Anatomy and relationships of Pachyrhachis problematicus,a primitive snake with hindlimbs

The anatomy of Pachyrhachis problematicus, an elongate, limb-reduced squamate from the Upper Cretaceous of Israel, is described and evaluated in detail. Previously considered a snake-like ''lizard'' of uncertain affinities, it is here shown to be the most primitive snake, and the sister-group to all other snakes. Pachyrhachis exhibits numerous derived characters uniting it with modern snakes (scolecophidians and alethinophidians): e.g. mobile premaxilla-maxilla articulation, braincase enclosed by frontals and parietals, sagittal parietal crest, absence of tympanic recess, single postdentary bone, over 140 presacral vertebrae, and complete loss of shoulder girdle and forelimb. However, it is more primitive than all modern snakes in retaining some strikingly primitive (lizard-like) features: presence of a jugal, squamosal, normal sacral attachment, and well-developed hindlimb composed of femur, tibia, fibula, and tarsals. Pachyrhachis provides additional support for the hypothesis that snakes are most closely related to Cretaceous marine lizards (mosasauroids). Almost all of the derived characters proposed to unite snakes and mosasauroids are highly developed in Pachyrhachis: the mobile mandibular symphysis, intramandibular joint, long and recurved pterygoid teeth, quadrate suspended by the supratemporal, loosely united pelvic elements (ilium, ischium, and pubis), and separate astragalus and calcaneum.     

Abbreviation of larval development and extension of brood care as key features of the evolution of freshwater Decapoda

The transition from marine to freshwater habitats is one of the major steps in the evolution of life. In the decapod crustaceans, four groups have colonized fresh water at different geological times since the Triassic, the freshwater shrimps, freshwater crayfish, freshwater crabs and freshwater anomurans. Some families have even colonized terrestrial habitats via the freshwater route or directly via the sea shore. Since none of these taxa has ever reinvaded its environment of origin the Decapoda appear particularly suitable to investigate life‐history adaptations to fresh water. Evolutionary comparison of marine, freshwater and terrestrial decapods suggests that the reduction of egg number, abbreviation of larval development, extension of brood care and lecithotrophy of the first posthatching life stages are key adaptations to fresh water. Marine decapods usually have high numbers of small eggs and develop through a prolonged planktonic larval cycle, whereas the production of small numbers of large eggs, direct development and extended brood care until the juvenile stage is the rule in freshwater crayfish, primary freshwater crabs and aeglid anomurans. The amphidromous freshwater shrimp and freshwater crab species and all terrestrial decapods that invaded land via the sea shore have retained ocean‐type planktonic development. Abbreviation of larval development and extension of brood care are interpreted as adaptations to the particularly strong variations of hydrodynamic parameters, physico‐chemical factors and phytoplankton availability in freshwater habitats. These life‐history changes increase fitness of the offspring and are obviously favoured by natural selection, explaining their multiple origins in fresh water. There is no evidence for their early evolution in the marine ancestors of the extant freshwater groups and a preadaptive role for the conquest of fresh water. The costs of the shift from relative r‐ to K‐strategy in freshwater decapods are traded‐off against fecundity, future reproduction and growth of females and perhaps against size of species but not against longevity of species. Direct development and extension of brood care is associated with the reduction of dispersal and gene flow among populations, which may explain the high degree of speciation and endemism in directly developing freshwater decapods. Direct development and extended brood care also favour the evolution of social systems, which in freshwater decapods range from simple subsocial organization to eusociality. Hermaphroditism and parthenogenesis, which have evolved in some terrestrial crayfish burrowers and invasive open water crayfish, respectively, may enable populations to adapt to restrictive or new environments by spatio‐temporal alteration of their socio‐ecological characteristics. Under conditions of rapid habitat loss, environmental pollution and global warming, the reduced dispersal ability of direct developers may turn into a severe disadvantage, posing a higher threat of extinction to freshwater crayfish, primary freshwater crabs, aeglids and landlocked freshwater shrimps as compared to amphidromous freshwater shrimps and secondary freshwater crabs.     

