Effect of biogeographic history on population vulnerability in European amphibians.

The genetic diversity of populations, which contributes greatly to their adaptive potential, is negatively affected by anthropogenic habitat fragmentation and destruction. However, continental-scale losses of genetic diversity also resulted from the population expansions that followed the end of the last glaciation, an element that is rarely considered in a conservation context. We addressed this issue in a meta-analysis in which we compared the spatial patterns of vulnerability of 18 widespread European amphibians in light of phylogeographic histories (glacial refugia and postglacial routes) and anthropogenic disturbances. Conservation statuses significantly worsened with distances from refugia, particularly in the context of industrial agriculture; human population density also had a negative effect. These findings suggest that features associated with the loss of genetic diversity in post-glacial amphibian populations (such as enhanced fixation load or depressed adaptive potential) may increase their susceptibility to current threats (e.g., habitat fragmentation and pesticide use). We propose that the phylogeographic status of populations (i.e., refugial vs. post-glacial) should be considered in conservation assessments for regional and national red lists.

The odd couple: contrasting phylogeographic patterns in two sympatric sibling species of woodlouse-­‐hunter spiders in the Canary Islands

Comparative phylogeography seeks for commonalities in the spatial demographic history of sympatric organisms to characterize the mechanisms that shaped such patterns. The unveiling of incongruent phylogeographic patterns in co-occurring species, on the other hand, may hint to overlooked differences in their life histories or microhabitat preferences. The woodlouse-hunter spiders of the genus Dysdera have undergone a major diversi cation on the Canary Islands. The species pair Dysdera alegranzaensis and Dysdera nesiotes are endemic to the island of Lanzarote and nearby islets, where they co-occur at most of their known localities. The two species stand in sharp contrast to other sympatric endemic Dysdera in showing no evidence of somatic (non-genitalic) differentiation. Phylogenetic and population genetic analyses of mitochondrial cox1 sequences from an exhaustive sample of D. alegranzaensis and D. nesiotes specimens, and additional mitochondrial (16S, L1, nad1) and nuclear genes (28S, H3) were analysed to reveal their phylogeographic patterns and clarify their phylogenetic relationships. Relaxed molecular clock models using ve calibration points were further used to estimate divergence times between species and populations. Striking differences in phylogeography and population structure between the two species were observed. Dysdera nesiotes displayed a metapopulation-like structure, while D. alegranzaensis was characterized by a weaker geographical structure but greater genetic divergences among its main haplotype lineages, suggesting more complex population dynamics. Our study con rms that co-distributed sibling species may exhibit contrasting phylogeographic patterns in the absence of somatic differentiation. Further ecological studies, however, will be necessary to clarify whether the contrasting phylogeographies may hint at an overlooked niche partitioning between the two species. In addition, further comparisons with available phylogeographic data of other eastern Canarian Dysdera endemics con rm the key role of lava ows in structuring local populations in oceanic islands and identify localities that acted as refugia during volcanic eruptions

Planarian (Platyhelminthes, Tricladida) Diversity and Molecular Markers: A New View of an Old Group

Planarians are a group of free-living platyhelminths (triclads) best-known largely due to long-standing regeneration and pattern formation research. However, the group"s diversity and evolutionary history has been mostly overlooked. A few taxonomists have focused on certain groups, resulting in the description of many species and the establishment of higher-level groups within the Tricladida. However, the scarcity of morphological features precludes inference of phylogenetic relationships among these taxa. The incorporation of molecular markers to study their diversity and phylogenetic relationships has facilitated disentangling many conundrums related to planarians and even allowed their use as phylogeographic model organisms. Here, we present some case examples ranging from delimiting species in an integrative style, and barcoding them, to analysing their evolutionary history on a lower scale to infer processes affecting biodiversity origin, or on a higher scale to understand the genus level or even higher relationships. In many cases, these studies have allowed proposing better classifications and resulted in taxonomical changes. We also explain shortcomings resulting in a lack of resolution or power to apply the most up-to-date data analyses. Next-generation sequencing methodologies may help improve this situation and accelerate their use as model organisms.

