Based on a study of 22 sites in northeastern Brazil, including the three main vegetation types, coastal Mata Atlântica (Zona da Mata), Caatinga and Brejos de Altitude (rain forest enclaves in Caatinga areas), we studied the distribution and habitat preferences of 456 crustose and microfoliose lichen species. Alpha-diversity ranged between three and 99 species per site, with Zona da Mata and Brejos de Altitude showing higher numbers than Caatinga sites. Beta-diversity (dissimilarity) was highest between Zona da Mata sites and, as a whole, the Zona da Mata showed the highest gamma-diversity, with a total of 334 species. Site ordination by non-metric multidimensional scaling (NMS), as well as cluster analysis, both using Sørensen's coefficient of dissimilarity, show that Zona da Mata and Caatinga sites have distinctive lichen species compositions, with the isolated Brejos de Altitude being more similar to coastal Zona da Mata than to Caatinga sites. Exposed Zona da Mata sites have certain species in common with Caatinga sites but overall cluster with the Zona da Mata sites. The transitional Agreste vegetation (one study site) also appears transitional between Zona da Mata and Caatinga in its lichen species composition. Indicator species analysis for each vegetation type was performed by applying a Monte-Carlo test. Other than ten ubiquitous taxa (found in all three vegetation types), 59 taxa were shared between Zona da Mata and Brejos de Altitude, 20 between Zona da Mata and Caatinga, and none between Brejos de Altitude and Caatinga. Dissimilarity values of Zona da Mata versus Brejos de Altitude sites were high (0.77 or 23% shared species on average), as were those of Zona da Mata versus Caatinga sites (average of 0.92 or 8% shared species). Zona da Mata lichens had a higher proportion of Arthoniomycetidae (Arthoniales: Arthoniaceae, Roccellaceae) and Chaetothyriomycetidae (Pyrenulales: Pyrenulaceae), as well as Porinaceae and Thelotremataceae; frequently trentepohlioid photobionts, predominantly transversely septate and/or narrow ascospores, and lack of lichen substances. Brejos de Altitude lichens showed a higher proportion of Dothideomycetiae (Trypetheliaceae) and Ostropomycetidae (Ostropales: Gomphillaceae and Graphidaceae), as well as Pilocarpaceae; ascospores were predominantly thick-walled or muriform and hyaline. Caatinga sites were dominated by Lecanoromycetidae (Lecanorales: Lecanoraceae; Teloschistales: Physciaceae) and Pertusariales (Pertusariaceae); taxa were chiefly associated with chlorococcoid photobionts, ascospores were megalosporous, non-septate and/or brown, and showed a predominance of certain cortical substances (atranorin, lichexanthone other xanthones, pulvinic acid derivates), as well as norstictic acid as medullary substance.
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