Biodiv Sci ›› 2023, Vol. 31 ›› Issue (12): 23314. DOI: 10.17520/biods.2023314
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Yanping Wang*()(), Minchu Zhang, Chengxiu Zhan
Received:
2023-09-04
Accepted:
2023-12-08
Online:
2023-12-20
Published:
2023-12-20
Contact:
E-mail: Yanping Wang, Minchu Zhang, Chengxiu Zhan. A review on the nested distribution pattern (nestedness): Analysis methods, mechanisms and conservation implications[J]. Biodiv Sci, 2023, 31(12): 23314.
Fig. 1 Sketch maps showing the nested distribution pattern (nestedness). (a) Perfect nestedness (from the most species-poor island I8 to the most species-rich island I1, the species assemblages on them are perfectly nested in turn); (b) Not perfect but significant nestdness. Sp stands for species, I for islands or fragmented patches. 1 indicates the occurrence of species on an island or fragmented patch, while 0 indicates a species does not occur on an island or fragmented patch.
简称Abbreviation | 全称 Full names | 术语解释 Explanations |
---|---|---|
NODF | 基于重叠和减少填充的嵌套测量 Nestedness metric based on overlap and decreasing fill | 由Almeida-Neto等( |
WNODF | 基于重叠和减少填充的加权嵌套测量Weighted nestedness metric based on overlap and decreasing fill | 由Almeida-Neto和Ulrich ( |
N0 | 物种缺失数量 No. of absences | 由Patterson和Atmar ( |
N1 | 物种出现数量 No. of presences | 由Cutler ( |
Ua | 非预期缺失数量 No. of unexpected absences | 由Cutler ( |
Up | 非预期出现数量 No. of unexpected presences | 由Cutler ( |
Ut | 非预期转换数量 No. of unexpected transformations | 由Cutler ( |
Nc | - | 由Wright和Reeves ( |
D | 偏离数量 No. of departures | 由Lomolino ( |
BR | 差异测量 Discrepancy measure | 由Brualdi和Sanderson ( |
T | 矩阵温度 Matrix temperature | 由Atmar和Patterson ( |
BINMATNEST | 二元矩阵温度嵌套计算器 Binary matrix nestedness temperature calculator | 由Rodríguez-Gironés和Santamaría ( |
HH | 超集数量 No. of supersets | 由Hausdorf和Hennig ( |
Table 1 Abbreviated nestedness metrics used in the article and their explanations
简称Abbreviation | 全称 Full names | 术语解释 Explanations |
---|---|---|
NODF | 基于重叠和减少填充的嵌套测量 Nestedness metric based on overlap and decreasing fill | 由Almeida-Neto等( |
WNODF | 基于重叠和减少填充的加权嵌套测量Weighted nestedness metric based on overlap and decreasing fill | 由Almeida-Neto和Ulrich ( |
N0 | 物种缺失数量 No. of absences | 由Patterson和Atmar ( |
N1 | 物种出现数量 No. of presences | 由Cutler ( |
Ua | 非预期缺失数量 No. of unexpected absences | 由Cutler ( |
Up | 非预期出现数量 No. of unexpected presences | 由Cutler ( |
Ut | 非预期转换数量 No. of unexpected transformations | 由Cutler ( |
Nc | - | 由Wright和Reeves ( |
D | 偏离数量 No. of departures | 由Lomolino ( |
BR | 差异测量 Discrepancy measure | 由Brualdi和Sanderson ( |
T | 矩阵温度 Matrix temperature | 由Atmar和Patterson ( |
BINMATNEST | 二元矩阵温度嵌套计算器 Binary matrix nestedness temperature calculator | 由Rodríguez-Gironés和Santamaría ( |
HH | 超集数量 No. of supersets | 由Hausdorf和Hennig ( |
嵌套指数分类Classification of nestedness metrics | 嵌套指数 Nestedness metrics | 属性 Characteristics | 参考文献 References |
---|---|---|---|
间隙嵌套指数 Gap metrics | N0、N1、Ua、Up、Ut、Nc、D、BR | 受矩阵转换、矩阵大小、形状和填充度的影响(Nc和BR除外); 样本量较小时, 计算的统计检验率较低 Gap metrics are affected by matrix transformation, matrix size, shape and fill (except for Nc and BR). They have low power at small sample size (small matrix size) | Patterson & Atmar, |
