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Athanasia Tzika

Senior Research Assistant in LANE

  • T: +41 22 379 67 75
  • office 4022a (Sciences III)
  • A Step-by-step Guide to Assemble a Reptilian Genome Chapter in "Methods in Molecular Biology - Avian and Reptilian Developmental Biology".

    abstract

    This volume discusses recent advances in avian and reptilian biology that have caused this diverse field to re-emerge. The chapters in this book are divided into 4 parts: genomics and transcriptomics, genetic manipulation, stem cells, and new model systems. Part I details how to perform genomic and transcriptomic analyses in birds and reptiles; Part II highlights technological advancements in avian genetic manipulation; Part III focuses on methods to handle pluripotent cells; and part IV looks at the emerging models in avian and reptilian developmental biology. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, Avian and Reptilian Developmental Biology: Methods and Protocols explores a variety of approaches and different sauropsid models that will help facilitate communication and collaboration among researchers, which in turn will progress this field forward.

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  • The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. Nucleic Acids Res. 2016 Jan 4;44(D1):D27-37. doi: 10.1093/nar/gkv1310. Epub 2015 Nov 28

    abstract

    The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article.

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  • Reptilian Transcriptomes v2.0: An Extensive Resource for Sauropsida Genomics and Transcriptomics. Genome Biol Evol 2015 Jun;7(6):1827-41. evv106. 10.1093/gbe/evv106. PMC4494049.

    abstract

    Despite the availability of deep-sequencing techniques, genomic and transcriptomic data remain unevenly distributed across phylogenetic groups. For example, reptiles are poorly represented in sequence databases, hindering functional evolutionary and developmental studies in these lineages substantially more diverse than mammals. In addition, different studies use different assembly and annotation protocols, inhibiting meaningful comparisons. Here, we present the "Reptilian Transcriptomes Database 2.0," which provides extensive annotation of transcriptomes and genomes from species covering the major reptilian lineages. To this end, we sequenced normalized complementary DNA libraries of multiple adult tissues and various embryonic stages of the leopard gecko and the corn snake and gathered published reptilian sequence data sets from representatives of the four extant orders of reptiles: Squamata (snakes and lizards), the tuatara, crocodiles, and turtles. The LANE runner 2.0 software was implemented to annotate all assemblies within a single integrated pipeline. We show that this approach increases the annotation completeness of the assembled transcriptomes/genomes. We then built large concatenated protein alignments of single-copy genes and inferred phylogenetic trees that support the positions of turtles and the tuatara as sister groups of Archosauria and Squamata, respectively. The Reptilian Transcriptomes Database 2.0 resource will be updated to include selected new data sets as they become available, thus making it a reference for differential expression studies, comparative genomics and transcriptomics, linkage mapping, molecular ecology, and phylogenomic analyses involving reptiles. The database is available at www.reptilian-transcriptomes.org and can be enquired using a wwwblast server installed at the University of Geneva.

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  • Two waves of anisotropic growth generate enlarged follicles in the spiny mouse. Evodevo 2014 ;5():33. 10.1186/2041-9139-5-33. 2041-9139-5-33. PMC4335386.

    abstract

    Mammals exhibit a remarkable variety of phenotypes and comparative studies using novel model species are needed to uncover the evolutionary developmental mechanisms generating this diversity. Here, we undertake a developmental biology and numerical modeling approach to investigate the development of skin appendages in the spiny mouse, Acomys dimidiatus.

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  • Retroviral envelope syncytin capture in an ancestrally diverged mammalian clade for placentation in the primitive Afrotherian tenrecs. Proc. Natl. Acad. Sci. U.S.A. 2014 Oct;111(41):E4332-41. 1412268111. 10.1073/pnas.1412268111. PMC4205661.

