LIVE-BIRTH IN VIPERS (VIPERIDAE) IS A KEY INNOVATION AND ADAPTATION TO GLOBAL COOLING DURING THE CENOZOIC

The identification of adaptations and key innovations has long interested biologists because they confer on organisms the ability to exploit previously unavailable ecological resources and respond to novel selective pressures. Although it can be extremely difficult to test for the effects of a character on the rate of lineage diversification, the convergent evolution of a character in multiple lineages provides an excellent opportunity to test for the effect of that character on lineage diversification. Here, I examine the effect of parity mode on the diversification of vipers, which have independently evolved viviparity in at least 13 lineages. I find strong statistical evidence that viviparous species diversify at a greater rate than oviparous species and correlate major decreases in the diversification rate of oviparous species with periods of global cooling, such as the Oligocene. These results suggest that the evolution of viviparity buffered live-bearing species against the negative effects of global climate change during the Cenozoic, and was a key innovation in the evolution and diversification of live-bearing vipers.     

EVOLUTION OF VIVIPARITY: A PHYLOGENETIC TEST OF THE COLD‐CLIMATE HYPOTHESIS IN PHRYNOSOMATID LIZARDS

The evolution of viviparity is a key life‐history transition in vertebrates, but the selective forces favoring its evolution are not fully understood. With >100 origins of viviparity, squamate reptiles (lizards and snakes) are ideal for addressing this issue. Some evidence from field and laboratory studies supports the “cold‐climate” hypothesis, wherein viviparity provides an advantage in cold environments by allowing mothers to maintain higher temperatures for developing embryos. Surprisingly, the cold‐climate hypothesis has not been tested using both climatic data and phylogenetic comparative methods. Here, we investigate the evolution of viviparity in the lizard family Phrynosomatidae using GIS‐based environmental data, an extensive phylogeny (117 species), and recently developed comparative methods. We find significant relationships between viviparity and lower temperatures during the warmest (egg‐laying) season, strongly supporting the cold‐climate hypothesis. Remarkably, we also find that viviparity tends to evolve more frequently at tropical latitudes, despite its association with cooler climates. Our results help explain this and two related patterns that seemingly contradict the cold‐climate hypothesis: the presence of viviparous species restricted to low‐elevation tropical regions and the paucity of viviparous species at high latitudes. Finally, we examine whether viviparous taxa may be at higher risk of extinction from anthropogenic climate change.     

Uterine epithelial cell changes during pregnancy in a marsupial (Sminthopsis crassicaudata; Dasyuridae)

Formation of a placenta requires intimate contact between the embryonic and maternal uterine epithelia in early pregnancy. Contact is accompanied by a characteristic suite of changes to the plasma membranes of uterine epithelial cells, termed the plasma membrane transformation. The plasma membrane transformation occurs in eutherian mammals and in viviparous (live‐bearing) squamate reptiles, and may be fundamental to the evolution of viviparity in amniotes. Marsupials provide an excellent opportunity to test the generality of this phenomenon. Here, we present the first detailed study of the plasma membrane transformation in a marsupial. We combine electron microscopy and immunohistochemistry to describe morphological and molecular features of uterine epithelial cells during pregnancy in the fat‐tailed dunnart (Sminthopsis crassicaudata; Dasyuridae). Cell morphology changes dramatically in S. crassicaudata during pregnancy. Apical microvilli are replaced by irregular blunt projections, then by spiky projections postimplantation. Cell surfaces flatten and ciliated cells are lost. Junctional complexes between adjacent cells increase in depth, then decrease just before implantation, which is consistent with junctional protein localization in this region of the cell membrane. The uterine cellular changes in S. crassicaudata are consistent with a plasma membrane transformation, and support the idea that this phenomenon is fundamental to the evolution of viviparity in amniote vertebrates. J. Morphol. 275:1081–1092, 2014. © 2014 Wiley Periodicals, Inc.     

