Past environmental changes have shaped the evolutionary and ecological diversity of extant organisms. Specifically, climatic fluctuations have made environmental conditions alternatively common or rare over time. Accordingly, most taxa have undergone restriction of their distribution to local refugia during habitat contraction, from which they could expand when suitable habitat became more common. Assessing how past restrictions in refugia have shaped species distributions and genetic diversity has motivated much research in evolutionary biology and biogeography. But there is still lack of clear synthesis on whether and how the taxonomic, functional and phylogenetic composition of extant multispecies assemblages retains the imprint of past restriction in refugia. We devised an original eco-evolutionary model to investigate the temporal dynamics of a regional species pool inhabiting a given habitat today, and which have experienced habitat reduction in the past. The model includes three components: (i) a demographic component driving stochastic changes in population sizes and extinctions due to habitat availability, (ii) a mutation and speciation component representing how divergent genotypes emerge and define new species over time, and (iii) a trait evolution component representing how trait values have changed across descendants over time. We used this model to simulate dynamics of multispecies assemblages that occupied a restricted refugia in the past and could expand their distribution subsequently. We characterized the past restriction in refugia in terms of two parameters representing the ending time of past refugia, and the extent of habitat restriction in the refugia. We characterized extant patterns of taxonomic, functional and phylogenetic diversity depending on these parameters. We found that extant relative abundances reflect the lasting influence of more recent refugia on demographic dynamics, while phylogenetic composition reflects the influence of more ancient habitat change. Extant functional diversity depends on the interplay between diversification dynamics and trait evolution, offering new options to jointly infer current trait adaptation and past trait evolution dynamics.

Aim Indian and Malagasy tropical rainforests share a common history that dates back to the fragmentation of Gondwana. We partitioned phylogenetic diversity across historical periods to uncover how such continental displacement led to the divergence of lineages, through vicariance and/or independent migration from other regions, influencing extant phylogenetic composition. Location Madagascar and South India (Western Ghats). Taxon Woody vascular plants (tracheophytes). Methods Using a time‐calibrated megaphylogeny, we partitioned the phylogenetic diversity of Indian and Malagasy tropical rainforest assemblages, across evolutionary periods defined based on milestone events in these regions of geological history. We decomposed the relative proportion of lineages with extant representatives in each area as well as in both areas, to quantify the common and separate biogeographical legacies in the two regions. We identified an excess or deficit of shared and unique lineages for each period and region. Results The proportion of shared lineages between Madagascar and India progressively decreased following the successive breakoff and isolation of Madagascar from the Indian‐Malagasy plate. Lineages unique to India are more numerous than expected at random in more recent time periods, whereas, lineages unique to Madagascar were significantly more present in older time periods. Main conclusions The flora of Madagascar harbours a greater number of ancient lineages than does the Western Ghats, consistent with the higher number of endemic families and genera of trees in Madagascar. More recent diversification in India could be related to the collision of India with Eurasia, which enabled subsequent biological interchanges.