    abstract

    Syncytins are fusogenic envelope (env) genes of retroviral origin that have been captured for a function in placentation. Syncytins have been identified in Euarchontoglires (primates, rodents, Leporidae) and Laurasiatheria (Carnivora, ruminants) placental mammals. Here, we searched for similar genes in species that retained characteristic features of primitive mammals, namely the Malagasy and mainland African Tenrecidae. They belong to the superorder Afrotheria, an early lineage that diverged from Euarchotonglires and Laurasiatheria 100 Mya, during the Cretaceous terrestrial revolution. An in silico search for env genes with full coding capacity within a Tenrecidae genome identified several candidates, with one displaying placenta-specific expression as revealed by RT-PCR analysis of a large panel of Setifer setosus tissues. Cloning of this endogenous retroviral env gene demonstrated fusogenicity in an ex vivo cell-cell fusion assay on a panel of mammalian cells. Refined analysis of placental architecture and ultrastructure combined with in situ hybridization demonstrated specific expression of the gene in multinucleate cellular masses and layers at the materno-fetal interface, consistent with a role in syncytium formation. This gene, which we named "syncytin-Ten1," is conserved among Tenrecidae, with evidence of purifying selection and conservation of fusogenic activity. To our knowledge, it is the first syncytin identified to date within the ancestrally diverged Afrotheria superorder.

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  • The genome sequence of the corn snake (Pantherophis guttatus), a valuable resource for EvoDevo studies in squamates. Int. J. Dev. Biol. 2014 ;58(10-12):881-8. 150060at. 10.1387/ijdb.150060at.

    abstract

    Squamates (snakes and lizards) exhibit a striking variety of phenotypes, with little known on their generative mechanisms. Studies aiming to understand the genetic basis of this wide diversity in morphology, physiology and ecology will greatly benefit from whole genome sequencing initiatives, as they provide the foundation for comparative analyses and improve our understanding of the evolution, development and diversification of traits. Here, we present the first draft genome of the corn snake Pantherophis guttatus, an oviparous snake that we promote as a particularly appropriate model species for evolutionary developmental studies in squamates. We sequenced 100-base paired-end reads from multiple individuals of a single family (parents and offspring) that produced a genome assembly of 1.53 gigabases (Gb), roughly covering 75% of the expected total genome size, and 297,768 scaffolds >1 Kb. We were able to fully retrieve 86, and partially another 106, of the 248 CEGMA core genes, indicating that a high genome completeness was achieved, even though the assembly is fragmented. Using MAKER2, we annotated 10,917 genes with high confidence (Annotation Edit Distance (AED)<1) and an additional 5,263 predicted genes matched with the species' transcriptome. Numerous colour and colour pattern morphs exist in P. guttatus, making it an ideal model to study the genetic determinism, development, and evolution of adaptive colour traits in reptiles. Using our draft genome and a Single-Nucleotide Polymorphism (SNP) calling approach, we confirmed the interval with the causative mutation for the amelanistic phenotype, a result supported by a parallel exome-based study.

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  • Multiple enhancers regulate Hoxd genes and the Hotdog LncRNA during cecum budding. Cell Rep 2013 Oct;5(1):137-50. S2211-1247(13)00500-7. 10.1016/j.celrep.2013.09.002.

    abstract

    Hox genes are required for the development of the intestinal cecum, a major organ of plant-eating species. We have analyzed the transcriptional regulation of Hoxd genes in cecal buds and show that they are controlled by a series of enhancers located in a gene desert flanking the HoxD cluster. The start site of two opposite long noncoding RNAs (lncRNAs), Hotdog and Twin of Hotdog, selectively contacts the expressed Hoxd genes in the framework of a topological domain, coinciding with robust transcription of these genes during cecum budding. Both lncRNAs are specifically transcribed in the cecum, albeit bearing no detectable function in trans. Hedgehogs have kept this regulatory potential despite the absence of the cecum, suggesting that these mechanisms are used in other developmental situations. In this context, we discuss the implementation of a common "budding toolkit" between the cecum and the limbs.

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  • Patterns of ossification in southern versus northern placental mammals. Evolution 2013 Jul;67(7):1994-2010. 10.1111/evo.12071.

