34 research outputs found
Mitochondrial genomes of acrodont lizards: timing of gene rearrangements and phylogenetic and biogeographic implications
<p>Abstract</p> <p>Background</p> <p>Acrodonta consists of Agamidae and Chamaeleonidae that have the characteristic acrodont dentition. These two families and Iguanidae <it>sensu lato </it>are members of infraorder Iguania. Phylogenetic relationships and historical biogeography of iguanian lizards still remain to be elucidated in spite of a number of morphological and molecular studies. This issue was addressed by sequencing complete mitochondrial genomes from 10 species that represent major lineages of acrodont lizards. This study also provided a good opportunity to compare molecular evolutionary modes of mitogenomes among different iguanian lineages.</p> <p>Results</p> <p>Acrodontan mitogenomes were found to be less conservative than iguanid counterparts with respect to gene arrangement features and rates of sequence evolution. Phylogenetic relationships were constructed with the mitogenomic sequence data and timing of gene rearrangements was inferred on it. The result suggested highly lineage-specific occurrence of several gene rearrangements, except for the translocation of the tRNA<sup>Pro </sup>gene from the 5' to 3' side of the control region, which likely occurred independently in both agamine and chamaeleonid lineages. Phylogenetic analyses strongly suggested the monophyly of Agamidae in relation to Chamaeleonidae and the non-monophyly of traditional genus <it>Chamaeleo </it>within Chamaeleonidae. <it>Uromastyx </it>and <it>Brookesia </it>were suggested to be the earliest shoot-off of Agamidae and Chamaeleonidae, respectively. Together with the results of relaxed-clock dating analyses, our molecular phylogeny was used to infer the origin of Acrodonta and historical biogeography of its descendant lineages. Our molecular data favored Gondwanan origin of Acrodonta, vicariant divergence of Agamidae and Chamaeleonidae in the drifting India-Madagascar landmass, and migration of the Agamidae to Eurasia with the Indian subcontinent, although Laurasian origin of Acrodonta was not strictly ruled out.</p> <p>Conclusions</p> <p>We detected distinct modes of mitogenomic evolution among iguanian families. Agamidae was highlighted in including a number of lineage-specific mitochondrial gene rearrangements. The mitogenomic data provided a certain level of resolution in reconstructing acrodontan phylogeny, although there still remain ambiguous relationships. Our biogeographic implications shed a light on the previous hypothesis of Gondwanan origin of Acrodonta by adding some new evidence and concreteness.</p
Sex chromosome evolution in snakes inferred from divergence patterns of two gametologous genes and chromosome distribution of sex chromosome-linked repetitive sequences
Molecular phylogenic trees of CTNNB1 gene. This figure shows neighbor-joining trees of CTNNB1 gene with the long alignment for 20 tetrapod species and the short alignment for 26 squamate species. (PDF 289 kb
Mitogenomic evaluation of the historical biogeography of cichlids toward reliable dating of teleostean divergences
<p>Abstract</p> <p>Background</p> <p>Recent advances in DNA sequencing and computation offer the opportunity for reliable estimates of divergence times between organisms based on molecular data. Bayesian estimations of divergence times that do not assume the molecular clock use time constraints at multiple nodes, usually based on the fossil records, as major boundary conditions. However, the fossil records of bony fishes may not adequately provide effective time constraints at multiple nodes. We explored an alternative source of time constraints in teleostean phylogeny by evaluating a biogeographic hypothesis concerning freshwater fishes from the family Cichlidae (Perciformes: Labroidei).</p> <p>Results</p> <p>We added new mitogenomic sequence data from six cichlid species and conducted phylogenetic analyses using a large mitogenomic data set. We found a reciprocal monophyly of African and Neotropical cichlids and their sister group relationship to some Malagasy taxa (Ptychochrominae <it>sensu </it>Sparks and Smith). All of these taxa clustered with a Malagasy + Indo/Sri Lankan clade (Etroplinae <it>sensu </it>Sparks and Smith). The results of the phylogenetic analyses and divergence time estimations between continental cichlid clades were much more congruent with Gondwanaland origin and Cretaceous vicariant divergences than with Cenozoic transmarine dispersal between major continents.</p> <p>Conclusion</p> <p>We propose to add the biogeographic assumption of cichlid divergences by continental fragmentation as effective time constraints in dating teleostean divergence times. We conducted divergence time estimations among teleosts by incorporating these additional time constraints and achieved a considerable reduction in credibility intervals in the estimated divergence times.</p