Evolution of vertebrate viviparity and specializations for fetal nutrition: A quantitative and qualitative analysis

Phylogenetic analyses indicate that viviparity (live‐bearing reproduction) has originated independently in more than 150 vertebrate lineages, including a minimum of 115 clades of extant squamate reptiles. Other evolutionary origins of viviparity include 13 origins among bony fishes, nine among chondrichthyans, eight in amphibians, one in Paleozoic placoderms, six among extinct reptiles, and one in mammals. The origins of viviparity range geologically from the mid‐Paleozoic through the Mesozoic to the Pleistocene. Substantial matrotrophy (maternal provision of nutrients to embryos during pregnancy) has arisen at least 33 times in these viviparous clades, with most (26) of these origins having occurred among fishes and amphibians. Convergent evolution in patterns of matrotrophy is widespread, as reflected by multiple independent origins of placentotrophy, histotrophy, oophagy, and embryophagy. Specializations for nutrient transfer to embryos are discontinuously distributed, reflecting the roles of phylogenetic inertia, exaptation (preadaptation), and constraint. Ancestral features that function in gas exchange and nutrition repeatedly and convergently have been co‐opted for nutrient transfer, often through minor modification of their components and changes in the timing of their expression (heterochrony). Studies on functional and evolutionary morphology continue to play a central role in our attempts to understand viviparity and mechanisms of fetal nutrition. J. Morphol. 276:961–990, 2015. © 2014 Wiley Periodicals, Inc.     

The effect of parity on morphological evolution among phrynosomatid lizards

The shift from egg laying to live‐bearing is one of the most well‐studied transitions in evolutionary biology. Few studies, however, have assessed the effect of this transition on morphological evolution. Here, we evaluated the effect of reproductive mode on the morphological evolution of 10 traits, among 108 species of phrynosomatid lizards. We assess whether the requirement for passing shelled eggs through the pelvic girdle has led to morphological constraints in oviparous species and whether long gestation times in viviparous species have led to constraints in locomotor morphology. We fit models to the data that vary both in their tempo (strength and rate of selection) and mode of evolution (Brownian or Ornstein‐Uhlenbeck) and estimates of trait optima. We found that most traits are best fit by a generalized multipeak OU model, suggesting differing trait optima for viviparous vs. oviparous species. Additionally, rates (σ²) of both pelvic girdle and forelimb trait evolution varied with parity; viviparous species had higher rates. Hindlimb traits, however, exhibited no difference in σ² between parity modes. In a functional context, our results suggest that the passage of shelled eggs constrains the morphology of the pelvic girdle, but we found no evidence of morphological constraint of the locomotor apparatus in viviparous species. Our results are consistent with recent lineage diversification analyses, leading to the conclusion that transitions to viviparity increase both lineage and morphological diversification.     

Tyrosine phosphorylated proteins in the reproductive tract of the viviparous lizard Eulamprus tympanum and the oviparous lizard Lampropholis guichenoti

Plastic changes occur in the morphology of the uterus at various stages of the reproductive cycle in both oviparous and viviparous lizards and these may be influenced by estrogen. Estrogen driven phosphorylation of effector proteins on tyrosine residues plays a major role in the plastic modulation of uterine anatomy and physiology in vertebrates. We used electrophoresis and Western blotting to characterize the phosphotyrosine protein profiles at various stages of the reproductive pathway in an oviparous lizard Lampropholis guichenoti and a viviparous lizard Eulamprus tympanum. L. guichenoti displayed major bands in the 200-35 kDa range and a triplet of bands of molecular masses 61 kDa, 52 kDa and 48 kDa in 50% of specimens and a 38 kDa band in all specimens. In contrast, E. tympanum samples all displayed a single major band at 40 kDa, which was significantly elevated at the early pregnancy stage. Somewhat paradoxically, the viviparous species, which has the more complex uterine epithelial changes during pregnancy, has the fewest phosphotyrosine bands, so how tyrosine phosphorylation is affected during the evolution of viviparity is not clear.     