温度嵌套指数 Temperature metrics | T、BINMATNEST | 不受矩阵转换的影响, 但会受矩阵大小和填充度的影响; 在矩阵中添加非嵌套的特有物种后, T指数会错误地识别出嵌套格局 Temperature metrics are affected by matrix size and fill, but not by matrix transformation. T metric incorrectly indicates an increase in nestedness with the addition of nonnested endemics to matrices | Atmar & Patterson, |
重叠嵌套指数 Overlap metrics | HH | 会受到异常值的过度影响, 且没有被标准化 HH is excessively affected by outliers and is not standardized | Hausdorf & Hennig, |
NODF | 基于行和列填充的标准化差异, 并且可以将总嵌套分解为由列和行分别进行计算; 不受矩阵大小、形状和填充度的影响 NODF is based on standardized differences in row and column fills. It can decompose total nestedness into a sum of the nestedness introduced by columns and by rows separately. NODF is not affected by matrix size, shape and fill | Almeida-Neto et al, | |
WNODF | 基于NODF的一种简单修改, 用于计算物种分布的多度矩阵数据是否嵌套; 不受矩阵大小、形状和填充度的影响 WNODF is a simple modification of NODF and used to determine the nestedness of the species-by-sites abundance matrix. It is not affected by matrix size, shape and fill | Almeida-Neto & Ulrich, | |
功能和谱系嵌套指数 Functional and phylogenetic metrics | phyloNODF | 用物种的系统发育建树解释谱系多样性; 不受矩阵大小、填充度以及树拓扑的影响 phyloNODF can be calculated if a phylogeny is used to account for differences in phylogenetic diversity. It is robust for matrix size, matrix fill, and tree topology | Melo et al, |
traitNODF | 用功能性状建树解释功能多样性; 不受矩阵大小、填充度以及树拓扑的影响 traitNODF can be calculated if a functional dendrogram constructed from species ecological traits is used to account for the functional diversity. It is robust for matrix size, matrix fill, and tree topology | Melo et al, |
Table 2 An overview of existing nestedness metrics
嵌套指数分类Classification of nestedness metrics | 嵌套指数 Nestedness metrics | 属性 Characteristics | 参考文献 References |
---|---|---|---|
间隙嵌套指数 Gap metrics | N0、N1、Ua、Up、Ut、Nc、D、BR | 受矩阵转换、矩阵大小、形状和填充度的影响(Nc和BR除外); 样本量较小时, 计算的统计检验率较低 Gap metrics are affected by matrix transformation, matrix size, shape and fill (except for Nc and BR). They have low power at small sample size (small matrix size) | Patterson & Atmar, |
温度嵌套指数 Temperature metrics | T、BINMATNEST | 不受矩阵转换的影响, 但会受矩阵大小和填充度的影响; 在矩阵中添加非嵌套的特有物种后, T指数会错误地识别出嵌套格局 Temperature metrics are affected by matrix size and fill, but not by matrix transformation. T metric incorrectly indicates an increase in nestedness with the addition of nonnested endemics to matrices | Atmar & Patterson, |
重叠嵌套指数 Overlap metrics | HH | 会受到异常值的过度影响, 且没有被标准化 HH is excessively affected by outliers and is not standardized | Hausdorf & Hennig, |
NODF | 基于行和列填充的标准化差异, 并且可以将总嵌套分解为由列和行分别进行计算; 不受矩阵大小、形状和填充度的影响 NODF is based on standardized differences in row and column fills. It can decompose total nestedness into a sum of the nestedness introduced by columns and by rows separately. NODF is not affected by matrix size, shape and fill | Almeida-Neto et al, | |
WNODF | 基于NODF的一种简单修改, 用于计算物种分布的多度矩阵数据是否嵌套; 不受矩阵大小、形状和填充度的影响 WNODF is a simple modification of NODF and used to determine the nestedness of the species-by-sites abundance matrix. It is not affected by matrix size, shape and fill | Almeida-Neto & Ulrich, | |
功能和谱系嵌套指数 Functional and phylogenetic metrics | phyloNODF | 用物种的系统发育建树解释谱系多样性; 不受矩阵大小、填充度以及树拓扑的影响 phyloNODF can be calculated if a phylogeny is used to account for differences in phylogenetic diversity. It is robust for matrix size, matrix fill, and tree topology | Melo et al, |
