Taxonomy and Distribution of Freshwater Pearl Mussels (Unionoida: Margaritiferidae) of the Russian Far East

The freshwater pearl mussel family Margaritiferidae includes 13 extant species, which are all listed by IUCN as endangered or vulnerable taxa. In this study, an extensive spatial sampling of Margaritifera spp. across the Russian Far East (Amur Basin, Kamchatka Peninsula, Kurile Archipelago and Sakhalin Island) was conducted for a revision of their taxonomy and distribution ranges. Based on their DNA sequences, shell and soft tissue morphology, three valid species were identified: Margaritifera dahurica (Middendorff, 1850), M. laevis (Haas, 1910) and M. middendorffi (Rosén, 1926). M. dahurica ranges across the Amur basin and some of the nearest river systems. M. laevis is distributed in Japan, Sakhalin Island and the Kurile Archipelago. M. middendorffi was previously considered an endemic species of the Kamchatka. However, it is widespread in the rivers of Kamchatka, Sakhalin Island, the Kurile Islands (across the Bussol Strait, which is the most significant biogeographical boundary within the archipelago), and, likely, in Japan. The Japanese species M. togakushiensis Kondo & Kobayashi, 2005 seems to be conspecific with M. middendorffi because of similar morphological patterns, small shell size (<100 mm long) and overlapped ranges, but it is in need of a separate revision. Phylogenetic analysis reveals that two NW Pacific margaritiferid species, M. laevis and M. middendorffi, formed a monophyletic 18S rDNA clade together with the North American species M. marrianae and M. falcata. The patterns that were found in these Margaritifera spp. are similar to those of freshwater fishes, indicating multiple colonizations of Eastern Asia by different mitochondrial lineages, including an ancient Beringian exchange between freshwater faunas across the Pacific.     

A molecular timescale for the evolution of the African freshwater fish family Kneriidae (Teleostei: Gonorynchiformes)

We re-examine the phylogenetic relationships of the family Kneriidae using whole mitogenome sequences across all four kneriid genera including the two recently recognized species of Cromeria (C. nilotica and C. occidentalis), and we provide a timescale to discuss the evolution of the family. The resulting phylogeny supports the monophyly of the family Kneriidae and the monophyly of the genus Cromeria. The two Cromeria species exhibit large genetic divergence (18.2%) that is comparable to those between Grasseichthys gabonensis and each two Cromeria species (16.9 and 19.0%). The three paedomorphic kneriid species (C. occidentalis, C. nilotica and G. gabonensis) do not form a monophyletic group, but the alternative hypothesis in which they are monophyletic cannot be statistically rejected. Two alternative relaxed molecular-clock Bayesian analyses, differing on how we time-calibrated the phylogenetic tree using the fossil record, support a Late Jurassic or Late Cretaceous origin of the African freshwater gonorynchiforms. The early diversification of the family Kneriidae is concomitant with the reductions or loss of several morphological characters that took place in a relatively short time interval of about 12–21 million years either during the Eocene or at the end of the Late Cretaceous.     

The rise to dominance of the angiosperm kingdom: dispersal,habitat widening and evolution during the Late Cretaceous of Europe

Coiffard, C. & Gomez, B. 2009: The rise to dominance of the angiosperm kingdom: dispersal, habitat widening and evolution during the Late Cretaceous of Europe. Lethaia, Vol. 43, pp. 164–169. The earliest fossil records of angiosperms in Europe occur in the Barremian and consist of freshwater wetland plants. From the Barremian onwards, angiosperms show a stepwise widening of their ecological range with the result that they inhabited most environments by the Cenomanian. Nevertheless, most angiosperms had still restricted habitats, while a few angiosperm trees were confined to disturbed environments, such as channel margins. A Wagner’s Parsimony Method analysis performed on a fossil plant and locality database from the Turonian to the Campanian of Europe indicates continued decrease in richness of ferns and gymnosperms compared with angiosperms, turnover between conifer and palm trees in freshwater‐related swamps at about the Cenomanian/Turonian boundary, and spreading of angiosperm trees through the floodplains. The ecological range of angiosperm trees was increased, being recorded in channel margins from the Cenomanian and spreading over floodplains (e.g. Platanaceae) and swamps (e.g. Arecaceae) by the Campanian. These new ecological ranges and successions went with innovative architectures, such as dicot trees and palm trees. Most living core angiosperm families had their earliest representatives in the Late Cretaceous, which should be considered as the dawn of modern angiosperm forests. □Core angiosperms, Europe, Late Cretaceous, palms, Wagner’s Parsimony Method.     

