The costs and benefits of larger brains in fishes

The astonishing diversity of brain sizes observed across the animal kingdom is typically explained in the context of trade-offs: the benefits of a larger brain, such as enhanced cognitive ability, are balanced against potential costs, such as increased energetic demands. Several hypotheses have been formulated in this framework, placing different emphasis on ecological, behavioural, or physiological aspects of trade-offs in brain size evolution. Within this body of work, there exists considerable taxonomic bias towards studies of birds and mammals, leaving some uncertainty about the generality of the respective arguments. Here, we test three of the most prominent such hypotheses, the 'expensive tissue', 'social brain' and 'cognitive buffer' hypotheses, in a large dataset of fishes, derived from a publicly available resource (FishBase). In accordance with predictions from the 'expensive tissue' and the 'social brain' hypothesis, larger brains co-occur with reduced fecundity and increased sociality in at least some Classes of fish. Contrary to expectations, however, lifespan is reduced in large-brained fishes, and there is a tendency for species that perform parental care to have smaller brains. As such, it appears that some potential costs (reduced fecundity) and benefits (increased sociality) of large brains are near universal to vertebrates, whereas others have more lineage-specific effects. We discuss our findings in the context of fundamental differences between the classically studied birds and mammals and the fishes we analyse here, namely divergent patterns of growth, parenting and neurogenesis. As such, our work highlights the need for a taxonomically diverse approach to any fundamental question in evolutionary biology.

SpeciesRax: A tool for maximum likelihood species tree inference from gene family trees under duplication, transfer, and loss

Species tree inference from gene family trees is becoming increasingly popular because it can account for discordance between the species tree and the corresponding gene family trees. In particular, methods that can account for multiple-copy gene families exhibit potential to leverage paralogy as informative signal. At present, there does not exist any widely adopted inference method for this purpose. Here, we present SpeciesRax, the first maximum likelihood method that can infer a rooted species tree from a set of gene family trees and can account for gene duplication, loss, and transfer events. By explicitly modeling events by which gene trees can depart from the species tree, SpeciesRax leverages the phylogenetic rooting signal in gene trees. SpeciesRax infers species tree branch lengths in units of expected substitutions per site and branch support values via paralogy-aware quartets extracted from the gene family trees. Using both empirical and simulated data sets we show that SpeciesRax is at least as accurate as the best competing methods while being one order of magnitude faster on large data sets at the same time. We used SpeciesRax to infer a biologically plausible rooted phylogeny of the vertebrates comprising 188 species from 31,612 gene families in 1 h using 40 cores. SpeciesRax is available under GNU GPL at https://github.com/BenoitMorel/GeneRax and on BioConda.

Supplementation of Bile Acids and Lipase in Broiler Diets for Better Nutrient Utilization and Performance: Potential Effects and Future Implications – A Review

Bile acids are used for better emulsification, digestion and absorption of dietary fat in chicken, especially in early life. Similarly, exogenous lipases have also been used for the improvement of physiological limitation of the chicken digestive system. Owing to potential of both bile acids and lipases, their use has been increased in recent years, for better emulsification of dietary fat and improvement of growth performance in broilers. In the past, pancreatic lipases were used for supplementation, but recently, microbial lipase is getting attention in poultry industry as a hydrolysis catalyst. Bile acids strengthen the defence mechanism of body against bacterial endotoxins and also play a key role in lipid regulation and sugar metabolism as signaling molecules. It has been demonstrated that bile acids and lipases may improve feed efficiency by enhancing digestive enzyme activity and ultimately leading to better fat digestion and absorption. Wide supplemental range of bile acids (0.004% to 0.25%) and lipases (0.01% to 0.1%) has been used in broiler diets for improvement of fat digestibility and their performance. Combinations of different bile acids have shown more potential to improve feed efficiency (by 7.14%) even at low (0.008%) levels as compared to any individual bile acid. Lipases at a lower level of 0.03% have exhibited more promising potential to improve fat digestibility and feed efficiency. However, contradicting results have been published in literature, which needs further investigations to elucidate various nutritional aspects of bile acids and lipase supplementation in broiler diet. This review focuses on providing insight on the mechanism of action and potential application of bile acids and lipases in broiler diets. Moreover, future implications of these additives in poultry nutrition for enhancing nutrient utilization and absorption are also discussed.

Integrative Studies of Sexual Selection in Manakins, a Clade of Charismatic Tropical Birds

The neotropical manakins (family Pipridae) provide a great opportunity for integrative studies of sexual selection as nearly all of the 51 species are lek-breeding, an extreme form of polygyny, and highly sexually dimorphic both in appearance and behavior. Male courtship displays are often elaborate and include auditory cues, both vocal and mechanical, as well as visual elements. In addition, the displays are often extremely rapid, highly acrobatic, and, in some species, multiple males perform coordinated displays that form the basis of long-term coalitions. Male manakins also exhibit unique neuroendocrine, physiological, and anatomical adaptations to support the performance of these complex displays and the maintenance of their intricate social systems. The Manakin Genomics Research Coordination Network (Manakin RCN, https://www.manakinsrcn.org) has brought together researchers (many in this symposium and this issue) from across disciplines to address the implications of sexual selection on evolution, ecology, behavior, and physiology in manakins. The objective of this paper is to present some of the most pertinent and integrative manakin research as well as introducing the papers presented in this issue. The results discussed at the manakin symposium, part of the 2021 Society for Integrative and Comparative Biology Conference, highlight the remarkable genomic, behavioral, and physiological adaptations as well as the evolutionary causes and consequences of strong sexual selection pressures that are evident in manakins.

Circuit mechanisms for colour vision in zebrafish

The use of spectral information in natural light to inform behaviour is one of the oldest and most fundamental abilities of visual systems. It long-predates animals' venture onto the land, and even the appearance of image-forming eyes. Accordingly, circuits for colour vision evolved under the surface of ancient oceans for hundreds of millions of years. These aquatic beginnings fundamentally underpin, and likely constrain, the organisation of modern visual systems. In contrast to our detailed circuit level understanding from diverse terrestrial vertebrates, however, comparatively little is known about their aquatic counterparts. Here, I summarise some of what is known about neural circuits for colour vision in fish, the most species-diverse group of vertebrates. With a focus on zebrafish, I will explore how their computational strategies are linked to the statistics of natural light in the underwater world, and how their study might help us understand vision in general, including in our own eyes.

Functional Characterization of the Lin28/let-7 Circuit During Forelimb Regeneration in Ambystoma mexicanum and Its Influence on Metabolic Reprogramming

The axolotl (Ambystoma mexicanum) is a caudate amphibian, which has an extraordinary ability to restore a wide variety of damaged structures by a process denominated epimorphosis. While the origin and potentiality of progenitor cells that take part during epimorphic regeneration are known to some extent, the metabolic changes experienced and their associated implications, remain unexplored. However, a circuit with a potential role as a modulator of cellular metabolism along regeneration is that formed by Lin28/let-7. In this study, we report two Lin28 paralogs and eight mature let-7 microRNAs encoded in the axolotl genome. Particularly, in the proliferative blastema stage amxLin28B is more abundant in the nuclei of blastemal cells, while the microRNAs amx-let-7c and amx-let-7a are most downregulated. Functional inhibition of Lin28 factors increase the levels of most mature let-7 microRNAs, consistent with an increment of intermediary metabolites of the Krebs cycle, and phenotypic alterations in the outgrowth of the blastema. In summary, we describe the primary components of the Lin28/let-7 circuit and their function during axolotl regeneration, acting upstream of metabolic reprogramming events.