    abstract

    Consensus on placental mammal phylogeny is fairly recent compared to that for vertebrates as a whole. A stable phylogenetic hypothesis enables investigation into the possibility that placental clades differ from one another in terms of their development. Here, we focus on the sequence of skeletal ossification as a possible source of developmental distinctiveness in "northern" (Laurasiatheria and Euarchontoglires) versus "southern" (Afrotheria and Xenarthra) placental clades. We contribute data on cranial and postcranial ossification events during growth in Afrotheria, including elephants, hyraxes, golden moles, tenrecs, sengis, and aardvarks. We use three different techniques to quantify sequence heterochrony: continuous method, sequence-ANOVA (analysis of variance) and event-paring/Parsimov. We show that afrotherians significantly differ from other placentals by an early ossification of the orbitosphenoid and caudal vertebrae. Our analysis also suggests that both southern placental groups show a greater degree of developmental variability; however, they rarely seem to vary in the same direction, especially regarding the shifts that differ statistically. The latter observation is inconsistent with the Atlantogenata hypothesis in which afrotherians are considered as the sister clade of xenarthrans. Interestingly, ancestral nodes for Laurasiatheria and Euarchontoglires show very similar trends and our results suggest that developmental homogeneity in some ossification sequences may be restricted to northern placental mammals (Boreoeutheria).

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  • Contrasted evolution of the vomeronasal receptor repertoires in mammals and squamate reptiles. Genome Biol Evol 2013 ;5(2):389-401. evt013. 10.1093/gbe/evt013. PMC3590772.

    abstract

    The vomeronasal organ (VNO) is an olfactory structure that detects pheromones and environmental cues. It consists of sensory neurons that express evolutionary unrelated groups of transmembrane chemoreceptors. The predominant V1R and V2R receptor repertoires are believed to detect airborne and water-soluble molecules, respectively. It has been suggested that the shift in habitat of early tetrapods from water to land is reflected by an increase in the ratio of V1R/V2R genes. Snakes, which have a very large VNO associated with a sophisticated tongue delivery system, are missing from this analysis. Here, we use RNA-seq and RNA in situ hybridization to study the diversity, evolution, and expression pattern of the corn snake vomeronasal receptor repertoires. Our analyses indicate that snakes and lizards retain an extremely limited number of V1R genes but exhibit a large number of V2R genes, including multiple lineages of reptile-specific and snake-specific expansions. We finally show that the peculiar bigenic pattern of V2R vomeronasal receptor gene transcription observed in mammals is conserved in squamate reptiles, hinting at an important but unknown functional role played by this expression strategy. Our results do not support the hypothesis that the shift to a vomeronasal receptor repertoire dominated by V1Rs in mammals reflects the evolutionary transition of early tetrapods from water to land. This study sheds light on the evolutionary dynamics of the vomeronasal receptor families in vertebrates and reveals how mammals and squamates differentially adapted the same ancestral vomeronasal repertoire to succeed in a terrestrial environment.

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  • Development and embryonic staging in non-model organisms: the case of an afrotherian mammal. J. Anat. 2013 Jan;222(1):2-18. 10.1111/j.1469-7580.2012.01509.x. PMC3552411.

    abstract

    Studies of evolutionary developmental biology commonly use 'model organisms' such as fruit flies or mice, and questions are often functional or epigenetic. Phylogenetic investigations, in contrast, typically use species that are less common and mostly deal with broad scale analyses in the tree of life. However, important evolutionary transformations have taken place at all taxonomic levels, resulting in such diverse forms as elephants and shrews. To understand the mechanisms underlying morphological diversification, broader sampling and comparative approaches are paramount. Using a simple, standardized protocol, we describe for the first time the development of soft tissues and some parts of the skeleton, using μCT-imaging of developmental series of Echinops telfairi and Tenrec ecaudatus, two tenrecid afrotherian mammals. The developmental timing of soft tissue and skeletal characters described for the tenrecids is briefly compared with that of other mammals, including mouse, echidna, and the opossum. We found relatively few heterochronic differences in development in the armadillo vs. tenrec, consistent with a close relationship of Xenarthra and Afrotheria. Ossification in T. ecaudatus continues well into the second half of overall gestation, resembling the pattern seen in other small mammals and differing markedly from the advanced state of ossification evident early in the gestation of elephants, sheep, and humans.

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  • Reptilian-transcriptome v1.0, a glimpse in the brain transcriptome of five divergent Sauropsida lineages and the phylogenetic position of turtles. Evodevo 2011 ;2(1):19. 2041-9139-2-19. 10.1186/2041-9139-2-19. PMC3192992.

    abstract

    Reptiles are largely under-represented in comparative genomics despite the fact that they are substantially more diverse in many respects than mammals. Given the high divergence of reptiles from classical model species, next-generation sequencing of their transcriptomes is an approach of choice for gene identification and annotation.

