D. James Harris

Can you bank on GenBank

Sequencing mitochondrial DNA (mtDNA) is now a routine laboratory procedure. Most journals insist that published sequences be submitted to data bases such as GenBank, where they are publicly available. But quality control of the raw data often depends solely on the original scientists. So just how reliable are the sequences in the data bases? According to a new paper by Forster in the Annals of Human Genetics, more than half of all published human mtDNA studies contain mistakes, a level so high that geneticists could be drawing incorrect conclusions in population and evolutionary studies. Much greater controls are needed, both from journals and from individual scientists. Fortunately, some new methods for detecting errors using phylogenetic networks have recently been proposed. How effective these are remains to be tested.

Complex estimates of evolutionary relationships in Tarentola mauritanica (Reptilia: Gekkonidae) derived from mitochondrial DNA sequences

Mitochondrial DNA (12S rRNA, 16S rRNA) sequences were analysed within Tarentola mauritanica and other selected species of Tarentola. Several highly genetically distinct lineages occur in North Africa, revealing phylogroups in southern and central Morocco, northern Morocco, Algeria, Tunisia, and Libya. A single haplotype characterizes populations across Spain, Portugal, Italy, Menorca, Crete, and Tunisia raising the possibility of an anthropogenic introduction followed by rapid population expansion throughout southern Europe. T. mauritanica is paraphyletic with respect to T. angustimentalis, a Canary islands endemic. The high genetic diversity observed across North Africa suggests T. mauritanica may represent a species complex.

Non-equilibrium estimates of gene flow inferred from nuclear genealogies suggest that Iberian and North African wall lizards (Podarcis spp.) are an assemblage of incipient species

BackgroundThe study of recently-diverged species offers significant challenges both in the definition of evolutionary entities and in the estimation of gene flow among them. Iberian and North African wall lizards (Podarcis) constitute a cryptic species complex for which previous assessments of mitochondrial DNA (mtDNA) and allozyme variation are concordant in describing the existence of several highly differentiated evolutionary units. However, these studies report important differences suggesting the occurrence of gene flow among forms. Here we study sequence variation in two nuclear introns, β-fibint7 and 6-Pgdint7, to further investigate overall evolutionary dynamics and test hypotheses related to species delimitation within this complex.ResultsBoth nuclear gene genealogies fail to define species as monophyletic. To discriminate between the effects of incomplete lineage sorting and gene flow in setting this pattern, we estimated migration rates among species using both FST-based estimators of gene flow, which assume migration-drift equilibrium, and a coalescent approach based on a model of divergence with gene flow. Equilibrium estimates of gene flow suggest widespread introgression between species, but coalescent estimates describe virtually zero admixture between most (but not all) species pairs. This suggests that although gene flow among forms may have occurred the main cause for species polyphyly is incomplete lineage sorting, implying that most forms have been isolated since their divergence. This observation is therefore in accordance with previous reports of strong differentiation based on mtDNA and allozyme data.ConclusionThese results corroborate most forms of Iberian and North African Podarcis as differentiated, although incipient, species, supporting a gradual view of speciation, according to which species may persist as distinct despite some permeability to genetic exchange and without having clearly definable genetic boundaries. Additionally, this study constitutes a warning against the misuse of equilibrium estimates of migration among recently-diverged groups.

Phylogeny and evolution of the green lizards, Lacerta spp. (Squamata: Lacertidae) based on mitochondrial and nuclear DNA sequences

Partial DNA sequences from three mitochondrial (cytochrome b , 12S rRNA and 16S rRNA) and two nuclear ( β -fibrinogen intron 7 and C- mos ) genes were used to estimate the phylogenetic relationships among all eight extant species of green lizards, Lacerta sensu stricto , and many currently recognized subspecies. All eight species form a monophyletic group. L. agilis , L. schreiberi and L. strigata are genetically well differentiated species. L. trilineata and L. pamphylica are not monophyletic units based on analyses of the β -fibrinogen intron 7. Lacerta media is closely related to some Lacerta trilineata . L. bilineata and L. viridis are closely related, and recognition of L. bilineata as a distinct species makes L. viridis paraphyletic also. For both L. bilineata and L. viridis , some subspecies appear to remain in their southern glacial refugia, while a single genetic entity shows successfully postglacial expansion. The topology derived from C- mos variation is concordant with that derived from mtDNA, with substitutions occurring at a similar rate to that of transversions in the rRNA genes. Although C- mos is typically used at deeper taxonomic levels it is also phylogenetically informative within green lizards. β -fibrinogen intron 7, typically used for assessing phylogenetic relationships among bird species, is a useful phylogenetic marker for reptiles also, showing considerable variation between species. There is not complete concordance between estimates of relationships derived from the mtDNA and nuclear markers, probably because rapid diversification led to incomplete lineage sorting in the green lizards. Introgression could also be occuring between some species.

