A general scenario of Hox gene inventory variation among major sarcopterygian lineages.
TL;DR: The Hox gene inventory for six sarcopterygian groups: lungfishes, caecilians, salamanders, snakes, turtles and crocodiles is determined by comprehensive PCR survey and genome walking, providing basis for future sequencing of the entire Hox clusters of these animals.
Abstract: Hox genes are known to play a key role in shaping the body plan of metazoans. Evolutionary dynamics of these genes is therefore essential in explaining patterns of evolutionary diversity. Among extant sarcopterygians comprising both lobe-finned fishes and tetrapods, our knowledge of the Hox genes and clusters has largely been restricted in several model organisms such as frogs, birds and mammals. Some evolutionary gaps still exist, especially for those groups with derived body morphology or occupying key positions on the tree of life, hindering our understanding of how Hox gene inventory varied along the sarcopterygian lineage. We determined the Hox gene inventory for six sarcopterygian groups: lungfishes, caecilians, salamanders, snakes, turtles and crocodiles by comprehensive PCR survey and genome walking. Variable Hox genes in each of the six sarcopterygian group representatives, compared to the human Hox gene inventory, were further validated for their presence/absence by PCR survey in a number of related species representing a broad evolutionary coverage of the group. Turtles, crocodiles, birds and placental mammals possess the same 39 Hox genes. HoxD12 is absent in snakes, amphibians and probably lungfishes. HoxB13 is lost in frogs and caecilians. Lobe-finned fishes, amphibians and squamate reptiles possess HoxC3. HoxC1 is only present in caecilians and lobe-finned fishes. Similar to coelacanths, lungfishes also possess HoxA14, which is only found in lobe-finned fishes to date. Our Hox gene variation data favor the lungfish-tetrapod, turtle-archosaur and frog-salamander relationships and imply that the loss of HoxD12 is not directly related to digit reduction. Our newly determined Hox inventory data provide a more complete scenario for evolutionary dynamics of Hox genes along the sarcopterygian lineage. Limbless, worm-like caecilians and snakes possess similar Hox gene inventories to animals with less derived body morphology, suggesting changes to their body morphology are likely due to other modifications rather than changes to Hox gene numbers. Furthermore, our results provide basis for future sequencing of the entire Hox clusters of these animals.
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TL;DR: It is argued that current evidences points that the 2R-WGD may not be linked to the origin of vertebrate innovations, but to their subsequent diversification in a broad variety of complex structures and functions that facilitated the successful transition from peaceful filter-feeding non-vertebrate ancestors to voracious vertebrate predators.
95 citations
TL;DR: An updated picture of the ancestral repertoires of the different lineages is drawn, a sort of “genome Hox bar-code” for most clades, to infer differential gene or cluster losses and gains that occurred during deuterostome evolution, which might be causally linked to the morphological changes that led to these widely diverse animal taxa.
Abstract: Hox genes, with their similar roles in animals as evolutionarily distant as humans and flies, have fascinated biologists since their discovery nearly 30 years ago. During the last two decades, reports on Hox genes from a still growing number of eumetazoan species have increased our knowledge on the Hox gene contents of a wide range of animal groups. In this review, we summarize the current Hox inventory among deuterostomes, not only in the well-known teleosts and tetrapods, but also in the earlier vertebrate and invertebrate groups. We draw an updated picture of the ancestral repertoires of the different lineages, a sort of “genome Hox bar-code” for most clades. This scenario allows us to infer differential gene or cluster losses and gains that occurred during deuterostome evolution, which might be causally linked to the morphological changes that led to these widely diverse animal taxa. Finally, we focus on the challenging family of posterior Hox genes, which probably originated through independent tandem duplication events at the origin of each of the ambulacrarian, cephalochordate and vertebrate/urochordate lineages.
85 citations
Cites background from "A general scenario of Hox gene inve..."
...Comparison of the Hox inventories of different tetrapods allows to infer a tetrapod ancestral condition of up to 41 genes [78], one more than previously thought [5], and an amniote ancestral condition of 40 Hox genes (after the loss of HoxC1; Figure 2), of which only the green anole (Anolis carolinensis) retains all of them [78,79], while mammals and the chicken have lost the HoxC3 gene independently....
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...This enabled Liang and colleagues [78] to reconstruct a more complete ancestral sarcopterygian Hox inventory, with a total of 43 Hox genes (Figure 2)....
