Juan Manuel Gorospe

Determining species boundaries is key for appropriately assessing biodiversity. However, the continuity of the speciation process makes delimiting species a difficult task, especially for recently diverged taxa. Furthermore, past introgression may leave traces that result in reticulate evolutionary patterns, challenging the estimation of species relationships. The fastest‐evolving biodiversity hotspot on Earth is the Páramo. Its flora in the tropical high Andes is known for extraordinarily high species richness and endemism. However, the recent origin, fast diversification and complex taxonomy of many genera challenge species delimitation and phylogenetic reconstruction. In this study, we reconstructed phylogenetic relationships and addressed the role of introgression in the diversification of Oritrophium s.s. (Asteraceae) based on phylogenomic data. We combined genomic, phenotypic and ecological data to test species boundaries and compared trajectories across the speciation continuum within the taxonomically complex ‘ O. peruvianum group’. We found that historical introgression played an important role in the evolution of Oritrophium s.s., and many of the taxa within the ‘ O. peruvianum group’ are at various stages of speciation. These results highlight the importance of testing for introgression to understand the diversification of recently evolved groups. Likewise, they suggest that heterogeneous speciation trajectories associated with geographic isolation and secondary contact, possibly during the Pleistocene, contributed to plant diversity in the tropical high Andes.

Summary: Mountains have highly heterogeneous environments that generate ample opportunities for lineage differentiation through ecological adaptation, geographic isolation and secondary contact. The geographic and ecological isolation of the afroalpine vegetation fragments on the East African mountain tops makes them an excellent system to study speciation. The initial diversification within the afroalpine endemic genus Dendrosenecio was shown to occur via allopatric divergence among four isolated mountain groups, but the potential role of ecological speciation within these groups and the role of gene flow in speciation remained uncertain. Here we extend the sampling of Dendrosenecio and use phylogenomics to assess the importance of gene flow in the diversification of the genus. Then, population genomics, demographic modelling and habitat differentiation analyses are used to study ecological speciation in two sister species occurring on Mount Kenya. We found that two sympatric sister species on Mt Kenya occupy distinct microhabitats, and our analyses support that they originated in situ via ecological speciation with gene flow. In addition, we obtained signals of admixture history between mountain groups. Taken together, these results suggest that geographic isolation shaped main lineages, while ecologically mediated speciation occurred within a single mountain.

Habitat stability is important for maintaining biodiversity by preventing species extinction, but this stability is being challenged by climate change. The tropical alpine ecosystem is currently one of the ecosystems most threatened by global warming, and the flora close to the permanent snow line is at high risk of extinction. The tropical alpine ecosystem, found in South and Central America, Malesia and Papuasia, Africa, and Hawaii, is of relatively young evolutionary age, and it has been exposed to changing climates since its origin, particularly during the Pleistocene. Estimating habitat loss and gain between the Last Glacial Maximum (LGM) and the present allows us to relate current biodiversity to past changes in climate and habitat stability. In order to do so, (i) we developed a unifying climate‐based delimitation of tropical alpine regions across continents, and (ii) we used this delimitation to assess the degree of habitat stability, that is, the overlap of suitable areas between the LGM and the present, in different tropical alpine regions. Finally, we discuss the link between habitat stability and tropical alpine plant diversity. Our climate‐based delimitation approach can be easily applied to other ecosystems using our developed code, facilitating macro‐comparative studies of habitat dynamics through time.