Phylogenetic relationships of Apodemus Kaup, 1829 (Rodentia: Muridae) species in the Eastern Mediterranean inferred from mitochondrial DNA, with emphasis on iranian species

Wood mice of the genus Apodemus are widely distributed in Eurasia, with the Eastern Mediterranean being considered as a hotspot. Indeed, numerous species have been documented in Iran, including A. witherbyi, A. hyrcanicus, A. uralensis, A. avicennicus, A. hermonensis, and A. arianus. In this study, 129 specimens were collected from different Iranian localities and two specimens from Afghanistan. The animals were identified taxonomically and their phylogenetic relationships were investigated using cytochrome b mitochondrial DNA sequences. Five species of the genus Apodemus were identified in Iran, including A. hyrcanicus, A. witherbyi, A. cf. ponticus, A. uralensis, and A. mystacinus, beside, A. pallipes from Afghanistan. This study found no evidence of A. flavicollis or A. sylvaticus in Iran, despite their occurrence in Turkey, shedding doubt on the status of A. flavicollis in Iran, Asia Minor, and the Levant. Phylogenetic analyses imply that A. witherbyi has priority over A. avicennicus, A. hermonensis, and A. iconicus. Estimation of the divergence time for these taxa suggests a separation at around 7.2 Ma for the subgenera Karstomys (including A. mystacinus and A. epimelas) and Sylvaemus (including A. flavicollis, A. sylvaticus, A. uralensis, A. pallipes, A. hyrcanicus, A. witherbyi, and A. cf. ponticus). Within the subgenus Karstomys, the divergence times for A. mystacinus and A. epimelas were between 3.0 and 6.1 Ma, and divergence times within the subgenus Sylvaemus were between 5.2 and 6.9 Ma for A. witherbyi and other species in this subgenus. It is postulated that vicariance events including the uplifting of the Zagros Mountains and Anatolian Plateau in the middle Miocene and climate oscillations during the Messinian Salinity Crisis besides formation of the Hyrcanian tertiary forests during the Neogene probably played substantial roles in the radiation and distribution of the genus Apodemus in the Eastern Mediterranean.

Geographic patterns of genetic variation in a broadly distributed marine vertebrate: new insights into loggerhead turtle stock structure from expanded mitochondrial DNA sequences

Previous genetic studies have demonstrated that natal homing shapes the stock structure of marine turtle nesting populations. However, widespread sharing of common haplotypes based on short segments of the mitochondrial control region often limits resolution of the demographic connectivity of populations. Recent studies employing longer control region sequences to resolve haplotype sharing have focused on regional assessments of genetic structure and phylogeography. Here we synthesize available control region sequences for loggerhead turtles from the Mediterranean Sea, Atlantic, and western Indian Ocean basins. These data represent six of the nine globally significant regional management units (RMUs) for the species and include novel sequence data from Brazil, Cape Verde, South Africa and Oman. Genetic tests of differentiation among 42 rookeries represented by short sequences (380 bp haplotypes from 3,486 samples) and 40 rookeries represented by long sequences (~800 bp haplotypes from 3,434 samples) supported the distinction of the six RMUs analyzed as well as recognition of at least 18 demographically independent management units (MUs) with respect to female natal homing. A total of 59 haplotypes were resolved. These haplotypes belonged to two highly divergent global lineages, with haplogroup I represented primarily by CC-A1, CC-A4, and CC-A11 variants and haplogroup II represented by CC-A2 and derived variants. Geographic distribution patterns of haplogroup II haplotypes and the nested position of CC-A11.6 from Oman among the Atlantic haplotypes invoke recent colonization of the Indian Ocean from the Atlantic for both global lineages. The haplotypes we confirmed for western Indian Ocean RMUs allow reinterpretation of previous mixed stock analysis and further suggest that contemporary migratory connectivity between the Indian and Atlantic Oceans occurs on a broader scale than previously hypothesized. This study represents a valuable model for conducting comprehensive international cooperative data management and research in marine ecology.

Phylogéographie comparée d’un système multitrophique : les parasitoïdes du genre Horismenus spp. ont-ils échappé au processus de domestication du haricot au Mexique?

