Colonization and diversification: towards a phylogeographic synthesis for the Canary Islands

Genetic diversity of an Azorean endemic and endangered plant species inferred from inter-simple sequence repeat markers

Knowledge of the levels and distribution of genetic diversity is important for designing conservation strategies for threatened and endangered species so as to guarantee sustainable survival of populations and to preserve their evolutionary potential. Picconia azorica is a valuable Azorean endemic species recently classified as endangered. To contribute with information useful for the establishment of conservation programmes, the genetic variability and differentiation among 230 samples from 11 populations collected in three Azorean islands was accessed with eight inter-simple sequence repeat markers. A total of 64 polymorphic loci were detected. The majority of genetic variability was found within populations and no genetic structure was detected between populations and between islands. Also the coefficient of genetic differentiation and the level of gene flow indicate that geographical distances do not act as barriers for gene flow. In order to ensure the survival of populations in situ and ex situ management practices should be considered, including artificial propagation through the use of plant tissue culture techniques, not only for the restoration of habitat but also for the sustainable use of its valuable wood.

The explosive radiation of Cheirolophus (Asteraceae, Cardueae) in Macaronesia

Background

Considered a biodiversity hotspot, the Canary Islands have been the key subjects of numerous evolutionary studies concerning a large variety of organisms. The genus Cheirolophus (Asteraceae) represents one of the largest plant radiations in the Canarian archipelago. In contrast, only a few species occur in the Mediterranean region, the putative ancestral area of the genus. Here, our main aim was to reconstruct the phylogenetic and biogeographic history of Cheirolophus with special focus on explaining the origin of the large Canarian radiation.

Results

We found significant incongruence in phylogenetic relationships between nuclear and plastid markers. Each dataset provided resolution at different levels in Cheirolophus: the nuclear markers resolved the backbone of the phylogeny while the plastid data provided better resolution within the Canarian clade. The origin of Cheirolophus was dated in the Mid-Late Miocene, followed by rapid diversification into the three main Mediterranean lineages and the Macaronesian clade. A decrease in diversification rates was inferred at the end of the Miocene, with a new increase in the Late Pliocene concurrent with the onset of the Mediterranean climate. Diversification within the Macaronesian clade started in the Early-Mid Pleistocene, with unusually high speciation rates giving rise to the extant insular diversity.

Conclusions

Climate-driven diversification likely explains the early evolutionary history of Cheirolophus in the Mediterranean region. It appears that the exceptionally high diversification rate in the Canarian clade was mainly driven by allopatric speciation (including intra- and interisland diversification). Several intrinsic (e.g. breeding system, polyploid origin, seed dispersal syndrome) and extrinsic (e.g. fragmented landscape, isolated habitats, climatic and geological changes) factors probably contributed to the progressive differentiation of populations resulting in numerous microendemisms. Finally, hybridization events and emerging ecological adaptation may have also reinforced the diversification process.

Intermediate geographic range facilitates speciation in European tree species

The possible influence of geographic range size on speciation remains a controversial subject in evolutionary ecology, with theory and data supporting positive, negative and bell-shaped relationships between speciation probability and ancestor range size. In this study, a surrogate of the speciation-range size relationship of extant European tree species (22 genera, 11 families) is obtained by comparing the range-size distribution of candidate ancestors (i.e.species which are thought to have originated new species) with that of relatives, controlling phylogenetic inertia and macroecological sampling bias. In this comparison, species range size is measured qualitatively using six categories. The candidate ancestors included seem to have speciated mainly through allopatric speciation, with fewer instances of hybridogenesis by allopolyploidy. The results show that speciation is significantly facilitated for species with intermediate range size. In the European tree flora, this pattern could be the result of multiple causes, including intermediate dispersal ability at these ranges. Descendant tree species tend to have narrow geographic ranges, a trend which arguably comes from limited dispersal ability in this case. Low dispersal ability could be common in new species as a consequence of widespread adaptation to stable habitats isolated by geographic barriers (“island habitats”) during allopatric speciation. This mechanism could be widespread among regional biotas and would facilitate narrow ranges in new species. This would provide a simple explanation to the observed abundance of narrow ranges in most macroecological species-range size distributions.

Signatures of volcanism and aridity in the evolution of an insular pine (Pinus canariensis Chr. Sm. Ex DC in Buch)

Oceanic islands of volcanic origin provide useful templates for the study of evolution because they are subjected to recurrent perturbations that generate steep environmental gradients that may promote adaptation. Here we combine population genetic data from nuclear genes with the analysis of environmental variation and phenotypic data from common gardens to disentangle the confounding effects of demography and selection to identify the factors of importance for the evolution of the insular pine P. canariensis. Eight nuclear genes were partially sequenced in a survey covering the entire species range, and phenotypic traits were measured in four common gardens from contrasting environments. The explanatory power of population substrate age and environmental indices were assessed against molecular and phenotypic diversity estimates. In addition, neutral genetic variability (FST) and the genetic differentiation of phenotypic variation (QST) were compared in order to identify the evolutionary forces acting on these traits. Two key factors in the evolution of the species were identified: (1) recurrent volcanic activity has left an imprint in the genetic diversity of the nuclear genes; (2) aridity in southern slopes promotes local adaptation in the driest localities of P. canariensis, despite high levels of gene flow among populations.