Convergence in pigmentation at multiple levels: mutations,genes and function

Convergence—the independent evolution of the same trait by two or more taxa—has long been of interest to evolutionary biologists, but only recently has the molecular basis of phenotypic convergence been identified. Here, we highlight studies of rapid evolution of cryptic coloration in vertebrates to demonstrate that phenotypic convergence can occur at multiple levels: mutations, genes and gene function. We first show that different genes can be responsible for convergent phenotypes even among closely related populations, for example, in the pale beach mice inhabiting Florida''s Gulf and Atlantic coasts. By contrast, the exact same mutation can create similar phenotypes in distantly related species such as mice and mammoths. Next, we show that different mutations in the same gene need not be functionally equivalent to produce similar phenotypes. For example, separate mutations produce divergent protein function but convergent pale coloration in two lizard species. Similarly, mutations that alter the expression of a gene in different ways can, nevertheless, result in similar phenotypes, as demonstrated by sister species of deer mice. Together these studies underscore the importance of identifying not only the genes, but also the precise mutations and their effects on protein function, that contribute to adaptation and highlight how convergence can occur at different genetic levels.     

Desmoglein‐2 during pregnancy and its role in the evolution of viviparity in a marsupial (Sminthopsis crassicaudata; Dasyuridae)

Attachment of the blastocyst and formation of the placenta during pregnancy is dependent on structural and cellular changes occurring in the uterine epithelium and in particular to the plasma membrane of these uterine cells. Desmosome expression decreases during pregnancy in eutherians and some squamates, presumably allowing for remodeling of the uterine epithelium and invasion of the trophoblast during implantation. Marsupials are a distinct mammalian amniote lineage of viviparity, with a short implantation or attachment period and varying levels of invasive placentation. To test the generality of changes to the uterine epithelium during pregnancy across mammals, we characterized the distribution of desmosomes in the uterine epithelial cells of a marsupial, Sminthopsis crassicaudata, using electron microscopy and immunohistochemistry. The absolute number of desmosomes along the lateral plasma membrane decreases during pregnancy and desmosomes are redistributed towards the apical region of the lateral plasma membrane as pregnancy proceeds, similar to what occurs during pregnancy in eutherian mammals. Despite the lower level of maternal investment in pregnancy and the noninvasive structure of fetal membranes in marsupials there are similarities in number and redistribution of desmosomes along the plasma membrane and changes to the morphology of the uterine epithelial cells suggesting that similar plasma membrane changes occur across all lineages of amniote vertebrates. J. Morphol. 276:261–272, 2015. © 2014 Wiley Periodicals, Inc.     

Evolution and Functional Characterisation of Melanopsins in a Deep-Sea Chimaera (Elephant Shark,Callorhinchus milii)

Non-visual photoreception in mammals is primarily mediated by two splice variants that derive from a single melanopsin (OPN4M) gene, whose expression is restricted to a subset of retinal ganglion cells. Physiologically, this sensory system regulates the photoentrainment of many biological rhythms, such as sleep via the melatonin endocrine system and pupil constriction. By contrast, melanopsin exists as two distinct lineages in non-mammals, opn4m and opn4x, and is broadly expressed in a wide range of tissue types, including the eye, brain, pineal gland and skin. Despite these findings, the evolution and function of melanopsin in early vertebrates are largely unknown. We, therefore, investigated the complement of opn4 classes present in the genome of a model deep-sea cartilaginous species, the elephant shark (Callorhinchus milii), as a representative vertebrate that resides at the base of the gnathostome (jawed vertebrate) lineage. We reveal that three melanopsin genes, opn4m1, opn4m2 and opn4x, are expressed in multiple tissues of the elephant shark. The two opn4m genes are likely to have arisen as a result of a lineage-specific duplication, whereas “long” and “short” splice variants are generated from a single opn4x gene. By using a heterologous expression system, we suggest that these genes encode functional photopigments that exhibit both “invertebrate-like” bistable and classical “vertebrate-like” monostable biochemical characteristics. We discuss the evolution and function of these melanopsin pigments within the context of the diverse photic and ecological environments inhabited by this chimaerid holocephalan, as well as the origin of non-visual sensory systems in early vertebrates.     

