Dryad

Introgression from modern hybrid varieties into landrace populations of maize (Zea mays ssp. mays L.) in central Italy

Introgression from modern hybrid varieties into landrace populations of maize (Zea mays ssp. mays L.) in central Italy Bitocchi, Elena Nanni, Laura Rossi, Monica Rau, Domenico Bellucci, Elisa Giardini, Alessandro Buonamici, Anna Vendramin, Giovanni G Papa, Roberto Landraces are domesticated local plant varieties that did not experienced a deliberate and intensive selection during a formal breeding programme. In Europe, maize landraces are still cultivated, particularly in marginal areas where traditional farming is often practised. Here, we have studied the evolution of flint maize landraces from central Italy over 50 years of on-farm cultivation, when dent hybrid varieties were introduced and their use was widespread. We have compared an â oldâ collection, obtained during the 1950s, before the introduction of hybrids, and a recent collection of maize landraces. For comparison, a sample of maize landraces from north Italy, and of improved germplasm, including hybrids and inbred lines were also used. A total of 296 genotypes were analysed using 21 microsatellites. Our results show that the maize landraces collected in the last 5-10 years have evolved directly from the flint landrace gene pool cultivated in central Italy before the introduction of modern hybrids. The population structure, diversity and linkage disequilibrium analyses indicate a significant amount of introgression from hybrid varieties into the recent landrace populations. No evidence of genetic erosion of the maize landraces was seen, suggesting that in-situ conservation of landraces is an efficient strategy for preserving genetic diversity. Finally, the level of introgression detected was very variable among recent landraces, with most of them showing a low level of introgression; this suggests that co-existence between different types of agriculture is possible, with the adoption of correct practices that are aimed at avoiding introgression from undesired genetic sources.

SSR data for maize landraces from Central Italy

SSR data for maize landraces from Central Italy Bitocchi, Elena Nanni, Laura Papa, Roberto

History and evolution of alpine plants endemic to the Qinghai-Tibetan Plateau: Aconitum gymnandrum (Ranunculaceae)

History and evolution of alpine plants endemic to the Qinghai-Tibetan Plateau: Aconitum gymnandrum (Ranunculaceae) Wang, Liuyang Abbott, Richard Zheng, Wei Chen, Ping Wang, Yujin Liu, Jianquan How Quaternary climatic oscillations affected range distributions and intraspecific divergence of alpine plants on the Qinghai-Tibetan Plateau (QTP) remains largely unknown. Here we report a survey of chloroplast (cp) and nuclear ribosomal (ITS) DNA variation aimed at exploring the phylogeographic history of the QTP alpine endemic Aconitum gymnandrum. We sequenced three cpDNA fragments (rpl20-rps12 intergenic spacer, the trnV intron and psbA-trnH spacer) and also the nuclear (ITS) region in 245 individuals from 23 populations sampled throughout the speciesâ range. Two distinct lineages with east and west geographical distributions respectively were identified from a phylogenetic analysis of ITS sequence variation and the divergence were estimated to be around 1.45 Ma. Nine chlorotypes that clustered into two major clades were broadly congruent in geographical distribution with the two ITS lineages, which was also supported by an analysis of molecular variance (AMOVA). Analysis of the spatial distribution of chlorotypes and coalescent simulation of chlorotype genealogies supported both an early Pleistocene origin of the two main cpDNA clades and the four-refugia hypothesis during the LGM. Two previous phylogeographic studies of QTP alpine plants indicated that such plants retreated to refugia at the eastern/south-eastern plateau edge during the LGM and/or previous glacial maxima. However, the results for A. gymnandrum suggest that at least some of these cold tolerant species may have also survived centrally on the QTP platform throughout the Quaternary.

ITS-1-20 intragroup.nxs

ITS-1-20 intragroup.nxs Wang, Liuyang Abbott, Richard Zheng, Wei Chen, Ping Wang, Yujin Liu, Jianquan

History and evolution of alpine plants endemic to the Qinghai-Tibetan Plateau: Aconitum gymnandrum (Ranunculaceae)

ITS intersubgenera_20080420.nxs

ITS intersubgenera_20080420.nxs Wang, Liuyang Abbott, Richard Zheng, Wei Chen, Ping Wang, Yujin Liu, Jianquan This file contain ITS sequences of A. gymnandrum and its close species

History and evolution of alpine plants endemic to the Qinghai-Tibetan Plateau: Aconitum gymnandrum (Ranunculaceae)

ITS-1-20 intragroup.meg

ITS-1-20 intragroup.meg Wang, Liuyang Abbott, Richard Zheng, Wei Chen, Ping Wang, Yujin Liu, Jianquan File include all different genotype within A. gymnandrum

ITS-1-20 intragroup.nxs

ITS-1-20 intragroup.nxs Wang, Liuyang Abbott, Richard Zheng, Wei Chen, Ping Wang, Yujin Liu, Jianquan Preparing input file for A. gymnandrum and its close species

History and evolution of alpine plants endemic to the Qinghai-Tibetan Plateau: Aconitum gymnandrum (Ranunculaceae)

ME-Aconitum_gymnandrum.pdf

ME-Aconitum_gymnandrum.pdf Wang, Liuyang Abbott, Richard Zheng, Wei Chen, Ping Wang, Yujin Liu, Jianquan Here I upload the final version of this paper. All data for this paper have been deposited in Genbank, and the corresponding Genbank number can be found in the paper.