Pronounced fixation, strong population differentiation and complex population history in the Canary Islands blue tit subspecies complex

Evolutionary molecular studies of island radiations may lead to insights in the role of vicariance, founder events, population size and drift in the processes of population differentiation. We evaluate the degree of population genetic differentiation and fixation of the Canary Islands blue tit subspecies complex using microsatellite markers and aim to get insights in the population history using coalescence based methods. The Canary Island populations were strongly genetically differentiated and had reduced diversity with pronounced fixation including many private alleles. In population structure models, the relationship between the central island populations (La Gomera, Tenerife and Gran Canaria) and El Hierro was difficult to disentangle whereas the two European populations showed consistent clustering, the two eastern islands (Fuerteventura and Lanzarote) and Morocco weak clustering, and La Palma a consistent unique lineage. Coalescence based models suggested that the European mainland forms an outgroup to the Afrocanarian population, a split between the western island group (La Palma and El Hierro) and the central island group, and recent splits between the three central islands, and between the two eastern islands and Morocco, respectively. It is clear that strong genetic drift and low level of concurrent gene flow among populations have shaped complex allelic patterns of fixation and skewed frequencies over the archipelago. However, understanding the population history remains challenging; in particular, the pattern of extreme divergence with low genetic diversity and yet unique genetic material in the Canary Island system requires an explanation. A potential scenario is population contractions of a historically large and genetically variable Afrocanarian population, with vicariance and drift following in the wake. The suggestion from sequence-based analyses of a Pleistocene extinction of a substantial part of North Africa and a Pleistocene/Holocene eastward re-colonisation of western North Africa from the Canaries remains possible.

Colonisation and diversification of the Zenaida Dove (Zenaida aurita) in the Antilles: phylogeography, contemporary gene flow and morphological divergence

Caribbean avifaunal biogeography has been mainly studied based on mitochondrial DNA. Here, we investigated both past and recent island differentiation and micro-evolutionary changes in the Zenaida Dove (Zenaida aurita) based on combined information from one mitochondrial (Cytochrome c Oxydase subunit I, COI) and 13 microsatellite markers and four morphological characters. This Caribbean endemic and abundant species has a large distribution, and two subspecies are supposed to occur: Z. a. zenaida in the Greater Antilles (GA) and Z. a. aurita in the Lesser Antilles (LA). Doves were sampled on two GA islands (Puerto Rico and the British Virgin Islands) and six LA islands (Saint Barthélemy, Guadeloupe, Les Saintes, Martinique, Saint Lucia and Barbados). Eleven COI haplotypes were observed that could be assembled in two distinct lineages, with six specific to GA, four to LA, the remaining one occurring in all islands. However, the level of divergence between those two lineages was too moderate to fully corroborate the existence of two subspecies. Colonisation of the studied islands appeared to be a recent process. However, both phenotypic and microsatellite data suggest that differentiation is already under way between all of them, partly associated with the existence of limited gene flow. No isolation by distance was observed. Differentiation for morphological traits was more pronounced than for neutral markers. These results suggest that despite recent colonisation, genetic drift and/or restricted gene flow are promoting differentiation for neutral markers. Variation in selective pressures between islands may explain the observed phenotypic differentiation.

Vulnerability to cavitation, hydraulic efficiency, growth and survival in an insular pine (Pinus canariensis)

BACKGROUND AND AIMS

It is widely accepted that hydraulic failure due to xylem embolism is a key factor contributing to drought-induced mortality in trees. In the present study, an attempt is made to disentangle phenotypic plasticity from genetic variation in hydraulic traits across the entire distribution area of a tree species to detect adaptation to local environments.

METHODS

A series of traits related to hydraulics (vulnerability to cavitation and hydraulic conductivity in branches), growth performance and leaf mass per area were assessed in eight Pinus canariensis populations growing in two common gardens under contrasting environments. In addition, the neutral genetic variability (FST) and the genetic differentiation of phenotypic variation (QST) were compared in order to identify the evolutionary forces acting on these traits.

KEY RESULTS

The variability for hydraulic traits was largely due to phenotypic plasticity. Nevertheless, the vulnerability to cavitation displayed a significant genetic variability (approx. 5 % of the explained variation), and a significant genetic × environment interaction (between 5 and 19 % of the explained variation). The strong correlation between vulnerability to cavitation and survival in the xeric common garden (r = -0·81; P < 0·05) suggests a role for the former in the adaptation to xeric environments. Populations from drier sites and higher temperature seasonality were less vulnerable to cavitation than those growing at mesic sites. No trade-off between xylem safety and efficiency was detected. QST of parameters of the vulnerability curve (0·365 for P50 and the slope of the vulnerability curve and 0·452 for P88) differed substantially from FST (0·091), indicating divergent selection. In contrast, genetic drift alone was found to be sufficient to explain patterns of differentiation for xylem efficiency and growth.

CONCLUSIONS

The ability of P. canariensis to inhabit a wide range of ecosystems seemed to be associated with high phenotypic plasticity and some degree of local adaptations of xylem and leaf traits. Resistance to cavitation conferred adaptive potential for this species to adapt successfully to xeric conditions.