Characterization of Squamate Olfactory Receptor Genes and Their Transcripts by the High-Throughput Sequencing Approach
The olfactory receptor (OR) genes represent the largest multigene family in the genome of terrestrial vertebrates. Here, the high-throughput next-generation sequencing (NGS) approach was applied to characterization of OR gene repertoires in the green anole lizard Anolis carolinensis and the Japanese four-lined ratsnake Elaphe quadrivirgata. Tagged polymerase chain reaction (PCR) products amplified from either genomic DNA or cDNA of the two species were used for parallel pyrosequencing, assembling, and screening for errors in PCR and pyrosequencing. Starting from the lizard genomic DNA, we accurately identified 56 of 136 OR genes that were identified from its draft genome sequence. These recovered genes were broadly distributed in the phylogenetic tree of vertebrate OR genes without severe biases toward particular OR families. Ninety-six OR genes were identified from the ratsnake genomic DNA, implying that the snake has more OR gene loci than the anole lizard in response to an increased need for the acuity of olfaction. This view is supported by the estimated number of OR genes in the Burmese python's draft genome (∼280), although squamates may generally have fewer OR genes than terrestrial mammals and amphibians. The OR gene repertoire of the python seems unique in that many class I OR genes are retained. The NGS approach also allowed us to identify candidates of highly expressed and silent OR gene copies in the lizard's olfactory epithelium. The approach will facilitate efficient and parallel characterization of considerable unbiased proportions of multigene family members and their transcripts from nonmodel organisms
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Whole-genome survey reveals extensive variation in genetic diversity and inbreeding levels among peregrine falcon subspecies
Article describes how, in efforts to prevent extinction, resource managers are often tasked with increasing genetic diversity in a population of concern to prevent inbreeding depression or improve adaptive potential in a changing environment. The authors used whole-genome resequencing to generate over two million single nucleotide polymorphisms (SNPs) from multiple individuals of all peregrine falcon subspecies
Uromastyx Merrem 1820
CLASSIFICATION OF <i>UROMASTYX</i> <p> We discuss the validity of the morphology-based classification of <i>Uromastyx</i> in the light of their molecular phylogeny. The molecular data support <i>Uromastyx</i> and <i>Leiolepis</i> forming a sister-group relationship as members of the most basal agamid lineage (57–88% bootstrap values; Fig. 5). Morphological studies since that conducted by Moody (1980) have pointed to this relationship, classifying them into a separate family Uromastycidae (Böhme, 1982), subfamily Uromastycinae (Borsuk-Bialynicka & Moody, 1984) or Leiolepidinae (Frost & Etheridge, 1989; Ananjeva, Dujsebayeva & Joger, 2001). To the best of our knowledge, molecu- lar studies have not provided sufficient resolution on this matter. Partial 12S or 16S rRNA gene sequences supported the sister relationship of <i>Uromastyx</i> and <i>Leiolepis</i>, but did not support the view that the clade represents one of the earliest agamid lineages (Honda <i>et al.</i>, 2000). A tree constructed by Macey <i>et al.</i> (2000) using gene regions similar to ours did not even support the clustering of the two genera, although their taxonomic representations were somewhat biased towards agamids other than <i>Uromastyx</i> and <i>Leiolepis</i>. Therefore, there still seems to be uncertainty in the placement of <i>Uromastyx</i> and <i>Leiolepis</i> in the Agamidae, and this should be investigated further with increased molecular data.</p> <p> The molecular phylogeny within the <i>Uromastyx</i> species (Fig. 5) is in good agreement generally with the most recent view based on morphology (Wilms, 2001). <i>U. hardwickii</i> represents the most basal lineage of the genus and the remaining taxa investigated grouped into the African and Arabian clades. However, as outlined earlier, there were a few discrepancies with respect to the phylogenetic affiliation of <i>U. macfadyeni</i>, <i>U. aegyptia</i> and <i>U. benti</i>. Morphological studies (Moody, 1987; Wilms, 2001) pointed to certain similarities of <i>U. macfadyeni</i> to <i>U. ocellata</i> and <i>U. ornata</i> of the Arabian clade, with the last 12–21 tail whorls made up of a continuous scale row and with fewer than 260 scales around the midbody.