Multiple origin of viviparity in Southeast Asian gastropods (Cerithioidea: Pachychilidae) and its evolutionary implications

This study aims at a better understanding of the evolutionary significance of viviparity in some freshwater gastropods. We use a phylogeny based on partial sequences of the mitochondrial 16S gene of representatives of the limnetic and pantropical Pachychilidae to infer the relationships within this particular group of cerithioideans and the evolution of reproductive strategies. The phylogeny presented herein implies a new systematization and suggests that viviparity has appeared three times among the Pachychilidae. This is supported by the finding of very distinct reproductive morphologies in different lineages of viviparous taxa that are exclusively found in Southeast Asia. Based on the observation that oviparity is the ancestral character state in this freshwater family, we conclude that viviparity has evolved subsequent to the exploration of freshwater. We present data showing that all Pachychilidae produce considerably larger but fewer egg capsules compared to most marine snails. In other studies on freshwater gastropods, this has been discussed as an adaptation to freshwater environments. In this context we hypothesize that the increased parental investment involved in the enlargement of eggs in concert with the reduction of clutch sizes was the driving factor that ultimately lead to the evolution of viviparity in the Asian taxa. Consequently, although not directly correlated with the colonization of the new adaptive zone, viviparity is strongly favored by other consequences of this step. Hence, we hypothesize that the production of large eggs, which is necessitated by the exploration of freshwater, represents a preadaptation existing in those ancestors from which viviparous pachychilid lineages eventually evolved in Southeast Asia.     

THE EVOLUTION OF OVIPARITY WITH EGG GUARDING AND VIVIPARITY IN LIZARDS AND SNAKES: A PHYLOGENETIC ANALYSIS

This paper investigates the evolution of viviparity and of egg guarding in lizards and snakes in which three modes of reproduction can be described: oviparity without egg guarding, oviparity with egg guarding, and viviparity. All possible transitions of reproductive modes were detected in each taxon using Maddison's method. We then tested two specific hypotheses. First, egg guarding can be regarded as an alternative to viviparity. A relatively frequent association of egg guarding and viviparous species in the same taxon may be due to similar environmental conditions or species characteristics leading to two different solutions. Second, egg guarding may facilitate the evolution of viviparity. This hypothesis is supported by the high frequency of viviparous species in taxa containing egg guarding species and by a tendency for prolonged uterine retention of eggs in brooding squamates. Our analyses demonstrate that the first hypothesis is the best supported. Egg guarding and viviparity most often evolved independently. If a major benefit of egg guarding is the repulsion of potential predators, size is one of the most obvious morphological characters that should be correlated with the evolution of reproductive modes. The two reproductive traits were correlated to a reduction in body size for viviparous species and an increase in body size for egg guarding species. This could partly explain why the evolution of these reproductive modes seems almost antagonist.     

Evolution of viviparity: what can Australian lizards tell us?

Historically, Australia has been important in the study of, and the development of hypotheses aimed at understanding, the evolution of viviparity in amniote vertebrates. Part of the importance of Australia in the field results from a rich fauna of skinks, including one of the broadest ranges of diversity of placental structures within one geographic region. During the last decade, we have focussed our studies on one lineage, the Eugongylus group of skinks of the subfamily Lygosominae because it contains oviparous species and some that exhibit complex placentae. Our specific objective has been to attempt to understand the fundamental steps required when viviparity, and ultimately complex placentae, evolve from oviparous ancestors. We have taken a three-prong approach: (1) detailed study of the morphology and ontogeny of the placentae of key species at the light microscope level; (2) study of changes in the uterus associated with pregnancy, or the plasma membrane transformation; and (3) measures of the net exchange of nutrients across the placenta or eggshell of key species. In turn, we have found that: (1) details of the morphology and ontogeny of placentae are more complex that originally envisaged, and that the early conclusions about a sequence in the evolution of complex placentae was naïve; (2) a plasma membrane transformation occurs in viviparous, but not oviparous lizards, and thus may be a fundamental feature of the evolution of viviparity in amniotes; and (3) species with more complex chorioallantoic placentae tend to transport more nutrients across the placenta during pregnancy than those with simpler chorioallantoic placentae but, because the correlation is not tight, the importance of the omphaloplacenta in transporting nutrients may have been overlooked. Also, the composition of yolk of highly matrotrophic species is broadly similar, but not identical, to the yolk of oviparous species. Some of the interpretation of our data within the context of our specific objective is not yet possible, pending the publication of a robust phylogeny of Eugongylus group skinks. Once such a phylogeny is available, we are in a position to propose specific hypotheses about the evolution of viviparity that can be tested using another lineage of amniotes, possibly Mabuya group skinks.     