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  • Consecutive Virgin Births in the New World Boid Snake, The Colombian Rainbow Boa, Epicrates maurus Journal of Heredity, 102(6):759-763

    abstract

    Until recently, facultative automictic parthenogenesis within the squamate reptiles exhibiting ZZ:ZW genetic sex determination has resulted in single reproductive events producing male (ZZ) or female (ZW) offspring. With the recent discovery of viable parthenogenetically produced female (WW) Boa constrictors, the existence of further parthenogenetic events resulting in WW females was questioned. Here, we provide genetic evidence for consecutive virgin births by a female Colombian rainbow boa (Epicrates maurus), resulting in the production of WW females likely through terminal fusion automixis. Samples were screened at 22 microsatellite loci with 12 amplifying unambiguous products. Of these, maternal heterozygosity was observed in 4, with the offspring differentially homozygous at each locus. This study documents the first record of parthenogenesis within the genus Epicrates, a second within the serpent lineage Boidae, and the third genetically confirmed case of consecutive virgin births of viable offspring within any vertebrate lineage. Unlike the recent record in Boa constrictors, the female described here was isolated from conspecifics from birth, demonstrating that males are not required to stimulate parthenogenetic reproduction in this species and possibly other Boas.

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  • Analysis of global and local population stratification of Finless Porpoises Neophocaena phocaenoides in Chinese waters Marine Biology, 158(8):1791-1804.

    abstract

    The existence of three distinct populations is widely accepted for the finless porpoise (Neophocaena phocaenoides) in Chinese waters: the Yellow Sea, Yangtze River, and South China Sea populations. Here, we use nine species-specific microsatellite loci, the complete mitochondrial DNA control region (912 bp), and the complete mitochondrial cytochrome b gene (1,140 bp) to further investigate potential population stratification in the Yellow Sea using 147 finless porpoise samples from the Bohai Sea and adjacent northern Yellow Sea, two regions that were largely underrepresented in previous genetic studies. Our F-statistics analyses confirm the previously described three populations, but further demonstrate significant genetic differentiation between the [Bohai + northern Yellow] Sea and the southern Yellow Sea. On the other hand, median-joining network analyses do not exhibit well-differentiated haplotype groups among different geographic populations, suggesting the existence of shared ancestral haplotypes. Levels of microsatellite diversity are moderate to high (mean HE = 0.794) among the 147 [Bohai + northern Yellow] Sea finless porpoises and no recent bottleneck was detected, whereas mtDNA control region and cytochrome b gene diversity is low to moderate. The microsatellite genotypic and mtDNA haplotypic data also confirm the presence of mother-calf pairs in single-net bycatch cases. The results presented here highlight the necessity to treat the [Bohai + northern Yellow] Sea population (highly impacted by anthropogenic threats) as a separate Management Unit.

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  • Development of a multiplex PCR assay for fine-scale population genetic analysis of the Komodo monitor Varanus komodoensis based on 18 polymorphic microsatellite loci. Mol Ecol Resour 2011 May;11(3):550-6. 10.1111/j.1755-0998.2011.02986.x.

    abstract

    Multiplex PCR assays for the coamplification of microsatellite loci allow rapid and cost-effective genetic analyses and the production of efficient screening protocols for international breeding programs. We constructed a partial genomic library enriched for di-nucleotide repeats and characterized 14 new microsatellite loci for the Komodo monitor (or Komodo dragon, Varanus komodoensis). Using these novel microsatellites and four previously described loci, we developed multiplex PCR assays that may be loaded on a genetic analyser in three separate panels. We tested the novel set of microsatellites for polymorphism using 69 individuals from three island populations and evaluated the resolving power of the entire panel of 18 loci by conducting (i) a preliminary assignment test to determine population(s) of origin and (ii) a parentage analysis for 43 captive Komodo monitors. This panel of polymorphic loci proved useful for both purposes and thus can be exploited for fine-scale population genetic analyses and as part of international captive breeding programs directed at maintaining genetically viable ex situ populations and reintroductions.

