; they could reproduce by parthenogenesis only as is known for hybrids of the D. pulex group, or continuously crossing with parents like some members of D. longispina group. However, poor parental D. korovchinskyi was not detected in the pond either morphologically or genetically. The exact vector of its past anthropogenic transportation to the Volga is unknown. Most probably, just ephippia of D. korovchinskyi were translocated replaced from the Khabarovsk Territory to the Samara Area somehow. This is the first report on hybrids within the D. curvirostris species complex. Here, we demonstrated that accurate studies with deep resolution increase the number of revealed cryptic invasions. We expect that the number of revealed cases of cryptic interspecific invasions will grow rapidly.

Bosminopsis deitersi (Crustacea: Cladocera) as an ancient species group: a revision

Water fleas (Crustacea: Cladocera) of the Family Bosminidae have been studied since the founding of paleolimnology and freshwater ecology. However, one species, Bosminopsis deitersi, stands out for its exceptional multicontinental range and broad ecological requirements. Here we use an integrated morphological and multilocus genetic approach to address the species problem in B. deitersi. We analyzed 32 populations of B. deitersi s. lat. Two nuclear and two mitochondrial loci were used to carry out the bGMYC, mPTP and STACEY algorithms for species delimitation. Detailed morphological study was also carried out across continents. The evidence indicated a widely distributed cryptic species in the Old World (Bosminopsis zernowi) that is genetically divergent from B. deitersi s.str. We revised the taxonomy and redescribed the species in this complex. Our sampling indicated that B. zernowi had weak genetic differentiation across its range. A molecular clock and biogeographic analysis with fossil calibrations suggested a Mesozoic origin for the Bosminopsis deitersi group. Our evidence rejects the single species hypothesis for B. deitersi and is consistent with an ancient species group (potentially Mesozoic) that shows marked morphological conservation. The family Bosminidae, then, has examples of both rapid morphological evolution (Holocene Bosmina), and morphological stasis (Bosminopsis).

Speciation in Daphnia

The microcrustacean Daphnia is arguably one of the most studied zooplankton species, having a well understood ecology, life history, and a relatively well studied evolutionary history. Despite this wealth of knowledge, species boundaries within closely related species in this genus often remain elusive and the major evolutionary forces driving the diversity of daphniids remain controversial. This genus contains more than 80 species with multiple cryptic species complexes, with many closely related species able to hybridize. Here, we review speciation research in Daphnia within the framework of current speciation theory. We evaluate the role of geography, ecology, and biology in restricting gene flow and promoting diversification. Of the 253 speciation studies on Daphnia, the majority of studies examine geographic barriers (55%). While evidence shows that geographic barriers play a role in species divergence, ecological barriers are also probably prominent in Daphnia speciation. We assess the contribution of ecological and nonecological reproductive isolating barriers between closely related species of Daphnia and found that none of the reproductive isolating barriers are restricting gene flow completely. Research on reproductive isolating barriers has disproportionally focused on two species complexes, the Daphnia pulex and Daphnia longispina species complexes. Finally, we identify areas of research that remain relatively unexplored and discuss future research directions that build our understanding of speciation in daphniids.

Unexpected mitochondrial lineage diversity within the genus Alonella Sars, 1862 (Crustacea: Cladocera) across the Northern Hemisphere

Representatives of the genus Alonella Sars (Crustacea: Cladocera: Chydorinae) belong to the smallest known water fleas. Although species of Alonella are widely distributed and often abundant in acidic and mountain water bodies, their diversity is poorly studied. Morphological and genetic approaches have been complicated by the minute size of these microcrustaceans. As a result, taxonomists have avoided revising these species. Here, we present genetic data on Alonella species diversity across the Northern Hemisphere with particular attention to the A. excisa species complex. We analyzed 82 16S rRNA sequences (all newly obtained), and 78 COI sequences (39 were newly obtained). The results revealed at least twelve divergent phylogenetic lineages, possible cryptic species, of Alonella, with different distribution patterns. As expected, the potential species diversity of this genus is significantly higher than traditionally accepted. The A. excisa complex is represented by nine divergent clades in the Northern Hemisphere, some of them have relatively broad distribution ranges and others are more locally distributed. Our results provide a genetic background for subsequent morphological analyses, formal descriptions of Alonella species and detailed phylogeographical studies.