Patterns and processes in complex landscapes: testing alternative biogeographical hypotheses through integrated analysis of phylogeography and community ecology in Hawai'i

The Island of Hawai'i is a dynamic assemblage of five volcanoes with wet forest habitat currently existing in four distinct natural regions that vary in area, age and geographical isolation. In this complex landscape, alternative assumptions of the relative importance of specific habitat characteristics on evolutionary and ecological processes predict strikingly different general patterns of local diversity and regional similarity. In this study, we compare alternative a priori hypotheses against observed patterns within two distinct biological systems and scales: community composition of wet forest vascular plant species and mitochondrial and nuclear genes of Drosophila sproati, a wet-forest-restricted endemic. All observed patterns display strong and similar regional structuring, with the greatest local diversity found in Kohala and the windward side of Mauna Loa, the least in Ka'ū and Kona, and a distinctive pattern of regional similarity that probably reflects the historical development of this habitat on the island. These observations largely corroborate a biogeographical model that integrates multiple lines of evidence, including climatic reconstruction, over those relying on single measures, such as current habitat configuration or substrate age. This method of testing alternative hypotheses across biological systems and scales is an innovative approach for understanding complex landscapes and should prove valuable in diverse biogeographical systems.

Founder takes all: density-dependent processes structure biodiversity

Density-dependent processes play a key role in the spatial structuring of biodiversity. Specifically, interrelated demographic processes, such as gene surfing, high-density blocking, and competitive exclusion, can generate striking geographic contrasts in the distributions of genes and species. Here, we propose that well-studied evolutionary and ecological biogeographic patterns of postglacial recolonization, progressive island colonization, microbial sectoring, and even the 'Out of Africa' pattern of human expansion, are fundamentally similar, underpinned by a 'founder takes all' density-dependent principle. Additionally, we hypothesize that older historic constraints of density-dependent processes are seen today in the dramatic biogeographic shifts that occur in response to human-mediated extinction events, whereby surviving lineages rapidly expand their ranges to replace extinct sister taxa.

Phylogeography and seed dispersal in islands: the case of Rumex bucephalophorus subsp. canariensis (Polygonaceae)

BACKGROUND AND AIMS

Rumex bucephalophorus subsp. canariensis is an endemic taxon to Macaronesia with diaspore polymorphism. The origin and colonizing route of this taxon in Macaronesia was studied using molecular data and information on diaspore types.

METHODS

Amplified fragment length polymorphism (AFLP) was used in 260 plants from 22 populations of R. bucephalophorus subsp. canariensis, four from the Madeiran archipelago and 18 from the Canary archipelago. Diaspore production was analysed in 9-50 plants from each population used for AFLP analysis. One hundred and one plants from the Madeiran archipelago and 375 plants from the Canary Islands were studied. For each plant the type of diaspore produced was recorded.

KEY RESULTS

Overall populations had low genetic diversity but they showed a geographical pattern of genetic diversity that was higher in the older eastern islands than in the younger western ones. Two types of dispersible diaspores were found: in the eastern Canary islands (Lanzarote, Fuerteventura and Gran Canaria), plants produced exclusively long-dispersible diaspores, whereas in the western Canary islands (Tenerife, La Gomera, El Hierro) and the Madeiran archipelago plants produced exclusively short-dispersible diaspores. Genetically, the studied populations fell into four main island groups: Lanzarote-Fuerteventura, Gran Canaria, Tenerife-El Hierro and La Gomera-Madeira archipelago.

CONCLUSIONS

A Moroccan origin of R. bucephalophorus subsp. canariensis is hypothesized with a colonization route from the eastern to the western islands. In addition, at least one gene flow event from La Gomera to the Madeiran archipelago has taken place. During the colonization process the type of dispersible diaspore changed so that dispersability decreased in populations of the westernmost islands.

Complete mitochondrial genomes from four subspecies of common chaffinch (Fringilla coelebs): new inferences about mitochondrial rate heterogeneity, neutral theory, and phylogenetic relationships within the order Passeriformes

We describe whole mitochondrial genome sequences from four subspecies of the common chaffinch (Fringilla coelebs), and compare them to 31 publicly available mitochondrial genome sequences from other Passeriformes. Rates and patterns of mitochondrial gene evolution are analyzed at different taxonomic levels within this avian order, and evidence is adduced for and against the nearly neutral theory of molecular evolution and the role of positive selection in shaping genetic variation of this small but critical genome. We find evidence of mitochondrial rate heterogeneity in birds as in other vertebrates, likely due to differences in mutational pressure across the genome. Unlike in gadine fish and some of the human mitochondrial work we do not observe strong support for the nearly neutral theory of molecular evolution; instead evidence from molecular clocks, distribution of dN/dS ratios at different levels of the taxonomic hierarchy and in different lineages, McDonald-Kreitman tests within Fringillidae, and site-specific tests of selection within Passeriformes, all point to a role for positive selection, especially for the complex I NADH dehydrogenase genes. The protein-coding mitogenome phylogeny of the order Passeriformes is broadly consistent with previously-reported molecular findings, but provides support for a sister relationship between the superfamilies Muscicapoidea and Passeroidea on a short basal internode of the Passerida where relationships have been difficult to resolve. An unexpected placement of the Paridae (represented by Hume's groundpecker) within the Muscicapoidea was observed. Consistent with other molecular studies the mtDNA phylogeny reveals paraphyly within the Muscicapoidea and a sister relationship of Fringilla with Carduelis rather than Emberiza.

