Latitudinal variation in genetic divergence of populations and the potential for future speciation

The increase in biological diversity with decreasing latitude is widely appreciated but the cause of the pattern is unknown. This pattern reflects latitudinal variation in both the origin of new species (cladogenesis) and the number of species that coexist. Here we address latitudinal variation in species origination, by examining population genetic processes that influence speciation. Previous data suggest a greater number of speciation events at lower latitudes. If speciation events occur more frequently at lower latitudes, we predicted that genetic divergence among populations within species, an important component of cladogenesis, should be greater among lower latitude populations. We tested this prediction using within-species patterns of mtDNA variation across 60 vertebrate species that collectively spanned six continents, two oceans, and 119 degrees latitude. We found greater genetic divergence of populations, controlling for geographic distance, at lower latitudes within species. This pattern remained statistically significant after removing populations that occur in localities previously covered by continental glaciers during the last glaciation. Results suggest that lower latitude populations within species exhibit greater evolutionary independence, increasing the likelihood that mutation, recombination, selection, and/or drift will lead to divergence of traits important for reproductive isolation and speciation. Results are consistent with a greater influence of seasonality, reduced energy, and/or glacial (Milankovitch) cycles acting on higher latitude populations, and represent one of the few tests of predictions of latitudinal variation in speciation rates using population genetic data.     

Evolution of temporal isolation in the wild: genetic divergence in timing of migration and breeding by introduced chinook salmon populations

Abstract. The timing of migration and breeding are key life-history traits; they are not only adaptations of populations to their environments, but can serve to increase reproductive isolation, facilitating further divergence among populations. As part of a study of divergence of chinook salmon, Oncorhynchus tshawytscha , populations, established in New Zealand from a common source in the early 1900s, we tested the hypotheses that the timing of migration and breeding are under genetic control and that the populations genetically differ in these traits despite phenotypic overlap in timing in the wild. Representatives of families from two populations were collected within a day or two of each other, reared in a common environment, and then released to sea from each of two different rivers, while other family representatives were retained in fresh water to maturity. The date of maturation of fish held in fresh water and the dates of return from the ocean and maturation of fish released to sea all showed significant differences between the two populations and among families within populations. The very high heritabilities and genetic correlations estimated for migration and maturation date indicated that these traits would respond rapidly to selection. Combined with the results of related studies on these chinook salmon populations, it appears that spawning time may not only evolve during the initial phases of divergence, but it may play an important role in accelerating divergence in other traits.     

马尾松和黄山松两个核基因位点的群体遗传多样性和种间分化

利用两个核基因座位C3H和GI, 对重叠分布于中国东南部的两个松属(Pinus)物种马尾松(P. massoniana)和黄山松(P. hwangshanensis)的22个群体88个个体进行了遗传多样性和种间分化模式研究。在这两个核基因座位上, 两种植物都表现出较低的核苷酸多样性水平(马尾松π_sil = 0.001 71; 黄山松π_sil = 0.003 40), 但是马尾松要显著低于黄山松; 在种内分化水平上, 马尾松的种内遗传分化也明显低于黄山松(马尾松F_ST = 0.059; 黄山松F_ST = 0.339)。这可能是由于黄山松的海拔分布高于马尾松, 而高海拔分布使黄山松的分布区域更加片段化, 促使其形成较高的种内遗传多样性和遗传分化。分子变异分析(AMOVA)发现, 两物种基于两个核基因座位的种间差异为48.86%, 而GI基因座位上的种间差异明显高于C3H座位(GI: 77.24%, C3H: 20.48%), 同时, 基因谱系显示两物种的共享单倍型仅在C3H座位上存在。结合这两个基因的功能, 推测GI基因可能在物种形成过程中受到了一定的选择压力, 因为GI基因参与调控植物的开花时间, 而C3H与木质素表达水平的调控有关。不同的选择压力使得GI的进化速度相对较快, 从而加速了黄山松和马尾松的物种分化。     

The impact of global climate change on genetic diversity within populations and species