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...Moreover, a PCR survey of the lungfish Protopterus annectens also found a HoxA14 gene ([78]; data from the lungfish are not included in Figure 2 because they lack clustering information, but they were taken into account to infer the ancestral condition)....
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...[78] also did not identify HoxC3 in crocodiles and turtles by degenerate PCR and it is absent from turtle genomes [80,81]....
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...bannanicus and the salamander Batrachuperus tibetanus [78], the amphibian ancestor probably had 40 genes, after losing HoxD12 from its tetrapod ancestor (Figure 2)....
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University of Oviedo1, Yale University2, University of Chicago3, Spanish National Research Council4, Flinders University5, State University of New York System6, University of South Alabama7, University of Florence8, University of California, Merced9, University of Mississippi10, University of British Columbia11, American Museum of Natural History12, University of Crete13
TL;DR: The genomes of two long-lived giant tortoises, including Lonesome George, reveal candidate genes and pathways associated with their development, gigantism and longevity and expands the understanding of the genomic determinants of ageing.
Abstract: Giant tortoises are among the longest-lived vertebrate animals and, as such, provide an excellent model to study traits like longevity and age-related diseases. However, genomic and molecular evolutionary information on giant tortoises is scarce. Here, we describe a global analysis of the genomes of Lonesome George-the iconic last member of Chelonoidis abingdonii-and the Aldabra giant tortoise (Aldabrachelys gigantea). Comparison of these genomes with those of related species, using both unsupervised and supervised analyses, led us to detect lineage-specific variants affecting DNA repair genes, inflammatory mediators and genes related to cancer development. Our study also hints at specific evolutionary strategies linked to increased lifespan, and expands our understanding of the genomic determinants of ageing. These new genome sequences also provide important resources to help the efforts for restoration of giant tortoise populations.
73 citations
TL;DR: The first full Hox gene sequences for any member of the Acipenseriformes, the American paddlefish, are presented and an independent WGD occurred in the paddlefish lineage, approximately 42 Ma based on sequences spanning the entire HoxA cluster and eight genes on the HoxD gene cluster.
Abstract: Vertebrates have experienced two rounds of whole-genome duplication (WGD) in the stem lineages of deep nodes within the group and a subsequent duplication event in the stem lineage of the teleosts—a highly diverse group of ray-finned fishes. Here, we present the first full Hox gene sequences for any member of the Acipenseriformes, the American paddlefish, and confirm that an independent WGD occurred in the paddlefish lineage, approximately 42 Ma based on sequences spanning the entire HoxA cluster and eight genes on the HoxD gene cluster. These clusters comprise different HOX loci and maintain conserved synteny relative to bichir, zebrafish, stickleback, and pufferfish, as well as human, mouse, and chick. We also provide a gene genealogy for the duplicated fzd8 gene in paddlefish and present evidence for the first Hox14 gene in any ray-finned fish. Taken together, these data demonstrate that the American paddlefish has an independently duplicated genome. Substitution patterns of the “alpha” paralogs on both the HoxA and HoxD gene clusters suggest transcriptional inactivation consistent with functional diploidization. Further, there are similarities in the pattern of sequence divergence among duplicated Hox genes in paddlefish and teleost lineages, even though they occurred independently approximately 200 Myr apart. We highlight implications on comparative analyses in the study of the “fin-limb transition” as well as gene and genome duplication in bony fishes, which includes all ray-finned fishes as well as the lobe-finned fishes and tetrapod vertebrates.
62 citations
TL;DR: All Hox gene clusters of Pantodon buchholzi, a member of the early branching teleost subdivision Osteoglossomorpha, are characterized and the term “tetralogy” is used to describe the homology relationship which exists between duplicated sequences which originate through a shared WGD but which diploidize into distinct paralogs from a common allelic pool independently in two lineages following speciation.
