Does organismal pedigree impact the magnitude of topological congruence among gene trees for unlinked loci?

One of the fundamental assumptions in the multi-locus approach to phylogeographic studies is that unlinked loci have independent genealogies. For this reason, congruence among gene trees from unlinked loci is normally interpreted as support for the existence of external forces that may have concordantly shaped the topology of multiple gene trees. However, it is also important to address and quantify the possibility that gene trees within a given species are all inherently constrained to some degree by their shared organismal pedigree, and thus in this strict sense are not entirely independent. Here we demonstrate by computer simulations that gene trees from a shared pedigree tend to display higher topological concordance than do gene trees from independent pedigrees with the same demographic parameters, but we also show that these constraining effects are normally minor in comparison to the much higher degree of topological concordance that can routinely emerge from external phylogeographic shaping forces. The topology-constraining effect of a shared pedigree decreases as effective population size increases, and becomes almost negligible in a random mating population of more than 1,000 individuals. Moreover, statistical detection of the pedigree effect requires a relatively large number of unlinked loci that far exceed what is typically used in current phylogeographic studies. Thus, with the possible exception of extremely small populations, multiple unlinked genes within a pedigree can indeed be assumed, for most practical purposes, to have independent genealogical histories.     

Statistical phylogeography

While studies of phylogeography and speciation in the past have largely focused on the documentation or detection of significant patterns of population genetic structure, the emerging field of statistical phylogeography aims to infer the history and processes underlying that structure, and to provide objective, rather than ad hoc explanations. Methods for parameter estimation are now commonly used to make inferences about demographic past. Although these approaches are well developed statistically, they typically pay little attention to geographical history. In contrast, methods that seek to reconstruct phylogeographic history are able to consider many alternative geographical scenarios, but are primarily nonstatistical, making inferences about particular biological processes without explicit reference to stochastically derived expectations. We advocate the merging of these two traditions so that statistical phylogeographic methods can provide an accurate representation of the past, consider a diverse array of processes, and yet yield a statistical estimate of that history. We discuss various conceptual issues associated with statistical phylogeographic inferences, considering especially the stochasticity of population genetic processes and assessing the confidence of phylogeographic conclusions. To this end, we present some empirical examples that utilize a statistical phylogeographic approach, and then by contrasting results from a coalescent-based approach to those from Templeton's nested cladistic analysis (NCA), we illustrate the importance of assessing error. Because NCA does not assess error in its inferences about historical processes or contemporary gene flow, we performed a small-scale study using simulated data to examine how our conclusions might be affected by such unconsidered errors. NCA did not identify the processes used to simulate the data, confusing among deterministic processes and the stochastic sorting of gene lineages. There is as yet insufficient justification of NCA's ability to accurately infer or distinguish among alternative processes. We close with a discussion of some unresolved problems of current statistical phylogeographic methods to propose areas in need of future development.     

Phylogeographic breaks in low-dispersal species: the emergence of concordance across gene trees

Computer simulations were used to investigate population conditions under which phylogeographic breaks in gene genealogies can be interpreted with confidence to infer the existence and location of historical barriers to gene flow in continuously distributed, low-dispersal species. We generated collections of haplotypic gene trees under a variety of demographic scenarios and analyzed them with regard to salient genealogical breaks in their spatial patterns. In the first part of the analysis, we estimated the frequency in which the spatial location of the deepest phylogeographic break between successive pairs of populations along a linear habitat coincided with a spatial physical barrier to dispersal. Results confirm previous reports that individual gene trees can show ‘haphazard’ phylogeographic discontinuities even in the absence of historical barriers to gene flow. In the second part of the analysis, we assessed the probability that pairs of gene genealogies from a set of population samples agree upon the location of a geographical barrier. Our findings extend earlier reports by demonstrating that spatially concordant phylogeographic breaks across independent neutral loci normally emerge only in the presence of longstanding historical barriers to gene flow. Genealogical concordance across multiple loci thus becomes a deciding criterion by which to distinguish between stochastic and deterministic causation in accounting for phylogeographic discontinuities in continuously distributed species.     