Cette étude vise à comparer l’histoire évolutive des parasitoïdes du genre Horismenus (Hymenoptera: Eulophidae) à celle de leurs hôtes bruches (Coleoptera: Bruchidae) et plante hôte (Phaseolus vulgaris L.) cultivée dans le contexte d’agriculture traditionnelle, au sein de son centre de domestication Mésoaméricain. Nous avons analysé la structure génétique de 23 populations de quatre espèces de parasitoïdes au Mexique, en utilisant un fragment du gène mitochondrial COI afin de les comparer aux structures précédemment publiées des hôtes bruches et du haricot commun. Nous avons prédit que les structures génétiques des populations d’hôtes (bruches et plante) et de parasitoïdes seraient similaires puisque également influencées par la migration entremise par l’humain (HMM) étant donnée que les parasitoïdes se développent telles que les bruches à l’intérieur des haricots. Compte tenu des stratégies de manipulation reproductive utilisées par l’alpha-protéobactérie endosymbionte Wolbachia spp. pour assurer sa transmission, la structure génétique des populations de parasitoïdes inférée à partir du génome mitochondrial devrait être altérée conséquemment à la transmission conjointe des mitochondries et des bactéries lors de la propagation de l’infection dans les populations de parasitoïdes. Les populations du parasitoïde H. missouriensis sont infectées par Wolbachia spp. Tel que prédit, ces populations ne sont pas différenciées (FST = 0,06), ce qui nous empêche d’inférer sur une histoire évolutive parallèle. Contrairement aux bruches, Acanthoscelides obtectus et A. ovelatus, la HMM n'est pas un processus contemporain qui influence la structure génétique des populations du parasitoïde H. depressus, étant donné la forte différenciation (FST = 0,34) qui existe entre ses populations. La structure génétique observée chez H. depressus est similaire à celle de sa plante hôte (i.e. dispersion aléatoire historique à partir d'un pool génique ancestral très diversifié) et est probablement le résultat d’un flux génique important en provenance des populations de parasitoïdes associées aux haricots spontanées à proximité des champs cultivés. L’étude de l’histoire évolutive intégrant plusieurs niveaux trophiques s’est avérée fructueuse dans la détection des différentes réponses évolutives entre les membres du module trophique face aux interactions humaines et parasitaires, et montre la pertinence d’analyser les systèmes écologiques dans leur ensemble.

Phylogéographie et conservation de deux espèces de petits félidés des Andes : le chat des pampas et le chat des Andes

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal

Phylogéographie comparée de la souris à pattes blanches et de la souris sylvestre, deux vecteurs de la maladie de Lyme au Québec

Mon étude vise à évaluer la propagation d’une zoonose en émergence au Québec, la maladie de Lyme, en conséquence du réchauffement climatique. Le pathogène responsable de cette infection, Borrelia burgdorferi, est transmis par l’intermédiaire d’une tique parasite, Ixodes scapularis, de plus en plus commune au Québec en raison de l’augmentation de la température moyenne du climat depuis les dernières décennies. Puisque la tique a une capacité de déplacement très restreinte, on s'attend à ce que sa dispersion soit liée à celle de son hôte primaire, soit la souris à pattes blanches (Peromyscus leucopus). Je décrirai donc d’abord les espèces impliquées, leur écologie et leur rôle dans ce système à trois niveaux (hôte/pathogène/vecteur). Puis, à l’aide de séquences d’ADN mitochondrial, je comparerai la phylogéographie des deux principales espèces de souris au Québec, la souris à pattes blanches et la souris sylvestre (P. maniculatus). Des analyses d’arbres et de réseaux d’haplotypes ont révélé des différences significatives dans la structure génétique et ainsi montré que les populations de P. leucopus seraient en expansion dans le sud du Québec. Cette étude nous a finalement permis d’émettre des hypothèses sur le patron d’établissement de la maladie de Lyme au Québec.

Population genetic diversity of the endemic Sardinian newt Euproctus platycephalus: implications for conservation

The Sardinian mountain newt Euproctus platycephalus, endemic to the island of Sardinia, (Italy), is considered a rare and threatened species and is classed as critically endangered by IUCN. It inhabits streams, small lakes and pools on the main mountain systems of the island. Threats from climatic and anthropogenic factors have raised concerns for the long-term survival of newt populations on the island. MtDNA sequencing was used to investigate the genetic population structure and phylogeography of this endemic species. Patterns of genetic variation were assessed by sequencing the complete Dloop region and part of the 12SrRNA, from 74 individuals representing four different populations. Analyses of molecular variance suggest that populations are significantly differentiated, and the distribution of haplotypes across the island shows strong geographical structuring. However, phylogenetic analyses also suggest that the Sardinian population consists of two distinct mtDNA groups, which may reflect ancient isolation and expansion events. Population structure, evolutionary history of the species and implications for the conservation of newt populations are discussed.