Chromosome-level genome assembly of Lethenteron reissneri provides insights into lamprey evolution

The reissner lamprey Lethenteron reissneri, belonging to the class Cyclostomata, serves as a bridge between invertebrates and jawed vertebrates, and is considered the sister group of jawed vertebrates. However, despite this evolutionary significance, the genetic mechanisms underlying the adaptive evolution of the lamprey lineage remain unclear. Here, we assembled a 1.06 Gb chromosome-level draft genome of L. reissneri, with 72 chromosomes (ranging in length from 4.5 Mb to 25.9 Mb) and a scaffold N50 length of 13.23 Mb. Genome quality comparisons revealed that the reissner lamprey genome has higher completeness and contiguity than the previously published sea lamprey and Japanese lamprey genomes. Moreover, reissner lamprey, sea lamprey, and Japanese lamprey species share similar transposable element profiles and Hox gene cluster compositions, suggesting that a burst of transposable element activity and whole genome duplication occurred before their divergence. Additionally, the Lip gene copy numbers, which have been studied for their functions in the host defence system, were found to be expanded uniquely in lamprey lineages, suggesting key roles for these genes in lamprey evolution and adaptation. We also identified two neural-related genes, Nrn1 and Unc13a, with copy number expansions in jawed vertebrates, which may be functionally relevant to the origin of lamprey brains. Hence, this study not only provides the first chromosome-level reference genome for Cyclostomata, but also highlights features of the unique biology and adaptive evolution of the lamprey lineage.

On some structural and evolutionary aspects of rDNA amplification in oogenesis of Trachemys scripta turtles

The features of rDNA amplification have been studied in oocytes of the red-eared slider Trachemys scripta using a number of specific histochemical and cytomolecular methods. A single nucleolus in early diplotene oocytes is associated with the nucleolus organizer region (NOR). With oocyte growth, the number of nucleoli increases dramatically and reaches hundreds by the lampbrush chromosome stage (pre-vitellogenesis). RNA-polymerase I, fibrillarin, and PCNA immunodetection in the amplified nucleoli and FISH of the 5'ETS probe to the oocyte nuclear content suggest pre-rRNA and rDNA synthesis in the nucleoli at all stages studied. This implies a continuous reproduction of the nucleoli during oocyte development from early diplotene up to vitellogenesis. The data obtained offer a different way for rDNA amplification and formation of extrachromosomal nucleoli in turtle oocytes compared with the amplified nucleoli formation in amphibian and fish oocytes. In the Sauropsida clade of Archelosauria, which includes turtles, crocodiles, and birds, rDNA function is known to be suppressed in avian oogenesis during the lampbrush stage (Gaginskaya et al. in Cytogenet Genome Res 124:251-267, 2009).

The KEAP1/NRF2 Signaling Pathway in Keratinization

Keratinization is a tissue adaptation, but aberrant keratinization is associated with skin disorders such as ichthyoses, atopic dermatitis, psoriasis, and acne. The disease phenotype stems from the interaction between genes and the environment; therefore, an understanding of the adaptation machinery may lead to a new appreciation of pathomechanisms. The KEAP1/NRF2 signaling pathway mediates the environmental responses of squamous epithelial tissue. The unpredicted outcome of the Keap1-null mutation in mice allowed us to revisit the basic principle of the biological process of keratinization: sulfur metabolism establishes unparalleled cytoprotection in the body wall of terrestrial mammals. We summarize the recent understanding of the KEAP1/NRF2 signaling pathway, which is a thiol-based sensor-effector apparatus, with particular focuses on epidermal differentiation in the context of the gene-environment interaction, the structure/function principles involved in KEAP1/NRF2 signaling, lessons from mouse models, and their pathological implications. This synthesis may provide insights into keratinization, which provides physical insulation and constitutes an essential innate integumentary defense system.

Phylogenetic and physiological signals in metazoan fossil biomolecules

Proteins, lipids, and sugars establish animal form and function. However, the preservation of biological signals in fossil organic matter is poorly understood. Here, we used high-resolution in situ Raman microspectroscopy to analyze the molecular compositions of 113 Phanerozoic metazoan fossils and sediments. Proteins, lipids, and sugars converge in composition during fossilization through lipoxidation and glycoxidation to form endogenous N-, O-, and S-heterocyclic polymers. Nonetheless, multivariate spectral analysis reveals molecular heterogeneities: The relative abundance of glycoxidation and lipoxidation products distinguishes different tissue types. Preserved chelating ligands are diagnostic of different modes of biomineralization. Amino acid-specific fossilization products retain phylogenetic information and capture higher-rank metazoan relationships. Molecular signals survive in deep time and provide a powerful tool for reconstructing the evolutionary history of animals.

Regulation of 14-3-3β/α gene expression in response to salinity, thermal, and bacterial stresses in Siberian sturgeon (Acipenser baeri)

The 14-3-3 proteins are a family of widely expressed acidic proteins, which are involved in the regulation of many biological processes of animals. However, no research regarding 14-3-3 has been described in sturgeon to date, one of the most primitive Actinopterygii species. Here, we identified the first 14-3-3 gene from Siberian sturgeon (Acipenser baeri), named Ab14-3-3β/α (GenBank Accession No. KY094076.1). The cDNA of Ab14-3-3β/α is 1212 bp in length, containing a 5'-untranslated region (UTR) of 82 bp, a 3'UTR of 392 bp, and an open reading frame (ORF) of 738 bp, encoding a polypeptide of 245 amino acids which contains a 14-3-3 homologs domain (PF00244). Phylogenetic analysis showed that the 14-3-3 gene product from Acipenser baeri is a counterpart of vertebrate 14-3-3β/α. The deduced Ab14-3-3β/α protein shares high identities of 46.5-95.5% with the homologs of other species. Ab14-3-3β/α mRNA was constitutively expressed in all examined tissues, with high expression levels in the blood and gill. Furthermore, the expression level of Ab14-3-3β/α mRNA increased significantly in the gill at 1 h under acute salinity shock by transfer of Siberian sturgeons from fresh water (FW) to 15 ppt. In fish subjected to a high temperature (31 °C), Ab14-3-3β/α showed a significant upregulation in the liver at 3 h compared with the control group (24 °C). A 4.85-fold increase of Ab14-3-3β/α expression in the spleen of Siberian sturgeon was observed at 24 h following Aeromonas hydrophila challenge. Collectively, these results indicated that Ab14-3-3β/α might play a certain role in sturgeon in response to some environmental stresses and bacterial challenge.