traitNODF | 用功能性状建树解释功能多样性; 不受矩阵大小、填充度以及树拓扑的影响 traitNODF can be calculated if a functional dendrogram constructed from species ecological traits is used to account for the functional diversity. It is robust for matrix size, matrix fill, and tree topology | Melo et al, |
Fig. 2 The distribution of nestedness studies across the world. The figure is based on the results of 269 nestedness studies (excluding articles purely describing nestedness methods and review articles) originated from databases such as Web of Science and CNKI based on the keywords “nestedness” “nested subset” “nested pattern” and “nested assemblage” as of October 31, 2023. Number 1-5 indicates the increasing number of nestedness studies.
Fig. 3 The number of nestedness studies published from 1986 to 2023. The figure is based on the results of 269 nestedness studies (excluding articles purely describing nestedness methods and review articles) originated from databases such as Web of Science and CNKI based on the keywords “nestedness” “nested subset” “nested pattern” and “nested assemblage” as of October 31, 2023.
Fig. 4 The distribution of nestedness studies based on the countries of researchers (the numbers in the figure represent the percentage of publications). The figure is based on the results of 269 nestedness studies (excluding articles purely describing nestedness methods and review articles) originated from databases such as Web of Science and CNKI based on the keywords “nestedness” “nested subset” “nested pattern” and “nested assemblage” as of October 31, 2023.
名称 Names | 简称 Abbreviation | 特点 Characteristics | 参考文献 References | ||
---|---|---|---|---|---|
行限制方式 Row constraint | 列限制方式 Column constraint | 其他名称 Other names | |||
Fixed-Fixed | FF | 固定 Fixed | 固定 Fixed | SIM9 | Connor & Simberloff, |
Fixed-Equiprobable | FE | 固定 Fixed | 允许列总数自由变化 Equiprobable | SIM2, R0, Random0 | Patterson & Atmar, |
Equiprobable-Fixed | EF | 允许行总数自由变化 Equiprobable | 固定 Fixed | SIM3 | Gotelli, |
Equiprobable-Equiprobable | EE | 允许行总数自由变化 Equiprobable | 允许列总数自由变化 Equiprobable | SIM1, R00 | Atmar & Patterson, |
Fixedincidence-Proportional | FP | 固定 Fixed | 与物种出现成比例变化 Proportional to species incidences | SIM5, R1, Random1 | Patterson & Atmar, |
Lognormal-Fixed | LF | 与物种多度取对数成比例变化 Following a lognormal species abundance distribution | 固定 Fixed | - | Ulrich & Gotelli, |
Incidence-Proportional | IP | 与物种出现成比例变化 Proportional to species incidences | 与物种出现成比例变化 Proportional to species incidences | SIM8, Model 2 | Gotelli, Bascompte et al, |
Abundance-Proportional | AP | - | 与物种相对多度成比例变化 Proportional to species relative abundances | Randnest | Jonsson, |
Equiprobable-Proportional | EP | 允许行总数自由变化 Equiprobable | 与物种出现成比例变化 Proportional to species incidences | - | Fischer & Lindenmayer, |
Proportional | P | 与物种相对多度成比例变化 Proportional to species relative abundances | 与承载能力成比例变化 Proportional to carrying capacities | Recol | Moore & Swihart, |
