Extensive mitochondrial introgression in North American Great Black-backed Gulls (Larus marinus) from the American Herring Gull (Larus smithsonianus) with little nuclear DNA impact.

Recent genetic studies have shown that introgression rates among loci may greatly vary according to their location in the genome. In particular, several cases of mito-nuclear discordances have been reported for a wide range of organisms. In the present study, we examine the causes of discordance between mitochondrial (mtDNA) and nuclear DNA introgression detected in North American populations of the Great Black-backed Gull (Larus marinus), a Holarctic species, from the Nearctic North American Herring Gull (Larus smithsonianus). Our results show that extensive unidirectional mtDNA introgression from Larus smithsonianus into Larus marinus in North America cannot be explained by ancestral polymorphism but most likely results from ancient hybridization events occurring when Larus marinus invaded the North America. Conversely, our nuclear DNA results based on 12 microsatellites detected very little introgression from Larus smithsonianus into North American Larus marinus. We discuss these results in the framework of demographic and selective mechanisms that have been postulated to explain mito-nuclear discrepancies. We were unable to demonstrate selection as the main cause of mito-nuclear introgression discordance but cannot dismiss the possible role of selection in the observed pattern. Among demographic explanations, only drift in small populations and bias in mate choice in an invasive context may explain our results. As it is often difficult to demonstrate that selection may be the main factor driving the introgression of mitochondrial DNA in natural populations, we advocate that evaluating alternative demographic neutral hypotheses may help to indirectly support or reject hypotheses invoking selective processes.

Molecular phylogenetics and historical biogeography of the west-palearctic common toads (Bufo bufo species complex).

In most pan-Eurasiatic species complexes, two phenomena have been traditionally considered key processes of their cladogenesis and biogeography. First, it is hypothesized that the origin and development of the Central Asian Deserts generated a biogeographic barrier that fragmented past continuous distributions in Eastern and Western domains. Second, Pleistocene glaciations have been proposed as the main process driving the regional diversification within each of these domains. The European common toad and its closest relatives provide an interesting opportunity to examine the relative contributions of these paleogeographic and paleoclimatic events to the phylogeny and biogeography of a widespread Eurasiatic group. We investigate this issue by applying a multiproxy approach combining information from molecular phylogenies, a multiple correspondence analysis of allozyme data and species distribution models. Our study includes 304 specimens from 164 populations, covering most of the distributional range of the Bufo bufo species complex in the Western Palearctic. The phylogenies (ML and Bayesian analyses) were based on a total of 1988 bp of mitochondrial DNA encompassing three genes (tRNAval, 16S and ND1). A dataset with 173 species of the family Bufonidae was assembled to estimate the separation of the two pan-Eurasiatic species complexes of Bufo and to date the main biogeographic events within the Bufo bufo species complex. The allozyme study included sixteen protein systems, corresponding to 21 presumptive loci. Finally, the distribution models were based on maximum entropy. Our distribution models show that Eastern and Western species complexes are greatly isolated by the Central Asian Deserts, and our dating estimates place this divergence during the Middle Miocene, a moment in which different sources of evidence document a major upturn of the aridification rate of Central Asia. This climate-driven process likely separated the Eastern and Western species. At the level of the Western Palearctic, our dating estimates place most of the deepest phylogenetic structure before the Pleistocene, indicating that Pleistocene glaciations did not have a major role in splitting the major lineages. At a shallow level, the glacial dynamics contributed unevenly to the genetic structuring of populations, with a strong influence in the European-Caucasian populations, and a more relaxed effect in the Iberian populations.

Speciation with gene flow in the large white-headed gulls: does selection counterbalance introgression?

We investigated the role of selection in generating and maintaining species distinctness in spite of ongoing gene flow, using two zones of secondary contact between large gull species in Europe (Larus argentatus and Larus cachinnans) and North America (Larus glaucescens and Larus occidentalis). We used the pattern of neutral genetic differentiation at nine microsatellite loci (F(ST)) as an indicator of expected changes under neutral processes and compared it with phenotypic differentiation (P(ST)) for a large number of traits (size, plumage melanism and coloration of bare parts). Even assuming very low heritability, interspecific divergence between L. glaucescens and L. occidentalis in plumage melanism and orbital ring colour clearly exceeded neutral differentiation. Similarly, melanism of the central primaries was highly divergent between L. argentatus and L. cachinnans. Such divergence is unlikely to have arisen randomly and is therefore attributed to spatially varying selection. Variation in plumage melanism in both transects agrees with Gloger's rule, which suggests that latitude (and associated sun and humidity gradients) could be the selective pressure shaping differentiation in plumage melanism. We suggest that strong species differentiation in orbital ring colour results from sexual selection. We conclude that these large gull species, along with other recently diverged species that hybridize after coming into secondary contact, may differ only in restricted regions of the genome that are undergoing strong disruptive selection because of their phenotypic effects.