Colliding fragment islands transport independent lineages of endemic rock-crawlers (Grylloblattodea: Grylloblattidae) in the Japanese archipelago

Fragment islands, viewed from the paradigm of island biogeographic theory, depend on continual immigration from continental sources to maintain levels of species diversity, or otherwise undergo a period of relaxation where species diversity declines to a lower equilibrium. Japan is a recently derived fragment island with a rich endemic flora and fauna. These endemic species have been described as paleoendemics, and conversely as recently derived Pleistocene colonists. Geological events in the Miocene period, notably the fragmentation and collision of islands, and the subsequent uplift of mountains in central Japan, provided opportunities for genetic isolation. More recently, cyclical climatic change during the Pliocene and Pleistocene periods led to intermittent land bridge connections to continental Asia. Here we investigate the pattern and timing of diversification in a diverse endemic lineage in order to test whether ongoing migration has sustained species diversity, whether there is evidence of relaxation, and how geological and climatic events are associated with lineage diversification. Using multi-locus genetic data, we test these hypotheses in a poorly dispersing, cold-adapted terrestrial insect lineage (Grylloblattodea: Grylloblattidae) sampled from Japan, Korea, and Russia. In phylogenetic analyses of concatenated data and a species tree approach, we find evidence of three deeply divergent lineages of rock-crawlers in Japan consistent with the pattern of island fragmentation from continental Asia. Tests of lineage diversification rates suggest that relaxation has not occurred and instead endemism has increased in the Japanese Grylloblattidae following mountain-building events in the Miocene. Although the importance of climate change in generating species diversity is a commonly held paradigm in Japanese biogeography, our analyses, including analyses of demographic change and phylogeographic range shifts in putative species, suggests that Pleistocene climatic change has had a limited effect on the diversification of rock-crawlers.

Interpreting the process behind endemism in China by integrating the phylogeography and ecological niche models of the Stachyridopsis ruficeps

An area of endemism (AOE) is a complex expression of the ecological and evolutionary history of a species. Here we aim to address the principal drivers of avian diversification in shaping patterns of endemism in China by integrating genetic, ecological, and distributional data on the Red-headed Tree Babbler (Stachyridopsis ruficeps), which is distributed across the eastern Himalayas and south China. We sequenced two mtDNA markers from 182 individuals representing all three of the primary AOEs in China. Phylogenetic inferences were used to reconstruct intraspecific phylogenetic relationships. Divergence time and population demography were estimated to gain insight into the evolutionary history of the species. We used Ecological niche modeling to predict species' distributions during the Last Glacial Maximum (LGM) and in the present. Finally, we also used two quantitative tests, an identity test and background test to assess the similarity of ecological niche preferences between adjacent lineages. We found five primary reciprocally monophyletic clades, typically separated approximately 0.2-2.27 MYA, of which three were deeply isolated endemic lineages located in the three AOEs. All phylogroups were detected to have undergone population expansion during the past 0.3 MY. Niche models showed discontinuous habitats, and there were three barriers of less suitable habitat during the LGM and in modern times. Ecoclimatic niches may diverge significantly even over recent timescales, as each phylogroup had a unique distribution, and unique niche characteristics. Vicariant events associated with geographical and ecological barriers, glacial refuges and ecological differentiation may be the main drivers forming the pattern of endemism in China.

Inferring multiple refugia and phylogeographical patterns in Pinus massoniana based on nucleotide sequence variation and DNA fingerprinting

BACKGROUND

Pinus massoniana, an ecologically and economically important conifer, is widespread across central and southern mainland China and Taiwan. In this study, we tested the central-marginal paradigm that predicts that the marginal populations tend to be less polymorphic than the central ones in their genetic composition, and examined a founders' effect in the island population.

METHODOLOGY/PRINCIPAL FINDINGS

We examined the phylogeography and population structuring of the P. massoniana based on nucleotide sequences of cpDNA atpB-rbcL intergenic spacer, intron regions of the AdhC2 locus, and microsatellite fingerprints. SAMOVA analysis of nucleotide sequences indicated that most genetic variants resided among geographical regions. High levels of genetic diversity in the marginal populations in the south region, a pattern seemingly contradicting the central-marginal paradigm, and the fixation of private haplotypes in most populations indicate that multiple refugia may have existed over the glacial maxima. STRUCTURE analyses on microsatellites revealed that genetic structure of mainland populations was mediated with recent genetic exchanges mostly via pollen flow, and that the genetic composition in east region was intermixed between south and west regions, a pattern likely shaped by gene introgression and maintenance of ancestral polymorphisms. As expected, the small island population in Taiwan was genetically differentiated from mainland populations.

CONCLUSIONS/SIGNIFICANCE

The marginal populations in south region possessed divergent gene pools, suggesting that the past glaciations might have low impacts on these populations at low latitudes. Estimates of ancestral population sizes interestingly reflect a recent expansion in mainland from a rather smaller population, a pattern that seemingly agrees with the pollen record.

Hybridization and population structure of the Culex pipiens complex in the islands of Macaronesia

The Culex pipiens complex includes two widespread mosquito vector species, Cx. pipiens and Cx. quinquefasciatus. The distribution of these species varies in latitude, with the former being present in temperate regions and the latter in tropical and subtropical regions. However, their distribution range overlaps in certain areas and interspecific hybridization has been documented. Genetic introgression between these species may have epidemiological repercussions for West Nile virus (WNV) transmission. Bayesian clustering analysis based on multilocus genotypes of 12 microsatellites was used to determine levels of hybridization between these two species in Macaronesian islands, the only contact zone described in West Africa. The distribution of the two species reflects both the islands' biogeography and historical aspects of human colonization. Madeira Island displayed a homogenous population of Cx. pipiens, whereas Cape Verde showed a more intriguing scenario with extensive hybridization. In the islands of Brava and Santiago, only Cx. quinquefasciatus was found, while in Fogo and Maio high hybrid rates (∼40%) between the two species were detected. Within the admixed populations, second-generation hybrids (∼50%) were identified suggesting a lack of isolation mechanisms. The observed levels of hybridization may locally potentiate the transmission to humans of zoonotic arboviruses such as WNV.