Rapid radiation in spiny lobsters (Palinurus spp) as revealed by classic and ABC methods using mtDNA and microsatellite data

Background: Molecular tools may help to uncover closely related and still diverging species from a wide variety of taxa and provide insight into the mechanisms, pace and geography of marine speciation. There is a certain controversy on the phylogeography and speciation modes of species-groups with an Eastern Atlantic-Western Indian Ocean distribution, with previous studies suggesting that older events (Miocene) and/or more recent (Pleistocene) oceanographic processes could have influenced the phylogeny of marine taxa. The spiny lobster genus Palinurus allows for testing among speciation hypotheses, since it has a particular distribution with two groups of three species each in the Northeastern Atlantic (P. elephas, P. mauritanicus and P. charlestoni) and Southeastern Atlantic and Southwestern Indian Oceans (P. gilchristi, P. delagoae and P. barbarae). In the present study, we obtain a more complete understanding of the phylogenetic relationships among these species through a combined dataset with both nuclear and mitochondrial markers, by testing alternative hypotheses on both the mutation rate and tree topology under the recently developed approximate Bayesian computation (ABC) methods. Results: Our analyses support a North-to-South speciation pattern in Palinurus with all the South-African species forming a monophyletic clade nested within the Northern Hemisphere species. Coalescent-based ABC methods allowed us to reject the previously proposed hypothesis of a Middle Miocene speciation event related with the closure of the Tethyan Seaway. Instead, divergence times obtained for Palinurus species using the combined mtDNA-microsatellite dataset and standard mutation rates for mtDNA agree with known glaciation-related processes occurring during the last 2 my. Conclusion: The Palinurus speciation pattern is a typical example of a series of rapid speciation events occurring within a group, with very short branches separating different species. Our results support the hypothesis that recent climate change-related oceanographic processes have influenced the phylogeny of marine taxa, with most Palinurus species originating during the last two million years. The present study highlights the value of new coalescent-based statistical methods such as ABC for testing different speciation hypotheses using molecular data.

Concordant Phylogeographies of 2 Malaria Vectors Attest to Common Spatial and Demographic Histories

The phylogeography of South American lineages is a topic of heated debate. Although a single process is unlikely to describe entire ecosystems, related species, which incur similar habitat limitations, can inform the history for a subsection of assemblages. We compared the phylogeographic patterns of the cytochrome oxidase I marker from Anopheles triannulatus (N = 72) and previous results for A. darlingi (N = 126) in a broad portion of their South American distributions. Both species share similar population subdivisions, with aggregations northeast of the Amazon River, in southern coastal Brazil and 2 regions in central Brazil. The average (ST) between these groups was 0.39 for A. triannulatus. Populations northeast of the Amazon and in southeastern Brazil are generally reciprocally monophyletic to the remaining groups. Based on these initial analyses, we constructed the a priori hypothesis that the Amazon and regions of high declivity pose geographic barriers to dispersal in these taxa. Mantel tests confirmed that these areas block gene flow for more than 1000 km for both species. The efficacy of these impediments was tested using landscape genetics, which could not reject our a priori hypothesis but did reject simpler scenarios. Results form summary statistics and phylogenetics suggest that both lineages originated in central Amazonia (south of the Amazon River) during the late Pleistocene (579 000 years ago) and that they followed the same paths of expansion into their contemporary distributions. These results may have implications for other species sharing similar ecological limitations but probably are not applicable as a general paradigm of Neotropical biogeography.

Spatial expansion and population structure of the neotropical malaria vector, Anopheles darlingi (Diptera: Culicidae)

Extensive population structuring is known to occur in Anopheles darlingi, the primary malaria vector of the Neotropics. We analysed the phylogeographic structure of the species using the mitochondrial cytochrome oxidase I marker. Diversity is divided into six main population groups in South America: Colombia, central Amazonia, southern Brazil, south-eastern Brazil, and two groups in north-east Brazil. The ancestral distribution of the taxon is hypothesized to be central Amazonia, and there is evidence of expansion from this region during the late Pleistocene. The expansion was not a homogeneous front, however, with at least four subgroups being formed due to geographic barriers. As the species spread, populations became isolated from each other by the Amazon River and the coastal mountain ranges of south-eastern Brazil and the Andes. Analyses incorporating distances around these barriers suggest that the entire South American range of An. darlingi is at mutation-dispersal-drift equilibrium. Because the species is distributed throughout such a broad area, the limited dispersal across some landscape types promotes differentiation between otherwise proximate populations. Moreover, samples from the An. darlingi holotype location in Rio de Janeiro State are substantially derived from all other populations, implying that there may be additional genetic differences of epidemiological relevance. The results obtained contribute to our understanding of gene flow in this species and allow the formulation of human mosquito health protocols in light of the potential population differences in vector capacity or tolerance to control strategies. (C) 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97, 854-866.