Fetal nutrition in lecithotrophic squamate reptiles: Toward a comprehensive model for evolution of viviparity and placentation

The primary pattern of embryonic nutrition for squamate reptiles is lecithotrophy; with few exceptions, all squamate embryos mobilize nutrients from yolk. The evolution of viviparity presents an opportunity for an additional source of embryonic nutrition through delivery of uterine secretions, or placentotrophy. This pattern of embryonic nutrition is thought to evolve through placental supplementation of lecithotrophy, followed by increasing dependence on placentotrophy. This review analyzes the relationship between reproductive mode and pattern of embryonic nutrition in three lecithotrophic viviparous species, and oviparous counterparts, for concordance with a current model for the evolution of viviparity and placentation. The assumptions of the model, that nutrients for oviparous embryos are mobilized from yolk, and that this source is not disrupted in the transition to viviparity, are supported for most nutrients. In contrast, calcium, an essential nutrient for embryonic development, is mobilized from both yolk and eggshell by oviparous embryos and reduction of eggshell calcium is correlated with viviparity. If embryonic fitness is compromised by disruption of a primary source of calcium, selection may not favor evolution of viviparity, yet viviparity has arisen independently in numerous squamate lineages. Studies of fetal nutrition in reproductively bimodal species suggest a resolution to this paradox. If uterine calcium secretion occurs during prolonged intrauterine egg retention, calcium placentotrophy evolves prior to viviparity as a replacement for eggshell calcium and embryonic nutrition will not be compromised. This hypothesis is integrated into the current model for evolution of viviparity and placentation to address the unique attributes of calcium nutrition. The sequence of events requires a shift in timing of uterine calcium secretion and the embryonic mechanism of calcium retrieval to be responsive to calcium availability. Regulation of uterine calcium secretion and the mechanism of embryonic uptake of calcium are important elements to understanding evolution of viviparity and placentation. J. Morphol., 2013. © 2013 Wiley Periodicals, Inc.     

Gene losses during human origins

Pseudogenization is a widespread phenomenon in genome evolution, and it has been proposed to serve as an engine of evolutionary change, especially during human origins (the “less-is-more” hypothesis). However, there has been no comprehensive analysis of human-specific pseudogenes. Furthermore, it is unclear whether pseudogenization itself can be selectively favored and thus play an active role in human evolution. Here we conduct a comparative genomic analysis and a literature survey to identify 80 nonprocessed pseudogenes that were inactivated in the human lineage after its separation from the chimpanzee lineage. Many functions are involved among these genes, with chemoreception and immune response being outstandingly overrepresented, suggesting potential species-specific features in these aspects of human physiology. To explore the possibility of adaptive pseudogenization, we focus on CASPASE12, a cysteinyl aspartate proteinase participating in inflammatory and innate immune response to endotoxins. We provide population genetic evidence that the nearly complete fixation of a null allele at CASPASE12 has been driven by positive selection, probably because the null allele confers protection from severe sepsis. We estimate that the selective advantage of the null allele is about 0.9% and the pseudogenization started shortly before the out-of-Africa migration of modern humans. Interestingly, two other genes related to sepsis were also pseudogenized in humans, possibly by selection. These adaptive gene losses might have occurred because of changes in our environment or genetic background that altered the threat from or response to sepsis. The identification and analysis of human-specific pseudogenes open the door for understanding the roles of gene losses in human origins, and the demonstration that gene loss itself can be adaptive supports and extends the “less-is-more” hypothesis.     