Data from: A new puddle frog (Phrynobatrachidae: Phrynobatrachus) from the Mambilla Plateau in eastern Nigeria

Data from: A new puddle frog (Phrynobatrachidae: Phrynobatrachus) from the Mambilla Plateau in eastern Nigeria Blackburn, David C A new species of puddle frog (Phrynobatrachus) is described from the Kurmin Danko Forest Reserve on the western edge of the Mambilla Plateau in eastern Nigeria. The new species is distinguished from both geographically proximate and closely related Phrynobatrachus species by the combination of its body size (larger than the closely related P. chukuchuku, P. manengoubensis, and P. werneri), degree of development of male traits, and a unique ventral colour pattern in males. Molecular phylogenetic analysis reveals that this new species is closely related to P. werneri and P. manengoubensis, which together with several other species form a clade restricted to the mountains of the Cameroon Volcanic Line. This new Phrynobatrachus is the first known amphibian species hypothesized as endemic to the Mambilla Plateau of eastern Nigeria.

Alignment of DNA sequences of Phrynobatrachus species

Alignment of DNA sequences of Phrynobatrachus species Blackburn, David C Alignment generated using ClustalX (gap cost = 15) of mitochondrial DNA sequences.

Data from: Description and phylogenetic relationships of two new species of miniature Arthroleptis (Anura: Arthroleptidae) from the Eastern Arc Mountains of Tanzania

Data from: Description and phylogenetic relationships of two new species of miniature Arthroleptis (Anura: Arthroleptidae) from the Eastern Arc Mountains of Tanzania Blackburn, David C I describe two new species of squeaker frog (Arthroleptidae: Arthroleptis) from the Eastern Arc Mountains of Tanzania. These new species are distinguished from other miniature Arthroleptis in the Eastern Arc Mountains by the combination of very small adult body size (< 15 mm snout–vent length), a pronounced dark inguinal spot, and color patterns unique to each species. The new species could be the smallest frog species known from East Africa and among the smallest species of Arthroleptis. An estimate of phylogeny on the basis of mitochondrial DNA sequences reveals that these morphologically cryptic species are sister taxa that compose a basal lineage within a clade of miniature Arthroleptis. Their description hints at a diverse cryptic amphibian fauna in the Eastern Arc Mountains that awaits additional discovery through molecular methods.

Alignment of mitochondrial data of miniature Arthroleptis

Alignment of mitochondrial data of miniature Arthroleptis Blackburn, David C Nexus file containing alignment generated via ClustalX of mitochondrial DNA sequence data.

Data from: Biogeography and evolution of body size and life history of African frogs: Phylogeny of squeakers (Arthroleptis) and long-ﬁngered frogs (Cardioglossa) estimated from mitochondrial data

Data from: Biogeography and evolution of body size and life history of African frogs: Phylogeny of squeakers (Arthroleptis) and long-ﬁngered frogs (Cardioglossa) estimated from mitochondrial data Blackburn, David C The evolutionary history of living African amphibians remains poorly understood. This study estimates the phylogeny within the frog genera Arthroleptis and Cardioglossa using approximately 2400 bases of mtDNA sequence data (12S, tRNA-Valine, and 16S genes) from half of the described species. Analyses are conducted using parsimony, maximum likelihood, and Bayesian methods. The effect of alignment on phylogeny estimation is explored by separately analyzing alignments generated with different gap costs and a consensus alignment. The consensus alignment results in species paraphyly, low nodal support, and incongruence with the results based on other alignments, which produced largely similar results. Most nodes in the phylogeny are highly supported, yet several topologies are inconsistent with previous hypotheses. The monophyly of Cardioglossa and of miniature species previously assigned to Schoutedenella was further examined using Templeton and Shimodaira–Hasegawa tests. Cardioglossa monophyly is rejected and C. aureoli is transferred to Arthroleptis. These tests do not reject Schoutedenella monophyly, but this hypothesis receives no support from non-parametric bootstrapping or Bayesian posterior probabilities. This phylogeny provides a framework for reconstructing historical biogeography and analyzing the evolution of body size and life history. Direct development and miniaturization appear at the base of Arthroleptis phylogeny concomitant with a range expansion from Central Africa to throughout most of sub-Saharan Africa.

Alignment generated using a gap cost of 20

Alignment generated using a gap cost of 20 Blackburn, David C

Alignment generated using a gap cost of 15

Alignment generated using a gap cost of 15 Blackburn, David C

Alignment generated using a gap cost of 10

Alignment generated using a gap cost of 10 Blackburn, David C

Alignment with character set denoting excluded base pairs

Alignment with character set denoting excluded base pairs Blackburn, David C Alignment with a charset specifying nucleotide positions differing between three alignments generated using different gap costs in ClustalX. These sites were excluded to make the consensus alignment.