</p> <p> In order to examine this further, we conducted the Kishino–Hasegawa test to compare the log-likelihood values between the ML tree topology of Figure 5 and some competing hypotheses in which <i>U. macfadyeni</i> clusters with either or both <i>U. ocellata</i> and <i>U. ornata</i> (Table 3). The results clearly rejected the competing hypotheses at the 1% significance level. We therefore suppose that the apparent similarities between <i>U. macfadyeni</i> and the latter two species may be due to convergent evolution through sharing similar ecological or climatic environments. These species are now distributed in neighbouring areas surrounding the Red Sea and the Gulf of Aden (Fig. 6).</p> <p> The nucleotide sequences (1503 bp) for the 25 taxa were analysed as described in the Material and methods. User-defined unrooted tree topologies were as follows: tree 1 for the ML tree topology as shown in Fig. 5, (Outgroup, Hard, ((Mac, (Gey, ((Aca1, Aca2), (Dis, Mali)))), ((Aeg, Mic), (Ben, ((Oce1, Oce2), Orn))))); tree 2, (Outgroup, Hard, ((Gey, ((Aca1, Aca2), (Dis, Mali))), ((Aeg, Mic), (Ben, (Mac, ((Oce1, Oce2), Orn)))))); tree 3, (Outgroup, Hard, ((Gey, ((Aca1, Aca2), (Dis, Mali))), ((Aeg, Mic), (Ben, (Orn, ((Oce1, Oce2), Mac)))))); and tree 4, (Outgroup, Hard, ((Gey, ((Aca1, Aca2), (Dis, Mali))), ((Aeg, Mic), (Ben, ((Oce1, Oce2), (Mac, Orn)))))). Refer to Fig. 5 for the tree topology of the outgroup and see the legend of Fig. 6 for abbreviations of <i>Uromastyx</i> taxa. Oce1 and Oce2 mean <i>U. ocellata</i> from Egypt and Sudan, respectively.</p> <p>†Natural logarithm of the likelihood value.</p> <p>‡Difference in lnL from that of the ML tree.</p> <p>§A standard error in lnL.</p> <p>¶An asterisk means that the corresponding phylogenetic hypothesis can be statistically rejected at the 1% significance level by the standard criterion of DlnL/SE> 2.58.</p> <p> <i>U. aegyptia</i> was considered to have a phylogenetic affinity to the African group because of their common features in external morphology, such as the last two to five tail whorls being made up of a continuous scale row (Moody, 1987; Wilms, 2001). However, this species has much higher midbody scale counts than do members of the African group (Wilms & Böhme, 2000a). The phylogenetic affiliation of <i>U. aegyptia</i> in the Arabian group (Fig. 5) may therefore be possible, though this is not conclusive due to the low bootstrap values (52–57%). It is noteworthy that the serological studies by Joger (1986) also suggested a closer relationship of <i>U. aegyptia</i> to <i>U. ocellata</i> and <i>U. ornata</i> than to <i>U. acanthinura</i> and <i>U. geyri</i>. Finally, the molecular phylogeny (Fig. 5) placed <i>U. benti</i> as sister to the <i>U. ocellata – U. ornata</i> clade, while <i>U. benti</i> was morphologically regarded as a sister taxon of <i>U. ocellata</i> with the exclusion of <i>U. ornata</i> (Wilms, 2001). We favour the molecular view in this respect because of its strong bootstrap values (98–99%).</p> <p> Treatment of a taxon as either a species or a subspecies has been changed frequently for members of the genus <i>Uromastyx</i>, and this may still be controversial. For example, Mertens (1962) classified <i>U. geyri</i> and <i>U. dispar</i> as subspecies of <i>U. acanthinura</i>, while Moody (1980) recognized them as full species. Thomas Wilms followed the former view in his book (Wilms, 1995) but later changed to the latter (Wilms, 2001). He also once recognized <i>U. ocellata</i>, <i>U. ornata</i> and <i>U. macfadyeni</i> as subspecies of <i>U. ocellata</i> (Wilms, 1995), while all of them have recently been treated as independent species (Wilms & Böhme, 2000c; Wilms, 2001). Conversely, <i>U. d. maliensis</i>, once recognized as an independent species (Joger & Lambert, 1996), has been revised to be a subspecies of <i>U. dispar</i> (Wilms & Böhme, 2000b).</p> <p> In all the above-mentioned points, our molecular phylogeny (Fig. 5) supports the most recent view in Wilms (2001), not only for the phylogenetic relationship but also for the level of divergence. The divergence times between <i>U. geyri</i>, <i>U. acanthinura</i> and <i>U. dispar</i>, as well as between <i>U. ocellata</i> and <i>U. ornata</i>, were much larger compared with those between <i>U. d. dispar</i> and <i>U. d. maliensis</i> (Table 2).