Javier Igea

University of Cambridge | Cam · Department of Plant Sciences

Speciation on islands, and particularly the divergence of species in situ, has long been debated. Here, we present one of the first, complete assessments of the geographic modes of speciation for the flora of a small oceanic island. Cocos Island (Costa Rica) is pristine; it is located 550 km off the Pacific coast of Central America. It harbours 189...

Species diversity varies greatly across the different taxonomic groups that comprise the Tree of Life (ToL). This imbalance is particularly conspicuous within angiosperms, but is largely unexplained. Seed mass is one trait that may help clarify why some lineages diversify more than others because it confers adaptation to different environments, whi...

Why is species diversity so unevenly distributed across different regions on Earth? Regional differences in biodiversity may stem from differences in rates of speciation and dispersal and colonization times, but these hypotheses have rarely been tested simultaneously at a global scale. Our study reveals the macroevolutionary routes that have genera...

Recent evidence has questioned whether the Latitudinal Diversity Gradient (LDG), whereby species richness increases towards the Equator, results in higher rates of speciation in the tropics. Allowing for time heterogeneity in speciation rate estimates for over 60,000 angiosperm species, we found that the LDG does not arise from variation in speciat...

Extinction threatens many species, yet is predicted by few factors across the plant Tree of Life (ToL). Taxon age is one factor that may associate with extinction if occupancy of geographic and adaptive zones varies with time, but evidence for such an association has been equivocal. Age-dependent occupancy can also influence diversification rates a...

Aim How mountains accumulate species diversity remains poorly understood, particularly the relative role of in situ cladogenesis compared with colonization from lower elevations. Here, we estimated the contributions of in situ cladogenesis and colonization in generating biodiversity of a large mountain plant radiation and determined the importance...

Topographic change shapes the evolution of biodiversity by influencing both habitat connectivity and habitat diversity as well as abiotic factors like climate. However, its role in creating global biodiversity gradients remains poorly characterized because geology, climate and evolutionary data have rarely been integrated across concordant timescal...

Premise: Recent, rapid radiations present a challenge for phylogenetic reconstruction. Fast successive speciation events typically lead to low sequence divergence and poorly resolved relationships with standard phylogenetic markers. Target sequence capture of many independent nuclear loci has the potential to improve phylogenetic resolution for ra...

Whole genome duplication or polyploidy is widespread amongst floras globally, but traditionally has been thought to have played a minor role in the evolution of island biodiversity, based on the low proportion of polyploid taxa present. We investigate five island systems (Juan Fernández, Galápagos, Canary Islands, Hawai'i, and New Zealand) to test...

Aim Different species assemblages of annual killifish possess replicated body size distributions yet have unique sets of species in each area of endemism. Here, we use models of trait evolution and historical biogeography to discover how size variation originated and has been restructured. Location South America. Taxon Austrolebias (Cyprinodontif...

The idea that populations must be geographically isolated (allopatric) to evolve into separate species has persisted for a long time. It is now clear that new species can also diverge despite ongoing genetic exchange, but few accepted cases of speciation in sympatry have held up when scrutinised using modern approaches. Here, we examined evidence f...

Although it is now widely accepted that speciation can occur in the face of continuous gene flow, with little or no spatial separation, the mechanisms and genomic architectures that permit such divergence are still debated. Here, we examined speciation in the face of gene flow in the Howea palms of Lord Howe Island, Australia. We built a genetic ma...

Recent evidence has questioned whether the Latitudinal Diversity Gradient (LDG), whereby species richness increases towards the Equator, results from higher rates of speciation in the tropics. Allowing for time heterogeneity in speciation rate estimates for over 28,000 angiosperm species, we found that the LDG does not arise from variation in speci...

Why is species diversity so unevenly distributed across different regions on Earth? Regional differences in biodiversity may stem from differences in rates of speciation and dispersal and colonization times, but these hypotheses have rarely been tested simultaneously at a global scale. Here we uncovered the routes that generated hotpots of mammal a...

Reconstructions of evolutionary and historical biogeographic processes can improve our understanding of how species assemblages developed and permit inference of ecological drivers affecting coexistence. We explore this approach in Austrolebias, a genus of annual fishes possessing a wide range of body sizes. Regional assemblages composed of differe...

Extinction threatens many species, yet few factors predict this risk across the plant Tree of Life (ToL). Taxon age is one factor that may associate with extinction if occupancy of geographic and adaptive zones varies with time, but evidence for such an association has been equivocal. Age-dependent occupancy can also influence diversification rates...

In 2008, a group of conservation scientists compiled a list of 100 priority questions for the conservation of the world's biodiversity [Sutherland et al. (2009) Conservation Biology, 23, 557–567]. However, now almost a decade later, no one has yet published a study gauging how much progress has been made in addressing these 100 high‐priority questi...