Discovery of fossil Ayu (<Emphasis Type="Italic">Plecoglossus altivelis</Emphasis>) from the Upper Miocene of Shimane Prefecture,Japan

The Ayu, Plecoglossus altivelis, comprising three subspecies, is the only species in the genus Plecoglossus in the family Osmeridae. Here, we describe for the first time the discovery of fossil specimens of P. altivelis from the Upper Miocene sediment of Matsue, Shimane Prefecture, Japan. The fossil individuals are subadult and have comb teeth in the second and third generations. These fossil specimens are clearly similar to the recent P. altivelis, the former’s meristic characters being included in the three recent subspecies. In terms of numbers of pectoral fin rays and vertebrae, the fossil specimens are more similar to the subspecies Plecoglossus altivelis ryukyuensis than the other subspecies, but they also show different dorsal fin shapes and anal fin ray counts. This discovery of fossil P. altivelis indicates the persistence of the species for at least 10 million years, from the Late Miocene to the present.     

Ancient DNA from an extinct Mediterranean micromammal—Hypnomys morpheus (Rodentia: Gliridae)—Provides insight into the biogeographic history of insular dormice

The dormice (Gliridae) are a family of rodents represented by relatively few extant species, though the family was much more species-rich during the Early Miocene. Intergeneric phylogenetic relationships among glirids in some cases remain unresolved, despite extensive molecular and morphological analyses. Uncertainty is greatest with respect to the relationships among fossil taxa and how extinct lineages are related to modern species. The fossil genus Hypnomys from the Balearic Islands (western Mediterranean Sea) includes the Late Pleistocene–Holocene species Hypnomys morpheus, which has variously been considered a close relative or subgenus of the extant Eliomys. In the present study, we sequenced ancient mitochondrial DNA from H. morpheus, which suggests a sister relationship with the extant members of Eliomys. In addition, the pairwise sequence variation between Hypnomys and Eliomys is higher than that observed between congeneric glirid species (e.g., many Graphiurus spp.), which allows us to reject the hypothesis that Hypnomys is a subgenus of Eliomys. Our molecular dating analyses suggest that Hypnomys and Eliomys diverged 13.67 million years ago (95% highest posterior density [HPD] = 7.39–20.07). The relatively early split between these genera together with the molar morphology of early representatives of Hypnomys points to a Middle-Late Miocene origin from a continental glirid with a complex molar pattern, such as Vasseuromys or a closely related genus.     

Chromosome-level genome assembly of Welwitschia mirabilis,a unique Namib Desert species

Welwitschia mirabilis, which is endemic to the Namib Desert, is the only living species within the family Welwitschiaceae. This species has an extremely long lifespan of up to 2,000 years and bears a single pair of opposite leaves that persist whilst alive. However, the underlying genetic mechanisms and evolution of the species remain poorly elucidated. Here, we report on a chromosome-level genome assembly for W. mirabilis, with a 6.30-Gb genome sequence and contig N50 of 27.50 Mb. In total, 39,019 protein-coding genes were predicted from the genome. Two brassinosteroid-related genes (BRI1 and CYCD3), key regulators of cell division and elongation, were strongly selected in W. mirabilis and may contribute to their long ever-growing leaves. Furthermore, 29 gene families in the mitogen-activated protein kinase signalling pathway showed significant expansion, which may contribute to the desert adaptations of the plant. Three positively selected genes (EHMT1, EIF4E, SOD2) may be involved in the mechanisms leading to long lifespan. Based on molecular clock dating and fossil calibrations, the divergence time of W. mirabilis and Gnetum montanum was estimated at ~123.5 million years ago. Reconstruction of population dynamics from genome data coincided well with the aridification of the Namib Desert. The genome sequence detailed in the current study provides insight into the evolution of W. mirabilis and should be an important resource for further study on gnetophyte and gymnosperm evolution.     