On the independent gene trees assumption in phylogenomic studies

Multilocus coalescent methods for inferring species trees or historical demographic parameters typically require the assumption that gene trees for sampled SNPs or DNA sequence loci are conditionally independent given their species tree. In practice, researchers have used different criteria to delimit “independent loci.” One criterion identifies sampled loci as being independent of each other if they undergo Mendelian independent assortment (IA criterion). O'Neill et al. (2013, Molecular Ecology, 22, 111–129) used this approach in their phylogeographic study of North American tiger salamander species complex. In two other studies, researchers developed a pair of related methods that employ an independent genealogies criterion (IG criterion), which considers the effects of population‐level recombination on correlations between the gene trees of intrachromosomal loci. Here, I explain these three methods, illustrate their use with example data, and evaluate their efficacies. I show that the IA approach is more conservative, is simpler to use and requires fewer assumptions than the IG approaches. However, IG approaches can identify much larger numbers of independent loci than the IA method, which, in turn, allows researchers to obtain more precise and accurate estimates of species trees and historical demographic parameters. A disadvantage of the IG methods is that they require an estimate of the population recombination rate. Despite their drawbacks, IA and IG approaches provide molecular ecologists with promising a priori methods for selecting SNPs or DNA sequence loci that likely meet the independence assumption in coalescent‐based phylogenomic studies.     

Comparative phylogeography of a coevolved community: concerted population expansions in Joshua trees and four yucca moths

Comparative phylogeographic studies have had mixed success in identifying common phylogeographic patterns among co-distributed organisms. Whereas some have found broadly similar patterns across a diverse array of taxa, others have found that the histories of different species are more idiosyncratic than congruent. The variation in the results of comparative phylogeographic studies could indicate that the extent to which sympatrically-distributed organisms share common biogeographic histories varies depending on the strength and specificity of ecological interactions between them. To test this hypothesis, we examined demographic and phylogeographic patterns in a highly specialized, coevolved community--Joshua trees (Yucca brevifolia) and their associated yucca moths. This tightly-integrated, mutually interdependent community is known to have experienced significant range changes at the end of the last glacial period, so there is a strong a priori expectation that these organisms will show common signatures of demographic and distributional changes over time. Using a database of >5000 GPS records for Joshua trees, and multi-locus DNA sequence data from the Joshua tree and four species of yucca moth, we combined paleaodistribution modeling with coalescent-based analyses of demographic and phylgeographic history. We extensively evaluated the power of our methods to infer past population size and distributional changes by evaluating the effect of different inference procedures on our results, comparing our palaeodistribution models to Pleistocene-aged packrat midden records, and simulating DNA sequence data under a variety of alternative demographic histories. Together the results indicate that these organisms have shared a common history of population expansion, and that these expansions were broadly coincident in time. However, contrary to our expectations, none of our analyses indicated significant range or population size reductions at the end of the last glacial period, and the inferred demographic changes substantially predate Holocene climate changes.     

Application of non-coding DNA regions in intraspecific analyses

In this review we discuss the use of non-coding DNA at the intraspecific level in plants. Both nuclear and organelle non-coding regions are widely used in interspecific phylogenetic approaches. However, they are also valuable in analyses on the intraspecific level. Besides taxonomy, that is, defining subspecies or varieties, large fields for the application of non-coding DNA are population genetic and phylogeographic studies. Population genetics tries to explain the genetic patterns within species mostly by the amount of extant gene flow among populations, while phylogeography explicitly tries to reconstruct historic events. Depending on the study different molecular markers can be used, varying between very fast evolving microsatellites or some more slowly changing regions like intergenic spacers and introns. Here, we focus mainly on the use of non-coding regions in phylogeographic analyses. Mostly used in this context are regions of the genomes of the chloroplasts and mitochondria. In phylogeography, the correct estimation of allele or haplotype relationships is particularly important. As tree-based methods are mostly insufficient to depict relationships within species, network approaches are better suitable to infer gene or locus genealogies. Problematic for phylogeographic studies are alleles shared among multiple species, which could result from either hybridization or incomplete lineage sorting. Especially the latter can severely influence the interpretation of the phylogeographic patterns. Therefore, it seems necessary for us to also include close relatives of the species under study in phylogeographic analyses. Not only the sample design but also the analysis methods are currently changing, as some new methods such as statistical phylogeography were emerging recently and widely used methods like nested clade analysis might not be reliable in every case. During the last few years, a multitude of studies were published, which mainly analyzed phylogeographic patterns in European and North American plants. Phylogeographic studies in other regions of the earth are still comparably rare, although questions like the influence of the ice age on the vegetation in the tropics or southern hemisphere are still open and phylogeography provides an excellent remedy to answer them.     