Angiosperm phylogenetic tree collapsed to monophyletic clades of ≤6000 species. The name of one representative species per clade is shown, and the numbers in parentheses indicate the number of species included in each clade. The BAMM analyses were carried out for six monophyletic clades (shown in red, yellow, green, blue, dark blue and pink) and on...

Phylogenetic tree of 13,577 angiosperm species with branch colours indicating the rate of seed mass evolution estimated with BAMM. Branches were scaled by speciation rate as determined by a BAMM analysis on a larger 19,703 tree. (TIF)

Prior and posterior distribution of the number of rate shifts in BAMM. a) the speciation/extinction and b) phenotypic evolution analyses for expectedNumberOfShifts = 25, 50 and 100 and 250. The analyses in the main text were carried out with expectedNumberOfShifts = 50 for both speciation/extinction and phenotypic evolution analyses. (TIF)

Comparison of the speciation rates at the tip of the tree obtained with the complete Zanne tree (29,703 species) and the seed size filtered tree (13,577 species). The dotted line represents the 1:1 reference line. (TIF)

Correlation of speciation with seed mass and seed mass rate of evolution in the clade-based analysis only considering congeneric species. (a) PGLS slope of the relationship of speciation rate—estimated with the method-of-moments estimator—with mean clade seed mass across 10 time slices. The size of the circles represents the number of clades in eac...

Correlation between speciation rate and rate of seed size evolution in a random sample of the BAMM posterior. The dotted line represents the Spearman correlation (ρ = 0.47, p-value < 0.001). (TIF)

Type I error analysis. We estimated the type I error rate of our analysis by simulating neutral traits on the angiosperm phylogenetic tree. We performed 1,000 simulations and then ran 1,000 STRAPP tests with each simulated dataset. We estimated the corresponding p-values for the association between traits and diversification and calculated the type...

Correlations between mean clade seed mass and speciation rate (estimated with RPANDA) across time slices. (a) 0 to 2 million years (myr); (b) 2 to 4 myr; (c) 4 to 6 myr; (d) 6 to 8 myr; (e) 8 to 10 myr; (f) 10 to 12 myr; (g) 12 to 14 myr; (h) 14 to 16 myr; (i) 16 to 18 myr; and (j) 18 to 20 myr. The degrees of freedom (df) are equivalent to the num...

Seed mass and its rate of evolution are associated with speciation in the clade-based analyses. (a) PGLS slope of the relationship between speciation rate (λ) from the method-of-moments estimator and the rate of seed mass evolution across 10 time slices. Circles are scaled to the number of clades in each time slice while colour indicates the signif...

Proposed effects of seed mass and other life history traits on diversification. (Solid lines). Dashed lines indicate correlations between life history traits. Numbers indicate reference where the link is proposed. (TIF)

Correlations between clade rate of seed size evolution and speciation rate (estimated with RPANDA) across time slices. (a) 0 to 2 million years (myr); (b) 2 to 4 myr; (c) 4 to 6 myr; (d) 6 to 8 myr; (e) 8 to 10 myr; (f) 10 to 12 myr; (g) 12 to 14 myr; (h) 14 to 16 myr; (i) 16 to 18 myr; and (j) 18 to 20 myr. The degrees of freedom (df) are equivale...

Correlation of (a) rate of seed mass evolution and (b) seed mass with net diversification rate (r) estimated using RPANDA in the clade-based analysis. The strength of correlations is shown as PGLS slopes and was calculated using mean clade-level seed mass across 10 time slices. The size of the circles represents the number of clades in each time sl...

Mean genus seed mass of strict annual (n = 214) and perennial (n = 793) genera. No significant difference between the means of the two groups was found when accounting for phylogeny (phylANOVA: p-value = 0.308, significance assessed with 1,000 random simulations). (TIF)

RPANDA diversification models for the clade-based analyses. For each 2-million year (myr) time slice, we counted the number of clades where the best-fitting model was either i) birth-death model with constant λ (speciation) and μ (extinction) (lambda.cst.mu.cst); pure birth model with constant λ (lambda.cst.mu0); pure birth model with exponential λ...

STRAPP correlations (rho) for 1,007 species of angiosperms with seed size, genome size (i.e., C-value), life cycle, height, woodiness data and rates of seed size, C-value and height evolution. Significant correlation are shown in bold and p-values are shown in parentheses. (DOCX)

STRAPP correlations of diversification and phenotypic traits for 1,007 angiosperm species. The distribution of the absolute difference in the observed correlation minus the null correlation is plotted for each trait. The coloured dotted lines indicate the mean of that distribution, and the black dotted line indicates 0; a distribution with mean = 0...