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  • Cryptic patterning of avian skin confers a developmental facility for loss of neck feathering PLoS Biology, 9(3).

    abstract

    Vertebrate skin is characterized by its patterned array of appendages, whether feathers, hairs, or scales. In avian skin the distribution of feathers occurs on two distinct spatial levels. Grouping of feathers within discrete tracts, with bare skin lying between the tracts, is termed the macropattern, while the smaller scale periodic spacing between individual feathers is referred to as the micropattern. The degree of integration between the patterning mechanisms that operate on these two scales during development and the mechanisms underlying the remarkable evolvability of skin macropatterns are unknown. A striking example of macropattern variation is the convergent loss of neck feathering in multiple species, a trait associated with heat tolerance in both wild and domestic birds. In chicken, a mutation called Naked neck is characterized by a reduction of body feathering and completely bare neck. Here we perform genetic fine mapping of the causative region and identify a large insertion associated with the Naked neck trait. A strong candidate gene in the critical interval, BMP12/GDF7, displays markedly elevated expression in Naked neck embryonic skin due to a cis-regulatory effect of the causative mutation. BMP family members inhibit embryonic feather formation by acting in a reaction-diffusion mechanism, and we find that selective production of retinoic acid by neck skin potentiates BMP signaling, making neck skin more sensitive than body skin to suppression of feather development. This selective production of retinoic acid by neck skin constitutes a cryptic pattern as its effects on feathering are not revealed until gross BMP levels are altered. This developmental modularity of neck and body skin allows simple quantitative changes in BMP levels to produce a sparsely feathered or bare neck while maintaining robust feather patterning on the body.

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  • Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses (a response to Vilella et al.’s correspondence) Genome Biology, 12: 401.

    abstract

    a response to Vilella et al.’s correspondence (A response to 2x genomes - depth does matter by MC Milinkovitch, R Helaers, E Depiereux, AC Tzika and T Gabaldón. Genome Biol 2010, 11:R16.)

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  • Molecular analyses of small cetacean samples from Peruvian fish markets Conservation Genetics, 11(6):2207-2218.

    abstract

    In the last 60 years, incidental entanglement in fishing gears (so called by-catch) became the main cause of mortality worldwide for small cetaceans and is pushing several populations and species to the verge of extinction. Thus, monitoring and quantifying by-catches is an important step towards proper and sustainable management of cetacean populations. Continuous studies indicated that by-catches and directed takes of small cetaceans in Peru greatly increased since 1985. Legal measures banning cetacean takes, enforced in 1994 and 1996, ironically made monitoring highly problematic as fishers continue catching these animals but utilize or dispose of carcasses clandes- tinely. Hence, in locations where cetaceans are landed covertly or already butchered, molecular genetic methods can provide the only means of identification of the species, sex, and sometimes the population of each sample. Here, we generate and analyse a fragment of the mitochondrial DNA cytochrome b gene and 5 nuclear microsatellite markers from 182 meat and skin samples of unidentified small cetaceans collected at three Peruvian markets between July 2006 and April 2007. Our results, compared to past surveys, indicate that Lagenorhynchus obscurus, Phocoena spinipinnis, Tursiops truncatus, Delphinus capensis, and D. delphis continue to be caught and marketed, but that the relative incidence of P. spinipinnis is highly reduced, pos- sibly because of population depletion. The small number of possible sampling duplicates demonstrates that a high monitoring frequency is required for a thorough evaluation of incidental catches in the area. A wide public debate on by-catch mitigation measures is greatly warranted in Peru.

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  • Historical constraints on vertebrate genome evolution. Genome Biol Evol 2010 ;2():13-8. 10.1093/gbe/evp052. PMC2839353.

    abstract

    Recent analyses indicated that genes with larger effect of knockout or mutation and with larger probability to revert to single copy after whole genome duplication are expressed earlier in development. Here, we further investigate whether tissue specificity of gene expression is constrained by the age of origin of the corresponding genes. We use 38 metazoan genomes and a comparative genomic application system to integrate inference of gene duplication with expression data from 17,503 human genes into a strictly phylogenetic framework. We show that the number of anatomical systems in which genes are expressed decreases steadily with decreased age of the genes' first appearance in the phylogeny: the oldest genes are expressed, on average, in twice as many anatomical systems than the genes gained recently in evolution. These results are robust to different sources of expression data, to different levels of the anatomical system hierarchy, and to the use of gene families rather than duplication events. Finally, we show that the rate of increase in gene tissue specificity correlates with the relative rate of increase in the maximum number of cell types in the corresponding taxa. Although subfunctionalization and increase in cell type number throughout evolution could constitute, respectively, the proximal and ultimate causes of this correlation, the two phenomena are intermingled. Our analyses identify a striking historical constraint in gene expression: the number of cell types in existence at the time of a gene appearance (through duplication or de novo origination) tends to determine its level of tissue specificity for tens or hundreds of millions of years.

