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Background  Species or clades may retain or shift their environmental niche space over evolutionary time. Understanding these processes offers insights into the environmental processes fuelling lineage diversification and might also provide information on past range dynamics of ecosystems. However, little is known about the relative contributions of niche conservatism versus niche divergence to species diversification in the tropics. Here, we examined broad-scale patterns of niche evolution within a Pliocene–Pleistocene clade of epiphytic  Bulbophyllum  orchids (30 spp.) whose collective distribution covers the northwest and eastern forest ecosystems of Madagascar.    Results  Using species occurrence data, ecological niche models, and multivariate analyses of contributing variables, we identified a three-state niche distribution character for the entire clade, coinciding with three major forest biomes  viz . phytogeographical provinces in Madagascar:  A , Northwest ‘Sambirano’;  B , ‘Eastern Lowlands’; and  C , ‘Central Highlands’. A time-calibrated phylogeny and Bayesian models of niche evolution were then used to detect general trends in the direction of niche change over the clade’s history (≤5.3 Ma). We found highest transitions rates between lowlands ( A  and  B ) and (mostly from  B ) into the highland ( C ), with extremely low rates out of the latter. Lowland-to-highland transitions occurred frequently during the Quaternary, suggesting that climate-induced vegetational shifts promoted niche transitions and ecological speciation at this time.    Conclusions  Our results reveal that niche transitions occurred frequently and asymmetrically within this Madagascan orchid clade, and in particular over Quaternary time scales. Intrinsic features germane to  Bulbophyllum  (e.g., high dispersal ability, drought tolerance, multiple photosynthetic pathways) as well as extrinsic factors (ecological, historical) likely interacted to generate the niche transition patterns observed. In sum, our results support the emerging idea of dramatic environmental and climatic fluctuations in Madagascar during the recent geological past, which overturns the long-held paradigm of long-term stability in tropical forest settings. The generality of the patterns and timings reported here awaits the availability of additional comparative studies in other Madagascan endemics.    Electronic supplementary material  The online version of this article (doi:10.1186/s12862-016-0586-3) contains supplementary material, which is available to authorized users.

Frequent but asymmetric niche shifts in Bulbophyllum orchids support environmental and climatic instability in Madagascar over Quaternary time scales