Mitochondrial DNA reveals the genealogical history of the snake-eyed lizards (Ophisops elegans and O. occidentalis) (Sauria: Lacertidae).

The snake-eyed lizards of the genus Ophisops (Lacertidae) have been through a series of taxonomical revisions, but still their phylogenetic relationships remain uncertain. In the present study we estimate the phylogeographic structure of O. elegans across its distributional range and we evaluate the relationships between O. elegans and the sympatric, in North Africa, species O. occidentalis, using partial mtDNA sequences (16S rRNA, COI, and cyt b). All phylogenetic analyses produced topologically identical trees where extant populations of O. elegans and O. occidentalis were found polyphyletic. Taking into account all the potential causes of polyphyly (introgressive hybridization, incomplete lineage sorting, and imperfect taxonomy) we suggest the inaccurate taxonomy as the most likely explanation for the observed pattern. Our results stress the need for re-evaluation of the current taxonomical status of these species and their subspecies. Furthermore, our biogeographic analyses and the estimated time of divergences suggest a late Miocene diversification within these species, where the present distribution of O. elegans and O. occidentalis was the result of several dispersal and vicariant events, which are associated with climatic oscillations (the late Miocene aridification of Asia and northern Africa) and paleogeographic barriers of late Miocene and Pliocene period.

Molecular and morphological patterns of introgression between two large white-headed gull species in a zone of recent secondary contact.

Incomplete reproductive isolation promotes gene flow between diverging taxa. However, any gene encoding for traits involved in the reproductive barriers will be less prone to introgression than neutral markers. Comparing introgression rates among loci is thus informative of the number and functions of loci involved in the reproductive barriers. This study aimed at identifying possible mechanisms of restriction to gene flow across a zone of recent secondary contact between Larus argentatus and Larus cachinnans by comparing introgression patterns for nine microsatellite loci, a fragment of mitochondrial DNA and a set of phenotypic traits. The low linkage disequilibrium between neutral nuclear markers indicated introgression without any barrier to gene flow. However, asymmetric introgression of mitochondrial DNA suggested that interspecific crosses may be more successful in one direction. The introgression rate for phenotypic traits was variable and low compared to neutral molecular markers. This was particularly evident in colouration of bare parts: individuals with intermediate colouration were scarcer in sympatry than expected if the genomes recombined freely. We hypothesized that one of these variables, the orbital ring colour, may play a role in mate choice, acting as an incomplete premating barrier through assortative mating. This study emphasizes that multilocus approaches are useful to discriminate among possible mechanisms responsible for the maintenance of hybrid zones.

Phenotypic variation in Galerida larks in Morocco: the role of history and natural selection.

The relative influences of history, natural selection and hybridization in shaping phenotypic variation in closely related taxa is a crucial issue in current evolutionary biology. In this study, we used as a model two sibling but paradoxically highly variable species of larks (Galerida theklae and Galerida cristata) of Morocco to separate the impacts of these evolutionary forces. In the former species, variation is manifested mainly in colouration, while in the latter, variation also encompasses bill size and shape. Mitochondrial and nuclear DNA sequencing were used to identify the historical relationships among the subspecies and species. According to our analyses, G. cristata and G. theklae diverged about 3.7 million years ago (Ma), and we found no evidence for a role of hybridization in maintaining their similarity. In G. theklae, there was no further subdivision, while in G. cristata two major mtDNA groups were identified (divergence approximately 1.1 Ma). These two lineages are parapatric and regroup, respectively, the three short-billed subspecies [G. (cristata) cristata] and the two long-billed subspecies [G. (cristata) randonii]. Patterns of morphological variation were then contrasted to this pattern of neutral relationships: we found that G. (c.) cristata was morphologically more similar to G. theklae than to G. (c.) randonii. Overall, these results point towards the prominent role of (i) natural selection and/or phenotypic plasticity in adapting the plumage to local conditions and (ii) natural selection in combination with historical isolation in driving the divergence in size and bill morphology in the crested larks.

Phylogenetic relationships within the Laridae (Charadriiformes: Aves) inferred from mitochondrial markers.

Gulls (Aves: Laridae) constitute a recent and cosmopolite family of well-studied seabirds for which a robust phylogeny is needed to perform comparative and biogeographical analyses. The present study, the first molecular phylogeny of all Larids species (N=53), is based on a combined segment of mtDNA (partial cytochrome b and control region). We discuss our phylogenetic tree in the light of previous suggestions based on morphological, behavioral, and plumage characters. Although the phylogeny is not fully resolved, it highlights several robust species groups and confirms or identifies for the first time some sister relationships that had never been suggested before. The Dolphin Gull (Leucophaeus scoresbii) for instance, is identified as the sister species of the Grey Gull (Larus modestus) and the Ross's Gull (Rhodostethia rosea) forms a monophyletic group with the Little Gull (Larus minutus). Our results clearly demonstrate that the genus Larus as currently defined is not monophyletic, since current taxonomy of gulls is based on the use of convergent phenotypic characters. We propose a new systematic arrangement that better reflects their evolutionary history.

