Diversification patterns of Solanum L. (Solanaceae), plant macroecology and responses to land-use change

Current patterns of biodiversity reflect, to a certain degree, the legacy effects of species adaptations to past environmental and geological settings. A more in-depth understanding of this history and the traits that shape it, therefore, will help us to improve our predictions of how species will respond to current environmental change. In this thesis, I apply different analytical approaches to a range of case studies at a variety of taxonomic and geographic scales to test the importance of this fundamental hypothesis. To examine the consequences of evolutionary and biogeographic history on the evolution of global biodiversity, in Chapter 2, I focus on the hyperdiverse plant genus Solanum (ca. 1300 species). This genus is an ideal case study since it combines a complete high-level phylogeny with global species distribution data, and covers an ecological spectrum from endemics to weeds. Chapter 2 shows that the vast diversity of Solanum is the result of at least two radiations. The majority of the lineages distributed in the Old World represent the most significant recent radiation, diversifying nearly twice as rapidly as any other group of solanums. This chapter also provides a brief comparison of the current approaches for modelling multi-rate diversification. In Chapter 3, I explore how the evolutionary legacy of colonisation, dispersal and climatic history have affected patterns of diversity in the genus. In this chapter, I show how successful colonisation of new areas and environmental changes can — but does not always — drive explosive diversification. In Chapter 3, I show how arid-adapted lineages within Solanum have benefited from widespread habitat drying over the last few million years. This successful expansion reveals the potential evolutionary capacity of this group to expand and colonise currently disturbed and open areas, which is supported by the spread of some species considered as weeds such as S. elaeagnifolium, S. torvum, S. nigrum. In Chapter 4, therefore, I undertake a global analysis to assess whether the climatic preferences that have shaped the macroevolution of Solanum are now also shaping plant macroecology worldwide. For this analysis, I broaden my taxonomic scope to consider all plants, analysing an extensive global database that I helped to compile on how terrestrial assemblages respond to land use change, using a simple and very coarse classification of land use. In this chapter, I demonstrate that species adapted to mesic conditions are highly sensitive to habitat conversion, compared with widespread arid and warmer-adapted species. These results show how land-use and climate change may favour similar species, thus potentially increasing the rate of homogenisation caused in the Anthropocene. As shown in Chapter 4 species’ responses to current environmental changes vary widely, depending on their ecological traits and climatic adaptations. This heterogeneity of responses could drive significant rearrangements in the composition of ecosystems, especially in the tropics where most of the species with narrow geographic and climatic ranges are found. In chapter 5, therefore, I quantify the impacts of land-use change on the composition of tropical assemblages using Colombia as a case study. In this chapter, I statistically analyse plant and animal data from 285 sites in Colombia to model how terrestrial assemblages are responding to land use change, using a much more finely resolved land-use classification than that used in Chapter 4. I combine these models with four projections of land use to investigate how diversity is expected to change under future scenarios associated with different climate change policies. Here I demonstrate that land-use change has driven an increasing change in the composition of the ecological assemblages in Colombia and that depending on the policies implemented in the future, this negative effect could continue, risking the quality of ecosystems unless the impacts are mitigated.Open Acces

MartiTracks: A Geometrical Approach for Identifying Geographical Patterns of Distribution

Panbiogeography represents an evolutionary approach to biogeography, using rational cost-efficient methods to reduce initial complexity to locality data, and depict general distribution patterns. However, few quantitative, and automated panbiogeographic methods exist. In this study, we propose a new algorithm, within a quantitative, geometrical framework, to perform panbiogeographical analyses as an alternative to more traditional methods. The algorithm first calculates a minimum spanning tree, an individual track for each species in a panbiogeographic context. Then the spatial congruence among segments of the minimum spanning trees is calculated using five congruence parameters, producing a general distribution pattern. In addition, the algorithm removes the ambiguity, and subjectivity often present in a manual panbiogeographic analysis. Results from two empirical examples using 61 species of the genus Bomarea (2340 records), and 1031 genera of both plants and animals (100118 records) distributed across the Northern Andes, demonstrated that a geometrical approach to panbiogeography is a feasible quantitative method to determine general distribution patterns for taxa, reducing complexity, and the time needed for managing large data sets

The PREDICTS database: a global database of how local terrestrial biodiversity responds to human impacts

Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species’ threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project – and avert – future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups – including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems – www.predicts.org.uk). We make site-level summary data available alongside this article. The full database will be publicly available in 2015

Basic units of congruence.

<p>Segments of the MSTs are the basic units of congruence between two species. Each segment belonging to the is defined as an edge that connects two endpoint vertices .</p

Decision rules of congruence.

<p>MartiTracks takes the minimum, and the maximum distances between segments to define the decision rules of congruence. Given two segments , and belonging to species and , respectively; two segments are congruent if: <b>A</b>. the first condition of congruence is fulfilled (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0018460#pone-0018460-g004" target="_blank">Figure 4A</a>), and if () and () are true. <b>B</b>. If both have intersecting points on or if both have intersecting points on (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0018460#pone-0018460-g004" target="_blank">Figure 4B</a>); and if (0dmax.linelmax.line) is true.</p

Conditions of congruence.

<p>MartiTracks considers two segments , and as congruent, <b>A</b>. if any of the vertices has an intersecting point on edge , or if any of the vertices has an intersecting point on edge <b>B</b>. if both vertices intersect on edge , or if both vertices intersect on edge . <b>C</b>. There is no congruence between segments if there is no intersecting points between them.</p

Distance from a point to a segment.

<p>The distance from point (P3) to segment (P1–P2) is calculated by the distance between point P3 and the intersecting point (P), resulting from the perpendicular extension of P3 towards segment (P1–P2).</p

Similarity index (SI).

<p>MartiTracks calculates the similarity among tracks through a similarity index (SI). Given two tracks , (either individual, or generalized tracks), the similarity index is the length of the congruent segments from to divided by the total length of the . In the same way the similarity index is the length of the congruent segments from to divided by the total length of the .</p