Radiating on oceanic islands: patterns and processes of speciation in the land snail genus Theba (Risso 1826)

Island radiations have played a major role in shaping our current understanding of allopatric, sympatric and parapatric speciation. However, the fact that species divergence correlates with island size emphasizes the importance of geographic isolation (allopatry) in speciation. Based on molecular and morphological data, we investigated the diversification of the land snail genus Theba on the two Canary Islands of Lanzarote and Fuerteventura. Due to the geological history of both islands, this study system provides ideal conditions to investigate the interplay of biogeography, dispersal ability and differentiation in generating species diversity. Our analyses demonstrated extensive cryptic diversification of Theba on these islands, probably driven mainly by non-adaptive allopatric differentiation and secondary gene flow. In a few cases, we observed a complete absence of gene flow among sympatrically distributed forms suggesting an advanced stage of speciation. On the Jandía peninsula genome scans suggested genotype-environment associations and potentially adaptive diversification of two closely related Theba species to different ecological environments. We found support for the idea that genetic differentiation was enhanced by divergent selection in different environments. The diversification of Theba on both islands is therefore best explained by a mixture of non-adaptive and adaptive speciation, promoted by ecological and geomorphological factors.

Phylogenetic relationships elucidate colonization patterns in the intertidal grazers Osilinus Philippi, 1847 and Phorcus Risso, 1826 (Gastropoda: Trochidae) in the northeastern Atlantic Ocean and Mediterranean Sea

Snails in the closely related trochid genera Phorcus Risso, 1826 and Osilinus Philippi, 1847 are ecologically important algal grazers in the intertidal zone of the northeastern Atlantic Ocean and Mediterranean Sea. Here we present the first complete molecular phylogeny for these genera, based on the nuclear 28S rRNA gene and the mitochondrial 16S rRNA and COI genes, and show that the current classification is erroneous. We recognize nine species in a single genus, Phorcus: estimated by BEAST analysis, this arose 30 (± 10) Ma; it consists of two subgenera, Phorcus and Osilinus, which we estimate diverged 14 (± 4.5) Ma. Osilinus kotschyi, from the Arabian and Red Seas, is not closely related and is tentatively referred to Priotrochus Fischer, 1879. Our phylogeny allows us to address biogeographical questions concerning the origins of the Mediterranean and Macaronesian species of this group. The former appear to have evolved from Atlantic ancestors that invaded the Mediterranean on several occasions after the Zanclean Flood, which ended the Messinian Salinity Crisis 5.3 Ma; whereas the latter arose from several colonizations of mainland Atlantic ancestors within the last 3 (± 1.5) Ma.

The relevance of gene flow in metapopulation dynamics of an oceanic island endemic, Olea europaea subsp. guanchica

Theoretical and empirical studies suggest that geographical isolation and extinction-recolonization dynamics are two factors causing strong genetic structure in metapopulations, but their consequences in species with high dispersal abilities have not been tested at large scales. Here, we investigated the effect of population age structure and isolation by distance in the patterns of genetic diversity in a wind-pollinated, zoochorous tree (Olea europaea subsp. guanchica) sporadically affected by volcanic events across the Canarian archipelago. Genetic variation was assessed at six nuclear microsatellites (nDNA) and six chloroplast fragments (cpDNA) in nine subpopulations sampled on four oceanic islands. Subpopulations occurring on more recent substrates were more differentiated than those on older substrates, but within-subpopulation genetic diversity was not significantly different between age groups for any type of marker. Isolation-by-distance differentiation was observed for nDNA but not for cpDNA, in agreement with other metapopulation studies. Contrary to the general trend for island systems, between-island differentiation was extremely low, and lower than differentiation between subpopulations on the same island. The pollen-to-seed ratio was close to one, two orders of magnitude lower than the average estimated for other wind-pollinated, animal-dispersed plants. Our results showed that population turnover and geographical isolation increased genetic differentiation relative to an island model at equilibrium, but overall genetic structure was unexpectedly weak for a species distributed among islands. This empirical study shows that extensive gene flow, particularly mediated by seeds, can ameliorate population subdivision resulting from extinction-recolonization dynamics and isolation by distance.

Tracing the temporal and spatial origins of island endemics in the Mediterranean region: a case study from the citrus family (Ruta L., Rutaceae)

Understanding the origin of island endemics is a central task of historical biogeography. Recent methodological advances provide a rigorous framework to determine the relative contribution of different biogeographic processes (e.g., vicariance, land migration, long-distance dispersal) to the origin of island endemics. With its complex but well-known history of microplate movements and climatic oscillations, the Mediterranean region (including the Mediterranean basin and Macaronesia) provides the geographic backdrop for the diversification of Ruta L., the type genus of Rutaceae (citrus family). Phylogenetic, molecular dating, and ancestral range reconstruction analyses were carried out to investigate the extent to which past geological connections and climatic history of the Mediterranean region explain the current distribution of species in Ruta, with emphasis on its island endemics. The analyses showed that Ruta invaded the region from the north well before the onset of the Mediterranean climate and diversified in situ as the climate became Mediterranean. The continental fragment island endemics of the genus originated via processes of land migration/vicariance driven by connections/disconnections between microplates, whereas the oceanic island endemics were the product of a single colonization event from the mainland followed by in situ diversification. This study emphasizes the need for an integrative, hypothesis-based approach to historical biogeography and stresses the importance of temporary land connections and colonization opportunity in the biotic assembly of continental fragment and oceanic islands, respectively.

