A Genetic Assessment of Ecological Restoration Success in Banksia attenuata

Rarely assessed in the success of ecological restoration projects is the maintenance of genetic variation in restored populations and, critically, their offspring. A founding population sourced from a limited genetic pool of nonlocal provenance seed can result in genetic bottlenecking and inbreeding, potentially reducing future population resilience and restoration success. We used microsatellite markers to assess the genetic variation of natural and restored populations, and their offspring, in Banksia attenuata R.Br. (Proteaceae), a keystone species of Banksia woodlands in south‐west Australia. Both natural and restored populations, and their offspring, displayed similarly high levels of heterozygosity (H_e range = 0.57–0.62) and allelic diversity (N_e range = 6.67–8.86) across 7 microsatellite loci. There was very weak population divergence (F_ST = 0.006) between the restored population and the adjacent natural population, indicating local provenance sourcing of seed. Genetic structuring within the natural population was weak, but detectable at 10 m and more strongly genetically structured than the restored population (Sp = 0.006 and 0.002, respectively). Complete outcrossing, low‐correlated paternity, and very low bi‐parental inbreeding were observed in both populations. Extensive pollen dispersal was observed within and among populations, with >50% of paternity assigned to sires beyond the local population. In a greenhouse experiment, differences in the overall performance of seedlings from natural and restored populations were negligible. Results indicate the successful genetic management of B. attenuata in this restoration project, from which general principles emphasizing the use of diverse local provenance seeds, genetic integration, and delivery of pollinator services are supported.     

Possible effects of interprotein variation in mean rate of amino acid substitution on the relationship of genetic distance with time since evolutionary divergence

Published data on mean rates of genetic divergence for a substantial number of protein molecules is used to examine the hypothetical effect of variations in these rates upon the expected relationship between evolutionary time and Nei's (1972, American Naturalist, 106: 283) genetic distance, D. Results indicate that at higher values D can be expected to deviate significantly from stochastic linearity with time. However, over the sort of time scale over which D values are normally estimated, deviation is slight and likely to be insignificant when compared to other potential sources of error. It is concluded that for most practical purposes interprotein differences in mean rates of amino acid substitution need not be taken into account when calibrating genetic distance estimates against evolutionary time.     

Contrasting patterns of morphological and neutral genetic divergence among geographically proximate populations of sockeye salmon Oncorhynchus nerka in Lake Aleknagik,Alaska

Levels of differentiation in morphological traits (age at maturity, body length at age, egg mass and body depth) and spawning time were examined in sockeye salmon Oncorhynchus nerka from three geographically proximate but physically distinct creeks in Lake Aleknagik, Alaska. Happy Creek fish had significantly greater values for most measured morphological traits, and Eagle Creek fish spawned significantly later than fish in the other creeks. Phenotypic differentiation between creeks, measured as P_ST, was then compared with microsatellite marker differentiation between creeks, measured as F_ST. No correlations were apparent between P_ST and F_ST values, and P_ST values were generally significantly larger than zero (P_ST= 0·0018–0·31) whereas F_ST values were not (F_ST=?0·0004 to 0·0016). The insignificant pair‐wise F_ST values between creek samples indicated that gene flow occurs between creeks, assuming the creek populations have reached migration–drift equilibrium. However, the strong homing behaviour of sockeye salmon precludes a scenario in which fish from the three creeks constitute a single population that segregates by body size. Rather, significant phenotypic differentiation suggests that strong divergent selection occurs on the phenotypic traits despite the homogenizing effects of gene flow.     

Ecological and life history characteristics predict population genetic divergence of two salmonids in the same landscape

Ecological and life history characteristics such as population size, dispersal pattern, and mating system mediate the influence of genetic drift and gene flow on population subdivision. Bull trout (Salvelinus confluentus) and mountain whitefish (Prosopium williamsoni) differ markedly in spawning location, population size and mating system. Based on these differences, we predicted that bull trout would have reduced genetic variation within and greater differentiation among populations compared with mountain whitefish. To test this hypothesis, we used microsatellite markers to determine patterns of genetic divergence for each species in the Clark Fork River, Montana, USA. As predicted, bull trout had a much greater proportion of genetic variation partitioned among populations than mountain whitefish. Among all sites, FST was seven times greater for bull trout (FST = 0.304 for bull trout, 0.042 for mountain whitefish. After removing genetically differentiated high mountain lake sites for each species FST, was 10 times greater for bull trout (FST = 0.176 for bull trout; FST = 0.018 for mountain whitefish). The same characteristics that affect dispersal patterns in these species also lead to predictions about the amount and scale of adaptive divergence among populations. We provide a theoretical framework that incorporates variation in ecological and life history factors, neutral divergence, and adaptive divergence to interpret how neutral and adaptive divergence might be correlates of ecological and life history factors.     