The anatomy of the upper cretaceous snake Najash rionegrina Apesteguía & Zaher, 2006, and the evolution of limblessness in snakes

Najash rionegrina Apesteguía & Zaher, 2006 , a terrestrial fossil snake from the Upper Cretaceous of Argentina, represents the first known snake with a sacrum associated with robust, well‐developed hind limbs. Najash rionegrina documents an important gap in the evolutionary development towards limblessness, because its phylogenetic affinities suggest that it is the sister group of all modern snakes, including the limbed Tethyan snakes Pachyrhachis, Haasiophis, and Eupodophis. The latter three limbed marine fossil snakes are shown to be more derived morphologically, because they lack a sacrum, but have articulated lymphapophyses, and their appendicular skeleton is enclosed by the rib cage, as in modern snakes.     

MMP‐13 (Matrix MetalloProteinase 13) expression might be an indicator for increased ECM remodeling and early signs of vertebral compression in farmed Atlantic salmon (Salmo salar L.)

Vertebral body compression is a common problem in commercial farming of Atlantic salmon. Although risk factors, such as vaccination and malnutrition, have been identified, the etiology is largely unknown. Histological studies of Atlantic salmon have shown that in a compressed deformity (platyspondyly) the length of the compact bone is reduced while the notochord start to form atypical chrondrogenic structures. In mammals, similar remodeling activities have been linked to inflammatory processes in the tissue. Hence, we wanted to investigate whether the compressed vertebrae in Atlantic salmon showed presence of local (IL‐1β, TNF‐α1), systemic (IgM) and chronic (MMP‐13, MMP‐9) immune responses (measured with quantitative PCR). Unvaccinated groups of Atlantic salmon that would later develop high or low prevalence of vertebral compression during on‐growth in seawater were sampled at seawater transfer, and 3 and 6 weeks after seawater transfer. In addition, compressed and normal vertebrae from the high deformity prevalence group were sampled 44 weeks after transfer to seawater. MMP‐13 was significantly up‐regulated in the group that developed a high prevalence of deformity, and also significantly up‐regulated in compressed vertebrae, 44 weeks after seawater transfer. In compressed vertebrae, MMP‐13 was equally up‐regulated in the notochord, compact bone and trabecular bone. The results of the present study suggest that MMP‐13 may serve as an early indicator for bone remodeling which may lead to vertebral compression, and that there is a relationship between the development of vertebral compression and increased remodeling activities in farmed Atlantic salmon.     

The role of local adaptation in shaping fish‐mussel coevolution

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Integrating molecular tools into freshwater ecology: developments and opportunities

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“Lucy” (A.L. 288‐1) had five sacral vertebrae

A “long‐backed” scenario of hominin vertebral evolution posits that early hominins possessed six lumbar vertebrae coupled with a high frequency of four sacral vertebrae (7:12‐13:6:4), a configuration acquired from a hominin‐panin last common ancestor (PLCA) having a vertebral formula of 7:13:6‐7:4. One founding line of evidence for this hypothesis is the recent assertion that the “Lucy” sacrum (A.L. 288‐1an, Australopithecus afarensis) consists of four sacral vertebrae and a partially‐fused first coccygeal vertebra (Co1), rather than five sacral vertebrae as in modern humans. This study reassesses the number of sacral vertebrae in Lucy by reexamining the distal end of A.L.288‐1an in the context of a comparative sample of modern human sacra and Co1 vertebrae, and the sacrum of A. sediba (MH2). Results demonstrate that, similar to S5 in modern humans and A. sediba, the last vertebra in A.L. 288‐1an exhibits inferiorly‐projecting (right side) cornua and a kidney‐shaped inferior body articular surface. This morphology is inconsistent with that of fused or isolated Co1 vertebrae in humans, which either lack cornua or possess only superiorly‐projecting cornua, and have more circularly‐shaped inferior body articular surfaces. The level at which the hiatus' apex is located is also more compatible with typical five‐element modern human sacra and A. sediba than if only four sacral vertebrae are present. Our observations suggest that A.L. 288‐1 possessed five sacral vertebrae as in modern humans; thus, sacral number in “Lucy” does not indicate a directional change in vertebral count that can provide information on the PLCA ancestral condition. Am J Phys Anthropol 156:295–303, 2015. © 2014 Wiley Periodicals, Inc.     

