Galápagos and Californian sea lions are separate species: Genetic analysis of the genus Zalophus and its implications for conservation management

Wolf JBW, Tautz D, Trillmich F. Galápagos and Californian sea lions are separate species: genetic analysis of the genus Zalophus and its implications for conservation management. Frontiers in Zoology. 2007;4(1): 20.Background: Accurate formal taxonomic designations are thought to be of critical importance for the conservation of endangered taxa. The Galápagos sea lion (GSL), being appreciated as a key element of the Galápagos marine ecosystem, has lately been listed as 'vulnerable' by the IUCN. To date there is, however, hardly any scientific evidence, whether it constitutes a separate entity from its abundant Californian neighbour (CSL). In this paper, we delineate the taxonomic relationships within the genus Zalophus being comprised of the Galápagos sea lion, the Californian sea lion and the already extinct Japanese sea lion (JSL). Results: Using a set of different phylogenetic reconstruction approaches, we find support for monophyly of all three taxa without evidence of reticulation events. Molecular clock estimates place time to common ancestry of the Galápagos sea lion and the Californian sea lion at about 2.3 ± 0.5 mya. Genetic separation is further suggested by diagnostic SNPs in the mitochondrial and nuclear genome. Microsatellite markers confirm this trend, showing numerous private alleles at most of the 25 investigated loci. Microsatellite-based estimates of genetic differentiation between the Galápagos sea lion and the Californian sea lion indicate significant genetic differentiation. Gene diversity is 14% lower in the Galápagos sea lion than in the Californian sea lion, but there is no evidence for recent bottleneck events in the Galápagos sea lion. Conclusion: Based on molecular evidence we build a case for classifying the Galápagos sea lion (Zalophus wollebaeki), the Californian sea lion (Zalophus californianus) and the Japanese sea lion (Zalophus japonicus) as true species. As morphological characters do not necessarily fully reflect the rapid divergence on the molecular level, the study can be considered as a test case for deriving species status from molecular evidence. We further use the results to discuss the role of genetics in conservation policy for an organism that already is under the general protection of the habitat it lives in

Molecular evolution of genes in avian genomes

Nam K, Mugal C, Nabholz B, et al. Molecular evolution of genes in avian genomes. Genome Biology. 2010;11(6): R68.Background: Obtaining a draft genome sequence of the zebra finch (Taeniopygia guttata), the second bird genome to be sequenced, provides the necessary resource for whole-genome comparative analysis of gene sequence evolution in a non-mammalian vertebrate lineage. To analyze basic molecular evolutionary processes during avian evolution, and to contrast these with the situation in mammals, we aligned the protein-coding sequences of 8,384 1:1 orthologs of chicken, zebra finch, a lizard and three mammalian species. Results: We found clear differences in the substitution rate at fourfold degenerate sites, being lowest in the ancestral bird lineage, intermediate in the chicken lineage and highest in the zebra finch lineage, possibly reflecting differences in generation time. We identified positively selected and/or rapidly evolving genes in avian lineages and found an overrepresentation of several functional classes, including anion transporter activity, calcium ion binding, cell adhesion and microtubule cytoskeleton. Conclusions: Focusing specifically on genes of neurological interest and genes differentially expressed in the unique vocal control nuclei of the songbird brain, we find a number of positively selected genes, including synaptic receptors. We found no evidence that selection for beneficial alleles is more efficient in regions of high recombination; in fact, there was a weak yet significant negative correlation between ω and recombination rate, which is in the direction predicted by the Hill-Robertson effect if slightly deleterious mutations contribute to protein evolution. These findings set the stage for studies of functional genetics of avian genes

General lack of global dosage compensation in ZZ/ZW systems? Broadening the perspective with RNA-seq