</p> HISTORICAL BIOGEOGRAPHY <p> Extant <i>Uromastyx</i> taxa of the African and Arabian groups are distributed allopatrically, with a considerable overlap of distribution only between <i>U. geyri</i> and <i>U. d. maliensis</i> (Fig. 6). In this section, we discuss how the <i>Uromastyx</i> species radiated and migrated to their current habitats, based on our molecular data together with geological and palaeoenvironmental evidence. The evolutionary framework thus constructed using representative sequences from each taxon will provide a basis for future phylogeographical analyses using many individuals with detailed locality information.</p> <p> Our molecular analyses suggested that <i>Uromastyx</i> and <i>Leiolepis</i> are sister genera (Fig. 5) and that they diverged from each other in the middle Eocene (40–50 Mya; Table 2). The oldest fossil record closely associated with these genera is <i>Mimeosaurus</i> of the Upper Cretaceous–Eocene of Mongolia (Moody, 1980), and is consistent with the above-mentioned divergence time. Moreover, all the extant species included in the genus <i>Leiolepis</i> inhabit south-east Asia. <i>U. hardwickii</i>, having diverged from the most basal position of the <i>Uromastyx</i> phylogeny (Fig. 5), inhabits south Asia. Thus, it is likely that direct ancestors of these genera lived in central–south Asia, from where the genus <i>Uromastyx</i> originated and migrated westward towards the hot and arid habitats suitable for their lifestyle (Fig. 6).</p> <p> From the late Cretaceous to the early Miocene (18–100 Mya) the African continent, including an area of the current Arabian Peninsula, had long been isolated from other continents (Rögl, 1998). Geological and palaeontological evidence (Rögl, 1998; Harzhauser, Piller & Steininger, 2002) consistently shows that plate tectonic activities connected Africa to Eurasia through closure of the Eastern Mediterranean seaway by approximately 18 Mya (the <i>Gomphotherium</i> Landbridge). This landbridge later became disconnected temporarily, but it has been continuously present since ~15 Mya.</p> <p> Our molecular analyses suggested that the Asian (<i>U. hardwickii</i>) and Afro-Arabian (the other species used) taxa diverged 25–29 Mya (Table 2). This is much earlier compared with the estimate for the formation of the <i>Gomphotherium</i> Landbridge. We therefore speculate that there was an initial stage of radiation of the <i>Uromastyx</i> lizards in the eastern Middle East before the formation of the landbridge, and that predecessors of the Afro-Arabian taxa derived from one of these diversified lineages. A few taxa from the eastern Middle East (e.g. <i>U. loricata</i> of Iraq and Iran and <i>U. thomasi</i> of Oman) were not included in our study. Morphological (Wilms, 2001 and refs. therein) and immunological (Joger, 1986) studies have suggested that these taxa diverged from basal positions next to that of <i>U. hardwickii</i> in the <i>Uromastyx</i> phylogeny.</p> <p> We estimated the African and Arabian groups of <i>Uromastyx</i> to have diverged 11–15 Mya (Table 2). North Africa was subjected to climatic changes towards aridity in the middle Miocene. Dry and open woodlands and the savanna emerged to interrupt the continuous African forest by the late middle Miocene (McClanahan & Young, 1996; MacDonald, 2003), and this may have facilitated faunal and floral exchanges eastwards and westwards (e.g. Fu, 1998; Caujapé- Castells & Jansen, 2003). Predecessors of the African <i>Uromastyx</i> group may have migrated to new xeric habitats in North Africa and diverged from the Arabian taxa (Fig. 6).</p> <p> The Arabian Peninsula began to separate from the remaining part of the African continent in the early Miocene as a tectonic consequence of the Afar mantle plume leading to the formation of the Red Sea, the Gulf of Aden and the East African Rift Valley (Girdler, 1991; Pudlo, Shandelmeier & Reynolds, 1997). This accompanied considerable uplifting of some mountain systems along the plate boundaries. The East African Rift Valley and associated mountain systems may have become terrestrial barriers, isolating <i>U. macfadyeni</i> of northern Somalia from its sister taxa of the African group. The estimated divergence time (10–12 Mya; Table 2) seems consistent with geological (Girdler, 1991) and palaeontological (Coppens, 1994) data in supporting this idea.