Pleistocene Branchiopods (Cladocera, Anostraca) from Transbaikalian Siberia Demonstrate Morphological and Ecological Stasis

Pleistocene water bodies have been studied using the paleolimnological approach, which traces environmental changes using particular subfossils as ecological proxies, rather than analysis of the paleocommunities themselves. Within a given taphocoenosis, the presence and quantity of animals are related to environmental conditions rather than to community types where relationships between taxa are stabilized during their long-term co-occurrence and are (at least partially) more important than the particular environmental conditions at the time of deposition, which may have experienced significant seasonal and inter-seasonal variations. Here, we analyze Branchiopoda (Crustacea) of two paleolocalities in the Transbaikalian Region of Russia: Urtuy (MIS3) and Nozhiy (older than 1.5 million years). Cladocerans Daphnia (Ctenodaphnia) magna, D. (C.) similis, D. (Daphnia) pulex, Ceriodaphnia pulchella-reticulata, C. laticaudata, Simocephalus sp., Moina cf. brachiata, M. macropopa clade, Chydorus cf. sphaericus, Capmtocercus sp. and anostracans Branchinecta cf. paludosa, and Streptocephalus (Streptocephalus) sp. are found in two localities. With the exception of the last taxon, which now occurs in the southern Holarctic, all other taxa inhabit the Transbaikalian Region. Within Eurasia, the steppe zone has the greatest diversity of large branchiopods and a high diversity of some cladocerans, such as subgenus Daphnia (Ctenodaphnia) and Moina sp. Here we demonstrated that the branchiopod community in shallow steppe water bodies has been unchanged since at least the Pleistocene, demonstrating long-term morphological and ecological stasis.

A new species group from the Daphnia curvirostris species complex (Cladocera: Anomopoda) from the eastern Palaearctic: taxonomy, phylogeny and phylogeography

The eastern Palaearctic is a centre of diversity for freshwater cladocerans (Crustacea), but little is known about the evolution and taxonomy of this diversity. Daphnia curvirostris is a Holarctic species complex that has most of its diversity in the eastern Palaearctic. We examined the phylogeography, rates of evolution and taxonomic status for each clade of the D. curvirostris complex using morphological and genetic evidence from four genes. The cybertaxonomical and morphological evidence supported an eastern Palaearctic clade, with at least four species (described here as the Daphnia korovchinskyi sp. nov. group) having diagnostic morphological characters. We also detected convergent morphological characters in the D. curvirostris complex that provided information about species boundaries. Two of the new species (Daphnia koreana sp. nov. and Daphnia ishidai sp. nov.) are known from single ponds and are threatened by human activity. Divergence time estimates suggested an ancient origin (12–28 Mya) for the D. korovchinskyi group, but these estimates are complicated by the small number of calibration points.

Crustacean remains from the Yuka mammoth raise questions about non-analogue freshwater communities in the Beringian region during the Pleistocene

Frozen permafrost Pleistocene mammal carcasses with soft tissue remains are subject to intensive study and help elucidate the palaeoenvironment where these animals lived. Here we present an inventory of the freshwater fauna and flora found in a sediment sample from the mummified Woolly Mammoth carcass found in August 2010, from the Oyogos Yar coast near the Kondratievo River in the Laptev Sea region, Sakha (Yakutia) Republic, NE Russia. Our study demonstrates that the waterbody where the carcass was buried could be characterized as a shallow pond or lake inhabited mainly by taxa which are present in this area today, but additionally by some branchiopod crustacean taxa currently absent or unusual in the region although they exist in the arid zone of Eurasia (steppes and semi-deserts). These findings suggest that some "non-analogue" crustacean communities co-existed with the "Mammoth fauna". Our findings raise questions about the nature of the waterbodies that existed in Beringia during the MIS3 climatic optimum when the mammoth was alive.

Phylogeography of Begonia luzhaiensis suggests both natural and anthropogenic causes for the marked population genetic structure

BACKGROUND

Sino-Vietnamese limestone karsts (SVLK) are a biodiversity hotspot rich in endemic plant species associated with caves and cave-like microhabitats. Based on phylogenetic studies of Begonia sect. Coelocentrum, a species-rich and characteristic SVLK clade, geographic isolation caused by extensive and continuous karstification was proposed as the major driving force triggering population diversification and geographic speciation. To test this proposition, population genetics and phylogeography of Begonia luzhaiensis were investigated using EST-SSR markers and the chloroplast trnC-ycf6 intergenic spacer.

RESULTS

F statistics, Bayesian clustering analysis, AMOVA, and PCoA of both data sets all indicated substantial population differentiation and significant isolation by distance. Nested clade phylogeographic analyses inferred that historical fragmentations have been prominent, congruent with Guangxi's geohistory of karstification as well as suggesting a mountain chain in northeastern Guangxi could have also acted as a major geographic barrier. A Bayesian skyline plot (BSP) indicated a slight decline in effective population size at 75,000 years ago (75 Kya), coinciding with the last glacial period during which the increased aridity in East Asia had retarded karstification, negatively affecting the populations of B. luzhaiensis. However, BSP detected a continuous and further population decline until the present time even though summer monsoons have resumed since the end of the last glacial maximum.

CONCLUSIONS

The microevolution patterns of B. luzhaiensis support that limited gene flow would have greatly enhanced the effects of random genetic drift and has been a major factor promoting diversification in Begonia, highly congruent with previous proposition. Based our study, we further propose that the arrival of Paleolithic Homo sapiens whose activities centered around limestone caves could have had further impacts on the populations of B. luzhaiensis, resulting in additional population decline. Further habitat destruction could have resulted from the transition from hunter gathering to food-producing societies ca. 20-10 Kya and the development of agriculture ca. 10 Kya in South China. Implications of the current study for SVLK plant conservation are also discussed.

