Deep reefs are not refugium for shallow-water fish communities in the southwestern Atlantic

1. The deep reef refugia hypothesis (DRRH) predicts that deep reef
ecosystems may act as refugium for the biota of disturbed shallow waters.
Because deep reefs are amongst the most understudied habitats on Earth,
formal tests of the DRRH remain scarce. If the DRRH is valid at the
community level, the diversity of species, functions and lineages of fish
communities of shallow reefs should be encapsulated in deep reefs. 2. We
tested the DRRH by assessing the taxonomic, functional and phylogenetic
diversity of 22 Brazilian fish communities between 2 and 62m depth. We
partitioned the gamma diversity of shallow (<30m) and deep reefs
(>30m) into independent alpha and beta components, accounted for
species’ abundance, and assessed if beta patterns were mostly driven by
spatial turnover or nestedness. 3. We recorded 3821 fishes belonging to 85
species and 36 families. Contrary to DRRH expectations, only 48% of the
species occurred in both shallow and deep reefs. Alpha diversity of rare
species was higher in deep reefs as expected, but alpha diversity of
typical and dominant species did not vary with depth. Alpha functional
diversity was higher in deep reefs only for rare and typical species, but
not for dominant species. Alpha phylogenetic diversity was consistently
higher in deep reefs, supporting DRRH expectations. 4. Profiles of
taxonomic, functional, and phylogenetic beta diversity indicated that deep
reefs were not more heterogeneous than shallow reefs, contradicting
expectations of biotic homogenization near sea surface. Furthermore,
pairwise beta diversity analyses revealed that the patterns were mostly
driven by spatial turnover rather than nestedness at any depth. 5.
Conclusions: Although some results support the DRRH, most
indicate that the shallow-water reef fish diversity are not fully
encapsulated in deep reefs. Every reef contributes significantly to the
regional diversity and must be managed and protected accordingly.

1. 深海礁庇护假说（Deep Reef Refugia Hypothesis, DRRH）预测，深海礁生态系统可作为受干扰浅水区生物群落的庇护所。由于深海礁是地球上研究程度最低的生境之一，针对DRRH的正式检验仍较为匮乏。若DRRH在群落层面成立，则浅礁鱼类群落的物种、功能与谱系多样性应当完全涵盖于深海礁之中。
2. 本研究通过评估22个巴西鱼类群落在2至62米水深下的分类多样性（taxonomic diversity）、功能多样性（functional diversity）与系统发育多样性（phylogenetic diversity），对DRRH进行了检验。我们将浅礁（水深<30米）与深海礁（水深>30米）的γ多样性（gamma diversity）拆分为相互独立的α多样性（alpha diversity）与β多样性（beta diversity）组分，同时纳入物种丰度信息，并检验了β多样性模式主要由空间周转（spatial turnover）还是嵌套结构（nestedness）驱动。
3. 本次调查共记录鱼类3821尾，隶属于85个物种、36个科。与DRRH的预期相悖，仅有48%的物种同时分布于浅礁与深海礁中。稀有物种的α多样性在深海礁中更高，符合预期，但典型与优势物种的α多样性并未随水深发生显著变化。仅在稀有与典型物种类群中，深海礁的α功能多样性显著高于浅礁，而优势物种类群未表现出该差异。α系统发育多样性在深海礁中始终显著更高，这一结果支持DRRH的预期。
4. 分类、功能与系统发育β多样性的分布特征显示，深海礁的群落异质性并未高于浅礁，这与近海面生物群落同质化的预期相悖。此外，成对β多样性分析显示，无论在何种水深下，β多样性模式主要由空间周转驱动，而非嵌套结构。
5. 结论：尽管部分研究结果支持DRRH，但绝大多数结果表明，浅礁珊瑚礁鱼类的多样性并未完全囊括于深海礁之中。每一类礁生境均对区域物种多样性具有重要贡献，因此应当据此开展针对性的管理与保护工作。