Molecular phylogeny and Holarctic diversification of the subtribe Calathina (Coleoptera: Carabidae: Sphodrini)

A molecular phylogeny of the subtribe Calathina was inferred from DNA sequence data from the mitochondrial cox1-cox2 region and the nuclear genes 28S and EF-1alpha. All lineages within Calathina from the Holarctic region were represented except for the monotypic subgenus Tachalus. Maximum Parsimony and Bayesian analyses of the combined data set showed that the subtribe is a monophyletic lineage that includes a single genus Calathus, where other taxa currently ranked as independent genera (Lindrothius, Synuchidius, Thermoscelis and Acalathus) are nested within this genus.Neocalathus and Lauricalathus, both subgenera of Calathus, were found to be polyphyletic and in need of taxonomic revision. The subtribe appears to have originated in the Mediterranean Basin and thereafter expanded into most parts of the Palearctic region, the Macaronesian archipelagos (at least five independent colonisation events), the Ethiopian highlands and the Nearctic region (at least two independent events).

Significance of ecological vicariance and long-distance dispersal in the diversification of Carex sect. Spirostachyae (Cyperaceae)

Plant disjunctions have provided one of the most intriguing distribution patterns historically addressed by biogeographers. Carex sect. Spirostachyae (Cyperaceae) displays an interesting pattern of disjunction to evaluate these scenarios, with species occurring in the main continental landmasses and in oceanic islands of the two hemispheres. Internal transcribed spacer and 5'-trnK intron plastid gene sequences were analyzed to determine (1) the times of diversification using penalized likelihood, and (2) reconstructions of the regions using maximum likelihood and Bayesian approaches of origin of sect. Spirostachyae and internal main lineages. The times for the diversification of sect. Spirostachyae are dated to between the end of the Eocene and the Oligocene, whereas the two main lineages are dated to between the end of the Oligocene and the beginning of Miocene. The phylogenetic analyses reveal a Mediterranean-Eurasian center of differentiation for sect. Spirostachyae and subsection Spirostachyae, whereas no clear, single ancestral area could be inferred for subsection Elatae. Both long-distance dispersal and ecological vicariance appear to have been involved in the evolutionary history of the disjunct distribution of the main lineages of sect. Spirostachyae. These organisms appear to have a special ability to colonize remote areas (through transoceanic and interhemispherical colonizations), but special long-distance dispersal mechanisms are not evident.

Paraphyly of organelle DNAs in Cycas Sect. Asiorientales due to ancient ancestral polymorphisms

Background

This study addresses the apportionment of genetic diversity between Cycas revoluta and C. taitungensis, species that constitute the section Asiorientales and represent a unique, basal lineage of the Laurasian genus Cycas. Fossil evidence indicates divergence of the section from the rest of Cycas at least 30 million years ago. Geographically, C. taitungensis is limited to Taiwan whereas C. revoluta is found in the Ryukyu Archipelago and on mainland China.

Results

The phylogenies of ribosomal ITS region of mtDNA and the intergenic spacer between atpB and rbcL genes of cpDNA were reconstructed. Phylogenetic analyses revealed paraphyly of both loci in the two species and also in the section Asiorientales. The lack of reciprocal monophyly between these long isolated sections is likely due to persistent shared ancestral polymorphisms. Molecular dating estimated that mt- and cp DNA lineages coalesced to the most recent common ancestors (TMRCA) about 327 (mt) and 204 MYA (cp), corresponding with the divergence of cycad sections in the Mesozoic.

Conclusion

Fates of newly derived mutations of cycads follow Klopfstein et al.'s surfing model where the majority of new mutations do not spread geographically and remain at low frequencies or are eventually lost by genetic drift. Only successful 'surfing mutations' reach very high frequencies and occupy a large portion of a species range. These mutations exist as dominant cytotypes across populations and species. Geographical subdivision is lacking in both species, even though recurrent gene flow by both pollen and seed is severely limited. In total, the contrasting levels between historical and ongoing gene flow, large population sizes, a long lifespan, and slow mutation rates in both organelle DNAs have all likely contributed to the unusually long duration of paraphyly in cycads.

Goats, birds, and emergent diseases: apparent and hidden effects of exotic species in an island environment

Exotic species can have devastating effects on recipient environments and even lead to the outbreak of emergent diseases. We present here several hidden effects that the introduction of goats has had on the Lesser Short-toed Lark, Calandrella rufescens, the commonest native bird inhabiting the island of Fuerteventura (Canary Islands). Vegetation structure varied with grazing pressure, and indeed, vegetation was all but eradicated from the locality with greatest goat densities, which was also where the lowest density of Lesser Short-toed Larks was recorded. The impact of habitat impoverishment, however, was partially compensated for by changes in the foraging behavior of birds, which benefited from the abundant food provided to goats on farms. Capture-resighting methods showed that birds visiting farms outnumbered the estimates for birds obtained in the surrounding natural habitat, suggesting that there was recruitment from a much larger area. Stable isotope analyses of feathers indicated that island birds feed largely on the maize supplied at goat farms, showing poorer body condition than birds from populations not associated with farms (peninsular Spain and Morocco). Moreover, larks from Fuerteventura had a very high prevalence of poxvirus lesions compared with other bird populations worldwide and may increase the risk of contracting the disease by feeding on farms, where they aggregate and coexist atypically with domestic birds. The island birds also had lower average productivity, which may be the consequence of the emergent disease and/or the poor nutritional state resulting from feeding on a low-protein diet. Diseased and non-diseased birds from Fuerteventura showed similar body condition and annual survival rates. However, the isotopic traces of delta 13C indicate that the diet of diseased birds was more uniform than that of non-diseased birds, being based on food from goat farms. Our results show how the combination of species frequently introduced onto islands (goats, poultry, and associated pathogens) can create ecological traps for native species that are not always easy to identify. Moreover, we stress that nutrition and infectious diseases are important determinants of the well-being and dynamics of animal populations, and thus health research must be included in the design of monitoring programs and conservation strategies.