The aquatic Lystrosaurus: A palaeontological myth

Evidence previously cited for the aquatic nature of the Triassic mammal‐like reptile Lystrosaurus is reviewed. It is concluded that this evidence does not constitute a convincing case.

General adaptations of aquatic tetrapods are reviewed and applied to the morphology of Lystrosaurus, in order to determine whether aquatic adaptations not previously sought in Lystrosaurus are present It is concluded that few or any such adaptations are present. Such as are, for example a widened knee and flared scapula blade, are as compatible with a digging function, as with swimming.

Nevertheless, the distinctive nature of the skull and to a lesser extent the postcranial skeleton of Lystrosaurus stands out, and several features require functional interpretation. These include: a downwardly‐directed and elongated snout, a short and high temporal region, a pear‐shaped external nasal opening bounded by a rugose ridge, slight dorsal flaring of the scapula, a powerful forelimb and wide knee joint These are dealt with elsewhere (King and Cluver, 1991).     

Predation on freshwater snails in Miocene Lake Steinheim: a trigger for intralacustrine evolution?

Shells of the freshwater gastropods Gyraulus trochiformis (Planorbidae or ramshorn snails) and Bania pseudoglobula (formerly Pseudamnicola, Hydrobiidae) from Miocene Steinheim Basin in SW Germany contain small holes with a mean diameter of 0.8 mm. Analyses of comparable holes are so far unknown from fossil or extant assemblages of freshwater shells. This analysis of the perforated shells suggests that the holes were not formed by post‐depositional or pure taphonomic processes. Instead, they were most likely produced by predators. This analysis widens the means for identification of predation on freshwater snail shells that can be used in other palaeolimnological studies. The co‐occurrence of fish teeth and perforated shells in the studied samples as well as the perforation features suggest that the predator was either barbel or tench fish. The correlation between shell sizes and hole diameters suggests a size relationship between predator and prey that may generally be related to gape‐limited fish predators. The co‐occurrence of perforated shells in these lake sediments with a dominance of large and armoured shells suggest that these larger shells with protuberances and knobs could not be crushed by the gape‐limited fish predators. This analysis is the basis for a hypothesis that the endemic evolution of Gyraulus in Lake Steinheim, with some varied forms of shell thickness and morphology, was triggered by a predator–prey relationship based on adaptations to avoid shell‐breaking predators.     

Chromosomal‐level assembly of Takifugu obscurus (Abe, 1949) genome using third‐generation DNA sequencing and Hi‐C analysis

The Tetraodontidae family are known to have relatively small and compact genomes compared to other vertebrates. The obscure puffer fish Takifugu obscurus is an anadromous species that migrates to freshwater from the sea for spawning. Thus the euryhaline characteristics of T. obscurus have been investigated to gain understanding of their survival ability, osmoregulation, and other homeostatic mechanisms in both freshwater and seawater. In this study, a high quality chromosome‐level reference genome for T. obscurus was constructed using long‐read Pacific Biosciences (PacBio) Sequel sequencing and a Hi‐C‐based chromatin contact map platform. The final genome assembly of T. obscurus is 381 Mb, with a contig N50 length of 3,296 kb and longest length of 10.7 Mb, from a total of 62 Gb of raw reads generated using single‐molecule real‐time sequencing technology from a PacBio Sequel platform. The PacBio data were further clustered into chromosome‐scale scaffolds using a Hi‐C approach, resulting in a 373 Mb genome assembly with a contig N50 length of 15.2 Mb and and longest length of 28 Mb. When we directly compared the 22 longest scaffolds of T. obscurus to the 22 chromosomes of the tiger puffer Takifugu rubripes, a clear one‐to‐one orthologous relationship was observed between the two species, supporting the chromosome‐level assembly of T. obscurus. This genome assembly can serve as a valuable genetic resource for exploring fugu‐specific compact genome characteristics, and will provide essential genomic information for understanding molecular adaptations to salinity fluctuations and the evolution of osmoregulatory mechanisms.     