Proportional-Proportional | PP | 与行和列的总数成比例变化, 而且行和列的总平均数与原始矩阵相同 Proportional to row and column totals, but the mean values of marginal totals match those of the original matrix | 与行和列的总数成比例变化, 而且行和列的总平均数与原始矩阵相同 Proportional to row and column totals, but the mean values of marginal totals match those of the original matrix | - | Ulrich & Gotelli, |
tipLabels | - | 不改变物种矩阵组成, 但会随机改变群落谱系构成的枝端结构 It shuffles the tip labels of the tree representation, but the site- by-species matrix is maintained intact | 不改变物种矩阵组成, 但会随机改变群落谱系构成的枝端结构 It shuffles the tip labels of the tree representation, but the site-by-species matrix is maintained intact | - | Melo et al, |
permRows | - | 随机改变矩阵的行(物种) Randomly reorders rows of the matrix | - | Melo et al, | |
permColumns | - | - | 随机改变矩阵的列(地点) Randomly reorders columns of the matrix | - | Melo et al, |
Table 3 Null models commonly used to infer the significance of nestedness
名称 Names | 简称 Abbreviation | 特点 Characteristics | 参考文献 References | ||
---|---|---|---|---|---|
行限制方式 Row constraint | 列限制方式 Column constraint | 其他名称 Other names | |||
Fixed-Fixed | FF | 固定 Fixed | 固定 Fixed | SIM9 | Connor & Simberloff, |
Fixed-Equiprobable | FE | 固定 Fixed | 允许列总数自由变化 Equiprobable | SIM2, R0, Random0 | Patterson & Atmar, |
Equiprobable-Fixed | EF | 允许行总数自由变化 Equiprobable | 固定 Fixed | SIM3 | Gotelli, |
Equiprobable-Equiprobable | EE | 允许行总数自由变化 Equiprobable | 允许列总数自由变化 Equiprobable | SIM1, R00 | Atmar & Patterson, |
Fixedincidence-Proportional | FP | 固定 Fixed | 与物种出现成比例变化 Proportional to species incidences | SIM5, R1, Random1 | Patterson & Atmar, |
Lognormal-Fixed | LF | 与物种多度取对数成比例变化 Following a lognormal species abundance distribution | 固定 Fixed | - | Ulrich & Gotelli, |
Incidence-Proportional | IP | 与物种出现成比例变化 Proportional to species incidences | 与物种出现成比例变化 Proportional to species incidences | SIM8, Model 2 | Gotelli, Bascompte et al, |
Abundance-Proportional | AP | - | 与物种相对多度成比例变化 Proportional to species relative abundances | Randnest | Jonsson, |
Equiprobable-Proportional | EP | 允许行总数自由变化 Equiprobable | 与物种出现成比例变化 Proportional to species incidences | - | Fischer & Lindenmayer, |
Proportional | P | 与物种相对多度成比例变化 Proportional to species relative abundances | 与承载能力成比例变化 Proportional to carrying capacities | Recol | Moore & Swihart, |
Proportional-Proportional | PP | 与行和列的总数成比例变化, 而且行和列的总平均数与原始矩阵相同 Proportional to row and column totals, but the mean values of marginal totals match those of the original matrix | 与行和列的总数成比例变化, 而且行和列的总平均数与原始矩阵相同 Proportional to row and column totals, but the mean values of marginal totals match those of the original matrix | - | Ulrich & Gotelli, |
tipLabels | - | 不改变物种矩阵组成, 但会随机改变群落谱系构成的枝端结构 It shuffles the tip labels of the tree representation, but the site- by-species matrix is maintained intact | 不改变物种矩阵组成, 但会随机改变群落谱系构成的枝端结构 It shuffles the tip labels of the tree representation, but the site-by-species matrix is maintained intact | - | Melo et al, |
permRows | - | 随机改变矩阵的行(物种) Randomly reorders rows of the matrix | - | Melo et al, | |
permColumns | - | - | 随机改变矩阵的列(地点) Randomly reorders columns of the matrix | - | Melo et al, |
假说Hypothesis | 前提或假设 Assumption | 预测 Prediction | 例子 Examples | |
---|---|---|---|---|
地点特征 Site properties | 物种特征 Species properties | |||