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  • Preliminary Genetic Status of the Spotted Seal Phoca largha in Liaodong Bay Based on Microsatellite and Mitochondrial DNA Analyses Trends in Evolutionary Biology, 2(6):33-38.

    abstract

    The Liaodong Bay spotted seal (Phoca largha) population experienced several drastic declines in the last 80 years. Recent studies are contradictory regarding the level of genetic diversity and population structure of P. largha, possibly because of the use of non-species-specific nuclear markers. Here, we report on i) the first isolation and characterization of 10 species-specific polymorphic microsatellite loci for the spotted seal, ii) sequences of a 572 bp mtDNA fragment in 25 Liaodong Bay individuals that we analyzed together with all published haplotypes from Liaodong Bay and Japan. Intermediate genetic diversity in microsatellite loci was found in the Liaodong Bay population and the effective population size estimates were 41.8 to 86.8 individuals. Low mtDNA genetic variability, especially nucleotide diversity, in the Liaodong Bay population was detected, but Bayesian skyline plots did not show any evidence of recent bottleneck. Both F-statistics and the haplotypic network indicate a clear differentiation between the Liaodong Bay and Japanese populations separated by a fixed mutation. Analysis of mtDNA data indicates that Liaodong Bay female seals show fidelity to their breeding site, and breeding time data suggest that this population is reproductively isolated from populations in other breeding areas. The observed low genetic diversity in mtDNA and the intermediate levels of nuclear microsatellite diversity, combined with the potential genetic isolation, suggest that the Liaodong Bay population might be at risk and that further investigation of the population genetics of spotted seals across their whole range is warranted for proper management of the species.

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  • 2x genomes — depth does matter. Genome Biol. 2010 ;11(2):R16. gb-2010-11-2-r16. 10.1186/gb-2010-11-2-r16. PMC2872876.

    abstract

    Given the availability of full genome sequences, mapping gene gains, duplications, and losses during evolution should theoretically be straightforward. However, this endeavor suffers from overemphasis on detecting conserved genome features, which in turn has led to sequencing multiple eutherian genomes with low coverage rather than fewer genomes with high-coverage and more even distribution in the phylogeny. Although limitations associated with analysis of low coverage genomes are recognized, they have not been quantified.

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  • Molecular genetic analysis of a captive-breeding program: the vulnerable endemic Jamaican yellow boa Conservation Genetics, 10 (1):69-77.

    abstract

    The endemic Jamaican boa (or “yellow boa”, Epicrates subflavus) is a vulnerable species of the Caribbean biodiversity hotspot whose natural populations greatly declined mainly due to predation by introduced species, human persecution, and habitat destruction. A captive breeding program was initiated in 1976 and rationalized in 2002 by the establishment of a European Endangered Species Program. During the last 30 years, more than 600 offspring, of which 80 are still alive today, have been produced and distributed among European host institutions and privates. Here, using nine nuclear microsatellite loci and a fragment of the mitochondrial cytochrome b gene, we (i) determine the natural population from which the founders originate, (ii) identify parental allocation errors and ambiguities in the studbook, and (iii) assess the genetic diversity and estimate levels of inbreeding of the current captive population based on loss of alleles, variance in reproductive success, and relatedness among individuals. Combining measures of relatedness derived from multilocus genotypes with practical parameters such as age of animals and localization of host institutions, we propose mating groups that would maximize genetic diversity in the captive population of the Jamaican boa. Our analyses provide guidance for a more efficient breeding program that, in turn, could be used as the starting point of a repatriation program to increase the probability of the species long-term survival.

