Geographic analysis of nucleotide diversity and song sparrow (Aves: Emberizidae) population history

Mitochondrial DNA (mtDNA) control-region (CR) sequences were analysed to address three questions regarding the evolution of geographical variation in song sparrows. (i) Are mtDNA sequences more informative about phylogenetic relationships and population history than previously published restriction fragment (RFLP) data? (ii) Are song sparrow CR sequences evolving in a selectively neutral manner? (iii) What do the haplotype cladogram and geographical pattern of nucleotide diversity (π) suggest about the recent evolutionary history of song sparrow populations? Results from phylogenetic analyses of CR sequences corroborate RFLP results and reveal instances in which haplotypes do not group by locality. Neutrality tests ( 51 ) suggest that song sparrow mtDNA is evolving in a selectively neutral manner, although exceptions are noted. A novel geographical pattern of π suggests a model of song sparrow population history involving multiple Pleistocene refugia and colonization of some formerly glaciated regions from multiple sources. Moreover, application of coalescence theory to the haplotype cladogram suggests that two different haplotypes (48NF and 151HA) may have predominated in different parts of the song sparrow's range. This model provides insight into the current distribution of song sparrow mtDNA haplotypes and may explain the discordance between evolutionary history inferred from mtDNA and morphology in this species.     

Genetic diversity and population structure in two species of sea cucumber: differing patterns according to mode of development

The population structure of two species of sea cucumber was examined based on mitochondrial DNA sequence analysis. Cucumaria miniata , a species with pelagic nonfeeding larvae lasting less than 2 weeks, and C. pseudocurata , a brooding species lacking a pelagic phase, both occur over similar wide ranges of the northeastern Pacific between Alaska and California. No significant genetic structuring was observed among C. miniata samples with 95% of the observed nucleotide variance attributable to that within population samples. Conversely, only 3.4% of the observed variance was attributed to that within C. pseudocurata population samples, with sampling sites typically greater than 100 km apart. At a finer scale, two C. pseudocurata population samples taken 5 km apart were not statistically different. A significant genetic disjunction was observed among populations of the brooding species, but not in species with pelagic larvae, north of Vancouver Island, Canada, corresponding to the splitting of the California and Alaska currents. Given the observed high levels of genetic diversity in northern samples, this genetic break indicates survival in northern, as well as southern, Pleistocene refugia. These results clearly demonstrate the effects that changes in life-history patterns can have on dispersal, population structure, and the potential for speciation events.     

Does vicariance shape biotas? Biogeographical tests of the vicariance model in the north‐west European land snail fauna

Aim To investigate the importance of vicariance in shaping the north‐west European land snail fauna. Location North‐west Europe. Methods We tested whether there is a non‐random congruence, i.e. a clustering of species ranges, using a Monte Carlo procedure with a null model that generates range data sets such that their range size distribution, the species richness distribution of the geographic cells and the spatial autocorrelation of the occurrences of a taxon approach the parameters in the real data set. Biotic elements, groups of species with similar ranges, were delimited with Model based Gaussian clustering. The prediction that closely related species belong to different biotic elements, has been tested with a chi‐square test. Results The distribution areas of the north‐west European land snail species are significantly clustered as predicted by the vicariance model. One widespread and seven regional biotic elements were identified. Contrary to the predictions of the vicariance model, closely related north‐west European land snail species belong significantly more often to the same biotic element than should be expected by chance. Main conclusions The clustering of closely related north‐west European land snail species within the same biotic element indicates that speciation modes other than vicariance were frequent or that the imprint of vicariance on the ranges was obscured by extensive post‐speciational dispersal. Extensive dispersal may have been caused by Pleistocene climatic fluctuations. The core areas of the regionally restricted biotic elements might indicate the positions of glacial refugia of land snails.     