A new species of fossil Mus (Rodentia, Muridae) from the Indian Himalaya: Evolutionary and phylogenetic implications

A new species of fossil Mus (Rodentia, Mammalia) is reported from the Late Pleistocene fluvio-lacustrine deposits of the Kumaun sector of Indian Himalaya. The fossiliferous horizon, medium-coarse grained sand lenses embedded in the massive carbonaceous mud, is exposed at locality Dulam and is Late Pleistocene (ca. 30 ka) in age. A new species, Mus dulamensis n. sp., is proposed. Characterized by strongly distorted and moderately elongated M¹ (about 170% of M² length) with prominent conules in front of the t₂, higher magnitude of stephanodonty (between the t₁ and t₄ and between the t₃ and t₆), moderately reduced M³ (about 56% of M² length) and stronger connection between the cusps, this species is distinct from all other species of the genus and is included in the “booduga group”. I suggest that M. dulamensis n. sp. is comparatively more derived than M. auctor, M. flynni, M. jacobsi and Mus sp. and it may have given rise to M. booduga or M. dunni. It is further suggested that presently living M. booduga and M. dunni are more specialized than Mus dulamensis n. sp.     

Roads to isolation: Similar genomic history patterns in two species of freshwater crabs with contrasting environmental tolerances and range sizes

Freshwater species often show high levels of endemism and risk of extinction owing to their limited dispersal abilities. This is exemplified by the stenotopic freshwater crab, Johora singaporensis which is one of the world's 100 most threatened species, and currently inhabits less than 0.01 km² of five low order hill streams within the highly urbanized island city‐state of Singapore. We compared populations of J. singaporensis with that of the non‐threatened, widespread, abundant, and eurytopic freshwater crab, Parathelphusa maculata, and found surprisingly high congruence between their population genomic histories. Based on 2,617 and 2,470 genome‐wide SNPs mined via the double‐digest restriction‐associated DNA sequencing method for ~90 individuals of J. singaporensis and P. maculata, respectively, the populations are strongly isolated (F_ST = 0.146–0.371), have low genetic diversity for both species (also for COI), and show signatures of recent genetic bottlenecks. The most genetically isolated populations for both species are separated from other populations by one of the oldest roads in Singapore. These results suggest that anthropogenic developments may have impacted stream‐dependent species in a uniform manner, regardless of ubiquity, habitat preference, or dispersal modes of the species. While signs of inbreeding were not detected for the critically endangered species, the genetic distinctiveness and low diversity of the populations call for genetic rescue and connecting corridors between the remaining fragments of the natural habitat.     

Testing fossil calibrations for vertebrate molecular trees

Lee, M. S. Y. & Skinner, A. (2011). Testing fossil calibrations for vertebrate molecular trees. —Zoologica Scripta, 40, 538–543.     

DNA taxonomy, cryptic speciation and diversification of the Neotropical-African liverwort, Marchesinia brachiata (Lejeuneaceae, Porellales)

The Neotropical-African liverwort Marchesinia brachiata has long been regarded as a polymorphic species. This hypothesis is examined using a dataset including sequences of the nuclear internal transcribed spacer region and the plastidic trnL–trnF region of 39 Marchesinia accessions. Maximum parsimony, maximum likelihood and Bayesian analyses indicate that Marchesinia robusta is nested within M. brachiata s.l. The molecular topologies support at least three partly sympatric biological species within M. brachiata s.l., the Neotropical M. bongardiana and M. languida, and the Neotropical-African M. brachiata s.s. These species are incompletely separated by subtle differences in underleaf shape and leaf dentation. Long branches within M. brachiata s.s. suggest ongoing speciation processes that are not yet reflected in distinguishable morphological variation. Divergence time estimates based on nrITS sequence variation and the liverwort fossil record indicate an establishment of the species M. bongardiana, M. brachiata, M. languida, M. madagassa, and M. robusta in the Late Oligocene and Miocene. The intraspecific diversity shows distinctive patterns with evidence for constant accumulation of genetic diversity in M. robusta and M. brachiata whereas M. bongardiana and M. languida likely went through a recent extinction or expansion process as indicated by the bottleneck pattern of genetic diversity. The tropical American-African disjunction of M. brachiata is the result of dispersal rather than Western Gondwanan vicariance.     