The Evolutionary History of The Orexin/Allatotropin GPCR Family: from Placozoa and Cnidaria to Vertebrata

Peptidic messengers constitute a highly diversified group of intercellular messengers widely distributed in nature that regulate a great number of physiological processes in Metazoa. Being crucial for life, it seem that they have appeared in the ancestral group from which Metazoa evolved, and were highly conserved along the evolutionary process. Peptides act mainly through G-protein coupled receptors (GPCRs), a family of transmembrane molecules. GPCRs are also widely distributed in nature being present in metazoan, but also in Choanoflagellata and Fungi. Among GPCRs, the Allatotropin/Orexin (AT/Ox) family is particularly characterized by the presence of the DRW motif in the second intracellular loop (IC Loop 2), and seems to be present in Cnidaria, Placozoa and in Bilateria, suggesting that it was present in the common ancestor of Metazoa. Looking for the evolutionary history of this GPCRs we searched for corresponding sequences in public databases. Our results suggest that AT/Ox receptors were highly conserved along evolutionary process, and that they are characterized by the presence of the E/DRWYAI motif at the IC Loop 2. Phylogenetic analyses show that AT/Ox family of receptors reflects evolutionary relationships that agree with current phylogenetic understanding in Actinopterygii and Sauropsida, including also the largely discussed position of Testudines.

ORTHOSCOPE: An Automatic Web Tool for Phylogenetically Inferring Bilaterian Orthogroups with User-Selected Taxa

Identification of orthologous or paralogous relationships of coding genes is fundamental to all aspects of comparative genomics. For accurate identification of orthologs among deeply diversified bilaterian lineages, precise estimation of gene trees is indispensable, given the complicated histories of genes over millions of years. By estimating gene trees, orthologs can be identified as members of an orthogroup, a set of genes descended from a single gene in the last common ancestor of all the species being considered. In addition to comparisons with a given species tree, purposeful taxonomic sampling increases the accuracy of gene tree estimation and orthogroup identification. Although some major phylogenetic relationships of bilaterians are gradually being unraveled, the scattering of published genomic data among separate web databases is becoming a significant hindrance to identification of orthogroups with appropriate taxonomic sampling. By integrating more than 250 metazoan gene models predicted in genome projects, we developed a web tool called ORTHOSCOPE to identify orthogroups of specific protein-coding genes within major bilaterian lineages. ORTHOSCOPE allows users to employ several sequences of a specific molecule and broadly accepted nodes included in a user-specified species tree as queries and to evaluate the reliability of estimated orthogroups based on topologies and node support values of estimated gene trees. A test analysis using data from 36 bilaterians was accomplished within 140 s. ORTHOSCOPE results can be used to evaluate orthologs identified by other stand-alone programs using genome-scale data. ORTHOSCOPE is freely available at https://www.orthoscope.jp or https://github.com/jun-inoue/orthoscope (last accessed December 28, 2018).

Evolution and Expression of S100A7 Gene in Vertebrates

The skin is the primary barrier between the internal organs of an organism and the environment, and it provides protection from ultraviolet (UV) radiation. According to the nocturnal bottleneck hypothesis, ungulates might have traversed to the grasslands and were exposed to UV radiation subsequent to the reduction in predation pressure. UV light exposure might have increased the S100A7 expression. In order to test whether the UV radiation is associated with the selection pressure on S100A7, we acquired the complete S100A7 DNA sequences from each of 42 vertebrate species. The results suggested that the evidence of diversifying selection in S100A7 occurred at the end of Mesozoic era, and the site of positive selection was observed in the branch of Artiodactyla (even-toed ungulates). In addition, we found that the transcription level of S100A7 in cashmere goat skin correlates with UV radiation. Our results indicated that S100A7 plays a role in the signaling between the skin genes and UV radiation during evolution.

Diverse Evolutionary Origins and Mechanisms of Lens Regeneration

In this review, we compare and contrast the three different forms of vertebrate lens regeneration: Wolffian lens regeneration, cornea-lens regeneration, and lens regeneration from lens epithelial cells. An examination of the diverse cellular origins of these lenses, their unique phylogenetic distribution, and the underlying molecular mechanisms, suggests that these different forms of lens regeneration evolved independently and utilize neither conserved nor convergent mechanisms to regulate these processes.

Expression of regulatory genes in the embryonic brain of a lizard and implications for understanding pallial organization and evolution

The comparison of gene expression patterns in the embryonic brain of mouse and chicken is being essential for understanding pallial organization. However, the scarcity of gene expression data in reptiles, crucial for understanding evolution, makes it difficult to identify homologues of pallial divisions in different amniotes. We cloned and analyzed the expression of the genes Emx1, Lhx2, Lhx9, and Tbr1 in the embryonic telencephalon of the lacertid lizard Psammodromus algirus. The comparative expression patterns of these genes, critical for pallial development, are better understood when using a recently proposed six‐part model of pallial divisions. The lizard medial pallium, expressing all genes, includes the medial and dorsomedial cortices, and the majority of the dorsal cortex, except the region of the lateral cortical superposition. The latter is rich in Lhx9 expression, being excluded as a candidate of dorsal or lateral pallia, and may belong to a distinct dorsolateral pallium, which extends from rostral to caudal levels. Thus, the neocortex homolog cannot be found in the classical reptilian dorsal cortex, but perhaps in a small Emx1‐expressing/Lhx9‐negative area at the front of the telencephalon, resembling the avian hyperpallium. The ventral pallium, expressing Lhx9, but not Emx1, gives rise to the dorsal ventricular ridge and appears comparable to the avian nidopallium. We also identified a distinct ventrocaudal pallial sector comparable to the avian arcopallium and to part of the mammalian pallial amygdala. These data open new venues for understanding the organization and evolution of the pallium.

Peritoneal bacterial infection repressed the expression of IL17D in Siberia sturgeon a chondrostean fish in the early immune response

IL17s are pro-inflammatory cytokines that play important roles in host fighting against extracellular bacteria and auto-immune and allergic diseases. IL17D is believed to be the most ancient IL17 member and its functions are far from clarity. Although it has been found in invertebrates, jawless fish, teleosts, and tetrapods, it has not been described in chondrostean fish. Moreover, there are discrepancies concerning its expression pattern in these animals. In this study, we cloned and characterized the cDNA of il17d in Siberia sturgeon (Acipenser baerii), a chondrostean fish and commercially important species in aquaculture. The sturgeon il17d cDNA encodes a deduced protein of 210aa. The classical characteristics of IL17, such as IL17 domain, cysteine and serine residues importantly for cystine-knot formation, and signal peptide, were observed in sturgeon IL17D. Phylogenetic analysis and multiple alignment suggest it is a counterpart of mammalian IL17D. However, in vivo studies demonstrated that the expression pattern of sturgeon il17d mRNA is different from that of other teleosts and jawless fish, and in most cases its expression was down-regulated at the early time points and gradually increasing at late time points when sturgeon were challenged with bacteria (Aernomas hydrophila or Staphylococcus aureus). The In vitro study by using primary spleen cells stimulated with polyI:C revealed a similar expression pattern to that in vivo studies, while the stimulation with β-glucan or LPS, which normally induced expression of il17d mRNA in target cells in vitro in other animals, did not show apparent changes in the expression of il17d mRNA. The results of present study indicated sturgeon IL17D may possess some different characteristics from its counterparts of other fish and invertebrates in the immune response, and may contribute to the understanding of IL17D functions in evolution as well as the potential use in sturgeon aquaculture.