Climate change at the landscape scale: predicting fine-grained spatial heterogeneity in warming and potential refugia for vegetation

Current predictions of how species will respond to climate change are based on coarse‐grained climate surfaces or idealized scenarios of uniform warming. These predictions may erroneously estimate the risk of extinction because they neglect to consider spatially heterogenous warming at the landscape scale or identify refugia where species can persist despite unfavourable regional climate. To address this issue, we investigated the heterogeneity in warming that has occurred in a 10 km × 10 km area from 1972 to 2007. We developed estimates by combining long‐term daily observations from a limited number of weather stations with a more spatially comprehensive dataset (40 sites) obtained during 2005–2006. We found that the spatial distribution of warming was greater inland, at lower elevations, away from streams, and at sites exposed to the northwest (NW). These differences corresponded with changes in weather patterns, such as an increasing frequency of hot, dry NW winds. As plant species were biased in the topographic and geographic locations they occupied, these differences meant that some species experienced more warming than others, and are at greater risk from climate change. This species bias could not be detected at coarser scales. The uneven seasonal nature of warming (e.g. more warming in winter, minimums increased more than maximums) means that climate change predictions will vary according to which predictors are selected in species distribution models. Models based on a limited set of predictors will produce erroneous predictions when the correct limiting factor is not selected, and this is difficult to avoid when temperature predictors are correlated because they are produced using elevation‐sensitive interpolations. The results reinforce the importance of downscaling coarse‐grained (∼50 km) temperature surfaces, and suggest that the accuracy of this process could be improved by considering regional weather patterns (wind speed, direction, humidity) and topographic exposure to key wind directions.     

Allozymic differentiation in the land snail Arianta arbustorum (Stylommatophora, Helicidae): historical inferences

The intraspecific genetic differentiation depends to a large part on historical factors. The mode of dispersal is an important determinant of the genetic diversity especially of newly founded populations. Fast long-distance colonization of formerly unsuitable habitats results in reduced genetic diversity and lineages originating from different glacial refugia form well-defined hybrid zones, where they meet. Slow dispersers, on the other hand, preserve their refugial genetic diversity. Paleontological findings and a previous analysis of mtDNA suggest that the land snail Arianta arbustorum, which today is widely spread across Europe, has survived the Pleistocene glaciations within the boundaries of permafrost. In the present paper, we asked, whether the differentiation of nuclear markers, i.e. allozymes, supports these results. We investigated the allozymic differentiation at 15 polymorphic loci in 14 Alpine and one English populations of the land snail A. arbustorum. Various tests of genetic population differentiation yielded ambiguous results. Allele frequencies differed significantly across populations and all but five pairwise F_ST values were significant. Genetic distances between populations were comparatively high. On the other hand, an exact test of population differentiation found no differences and the assignment of individuals to their populations of origin was poor. This indicates that allozymic differentiation is constrained. Whether these constraints are of natural or methodological nature remains open. Matrices of genetic and geographical distances were correlated only after removal of the English population from the analysis. Similarly, with one exception F_ST values increased as the number of regions included in the calculations increased. Thus, on a regional scale, we largely observed a pattern of isolation by distance, which does no longer hold on a larger scale. This is well in accordance with the previous findings based on mtDNA. Mitochondrial lineages were widely distributed across Europe and overlapped extensively. Considering the low potential for dispersal of a land snail, the patchy distribution of lineages, and the high genetic diversity also found in the present study suggests that A. arbustorum has survived the Pleistocene within the boundaries of permafrost.     

Stable Heliconius butterfly hybrid zones are correlated with a local rainfall peak at the edge of the Amazon basin

Multilocus clines between Müllerian mimetic races of Heliconius butterflies provide a classic example of the maintenance of hybrid zones and their importance in speciation. Concordant hybrid zones in the mimics Heliconius erato and H. melpomene in northern Peru were carefully documented in the 1980s, and this prior work now permits a historical analysis of the movement or stasis of the zones. Previous work predicted that these zones might be moving toward the Andes due to selective asymmetry. Extensive deforestation and climate change might also be expected to affect the positions and widths of the hybrid zones. We show that the positions and shapes of these hybrid zones have instead remained remarkably stable between 1985 and 2012. The stability of this interaction strongly implicates continued selection, rather than neutral mixing following secondary contact. The stability of cline widths and strong linkage disequilibria (gametic correlation coefficients R_max = 0.35–0.56 among unlinked loci) over 25 years suggest that mimetic selection pressures on each color pattern locus have remained approximately constant (s ≈ 0.13–0.40 per locus in both species). Exceptionally high levels of precipitation at the edge of the easternmost Andes may act as a population density trough for butterflies, trapping the hybrid zones at the foot of the mountains, and preventing movement. As such, our results falsify one prediction of the Pleistocene Refugium theory: That the ranges of divergent species or subspecies should be centered on regions characterized by maxima of rainfall, with hybrid zones falling in more arid regions between them.     