Characterization of demographic expansions from pairwise comparisons of linked microsatellite haplotypes

This work extends the methods of demographic inference based on the distribution of pairwise genetic differences between individuals (mismatch distribution) to the case of linked microsatellite data. Population genetics theory describes the distribution of mutations among a sample of genes under different demographic scenarios. However, the actual number of mutations can rarely be deduced from DNA polymorphisms. The inclusion of mutation models in theoretical predictions can improve the performance of statistical methods. We have developed a maximum-pseudolikelihood estimator for the parameters that characterize a demographic expansion for a series of linked loci evolving under a stepwise mutation model. Those loci would correspond to DNA polymorphisms of linked microsatellites (such as those found on the Y chromosome or the chloroplast genome). The proposed method was evaluated with simulated data sets and with a data set of chloroplast microsatellites that showed signal for demographic expansion in a previous study. The results show that inclusion of a mutational model in the analysis improves the estimates of the age of expansion in the case of older expansions.

Genetic diversity and differentiation processes in the ploidy series of Olea europaea L.: a multiscale approach from subspecies to insular populations

Geographical isolation and polyploidization are central concepts in plant evolution. The hierarchical organization of archipelagos in this study provides a framework for testing the evolutionary consequences for polyploid taxa and populations occurring in isolation. Using amplified fragment length polymorphism and simple sequence repeat markers, we determined the genetic diversity and differentiation patterns at three levels of geographical isolation in Olea europaea: mainland-archipelagos, islands within an archipelago, and populations within an island. At the subspecies scale, the hexaploid ssp. maroccana (southwest Morocco) exhibited higher genetic diversity than the insular counterparts. In contrast, the tetraploid ssp. cerasiformis (Madeira) displayed values similar to those obtained for the diploid ssp. guanchica (Canary Islands). Geographical isolation was associated with a high genetic differentiation at this scale. In the Canarian archipelago, the stepping-stone model of differentiation suggested in a previous study was partially supported. Within the western lineage, an east-to-west differentiation pattern was confirmed. Conversely, the easternmost populations were more related to the mainland ssp. europaea than to the western guanchica lineage. Genetic diversity across the Canarian archipelago was significantly correlated with the date of the last volcanic activity in the area/island where each population occurs. At the island scale, this pattern was not confirmed in older islands (Tenerife and Madeira), where populations were genetically homogeneous. In contrast, founder effects resulted in low genetic diversity and marked genetic differentiation among populations of the youngest island, La Palma.

The origin of clonal diversity and structure of Populus alba in Sardinia: evidence from nuclear and plastid microsatellite markers

BACKGROUND AND AIMS

Populus alba is a thermophilic forest tree present in the Mediterranean basin. Its habitat is highly fragmented and its distribution range has been subject to long-term human interference, resulting in debate surrounding whether certain populations are native or exotic in origin. In particular, populations from the islands of Corsica and Sardinia are of uncertain origin. While populations of P. alba mainly reproduce sexually, clonal reproduction is also common. The aims of this study were to locate and molecularly characterize the poorly studied island populations of P. alba and compare these with samples from various spatial scales, in order to provide information on the genetic structure and phylogeography of this species. This information will provide evidence on whether the species is native to Sardinia, which is important for the development of conservation strategies.

METHODS

DNA extracts were obtained from the following P. alba trees: 159 from Sardinia, 47 from Ticino regional park (northern Italy), 15 acquired from an Italian Germoplasm Bank (IRC; Italian Reference Collection) and 28 from the Mediterranean basin (MB). Genetic polymorphisms were revealed at nuclear and chloroplast DNA (cpDNA) microsatellite loci, both at the island scale (Sardinia) and at broader scales, for comparative assessment of the genetic and genotypic diversity and phylogeography.

KEY RESULTS

Based on nuclear microsatellite loci, Sardinian white poplar consists of a small number of genets (26), each of which is represented by several ramets. Despite the uniqueness of the Sardinian haplotypes and the very low value of genetic diversity at the cpDNA level (vK = 0.15), the HT (0.60) and the AR (3.61) values, estimated at the nuclear level for Sardinia, were comparable with those of the other populations and collections.

CONCLUSIONS

The uniqueness of the cpDNA haplotypes, the prevalence of clonality and the restricted number of genets recorded suggest that Sardinian white poplar could be a floristic relict of the native flora of the island, which has spread through available habitats on the island mainly by means of vegetative propagation and human activities.