被动取样 Passive sampling | 容纳力 Carrying capacities | 地区多度(常见种/偶见种) Regional abundance (common/rare species) | 地区的物种多度决定了岛屿占有情况, 因为常见种与偶见种相比更容易被调查到 Regional abundance predicts island occupancy because rare species are less likely to be sampled in a given area than common species | Andrén, |
选择性灭绝 Selective extinction | 容纳力 Carrying capacities | 灭绝敏感性(最小面积需求、体型大小、地理分布范围等) Extinction sensitivity (e.g., minimum area requirement, body size, and geographic range size) | 研究地点的面积决定了物种在生境中的选择性出现, 因为最小面积需求大或具有其他易灭绝特征的物种更容易发生灭绝 Area is the main factor explaining species nestedness because species with large minimum area requirements and other extinction-prone traits have greater extinction risk | Patterson & Atmar, |
选择性迁移 Selective colonization | 隔离度 Isolation | 扩散能力 Dispersal ability | 研究地点的隔离度和物种的扩散能力(如身体大小、游泳能力)决定了物种在生境中的选择性出现 Selective occupancy of islands according to island isolation and species traits related to dispersal capacity (e.g., body size, swimming ability) | Darlington, |
栖息地嵌套 Habitat nestedness | 栖息地异质性 Habitat heterogeneity | 栖息地专属性 Degree of specialization | 与栖息地特化种相比, 栖息地通才在面积小或资源少的斑块中具有较高的出现率 Compared with specialist species, generalist species can occupy higher proportion of smaller and/or resource poor patches | Wright & Reeves, |
人为干扰 Human disturbance | 干扰大小 Degree of disturbance | 干扰容忍性 Disturbance tolerances | 物种在栖息地中的出现由人为干扰决定, 因为对干扰敏感性高的物种更容易发生灭绝 Human disturbance predicts island occupancy because species vulnerable to disturbance are more likely to extinct | Fernández-Juricic, |
Table 4 Common hypotheses for explaining the nested subset pattern (nestedness)
假说Hypothesis | 前提或假设 Assumption | 预测 Prediction | 例子 Examples | |
---|---|---|---|---|
地点特征 Site properties | 物种特征 Species properties | |||
被动取样 Passive sampling | 容纳力 Carrying capacities | 地区多度(常见种/偶见种) Regional abundance (common/rare species) | 地区的物种多度决定了岛屿占有情况, 因为常见种与偶见种相比更容易被调查到 Regional abundance predicts island occupancy because rare species are less likely to be sampled in a given area than common species | Andrén, |
选择性灭绝 Selective extinction | 容纳力 Carrying capacities | 灭绝敏感性(最小面积需求、体型大小、地理分布范围等) Extinction sensitivity (e.g., minimum area requirement, body size, and geographic range size) | 研究地点的面积决定了物种在生境中的选择性出现, 因为最小面积需求大或具有其他易灭绝特征的物种更容易发生灭绝 Area is the main factor explaining species nestedness because species with large minimum area requirements and other extinction-prone traits have greater extinction risk | Patterson & Atmar, |
选择性迁移 Selective colonization | 隔离度 Isolation | 扩散能力 Dispersal ability | 研究地点的隔离度和物种的扩散能力(如身体大小、游泳能力)决定了物种在生境中的选择性出现 Selective occupancy of islands according to island isolation and species traits related to dispersal capacity (e.g., body size, swimming ability) | Darlington, |
栖息地嵌套 Habitat nestedness | 栖息地异质性 Habitat heterogeneity | 栖息地专属性 Degree of specialization | 与栖息地特化种相比, 栖息地通才在面积小或资源少的斑块中具有较高的出现率 Compared with specialist species, generalist species can occupy higher proportion of smaller and/or resource poor patches | Wright & Reeves, |
人为干扰 Human disturbance | 干扰大小 Degree of disturbance | 干扰容忍性 Disturbance tolerances | 物种在栖息地中的出现由人为干扰决定, 因为对干扰敏感性高的物种更容易发生灭绝 Human disturbance predicts island occupancy because species vulnerable to disturbance are more likely to extinct | Fernández-Juricic, |
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