Fused mid‐caudal vertebrae in the titanosaur Uberabatitan ribeiroi from the Late Cretaceous of Brazil and other bone lesions

Bone pathology in the titanosaur dinosaur Uberabatitan ribeiroi from the Marília Formation (Bauru Group, Late Cretaceous) of Uberaba city (Minas Gerais State, Brazil) is analysed here. They include two fused procoelous mid‐caudal vertebrae (CPPLIP‐1020) and a haemal arch (CPPLIP‐1006) of the middle section of the tail with a healing fracture callus. The analyses of the caudal vertebrae CPPLIP‐1020 of Uberabatitan permit us to recognize the following signs, based on CT scan and external macroscopic observations: (1) ossified longitudinal tendons; (2) likely ossified intervertebral disc, producing fused vertebral bodies; (3) fused right zygapophyseal process with a laterally developed osteophyte affecting this joint; (4) osteophytes and exostoses at different portions of the vertebrae; (5) cloacae, bone erosion and likely internal infection. According to all the processes observed in these caudals, we could not discard at least two possibilities for the diagnosis of the fused vertebrae. It could be the result of a spondyloarthropathy process (considering most of the observed signs) or possibly have been associated with an infection (e.g. discospondylitis/infections spondylitis or septic arthritis). The bone lesion record in Uberabatitan ribeiroi from the Late Cretaceous of Brazil increases the range of study of titanosaur dinosaurs, which although have a large fossil record, have few pathological studies.     

Rose bitterling (Rhodeus ocellatus) embryos parasitize freshwater mussels by competing for nutrients and oxygen

Spence, R. and Smith, C. 2011. Rose bitterling (Rhodeus ocellatus) embryos parasitize freshwater mussels by competing for nutrients and oxygen. —Acta Zoologica (Stockholm) 00 : 1–6. Understanding how parasites inflict fitness costs on their hosts is a key question in host–parasite biology. Rose bitterling (Rhodeus ocellatus) are small cyprinid fish that place their eggs in the gills of living freshwater mussels. The embryos complete their development inside the mussel gill and emerge as free‐swimming larvae after approximately 4 weeks. Bitterling show a range of specialized adaptations for using mussels as a spawning substrate, and the presence of bitterling embryos has been shown to retard the growth of mussels. We compared the development and survival of embryos incubated in either mussels or Petri dishes and exposed to either nutrient‐rich or nutrient‐poor pond water. Embryonic development rate was significantly faster in Petri dishes, probably as a result of oxygen limitation in mussel gills. Embryo survival rate was significantly higher in nutrient‐rich than filtered water, suggesting that the embryos obtained a nutritional benefit prior to emergence from the host. The results imply that bitterling embryos compete for oxygen and nutrients with their host mussel, as well as each other, and in this way, impose a growth cost on mussels.     

Oldest known Varanus (Squamata: Varanidae) from the Upper Eocene and Lower Oligocene of Egypt: support for an African origin of the genus

Abstract: A large collection of lizard vertebrae from northern Africa represents the oldest unambiguous occurrence of the genus Varanus. The fossils come from late Eocene and early Oligocene freshwater deposits of the Fayum, Egypt, an area noted for many significant primate finds. The recovery and identification of this material indicate that the genus Varanus arose in Africa, before dispersing to Australia and Asia. This dispersal occurred prior to the early to mid‐Miocene, by which time fossil Varanus are known from Australia and Eurasia. Although the dispersal route remains unknown, the lizard material reported here supports the hypothesis that a corridor existed allowing freshwater and terrestrial organisms to cross from Africa to Asia.     

Biogeography,habitat transitions and hybridization in a radiation of South American silverside fishes revealed by mitochondrial and genomic RAD data

Rivers and lake systems in the southern cone of South America have been widely influenced by historical glaciations, carrying important implications for the evolution of aquatic organisms, including prompting transitions between marine and freshwater habitats and by triggering hybridization among incipient species via waterway connectivity and stream capture events. Silverside fishes (Odontesthes) in the region comprise a radiation of 19 marine and freshwater species that have been hypothesized on the basis of morphological or mitochondrial DNA data to have either transitioned repeatedly into continental waters from the sea or colonized marine habitats following freshwater diversification. New double digest restriction‐site associated DNA data presented here provide a robust framework to investigate the biogeographical history of and habitat transitions in Odontesthes. We show that Odontesthes silversides originally diversified in the Pacific but independently colonized the Atlantic three times, producing three independent marine‐to‐freshwater transitions. Our results also indicate recent introgression of marine mitochondrial haplotypes into two freshwater clades, with more recurring instances of hybridization among Atlantic‐ versus Pacific‐slope species. In Pacific freshwater drainages, hybridization with a marine species appears to be geographically isolated and may be related to glaciation events. Substantial structural differences of estuarine gradients between these two geographical areas may have influenced the frequency, intensity and evolutionary effects of hybridization events.     