Isolation and characterization of two different 5S rDNA in Anguilla anguilla and in Anguilla rostrata: possible markers of evolutionary divergence

We cloned and sequenced the HaeIII 350‐bp 5S ribosomal DNA (rDNA) band of Anguilla rostrata and designed specific primers from this sequence. Polymerase chain reaction performed with these primers is able to distinguish DNA samples obtained from European (Anguilla anguilla) and American (Anguilla rostrata) eels. Two amplicons of 1200 bp and 600 bp were obtained, respectively, from A. rostrata and A. anguilla, and the whole 5S rDNA repeated unit from these eels was cloned and sequenced. Southern blot experiments, using four different restriction enzymes and the 5S nontranscribed spacers regions as probe, are able to point out specific diversity in these eels.     

Genetic divergence without spatial isolation in polecat Mustela putorius populations

Understanding how genetic divergence could exist without spatial isolation is a fundamental issue in biology. Although carnivores have previously been considered as having a weak genetic variability, polecats Mustela putorius from eight distinct populations exhibited both a strong polymorphism (17.5–22.5%) and a substantial allele effective number reaching N_e=1.12. Heterozygosity ranging from H_o=0.031–0.063 significantly differed among populations, while the mean F_IS averaging 0.388 stressed a real deficiency of heterozygotes. Observed heterozygosity levels among populations did not correlate with any habitat types but were clearly associated with habitat diversity index. The habitat structure in polecat home range corresponded to habitat mosaic structure in which discrete habitat types alternated causing multifactorial constraints that may favour heterozygosity. Allozymic frequencies within populations did not vary with dominant habitat. But in the Tyrosinase‐1, the rare homozygote BB, resulting in a ‘dark’ phenotype, was found much more in deciduous woods than the homozygote AA showing the ‘typical’ pattern. Thus, the genetic basis for a character differentiation was here evidenced in a remarkable situation without spatial isolation. Further, the very low proportion of heterozygotes for this locus suggests a disruptive effect and supports the prediction of intermediate phenotypes being at a disadvantage. This heterozygote deficit may also result from an assortative mating intra phenotype (homogamy). The divergence in polecat phenotypes showed that genetic differentiation can be induced by subtle variations in environment, a situation that is likely to be frequent in most natural populations, and emphasized the adaptive nature of habitat preference.     

Evolutionary divergence of ribosomal internal transcribed spacer 2 in lizards

Internal transcribed spacers 1 and 2 (ITS1 and ITS2) are known to play an important role in rRNA maturation, yet the mechanism of their action is still not completely understood. Comparison of the ITS1 and ITS2 nucleotide sequences for various organisms reveals conserved regions, which are potentially involved in rRNA biogenesis, and yields new information about the evolutionary divergence of the corresponding region of the genome. The rDNA fragments containing ITS2 were amplified, cloned, and sequenced for three lizard species: Darevskia armeniaca, Lacerta strigata (Lacertidae), and Agama caucasia (Agamidae). The lizard ITS2 sequences were compared with their counterparts from other organisms and proved to contain not only universally conserved elements characteristic of the consensus secondary structure of vertebrate ITS2, but also lizard-specific regions. Comparison of the ITS2 size and the distribution of homologous regions for the two lizard families made it possible to assume that evolution of the modern species involved duplication of ITS2 in the genome of their common ancestor.     