Genetic diversity provides the basic substrate for evolution, yet few studies assess the impacts of global climate change (GCC) on intraspecific genetic variation. In this review, we highlight the importance of incorporating neutral and non‐neutral genetic diversity when assessing the impacts of GCC, for example, in studies that aim to predict the future distribution and fate of a species or ecological community. Specifically, we address the following questions: Why study the effects of GCC on intraspecific genetic diversity? How does GCC affect genetic diversity? How is the effect of GCC on genetic diversity currently studied? Where is potential for future research? For each of these questions, we provide a general background and highlight case studies across the animal, plant and microbial kingdoms. We further discuss how cryptic diversity can affect GCC assessments, how genetic diversity can be integrated into studies that aim to predict species' responses on GCC and how conservation efforts related to GCC can incorporate and profit from inclusion of genetic diversity assessments. We argue that studying the fate of intraspecifc genetic diversity is an indispensable and logical venture if we are to fully understand the consequences of GCC on biodiversity on all levels.     

The devil's in the details: genetic and phenotypic divergence between artificial and native populations of the endangered pupfish (Cyprinodon diabolis)

Propagation of threatened or endangered species in artificial habitats is a common strategy for reducing the probability of extinction by demographic or stochastic forces. Differential selection, founder effects and genetic drift can conspire to cause artificial populations to differ irreversibly from native populations for characters important for fitness, thereby compromising conservation efforts. Here we show that artificial propagation of the endangered Devil's Hole pupfish Cyprinodon diabolis resulted in rapid divergence for phenotypic and genetic characteristics despite attempts to replicate key characteristics of the species' native habitat when designing the artificial environments. Although differences in behavior and morphology between the native pool population and the two artificial pools may reflect phenotypic plasticity, the results underscore the need to monitor and control (to the extent possible) closely the evolutionary process when propagating native species in artificial pools for multiple generations.     

Non-equilibrium gene frequency divergence: persistent founder effects in natural populations

The estimation of gene flow using gene frequency divergence information has become increasingly popular because of the difficulty involved in the direct determination of gene flow among populations. The present study examined allozyme gene frequencies in populations of eighteen aquatic invertebrate taxa at two sites in northern Canada. Gene frequencies at polymorpic loci were significantly different among 8–31 localized populations of all species at Igloolik and among 10–36 populations at Churchill confirming the generality of gene pool fragmentation in pond-dwelling organisms. Measures of gene flow estimated from gene frequency divergence, which assume that gene frequency distributions are at equilibrium, were inconsistent with the probable dispersal capacities of taxa. This provoked an examination of historical events as alternative explanations. Both theory and computer simulations demonstrated that when populations grow rapidly in size after founding from few individuals, the gene frequency divergence established during colonization is resistant to decay by gene exchange. Our work suggests that gene frequency distributions are often not in equilibrium and that caution should be employed in attempts to infer gene flow from them in natural populations.     

On the degree of genetic divergence in Drosophila ananassae populations transferred to laboratory conditions

Twelve natural populations of Drosophila ananassae were sampled and laboratory populations were derived. All the populations were maintained in food bottles in the laboratory for ten generations by transferring fifty flies (females and males in equal number) in each generation. After ten generations they were analysed chromosomally to determine the frequency of different chromosome arrangements. The results show that there is significant variation in the frequencies of chromosome arrangements and in the level of inversion heterozygosity. Although some of the populations became mo-nomorphic for certain inversions, in general all populations remained polymorphic even after ten generations. The degree of genetic differentiation in the populations after they were transferred to laboratory conditions has been estimated by calculating genetic identity and distance between the initial and final populations based on the differences in chromosome arrangement frequencies. The estimates of I and D suggest that there is considerable variation in the degree of genetic divergence in D. ananassae populations. Some populations have remained unchanged while others have diverged to a considerable extent.     