Recent developments in genetic data analysis: what can they tell us about human demographic history?

Over the last decade, a number of new methods of population genetic analysis based on likelihood have been introduced. This review describes and explains the general statistical techniques that have recently been used, and discusses the underlying population genetic models. Experimental papers that use these methods to infer human demographic and phylogeographic history are reviewed. It appears that the use of likelihood has hitherto had little impact in the field of human population genetics, which is still primarily driven by more traditional approaches. However, with the current uncertainty about the effects of natural selection, population structure and ascertainment of single-nucleotide polymorphism markers, it is suggested that likelihood-based methods may have a greater impact in the future.     

Natural selection on mitochondrial DNA in Parus and its relevance for phylogeographic studies

I examined mitochondrial ND2 sequences in species of tits (genus Parus) to determine whether substitutions were neutral or under selection. Haplotype trees in these species are shallow and geographically unstructured, which could be a signature of recent demographic expansion or purifying selection. McDonald-Kreitman tests revealed a pattern of excess replacement polymorphisms for closely related taxa. Replacement substitutions tended to be less common in the basal parts of haplotype trees, suggesting that they are selected against over evolutionary time. Thus, the pattern of selection is consistent with a model of mildly deleterious haplotypes. To investigate the significance of this selection, the ND2 gene was subdivided into surface and transmembrane portions, and synonymous-non-synonymous sites, and F(ST)-values (the amount of variance distributed among populations) computed for each. Among sampling localities in P. major, both partitions gave similar estimates of F(ST), which is consistent with demographic expansion as the cause of the shallow trees. In P. montanus, two localities contained high percentages of individuals that had a single replacement substitution in the transmembrane portion of the gene, which inflated F(ST)-values relative to the surface sites. Thus, the interpretation of the genetic differentiation of these two sites could be either geographical isolation or selection. Given that the sole substitution causing the high F(ST)-values was a replacement one, selection is implicated. However, this substitution occurred in only 2 of 12 localities, revealing that overall the phylogeographic pattern was not biased by selection, once the cause of the two high pairwise F(ST)-comparisons was recognized. Investigators should consider the source of significant genetic heterogeneity within species, to determine if the variation is likely caused by demographic isolation or selection. However, it seems unlikely that most phylogeographic analyses are invalidated by the effects of natural selection.     

Test for simultaneous divergence using approximate Bayesian computation

Comparative phylogeographic studies often reveal disparate levels of sequence divergence between lineages spanning a common geographic barrier, leading to the conclusion that isolation was nonsynchronous. However, only rarely do researchers account for the expected variance associated with ancestral coalescence and among-taxon variation in demographic history. We introduce a flexible approximate Bayesian computational (ABC) framework that can test for simultaneous divergence (TSD) using a hierarchical model that incorporates idiosyncratic differences in demographic history across taxon pairs. The method is tested across a range of conditions and is shown to be accurate even with single-locus mitochondrial DNA (mtDNA) data. We apply this method to a landmark dataset of putative simultaneous vicariance, eight geminate echinoid taxon pairs thought to have been split by the Isthmus of Panama 3.1 million years ago. The ABC posterior estimates are not consistent with a history of simultaneous vicariance given these data. Subsequent ABC estimates under a constrained model that assumes two divergence times across the eight taxon pairs suggests simultaneous divergence 3.1 million years ago in seven of the taxon pairs and a more recent divergence in the remaining taxon pair. These ABC estimates on the simultaneous divergence of the seven taxon pairs correspond to a DNA substitution rate of approximately 1.59% per lineage per million years at the mtDNA cytochrome oxidase I gene. This ABC framework can easily be modified to analyze single taxon-pair datasets and/or be expanded to include multiple loci, migration, recombination, and other idiosyncratic demographic histories. The flexible aspect of ABC and its built-in evaluation of estimator bias and statistical power has the potential to greatly enhance statistical rigor in phylogeographic studies.     