Mitochondrial phylogeography of Testudo graeca in the Western Mediterranean: Old complex divergence in North Africa and recent arrival in Europe

We investigated the mitochondrial phylogeography of spur-thighed tortoises (Testudo graeca) in the Western Mediterranean. In North Africa, four major lineages (A-D) occur that together constitute a well-supported clade corresponding to one of the six major clades within T. graeca; the North African clade is sister to a Caucasian clade representing the subspecies T. g. armeniaca. Phylogenetic relationships between the North African lineages are badly resolved. Lineage A is distributed in Tunisia and adjacent Algeria, lineage B in Algeria and northern Morocco, lineage C in the Libyan Cyrenaica Peninsula, and lineage D north of the High Atlas Mts. and in the Souss Valley (southern Morocco). Lineage B is subdivided into two subgroups, B1 (eastern Morocco and Algeria) and B2 (north-western Morocco). Italian tortoises harbour haplotypes of lineage A, Spanish tortoises of subgroup B1. Based on a relaxed molecular clock calibrated with fossil evidence, the six major mtDNA clades of T. graeca are estimated to have diverged approximately 4.2-1.8 Ma ago; the split between the clades representing the eastern subspecies T. g. ibera and T. g. terrestris is younger than the split between Western Mediterranean tortoises and T. g. armeniaca. The Western Mediterranean lineages A-D were dated to have diverged at least 1.4-1.1 Ma ago; B1 and B2 split approximately 0.7 Ma ago. Our results suggest that Italian and Spanish tortoises were either introduced or originated from trans-oceanic dispersal in historic or prehistoric times. Spur-thighed tortoises invaded North Africa probably across Near Eastern landbridges that emerged in the Late Tertiary. Their diversification in North Africa seems to be correlated with habitat aridization cycles during the Pleistocene. The ranges of the Western Mediterranean lineages largely correspond to the distribution of morphologically defined subspecies in North Africa, with exception of T. g. graeca and T. g. whitei, and of T. g. lamberti and T. g. marokkensis, which are not differentiated. We propose to lump the first two subspecies under the name of T. g. graeca and the latter under the name of T. g. marokkensis. The complex differentiation of spur-thighed tortoises in North Africa implies that the model of a bipartite east-west differentiation, as proposed for other Maghrebian amphibians and reptiles, may be too simplistic, reflecting incomplete locality sampling rather than actual phylogeographic differentiation.

Systematic and phylogeographical assessment of the Acanthodactylus erythrurus group (Reptilia: Lacertidae) based on phylogenetic analyses of mitochondrial and nuclear DNA.

We have used mitochondrial 12S rRNA, 16S rRNA and nuclear beta-fibrinogen (intron 7) sequences to investigate the phylogenetic and phylogeographic relationships between Acanthodactylus erythrurus group species (except for A. boueti). The phylogenetic analyses of the Acanthodactylus genus did not cluster A. guineensis and A. savignyi with the remaining species of the group (A. blanci, A. lineomaculatus and A. erythrurus). Within the A. erythrurus group, the results of the mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) showed a complex phylogeny with geographic structure, but it was not congruent with the present taxonomy. Some taxonomic units, such as A. blanci, A. lineomaculatus, A. e. atlanticus and A. e. belli did not form monophyletic genetic units. The application of a molecular clock suggested that the uplift of the Atlas Mountains in the mid-late Miocene and the reopening of the Strait of Gibraltar could be major biogeographic events responsible for the genetic differentiation in the group. Additionally, diverse micro-evolutionary patterns due to the recent contraction/expansion phases of the habitats in North Africa associated with the high dispersal capabilities of these lizards could be related to the complex phylogenetic patterns observed.