Estimation of divergence times for major lineages of primate species

Although the phylogenetic relationships of major lineages of primate species are relatively well established, the times of divergence of these lineages as estimated by molecular data are still controversial. This controversy has been generated in part because different authors have used different types of molecular data, different statistical methods, and different calibration points. We have therefore examined the effects of these factors on the estimates of divergence times and reached the following conclusions: (1) It is advisable to concatenate many gene sequences and use a multigene gamma distance for estimating divergence times rather than using the individual gene approach. (2) When sequence data from many nuclear genes are available, protein sequences appear to give more robust estimates than DNA sequences. (3) Nuclear proteins are generally more suitable than mitochondrial proteins for time estimation. (4) It is important first to construct a phylogenetic tree for a group of species using some outgroups and then estimate the branch lengths. (5) It appears to be better to use a few reliable calibration points rather than many unreliable ones. Considering all these factors and using two calibration points, we estimated that the human lineage diverged from the chimpanzee, gorilla, orangutan, Old World monkey, and New World monkey lineages approximately 6 MYA (with a range of 5-7), 7 MYA (range, 6-8), 13 MYA (range, 12-15), 23 MYA (range, 21-25), and 33 MYA (range 32-36).     

The genetic divergence of three populations

This paper considers the effect of the genetic divergence on the genetic composition of three samples drawn from three populations at some time after the populations had split. It generalizes the two-sample case studied earlier by Watterson (1985a). Under the assumptions that (i) mating is at random, (ii) the genes at a locus can be any of infinitely many alleles and all mutants are assumed to be new alleles, and (iii) no selective differences exist, we find the probability distribution of the sample gene configurations. From this distribution the single-sample allelic distribution after one-step and two-step bottlenecks and the allelic distribution in the two-sample case can be obtained as marginal distributions. Some numerical results on the number of alleles in common in the three samples are compared with those obtained by Watterson's simulation method; the agreement is excellent. Also, the probability that the three samples are monomorphic for the same allele is found, and numerical examples are given.     

The genetic divergence of two populations

When a population splits in two and the resulting populations evolve independently, genetic divergence may occur due to mutation and genetic drift. This paper considers the influence these factors have on the genetic composition of two samples drawn from the respective populations at some time after the split. Analytical formulas and numerical examples are given of (i) the probability distribution and moments of the allele frequencies, (ii) the number of alleles in common between the samples, and (iii) the probability that the samples are monomorphic.     

Environmental factors associated with genetic and phenotypic divergence among sympatric populations of Arctic charr (Salvelinus alpinus)

The mechanisms by which phenotypic and genetic divergence may occur among sympatric, conspecific populations have been widely discussed but are still not well understood. Possible mechanisms include assortative mating based on morphology or variation in the reproductive behaviour of phenotypes, and both have been suggested to be relevant to the differentiation of salmonid populations in post-glacial lakes. Here, we studied Arctic charr (Salvelinus alpinus) in Windermere, where putative populations are defined by spatial and temporal variation in spawning. Genetic differentiation was assessed based on nine microsatellite loci, and phenotypic variation was assessed from morphometric characters. We test hypotheses about the relative role of morphology, spawning season and spawning habitat in the evolution of genetic divergence among these populations. Distinct from other lake systems, we find that both morphological and genetic differentiation are restricted primarily to one of two interconnecting basins, that genetic and morphological differentiation are decoupled in this lake and that both phenotype and environment have changed over the last 20 years. The implication is that breeding habitat plays a primary role in isolating populations that differentiate by drift and that phenotypically plastic changes, potentially related to foraging specializations, have either become secondarily decoupled from the genetically defined populations or were never fundamental in driving the evolution of genetic diversity in the Windermere system.     

The distribution of the coalescence time and the number of pairwise nucleotide differences in a model of population divergence or speciation with an initial period of gene flow

This paper is concerned with a model of “isolation with an initial period of migration”, where a panmictic ancestral population split into n descendant populations which exchanged migrants symmetrically at a constant rate for a period of time and subsequently became completely isolated. In the limit as the population split occurred an infinitely long time ago, the model becomes an “isolation after migration” model, describing completely isolated descendant populations which arose from a subdivided ancestral population. The probability density function of the coalescence time of a pair of genes and the probability distribution of the number of pairwise nucleotide differences are derived for both models. Whilst these are theoretical results of interest in their own right, they also give an exact analytical expression for the likelihood, for data consisting of the numbers of nucleotide differences between pairs of DNA sequences where each pair is at a different, independent locus. The behaviour of the distribution of the number of pairwise nucleotide differences under these models is illustrated and compared to the corresponding distributions under the “isolation with migration” and “complete isolation” models. It is shown that the distribution of the number of nucleotide differences between a pair of DNA sequences from different descendant populations in the model of “isolation with an initial period of migration” can be quite different from that under the “isolation with migration model”, even if the average migration rate over time (and hence the total number of migrants) is the same in both scenarios. It is also illustrated how the results can be extended to other demographic scenarios that can be described by a combination of isolated panmictic populations and “symmetric island” models.     