鸟类分子系统地理学研究进展

分子系统地理学是当代生物地理学的重要分支,是以分子生物学方法重建种内和种上水平的系统发育关系,阐释进化历史,并通过分析近缘生物类群的系统发育关系与其空间和时间分布格局间的相关性构建生物区系历史的研究,是分子生物学与生物地理学结合的产物。中性进化学说和溯祖理论分析的建立,以及线粒体DNA和微卫星标记等分子遗传标记的应用,为分子系统地理学研究的开展提供了理论和实践基础。近年来,分子系统地理方法在鸟类学研究中的应用揭示了许多不同于传统认知的发现,为准确而深入的了解鸟类分子系统地理格局的差异和不同类群的起源中心提供了新颖的证据。目前的研究多从隔离分化说和扩散说的角度对鸟类分子系统地理格局的成因进行分析,而迁徙行为不同对鸟类系统地理格局的影响为成因的解释提供了新的角度。结合区域特点的比较分子系统地理研究,在更广泛的地域和更多类群中开展研究是我国鸟类分子系统地理研究的方向。此外,展望了第二代测序技术对分子生态生物地理研究具有的潜在促进作用。     

复杂疾病全基因组关联研究进展——遗传统计分析

2005年, Science杂志首次报道了有关人类年龄相关性黄斑变性的全基因组关联研究, 此后有关肥胖、2型糖尿病、冠心病、阿尔茨海默病等一系列复杂疾病的全基因组关联研究被陆续报道, 这一阶段被称为人类全基因组关联研究的第一次浪潮。文章分别介绍了全基因组关联研究统计分析的方法、软件和应用实例; 比较了关联分析中多重检验的P值调整方法, 包括Bonferroni、递减的Bonferroni校正法、模拟运算法和控制错误发现率的方法; 还讨论了人群混杂对关联分析结果可能产生的影响及原理, 以及全基因组关联研究中控制人群混杂的方法的研究进展和应用实例。在全基因组关联研究的第一次浪潮中, 应用经典的遗传统计方法发现了许多基因-表型之间的关联并且能够对这些关联做出解释, 其中包括许多基因组中的未知基因和染色体区域。然而, 全基因组关联研究的继续发展需要进一步阐述基因组内基因之间相互作用、基因-基因之间的复杂作用网络与环境因素的相互作用在复杂疾病发生中的作用, 现有的统计分析方法肯定不能满足需要, 开发更为高级的统计分析方法势在必行。最后, 文章还给出了全基因组关联研究统计分析软件的相关网站信息。     

Recent and ongoing selection in the human genome

The recent availability of genome-scale genotyping data has led to the identification of regions of the human genome that seem to have been targeted by selection. These findings have increased our understanding of the evolutionary forces that affect the human genome, have augmented our knowledge of gene function and promise to increase our understanding of the genetic basis of disease. However, inferences of selection are challenged by several confounding factors, especially the complex demographic history of human populations, and concordance between studies is variable. Although such studies will always be associated with some uncertainty, steps can be taken to minimize the effects of confounding factors and improve our interpretation of their findings.     