Male pregnancy in seahorses and pipefish: beyond the mammalian model

Pregnancy has been traditionally defined as the period during which developing embryos are incubated in the body after egg-sperm union. Despite strong similarities between viviparity in mammals and other vertebrate groups, researchers have historically been reluctant to use the term pregnancy for non-mammals in recognition of the highly developed form of viviparity in eutherians. Syngnathid fishes (seahorses and pipefishes) have a unique reproductive system, where the male incubates developing embryos in a specialized brooding structure in which they are aerated, osmoregulated, protected and likely provisioned during their development. Recent insights into physiological, morphological and genetic changes associated with syngnathid reproduction provide compelling evidence that male incubation in these species is a highly specialized form of reproduction akin to other forms of viviparity. Here, we review these recent advances, highlighting similarities and differences between seahorse and mammalian pregnancy. Understanding the changes associated with the parallel evolution of male pregnancy in the two major syngnathid lineages will help to identify key innovations that facilitated the development of this unique form of reproduction and, through comparison with other forms of live bearing, may allow the identification of a common set of characteristics shared by all viviparous organisms.     

Sequence and organization of coelacanth neurohypophysial hormone genes: Evolutionary history of the vertebrate neurohypophysial hormone gene locus

Background  

The mammalian neurohypophysial hormones, vasopressin and oxytocin are involved in osmoregulation and uterine smooth muscle contraction respectively. All jawed vertebrates contain at least one homolog each of vasopressin and oxytocin whereas jawless vertebrates contain a single neurohypophysial hormone called vasotocin. The vasopressin homolog in non-mammalian vertebrates is vasotocin; and the oxytocin homolog is mesotocin in non-eutherian tetrapods, mesotocin and [Phe²]mesotocin in lungfishes, and isotocin in ray-finned fishes. The genes encoding vasopressin and oxytocin genes are closely linked in the human and rodent genomes in a tail-to-tail orientation. In contrast, their pufferfish homologs (vasotocin and isotocin) are located on the same strand of DNA with isotocin gene located upstream of vasotocin gene separated by five genes, suggesting that this locus has experienced rearrangements in either mammalian or ray-finned fish lineage, or in both lineages. The coelacanths occupy a unique phylogenetic position close to the divergence of the mammalian and ray-finned fish lineages.     

Phylogenomics of trophically diverse cichlids disentangles processes driving adaptive radiation and repeated trophic transitions

Cichlid fishes of the tribe Tropheini are a striking case of adaptive radiation, exemplifying multiple trophic transitions between herbivory and carnivory occurring in sympatry with other established cichlid lineages. Tropheini evolved highly specialized eco‐morphologies to exploit similar trophic niches in different ways repeatedly and rapidly. To better understand the evolutionary history and trophic adaptations of this lineage, we generated a dataset of 532 targeted loci from 21 out of the 22 described Tropheini species. We resolved the Tropheini into seven monophyletic genera and discovered one to be polyphyletic. The polyphyletic genus, Petrochromis, represents three convergent origins of the algae grazing trophic specialization. This repeated evolution of grazing may have been facilitated by adaptive introgression as we found evidence for gene flow among algae grazing genera. We also found evidence of gene flow among algae browsing genera, but gene flow was restricted between herbivorous and carnivorous genera. Furthermore, we observed no evidence supporting a hybrid origin of this radiation. Our molecular evolutionary analyses suggest that opsin genes likely evolved in response to selection pressures associated with trophic ecology in the Tropheini. We found surprisingly little evidence of positive selection in coding regions of jaw‐shaping genes in this trophically diverse lineage. This suggests low degrees of freedom for further change in these genes, and possibly a larger role for regulatory variation in driving jaw adaptations. Our study emphasizes Tropheini cichlids as an important model for studying the evolution of trophic specialization and its role in speciation.