Phylogenetic tree of 353 angiosperm families with representatives in our analyses. The red bars indicate the levels of sampling for each family. (TIF)

Correlation of mean speciation and mean phenotypic rates across all the branches of the angiosperm phylogenetic tree. The dotted line is the ordinary least squares regression (R2 = 0.31, p-value < 0.001). (TIF)

Correlations between mean clade seed mass and speciation rate (estimated with the method-of-moments estimator) across time slices. (a) 0 to 2 million years (myr); (b) 2 to 4 myr; (c) 4 to 6 myr; (d) 6 to 8 myr; (e) 8 to 10 myr; (f) 10 to 12 myr; (g) 12 to 14 myr; (h) 14 to 16 myr; (i) 16 to 18 myr; and (j) 18 to 20 myr. (TIF)

Correlations between clade rate of seed size evolution and speciation rate (estimated with the method-of-moments estimator) across time slices. (a) 0 to 2 million years (myr); (b) 2 to 4 myr; (c) 4 to 6 myr; (d) 6 to 8 myr; (e) 8 to 10 myr; (f) 10 to 12 myr; (g) 12 to 14 myr; (h) 14 to 16 myr; (i) 16 to 18 myr; and (j) 18 to 20 myr. (TIF)

Correlations of seed size and other phenotypic traits. Trait values were obtained from a 1,007 species tree where all species had data for seed size, C-value and plant height. The values are the slopes of the PGLS regressions and asterisks denote statistically significant correlations (p-value < 0.05). (DOCX)

Correlations of seed size rate of evolution and other phenotypic rates of evolution. Rate values were obtained from a 1,007 species tree where all species had data for seed size, C-value and plant height. The values are the slopes of the PGLS regressions and asterisks denote statistically significant correlations (p-value < 0.05). (DOCX)

Species diversity varies greatly across the different taxonomic groups that comprise the Tree of Life (ToL). This imbalance is particularly conspicuous within angiosperms, but is largely unexplained. Seed mass is one trait that may help clarify why some lineages diversify more than others because it confers adaptation to different environments, whi...

Background All vertebrates initially feed their offspring using yolk reserves. In some live-bearing species these yolk reserves may be supplemented with extra nutrition via a placenta. Sharks belonging to the Carcharhinidae family are all live-bearing, and with the exception of the tiger shark (Galeocerdo cuvier), develop placental connections afte...

The Pyrenean desman (Galemys pyrenaicus) is a small semi-aquatic mammal endemic to the Iberian Peninsula. The species has recently experienced a strong decline and some of its populations are severely threatened with extinction. To help in the preservation of this species, it is critical to understand its genetic structure and main evolutionary uni...

Ecological speciation requires divergent selection, reproductive isolation, and a genetic mechanism to link the two. We examined the role of gene expression and coding sequence evolution in this process using two species of Howea palms that have diverged sympatrically on Lord Howe Island, Australia. These palms are associated with distinct soil typ...

Species richness is distributed unevenly across the tree of life and this may be influenced by the evolution of novel phenotypes that promote diversification. Viviparity has originated ~150 times in vertebrates and is considered to be an adaptation to highly variable environments. Likewise, possessing an annual life cycle is common in plants and in...

Background Multilocus data are becoming increasingly important in determining the phylogeny of closely related species and delimiting species. In species complexes where unequivocal fossil calibrations are not available, rigorous dating of the coalescence-based species trees requires accurate mutation rates of the loci under study but, generally, t...

One of the major challenges in the analysis of closely related species, speciation and phylogeography is the identification of variable sequence markers that allow the determination of genealogical relationships in multiple genomic regions using coalescent and species tree approaches. Rodent species represent nearly half of the mammalian diversity,...

Background Species with strict ecological requirements may provide new insights into the forces that shaped the geographic variation of genetic diversity. The Pyrenean desman, Galemys pyrenaicus, is a small semi-aquatic mammal that inhabits clean streams of the northern half of the Iberian Peninsula and is endangered in most of its geographic range...

The Pyrenean desman (Galemys pyrenaicus) is a threatened semi-aquatic mammal of which we ignore some basics aspects of its genetic diversity and structure. Moreover, there is limited updated information about its distribution. In this study, we sampled the rivers and streams a priori favorable for this species in the three National Parks with previ...

Final set of 224 introns selected for the phylogeny of closely related mammalian species. The first page of each intron lists the following information: description (function of the gene to which the intron belongs), gene name according to the HUGO Gene Nomenclature Committee (in parenthesis), intron number, chromosome where it is located in Homo s...

Multilocus phylogenies can be used to infer the species tree of a group of closely related species. In species trees, the nodes represent the actual separation between species, thus providing essential information about their evolutionary history. In addition, multilocus phylogenies can help in analyses of species delimitation, gene flow and geneti...

We introduce a new phylogenetic comparison method that measures overall differences in the relative branch length and topology of two phylogenetic trees. To do this, the algorithm first scales one of the trees to have a global divergence as similar as possible to the other tree. Then, the branch length distance, which takes differences in topology...