Unexpected endemism in the Daphnia longispina complex (Crustacea: Cladocera) in Southern Siberia

The biological significance of regional cladoceran morphotypes in the montane regions of the central Palearctic remains poorly understood. In the Holarctic Daphnia longispina complex (Cladocera: Daphniidae), several variants, lineages and species have been proposed as endemic for Southern Siberia. Daphnia turbinata Sars, for example, named after its unusual head shape, is known only from Southern Siberia. Here we sequence DNA of Daphnia from three mitochondrial genes (12S rRNA, 16S rRNA, and NADH dehydrogenase subunit 2, ND2) from 57 localities in Russia and Mongolia (the majority being from Southern Siberia) and place them in evolutionary context with existing data. Our aim was to examine regional endemism of the Daphnia longispina complex in Southern Siberian; to improve the phylogenetic understanding with improved taxonomic and regional sampling, and to better understand the influence of Pleistocene glaciation on the biogeography of these lineages. At least three lineages showed genetic evidence for endemism in Southern Siberia. There was strong support for D. turbinata as a sister lineage to to D. longispina/D. dentifera. Another endemic, Siberian D. cf. longispina, is a sister group to the longispina group in general. Within D. longispina s. str. there was an endemic Siberian clade with a western range boundary near the Yenisei River Basin. Gene flow estimates among populations (based on F_ST values) were very low for clades of D. longispina on a regional (the original 12S dataset), and on a pan-Eurasian (the extended 12S dataset) scale. Negative values of Fu’s F_S and Tajima’s D tests prevailed for the species examined with significant values found for two D. longispina clades, D. dentifera, D. galeata and D. cristata. Our results support the notion that Southern Siberia is an important biogeographic region for cladocerans as it contained unexpected diversity of endemics (such as D. turbinata, D. cf. longispina and lineages of D. umbra and D. longsipina s.str.) and from being the geographic meeting place of expanding postglacial lineages from eastern and western refugia.

Contrasting endemism in pond-dwelling cyclic parthenogens: the Daphnia curvirostris species group (Crustacea: Cladocera)

Pond-dwelling cyclic parthenogens are often proposed to be highly vagile. However, the Holarctic biogeography of parthenogens has been hampered by very limited sampling in the eastern Palearctic. Here we examine the geographic boundaries, diversity, and connectivity across the Palearctic for the Daphnia curvirostris complex (Cladocera: Daphniidae). Nuclear (HSP90) and mitochondrial (ND2) sequence data supported the existence of five main clades (most of which corresponded to presumptive species) with one eastern Palearctic clade being novel to this study (the average mitochondrial genetic divergence from known species was 19.2%). D. curvirostris s.s. was geographically widespread in the Palearctic, with a population genetic signature consistent with postglacial expansion. The Eastern Palearctic had local nine endemic species and/or subclades (other Holarctic regions lacked more than one endemic subclade). Even though several endemic species appeared to have survived Pleistocene glaciation in the eastern Palearctic, much of the Palearctic has been recolonized by D. curvirostris s.str. from a Western Palearctic refugium. A disjunct population in Mexico also shared its haplotypes with D. curvirostris s.str., consistent with a recent introduction. The only apparently endemic North American lineage was detected in a thermally disturbed pond system in northwestern Alaska. Our results for pond-dwelling cyclic parthenogens further support the hypothesis that the Eastern Palearctic is a diversity hotspot for freshwater invertebrates.

Contrasting phylogeographic patterns and demographic history in closely related species of Daphnia longispina group (Crustacea: Cladocera) with focus on North-Eastern Eurasia

Species with large geographic distributions present a challenge for phylogeographic studies due to the logistic difficulties of obtaining adequate samples. Daphnia O.F. Müller (Anomopoda: Daphniidae) is a model genus for evolutionary biology and ecology, but many regions such as the remote areas of Siberia, remain poorly studied. Here we examined genetic polymorphism in the ribosomal 12S and the protein-coding ND2 mitochondrial genes of three closely related taxa of the Daphnia (Daphnia) longispina complex, namely D. galeata Sars, D. longispina O.F. Müller and D. dentifera Forbes. We estimated the phylogenetic relationships among these taxa based on a concatenated alignment of these two genes. Using sequences from the present study and those available in GenBank, we investigated the geographic distributions of the mitochondrial haplotypes of these species and proposed an evolutionary scenario for each taxon. Network structures, haplotype distribution patterns, and FST values indicated significant differences in the evolutionary history of the examined species. Our analysis of D. galeata populations confirmed its recent and fast expansion, without a previous phase of a strong population disconnection. In contrast, the high haplotype diversity in D. dentifera and D. longispina could be explained by the survival of different phylogroups in several glacial refugia located in different geographic regions. For all studied species, maximum haplotype diversity was recorded in the remote regions of Siberia-lakes of the Yenisei River and Transbaikalia. Our study is an important step in our understanding of the evolutionary history of the Daphnia longispina group and provides further evidence of the biogeographic significance of Siberia for freshwater taxa.