MOLECULAR CHARACTERIZATION OF HEPATOZOON SPECIES IN REPTILES FROM THE SEYCHELLES

Abstract Hepatozoon parasites were examined for the first time in reptiles from the Seychelles Islands. Although both prevalence and intensity were low, Hepatozoon species were detected in individuals from 2 endemic species, the lizard Mabuya wrightii and the snake Lycognathophis seychellensis. This was confirmed using visual identification and through sequencing part of the 18s rRNA gene. Phylogenetic analysis indicates that the Hepatozoon on the Seychelles form a monophyletic lineage, although more data are clearly needed to stabilize estimates of relationships based on this marker.

Molecular survey of Hepatozoon Species in Lizards From North Africa

Abstract The prevalence of Hepatozoon parasites in 460 lizards from North Africa was studied by amplification and sequencing of the 18S rRNA gene. The phylogenetic analysis of the 18S rRNA gene provides new insights into the phylogeny of these parasites with multiple genetically distinct lineages recovered. Parasite prevalence differed significantly between lacertid lizards and geckos. Our results show that there is limited host specificity and no clear relation to the geographical distribution of Hepatozoon parasites.

Phylogeny of North African Agama lizards (Reptilia: Agamidae) and the role of the Sahara desert in vertebrate speciation

The origin of Saharan biodiversity is poorly understood, in part because the geological and paleoclimatic events that presumably shaped species diversity are still controversial, but also because few studies have explored causal explanations for the origin of Saharan diversity using a phylogenetic framework. Here, we use mtDNA (16S and ND4 genes) and nDNA (MC1R and CMOS genes) to infer the relationships and biogeographic history of North African agamas (genus Agama). Agamas are conspicuous, diverse and abundant African lizards that also occur in the Saharan xeric and mesic environments. Our results revealed the presence of three Agama lineages in North Africa: one Afrotropical, one Sahelo-Saharan, and one broadly distributed in North Africa and mainly Saharan. Southern Mauritania contains the highest known diversity, with all three lineages present. Results suggest that agamas colonized the Sahara twice, but only one lineage was able to radiate and diversify there. Species in the Saharan lineage are mostly allopatric, and their splitting, genetic diversity and distribution are greatly explained by mountain ranges. One species in this lineage has colonized the Mediterranean climatic zone (A. impalearis), and another one the Sahel savannah (A. boueti). The other lineage to colonize the Sahara corresponds to A. boulengeri, an eminently Sahelian species that also inhabits Saharan mountain ranges in Mauritania and Mali. Phylogenetic analyses indicate that allopatric montane populations within some currently recognized species are also genetically divergent. Our study therefore concludes that vicariant speciation is a leading motor of species diversification in the area: Inside the Sahara, associated to mountain-ranges isolated by dune seas and bare plains; outside, associated to less harsh climates to the North and South. Paleoclimatic oscillations are suggested as causal explanations of the vicariant distribution and origin of species. Agamas are thought to have colonized northern Africa during wet periods, with subsequent dry periods fragmenting species distribution and leading to allopatric populations associated to milder and wetter climates in the Mediterranean, Sahel, and in Saharan mountains, in an island-model fashion. Finally, our results support the synonymization of A. castroviejoi with A. boueti, the reciprocal monophyly of all other North African agamas, and suggest one candidate species within A. boulengeri.

Molecular phylogeny, biogeography and insights into the origin of parthenogenesis in the Neotropical genus Leposoma (Squamata: Gymnophthalmidae): Ancient links between the Atlantic Forest and Amazonia

Leposoma is a conspicuous component of leaf litter herpetofauna of South and Central American rainforests. The 15 bisexual and one parthenogenetic species are allocated to the parietale and scincoides groups based on morphology. Phylogenetic analyses of 1830 bp (mtDNA+nuclear) were performed on 63 specimens of four species from Amazonian and Panamanian rainforests, and six species and one undescribed form from the Atlantic Forest. Different methods of tree reconstruction were explored, with Anotosaura vanzolinia and Colobosauroides cearensis as outgroups. The monophyly of the parietale and scincoides groups is strongly supported. Contrary to previous hypotheses suggesting a recent contact between Atlantic and Amazon forests, our estimates point to an initial split in Miocene. The position of Leposoma baturitensis, endemic to relictual forests in the semiarid Caatingas northeastern Brazil, and its divergence from the remaining species of the Atlantic Forest, suggests an ancient isolation with no indication of a secondary contact with forests of the eastern coast. Our data do not permit unambiguous assignment of parental species of the unisexual Leposoma percarinatum or the mechanism involved in the origin of parthenogenesis, but revealed two highly divergent diploid and triploid lineages within L. percarinatum, indicating that the unisexuals represent a species complex.