Optical influence of oil droplets on cone photoreceptor sensitivity

Oil droplets are spherical organelles found in the cone photoreceptors of vertebrates. They are generally assumed to focus incident light into the outer segment, and thereby improve light catch because of the droplets' spherical lens-like shape. However, using full-wave optical simulations of physiologically realistic cone photoreceptors from birds, frogs and turtles, we find that pigmented oil droplets actually drastically reduce the transmission of light into the outer segment integrated across the full visible wavelength range of each species. Only transparent oil droplets improve light catch into the outer segments, and any enhancement is critically dependent on the refractive index, diameter of the oil droplet, and diameter and length of the outer segment. Furthermore, oil droplets are not the only optical elements found in cone inner segments. The ellipsoid, a dense aggregation of mitochondria situated immediately prior to the oil droplet, mitigates the loss of light at the oil droplet surface. We describe a framework for integrating these optical phenomena into simple models of receptor sensitivity, and the relevance of these observations to evolutionary appearance and loss of oil droplets is discussed.

Identification of a mammalian silicon transporter

Silicon (Si) has long been known to play a major physiological and structural role in certain organisms, including diatoms, sponges, and many higher plants, leading to the recent identification of multiple proteins responsible for Si transport in a range of algal and plant species. In mammals, despite several convincing studies suggesting that silicon is an important factor in bone development and connective tissue health, there is a critical lack of understanding about the biochemical pathways that enable Si homeostasis. Here we report the identification of a mammalian efflux Si transporter, namely Slc34a2 (also termed NaPiIIb), a known sodium-phosphate cotransporter, which was upregulated in rat kidney following chronic dietary Si deprivation. Normal rat renal epithelium demonstrated punctate expression of Slc34a2, and when the protein was heterologously expressed in Xenopus laevis oocytes, Si efflux activity (i.e., movement of Si out of cells) was induced and was quantitatively similar to that induced by the known plant Si transporter OsLsi2 in the same expression system. Interestingly, Si efflux appeared saturable over time, but it did not vary as a function of extracellular HPO42− or Na⁺ concentration, suggesting that Slc34a2 harbors a functionally independent transport site for Si operating in the reverse direction to the site for phosphate. Indeed, in rats with dietary Si depletion-induced upregulation of transporter expression, there was increased urinary phosphate excretion. This is the first evidence of an active Si transport protein in mammals and points towards an important role for Si in vertebrates and explains interactions between dietary phosphate and silicon.

Acute effects of temperature and hypercarbia on cutaneous and branchial gas exchange in the South American lungfish, Lepidosiren paradoxa

The South American lungfish, Lepidosiren paradoxa inhabits seasonal environments in the Central Amazon and Paraná-Paraguay basins that undergo significant oscillations in temperature throughout the year. They rely on different gas exchange organs, such as gills and skin for aquatic gas exchange while their truly bilateral lungs are responsible for aerial gas exchange; however, there are no data available on the individual contributions of the skin and the gills to total aquatic gas exchange in L. paradoxa. Thus, in the present study we quantify the relative contributions of skin and gills on total aquatic gas exchange during warm (35°C) and cold exposure (20°C) in addition to the effects of aerial and aquatic hypercarbia on aquatic gas exchange and gill ventilation rate (f_G; 25°C), respectively. Elevated temperature (35°C) caused a significant increase in the contribution of cutaneous (from 0.61±0.13 to 1.34±0.26ml. STPD.h^-1kg^-1) and branchial (from 0.54±0.17 to 1.73±0.53ml. STPD.h^-1kg^-1) gas exchange for V̇CO₂ relative to the lower temperature (20°C), while V̇O₂ remained relatively unchanged. L. paradoxa exhibited a greater branchial contribution in relation to total aquatic gas exchange at lower temperatures (20 and 25°C) for oxygen uptake. Aerial hypercarbia decreased branchial V̇O₂ whereas branchial V̇CO₂ was significantly increased. Progressive increases in aquatic hypercarbia did not affect f_G. This response is in contrast to increases in pulmonary ventilation that may offset any increase in arterial partial pressure of CO₂ owing to CO₂ loading through the animals' branchial surface. Thus, despite their reduced contribution to total gas exchange, cutaneous and branchial gas exchange in L. paradoxa can be significantly affected by temperature and aerial hypercarbia.

The Identification of the Closest Living Relative(s) of Tetrapods: Phylogenomic Lessons for Resolving Short Ancient Internodes

Identifying the closest living relative(s) of tetrapods is an important, yet still contested question in vertebrate phylogenetics. Three hypotheses are possible and ruling out alternatives has proven difficult even with large molecular data sets due to weak phylogenetic signal coupled nonphylogenetic noise resulting from relatively rapid speciation events that occurred a long time ago ([Formula: see text]400 Ma). Here, we revisit the identity of the closest living relative of land vertebrates from a phylogenomic perspective and include new genomic data for all extant lungfish genera. RNA-seq proves to be a great alternative to genomic sequencing, which currently is technically not feasible in lungfishes due to their huge (50-130 Gb) and repetitive genomes. We examined the most important sources of systematic error, namely long-branch attraction (LBA), compositional heterogeneity and distribution of missing data and applied different correction techniques. A multispecies coalescent approach is used to account for deep coalescence that might come from the short and deep internodes separating early sarcopterygian splits. Concatenation methods favored lungfishes as the closest living relatives of tetrapods with strong statistical support. Amino acid profile mixture models can unambiguously resolve this difficult internode thanks to their ability to avoid systematic error. We assessed the performance of different site-heterogeneous models and data partitioning and compared the ability of different strategies designed to overcome LBA, including taxon manipulation, reduction of among-lineage rate heterogeneity and removal of fast-evolving or compositionally heterogeneous positions. The identification of lungfish as sister group of tetrapods is robust regarding the effects of nonstationary composition and distribution of missing data. The multispecies coalescent method reconstructed strongly supported topologies that were congruent with concatenation, despite pervasive gene tree heterogeneity. We reject alternative topologies for early sarcopterygian relationships by increasing the signal-to-noise ratio in our alignments. The analytical pipeline outlined here combines probabilistic phylogenomic inference with methods for evaluating data quality, model adequacy, and assessing systematic error, and thus is likely to help resolve similarly difficult internodes in the tree of life. [Coalescence; coelacanth; compositional heterogeneity; gene tree; long-branch attraction; lungfish; missing data; model misspecification; phylogenomic; species tree; systematic error.].

