David James Harris

Ancient introgression of Lepus timidus mtDNA into L. granatensis and L. europaeus in the Iberian Peninsula.

A 587 bp fragment of cytochrome b sequences from 90 individuals of 15 hare (Lepus) species and two outgroups were phylogenetically analysed and compared to an analysis derived from 474 bp sequences of the nuclear transferrin gene. Mountain hare (Lepus timidus) type mtDNA was observed in L. granatensis and L. europaeus from the Iberian Peninsula, far away from the extant distributional range of L. timidus. In addition to these two hare species, other hare species may also contain mtDNA from L. timidus. This species may have introgressed with other species of Lepus that occur within its present range, or where fossils indicate its historical presence during glacial periods. L. timidus mtDNA is common in the northern part of the L. granatensis range. Finally, we reassessed the phylogenetic relationships of the five European hare species based on both mitochondrial and nuclear DNA sequences.

DNA barcoding reveals cryptic diversity in marine hydroids (Cnidaria, Hydrozoa) from coastal and deep-sea environments

Fifty‐six sequences of the mitochondrial 16S RNA gene were generated for hydroids, belonging to six nominal families — Eudendriidae, Lafoeidae, Haleciidae, Sertulariidae, Plumulariidae and Aglaopheniidae — collected from bathyal environments of the Gulf of Cadiz (22 haplotypes), Greenland (1 haplotype), Azores (1 haplotype), the shallow waters of the UK (17 haplotypes) and Portugal (2 haplotypes). When combined and analysed with 68 additional sequences published in GenBank, corresponding to 63 nominal species of these families (nine species in common between the GenBank sequences and those presented by the authors), cryptic species were detected (e.g. two species of Nemertesia and other of Lafoea), as well as apparent cases of conspecificity (e.g. Nemertesia antennina and N. perrieri and Aglaophenia octodonta, A. pluma and A. tubiformis). Other taxonomic inconsistencies were found in the data including cases where species from different genera clustered together (e.g. Sertularia cupressina, Thuiaria thuja, Abietinaria abietina and Ab. filicula). The mitochondrial 16S rRNA proved to be a useful DNA ‘barcode’ gene for hydroids, not only allowing discrimination of species, but also in some cases of populations, genera and families, and their intra‐ or interphylogenetic associations. Although still under‐represented in public data bases, the 16S rRNA gene is starting to be used frequently in the study of hydroids. These data provide powerful complementary evidence for advancing our understanding of hydrozoan systematics.

Contrasting patterns of population subdivision and historical demography in three western Mediterranean lizard species inferred from mitochondrial DNA variation.

Pleistocene climatic oscillations were a major force shaping genetic variability in many taxa. We analyse the relative effects of the ice ages across a latitudinal gradient in the Western Mediterranean region, testing two main predictions: (i) species with historical distributions in northern latitudes should have experienced greater loss of suitable habitat, resulting in higher extinction of historical lineages than species distributed in southern latitudes, where the effects of the ice ages were not as drastic. This would be reflected in the observation of lower diversity and number of differentiated lineages in northern areas. (ii) a signature of demographic expansion following the climate amelioration should be obvious in northern species, whereas in the south evidence of long‐term effective population size stability should be observed. We used as models three species of wall lizards (Podarcis bocagei, Podarcis carbonelli and Podarcis vaucheri) that replace each other along the study area. We investigated the patterns of mitochondrial DNA diversity and subdivision and obtained demographic parameter estimates for each species. Our results suggest that P. bocagei, the northernmost species, bears low genetic diversity, a shallow coalescent history and marks of a demographic expansion. In contrast, P. vaucheri, the species with a southernmost distribution, shows deeper coalescence events, complex geographical substructure and no evidence for population growth. The species with an intermediate distribution, P. carbonelli, shows average levels of diversity, substructure and population growth. Taken together, these results conform to our main predictions and are explained by a differential influence of the ice ages on distinct latitudes.

Assessment of genetic diversity within Acanthodactylus erythrurus (Reptilia: Lacertidae) in Morocco and the Iberian Peninsula using mitochondrial DNA sequence data

Vielliard, J.M.E., Cardoso, A.J. (1996): Adaptacao de sinais sonoros de anfibios e aves a ambientes de riachos com corredeiras. In: Herpetologia Neotropical: Actas del II Congresso Latinoamericano de Herpetologia, Vol. II, p. 97-119. Pefaur, J.E., Ed., Merida, Univ. de los Andes, Consejo de Publ., Consejo de Desarrolo Cientifico, Humanistico y Tecnologico. Weygoldt, P., Carvalho e Silva, S.P. (1992): Mating and oviposition in the hylodine frog Crossodactylus gaudichaudii (Anura: Leptodactylidae). Amphibia-Reptilia 13: 35-45.