The West Indies as a laboratory of biogeography and evolution

Islands have long provided material and inspiration for the study of evolution and ecology. The West Indies are complex historically and geographically, providing a rich backdrop for the analysis of colonization, diversification and extinction of species. They are sufficiently isolated to sustain endemic forms and close enough to sources of colonists to develop a dynamic interaction with surrounding continental regions. The Greater Antilles comprise old fragments of continental crust, some very large; the Lesser Antilles are a more recent volcanic island arc, and the low-lying Bahama Islands are scattered on a shallow oceanic platform. Dating of island lineages using molecular methods indicates over-water dispersal of most inhabitants of the West Indies, although direct connections with what is now southern Mexico in the Early Tertiary, and subsequent land bridges or stepping stone islands linking to Central and South America might also have facilitated colonization. Species-area relationships within the West Indies suggest a strong role for endemic radiations and extinction in shaping patterns of diversity. Diversification is promoted by opportunities for allopatric divergence between islands, or within the large islands of the Greater Antilles, with a classic example provided by the Anolis lizards. The timing of colonization events using molecular clocks permits analysis of colonization-extinction dynamics by means of species accumulation curves. These indicate low rates of colonization and extinction for reptiles and amphibians in the Greater Antilles, with estimated average persistence times of lineages in the West Indies exceeding 30Myr. Even though individual island populations of birds might persist an average of 2Myr on larger islands in the Lesser Antilles, recolonization from within the archipelago appears to maintain avian lineages within the island chain indefinitely. Birds of the Lesser Antilles also provide evidence of a mass extinction event within the past million years, emphasizing the time-heterogeneity of historical processes. Geographical dynamics are matched by ecological changes in the distribution of species within islands over time resulting from adaptive radiation and shifts in habitat, often following repeatable patterns. Although extinction is relatively infrequent under natural conditions, changes in island environments as a result of human activities have exterminated many populations and others--especially old, endemic species--remain vulnerable. Conservation efforts are strengthened by recognition of aesthetic, cultural and scientific values of the unique flora and fauna of the West Indies.

Colonization and diversification of Galápagos terrestrial fauna: a phylogenetic and biogeographical synthesis

Remote oceanic islands have long been recognized as natural models for the study of evolutionary processes involved in diversification. Their remoteness provides opportunities for isolation and divergence of populations, which make islands remarkable settings for the study of diversification. Groups of islands may share a relatively similar geological history and comparable climate, but their inhabitants experience subtly different environments and have distinct evolutionary histories, offering the potential for comparative studies. A range of organisms have colonized the Galápagos Islands, and various lineages have radiated throughout the archipelago to form unique assemblages. This review pays particular attention to molecular phylogenetic studies of Galápagos terrestrial fauna. We find that most of the Galápagos terrestrial fauna have diversified in parallel to the geological formation of the islands. Lineages have occasionally diversified within islands, and the clearest cases occur in taxa with very low vagility and on large islands with diverse habitats. Ecology and habitat specialization appear to be critical in speciation both within and between islands. Although the number of phylogenetic studies is continuously increasing, studies of natural history, ecology, evolution and behaviour are essential to completely reveal how diversification proceeded on these islands.

Nuclear and mitochondrial sequences confirm complex colonization patterns and clear species boundaries for flightless weevils in the Galápagos archipelago

Nuclear sequence data were collected from endemic Galápagos species and an introduced close relative, and contrasted with mitochondrial DNA sequences, continuing investigation into the colonization history and modes of diversification in the weevil genus Galapaganus. The current combined phylogeny together with previously published penalized likelihood age estimates builds a complex picture of the archipelago's colonization history. The present reconstruction relies on submerged platforms to explain the early divergence of the young southern Isabela endemics or the Española or San Cristobal populations. Diversity is later built through inter-island divergence starting on older islands and continuing on two simultaneous tracks towards younger islands. The amount of diversity generated through intra-island processes is skewed towards older islands, suggesting that island age significantly influences diversity. Phylogenetic concordance between nuclear and mitochondrial datasets and well-supported monophyletic species in mitochondrial derived topologies appear to reject the possibility of inter-species hybridization. These clear species boundaries might be related to the tight host associations of adult weevils in discrete ecological zones. If shared hosts facilitate hybridization, then host- or habitat-promoted divergences could prevent it, even in the case of species that share islands, since the altitudinal partitioning of habitats minimizes range overlap.

Timing and tempo of early and successive adaptive radiations in Macaronesia

The flora of Macaronesia, which encompasses five Atlantic archipelagos (Azores, Canaries, Madeira, Cape Verde, and Salvage), is exceptionally rich and diverse.

Spectacular radiation of numerous endemic plant groups has made the Macaronesian islands an outstanding area for studies of evolution and speciation. Despite intensive investigation in the last 15 years, absolute age and rate of diversification are poorly known for the flora of Macaronesia. Here we report molecular divergence estimates and rates of diversification for five representative, putative rapid radiations of monophyletic endemic plant lineages across the core eudicot clade of flowering plants. Three discrete windows of colonization during the Miocene and early Pliocene are suggested for these lineages, all of which are inferred to have had a single colonization event followed by rapid radiation. Subsequent inter-archipelago dispersal events into Madeira and the Cape Verdes took place very recently during the late Pliocene and Pleistocene after initial diversification on the Canary Islands. The tempo of adaptive radiations differs among the groups, but is relatively rapid compared to continental and other island radiations. Our results demonstrate that opportunity for island colonization and successful radiation may have been constrained to discrete time periods of profound climatic and geological changes in northern African and the Mediterranean.