Alignment representing consensus of three other alignments

Alignment representing consensus of three other alignments Blackburn, David C Consensus alignment generated by removing nucleotide positions for which the alignment differed when comparing three alignments generated via ClustalX (with gap costs of 10, 15, and 20).

Data from: Complete mitochondrial DNA replacement in a Lake Tanganyika cichlid fish

Data from: Complete mitochondrial DNA replacement in a Lake Tanganyika cichlid fish Nevado, Bruno Koblmuller, S. Sturmbauer, Christian Snoeks, Jos Usano-Alemany, Jaime Verheyen, Erik We used nuclear and mitochondrial DNA sequences from specimens collected throughout Lake Tanganyika to clarify the evolutionary relationship between Lamprologus callipterus and Neolamprologus fasciatus. The nuclear data supports the reciprocal monophyly of these two shell breeding lamprologine cichlids. However, mitochondrial DNA (mtDNA) sequences show that 1) L. callipterus includes two divergent and geographically disjunct (North-South) mtDNA lineages; and that 2) N. fasciatus individuals cluster in a lineage sister group to the northern lineage of L. callipterus. The two mtDNA lineages of L. callipterus diverged c. 684 Kya to 1.2 Mya, coinciding with a major water level low stand in Lake Tanganyika, which divided the lake into isolated sub-lakes. This suggests that the two mtDNA lineages originated as the result of the separation of L. callipterus populations in different sub-basins. The incongruent phylogenetic position of N. fasciatus can best be explained by an ancient unidirectional introgression from L. callipterus into N. fasciatus. Remarkably, our data indicate that this event resulted in the complete mtDNA replacement in N. fasciatus. Our data suggest that hybridization occurred soon after the divergence of the two L. callipterus mtDNA lineages, probably still during the water level low stand, and that subsequently the invading mtDNA lineage spread throughout the lake.

nuclear phylogeny

nuclear phylogeny Nevado, Bruno File used for inference of nuclearDNA relationships of focal species (L. callipterus and N. fasciatus) within Lamprologini. Specimens names correspond to isolate names in SOM file 1 of the paper. For commands given to MrBayes when reading this file see ReadMe below.

Data from: Phenotypic correlates of Clock gene variation in a wild blue tit population: evidence for a role in seasonal timing of reproduction

Data from: Phenotypic correlates of Clock gene variation in a wild blue tit population: evidence for a role in seasonal timing of reproduction Liedvogel, Miriam Szulkin, Marta Knowles, Sarah Wood, Matt Sheldon, Ben The timing of reproduction in birds varies considerably within populations and is often under strong natural selection. Individual timing within years is dependent on a range of environmental factors in addition to having an additive genetic basis. In vertebrates, an increasing amount is known about the molecular basis for variation in biological timing. The Clock gene includes a variable poly-glutamine (poly-Q) repeat influencing behaviour and physiology. Recent work in birds, fish and insects has demonstrated associations between Clock genotype and latitude across populations, which match latitudinal variation in breeding time. In this study, we investigated the phenotypic correlates of variation in Clock genotype within a single blue tit Cyanistes caeruleus population over two successive breeding seasons. In females, but not in males, we observed a general trend for birds with fewer poly-Q repeats to breed earlier in the season. Incubation duration was shorter in both females and males with fewer repeats at the polymorphic Clock locus. Poly-Q Clock allele-frequency was homogenously distributed within the study population and did not exhibit any consistent environment-related variation. We further tested for effects of Clock genotype on reproductive success and survival, and found that females with fewer poly-Q repeats produced a higher number of fledged offspring. Our results therefore suggest that (i) selection in females, but not in males, for fewer poly-Q repeats may be operating, (ii) the across-population associations in timing of breeding involving this locus might be linked to variation within populations, and (iii) the Clock gene might be involved in local adaptation to seasonal environments.

Clock genotype for blue tit breeding population 2006-2007

Clock genotype for blue tit breeding population 2006-2007 Liedvogel, Miriam Szulkin, Marta Knowles, Sarah Wood, Matt Sheldon, Ben The file contains genotyping data and relevant covariates for the blue tit population breeding in Wytham woods 2006 and 2007.