Trade‐offs in osmoregulation and parallel shifts in molecular function follow ecological transitions to freshwater in the Alewife

Adaptation to freshwater may be expected to reduce performance in seawater because these environments represent opposing selective regimes. We tested for such a trade‐off in populations of the Alewife (Alosa pseudoharengus). Alewives are ancestrally anadromous, and multiple populations have been independently restricted to freshwater (landlocked). We conducted salinity challenge experiments, whereby juvenile Alewives from one anadromous and multiple landlocked populations were exposed to freshwater and seawater on acute and acclimation timescales. In response to acute salinity challenge trials, independently derived landlocked populations varied in the degree to which seawater tolerance has been lost. In laboratory‐acclimation experiments, landlocked Alewives exhibited improved freshwater tolerance, which was correlated with reductions in seawater tolerance and hypo‐osmotic balance, suggesting that trade‐offs in osmoregulation may be associated with local adaptation to freshwater. We detected differentiation between life‐history forms in the expression of an ion‐uptake gene (NHE3), and in gill Na⁺/K⁺‐ATPase activity. Trade‐offs in osmoregulation, therefore, may be mediated by differentiation in ion‐uptake and salt‐secreting pathways.     

The insect trace fossil Tonganoxichnus from the middle Pennsylvanian of Indiana: Paleobiologic and paleoenvironmental implications

The ichnogenus Tonganoxichnus, produced by one or more monuran insect taxa, is now recorded from the Middle Pennsylvanian Mansfield Formation of Indiana. Tonganoxichnus is a resting trace that has three important implications. First, it represents a recurrent behavioral pattern in Upper Carboniferous to Lower Permian marginal marine environments of North America. Second, it provides finely resolved anatomical information for axial and appendicular body structures and behaviors that are difficult to determine from body‐fossil material alone. Third, integrated sedimentologic and ichnologic observations indicate that the Tonganoxichnus assemblage, inclusive of other ichnotaxa, is common in tidal rhythmites that were developed under freshwater conditions, probably in the innermost part of estuarine systems, close to or at the fluvioestuarine transition.     

Life‐history strategy,with ctenidial and pallial larval brooding,of the troglodytic ‘living fossil’ Congeria kusceri (Bivalvia: Dreissenidae) from the subterranean Dinaric Alpine karst of Croatia

Among freshwater bivalves, the brooding of embryos and larvae within the maternal ctenidia is well known. Exceptions to this generalization are the non‐brooding freshwater and estuarine species of Dreissena and Mytilopsis, respectively. It was reported that the freshwater troglodytic cousin, Congeria kusceri Bole, 1962, of these dreissenids does not brood either. It is herein demonstrated that C. kusceri undergoes one reproductive cycle each year. Sexes are separate, with an early male and later female bias. A small percentage (2.14%) of individuals is hermaphroditic. The gonads mature over summer from May to November. Spawning commences in September, when females release mature oocytes into their ctenidia and inhale sperm from mature males. Here the oocytes are fertilized, and develop within interfilamentary marsupia. Ctenidial tissues glandularize, and may provide a source of maternal nutrition for the embryos. At the late prodissoconch‐1 or prodissoconch‐2 stage (PR2, ~220 μm), larvae are released into the infrabranchial chamber via a birth channel along the outer edge of the ventral marginal food groove of both inner demibranchs. Here, they are brooded further in mantle pouches located beneath the inhalant siphon. Subsequently, after the PR2 stage (nepioconch/dissoconch), they are released from the inhalant siphon and assume an independent life as crawling juveniles. Such juveniles may be found amongst clusters of adults. Not only is C. kusceri unique amongst the Dreissenidae in possessing the capacity to brood internally fertilized ova, but it is also exceptional amongst the Bivalvia in possessing the described methods of brooding and birth. Explanations for both lie in its troglodytic lifestyle, decadal length longevity and habitat: that of byssal attachment to the hard surfaces of underground freshwater rivers, caves, pits, and sinkholes in the Tethyan arc of the Dinaric karst. Internal fertilization of a few large yolky eggs, lecithotrophic larvae, ctenidial brooding, and secondary pallial parental care represent relatively recent, Late Miocene, evolutionary adaptations from a Tethyan lentic ancestor.     