Determination of genetic diversity within the insular lizard Podarcis tiliguerta using mtDNA sequence data, with a reassessment of the phylogeny of Podarcis

Despite being the predominant reptile group in Southern Europe, the taxonomy of Podarcis Wall lizards is both complex and unstable. Recent attempts to estimate a phylogeny for the genus using molecular methods have been largely unsuccessful, with many poorly resolved nodes and widely different estimates from different studies (Harris and Arnold, 1999; Oliverio et al., 2000; Poulakakis et al., 2003). One possible reason for this is that presently accepted forms may well be species complexes — Podarcis hispanica∗ (Steindachner, 1879) contains several highly genetically distinct lineages all of which may deserve species status based on mitochondrial (Harris and Sa-Sousa, 2002; Harris et al., 2002) and protein electrophoretic data (Pinho et al., 2003). Podarcis erhardii (Bedriaga, 1882) is also probably a species complex (Poulakakis et al., 2003), Podarcis sicula and Podarcis melisellensis contain considerable genetic diversity (Podnar et al., 2004, 2005) although Podarcis lilfordi (Günter,

Modelling the partially unknown distribution of wall lizards (Podarcis) in North Africa: ecological affinities, potential areas of occurrence, and methodological constraints

Species distribution modelling (SDM) is a powerful tool to investigate various biological questions with a spa- tial component, but is also sensitive to presence-data characteristics, particularly data precision and clustering. Here, we in- vestigate the effect of these two factors on SDM using Maxent as the modelling technique and wall lizards (genus Podarcis Wagler, 1830) from North Africa as a model system. Podarcis are not ubiquitous in Africa as they are in Europe, but their ecological and distributional characteristics in this area are poorly known. Our results show that the most impor- tant environmental factors related to the distribution of this genus in North Africa are humidity, habitat type, and tempera- ture. The areas of potential distribution predicted by models based on data sets with different precision and clustering characteristics show high relatedness to coastal areas and mountain ranges and extend to areas were presence records for these lizards are lacking. Our comparison of models based on different data sets indicates that finer scale models, even if based on fewer presence locations, outperform coarser scale ones. Data clustering does not have a negative effect on model performance, but is rather overcome by sample-size effects. Similar approaches may be of general application to other stenoic species for which available locations are scarce in comparison with the extension of the study area.

Evolutionary history of the genus Tarentola (Gekkota: Phyllodactylidae) from the Mediterranean Basin, estimated using multilocus sequence data

BackgroundThe pronounced morphological conservatism within Tarentola geckos contrasted with a high genetic variation in North Africa, has led to the hypothesis that this group could represent a cryptic species complex, a challenging system to study especially when trying to define distinct evolutionary entities and address biogeographic hypotheses. In the present work we have re-examined the phylogenetic and phylogeographic relationships between and within all Mediterranean species of Tarentola, placing the genealogies obtained into a temporal framework. In order to do this, we have investigated the sequence variation of two mitochondrial (12S rRNA and 16S rRNA), and four nuclear markers (ACM4, PDC, MC1R, and RAG2) for 384 individuals of all known Mediterranean Tarentola species, so that their evolutionary history could be assessed.ResultsOf all three generated genealogies (combined mtDNA, combined nDNA, and mtDNA+nDNA) we prefer the phylogenetic relationships obtained when all genetic markers are combined. A total of 133 individuals, and 2,901 bp of sequence length, were used in this analysis. The phylogeny obtained for Tarentola presents deep branches, with T. annularis, T. ephippiata and T. chazaliae occupying a basal position and splitting from the remaining species around 15.38 Mya. Tarentola boehmei is sister to all other Mediterranean species, from which it split around 11.38 Mya. There are also two other major groups: 1) the T. mauritanica complex present in North Africa and Europe; and 2) the clade formed by the T. fascicularis/deserti complex, T. neglecta and T. mindiae, occurring only in North Africa. The cladogenesis between these two groups occurred around 8.69 Mya, coincident with the late Miocene. Contrary to what was initially proposed, T. neglecta and T. mindiae are sister taxa to both T. fascicularis and T. deserti.ConclusionsAt least in the Iberian Peninsula and Northwest Africa, the lineages obtained have some geographic coherency, whilst the evolutionary history of the forms from Northeast Africa remains unclear, with a paraphyletic T. fascicularis with respect to T. deserti. The separation between the T. mauritanica complex and the clade formed by the T. fascicularis/deserti complex, T. neglecta and T. mindiae is coincident with the uplift of the Atlas Mountain chain, and the establishment of two distinct bioclimatic regions on each side of the barrier.