Phylogeography of a game species: the red-crested pochard (Netta rufina) and consequences for its management.

Western European populations of red-crested pochard (Netta rufina) are characterized by low size and high fragmentation, which accentuate their sensitivity to hunting. Uncertainties regarding the demographic trends of these populations highlight the need for pertinent hunting regulations. This requires identification of the limits of the populations under exploitation, i.e. delimiting a management unit. We used the left domain of the mitochondrial control region and seven nuclear loci (four microsatellites and three introns) to assess the level of genetic structure and demographic independence between the fragmented Western European and the large Central Asian populations. The second objective was to investigate the colonization history of the Western European populations. This study demonstrated that the Western European populations of red-crested pochard constitute a separate demographic conservation unit relative to the Asian population as a result of very low female dispersal (mitochondrial DNA: PhiST = 0.152). A morphometric analysis further suggested that Central Asian and Western European specimens of both sexes originate from different pools of individuals. Male dispersal seems higher than female dispersal, as suggested by the lack of clear genetic structure for the nuclear markers at this continental scale. Genetic data, in conjunction with historical demographic data, indicate that the current Western European populations probably originate from a recent colonization from Central Asia. As numbers of red-crested pochards in Western Europe cannot be efficiently supplemented by immigration from the larger Asian populations, a management plan regulating the harvest in Western Europe is required.

Sire coloration influences offspring survival under predation risk in the moorfrog.

When breeding, male moor frogs Rana arvalis develop a bright blue dorsal coloration which varies in intensity between males. We tested whether this colour acts as a potential signal of a male's genetic quality to female moor frogs by artificially crossing pairs of males differing in the extent of the blue coloration to the same female. Maternal half-sibships provide a powerful means to detect paternal genetic effects on offspring as they control for other potentially confounding variables. We assayed the ability of offspring to survive an ecologically realistic test of fitness by exposing them to predation by the larvae of the predatory water beetle Dytiscus marginalis. Although sire's coloration did not influence tadpole body size, it did affect their ability to survive the predation trial. Offspring of bright blue males had higher survival than those of dull males when exposed to large predators, which were more voracious predators than smaller ones. Our results indicate that paternal secondary sexual traits provide information about genetic effects on offspring fitness in this species, but suggest that these effects may be context-dependent. Variable selection caused by contextual dependence may have important consequences for the evolution of female choice rules, and for the maintenance of genetic variation for both male trait and female preference.

Slow rate of evolution in the mitochondrial control region of gulls (Aves: Laridae).

We sequenced part of the mitochondrial control region and the cytochrome b gene in 72 specimens from 32 gull species (Laridae, Larini) and 2 outgroup representatives (terns: Laridae, Sternini). Our control region segment spanned the conserved central domain II and the usually hypervariable 3' domain III. Apart from some heteroplasmy at the 3' end of the control region, domain III was not more variable than domain II or the cytochrome b gene. Furthermore, variation in the tempo of evolution of domain III was apparent between phyletic species groups. The lack of variation of the gull control region could not be explained by an increase in the proportion of conserved sequences in these birds, and the gull control region showed an organization similar to those of other avian control regions studied to date. A novel invariant direct repeat was identified in domain II of gulls, and in domain III, two to three inverted, sometimes imperfect, repeats are able to form a significantly stable stem-and-loop structure. These putative secondary structures have not been reported before, and a comparison between species groups showed that they are more stable in the group with the more conserved control region. The unusually slow rate of evolution of control region part III of the gulls could thus be partly explained by the existence of secondary structures in domain III of these species.

Genetic structure of avian populations--allozymes revisited.

Selection on allozymes has sometimes been advanced as one explanation for the low levels of population differentiation detected in avian populations by the use of enzymatic markers. Comparisons of the amount of population subdivision (estimated by FST values or analogous indices) measured by enzymatic and mitochondrial DNA (mtDNA) markers in birds were seen as evidence for this because mtDNA typically produces a more structured picture of population subdivisions. In fact, when taking into account the smaller effective population size of mtDNA, nuclear and mitochondrial markers give concordant results. Some discrepancies still exist, but I suggest that some might originate from different amounts of nuclear vs. mitochondrial gene flow due to partial reproductive isolation. Variable number of tandem repeat (VNTR) loci do not provide a dramatically different picture of population structures in birds compared to allozymes. Although more tests are needed, such as comparing the amount of genetic structure detected in the same populations with allozymes and microsatellites, the low levels of population subdivision measured with allozymes in birds seem to reflect historical and demographic processes and would not appear to result from any peculiarities of bird enzymatic loci.