ChapterFourteenPhylogeography[3rdpart]

1、Definition 1: Demographic inference that takes into account the stochasticity of genetic processes.Definition 2: Studies focused on the processes generating patterns of genetic variation within and among closely related species.Statistical phylogeography種群突變參數(shù) = 4Ne?？赏ㄟ^基于溯祖模型的軟件（例如，Lamarc: Kuhner, 2

2、006）對已知的DNA序列進行計算獲得。當恒定的有效種群大小不是一個合理的假設(shè)時，值可作為種群增長參數(shù)的一個估計值。The universe of potential historical scenarios that might be considered in statistical phylogeography is huge. As represented here on the surface of the sphere, there is a continuous array of possible demographic processes and associated para

3、meter values. Depending on the trajectory of a populations history over time (i.e., the path traversed through the sphere), a simple model such as contiguous range expansion (shown on the left) might provide an accurate simplified representation, whereas in other cases, a more complex model that inc

4、orporates different evolutionary processes at varying time points (shown on the right) would be needed for statistical phylogeographic analyses.The coalescent process was used to evaluate the probability that n gene lineages would fail to coalesce within population lineages representing purported al

5、lopatric ancestral refugial-source populations, hence, producing a discordance between the gene and population tree. purported 傳說的, 據(jù)說的Schematic representations of a gene tree contained within a population tree; an arrow identifies the discordance between the gene and population trees. This discord

6、can easily be quantified by counting the number of deep coalescents (Maddison 1997), or the failure of gene lineages to coalesce within their respective population lineages (assuming that there is no gene flow among the populations).The amount of discordance between a gene tree and the population mo

7、del was measured by s, the minimum number of sorting events required to produce the genealogy within a given model of divergence (Slatkin and Maddison 1989). The s-value is a measure of the number of parsimony steps in a character (where the source population for the haplotype is the character state

8、) for a reconstructed gene tree, such that more discordance between the population and gene trees leads to a higher s-value. If it is assumed that the populations have been separated for a long time (and N sample size), the only process causing discordance is migration; otherwise, incomplete lineage

9、 sorting (from multiple refugia) may contribute to the differences. A gene genealogy may be different from the species phylogeny. This phenomenon is called incomplete lineage sorting (ILS).Incomplete lineage sorting can cause serious difficulties for phylogenetic inference.Traditionally, incomplete

10、lineage sorting (ILS) is said to produce a difference between a gene tree and a species tree although the gene of course, could be any genomic segment of interest. 一個基因樹可能不同于物種譜系樹或種群樹，這一現(xiàn)象稱作不完全譜系分選或譜系揀選不徹底（incomplete lineage sorting, ILS）。A three-species phylogeny for species X, Y, and Z, with ances

11、tral species XY and XYZ. Individuals x1, y1, and z1 have a genealogy that reflects the species tree (light gray), but individuals x2, y2, and z2 have a genealogy with a discordant topology (dark gray).Alternative historical scenarios were represented as different population treesThe null hypothesis

12、of a single ancestral source population was modeled where each individual, contemporary sky-island population corresponded to a population in the population tree.A single ancestral population as represented by a fragmentation modelThe alternative hypothesis of multiple ancestral populations, was mod

13、eled with groups of sky-island populations treated essentially as a single population if they were colonized from the same ancestral refugial-source population. Gene trees simulated by a neutral coalescent process under the fragmentation model (a) were used to derive an expected distribution for the

14、 amount of discord that would be predicted between a genealogy and a population tree representing the allopatric refugia model (b), when the data have actually evolved under a history in which the contemporary populations were derived from a single ancestral source. The discord between the reconstru

15、cted gene tree and the allopatric refuge model was then compared to this expected distribution.Multiple ancestral populations, using an allopatric refuge model (groupings of populations were identified from previous phylogeographic analysesThe timing of gene divergence generally overestimates popula

16、tion divergence times. The discrepancy between gene and population divergence is less for events in the more distant past (a) compared to the effect on estimates of recent divergence times (b) where the difference between and T represents a much larger proportion of the estimated population divergen