Morphology, development and heterochrony of the carapace of Giant Amazon River Turtle Podocnemis expansa (Testudines, Podocnemidae)

Abstract: With aim to report the ontogeny of the osseous elements of the carapace in Peurodiras, 62 embryos and 43 nestlings of Podocnemis expansa were collected and submitted to the clearing and staining technique of bones and cartilages and study of serial histological slices. The carapace has mixed osseous structure of endo and exoskeleton, formed by 8 pairs of costal bones associated with ribs, 7 neural bones associated with neural arches, 11 pairs of peripheral bones, 1 nuchal, 1 pygal and 1 suprapygal. This structure begins its formation in the beginning of stage 16 with the ossification of the periosteal collar of the ribs. With exception of the peripheral bones, the other ones begin their ossification during the embrionary period. In histologic investigation it was found that the costal bones and neural bones have a close relation to the endoskeleton components, originating themselves as intramembranous expansions of the periosteal collar of the ribs and neural arches, respectively. The condensation of the mesenchyme adjacent to the periosteal collar induces the formation of spikes that grow in trabeculae permeated by fibroblasts below the dermis. The nuchal bone also ossifies in an intramembranous way, but does not show direct relation to the endoskeleton. Such information confirms those related to the other Pleurodira, mainly with Podocnemis unifilis, sometimes with conspicuous variations in the chronology of the ossification events. The formation of dermal plates in the carapace of Pleurodira and Criptodira follow the same pattern.

Structure and vascularization of the ventricular myocardium in Holocephali: their evolutionary significance

It was generally assumed that the ventricle of the primitive vertebrate heart was composed of trabeculated, or spongy, myocardium, supplied by oxygen-poor luminal blood. In addition, it was presumed that the mixed ventricular myocardium, consisting of a compacta and a spongiosa, and its supply through coronary arteries appeared several times throughout fish evolution. Recent work has suggested, however, that a fully vascularized, mixed myocardium may be the primitive condition in gnathostomes. The present study of the heart ventricles of four holocephalan species aimed to clarify this controversy. Our observations showed that the ventricular myocardium of Chimaera monstrosa and Harriotta raleighana consists of a very thin compacta overlying a widespread spongiosa. The ventricle of Hydrolagus affinis is composed exclusively of trabeculated myocardium. In these three species there is a well-developed coronary artery system. The main coronary artery trunks run along the outflow tract, giving off subepicardial ventricular arteries. The trabeculae of the spongiosa are irrigated by branches of the subepicardial arteries and by penetrating arterial vessels arising directly from the main coronary trunks at the level of the conoventricular junction. The ventricle of Rhinochimaera atlantica has only spongy myocardium supplied by luminal blood. Small coronary arterial vessels are present in the subepicardium, but they do not enter the myocardial trabeculae. The present findings show for the first time that in a wild living vertebrate species, specifically H. affinis, an extensive coronary artery system supplying the whole cardiac ventricle exists in the absence of a well-developed compact ventricular myocardium. This is consistent with the notion derived from experimental work that myocardial cell proliferation and coronary vascular growth rely on distinct developmental programs. Our observations, together with data in the literature on elasmobranchs, support the view that the mixed ventricular myocardium is primitive for chondrichthyans. The reduction or even lack of compacta in holocephali has to be regarded as a derived anatomical trait. Our findings also fit in with the view that the mixed myocardium was the primitive condition in gnathostomes, and that the absence of compact ventricular myocardium in different actinopterygian groups is the result of a repeated loss of such type of cardiac muscle during fish evolution.

Brain - Endocast Relationship in the Australian Lungfish, Neoceratodus forsteri, Elucidated from Tomographic Data (Sarcopterygii: Dipnoi)

Although the brains of the three extant lungfish genera have been previously described, the spatial relationship between the brain and the neurocranium has never before been fully described nor quantified. Through the application of virtual microtomography (μCT) and 3D rendering software, we describe aspects of the gross anatomy of the brain and labyrinth region in the Australian lungfish, Neoceratodus forsteri and compare this to previous accounts. Unexpected characters in this specimen include short olfactory peduncles connecting the olfactory bulbs to the telencephalon, and an oblong telencephalon. Furthermore, we illustrate the endocast (the mould of the internal space of the neurocranial cavity) of Neoceratodus, also describing and quantifying the brain-endocast relationship in a lungfish for the first time. Overall, the brain of the Australian lungfish closely matches the size and shape of the endocast cavity housing it, filling more than four fifths of the total volume. The forebrain and labyrinth regions of the brain correspond very well to the endocast morphology, while the midbrain and hindbrain do not fit so closely. Our results cast light on the gross neural and endocast anatomy in lungfishes, and are likely to have particular significance for palaeoneurologists studying fossil taxa.

Early Vertebrate Evolution of the Host Restriction Factor Tetherin

Tetherin is an interferon-inducible restriction factor targeting a broad range of enveloped viruses. Its antiviral activity depends on an unusual topology comprising an N-terminal transmembrane domain (TMD) followed by an extracellular coiled-coil region and a C-terminal glycosylphosphatidylinositol (GPI) anchor. One of the two membrane anchors is inserted into assembling virions, while the other remains in the plasma membrane of the infected cell. Thus, tetherin entraps budding viruses by physically bridging viral and cellular membranes. Although tetherin restricts the release of a large variety of diverse human and animal viruses, only mammalian orthologs have been described to date. Here, we examined the evolutionary origin of this protein and demonstrate that tetherin orthologs are also found in fish, reptiles, and birds. Notably, alligator tetherin efficiently blocks the release of retroviral particles. Thus, tetherin emerged early during vertebrate evolution and acquired its antiviral activity before the mammal/reptile divergence. Although there is only limited sequence homology, all orthologs share the typical topology. Two unrelated proteins of the slime mold Dictyostelium discoideum also adopt a tetherin-like configuration with an N-terminal TMD and a C-terminal GPI anchor. However, these proteins showed no evidence for convergent evolution and failed to inhibit virion release. In summary, our findings demonstrate that tetherin emerged at least 450 million years ago and is more widespread than previously anticipated. The early evolution of antiviral activity together with the high topology conservation but low sequence homology suggests that restriction of virus release is the primary function of tetherin.

IMPORTANCE

The continuous arms race with viruses has driven the evolution of a variety of cell-intrinsic immunity factors that inhibit different steps of the viral replication cycle. One of these restriction factors, tetherin, inhibits the release of newly formed progeny virions from infected cells. Although tetherin targets a broad range of enveloped viruses, including retro-, filo-, herpes-, and arenaviruses, the evolutionary origin of this restriction factor and its antiviral activity remained obscure. Here, we examined diverse vertebrate genomes for genes encoding cellular proteins that share with tetherin the highly unusual combination of an N-terminal transmembrane domain and a C-terminal glycosylphosphatidylinositol anchor. We show that tetherin orthologs are found in fish, reptiles, and birds and demonstrate that alligator tetherin efficiently inhibits the release of retroviral particles. Our findings identify tetherin as an evolutionarily ancient restriction factor and provide new important insights into the continuous arms race between viruses and their hosts.