Quantitative trait data of Lythrum salicaria

Quantitative trait data of Lythrum salicaria Chun, Young Jin Nason, John Moloney, Kirk

Data from: Comparison of quantitative and molecular genetic variation of native vs. invasive populations of purple loosestrife (Lythrum salicaria L., Lythraceae)

Data from: Comparison of quantitative and molecular genetic variation of native vs. invasive populations of purple loosestrife (Lythrum salicaria L., Lythraceae) Chun, Young Jin Nason, John Moloney, Kirk Study of adaptive evolutionary changes in populations of invasive species can be advanced through the joint application of quantitative and population genetic methods. Using purple loosestrife as a model system, we investigated the relative roles of natural selection, genetic drift, and gene flow in the invasive process by contrasting phenotypic and neutral genetic differentiation among native European and invasive North American populations (QST - FST analysis). Our results indicate that invasive and native populations harbor comparable levels of AFLP variation, a pattern consistent with multiple independent introductions from a diverse European gene pool. However, it was observed that the genetic variation reduced during subsequent invasion, perhaps by founder effects and genetic drift. Comparison of genetically-based quantitative trait differentiation (QST) to its expectation under neutrality (FST) revealed no evidence of disruptive selection (QST > FST) or stabilizing selection (QST < FST). One exception was found for only one trait (the number of stems) showing significant sign of stabilizing selection across all populations. It suggests that the difficulties in distinguishing the effects of non-adaptive population processes and natural selection. Multiple introductions of purple loosestrife may have created a genetic mixture from diverse source populations and increased population genetic diversity, but its link to the adaptive differentiation of invasive North American populations needs further research.

AFLP data of Lythrum salicaria

AFLP data of Lythrum salicaria Chun, Young Jin Nason, John Moloney, Kirk

Data from: Inter-population variation in mating system and late-stage inbreeding depression in Magnolia stellata

Data from: Inter-population variation in mating system and late-stage inbreeding depression in Magnolia stellata Tamaki, Ichiro Ishida, Kiyoshi Setsuko, Suzuki Tomaru, Nobuhiro Inbreeding has the potential to cause evolutionary changes in populations, although these changes are likely to drive populations to extinction through inbreeding depression and reductions in genetic diversity. We investigated the mating system and late-stage inbreeding depression (δ) in 10 populations of Magnolia stellata using nine microsatellite markers and evaluated the effects of population size and the degree of population isolation through inbreeding and inbreeding depression on the persistence of populations. The outcrossing rates were very similar (~0.7) among populations, but the correlations of paternity, fractions of biparental inbreeding and inbreeding coefficients at the seed stage (FS) varied among populations, suggesting that the level of outcrossing was similar among populations, while the quality of it was not. A significant negative correlation was detected between FS and population size. The average value of δ was 0.709, and the values in six of the 10 populations were significant. The values of δ differed among populations, although clear relationships with population size and the degree of population isolation were not detected. However, in one population, which was very small and located in the edge of the species' range, we obtained a very low value of δ (-0.096), which may be indicative of purging or the fixation of deleterious alleles. Existing M. stellata populations that are small (and thus might be expected to have higher frequencies of inbreeding) and have large values of δ may be in danger of declining, even if the populations are located within the central region of the species range.

GenotypeData100304.txt

GenotypeData100304.txt Tamaki, Ichiro Ishida, Kiyoshi Setsuko, Suzuki Tomaru, Nobuhiro This data is simple tab delimited text and its line break style is UNIX. It contains 9 microsatellite genotypes of 142 maternal trees and 1216 their seeds. In column headings, pop, family, fruit indicates population code, family and fruit ID, respectively. Fruit ID, whose value is 0, indicates that the individual is the maternal tree of seeds that has the same family ID of it. Lia and Lib indicates first and second alleles of the loci, respectively. Li_oc and Lall_oc indicates the outcrossing status of ith locus and over all loci. For example, if the value of L1_oc is 0 or 1, the status of first locus is selfed or outcrossed, respectively. NA indicates no data.

Data from: Identifying footprints of selection in stocked brown trout populations: a spatio-temporal approach

Data from: Identifying footprints of selection in stocked brown trout populations: a spatio-temporal approach Hansen, Michael Meier, Kristian Mensberg, Karen-Lise Studies of interactions between farmed and wild salmonid fishes have suggested reduced fitness of farmed strains in the wild, but evidence for selection at the genic level is lacking. We studied three brown trout populations in Denmark which have been significantly admixed with stocked hatchery trout (19 to 64%), along with two hatchery strains used for stocking. The wild populations were represented by contemporary samples (2000-2006) and two of them by historical samples (1943-1956). We analyzed 61 microsatellite loci, nine of which showed putative functional relationships (EST-linked or quantitative trait loci). FST based outlier tests provided support for diversifying selection at chromosome regions marked by three loci, two anonymous and one EST-linked. Patterns of differentiation suggested that the loci were candidates for being under diversifying hitch-hiking selection in hatchery versus wild environments. Analysis of hatchery strain admixture proportions showed that in one wild population, two of the loci showed significantly lower admixture proportions than the putatively neutral loci, implying contemporary selection against alleles introduced by hatchery strain trout. In the most strongly admixed population, however, there was no evidence for selection, possibly due to immigration by stocked trout overcoming selection against hatchery-derived alleles or supportive breeding practices allowing hatchery strain trout to escape natural selection. To our knowledge, this is the first study demonstrating footprints of selection in wild salmonid populations subject to spawning intrusion by farmed fish.