Contrasting population genetic structure among freshwater‐resident and anadromous lampreys: the role of demographic history,differential dispersal and anthropogenic barriers to movement

The tendency of many species to abandon migration remains a poorly understood aspect of evolutionary biology that may play an important role in promoting species radiation by both allopatric and sympatric mechanisms. Anadromy inherently offers an opportunity for the colonization of freshwater environments, and the shift from an anadromous to a wholly freshwater life history has occurred in many families of fishes. Freshwater‐resident forms have arisen repeatedly among lampreys (within the Petromyzontidae and Mordaciidae), and there has been much debate as to whether anadromous lampreys, and their derived freshwater‐resident analogues, constitute distinct species or are divergent ecotypes of polymorphic species. Samples of 543 European river lamprey Lampetra fluviatilis (mostly from anadromous populations) and freshwater European brook lamprey Lampetra planeri from across 18 sites, primarily in the British Isles, were investigated for 13 polymorphic microsatellite DNA loci, and 108 samples from six of these sites were sequenced for 829 bp of mitochondrial DNA (mtDNA). We found contrasting patterns of population structure for mtDNA and microsatellite DNA markers, such that low diversity and little structure were seen for all populations for mtDNA (consistent with a recent founder expansion event), while fine‐scale structuring was evident for nuclear markers. Strong differentiation for microsatellite DNA loci was seen among freshwater‐resident L. planeri populations and between L. fluviatilis and L. planeri in most cases, but little structure was evident among anadromous L. fluviatilis populations. We conclude that postglacial colonization founded multiple freshwater‐resident populations with strong habitat fidelity and limited dispersal tendencies that became highly differentiated, a pattern that was likely intensified by anthropogenic barriers.     

MYCOSPORINE‐LIKE AMINO ACIDS AND PHYLOGENIES IN GREEN ALGAE: PRASIOLA AND ITS RELATIVES FROM THE TREBOUXIOPHYCEAE (CHLOROPHYTA)1

A UV‐absorbing mycosporine‐like amino acid (324 nm‐MAA), so far only known from the green macroalgal genus Prasiola (Trebouxiophyceae), was also identified in other morphologically diverse green algae closely related to Prasiola spp. in 18S rDNA phylogenies. Using HPLC, a second UV‐absorbing compound was found only in Myrmecia incisa Reisigal among all studied strains. This substance showed an absorption maximum at 322 nm and hence was designated as putative 322 nm‐MAA. Preliminary UV‐exposure experiments indicated that all species containing one or the other MAA showed a strong accumulation of the respective compound, thus supporting their function as putative UV sunscreen. Both UV‐absorbing substances were only identified in the studied members of the Trebouxiophyceae but were absent in members of the Ulvophyceae and Chlorophyceae. When mapped on an 18S rDNA phylogeny, the distribution of 324 nm‐MAA was found to be scattered within the Trebouxiophyceae but was consistent with a distribution that follows phylogenetic patterns rather than ecological adaptations. The 324 nm‐MAA was also detected in two phylogenetically related species from freshwater as well as from subaerial habitats, Watanabea reniformis Hanagata et al. and isolate UR7/5, which were phylogenetically independent of Prasiola and its closer allies. MAAs were absent in another Trebouxiophyceae clade comprising lichen photobionts (Coccomyxa pringsheimii Jaag) as well as freshwater picoplanktonic algae (Choricystis minor (Skuja) Fott). The data presented suggest a chemotaxonomic value of the 324 nm‐MAA in green algal taxonomy. To address the paraphyly of the genus Myrmecia Printz as presently circumscribed, we propose the new combination Lobosphaera incisa.