Progressive alignment of genomic signals by multiple dynamic time warping

This paper presents the utilization of progressive alignment principle for positional adjustment of a set of genomic signals with different lengths. The new method of multiple alignment of signals based on dynamic time warping is tested for the purpose of evaluating the similarity of different length genes in phylogenetic studies. Two sets of phylogenetic markers were used to demonstrate the effectiveness of the evaluation of intraspecies and interspecies genetic variability. The part of the proposed method is modification of pairwise alignment of two signals by dynamic time warping with using correlation in a sliding window. The correlation based dynamic time warping allows more accurate alignment dependent on local homologies in sequences without the need of scoring matrix or evolutionary models, because mutual similarities of residues are included in the numerical code of signals.

The first virtual cranial endocast of a lungfish (sarcopterygii: dipnoi)

Lungfish, or dipnoans, have a history spanning over 400 million years and are the closest living sister taxon to the tetrapods. Most Devonian lungfish had heavily ossified endoskeletons, whereas most Mesozoic and Cenozoic lungfish had largely cartilaginous endoskeletons and are usually known only from isolated tooth plates or disarticulated bone fragments. There is thus a substantial temporal and evolutionary gap in our understanding of lungfish endoskeletal morphology, between the diverse and highly variable Devonian forms on the one hand and the three extant genera on the other. Here we present a virtual cranial endocast of Rhinodipterus kimberleyensis, from the Late Devonian Gogo Formation of Australia, one of the most derived fossil dipnoans with a well-ossified braincase. This endocast, generated from a Computed Microtomography (µCT) scan of the skull, is the first virtual endocast of any lungfish published, and only the third fossil dipnoan endocast to be illustrated in its entirety. Key features include long olfactory canals, a telencephalic cavity with a moderate degree of ventral expansion, large suparaotic cavities, and moderately enlarged utricular recesses. It has numerous similarities to the endocasts of Chirodipterus wildungensis and Griphognathus whitei, and to a lesser degree to 'Chirodipterus' australis and Dipnorhynchus sussmilchi. Among extant lungfish, it consistently resembles Neoceratodus more closely than Lepidosiren and Protopterus. Several trends in the evolution of the brains and labyrinth regions in dipnoans, such as the expansions of the utricular recess and telencephalic regions over time, are identified and discussed.

Heterogeneous tempo and mode of conserved noncoding sequence evolution among four mammalian orders

Conserved noncoding sequences (CNSs) of vertebrates are considered to be closely linked with protein-coding gene regulatory functions. We examined the abundance and genomic distribution of CNSs in four mammalian orders: primates, rodents, carnivores, and cetartiodactyls. We defined the two thresholds for CNS using conservation level of coding genes; using all the three coding positions and using only first and second codon positions. The abundance of CNSs varied among lineages, with primates and rodents having highest and lowest number of CNSs, respectively, whereas carnivores and cetartiodactyls had intermediate values. These CNSs cover 1.3-5.5% of the mammalian genomes and have signatures of selective constraints that are stronger in more ancestral than the recent ones. Evolution of new CNSs as well as retention of ancestral CNSs contribute to the differences in abundance. The genomic distribution of CNSs is dynamic with higher proportions of rodent and primate CNSs located in the introns compared with carnivores and cetartiodactyls. In fact, 19% of orthologous single-copy CNSs between human and dog are located in different genomic regions. If CNSs can be considered as candidates of gene expression regulatory sequences, heterogeneity of CNSs among the four mammalian orders may have played an important role in creating the order-specific phenotypes. Fewer CNSs in rodents suggest that rodent diversity is related to lower regulatory conservation. With CNSs shown to cluster around genes involved in nervous systems and the higher number of primate CNSs, our result suggests that CNSs may be involved in the higher complexity of the primate nervous system.

Conserved localization of Pax6 and Pax7 transcripts in the brain of representatives of sarcopterygian vertebrates during development supports homologous brain regionalization

Many of the genes involved in brain patterning during development are highly conserved in vertebrates and similarities in their expression patterns help to recognize homologous cell types or brain regions. Among these genes, Pax6 and Pax7 are expressed in regionally restricted patterns in the brain and are essential for its development. In the present immunohistochemical study we analyzed the distribution of Pax6 and Pax7 cells in the brain of six representative species of tetrapods and lungfishes, the closest living relatives of tetrapods, at several developmental stages. The distribution patterns of these transcription factors were largely comparable across species. In all species only Pax6 was expressed in the telencephalon, including the olfactory bulbs, septum, striatum, and amygdaloid complex. In the diencephalon, Pax6 and Pax7 were distinct in the alar and basal parts, mainly in prosomeres 1 and 3. Pax7 specifically labeled cells in the optic tectum (superior colliculus) and Pax6, but not Pax7, cells were found in the tegmentum. Pax6 was found in most granule cells of the cerebellum and Pax7 labeling was detected in cells of the ventricular zone of the rostral alar plate and in migrated cells in the basal plate, including the griseum centrale and the interpeduncular nucleus. Caudally, Pax6 cells formed a column, whereas the ventricular zone of the alar plate expressed Pax7. Since the observed Pax6 and Pax7 expression patterns are largely conserved they can be used to identify subdivisions in the brain across vertebrates that are not clearly discernible with classical techniques.

Combinatorial expression of Lef1, Lhx2, Lhx5, Lhx9, Lmo3, Lmo4, and Prox1 helps to identify comparable subdivisions in the developing hippocampal formation of mouse and chicken

We carried out a study of the expression patterns of seven developmental regulatory genes (Lef1, Lhx2, Lhx9, Lhx5, Lmo3, Lmo4, and Prox1), in combination with topological position, to identify the medial pallial derivatives, define its major subdivisions, and compare them between mouse and chicken. In both species, the medial pallium is defined as a pallial sector adjacent to the cortical hem and roof plate/choroid tela, showing moderate to strong ventricular zone expression of Lef1, Lhx2, and Lhx9, but not Lhx5. Based on this, the hippocampal formation (indusium griseum, dentate gyrus, Ammon's horn fields, and subiculum), the medial entorhinal cortex, and part of the amygdalo-hippocampal transition area of mouse appeared to derive from the medial pallium. In the chicken, based on the same position and gene expression profile, we propose that the hippocampus (including the V-shaped area), the parahippocampal area (including its caudolateral part), the entorhinal cortex, and the amygdalo-hippocampal transition area are medial pallial derivatives. Moreover, the combinatorial expression of Lef1, Prox1, Lmo4, and Lmo3 allowed the identification of dentate gyrus/CA3-like, CA1/subicular-like, and medial entorhinal-like comparable sectors in mouse and chicken, and point to the existence of mostly conserved molecular networks involved in hippocampal complex development. Notably, while the mouse medial entorhinal cortex derives from the medial pallium (similarly to the hippocampal formation, both being involved in spatial navigation and spatial memory), the lateral entorhinal cortex (involved in processing non-spatial, contextual information) appears to derive from a distinct dorsolateral caudal pallial sector.