Hansen et al 2010 MEC.xlsx

Hansen et al 2010 MEC.xlsx Hansen, Michael Meier, Kristian Mensberg, Karen-Lise Brown trout microsatellite data (61 loci). The data set consists of samples from three wild brown trout populations in Western Jutland, Denmark, along with samples from two hatchery strains used for stocking. The samples of wild trout populations consist of contemporary samples (2000-2006). Moreover, two of the populations are also represented by historical samples from 1943-1956. See Hansen et al. (2010) for further details. The data file is in MSA format [Dieringer D, Schlotterer C (2003) Microsatellite Analyser (msa): a platform independent analysis tool for large microsatellite data sets. Molecular Ecology Notes, 3, 167–169].

Data from: Sixty years of anthropogenic pressure: a spatio-temporal genetic analysis of brown trout populations subject to stocking and population declines

Data from: Sixty years of anthropogenic pressure: a spatio-temporal genetic analysis of brown trout populations subject to stocking and population declines Hansen, Michael Fraser, Dylan Meier, Kristian Mensberg, Karen-Lise Analyses of historical samples can provide invaluable information on changes to the genetic composition of natural populations resulting from human activities. Here, we analyze 21 microsatellite loci in historical (archived scales from 1927-1956) and contemporary samples of brown trout (Salmo trutta) from six neighbouring rivers in Denmark, to compare the genetic structure of wild populations before and after population declines and stocking with non-local strains of hatchery trout. We show that all populations have been strongly affected by stocking, with admixture proportions ranging from 14 to 64%. Historical population genetic structure was characterized by isolation-by-distance and by positive correlations between historical effective population sizes and habitat area within river systems. Contemporary population genetic structure still showed isolation-by-distance, but also reflected differences among populations in hatchery trout admixture proportions. Despite significant changes to the genetic composition within populations over time, dispersal rates among populations were roughly similar before and after stocking. We also assessed whether population declines or introgression by hatchery strain trout should be the most significant conservation concern in this system. Based on theoretical considerations, we argue that population declines have had limited negative effects for the persistence of adaptive variation, but admixture with hatchery trout may have resulted in reduced local adaptation. Collectively, our study demonstrates the usefulness of analyzing historical samples for identifying the most important consequences of human activities on the genetic structure of wild populations.

Brown trout microsatellite data

Brown trout microsatellite data Hansen, Michael Fraser, Dylan Meier, Kristian Mensberg, Karen-Lise The file contains microsatellite data (21 loci) from six wild brown trout populations in Western Jutland, Denmark, along with samples from two hatchery strains used for stocking the rivers. The samples from the wild populations consist of contemporary samples (2000-2006) and historical pre-stocking samples (1927-1956), the latter obtained by analyzing DNA from archived scale samples. See Hansen et al. (2009) for further details on the data and study. The file format is MSA [Dieringer D, Schlotterer C (2003) Microsatellite Analyser (msa): a platform independent analysis tool for large microsatellite data sets. Molecular Ecology Notes, 3, 167–169].

Data from: Elucidating the role of genetic drift and directional natural selection in genetic differentiation of cork oak (Quercus suber L.)

Data from: Elucidating the role of genetic drift and directional natural selection in genetic differentiation of cork oak (Quercus suber L.) Ramírez-Valiente, José Alberto Lorenzo, Zaida Soto, Álvaro Valladares, Fernando Gil, Luis Aranda, Ismael Drought is the main selection agent in Mediterranean ecosystems and it is been suggested as an important evolutionary force responsible for population diversification in these environments. However, population divergence in quantitative traits can be driven by either directional natural selection, genetic drift or both. To investigate the roles of these forces on among-population divergence in ecophysiological traits related to drought tolerance (Δ13C, SLA, leaf size, Nmass), we compared molecular and quantitative genetic differentiation among thirteen cork oak (Quercus suber L.) populations spanning over a gradient of rainfall and temperature. Population differentiation for height, specific leaf area and leaf nitrogen content far exceeded the molecular differentiation measured by six nuclear microsatellites and was associated with the climatic gradient in among-year rainfall variation. These results suggest (1) these traits are subjected to directional selection and (2) the genetic differences among populations are partly due to adaptation to the rainfall unpredictability at the place of origin. By contrast, the low among population divergence found in stem diameter, annual growth and carbon isotopic discrimination (a surrogate for water use efficiency) and the weak association with the environmental gradient suggest low or no directional selection on these traits under dry conditions. Among-population differentiation for neutral markers was not a good predictor for differentiation regarding the quantitative traits studied here, but for leaf size. The observed correlation between the genetic differentiation for leaf size and that for molecular markers was exclusively due to the association between leaf size and microsatellite QpZAG46, which suggests a possible linkage between microsatellite QpZAG46 and genes encoding for leaf size.