Geographic variation in male courtship acoustics and genetic divergence of populations of the Cotesia flavipes species complex

Courtship behaviors of insect populations can vary across the range of a species. Populations exhibiting divergent courtship behavior may indicate genetic divergence or cryptic species. Courtship acoustic signals produced by male wing fanning and genetic structure (using amplified fragment length polymorphisms) were examined for seven allopatric populations of the Cotesia flavipes (Hymenoptera: Braconidae) species complex, using four C. sesamiae (Cameron) and three C. flavipes Cameron populations. Members of this species complex parasitize lepidopteran pests in gramineous crops including sugarcane, maize, and rice . Significant variation was detected in courtship acoustic signals and genetic structure among populations of both species. For C. sesamiae, courtship acoustic signals varied more between populations of two biotypes that were collected near an area of sympatry. The two biotypes of C. sesamiae were also genetically divergent. For C. flavipes, significant differences in acoustic signals and genetic structure occurred among allopatric populations; these differences support the recent designation of one population as a new species. Courtship acoustics play a role in reproductive isolation in this species complex, and are likely used in conjunction with chemical signals. Ecological factors such as host range and host plant use may also influence the divergence of both courtship acoustic signals and genetic structure among populations in the C. flavipes complex.     

The influence of gene flow and drift on genetic and phenotypic divergence in two species of Zosterops in Vanuatu

Colonization of an archipelago sets the stage for adaptive radiation. However, some archipelagos are home to spectacular radiations, while others have much lower levels of diversification. The amount of gene flow among allopatric populations is one factor proposed to contribute to this variation. In island colonizing birds, selection for reduced dispersal ability is predicted to produce changing patterns of regional population genetic structure as gene flow-dominated systems give way to drift-mediated divergence. If this transition is important in facilitating phenotypic divergence, levels of genetic and phenotypic divergence should be associated. We consider population genetic structure and phenotypic divergence among two co-distributed, congeneric (Genus: Zosterops) bird species inhabiting the Vanuatu archipelago. The more recent colonist, Z. lateralis, exhibits genetic patterns consistent with a strong influence of distance-mediated gene flow. However, complex patterns of asymmetrical gene flow indicate variation in dispersal ability or inclination among populations. The endemic species, Z. flavifrons, shows only a partial transition towards a drift-mediated system, despite a long evolutionary history on the archipelago. We find no strong evidence that gene flow constrains phenotypic divergence in either species, suggesting that levels of inter-island gene flow do not explain the absence of a radiation across this archipelago.     

Geographic variation and divergence of songs in the Olive Sparrow species complex

Phenotypic traits such as songs are important in species recognition. Variation in acoustic traits can form barriers to gene flow and promote speciation. Therefore, understanding song divergence is crucial in groups with controversial taxonomy such as Olive Sparrows (Arremonops rufivirgatus), a widespread Neotropical species of songbird with multiple allopatric populations. Taxonomic authorities disagree on the number of Olive Sparrow subspecies, placing them into either two or three main groups. These groups may represent separate species based on morphological traits, but trait divergence within the complex has not been examined. We studied geographic variation in the characteristics of the songs of Olive Sparrows at two geographical levels: among three proposed groups and among five allopatric populations. In a second analysis, we evaluated the strength of acoustic divergence within the complex by comparing acoustic distances among groups and allopatric populations of Olive Sparrows with the acoustic distance among three recognized species in the genus Arremonops. We analyzed 802 songs from 174 individuals across 81 locations and measured 12 variables to describe the fine structural characteristics of the songs of Olive Sparrows, Green-backed Sparrows (A. chloronotus), Black-striped Sparrows (A. conirostris), and Tocuyo Sparrows (A. tocuyensis). We found significant acoustic variation in the Olive Sparrow complex at both geographical levels. Our divergence analysis also revealed that vocal divergence within the complex is similar to or greater than that found between recognized species in the genus. Together, these results suggest that acoustic diversity within the Olive Sparrow complex probably originated by isolation in tandem with selective and/or non-selective factors.     