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  • Population genetics of Galápagos land iguana (genus Conolophus) remnant populations. Mol. Ecol. 2008 Dec;17(23):4943-52. MEC3967. 10.1111/j.1365-294X.2008.03967.x.

    abstract

    The Galápagos land iguanas (genus Conolophus) have faced significant anthropogenic disturbances since the 17th century, leading to severe reduction of some populations and the extinction of others. Conservation activities, including the repatriation of captive-bred animals to depleted areas, have been ongoing since the late 1970s, but genetic information has not been extensively incorporated. Here we use nine species-specific microsatellite loci of 703 land iguanas from the six islands where the species occur today to characterize the genetic diversity within, and the levels of genetic differentiation among, current populations as well as test previous hypotheses about accidental translocations associated with early conservation efforts. Our analyses indicate that (i) five populations of iguanas represent distinct conservation units (one of them being the recently discovered rosada form) and could warrant species status, (ii) some individuals from North Seymour previously assumed to be from the natural Baltra population appear related to both Isabela and Santa Cruz populations, and (iii) the five different management units exhibit considerably different levels of intrapopulation genetic diversity, with the Plaza Sur and Santa Fe populations particularly low. Although the initial captive breeding programmes, coupled with intensive efforts to eradicate introduced species, saved several land iguana populations from extinction, our molecular results provide objective data for improving continuing in situ species survival plans and population management for this spectacular and emblematic reptile.

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  • Characterization of microsatellite loci in the European pond turtle Emys orbicularis. Mol Ecol Resour 2009 Jan;9(1):189-91. 10.1111/j.1755-0998.2008.02205.x.

    abstract

    A set of eight highly polymorphic microsatellite markers was isolated and characterized from a genomic library enriched for dinucleotide repeats in the European pond turtle, Emys orbicularis. The markers were tested for polymorphism in a total of 33 turtles sampled in two natural ponds in the nature reserve of Kerkini, northern Greece. Number of alleles varied from 10 to 18, and expected heterozygosity ranged between 0.738 and 0.921. This novel set of loci will be particularly useful to assess fine-scale population structure and for parentage analysis in E. orbicularis.

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  • Mapping gene gains and losses among metazoan full genomes using an integrated phylogenetic framework Chapter 9 in “Evolution after Gene Duplication” Editors Dittmar K. and Liberles D. A., Wiley-Blackwell.

    abstract

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  • Population structure of an endemic vulnerable species, the Jamaican boa (Epicrates subflavus). Mol. Ecol. 2008 Jan;17(2):533-44. MEC3588. 10.1111/j.1365-294X.2007.03588.x.

    abstract

    The Jamaican boa (Epicrates subflavus; also called Yellow boa) is an endemic species whose natural populations greatly and constantly declined since the late 19th century, mainly because of predation by introduced species, human persecution, and habitat destruction. In-situ conservation of the Jamaican boa is seriously hindered by the lack of information on demographic and ecological parameters as well as by a poor understanding of the population structure and species distribution in the wild. Here, using nine nuclear microsatellite loci and a fragment of the mitochondrial cytochrome b gene from 87 wild-born individuals, we present the first molecular genetic analyses focusing on the diversity and structure of the natural populations of the Jamaican boa. A model-based clustering analysis of multilocus microsatellite genotypes identifies three groups that are also significantly differentiated on the basis of F-statistics. Similarly, haplotypic network reconstruction methods applied on the cytochrome b haplotypes isolated here identify two well-differentiated haplogroups separated by four to six fixed mutations. Bayesian and metaGA analyses of the mitochondrial data set combined with sequences from other Boidae species indicate that rooting of the haplotypic network occurs most likely between the two defined haplogroups. Both analyses (based on nuclear and mitochondrial markers) underline an Eastern vs. (Western + Central) pattern of differentiation in agreement with geological data and patterns of differentiation uncovered in other vertebrate and invertebrate Jamaican species. Our results provide important insights for improving management of ex-situ captive populations and for guiding the development of proper in-situ species survival and habitat management plans for this spectacular, yet poorly known and vulnerable, snake.

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  • A Pragmatic Approach for Selecting Evo-Devo Model Species in Amniotes Chapter 7 in “Evolving Pathways: Key Themes in Evolutionary Developmental Biology.

    abstract

    One major classical justification of using a model metazoan species for experimentation has been that discoveries of biological phenomena in that species could be extrapolated to other multicellular species. Because the chances that this extrapolation is valid in humans depend on the phylogenetic distance between humans and the model species, many researchers have somewhat sacrificed the major benefits of small size, short generation time and ease of manipulation that characterise some invertebrates in order to use species that humans can more readily relate to, such as the laboratory mouse (Mus musculus). However, the community of biologists has continued to use additional model species because each of the selected taxa have specific features that make experimental manipulation easier (e.g. easy-to-score morphological variation and giant polytene chromosomes in Drosophila melanogaster, or accurate description of the largely invariant complete cell lineage and full neural connectivity in the roundworm Caenorhabditis elegans).