Data from: Spatial genetic structure in continuous and fragmented populations of Pinus pinaster Aiton

Data from: Spatial genetic structure in continuous and fragmented populations of Pinus pinaster Aiton de-Lucas, Ana González-Martínez, Santiago Vendramin, Giovanni G Hidalgo, Elena Heuertz, Myriam Habitat fragmentation, i.e., the reduction of populations into small isolated remnants, is expected to increase spatial genetic structure (SGS) in plant populations through non-random mating, lower population densities and potential aggregation of reproductive individuals. We investigated the effects of population size reduction and genetic isolation on SGS in maritime pine (Pinus pinaster Aiton) using a combined experimental and simulation approach. Maritime pine is a wind-pollinated conifer which has a scattered distribution in the Iberian Peninsula due to forest fires and habitat fragmentation. Five highly polymorphic nuclear microsatellites were genotyped in a total of 394 individuals from two population pairs from the Iberian Peninsula, formed by one continuous and one fragmented population each. In agreement with predictions, SGS was significant and stronger in fragments (Sp=0.020 and Sp=0.026) than in continuous populations, where significant SGS was detected for one population only (Sp=0.010). Simulations suggested that under fat-tailed dispersal, small population size is a stronger determinant of SGS than genetic isolation, while under normal dispersal, genetic isolation has a stronger effect. SGS was always stronger in real populations than in simulations, except if unrealistically narrow dispersal and/or high variance of reproductive success were modelled (even when accounting for potential overestimation of SGS in real populations due to short-distance sampling). This suggests that factors such as non-random mating or selection not considered in the simulations were additionally operating on SGS in Iberian maritime pine populations.

Microsatellite genotypes for Pinus pinaster. Spatial genetic structure in Spain

Microsatellite genotypes for Pinus pinaster. Spatial genetic structure in Spain de-Lucas, Ana González-Martínez, Santiago Vendramin, Giovanni G Hidalgo, Elena Heuertz, Myriam

Data from: Allopatric origin of cryptic butterfly species that were discovered feeding on distinct host plants in sympatry

Data from: Allopatric origin of cryptic butterfly species that were discovered feeding on distinct host plants in sympatry McBride, Carolyn van Velzen, Robin Larsen, Torben Surveys of tropical insects are increasingly uncovering cryptic species - morphologically similar yet reproductively isolated taxa once thought to comprise a single interbreeding entity. The vast majority of such species are described from a single location. This leaves us with little information on geographic range and intraspecific variation and limits our ability to infer the forces responsible for generating such diversity. For example, in herbivorous and parasitic insects, multiple specialists are often discovered within what were thought to be single more generalized species. Host shifts are likely to have contributed to speciation in these cases. But when and where did those shifts occur, and were they facilitated by geographic isolation? We attempted to answer these questions for two cryptic species within the butterfly Cymothoe egesta that were recently discovered on different host plants in central Cameroon. We first used mtDNA markers to separate individuals collected on the two hosts within Cameroon and then extended our analysis to incorporate individuals collected across the entire pan-Afrotropical range of the original taxon. To our surprise, we found that the species are almost entirely allopatric, dividing the original range and overlapping only in the narrow zone of West-Central Africa where they were first discovered in sympatry. This finding, combined with analyses of genetic variation within each butterfly species, strongly suggests that speciation occurred in allopatry, probably during the Pleistocene. We discuss the implications of our results for understanding speciation among other cryptic species recently discovered in the tropics and argue that more work is needed on geographic patterns and host usage in such taxa.

C.egesta_alignment_4Dryad.nex

C.egesta_alignment_4Dryad.nex McBride, Carolyn van Velzen, Robin Larsen, Torben Alignment file used for phylogenetic and population genetic analyses on "phylogenetic" dataset described in the article.

Data from: Dispersal to or from an African biodiversity hotspot?

Data from: Dispersal to or from an African biodiversity hotspot? Blackburn, David Measey, John Biodiversity hotspots are centers of endemism and thus contain many range-restricted species. In addition, within these hotspots are often widespread species that might have originated within a hotspot before dispersing to neighboring or distant regions. We test this hypothesis through a phylogeographic analysis of a miniature leaf litter frog, Arthroleptis xenodactyloides, that has a large distribution throughout the Eastern Arc, a biodiversity hotspot, and other regions in East Africa. Maximum likelihood and Bayesian estimates of the mitochondrial gene phylogeny are used as a proxy for understanding the evolutionary history of diversification and the historical relationships between populations. The north-south range of this species extends for approximately 1900 km; our sampling covers approximately 85% of this range. Using phylogenetic comparative methods, we estimate the region of origin and direction of dispersal within A. xenodactyloides. We compare contrasting hypotheses of latitudinal range expansion using bayes factors. The ancestral region of origin of A. xenodactyloides is reconstructed as having occurred within the Eastern Arc before dispersing southwards into the Southern Rift mountains, probably in the Pleistocene. The phylogeographic structure within this leaf litter frog is surprisingly similar to that of forest birds, revealing that similar geographic features might have had a driving role in diversification of these very dissimilar taxa. Latitudinal expansion occurred early in the evolutionary history of A. xenodactyloides and may indicate that physiological adaptation facilitated its wide geographic distribution.