Forest-obligate Sabethes mosquitoes suggest palaeoecological perturbations

The origin of tropical forest diversity has been hotly debated for decades. Although specific mechanisms vary, many such explanations propose some vicariance in the distribution of species during glacial cycles and several have been supported by genetic evidence in Neotropical taxa. However, no consensus exists with regard to the extent or time frame of the vicariance events. Here, we analyse the cytochrome oxidase II mitochondrial gene of 250 Sabethes albiprivus B mosquitoes sampled from western Sao Paulo in Brazil. There was very low population structuring among collection sites (Phi(ST) = 0.03, P = 0.04). Historic demographic analyses and the contemporary geographic distribution of genetic diversity suggest that the populations sampled are not at demographic equilibrium. Three distinct mitochondrial clades were observed in the samples, one of which differed significantly in its geographic distribution relative to the other two within a small sampling area (similar to 70 x 35 km). This fact, supported by the inability of maximum likelihood analyses to achieve adequate fits to simple models for the population demography of the species, suggests a more complex history, possibly involving disjunct forest refugia. This hypothesis is supported by a genetic signal of recent population growth, which is expected if population sizes of this forest-obligate insect increased during the forest expansions that followed glacial periods. Although a time frame cannot be reliably inferred for the vicariance event leading to the three genetic clades, molecular clock estimates place this at similar to 1 Myr before present.

Coalescent analysis of mtDNA indicates Pleistocene divergence among three species of howler monkey (Alouatta spp.) and population subdivision within the Atlantic Coastal Forest species, A. guariba

We have used coalescent analysis of mtDNA cytochrome b (cyt b) sequences to estimate times of divergence of three species of Alouatta-A. caraya, A. belzebul, and A. guariba-which are in close geographic proximity. A. caraya is inferred to have diverged from the A. guariba/A. belzebul clade approximately 3.83 million years ago (MYA), with the later pair diverging approximately 1.55 MYA. These dates are much more recent than previous dates based on molecular-clock methods. In addition, analyses of new sequences from the Atlantic Coastal Forest species A. guariba indicate the presence of two distinct haplogroups corresponding to northern and southern populations with both haplogroups occurring in sympatry within Sao Paulo state. The time of divergence of these two haplogroups is estimated to be 1.2 MYA and so follows quite closely after the divergence of A. guariba and A. belzebul. These more recent dates point to the importance of Pleistocene environmental events as important factors in the diversification of A. belzebul and A. guariba. We discuss the diversification of the three Alouatta species in the context of recent models of climatic change and with regard to recent molecular phylogeographic analyses of other animal groups distributed in Brazil.

The genetic effects of Late Quaternary climatic changes over a tropical latitudinal gradient: diversification of an Atlantic Forest passerine

The increase in biodiversity from high to low latitudes is a widely recognized biogeographical pattern. According to the latitudinal gradient hypothesis (LGH), this pattern was shaped by differential effects of Late Quaternary climatic changes across a latitudinal gradient. Here, we evaluate the effects of climatic changes across a tropical latitudinal gradient and its implications to diversification of an Atlantic Forest (AF) endemic passerine. We studied the intraspecific diversification and historical demography of Sclerurus scansor, based on mitochondrial (ND2, ND3 and cytb) and nuclear (FIB7) gene sequences. Phylogenetic analyses recovered three well-supported clades associated with distinct latitudinal zones. Coalescent-based methods were applied to estimate divergence times and changes in effective population sizes. Estimates of divergence times indicate that intraspecific diversification took place during Middle-Late Pleistocene. Distinct demographic scenarios were identified, with the southern lineage exhibiting a clear signature of demographic expansion, while the central one remained more stable. The northern lineage, contrasting with LGH predictions, exhibited a clear sign of a recent bottleneck. Our results suggest that different AF regions reacted distinctly, even in opposite ways, under the same climatic period, producing simultaneously favourable scenarios for isolation and contact among populations.