Deep evolutionary lineages in a Western Mediterranean snake (Vipera latastei/monticola group) and high genetic structuring in Southern Iberian populations.

Phylogeographic studies during the last decade confirmed an internal complexity of the Iberian Peninsula and northern Maghreb as refugial areas during the Miocene to Pleistocene period. Species with low vagility that experienced the complex climatic and palaeogeographic processes occurred in the Western Mediterranean Basin are excellent candidates to study the extent of lineage diversification in this region. We applied phylogenetic analyses based on mitochondrial data to infer the evolutionary history of Vipera latastei/monticola and identify the major biogeographic events structuring the genetic diversity within this group. We obtained a well-resolved phylogeny, with four highly divergent lineages (one African and three Iberian) that originated in the Tertiary. Coalescence-based estimations suggest that the differentiation of the four major lineages in V. latastei/monticola corresponds to the Messinian salinity crisis and the reopening of the Strait of Gibraltar during the Miocene. Subsequent Pliocene and Pleistocene climatic oscillations continued to isolate both Iberian and Maghrebian populations and led to a high genetic structuring in this group, particularly in Southern Iberia, a complex palaeogeographic and topographic region with high endemism levels. This study does not support the current taxonomy of the group, thus suggesting that an integrative evaluation of Iberian and African populations is needed to resolve its systematics.

Evidence for genetic similarity of two allopatric European hares (Lepus corsicanus and L. castroviejoi) inferred from nuclear DNA sequences

During the Pleistocene, the severe climatic changes induced major shifts in species distributions, forcing them to retract, expand, displace and/or fragment their ranges (Hewitt, 1996). In Europe, these continuous oscillations led to the production of greater subspecific and specific diversity in the southern peninsulas since they were the major ice age refugial areas (Hewitt, 1999). Hares (genus Lepus) seem to perfectly demonstrate these phenomena. Despite earlier controversies, the latest taxonomic view accepts five species of genus Lepus occurring naturally in Europe: L. europaeus, L. timidus, L. granatensis, L. castroviejoi, and L. corsicanus (Mitchell-Jones et al., 1999). Of these species, the latter two have allopatric and restricted ranges, L. castroviejoi in the Cantabrian Mountains of the Iberian Peninsula and L. corsicanus in the Apennines from central and southern Italy and also in Sicily (Fig. 1). These two southern European endemisms occupy highly specialized patches of scarce habitat and thus the establishment of suitable conservation mechanisms is a major concern (e.g., Temple and Terry, 2007). Several molecular studies have tried to clarify the evolutionary relationships between the European hare species (e.g., Perez-Suarez et al., 1994; Thulin et al., 1997a; Pierpaoli et al., 1999; Suchentrunk et al., 1999; Alves et al., 2000; Estonba et al., 2006; Ben Slimen et al., 2005). However,

Phylogeography and genetic diversity of Psammophis schokari (Serpentes) in North Africa based on mitochondrial DNA sequences

ABSTRACT The snake Psammophis schokari has a widespread distribution across North Africa, and in Morocco/Western Sahara is represented by three different morphotypes: striped, unicoloured and the Western-Sahara morph. ND4 mitochondrial DNA sequences from 28 specimens comprising 20 P. shokari, two P. aegyptius, one P. elegans, two P. sibilans, one P. condanarus and two outgroups were analysed. Within P. schokari we identified four genetic lineages (Morocco/Western Sahara, Mauritania, Algeria and Israel) with a genetic divergence ranging from 4–5%, less than that typically found between different species. Surprisingly, Moroccan/Western Sahara and Algerian lineages are the most divergent ones. This geographic substructuring may be due to severe climate changes in the Sahara desert between the Miocene and Pleistocene associated with expansion/contraction phases of this desert. Psammophis aegyptius is the sister-taxon of Psammophis schokari with a high level of genetic divergence between them (10.7%) supporting the recognition of P. aegyptius as a distinct species. The three Moroccan/Western Sahara colour morphotypes form one genetic lineage, indicating that colour pattern does not reflect a different phylogenetic history, and is probably an ecological adaptation to the local environment.