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.     

皱大球蚧(Eulecanium kuwanai)和瘤坚大球蚧(Eulecanium gigantean)地理种群的RAPD遗传分化

采用RAPD技术测定分析了河北省皱大球蚧和瘤坚大球蚧8个地理种群的遗传结构。结果表明：5种引物在8个种群中共产生了65条RAPD标记,各地理种群之间没有产生各自的特征标记;不同种群间的遗传相似程度与其地理间距呈反比;种群内的遗传相似程度比种间高。Shannon信息指数表明,皱大球蚧的平均遗传多样性高于瘤坚大球蚧,分别为0.3456和0.3225说明物种不同,其变异程度也不同。     

Estimating divergence time with the use of microsatellite genetic distances: impacts of population growth and gene flow

Genetic distances play an important role in estimating divergence time of bifurcated populations. However, they can be greatly affected by demographic processes, such as migration and population dynamics, which complicate their interpretation. For example, the widely used distance for microsatellite loci, (deltamu)2, assumes constant population size, no gene flow, and mutation-drift equilibrium. It is shown here that (deltamu)2 strongly underestimates divergence time if populations are growing and/or connected by gene flow. In recent publications, the average estimate of divergence time between African and non-African populations obtained by using (deltamu)2 is about 34,000 years, although archaeological data show a much earlier presence of modern humans out of Africa. I introduce a different estimator of population separation time based on microsatellite statistics, T(D), that does not assume mutation-drift equilibrium, is independent of population dynamics in the absence of gene flow, and is robust to weak migration flow for growing populations. However, it requires a knowledge of the variance in the number of repeats at the beginning of population separation, V(0). One way to overcome this problem is to find minimal and maximal bounds for the variance and thus obtain the earliest and latest bounds for divergence time (this is not a confidence interval, and it simply reflects an uncertainty about the value of V(0) in an ancestral population). Another way to avoid the uncertainty is to choose from among present populations a reference whose variation is presumably close to what it might have been in an ancestral population. A different approach for using T(D) is to estimate the time difference between adjacent nodes on a phylogenetic population tree. Using data on variation at autosomal short tandem repeat loci with di-, tri-, and tetranucleotide repeats in worldwide populations, T(D) gives an estimate of 57,000 years for the separation of the out-of-Africa branch of modern humans from Africans based on the value of V(0) in the Southern American Indian populations; the earliest bound for this event has been estimated to be about 135,000 years. The data also suggest that the Asian and European populations diverged from each other about 20,000 years, after the occurrence of the out-of-Africa branch.     

日本稻蝗、中华稻蝗和赤胫伪稻蝗地理种群的RAPD遗传分化研究

运用10个RAPD引物对日本稻蝗(Oxya japonica)、中华稻蝗(Oxya chinensis)和赤胫伪稻蝗(Pseudoxya diminuta)的种群遗传分化进行分析。10个随机引物共产生135条带,扩增谱带具有明显的属、种间多态性。Shannon信息指数表明中华稻蝗遗传多样性水平较高(2．693),日本稻蝗次之(2.319),赤胫伪稻蝗最低(1．042)。中华稻蝗和日本稻蝗的不同地理居群出现遗传分化,由Shannon信息指数估算的种群间遗传分化系数分别为20．7％,42．4％。用UPGMA和NJ法对Nei’s遗传距离作聚类分析,构建分子系统树。系统树显示：同一种群的不同个体优先相聚,而后,同一种的不同种群依次相聚;日本稻蝗广西南宁种群和广东广州种群首先聚为一支,陕西西安种群和浙江杭州种群聚为另一支,两支相聚后与中华稻蝗聚在一起,最后与赤胫伪稻蝗相聚。聚类结果表明：不同地域日本稻蝗亲缘关系的远近与地理距离呈现一定的相关趋势,日本稻蝗与中华稻蝗亲缘关系较近,Nei’S遗传距离平均为0．142,而赤胫伪稻蝗与它们关系较远,Nei’s遗传距离平均为0．451。聚类图所显示的物种间亲缘关系的远近程度与形态分类学和细胞分类学结果相一致。