Phylogeny and diversification of the cloud forest Morpho sulkowskyi group (Lepidoptera,Nymphalidae) in the evolving Andes

The monophyletic Morpho sulkowskyi butterfly group, endemic of Andean cloud forests, was studied to test the respective contributions of Mio‐Pliocene intense uplift period and Pleistocene glacial cycles on Andean biodiversity. We sampled nine taxa covering the whole geographical range of the group. Two mitochondrial and two nuclear genes were analysed using a Bayesian method. We established a dated phylogeny of the group using a relaxed clock method and a wide‐outgroup approach. To discriminate between two hypotheses, we used a biogeographical probabilistic method. Results suggest that the ancestor of the M. sulkowskyi group originated during the Middle–Late Miocene uplift of the Eastern Cordillera in northern Peru. Biogeographical inference suggests that the M. sulkowskyi and Morpho lympharis clades diverged in the northern Peruvian Andes. The subsequent divergences, from the Late Miocene to the Late Pliocene, should have resulted from a dispersal towards the Northern Andes (M. sulkowskyi clade), after the closure of the West Andean Portal separating the Central and Northern Andes, and a southwards dispersal along the Peruvian and Bolivian Eastern Cordilleras (M. lympharis clade). Only a few divergences occurred at the very end of the Pliocene or during the Pleistocene, a period when the more recent uplifts interfered with Pleistocene glacial cycles.     

Identification of Mycobacterium species from apparently healthy freshwater aquarium fish using partial sequencing and PCR‐RFLP analysis of heat shock protein (hsp65) gene

The present study analysed the incidence of mycobacteria in apparently healthy looking freshwater aquarium fish in Uttar Pradesh (State), India. Sixty fish belonging to eight different species were collected from six aquarium shops in different cities and processed for isolation of Mycobacterium species. Using the initial protocol of decontamination of tissue homogenates (with 1N HCl & 2N NaOH) and incubation at 30°C for 2 months, Mycobacterium sp. was isolated from 25% of the fish. The isolates were identified by standard biochemical tests. A 441 bp fragment of the hsp65 gene was amplified and digested by two fastdigest restriction enzymes, BstEII and HaeIII. Digested products were analysed using agarose gel electrophoresis. Sequencing of amplified fragments of the hsp65 gene was also performed. Isolates were identified as: five isolates of M. abscessus, three M. gordonae, two M. fortuitum, two M. conceptionense, two M. parascrofulaceum, and one isolate of M. senegalense. Mycobacterial incidence in apparently healthy looking freshwater aquarium fish is dreadful and the study is relevant because of the mycobacterial diversity related to aquarium fish and its zoonotic importance. All Mycobacterium species isolated in this study are well known pathogens in humans as well as fish.     

Niche partitioning between close relatives suggests trade‐offs between adaptation to local environments and competition

Niche partitioning among close relatives may reflect trade‐offs underlying species divergence and coexistence (e.g., between stress tolerance and competitive ability). We quantified the effects of habitat and congeneric species interactions on fitness for two closely related herbaceous plant species, Mimulus guttatus and Mimulus laciniatus, in three common habitat types within their sympatric range. Drought stress strongly reduced survival of M. guttatus in fast‐drying seeps occupied by M. laciniatus, suggesting that divergent habitat adaptation maintains this niche boundary. However, neither seedling performance nor congeneric competition explained the absence of M. laciniatus from shady streams where M. guttatus thrives. M. laciniatus may be excluded from this habitat by competition with other species in the community or mature M. guttatus. Species performance and competitive ability were similar in sympatric meadows where plant community stature and the growing season length are intermediate between seeps and streams. Stochastic effects (e.g., dispersal among habitats or temporal variation) may contribute to coexistence in this habitat. Habitat adaptation, species interactions, and stochastic mechanisms influence sympatric distributions for these recently diverged species.     