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  • MANTIS: a phylogenetic framework for multi-species genome comparisons. Bioinformatics 2008 Jan;24(2):151-7. btm567. 10.1093/bioinformatics/btm567.

    abstract

    Practitioners of comparative genomics face huge analytical challenges as whole genome sequences and functional/expression data accumulate. Furthermore, the field would greatly benefit from a better integration of this wealth of data with evolutionary concepts.

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  • Escaping the mouse trap: the selection of new Evo-Devo model species. J. Exp. Zool. B Mol. Dev. Evol. 2007 Jul;308(4):337-46. 10.1002/jez.b.21180.

    abstract

    Among the many, sometimes contradictory, criteria that have been used for promoting model species, the most prominent has probably been their relevance for understanding human biology. Recently however, the debate has partly shifted from the search for evolutionary conservation (medicine-driven models) to a better understanding of the generative mechanisms underlying biological diversity (Evo-Devo-driven models). Integration of multiple disciplines, beyond developmental genetics and evolutionary molecular genetics, as well as of innovative technologies will help biologists to open the massive realm of living species to genome manipulation and phenotypic investigation. However, a consensual list of model species must still be reached for optimizing the interplay between in silico analyses and in vivo experiments, and we claim that the Evo-Devo community should play a more energetic role in this endeavor. We discuss here a few criteria and limitations of major relevance to the choice of model species for Evo-Devo studies, and promote the use of a pragmatic approach. Finally, given the difficulties related to manipulating and breeding model species, we suggest the development of Evo-Devo virtual zoos maintaining breeding colonies of a selected set of species and from which eggs or staged embryos are available on order.

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  • Evidence for male dispersal along the coasts but no migration in pelagic waters in dusky dolphins (Lagenorhynchus obscurus). Mol. Ecol. 2005 Jan;14(1):107-21. MEC2407. 10.1111/j.1365-294X.2004.02407.x.

    abstract

    Using nine nuclear species-specific microsatellite loci and two mitochondrial gene fragments (cytochrome b and control region), we investigated the processes that have shaped the geographical distribution of genetic diversity exhibited by contemporary dusky dolphin (Lagenorhynchus obscurus) populations. A total of 221 individuals from four locations (Peru, Argentina, southern Africa, and New Zealand) were assayed, covering most of the species' distribution range. Although our analyses identify a general demographic decline in the Peruvian dusky dolphin stock (recently affected by high natural and human-induced mortality levels), comparison between the different molecular markers hint at an ancient bottleneck that predates recent El Niño oscillations and human exploitation. Moreover, we find evidence of a difference in dispersal behaviour of dusky dolphins along the South American coast and across the Atlantic. While data in Peruvian and Argentine waters are best explained by male-specific gene flow between these two populations, our analyses suggest that dusky dolphins from Argentina and southern Africa recently separated from an ancestral Atlantic population and, since then, diverged without considerable gene flow. The inclusion of a few New Zealand samples further confirms the low levels of genetic differentiation among most dusky dolphin populations. Only the Peruvian dusky dolphin stock is highly differentiated, especially at mitochondrial loci, suggesting that major fluctuations in its population size have led to an increased rate of genetic drift.

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  • Species identification of Chilean Artemia populations based on mitochondrial DNA RFLP analysis Journal of Biogeography, 31:547-555.

    abstract

    Two species of the brine shrimp, namely Artemia franciscana Kellogg and A. persimilis Piccinelli and Prosdocimi, inhabit Chile. Most studies so far have shown that A. franciscana is the most widely distributed species in Chile, with A. persimilis present only in Chilean Patagonia. In general, there is good agreement between morphological and genetic comparisons of Chilean populations with respect to species discrimination. However, a number of results indicate an overlap with some populations tending to diverge from A. franciscana and/or resembling A. persimilis. Prior to the mid 90's the use of DNA markers in Artemia was rather limited, despite their successful application in numerous other species. In this study, we investigate whether the conclusions drawn from traditional comparative tools are congruent with the pattern of genetic divergence depicted by DNA analysis at the mitochondrial level.

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