</p> <p> Within the Arabian group, <i>U. aegyptia</i> first diverged from the other members 12–14 Mya (Table 2) and this species is now widely distributed in the Arabian Peninsula and northern Egypt. Molecular data also suggested that <i>U. benti</i> diverged from <i>U. ocellata</i> and <i>U. ornata</i> 9–10 Mya and that the latter two species diverged from each other 7–8 Mya (Table 2). A possible geological factor that may have been associated with the former divergence is the elevation of the Yemen Plateau (Geoffroy, Huchon & Khanbari, 1998). However, the considerable uplifting of the Yemen Plateau may have already occurred in the early Miocene, somewhat earlier than the estimated divergence time (9–10 Mya). We therefore withhold a conclusion on this matter until more molecular and geological data become available.</p> <p> Geological influence on the divergence between <i>U. ocellata</i> and <i>U. ornata</i> seems much clearer. Since the current distribution ranges for <i>U. ocellata</i> and <i>U. ornata</i> are separated by the Red Sea, their divergence has been hypothesized to be due to the habitat fragmentation caused by the expansion of the Red Sea (Wilms, 2001). Our study supports this hypothesis by showing that the estimated divergence time between the two species (7–8 Mya) corresponds well to the geological timing for the expansion of the Red Sea (Girdler, 1991; Pudlo <i>et al.</i>, 1997; refs. therein). The oceanic accretion may have started in the middle Miocene (12– 13 Mya), while evidence from sedimentary rocks suggests that seawater had come in to the northern region of the Red Sea by at least 5 Mya (Ross & Schlee, 1973).</p> <p> Our molecular data pointed to much more recent times for the divergences between members of the African group other than <i>U. macfadyeni</i> (Table 2). By the early Pliocene (around 5 Mya), the trend for a cooler and drier environment was well established in North Africa with expansion of the grassland (MacDonald, 2003). After 2.8 Mya, there were repeated global cycles of warming and cooling and this is believed to have accelerated speciation for a variety of terrestrial and marine animals (Agusti, Rook & Andrews, 1999; deMenocal & Brown, 1999). Especially during the late Pliocene (around 2.4 and 1.8 Mya), further cooling and drying resulted in a major expansion of grassland and desert environments (McClanahan & Young, 1996). We suggest that such climatic fluctuations could have caused the habitat fragmentation and isolation of local populations, leading to the speciation between <i>U. geyri</i>, <i>U. acanthinura</i> and <i>U. dispar</i>.</p>Published as part of <i>Amer, Sayed A. M. & Kumazawa, Yoshinori, 2005, Mitochondrial DNA sequences of the Afro-Arabian spiny-tailed lizards (genus Uromastyx; family Agamidae): phylogenetic analyses and evolution of gene arrangements, pp. 247-260 in Biological Journal of the Linnean Society 85</i> on pages 254-257, DOI: 10.1111/j.1095-8312.2005.00485.x, <a href="http://zenodo.org/record/7846312">http://zenodo.org/record/7846312</a>
Evolution of the Noncoding Features of Sea Snake Mitochondrial Genomes within Elapidae
Mitochondrial genomes of four elapid snakes (three marine species [Emydocephalus ijimae, Hydrophis ornatus, and Hydrophis melanocephalus], and one terrestrial species [Sinomicrurus japonicus]) were completely sequenced by a combination of Sanger sequencing, next-generation sequencing and Nanopore sequencing. Nanopore sequencing was especially effective in accurately reading through long tandem repeats in these genomes. This led us to show that major noncoding regions in the mitochondrial genomes of those three sea snakes contain considerably long tandem duplications, unlike the mitochondrial genomes previously reported for same and other sea snake species. We also found a transposition of the light-strand replication origin within a tRNA gene cluster for the three sea snakes. This change can be explained by the Tandem Duplication—Random Loss model, which was further supported by remnant intervening sequences between tRNA genes. Mitochondrial genomes of true snakes (Alethinophidia) have been shown to contain duplicate major noncoding regions, each of which includes the control region necessary for regulating the heavy-strand replication and transcription from both strands. However, the control region completely disappeared from one of the two major noncoding regions for two Hydrophis sea snakes, posing evolutionary questions on the roles of duplicate control regions in snake mitochondrial genomes. The timing and molecular mechanisms for these changes are discussed based on the elapid phylogeny
Additional file 2: of Variation and evolution of polyadenylation profiles in sauropsid mitochondrial mRNAs as deduced from the high-throughput RNA sequencing
A Perl script named polyA_seq.pl used to find oligoA-containing reads. (TXT 1 kb