丹霞梧桐群体遗传结构及其遗传分化

丹霞梧桐(Firmiana danxiaensis)是分布于我国韶关地区北部丹霞地貌的特有物种, 其分布范围狭窄, 种群数量小。本文利用EST-SSR分子标记位点, 分析丹霞梧桐群体(丹霞山组群和南雄组群)的遗传多样性和遗传结构, 研究群体的分化历史, 探讨该物种的可能分布和科学保护策略。结果表明: 丹霞梧桐总的遗传多样性中等(Ht = 0.631), 群体内遗传多样性较高(Hs = 0.546), 遗传变异主要存在于群体内(79.66%), 但不同地理组群间存在显著的遗传分化(F_ST = 0.150)。长期地理隔离和现代人为干扰是形成丹霞梧桐当前遗传变异模式的主要原因。STRUCTURE分析可将研究群体划分为清晰的两个基因库(gene pool), 其遗传结构与系统发育地理格局之间有密切关系。丹霞梧桐不同地理群体经历了独立的进化路线, 但丹霞山群体的杂合性高, 遗传背景更为复杂。近似贝叶斯运算法(Approximate Bayesian Computation, ABC)分析表明, 丹霞山和南雄地理群体在10万年前由同一个祖先群体分化而来, 分化时有效群体大小分别为7,290和5,550。结合丹霞梧桐的遗传变异和生态位信息, 可推测丹霞梧桐曾广泛分布于南岭地区, 受第四纪第三次亚冰期的影响, 南岭北部的丹霞梧桐群体因气候剧烈变化而灭绝, 仅在南岭南部适宜的环境中得以保存并繁衍至今, 丹霞山和南雄是丹霞梧桐最主要的两个冰期避难所。在全面掌握丹霞梧桐的自然分布, 开展就地保护的基础上, 通过建立种质资源圃、人工种苗扩繁、自然回归试验等措施, 对于该物种的异地保护、种群恢复和开发利用具有重要意义。     

Interpopulation variation in predator foraging behaviour promotes the evolutionary divergence of prey

Despite intensive investigation of the role of predation on evolutionary processes, few studies have questioned the possibility of the evolutionary divergence of prey populations in response to interpopulation variation in predator foraging behaviour. In an interaction between a seed-predatory insect, the camellia weevil (Curculio camelliae), and its host plant, the Japanese camellia (Camellia japonica), I tested whether the evolutionary differentiation of the plant's defensive trait, pericarp thickness, was related to the interpopulation variation in the foraging behaviour of female weevils. I found that the preference of weevils for the plant fruit based on pericarp thickness varied across 13 populations in Japan. Importantly, variation in weevil behaviour explained interpopulation variation in pericarp thickness and the direction/strength of natural selection on the trait. Overall, I show that adaptive foraging of predators can result in the evolutionary divergence of predator-prey interactions.     

The role of habitat choice in micro‐evolutionary dynamics: An experimental study on the Mediterranean killifish Aphanius fasciatus (Cyprinodontidae)

Habitat choice is defined as a nonrandom distribution of genotypes in different microhabitats. Therefore, it could exert a great impact on the genetic variance of natural populations by promoting genetic divergence, local adaptation, and may even lead to sympatric speciation. Despite this potential role in micro‐ and macro‐evolutionary processes, there is little empirical evidence that the various genotypes within a population may differ in habitat choice‐related behaviors. Here, we tested whether habitat choice may have contributed to genetic divergence within a local population of the Mediterranean killifish Aphanius fasciatus, which emerged between groups inhabiting microhabitats with different oxygen concentrations during previous field studies. In a first experiment, we studied the distribution of individuals in conditions of hypoxia and normoxia to test whether they had a different ability to shy away from a hypoxic environment; in a second experiment, we analyzed the individual behavior of fish separately in the two conditions, to verify whether they showed peculiar behavioral responses linked to a possible differential distribution. We then analyzed the six allozyme loci, whose allelic and genotypic frequencies were significantly divergent in the previous studies. In the first test, we found that the distribution of the two homozygote genotypes of the glucose‐6‐phosphate isomerase‐1 locus (GPI‐1) was significantly different between the hypoxic and the normoxic conditions. During the second test, all individuals were more active in hypoxic conditions, but the two GPI‐1 homozygotes showed a significant difference in time spent performing surface breathing, which was consistent with their distribution observed in the first experiment. These results provide evidence that individual behavioral traits, related to genetic features, may lead to a nonrandom distribution of genotypes in heterogeneous although contiguous microhabitats and, consequently, that habitat choice can play a significant role in driving the micro‐evolutionary dynamics of this species.     