Aligned DNA sequences of Arthroleptis xenodactyloides

Aligned DNA sequences of Arthroleptis xenodactyloides Blackburn, David C Measey, G. John A nexus file containing aligned mitochondrial DNA sequences of Arthroleptis xenodactyloides and related species. Sequences aligned using ClustalX and then trimmed.

Data from: Mitochondrial and microsatellite DNA markers reveal a Balkanic origin for the highly invasive Horse-Chestnut leaf miner Cameraria ohridella (Lepidoptera, Gracillariidae)

Data from: Mitochondrial and microsatellite DNA markers reveal a Balkanic origin for the highly invasive Horse-Chestnut leaf miner Cameraria ohridella (Lepidoptera, Gracillariidae) Valade, Romain Kenis, Marc Hernandez-Lopez, Antonio Augustin, Sylvie Mena, Neus Mari Magnoux, Emmanuelle Rougerie, Rodolphe Lakatos, Ferenc Roques, Alain Lopez-Vaamonde, Carlos Biological invasions usually start with a small number of founder individuals. These founders are likely to represent a small fraction of the total genetic diversity found in the source population. Our study set out to trace genetically the geographical origin of the horse-chestnut leafminer, Cameraria ohridella, an invasive microlepidopteran whose area of origin is still unkown. Since its discovery in Macedonia twenty years ago, this insect has experienced an explosive westward range expansion, progressively colonizing all of Central and Western Europe. We used cytochrome oxidase I sequences (DNA barcode fragment) and a set of six polymorphic microsatellites to assess the genetic variability of C. ohridella populations, and to test the hypothesis that C. ohridella derives from the southern Balkans (Albania, Macedonia and Greece). Analysis of mtDNA of 486 individuals from 88 localities allowed us to identify 25 geographically structured haplotypes. In addition, 480 individuals from 16 populations from Europe and the southern Balkans were genotyped for 6 polymorphic microsatellite loci. High haplotype diversity and low measures of nucleotide diversities including a significantly negative Tajima's D indicate that C. ohridella has experienced rapid population expansion during its dispersal across Europe. Both mtDNA and microsatellites show a reduction in genetic diversity of C. ohridella populations sampled from artificial habitats (e.g. planted trees in public parks, gardens, along roads in urban or sub-urban areas) across Europe compared to C. ohridella sampled in natural stands of horse-chestnuts in the southern Balkans. These findings suggest that European populations of C. ohridella may indeed derive from the southern Balkans.

Data from: Mating system variability in a mouthbrooding cichlid fish from a tropical lake

Data from: Mating system variability in a mouthbrooding cichlid fish from a tropical lake Sefc, Kristina Hermann, Caroline Koblmuller, S. Intraspecific variability in mating behavior and disparities between social and reproductive behavior add complexity to the description of animal mating systems. A previously published field study on a population of the maternally mouthbrooding cichlid fish Ctenochromis horei in the north of Lake Tanganyika suggested mate monopolization by the most dominant male. In the present study, genetic reconstructions of paternity in a population in the south of the lake provided no evidence for male mate monopolization, as none of the inferred sires had offspring in more than one brood. The ability to reconstruct sire genotypes from offspring alleles was confirmed by computer simulations. Multiple paternity occurred in several broods and was significantly more frequent in the sample taken in the rainy season than in the dry season sample (100% of broods versus 12.5%, respectively; p = 0.0014). The data suggest geographic and temporal variation in the mating behavior of C. horei despite its continuous year-round reproduction, invariable brood care behavior and habitat-specific distribution in the relatively constant and confined environment of a tropical lake. Moreover, our data show that inferences on the distribution of male reproductive success, if based on each geographical or temporal data set alone, would fail to describe the potential for sexual selection in this species.

microsatellite alleles sizes of mothers and brood, and of the population sample.xls

microsatellite alleles sizes of mothers and brood, and of the population sample.xls Sefc, Kristina Hermann, Caroline Koblmuller, S. The table contains microsatellite allele sizes of mothers and their broods, and of the population sample. The data were used to reconstruct the number of sires per brood. Offspring sample IDs are prefixed by a 'C'.

Data from: Amphibian chytridiomycosis in Japan: distribution, haplotypes, and possible entry into Japan