Speciation in Mediterranean refugia and post‐glacial expansion of Zerynthia polyxena (Lepidoptera,Papilionidae)

Migration of populations to and from glacial refugia is responsible for various cases of speciation and subspeciation in Europe. The pattern of distribution and the degree of diversification between lineages originated by isolation in different glacial refugia usually depends on ecological traits, especially to their dispersal ability. Zerynthia polyxena is a philopatric species, scattered in small populations and rarely colonizing mountain areas. These characteristics probably caused repeated isolation during the Quaternary and may have favoured diversification. Actually two studies, based on both morphological and genetic data, suggest the existence of two highly distinct lineages in Europe having in Northern Italy their contact zone. In this study, I applied geometric morphometrics to male genitalia and demonstrated that (i) two morphotypes exist in Europe approximately facing on the two sides of the Po River; (ii) the two lineages probably survived glaciations in Italy and the Balkan Peninsula, respectively; then the Balkans lineage expanded to Central and Eastern Europe; (iii) no hybrid populations seem to exist in the contact area and, in one locality at least, the two lineages live in sympatry without any evidence of intermediates. These results suggest that (i) two sister species of Zerynthia exist in Europe. Accordingly, Papilio cassandra Geyer, 1828 is reinstated, as Zerynthia cassandra stat. rev., as the species to which the Zerynthia from Italy South of the Po River belong. Male genitalia differences with Zerynthia polyxena are described.     

The role of topography in structuring the demographic history of the pine processionary moth,Thaumetopoea pityocampa (Lepidoptera: Notodontidae)

Aim We investigated the Quaternary history of the pine processionary moth, Thaumetopoea pityocampa, an oligophagous insect currently expanding its range. We tested the potential role played by mountain ranges during the post‐glacial recolonization of western Europe. Location Western Europe, with a focus on the Pyrenees, Massif Central and western Alps. Methods Maternal genetic structure was investigated using a fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene. We analysed 412 individuals from 61 locations and performed maximum likelihood and maximum parsimony phylogenetic analyses and hierarchical analysis of molecular variance, and we investigated signs of past expansion. Results A strong phylogeographic pattern was found, with two deeply divergent clades. Surprisingly, these clades were not separated by the Pyrenees but rather were distributed from western to central Iberia and from eastern Iberia to the Italian Peninsula, respectively. This latter group consisted of three shallowly divergent lineages that exhibited strong geographic structure and independent population expansions. The three identified lineages occurred: (1) on both sides of the Pyrenean range, with more genetically diverse populations in the east, (2) from eastern Iberia to western France, with a higher genetic diversity in the south, and (3) from the western Massif Central to Italy. Admixture areas were found at the foot of the Pyrenees and Massif Central. Main conclusions The identified genetic lineages were geographically structured, but surprisingly the unsuitable high‐elevation areas of the main mountainous ranges were not responsible for the spatial separation of genetic groups. Rather than acting as barriers to dispersal, mountains appear to have served as refugia during the Pleistocene glaciations, and current distributions largely reflect expansion from these bottlenecked refugial populations. The western and central Iberian clade did not contribute to the northward post‐glacial recolonization of Europe, yet its northern limit does not correspond to the Pyrenees. The different contributions of the identified refugia to post‐glacial expansion might be explained by differences in host plant species richness. For example, the Pyrenean lineage could have been trapped elevationally by tracking montane pines, while the eastern Iberian lineage could have expanded latitudinally by tracking thermophilic lowland pine species.     