Using genes as characters and a parsimony analysis to explore the phylogenetic position of turtles

The phylogenetic position of turtles within the vertebrate tree of life remains controversial. Conflicting conclusions from different studies are likely a consequence of systematic error in the tree construction process, rather than random error from small amounts of data. Using genomic data, we evaluate the phylogenetic position of turtles with both conventional concatenated data analysis and a "genes as characters" approach. Two datasets were constructed, one with seven species (human, opossum, zebra finch, chicken, green anole, Chinese pond turtle, and western clawed frog) and 4584 orthologous genes, and the second with four additional species (soft-shelled turtle, Nile crocodile, royal python, and tuatara) but only 1638 genes. Our concatenated data analysis strongly supported turtle as the sister-group to archosaurs (the archosaur hypothesis), similar to several recent genomic data based studies using similar methods. When using genes as characters and gene trees as character-state trees with equal weighting for each gene, however, our parsimony analysis suggested that turtles are possibly sister-group to diapsids, archosaurs, or lepidosaurs. None of these resolutions were strongly supported by bootstraps. Furthermore, our incongruence analysis clearly demonstrated that there is a large amount of inconsistency among genes and most of the conflict relates to the placement of turtles. We conclude that the uncertain placement of turtles is a reflection of the true state of nature. Concatenated data analysis of large and heterogeneous datasets likely suffers from systematic error and over-estimates of confidence as a consequence of a large number of characters. Using genes as characters offers an alternative for phylogenomic analysis. It has potential to reduce systematic error, such as data heterogeneity and long-branch attraction, and it can also avoid problems associated with computation time and model selection. Finally, treating genes as characters provides a convenient method for examining gene and genome evolution.

Endocrine-disrupting chemical exposure and the American alligator: a review of the potential role of environmental estrogens on the immune system of a top trophic carnivore

Endocrine-disrupting chemicals (EDCs) alter cellular and organ system homeostasis by interfering with the body's normal physiologic processes. Numerous studies have identified environmental estrogens as modulators of EDC-related processes in crocodilians, notably in sex determination. Other broader studies have shown that environmental estrogens dysregulate normal immune function in mammals, birds, turtles, lizards, fish, and invertebrates; however, the effects of such estrogenic exposures on alligator immune function have not been elucidated. Alligators occupy a top trophic status, which may give them untapped utility as indicators of environmental quality. Environmental estrogens are also prevalent in the waters they occupy. Understanding the effects of these EDCs on alligator immunity is critical for managing and assessing changes in their health and is thus the focus of this review.

Estimating the rate of irreversibility in protein evolution

Whether or not evolutionary change is inherently irreversible remains a controversial topic. Some examples of evolutionary irreversibility are known; however, this question has not been comprehensively addressed at the molecular level. Here, we use data from 221 human genes with known pathogenic mutations to estimate the rate of irreversibility in protein evolution. For these genes, we reconstruct ancestral amino acid sequences along the mammalian phylogeny and identify ancestral amino acid states that match known pathogenic mutations. Such cases represent inherent evolutionary irreversibility because, at the present moment, reversals to these ancestral amino acid states are impossible for the human lineage. We estimate that approximately 10% of all amino acid substitutions along the mammalian phylogeny are irreversible, such that a return to the ancestral amino acid state would lead to a pathogenic phenotype. For a subset of 51 genes with high rates of irreversibility, as much as 40% of all amino acid evolution was estimated to be irreversible. Because pathogenic phenotypes do not resemble ancestral phenotypes, the molecular nature of the high rate of irreversibility in proteins is best explained by evolution with a high prevalence of compensatory, epistatic interactions between amino acid sites. Under such mode of protein evolution, once an amino acid substitution is fixed, the probability of its reversal declines as the protein sequence accumulates changes that affect the phenotypic manifestation of the ancestral state. The prevalence of epistasis in evolution indicates that the observed high rate of irreversibility in protein evolution is an inherent property of protein structure and function.

Pattern and polarity in the development and evolution of the gnathostome jaw: both conservation and heterotopy in the branchial arches of the shark, Scyliorhinus canicula

The acquisition of jaws constitutes a landmark event in vertebrate evolution, one that in large part potentiated their success and diversification. Jaw development and patterning involves an intricate spatiotemporal series of reciprocal inductive and responsive interactions between the cephalic epithelia and the cranial neural crest (CNC) and cephalic mesodermal mesenchyme. The coordinated regulation of these interactions is critical for both the ontogenetic registration of the jaws and the evolutionary elaboration of variable jaw morphologies and designs. Current models of jaw development and evolution have been built on molecular and cellular evidence gathered mostly in amniotes such as mice, chicks and humans, and augmented by a much smaller body of work on the zebrafish. These have been partnered by essential work attempting to understand the origins of jaws that has focused on the jawless lamprey. Chondrichthyans (cartilaginous fish) are the most distant group to amniotes within extant gnathostomes, and comprise the crucial clade uniting amniotes and agnathans; yet despite their critical phylogenetic position, evidence of the molecular and cellular underpinnings of jaw development in chondrichthyans is still lacking. Recent advances in genome and molecular developmental biology of the lesser spotted dogfish shark, Scyliorhinus canicula, make it ideal for the molecular study of chondrichthyan jaw development. Here, following the 'Hinge and Caps' model of jaw development, we have investigated evidence of heterotopic (relative changes in position) and heterochronic (relative changes in timing) shifts in gene expression, relative to amniotes, in the jaw primordia of S. canicula embryos. We demonstrate the presence of clear proximo-distal polarity in gene expression patterns in the shark embryo, thus establishing a baseline molecular baüplan for branchial arch-derived jaw development and further validating the utility of the 'Hinge and Caps' model in comparative studies of jaw development and evolution. Moreover, we correlate gene expression patterns with the absence of a lambdoidal junction (formed where the maxillary first arch meets the frontonasal processes) in chondrichthyans, further highlighting the importance of this region for the development and evolution of jaw structure in advanced gnathostomes.

Co-orthology of Pax4 and Pax6 to the fly eyeless gene: molecular phylogenetic, comparative genomic, and embryological analyses

The functional equivalence of Pax6/eyeless genes across distantly related animal phyla has been one of central findings on which evo-devo studies is based. In this study, we show that Pax4, in addition to Pax6, is a vertebrate ortholog of the fly eyeless gene (and its duplicate, twin of eyeless [toy] gene, unique to Insecta). Molecular phylogenetic trees published to date placed the Pax4 gene outside the Pax6/eyeless subgroup as if the Pax4 gene originated from a gene duplication before the origin of bilaterians. However, Pax4 genes had only been reported for mammals. Our molecular phylogenetic analysis, including previously unidentified teleost fish pax4 genes, equally supported two scenarios: one with the Pax4-Pax6 duplication early in vertebrate evolution and the other with this duplication before the bilaterian radiation. We then investigated gene compositions in the genomic regions containing Pax4 and Pax6, and identified (1) conserved synteny between these two regions, suggesting that the Pax4-Pax6 split was caused by a large-scale duplication and (2) its timing within early vertebrate evolution based on the duplication timing of the members of neighboring gene families. Our results are consistent with the so-called two-round genome duplications in early vertebrates. Overall, the Pax6/eyeless ortholog is merely part of a 2:2 orthology relationship between vertebrates (with Pax4 and Pax6) and the fly (with eyeless and toy). In this context, evolution of transcriptional regulation associated with the Pax4-Pax6 split is also discussed in light of the zebrafish pax4 expression pattern that is analyzed here for the first time.