Phylogeography and conservation genetics of the Columbia spotted frog (Rana luteiventris; Amphibia, Ranidae)

The Columbia spotted frog (Rana luteiventris) has a widespread distribution in western Canada and the western US, although the southern reach of its range is highly fragmented into several isolated populations. Threats from various factors have raised concerns regarding the long-term survival of many small, isolated populations. Here, we report a study designed to determine the phylogeographic and conservation genetic parameters of R. luteiventris in the western US. Mitochondrial DNA (mtDNA) sequences were examined for phylogeographic structuring using phylogenetic reconstruction methods, coupled with networking and nested clade analyses. These methods permitted a distinction to be made between historic and demographic forces acting to generate geographical patterning of genetic variation. Phylogenetic analysis revealed four geographically correlated monophyletic clades. Three of these clades correspond to well-defined, nonoverlapping geographical locations in the fragmented portion of the range. The other is comprised of all samples collected from the contiguous range and includes one isolate from northern Wyoming. Networking and nested clade analyses confirmed these results and revealed that historical processes, such as range expansion and vicariance, rather than recurrent gene flow are likely responsible for observed patterns of genetic variation. A measure of genetic variation (theta = 4N(e)mu) revealed that R. luteiventris populations in Utah have a relatively low amount of genetic variation compared with populations in the continuous portion of the range.     

In defence of model‐based inference in phylogeography

Recent papers have promoted the view that model‐based methods in general, and those based on Approximate Bayesian Computation (ABC) in particular, are flawed in a number of ways, and are therefore inappropriate for the analysis of phylogeographic data. These papers further argue that Nested Clade Phylogeographic Analysis (NCPA) offers the best approach in statistical phylogeography. In order to remove the confusion and misconceptions introduced by these papers, we justify and explain the reasoning behind model‐based inference. We argue that ABC is a statistically valid approach, alongside other computational statistical techniques that have been successfully used to infer parameters and compare models in population genetics. We also examine the NCPA method and highlight numerous deficiencies, either when used with single or multiple loci. We further show that the ages of clades are carelessly used to infer ages of demographic events, that these ages are estimated under a simple model of panmixia and population stationarity but are then used under different and unspecified models to test hypotheses, a usage the invalidates these testing procedures. We conclude by encouraging researchers to study and use model‐based inference in population genetics.     

A practical introduction to sequentially Markovian coalescent methods for estimating demographic history from genomic data

A common goal of population genomics and molecular ecology is to reconstruct the demographic history of a species of interest. A pair of powerful tools based on the sequentially Markovian coalescent have been developed to infer past population sizes using genome sequences. These methods are most useful when sequences are available for only a limited number of genomes and when the aim is to study ancient demographic events. The results of these analyses can be difficult to interpret accurately, because doing so requires some understanding of their theoretical basis and of their sensitivity to confounding factors. In this practical review, we explain some of the key concepts underpinning the pairwise and multiple sequentially Markovian coalescent methods (PSMC and MSMC, respectively). We relate these concepts to the use and interpretation of these methods, and we explain how the choice of different parameter values by the user can affect the accuracy and precision of the inferences. Based on our survey of 100 PSMC studies and 30 MSMC studies, we describe how the two methods are used in practice. Readers of this article will become familiar with the principles, practice, and interpretation of the sequentially Markovian coalescent for inferring demographic history.     

Gene flow between vicariant tree species: insights into savanna-forest evolutionary relationships

Studying the genetic structure of vicariant species (i.e., closely related species that occupy ecologically distinct yet adjacent habitats) can shed light on the evolution and divergence of species with different ecological requirements. A previous phylogeographic study identified chloroplast DNA haplotype sharing between two vicariant tree species, one from forest (Hymenaea courbaril) and one from savanna (H. stigonocarpa) habitats. These species co-occur in the Brazilian Cerrado, a biome that encompasses forest patches and riverine forests within a savanna matrix. In order to investigate the evolutionary processes involved in the genetic divergence of these trees, we used nuclear microsatellite markers, statistical methods including approximate Bayesian computation (ABC), and leaf morphology to analyze neighboring and distant populations. Bayesian analysis revealed admixture between the species. ABC analysis supported the scenarios with the occurrence of gene flow between species during the Last Glacial Maximum or from the Holocene to the present, when compared to alternative scenarios of no gene flow or constant gene flow since divergence. However, putative hybrids did not exhibit intermediate leaflet morphology, which could be related to distinct selective pressures maintaining species integrity even in the face of gene flow. Our results suggest that despite morphological differences between savanna and forest species, interspecific barriers to gene flow might not be fully developed between vicariant tree species and that interspecific hybridization in trees from Cerrado biome may be an underdiagnosed process.     