17、ce time.year before presentSchematic describing the process of generating alternative biogeographical hypotheses using palaeodistribution models and of testing them using coalescent simulations and empirical genetic data. In (e) and (f) the gradient from red to white differentiates areas with predic

18、ted high to low suitability, respectively, for the species in question.統(tǒng)計譜系地理學統(tǒng)計譜系地理學零假設(shè)：當前動物地理分布格局是基于同一祖先的后裔廣泛分布區(qū)域經(jīng)歷生境片段化后形成。1個采樣點對應種群樹中的1個種群，構(gòu)建一個種群樹，所有種群直接源自一共同祖先種群（即種群破碎化模型）。種群破碎化模型的構(gòu)建從一個Mesquite軟件默認的種群樹開始（該默認種群樹是軟件基于每個種群所包含的單倍型經(jīng)過溯祖模擬過程構(gòu)建的）。備擇假設(shè)：當前動物地理分布格局由不同冰期生物種遺區(qū)分別演化而來。這時，零假設(shè)中的種群根據(jù)基因譜系樹（基于實驗獲得

19、的真實單倍型序列構(gòu)建的ML樹或Bayes樹）并結(jié)合地理區(qū)域劃分（更普遍）、景觀特征或形態(tài)學特征等人為歸并成若干較大的種群，利用Mesquite軟件基于歸并后的每個較大的種群中所包含的單倍型（基因）經(jīng)過溯祖模擬過程構(gòu)建備擇假設(shè)種群樹（即種群分異模型models of population divergence，選擇軟件默認樹）。 分析步驟：分析步驟：1 Mesquite運算過程中需要有效種群大小參數(shù)Ne。Ne可通過種群突變參數(shù)計算獲得, = 4Ne?？赏ㄟ^基于溯祖模型的軟件（例如，Lamarc: Kuhner, 2006；Fluctuate 1.4: Kuhner et al. 1995）對已知

20、的DNA序列進行計算獲得。注意，每一個種群（即每個采樣點）來自的Ne值都要計算。當恒定的有效種群大小不是一個合理的假設(shè)時，值可作為種群增長參數(shù)的一個估計值。如果有效種群大小是恒定的，則可利用Arlequin中值的Watteson估計量（Wattesons estimator）直接從隔離點（segregating sites）的分布估算，或者利用DnaSP在DNA單倍型中基于核苷酸多樣性（ ）的配對差異（pairwise differences）估算而得。注意，突變率必須是已知的（例如，昆蟲的mtDNA的分異率是每百萬年2%）。利用軟件Fluctuate 1.4 (Kuhner et al. 1

21、995) 可以估算每一個種群和地區(qū)的每點（per site）值。2 構(gòu)建種群分異模型（包括冰后期種遺區(qū)模型和種群破碎化模型。前者可由Mesquite推斷出（Tree search: Taxa&TreesMake New Trees Block FromOther ChoicesTree Search; or Cluster analysis: Taxa&TreesMake New Trees Block FromOther ChoicesCluster Analysis. 詳見后面），后者通過軟件手工處理前者得到）。以樹長的變化范圍來估算種群分異時間。Mesquite利用世代數(shù)

22、代表分枝長度，所有首先將年代轉(zhuǎn)換成世代數(shù)。不同物種，一個世代等于1年或幾年等不同年代。3 基于每個種群分異模型，根據(jù)實驗室獲得的序列數(shù)據(jù)通過溯祖模擬過程構(gòu)建種群分異模型各自的基因樹（基因樹數(shù)量等同于種群分異模型數(shù)量，因為每個種群分異模型只模擬1個基因樹。在此模擬的基因樹上將進一步模擬基因矩陣。Select CharactersMake New Matrix FromOther Choices., then indicate Simulated Matrices on Trees詳見后面）。4 基于步驟3的基因樹、中性溯祖過程、DNA替換模型（ModelTest）及有效種群大小Ne，基于每個基因樹模擬1000個（可自定義個數(shù)）DNA序列數(shù)據(jù)（即基因矩陣）。5 根據(jù)模擬的基因矩陣，利用PAUP*4.10b構(gòu)建ML基因樹。對應于每個種