Sea water transport and submersion tolerance as dispersal strategies for the invasive ground beetle Merizodus soledadinus (Carabidae)

The alien ground beetle Merizodus soledadinus was introduced to the sub-Antarctic Kerguelen Islands in 1913. It colonized several small islands and islets of this archipelago, without any apparent human assistance in some locations, and crossed several large rivers and alluvial plains. As aggregations of this species on the tidal drift line are common at the Kerguelen Islands, the present work examined whether adult individuals of M. soledadinus could disperse by flotation on the sea. Different sample sizes of ground beetles (from 1 to 10) were placed on sea water at 8°C in plastic vials. Survival (50% lethal times) significantly increased from 2.1 ± 0.2 days for single beetles to 6.5 ± 0.3 days for groups of 10 beetles per vial, with there being no difference in the survival duration for groups of 2, 5, and 10 beetles per vial. Similar survival durations were found for beetles in vials with artificially agitated water and controls. In addition, the duration of survival was twice as high under freshwater versus sea water conditions, when groups of 10 adults were used. Finally, the survival to total submersion in freshwater was evaluated, and ranged from 3 to 4 days. This ability to survive extended periods both floating on and/or submerged beneath salt and freshwater conditions, indicates the presence of a successful dispersal mechanism, which may facilitate the dispersal range of M. soledadinus across the Kerguelen Islands, comprising over 300 islands and islets in total.     

Molecular evidence for long-distance dispersal in the New Zealand pteridophyte flora

Aim To examine the relative importance of long‐distance dispersal in shaping the New Zealand pteridophyte (ferns and lycophytes) flora and its relationships with other floras, with the null hypothesis that the extant New Zealand pteridophyte flora has been isolated since New Zealand’s separation from Gondwana. Location New Zealand. Methods rbcL DNA sequences were assembled for 31 New Zealand pteridophyte genera, with each genus represented by one New Zealand species and the most closely related non‐New Zealand species for which data were available. Maximum‐likelihood, maximum‐parsimony, and Bayesian analysis phylograms were constructed and used as input for r 8s molecular dating, along with 23 fossil calibrations. Divergence estimates less than conservatively recent ages for New Zealand’s geological isolation, namely H_o > 30 Ma for pairs involving New Caledonian and Norfolk Island species and H_o > 55 Ma for all others, were taken as rejection of the null hypothesis. Results The null hypothesis was rejected for all pairs except, under some parameter conditions, for those involving the New Zealand species Cardiomanes reniforme, Lindsaea trichomanoides, Loxsoma cunninghamii, Lygodium articulatum, Marattia salicina, and Pteris comans. However, the Lindsaea and Pteris results probably reflect the absence in the analyses of closely related non‐New Zealand samples, while the Marattia divergence was highly contingent on which fossil calibrations were used. Main conclusions Rejection of the null hypothesis for the majority of pairs implies that the extant New Zealand lineage has undergone long‐distance dispersal either into or out of New Zealand. The notion of a long isolation since geological separation can, therefore, be dismissed for much of New Zealand’s pteridophyte flora. The analyses do not identify the direction of the long‐distance dispersal, and these New Zealand lineages could have had vicariant origins with subsequent long‐distance emigration. However, the alternative that many extant New Zealand pteridophyte lineages only arrived by long‐distance immigration after geological isolation seems likely.     

Survival and behaviour of juvenile unionid mussels exposed to thermal stress and dewatering in the presence of a sediment temperature gradient

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DESCRIPTION OF TYRANNODINIUM GEN. NOV., A FRESHWATER DINOFLAGELLATE CLOSELY RELATED TO THE MARINE PFIESTERIA‐LIKE SPECIES1

On the basis of morphological (light and electron microscopy) as well molecular data, we show that the widely distributed freshwater dinoflagellate presently known as Peridiniopsis berolinensis is a member of the family Pfiesteriaceae, an otherwise marine and estuarine family of dinoflagellates. P. berolinensis is a close relative of the marine species, which it resembles in morphology, mode of swimming, food‐uptake mechanism, and partial LSU rRNA sequences. It differs from all known genera of the family in plate tabulation. P. berolinensis is only distantly related to the type species of Peridiniopsis, P. borgei, and is therefore transferred to the new genus Tyrannodinium as T. berolinense comb. nov. T. berolinense is a very common freshwater flagellate that feeds vigorously on other protists and is able to consume injured metazoans much larger than itself. Production of toxins has not been reported.     