Abstract: Numerous ancient whole-genome duplications (WGD) have occurred during eukaryote evolution. In vertebrates, duplicated developmental genes and their functional divergence have had important consequences for morphological evolution. Although two vertebrate WGD events (1R/2R) occurred over 525 Ma, we have focused on the more recent 3R or TGD (teleost genome duplication) event which occurred approximately 350 Ma in a common ancestor of over 26,000 species of teleost fishes. Through a combination of whole genome and bacterial artificial chromosome clone sequencing we characterized all Hox gene clusters of Pantodon buchholzi, a member of the early branching teleost subdivision Osteoglossomorpha. We find 45 Hox genes organized in only five clusters indicating that Pantodon has suffered more Hox cluster loss than other known species. Despite strong evidence for homology of the five Pantodon clusters to the four canonical pre-TGD vertebrate clusters (one HoxA, two HoxB, one HoxC, and one HoxD), we were unable to confidently resolve 1:1 orthology relationships between four of the Pantodon clusters and the eight post-TGD clusters of other teleosts. Phylogenetic analysis revealed that many Pantodon genes segregate outside the conventional "a" and "b" post-TGD orthology groups, that extensive topological incongruence exists between genes physically linked on a single cluster, and that signal divergence causes ambivalence in assigning 1:1 orthology in concatenated Hox cluster analyses. Out of several possible explanations for this phenomenon we favor a model which keeps with the prevailing view of a single TGD prior to teleost radiation, but which also considers the timing of diploidization after duplication, relative to speciation events. We suggest that although the duplicated hoxa clusters diploidized prior to divergence of osteoglossomorphs, the duplicated hoxb, hoxc, and hoxd clusters concluded diploidization independently in osteoglossomorphs and other teleosts. We use the term "tetralogy" to describe the homology relationship which exists between duplicated sequences which originate through a shared WGD, but which diploidize into distinct paralogs from a common allelic pool independently in two lineages following speciation.
40 citations
Cites background from "A general scenario of Hox gene inve..."
...Teleost Hox cluster evolution appears to be significantly more dynamic than other gnathostome vertebrates which almost invariably retain the four ancestral Hox clusters with relatively few independent gene losses in different lineages (Liang et al. 2011)....
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References
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TL;DR: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved and modifications are incorporated into a new program, CLUSTAL W, which is freely available.
Abstract: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. Firstly, individual weights are assigned to each sequence in a partial alignment in order to down-weight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions. These modifications are incorporated into a new program, CLUSTAL W which is freely available.
63,427 citations
TL;DR: Version 4 of MEGA software expands on the existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses.
Abstract: We announce the release of the fourth version of MEGA software, which expands on the existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. Version 4 includes a unique facility to generate captions, written in figure legend format, in order to provide natural language descriptions of the models and methods used in the analyses. This facility aims to promote a better understanding of the underlying assumptions used in analyses, and of the results generated. Another new feature is the Maximum Composite Likelihood (MCL) method for estimating evolutionary distances between all pairs of sequences simultaneously, with and without incorporating rate variation among sites and substitution pattern heterogeneities among lineages. This MCL method also can be used to estimate transition/transversion bias and nucleotide substitution pattern without knowledge of the phylogenetic tree. This new version is a native 32-bit Windows application with multi-threading and multi-user supports, and it is also available to run in a Linux desktop environment (via the Wine compatibility layer) and on Intel-based Macintosh computers under the Parallels program. The current version of MEGA is available free of charge at (http://www.megasoftware.net).
29,021 citations
Additional excerpts
...0 [50] with either K2P (for nucleic acid) or JTT (for protein) distances....
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Book•
01 Jan 1986
TL;DR: The world of amphibians has a rich evolutionary history and the potential for the future of the amphibian species as mentioned in this paper, which includes reproductive strategies, reproductive cycles, reproductive mode, quantitative aspects, parental care, evolution of reproductive strategies courtship and mating - location of breeding site, secondary sexual characters, courtship behaviour, fertilization and oviposition, sexual selection, sexual evolution of mating systems vocalization - anuran communication system, mechanisms of sound production and reception, kinds of vocalizations and their functions, abiotic factors affecting vocalization, phylogenetic implications of vocalization eggs
Abstract: Introduction to amphibia - the world of amphibians, historical resume, prospects for the future. Part 1 Life History: reproductive strategies - reproductive cycles, reproductive mode, quantitative aspects, parental care, evolution of reproductive strategies courtship and mating - location of breeding site, secondary sexual characters, courtship behaviour, fertilization and oviposition, sexual selection, evolution of mating systems vocalization - anuran communication system, mechanisms of sound production and reception, kinds of vocalizations and their functions, abiotic factors affecting vocalization, interspecific significance of vocalization, phylogenetic implications of vocalization eggs and development - spermatozoa and fertilization, egg structure, egg development, hatching and birth, development and amphibian diversity larvae - morphology of larvae, adaptive types of larvae, physiology and ecology, social behaviour, evolutionary significance of larvae metamorphosis - endocrine control, other biochemical changes, morphological changes, neoteny, ecological and evolutionary significance of metamorphosis. Part 2 Ecology: relationships with the environment - water economy, temperature, gas exchange, energy metabolism and energy budgets, ecological synthesis food and feeding - prey selection, location of prey, capture of prey, evolution of prey-capturing mechanisms and strategies enemies and defence - diseases, parasites, predators, anti-predator mechanisms, evolution of defence mechanisms population biology - characteristics of individuals, movements and territoriality, demography, factors regulating populations community ecology and species diversity - community structure, species diversity, evolution of amphibian communities. Part 3 Morphology: musculoskeletal system - skull and hyobranchium, axial system, appendicular system, integration of functional units integumentary, sensory and visceral systems - integument, sensory receptor systems, nervous system, circulatory and respiratory systems, urogenital system, digestive system, endocrine glands, evolutionary considerations. Part 4 Evolution: origin and early evolution - nature of a tetrapod, primitive tetrapods, tetrapod affinities (lungfishes or lobe-fins?), diversity and evolution of early tetrapods, status of the lissamphibia cytogenetic, molecular and genomic evolution - cytogenetics, molecular evolution, genomic evolution phylogeny - caudata, gymnophiona, anura biogeography - biogeographic principles, historical setting, lissamphibia, caudata, gymnophiona, anura classification.