Isolation by adaptation in Neochlamisus leaf beetles: host-related selection promotes neutral genomic divergence

This study tests how divergent natural selection promotes genomic differentiation during ecological speciation. Specifically, we use adaptive ecological divergence (here, population divergence in host plant use and preference) as a proxy for selection strength and evaluate the correlation between levels of adaptive and genetic differentiation across pairwise population comparisons. Positive correlations would reveal the pattern predicted by our hypothesis, that of 'isolation by adaptation' (IBA). Notably, IBA is predicted not only for selected loci but also for neutral loci. This may reflect the effects of divergent selection on neutral loci that are 'loosely linked' to divergently selected loci or on geneflow restriction that facilitates genetic drift at all loci, including neutral loci that are completely unlinked to those evolving under divergent selection. Here, we evaluate IBA in maple- and willow-associated populations of Neochlamisus bebbianae leaf beetles. To do so, we collected host preference data to construct adaptive divergence indices and used AFLPs (amplified fragment length polymorphisms) and mitochondrial sequences to quantify genetic differentiation. Partial Mantel tests showed significant IBA in 'pooled' analyses of putatively neutral and of putatively selected ('outlier') AFLP loci. This pattern was also recovered in 12% of 'locus-specific' analyses that separately evaluated genetic differentiation at individual neutral loci. These results provided evidence for widespread effects of selection on neutral genomic divergence. Our collective findings indicate that host-related selection may play important roles in the population genomic differentiation of both neutral and selected gene regions in herbivorous insects.     

双子叶植物幼苗类型及其可能的演化关系

根据幼苗形态特征,把双子叶植物幼苗划分为18个类型9个亚型,用图解释了幼苗类型之间的进化关系。双子叶植物幼苗类型进化的主线是:暗罗型（子叶具吸收功能,留土）→紫玉盘型（子叶具吸收功能,留于种壳中,下胚轴伸长）→木兰型（子叶具吸收兼光合功能）→蜡梅型（子叶具光合功能）→樱型（子叶具光合兼贮藏功能）→樟型（子叶具贮藏功能）,其他类型或亚型则为进化的旁支或盲支。根据幼苗类型来判断,现存被子植物最古老的科应为番荔枝科。     

Genetic diversity within and among two Argentinean and one Mexican species of Acacia (Fabaceae)

Acacia is a pantropical genus comprising > 1450 species. Following Vassal's treatment Acacia is considered as a single genus with three subgenera (Acacia, Aculeiferum and Phyllodineae). Acacia caven, A. curvifructa and A. farnesiana belong to subgenus Acacia and the relationship between them is controversial. The aim of this study was to elucidate the relationship between the three species using amplified fragment length polymorphism, analysing 15 populations of these species, and to compare the results obtained with those from a morphological analysis. Genetic diversity indices (percentage of polymorphic loci, genetic diversity) showed that genetic variation in A. caven is higher than that in A. curvifructa and A. farnesiana. Of the total genetic diversity in A. caven and A. farnesiana, most is found within populations (∼70%). Analysis with STRUCTURE showed that the optimal number of clusters (K) was ten, and in all cases where populations were grouped they were geographically close and/or belong to the same variety. The morphological canonical discriminant analysis did not result in a separation between all individuals, indicating that they do not harbour consistent morphological discontinuities. Altogether, the results of our molecular analyses showed the existence of significant differences between A. caven, A. curvifructa and A. farnesiana, which argues for recognizing them as different species. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 177 , 593–606.     

The Baldwin effect and genetic assimilation: revisiting two mechanisms of evolutionary change mediated by phenotypic plasticity

Two different, but related, evolutionary theories pertaining to phenotypic plasticity were proposed by James Mark Baldwin and Conrad Hal Waddington. Unfortunately, these theories are often confused with one another. Baldwin's notion of organic selection posits that plasticity influences whether an individual will survive in a new environment, thus dictating the course of future evolution. Heritable variations can then be selected upon to direct phenotypic evolution (i.e., "orthoplasy"). The combination of these two processes (organic selection and orthoplasy) is now commonly referred to as the "Baldwin effect." Alternately, Waddington's genetic assimilation is a process whereby an environmentally induced phenotype, or "acquired character," becomes canalized through selection acting upon the developmental system. Genetic accommodation is a modern term used to describe the process of heritable changes that occur in response to a novel induction. Genetic accommodation is a key component of the Baldwin effect, and genetic assimilation is a type of genetic accommodation. I here define both the Baldwin effect and genetic assimilation in terms of genetic accommodation, describe cases in which either should occur in nature, and propose that each could play a role in evolutionary diversification.     

Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis)

The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction‐site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small N_e (range = 2.1–89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome‐wide divergence. Nonetheless, outlier tests identified 3.6–6.6% of loci as high F_ST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high F_ST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small N_e in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential.     

Vicariance divergence and gene flow among islet populations of an endemic lizard

Allopatry and allopatric speciation can arise through two different mechanisms: vicariance or colonization through dispersal. Distinguishing between these different allopatric mechanisms is difficult and one of the major challenges in biogeographical research. Here, we address whether allopatric isolation in an endemic island lizard is the result of vicariance or dispersal. We estimated the amount and direction of gene flow during the divergence of isolated islet populations and subspecies of the endemic Skyros wall lizard Podarcis gaigeae, a phenotypically variable species that inhabits a major island and small islets in the Greek archipelago. We applied isolation-with-migration models to estimate population divergence times, population sizes and gene flow between islet-mainland population pairs. Divergence times were significantly correlated with independently estimated geological divergence times. This correlation strongly supports a vicariance scenario where islet populations have sequentially become isolated from the major island. We did not find evidence for significant gene flow within P. g. gaigeae. However, gene-flow estimates from the islet to the mainland populations were positively affected by islet area and negatively by distance between the islet and mainland. We also found evidence for gene flow from one subspecies (P. g. weigandi) into another (P. g. gaigeae), but not in the other direction. Ongoing gene flow between the subspecies suggests that even in this geographically allopatric scenario with the sea posing a strong barrier to dispersal, divergence with some gene flow is still feasible.     

Molecular phylogenies and divergence times of sea urchin species of Strongylocentrotidae,Echinoida

Sea urchins of the family Strongylocentrotidae have been important model systems in many fields of basic biology, yet knowledge of their evolutionary identities such as the phylogenetic relationships and divergence times remains limited. Here, I inferred molecular phylogenies of seven Strongylocentrotid species (Strongylocentrotus franciscanus, S. nudus, S. purpuratus, S. intermedius, S. droebachiensis, S. pallidus, and Hemicentrotus pulcherrimus) from the analyses of mitochondrial DNA sequences of 12SrDNA (349 nt), 12SrDNA-tRNA(gln) region (862 nt), and a combined sequence of cytochrome oxidase subunit I (COI, 1080 nt) and NADH dehydrogenase subunit I (NDI, 742 nt). The rate of sequence evolution and divergence times for each species were then estimated from the trees with reference to the time of separation between Strongylocentrotidae and Parechinidae, 35 to 50 MYA. The three trees agree well with each other, and the phylogeny is summarized by ((S. franciscanus, S. nudus), (H. pulcherrimus (S. purpuratus, S. intermedius (S. droebachiensis, S. pallidus)))). It is notable that the genus Strongylocentrotus consists of two distinct clades and that H. pulcherrimus branches off within Strongylocentrotus, implying assignment of a separate, monospecific genus to this species inappropriate. The rate of sequence evolution is calibrated to be 0.24%-0.34%/Myr in 12SrDNA, 0.25%-0.36%/Myr in 12SrDNA-tRNA(gln), and 0.65%-0.93%/Myr in COI-NDI combined sequences. S. purpuratus, in particular, shows the significantly higher rate of evolution in the 12SrDNA and 12SrDNA-tRNA(gln) regions compared to other species, suggesting careful use of its sequences in comparative studies. The two clades of Strongylocentrotidae seem to have split 13-19 MYA, and H. pulcherrimus branched off 7.2-14 MYA. In the former clade, S. franciscanus and S. nudus separated 5.7-8.1 MYA. In the latter clade, S. purpuratus, S. intermedius, and the clade of S. droebachiensis and S. pallidus diverged approximately 4.6-12 MYA, and the last two closest species separated 2.1-3.1 MYA.