Data from: Amphibian chytridiomycosis in Japan: distribution, haplotypes, and possible entry into Japan Goka, Koichi Yokoyama, Jun Une, Yumi Kuroki, Toshiro Suzuki, Kazutaka Nakahara, Miri Kobayashi, Arei Inaba, Shigeki Mizutani, Tomoo Hyatt, Alex A serious disease of amphibians caused by the chytrid fungus Batrachochytrium dendrobatidis was first found in Japan in December 2006 in imported pet frogs. This was the first report of chytridiomycosis in Asia. To assess the risk of pandemic chytridiomycosis to Japanese frogs, we surveyed the distribution of the fungus among captive and wild frog populations. We established a nested PCR assay that uses two pairs of PCR primers to amplify the internal transcribed spacer (ITS) region of a ribosomal RNA cassette to detect mild fungal infections from as little as 0.001 pg (1 fg) of B. dendrobatidis DNA. We collected swab samples from 265 amphibians sold at pet shops, 294 bred at institutes, and 2,103 collected at field sites from northern to southwestern Japan. We detected infections in native and exotic species, both in captivity and in the field. Sequencing of PCR products revealed 26 haplotypes of the B. dendrobatidis ITS region. Phylogenetic analysis showed that 3 of these haplotypes were specific to the Japanese giant salamander (Andrias japonicus) and appeared to have established a commensal relationship with this native amphibian. Many other haplotypes were carried by alien amphibians. The highest genetic diversity of B. dendrobatidis was found in the American bullfrog (Rana catesbeiana). Some strains of B. dendrobatidis appeared to be endemic to Japanese native amphibians, but many alien strains are being introduced into Japan via imported amphibians. To improve chytridiomycosis risk management, we must consider the risk of B. dendrobatidis changing hosts as a result of anthropogenic disturbance of the host-specific distribution of the fungus.

Data from: Temporal variation in the genetic structure of a drone congregation area: An insight into the population dynamics of wild African honeybees (Apis mellifera scutellata)

Data from: Temporal variation in the genetic structure of a drone congregation area: An insight into the population dynamics of wild African honeybees (Apis mellifera scutellata) Jaffe, Rodolfo Dietemann, Vincent Crewe, Robin Moritz, Robin The mating system of the honeybee (Apis mellifera) has been regarded as one of the most panmictic in the animal kingdom, with thousands of males aggregating in drone congregation areas (DCAs) that virgin queens visit to mate with tens of partners. Although males from many colonies gather at such congregations, the temporal changes in the colonies contributing drones remain unknown. Yet, changes in the DCAs' genetic structure will ultimately determine population gene flow and effective population size. By repeatedly sampling drones from an African DCA over a period of three years, we studied the temporal changes in the genetic structure of a wild honeybee population. Using three sets of tightly linked microsatellite markers, we were able to reconstruct individual queen genotypes with a high accuracy, follow them through time and estimate their rate of replacement. The number of queens contributing drones to the DCA varied from 12 to 72 and was correlated with temperature and rainfall. We found that more than 80% of these queens were replaced by mostly unrelated ones in successive eight months sampling intervals, which resulted in a clear temporal genetic differentiation of the DCA. Our results suggest that the frequent long range migration of colonies without nest-site fidelity is the main driver of this high queen turnover. DCAs of African honeybees should thus be regarded as extremely dynamic systems which together with migration boost the effective population size and maintain a high genetic diversity in the population.

Table S2

Table S2 Jaffe, Rodolfo Dietemann, Vincent Crewe, Robin Moritz, Robin Arlequin input file containing the multilocus genotype of 510 Apis mellifera scutellata drones collected at a single DCA over a period of 3 years. The 12 loci employed for genotyping are shown in the first line. The collection date of each sample is given as Ma, No, Ap, Se and De, referring to March 2004, November 2004, April 2007, September 2007 and December 2007, respectively.

Table S1

Table S1 Jaffe, Rodolfo Dietemann, Vincent Crewe, Robin Moritz, Robin

Fig. S1

Fig. S1 Jaffe, Rodolfo Dietemann, Vincent Crewe, Robin Moritz, Robin

Data from: Climatic stability and genetic divergence in the tropical insular lizard Anolis krugi, the Puerto Rican "Lagartijo Jardinero de la Montaña"

Data from: Climatic stability and genetic divergence in the tropical insular lizard Anolis krugi, the Puerto Rican "Lagartijo Jardinero de la Montaña" Rodríguez, Javier Jezkova, Tereza Leal, Manuel Two factors that can lead to geographic structuring in conspecific populations are barriers to dispersal and climatic stability. Populations that occur in different physiographic regions may be restricted to those areas by physical and/or ecological barriers, which may facilitate the formation of phylogeographic clades. Long-term climatic stability can also promote genetic diversification, because new clades are likely to evolve in areas that experience lesser climatic shifts. We conducted a phylogeographic study of the Puerto Rican lizard Anolis krugi to assess whether populations of this anole show genetic discontinuities across the species' range, and if they do, whether these breaks coincide with the boundaries of the five physiographic regions of Puerto Rico. We also assessed whether interpopulation genetic distances in A. krugi are positively correlated with relative climatic stability in the island. Anolis krugi exhibits genetic structuring, but the phylogroups do not correspond to the physiographic regions of Puerto Rico. We used climatic reconstructions of two environmental extremes of the Quaternary period, the present conditions and those during the last glacial maximum, to quantify the degree of climatic stability between sampling locations. We documented positive correlations between genetic distances and relative climatic stability, although these associations were not significant when corrected for autocorrelation. The approach that we employed to assess the relationship between climatic stability and the genetic architecture of A. krugi can also be used to investigate the impact of factors such as the spatial distribution of food sources, parasites, predators or competitors on the genetic landscape of a species.