4,015 citations
American Museum of Natural History1, Columbia University2, University of Hamburg3, Sao Paulo State University4, University of Richmond5, University of the Western Cape6, Natural History Museum7, University of Texas at Arlington8, Yahoo!9, Florida Fish and Wildlife Conservation Commission10, California Academy of Sciences11, University of Michigan12, National University of Colombia13, McGill University14
TL;DR: A new taxonomy of living amphibians is proposed to correct the deficiencies of the old one, based on the largest phylogenetic analysis of living Amphibia so far accomplished, and many subsidiary taxa are demonstrated to be nonmonophyletic.
Abstract: The evidentiary basis of the currently accepted classification of living amphibians is discussed and shown not to warrant the degree of authority conferred on it by use and tradition. A new taxonomy of living amphibians is proposed to correct the deficiencies of the old one. This new taxonomy is based on the largest phylogenetic analysis of living Amphibia so far accomplished. We combined the comparative anatomical character evidence of Haas (2003) with DNA sequences from the mitochondrial transcription unit H1 (12S and 16S ribosomal RNA and tRNAValine genes, ≈ 2,400 bp of mitochondrial sequences) and the nuclear genes histone H3, rhodopsin, tyrosinase, and seven in absentia, and the large ribosomal subunit 28S (≈ 2,300 bp of nuclear sequences; ca. 1.8 million base pairs; x = 3.7 kb/terminal). The dataset includes 532 terminals sampled from 522 species representative of the global diversity of amphibians as well as seven of the closest living relatives of amphibians for outgroup comparisons. The...
1,994 citations
"A general scenario of Hox gene inve..." refers result in this paper
...The retention of HoxC1 in caecilians but not in frogs and salamanders implied that among the three living amphibian groups, caecilians are more distantly related to frogs and salamanders, supporting the Batrachia hypothesis (a frog+salamander clade) advocated by most recent molecular studies [45-48]....
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TL;DR: Genome analysis provides a greatly improved fish gene catalogue, including identifying key genes previously thought to be absent in fish, and reconstructs much of the evolutionary history of ancient and recent chromosome rearrangements leading to the modern human karyotype.
Abstract: Tetraodon nigroviridis is a freshwater puffer fish with the smallest known vertebrate genome. Here, we report a draft genome sequence with long-range linkage and substantial anchoring to the 21 Tetraodon chromosomes. Genome analysis provides a greatly improved fish gene catalogue, including identifying key genes previously thought to be absent in fish. Comparison with other vertebrates and a urochordate indicates that fish proteins have diverged markedly faster than their mammalian homologues. Comparison with the human genome suggests ∼900 previously unannotated human genes. Analysis of the Tetraodon and human genomes shows that whole-genome duplication occurred in the teleost fish lineage, subsequent to its divergence from mammals. The analysis also makes it possible to infer the basic structure of the ancestral bony vertebrate genome, which was composed of 12 chromosomes, and to reconstruct much of the evolutionary history of ancient and recent chromosome rearrangements leading to the modern human karyotype.
1,889 citations
"A general scenario of Hox gene inve..." refers background in this paper
...There are three or four clusters in chondrichthyans [8-10], four clusters in lobe-finned fishes [11-13] and tetrapods [14,15], up to eight in ray-finned fishes [16-20] and ~14 in tetraploid salmonid species [21]....
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