Mating system,pollen and propagule dispersal,and spatial genetic structure in a high-density population of the mangrove tree Kandelia candel

Mangrove tree species form ecologically and economically important forests along the tropical and subtropical coastlines of the world. Although low intrapopulation genetic diversity and high interpopulation genetic differentiation have been detected in most mangrove tree species, no direct investigation of pollen and propagule dispersal through paternity and/or parentage analysis and spatial genetic structure within populations has been conducted. We surveyed the mating system, pollen and propagule dispersal, and spatial genetic structure in a natural population of Kandelia candel, one of the typical viviparous mangrove tree species, using nuclear and chloroplast microsatellite markers. High diversity and outcrossing rates were observed. Paternity and parentage analysis and modelling estimations revealed the presence of an extremely short-distance component of pollen and propagule dispersal (pollen: 15.2 ± 14.9 m (SD) by paternity analysis and 34.4 m by modelling; propagule: 9.4 ± 13.8 m (SD) by parentage analysis, and 18.6 m by modelling). Genetic structure was significant at short distances, and a clumped distribution of chloroplast microsatellite genotypes was seen in K. candel adults. We conclude that the K. candel population was initiated by limited propagule founders from outside by long-distance dispersal followed by limited propagule dispersal from the founders, resulting in a half-sib family structure.     

Speciation and dietary specialization in Drupa,a genus of predatory marine snails (Gastropoda: Muricidae)

Claremont, M., Reid, D.G. & Williams, S.T. (2012) Speciation and dietary specialization in Drupa, a genus of predatory marine snails (Gastropoda: Muricidae). —Zoologica Scripta, 41, 137–149. We test the competing predictions of allopatric speciation and of ecological speciation by dietary specialization in Drupa, an Indo‐Pacific genus of carnivorous marine gastropods in the family Muricidae. We use a well‐resolved molecular phylogeny (reconstructed from one nuclear and two mitochondrial genes) to show the validity of the traditional species D. elegans, D. rubusidaeus, D. clathrata, D. morum and D. speciosa.‘Drupa ricinus’ is shown to consist of three species: D. ricinus s. s., D. albolabris and a new species, possibly endemic to Japan. ‘Purpura’aperta is transferred to Drupa. Despite potential widespread dispersal and a high degree of range overlap among sister species, range sizes between sister species are highly asymmetric, suggesting that speciation has been predominately peripatric. The exception is the sister pair D. ricinus s. s. and D. albolabris, which have symmetric range sizes and are sympatric over broad Indo‐Pacific ranges. Such symmetry and extensive sympatry are contrary to the predictions of the (peripatric) allopatric model of speciation. Nevertheless, contrary to the predictions of an ecological speciation model based upon dietary specialization, broad dietary range appears to be identical between the species. Small differences in microhabitat preferences (or hypothetical dietary specialization at a fine taxonomic scale) may have been significant in the speciation process or, if initial divergence was allopatric, in permitting subsequent sympatry. Broad dietary shifts appear to have accompanied more ancient divergences within the genus Drupa.     

Longgupo: EarlyHomo colonizer or late plioceneLufengpithecus survivor in south China?

A fragment of mandible and a maxillary incisor of different individuals from the Longgupo Cave, China have been cited as evidence of an early dispersal ofHomo from Africa to Asia. More specifically, these specimens are said to resemble “Homo ergaster” orHomo habilis, rather than the species usually thought to be the first Asian colonizer,Homo erectus. If this supposition is correct, it calls into question which hominid (sensu stricto) first left Africa, and why hominids became a colonizing species. Furthermore, the Longgupo remains have been used to buttress the argument thatHomo erectus evolved uniquely in Asia and was not involved in the origins of modern humans. We question this whole line of argument because the mandibular fragment cannot be distinguished from penecontemporary fossil apes, especially the Late Miocene-Pliocene Chinese genusLufengpithecus, while the incisor is indistinguishable from those of recent and living east Asian people and may be intrusive in the deposit. We believe that the Longgupo mandible represents the relic survival of a Late Miocene ape lineage into a period just prior to the dispersal of hominids into southeastern Asia, with some female dental features that parallel the hominid condition. If the Longgupo mandibular fragment represents a member of theLufengpithecus clade, it demonstrates that hominoids other thanGigantopithecus and the direct ancestor of the orangutan persisted in east Asia into the Late Pliocene, while all other Eurasian large-bodied hominoids disappeared in the Late Miocene.