A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic lissamphibia

In resolving the vertebrate tree of life, two fundamental questions remain: 1) what is the phylogenetic position of turtles within amniotes, and 2) what are the relationships between the three major lissamphibian (extant amphibian) groups? These relationships have historically been difficult to resolve, with five different hypotheses proposed for turtle placement, and four proposed branching patterns within Lissamphibia. We compiled a large cDNA/EST dataset for vertebrates (75 genes for 129 taxa) to address these outstanding questions. Gene-specific phylogenetic analyses revealed a great deal of variation in preferred topology, resulting in topologically ambiguous conclusions from the combined dataset. Due to consistent preferences for the same divergent topologies across genes, we suspected systematic phylogenetic error as a cause of some variation. Accordingly, we developed and tested a novel statistical method that identifies sites that have a high probability of containing biased signal for a specific phylogenetic relationship. After removing putatively biased sites, support emerged for a sister relationship between turtles and either crocodilians or archosaurs, as well as for a caecilian-salamander sister relationship within Lissamphibia, with Lissamphibia potentially paraphyletic.

Genetic diversity, endemism and phylogeny of lampreys within the genus Lampetra sensu stricto (Petromyzontiformes: Petromyzontidae) in western North America

Phylogenetic structure of four Lampetra species from the Pacific drainage of North America (western brook lamprey Lampetra richardsoni, Pacific brook lamprey Lampetra pacifica, river lamprey Lampetra ayresii and Kern brook lamprey Lampetra hubbsi) and unidentified Lampetra specimens (referred to as Lampetra sp.) from 36 locations was estimated using the mitochondrial cytochrome b gene. Maximum parsimony and Bayesian inferences did not correspond with any taxonomic scheme proposed to date. Rather, although L. richardsoni (from Alaska to California) and L. ayresii (from British Columbia to California) together constituted a well-supported clade distinct from several genetically divergent Lampetra populations in Oregon and California, these two species were not reciprocally monophyletic. The genetically divergent populations included L. pacifica (from the Columbia River basin) and L. hubbsi (from the Kern River basin) and four Lampetra sp. populations in Oregon (Siuslaw River and Fourmile Creek) and California (Kelsey and Mark West Creeks). These four Lampetra sp. populations showed genetic divergence between 2.3 and 5.7% from any known species (and up to 8.0% from each other), and may represent morphologically cryptic and thus previously undescribed species. A fifth population (from Paynes Creek, California) may represent a range extension of L. hubbsi into the Upper Sacramento River.

Sturgeons, sharks, and rays have multifocal crystalline lenses and similar lens suspension apparatuses

Crystalline lenses with multiple focal lengths in monochromatic light (multifocal lenses) are present in many vertebrate groups. These lenses compensate for chromatic aberration and create well-focused color images. Stabilization of the lens within the eye and the ability to adjust focus are further requirements for vision in high detail. We investigated the occurrence of multifocal lenses by photorefractometry and lens suspension structures by light and electron microscopy in sturgeons (Acipenseriformes, Chondrostei) as well as sharks and rays (Elasmobranchii, Chondrichthyes). Multifocal lenses were found in two more major vertebrate groups, the Chondrostei represented by Acipenseriformes and Chondrichthyes represented by Elasmobranchii. The lens suspension structures of sturgeons, sharks, and rays are more complex than described previously. The lens is suspended by many delicate suspensory fibers in association with a ventral papilla in all groups studied. The arrangements of the suspensory fibers are most similar between sturgeons and sharks. In rays, the lens is suspended by a smaller ventral papilla and the suspensory fibers are arranged more concentrically to the lens.

Mechanisms of sperm storage in the female reproductive tract: an interspecies comparison

Once semen has been collected for artificial insemination, it is diluted into extenders designed to prevent its deterioration over the period prior to insemination. If the semen is not frozen, the extenders provide protection for a period of a few hours to a few days, depending on species. Despite the efforts of biotechnologists to increase the duration of storage without compromising fertility, there has been relatively little progress for many years. However, comparative studies in diverse species have revealed that long-term sperm storage (up to months and years) within the female reproductive tract is relatively commonplace in reptiles, fishes, birds and amphibians. Even among mammals, some species of bat have evolved mechanisms for storing spermatozoa for several months in the uterus or oviduct so that they can mate in the autumn but postpone fertilization until the spring. We currently know little about the mechanisms that support such long-term sperm storage, mainly because evidence from such species is either absent or fragmentary. Nevertheless, parallels between mammalian and other systems, where spermatozoa are sequestered in sperm storage tubules, suggest that the enclosure of spermatozoa within pockets of epithelial cells may be sufficient to achieve long-term sperm storage. In addition, recent evidence from sperm-storing bats has suggested an alternative, or additional, hypothesis that the modulation of apoptosis within epithelial cells is important in controlling sperm survival. Despite a lack of direct experimental evidence from a wide variety of species, I propose that there is now enough evidence to warrant investigation of these hypotheses.

In vivo strains in the femur of the Virginia opossum (Didelphis virginiana) during terrestrial locomotion: testing hypotheses of evolutionary shifts in mammalian bone loading and design

Terrestrial locomotion can impose substantial loads on vertebrate limbs. Previous studies have shown that limb bones from cursorial species of eutherian mammals experience high bending loads with minimal torsion, whereas the limb bones of non-avian reptiles (and amphibians) exhibit considerable torsion in addition to bending. It has been hypothesized that these differences in loading regime are related to the difference in limb posture between upright mammals and sprawling reptiles, and that the loading patterns observed in non-avian reptiles may be ancestral for tetrapod vertebrates. To evaluate whether non-cursorial mammals show loading patterns more similar to those of sprawling lineages, we measured in vivo strains in the femur during terrestrial locomotion of the Virginia opossum (Didelphis virginiana), a marsupial that uses more crouched limb posture than most mammals from which bone strains have been recorded, and which belongs to a clade phylogenetically between reptiles and the eutherian mammals studied previously. The presence of substantial torsion in the femur of opossums, similar to non-avian reptiles, would suggest that this loading regime likely reflects an ancestral condition for tetrapod limb bone design. Strain recordings indicate the presence of both bending and appreciable torsion (shear strain: 419.1 ± 212.8 με) in the opossum femur, with planar strain analyses showing neutral axis orientations that placed the lateral aspect of the femur in tension at the time of peak strains. Such mediolateral bending was unexpected for a mammal running with near-parasagittal limb kinematics. Shear strains were similar in magnitude to peak compressive axial strains, with opossum femora experiencing similar bending loads but higher levels of torsion compared with most previously studied mammals. Analyses of peak femoral strains led to estimated safety factor ranges of 5.1-7.2 in bending and 5.5-7.3 in torsion, somewhat higher than typical mammalian values for bending, but approaching typical reptilian values for shear. Loading patterns of opossum limb bones therefore appear intermediate in some respects between those of eutherian mammals and non-avian reptiles, providing further support for hypotheses that high torsion and elevated limb bone safety factors may represent persistent ancestral conditions in the evolution of tetrapod limb bone loading and design.