Birds and Barriers: present and past seas are dominant correlates of avian turnover in the Indo-Australia Archipelago.

<strong>Appendix S1.</strong> R code used in analyses with associated data <br> <strong>Abstract</strong> The Indo-Australian Archipelago (IAA) is a geologically dynamic area of high biotic endemism that spans the continental shelves of Sunda and Sahul and intervening oceanic islands. We provide a comprehensive quantitative assessment of how bird communities are structured across the IAA using beta diversity indices. We focus on three key questions. Are the islands of Wallacea a biogeographically cohesive unit or a more heterogeneous transition zone? Is the rich biota of New Guinea and the East Melanesian islands most closely linked to that of Sunda, Sahul or Wallacea? What are the geographic and environmental correlates of biotic structuring across the region and how does this compare with determinants of plant diversity? We measure the dissimilarity of bird species composition between eleven major areas within the IAA using a new compilation of distribution data and calculate taxonomic beta diversity at species, genera, and family levels. To compare with recent analyses of plants, we analysed potential correlates of turnover, focusing on geographic proximity, sea barriers, land area, and climatic variation. We also used connectivity analyses to estimate the minimum number of connection events needed to explain the current distribution of shared taxa. We found that islands recently connected by land have lower beta diversity than oceanic islands. Additionally, avifaunas on the islands of Wallacea have little biotic cohesion, reflecting their complex geological history. The avifaunas of New Guinea and the Eastern Melanesian islands are very distinctive. Where New Guinea birds are most similar to Australia, East Melanesian birds are more similar to either Sahul or Wallacea, depending on taxonomic level. Isolation through space and time had the strongest influence on avifaunal turnover at all taxonomic scales, in contrast to plants for which climatic variation was the strongest predictor. Further analyses incorporating phylogeny, biome, trait, and biotic interaction data are needed to investigate the processes that have caused biotic turnover across this fascinating biogeographic region.

**附录S1** 本研究分析所用的R代码及配套数据集
**摘要** 印澳群岛（Indo-Australian Archipelago, IAA）是一个地质活动活跃、生物特有性极高的区域，涵盖巽他陆架（Sunda）、萨胡尔陆架（Sahul）及其间的大洋岛屿。本研究借助β多样性指数（beta diversity indices），对印澳群岛内鸟类群落的组构模式开展了全面的定量评估。我们聚焦于三个核心科学问题：其一，华莱士区（Wallacea）的岛屿是否构成一个生物地理上的连贯单元，抑或是一个更为异质的过渡带？其二，新几内亚与东美拉尼西亚群岛的丰富生物区系，与巽他、萨胡尔或华莱士区的生物区系亲缘关系最近？其三，整个区域内生物组构的地理与环境关联因子是什么，且这一结果与植物多样性的决定因子有何异同？

本研究基于全新编制的分布数据集合，测算印澳群岛内11个主要区域间鸟类物种组成的差异度，并分别在物种、属及科水平上计算分类学β多样性。为与近期的植物研究分析进行对比，我们分析了鸟类区系更替的潜在关联因子，重点考察地理邻近性、海洋阻隔、陆地面积及气候变异。此外，我们还借助连通性分析，估算解释当前共有类群分布格局所需的最少连通事件数。

研究发现，近期通过陆地相连的岛屿，其β多样性低于大洋岛屿。此外，华莱士区岛屿的鸟类区系几乎不存在生物连贯性，这反映了其复杂的地质历史。新几内亚与东美拉尼西亚群岛的鸟类区系极具独特性。当新几内亚鸟类与澳大利亚鸟类相似度最高时，东美拉尼西亚鸟类的亲缘类群则依分类学水平的不同，更接近萨胡尔或华莱士区的类群。

与以气候变异为最强预测因子的植物类群不同，时空隔离对所有分类学尺度下的鸟类区系更替均具有最显著的影响。未来需整合系统发育、生物群区、功能性状及生物互作数据开展进一步分析，以探究驱动这一极具研究价值的生物地理区域内生物区系更替的具体过程。