Background Species with heteromorphic sex chromosomes face the challenge of large-scale imbalance in gene dose. Microarray-based studies in several independent male heterogametic XX/XY systems suggest that dosage compensation mechanisms are in place to mitigate the detrimental effects of gene dose differences. However, recent genomic research on female heterogametic ZZ/ZW systems has generated surprising results. In two bird species and one lepidopteran no evidence for a global dosage compensating mechanism has been found. The recent advent of massively parallel RNA sequencing now opens up the possibility to gauge the generality of this observation with a broader phylogenetic sampling. It further allows assessing the validity of microarray-based inference on dosage compensation with a novel technology. Results We here expemplify this approach using massively parallel sequencing on barcoded individuals of a bird species, the European crow (Corvus corone), where previously no genetic resources were available. Testing for Z-linkage with quantitative PCR (qPCR,) we first establish that orthology with distantly related species (chicken, zebra finch) can be used as a good predictor for chromosomal affiliation of a gene. We then use a digital measure of gene expression (RNA-seq) on brain transcriptome and confirm a global lack of dosage compensation on the Z chromosome. RNA-seq estimates of male-to-female (m:f) expression difference on the Z compare well to previous microarray-based estimates in birds and lepidopterans. The data further lends support that an up-regulation of female Z-linked genes conveys partial compensation and suggest a relationship between sex-bias and absolute expression level of a gene. Correlation of sex-biased gene expression on the Z chromosome across all three bird species further suggests that the degree of compensation has been partly conserved across 100 million years of avian evolution. Conclusions This work demonstrates that the study of dosage compensation has become amenable to species where previously no genetic resources were available. Massively parallele transcriptome sequencing allows re-assessing the degree of dosage compensation with a novel tool in well-studies species and, in addition, gain valuable insights into the generality of mechanisms across independent taxonomic group for both the XX/XY and ZZ/ZW system

Genomics and the challenging translation into conservation practice

he global loss of biodiversity continues at an alarming rate. Genomic approaches have been suggested as a promising tool for conservation practice as scaling up to genome-wide data can improve traditional conservation genetic inferences and provide qualitatively novel insights. However, the generation of genomic data and subsequent analyses and interpretations remain challenging and largely confined to academic research in ecology and evolution. This generates a gap between basic research and applicable solutions for conservation managers faced with multifaceted problems. Before the real-world conservation potential of genomic research can be realized, we suggest that current infrastructures need to be modified, methods must mature, analytical pipelines need to be developed, and successful case studies must be disseminated to practitioners.Peer reviewe

A) Neighbour-joining tree of mitochondrial DNA showing genetic relationships among rookeries of Galápagos sea lions

Genetic distances between rookeries are based on corrected mean pair-wise sequence comparisons of the mitochondrial control region. B) 50 percent Neighbour-joining bootstrap consensus tree based on Goodman's Rst at the rookery level for 22 microsatellite loci. Bootstrap support values (5000 replicates) are shown above the nodes. Abbreviations: GFS = Galápagos fur seal, letter codes represent sampled populations (see Fig. 1)<p><b>Copyright information:</b></p><p>Taken from "Tracing early stages of species differentiation: Ecological, morphological and genetic divergence of Galápagos sea lion populations"</p><p>http://www.biomedcentral.com/1471-2148/8/150</p><p>BMC Evolutionary Biology 2008;8():150-150.</p><p>Published online 16 May 2008</p><p>PMCID:PMC2408593.</p><p></p

Isotopic biplot showing mean (± 95% CI) of δC and δN values from juvenile Galápagos sea lions (circles) and Galápagos fur seals (square) collected in different rookeries across the Galápagos Islands

The corresponding habitat of each rookery is indicated by colour (white = Centre, grey = West).<p><b>Copyright information:</b></p><p>Taken from "Tracing early stages of species differentiation: Ecological, morphological and genetic divergence of Galápagos sea lion populations"</p><p>http://www.biomedcentral.com/1471-2148/8/150</p><p>BMC Evolutionary Biology 2008;8():150-150.</p><p>Published online 16 May 2008</p><p>PMCID:PMC2408593.</p><p></p

Relationship of geographic distance (logarithm of shortest swimming distance) and genetic distance of the mitochondrial (mtDNA) and nuclear marker (microsatellites)

Triangles symbolize pair-wise comparisons between rookeries that share the same habitat. Filled circles stand for comparisons across habitats. The shaded area indicates the range of geographic distances that is characteristic for both intra- and inter-habitat specific pairwise comparisons. Dotted brackets visualise the value range of genetic distances from within habitat comparisons, solid brackets from between habitat comparisons.<p><b>Copyright information:</b></p><p>Taken from "Tracing early stages of species differentiation: Ecological, morphological and genetic divergence of Galápagos sea lion populations"</p><p>http://www.biomedcentral.com/1471-2148/8/150</p><p>BMC Evolutionary Biology 2008;8():150-150.</p><p>Published online 16 May 2008</p><p>PMCID:PMC2408593.</p><p></p

Genomics in Conservation: Case Studies and Bridging the Gap between Data and Application Reply

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