Phylogeography of Podocarpus matudae (Podocarpaceae): pre‐Quaternary relicts in northern Mesoamerican cloud forests

Aim Cloud forests of northern Mesoamerica represent the northern and southern limit of the contact zone between species otherwise characteristic of North or South America. Several phylogeographic studies featuring temperate conifer species have improved our understanding of species responses to environmental changes. In contrast, conifer species that presumably colonized northern Mesoamerica from South America are far less studied. A phylogeographic study of Podocarpus matudae (Podocarpaceae) was conducted to identify any major evolutionary divergences or disjunctions across its range and to determine if its current distribution is associated with pre‐Quaternary climatic and/or long‐distance dispersal events. Location Northern Mesoamerica (Mexico and Guatemala). Methods Sixteen populations (157 individuals) of P. matudae were screened for variation at two plastid DNA markers. The intra‐specific phylogenetic relationships among haplotypes were reconstructed using Bayesian inference. Population genetic analyses were undertaken to gain insight into the evolutionary history of these populations. To test whether genetic divergence among populations occurred at different time‐scales plastid DNA sequence data and fossil‐ and coalescent‐based calibrations were integrated. Results The combination of plastid markers yielded 11 haplotypes. Differentiation among populations based on DNA variation (G_ST) (0.707, SE 0.0807) indicated a clear population structure in P. matudae. Differentiation for ordered alleles (N_ST) (0.811, SE 0.0732) was higher than that for G_ST, indicating phylogeographical structure in P. matudae. Most of the total variation (81.3%, P < 0.0001) was explained by differences among populations. The estimated divergence time between the unique haplotypes from a Guatemalan population and the two most common haplotypes from the Sierra Madre Oriental in Mexico was between 10 and 20 Ma, and further haplotype divergence in the poorly resolved clade of the Sierra Madre Oriental occurred between 3 and 0.5 Ma. Main conclusions Divergence estimations support the hypothesis that extant Podocarpus matudae populations are pre‐Quaternary relicts. This finding is consistent with fossil and pollen data that support a Miocene age for temperate floristic elements in Mesoamerican cloud forests, whereas further haplotype divergence within the Sierra Madre Oriental, Chiapas and Guatemala occurred more recently, coinciding with Pleistocene cloud forest refugia.     

HOLARCTIC PHYLOGEOGRAPHY OF AN ASEXUAL SPECIES COMPLEX I. MITOCHONDRIAL DNA VARIATION IN ARCTIC DAPHNIA

Pleistocene glacial cycles undoubtedly altered the evolutionary trajectories of many taxa, yet few studies have examined the impact of such events on genetic differentiation and phylogeography at large geographic scales. Here we present the results of a circumarctic survey of mitochondrial DNA diversity in members of the Daphnia pulex complex. The analysis involved the survey of restriction site polymorphisms in a 2100-bp fragment of the NADH-4 (ND4) and NADH-5 (ND5) genes for 276 populations representing the two major groups (tenebrosa and pulicaria) in this complex across their Holarctic range. A comparison of the distribution patterns for seven clades in this complex revealed very clear phylogeographic structuring. Most notably, pulicaria group lineages were restricted primarily to the Nearctic, with some colonization of formerly glaciated portions of northern Europe. This group was not detected from vast expanses of northern Eurasia, including the Beringian glacial refuge. In contrast, tenebrosa group haplotypes showed considerable intercontinental divergence between Eurasian and North American lineages, but were absent from Greenland and Iceland, as well as the Canadian arctic archipelago. Dispersal in Eurasia was primarily in a westerly direction from Beringia, whereas dispersal in the Nearctic followed proglacial drainage patterns. Long-distance dispersal of certain lineages was observed in both groups, and variation in haplotype richness and nucleotide diversity allowed us to make inferences about the positioning of putative glacial refugia. Overall, the phylogeographic pattern of diversification in this arctic complex is characterized by the apparently unique postglacial histories for each clade, indicating that even closely allied taxa can respond independently to the allopatric effects of glacial cycles. This is in sharp contrast to other phylogeographic studies of species assemblages from more southern (unglaciated) latitudes, which are often characterized by concordant patterns.