It's about time: divergence, demography, and the evolution of developmental modes in marine invertebrates

Differences in larval developmental mode are predicted to affect ecological and evolutionary processes ranging from gene flow and population bottlenecks to rates of population recovery from anthropogenic disturbance and capacity for local adaptation. The most powerful tests of these predictions use comparisons among species to ask how phylogeographic patterns are correlated with the evolution and loss of prolonged planktonic larval development. An important and largely untested assumption of these studies is that interspecific differences in population genetic structure are mainly caused by differences in dispersal and gene flow (rather than by differences in divergence times among populations or changes in effective population sizes), and that species with similar patterns of spatial genetic variation have similar underlying temporal demographic histories. Teasing apart these temporal and spatial patterns is important for understanding the causes and consequences of evolutionary changes in larval developmental mode. New analytical methods that use the coalescent history of allelic diversity can reveal these temporal patterns, test the strength of traditional population-genetic explanations for variation in spatial structure based on differences in dispersal, and identify strongly supported alternative explanations for spatial structure based on demographic history rather than on gene flow alone. We briefly review some of these recent analytical developments, and show their potential for refining ideas about the correspondence between the evolution of larval developmental mode, population demographic history, and spatial genetic variation.     

Patterns of gene flow and population genetic structure in the canyon treefrog, Hyla arenicolor (Cope)

Patterns of gene flow and genetic structuring were examined in the canyon treefrog, Hyla arenicolor (Cope). Hierarchical analysis of genetic variation was performed on mitochondrial cytochrome b haplotypes from 323 individuals, representing 32 populations from previously described phylogeographic regions. Results from AMOVA revealed that 60.4-78.9% of the recovered genetic variation was the result of differences in the appointment of genetic variation between subdivisions of the primary phylogeographic regions. In contrast, populations only contained between 13.9 and 30.1% of the observed haplotypic variation. Gene flow estimates based on calculations of phi ST revealed moderate levels of gene flow within phylogeographic regions, but there was no evidence of gene flow between these regions, suggesting that geographical boundaries were probably important in the formation of phylogeographic structure in H. arenicolor. Phylogeographic regions exhibited very different patterns of gene flow. One region showed evidence of recent colonization. Another region exhibited very limited gene flow. Moderate to high estimates of gene flow were obtained for populations from two distinct phylogeographic regions characterized by mesic and xeric environments. Isolation by distance was observed in both regions suggesting that these regions are in genetic equilibrium. Because gene flow is extremely unlikely between the populations in the xeric region, this result is interpreted as historical gene flow. These results indicate that isolation-by-distance effects may still be observed even when population genetic structure and gene flow are the result of historical association.     

Identifying main evolutionary mechanisms shaping genetic variation of Leuciscus cephalus L. 1758 (Cyprinidae) in western Greece: discordance between methods.

Numerous methods can be used in intraspecific phylogeographic studies to infer the evolutionary mechanisms that shaped observed genetic variation in populations. However, these methods are scarcely used jointly, and the evolutionary outcomes they could propose are not fully compared. In this study, using a chub (Leuciscus cephalus; Cyprinidae) mitochondrial DNA data set (13 populations in Western Greece, 14 haplotypes), we compare three distinct 'historical' methods that could possibly infer relative importance of basic evolutionary mechanisms (isolation vs migration) shaping genetic variation: the nested clade analysis, the psi-test and the 'mismatch distributions'. Taking together, interpretations of these analyses allow to draw a picture of the evolutionary history of chub in Western Greece based on isolation and genetic drift for higher clades. However, results issued each method can differ for low differentiated clades. We discuss such differences and suggest that methods should be used jointly in phylogeographic studies for a better evaluation of the evolutionary mechanisms that shaped genetic variation.