Aim: The tribe Antirrhineae, including snapdragons, toadflaxes and relatives, is widely distributed across the Northern Hemisphere and the Neotropics. It displays an uneven distribution of diversity, with more than 50% of species and subspecies in the Mediterranean Region. Here we conducted the first detailed, worldwide biogeographic analysis of the Antirrhineae and tested two alternative hypotheses (time‐for‐speciation versus diversification rate differences) to explain the uneven distribution of diversity.Location: Worldwide, with a focus on the Mediterranean Region.Taxon: Tribe Antirrhineae (Plantaginaceae).Methods: A phylogenetic biogeographic approach was taken, accounting for area connections through time. Ancestral ranges, dispersal events, speciation and lineage accumulation within areas were estimated. Diversification rates for taxa present and absent in the Mediterranean Region were compared, accounting for the effect of a floral key innovation (nectar spur).Results: A proto‐Mediterranean origin in the Late Eocene was estimated, and the Mediterranean Region stood out as the main centre for speciation and dispersal. Congruent patterns of long‐distance dispersal from the Mediterranean Region to North America were recovered for at least two amphiatlantic clades. A significant floristic exchange between the Mediterranean and south‐western Asia was detected. We found no evidence of different diversification rates between lineages inside and outside the Mediterranean Region.Main conclusions: The Mediterranean Region played a key role in the origin of the current distribution of the Antirrhineae. However, the higher species richness found in this region appears to be the result of a time‐for‐speciation effect rather than that of increased diversification rates. The establishment of current Mediterranean climates in the Northern Hemisphere appears to have contributed to the recent diversification of the group, in combination with colonization of adjacent regions with arid and semi‐arid climates.

Aim: The tribe Antirrhineae, including snapdragons, toadflaxes and relatives, is a model group for plant evolutionary research. It is widely distributed across the Northern Hemisphere and the Neotropics, but displays an uneven distribution of diversity, with more than 50% of species and subspecies in the Mediterranean Region. Here we conducted the first detailed, worldwide biogeographic analysis of the Antirrhineae and tested two alternative hypotheses (time-for-speciation vs. diversification rate differences) to explain the uneven distribution of diversity.Location: Worldwide, with a focus on the Mediterranean Region.Taxon: tribe Antirrhineae (Plantaginaceae).Methods: A phylogenetic biogeographic approach was taken, accounting for area connections through time. Ancestral ranges, dispersal events, speciation and lineage accumulation within areas were estimated. Diversification rates for taxa present and absent in the Mediterranean Region were compared, accounting for the effect of a floral key innovation (nectar spur).Results: A proto-Mediterranean origin in the Late Eocene was estimated, and the Mediterranean Region stood out as the main centre for speciation and dispersal. Congruent patterns of long-distance dispersal from the Mediterranean Region to North America were recovered for at least two amphiatlantic clades. A significant floristic exchange between the Mediterranean and south-western Asia was detected. We found no evidence of different diversification rates between lineages inside and outside the Mediterranean Region.Main conclusions: The Mediterranean Region played a key role in the origin of the current distribution of the Antirrhineae. However, the higher species richness found in this region appears to be the result of a time-for-speciation effect rather than of increased diversification rates. The establishment of current mediterranean climates in the Northern Hemisphere appears to have contributed to the recent diversification of the group, in combination with colonisation of adjacent regions with arid and semi-arid climates.

El objetivo de este trabajo fue proponer una metodología que permita medir cuantitativamente los efectos de actividades de restauración a escala de paisaje, comparando una condición inicial de conservación, con otra condición ideal, denominada paisaje de referencia, creada proyectando los cambios esperados por la restauración. Definido el paisaje de referencia se propuso evaluar índices de paisaje que permitieran cuantificar la ganancia en conservación lograda por la restauración. Para ello, se trabajó en una cuenca con alto grado de conservación. Los índices usados fueron: efecto borde, índice de diversidad del paisaje, índice de forma e índice de continuidad espacial, aplicándose cada uno de ellos a la condición inicial y al paisaje de referencia. Para el caso estudiado, el paisaje de referencia fue simple y sencillo de definir debido a la vasta información relativa a los bosques de la zona. En la etapa de evaluación de los índices del paisaje usado, los que presentaron el mejor desempeño para cuantificar la mejora en conservación fueron el de efecto borde y el de continuidad del paisaje. El índice de forma, en cambio, generó valores confusos entre la condición inicial y el paisaje de referencia, ya que el valor del índice aumenta o empeora solo por el aumento de la superficie. Así también el índice de diversidad obliga a un análisis complejo, principalmente porque la restauración modifica el número de clases de la condición inicial respecto al paisaje de referencia.