Exploring the tempo of species diversification in legumes

Koenen, Erik J. M.; Vos, Jurriaan M. de; Atchison, Guy W.; Simon, Marcelo F.; Schrire, Brian; Souza, Élvia Rodrigues de; Queiroz, Luciano Paganucci de; Hughes, Colin E.

doi:10.1016/j.sajb.2013.07.005

Cited by 53 publications

(52 citation statements)

References 72 publications

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“…2A). This topology is generally consistent with previous studies (Wojciechowski et al, 2004;Bruneau et al, 2008;Bello et al, 2009;Cardoso et al, 2013;Koenen et al, 2013).…”

Section: Fabalessupporting

confidence: 93%

Phylogeny of the Rosidae: A dense taxon sampling analysis

Sun

Naeem

et al. 2016

J of Sytematics Evolution

125

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Rosidae, a clade of approximately 90 000 species of angiosperms, exhibits remarkable morphological diversity and extraordinary heterogeneity in habitats and life forms. Resolving phylogenetic relationships within Rosidae has been difficult, in large part due to nested radiations and the enormous size of the clade. Current estimates of phylogeny contain areas of poor resolution and/or support, and there have been few attempts to synthesize the available data into a comprehensive view of Rosidae phylogeny. We aim to improve understanding of the phylogeny of Rosidae with a dense sampling scheme using both newly generated sequences and data from GenBank of the chloroplast rbcL, atpB, and matK genes and the mitochondrial matR gene. We combined sequences from 9300 species, representing 2775 genera, 138 families, and 17 orders into a supermatrix. Although 59.26% of the cells in the supermatrix have no data, our results generally agree with previous estimates of Rosidae phylogeny and provide greater resolution and support in several areas of the topology. Several noteworthy phylogenetic relationships are recovered, including some novel relationships. Two families (Euphorbiaceae and Salvadoraceae) and 467 genera are recovered as non-monophyletic in our sampling, suggesting the need for future systematic studies of these groups. Our study shows the value of a botanically informed bioinformatics approach and dense taxonomic sampling for resolving rosid relationships. The resulting tree provides a starting point for large-scale analyses of the evolutionary patterns within Rosidae.Key words: phylogeny, rapid radiation, Rosidae, supermatrix.With approximately 90 000 species (estimated from Hinchliff et al., 2015), 135-140 families, and 17 orders (Soltis et al., 2005;APG III, 2009;APG IV, 2016), Rosidae contains at least one quarter of all angiosperm species and approximately 39% of eudicot species diversity (Magall on et al., 1999;Wang et al., 2009). Molecular dating indicates that Rosidae originated in the Early to Late Cretaceous, between 115 and 93 million years ago (Mya), followed by rapid diversification resulting in the Fabidae and Malvidae crown groups approximately 112 to 91 Mya (Albian to Coniacian) and 109 to 83 Mya (Cenomanian to Santonian), respectively (Wang et al., 2009;Bell et al., 2010), with major lineages diversifying in perhaps as little as 4 to 5 million years (Wang et al., 2009;Soltis et al., 2010). The radiations in Rosidae also represent the rapid rise of angiosperm-dominated forests and associated co-diversification events that have profoundly shaped much of the current terrestrial biodiversity (Wang et al., 2009).This extraordinarily diverse clade exhibits enormous heterogeneity in habitats and life forms, including herbs, shrubs, trees, vines, aquatics, succulents, and parasites. Species of Rosidae generally have bitegmic, crassinucellate ovules, distinguishing them from Asteridae, which are generally characterized by unitegmic, tenuinucellate ovules. Moreover, some members possess novel bio...

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“…2A). This topology is generally consistent with previous studies (Wojciechowski et al, 2004;Bruneau et al, 2008;Bello et al, 2009;Cardoso et al, 2013;Koenen et al, 2013).…”

Section: Fabalessupporting

confidence: 93%

Phylogeny of the Rosidae: A dense taxon sampling analysis

Sun

Naeem

et al. 2016

J of Sytematics Evolution

125

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“…They analyzed the genus Dianthus (carnations, Caryophyllaceae) and found net diversification rates of up to 16 new species per species per million years. This puts them well above 11 other plant groups, the highest rate of which was for Andean Lupinus (lupins, Fabaceae) at approximately 2 (Hughes & Eastwood ; Koenen et al ). For birds, the record holders are the Southeast Asian Zosterops (White‐eyes, Zosteropidae), at 2.6 new species per species per million years.…”

Section: Discussionmentioning

confidence: 90%

“…puts them well above 11 other plant groups, the highest rate of which was for Andean Lupinus (lupins, Fabaceae) at approximately 2 (Hughes & Eastwood 2006;Koenen et al 2013). For birds, the record holders are the Southeast Asian Zosterops (White-eyes, Zosteropidae), at 2.6 new species per species per million years.…”

Section: Diversification Ratesmentioning

confidence: 95%

Estimating the normal background rate of species extinction

Vos

Joppa

Gittleman

et al. 2014

Conservation Biology

467

223

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A key measure of humanity's global impact is by how much it has increased species extinction rates. Familiar statements are that these are 100-1000 times pre-human or background extinction levels. Estimating recent rates is straightforward, but establishing a background rate for comparison is not. Previous researchers chose an approximate benchmark of 1 extinction per million species per year (E/MSY). We explored disparate lines of evidence that suggest a substantially lower estimate. Fossil data yield direct estimates of extinction rates, but they are temporally coarse, mostly limited to marine hard-bodied taxa, and generally involve genera not species. Based on these data, typical background loss is 0.01 genera per million genera per year. Molecular phylogenies are available for more taxa and ecosystems, but it is debated whether they can be used to estimate separately speciation and extinction rates. We selected data to address known concerns and used them to determine median extinction estimates from statistical distributions of probable values for terrestrial plants and animals. We then created simulations to explore effects of violating model assumptions. Finally, we compiled estimates of diversification-the difference between speciation and extinction rates for different taxa. Median estimates of extinction rates ranged from 0.023 to 0.135 E/MSY. Simulation results suggested over- and under-estimation of extinction from individual phylogenies partially canceled each other out when large sets of phylogenies were analyzed. There was no evidence for recent and widespread pre-human overall declines in diversity. This implies that average extinction rates are less than average diversification rates. Median diversification rates were 0.05-0.2 new species per million species per year. On the basis of these results, we concluded that typical rates of background extinction may be closer to 0.1 E/MSY. Thus, current extinction rates are 1,000 times higher than natural background rates of extinction and future rates are likely to be 10,000 times higher.

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“…For example, the high species diversity in the California Floristic Province is associated with lower rates of extinction more than elevated speciation or immigration, using models in which rates of lineage birth, death, and movement are dependent on geographic occupancy but not time (53). Assembly of the Cerrado biome in Brazil has been characterized by recent (late Miocene onward) in situ adaptation of lineages to fire resistance (54), with some clades, especially in the campos rupestres highlands, showing evidence of endemic radiation [e.g., Mimosa (54,55), Calliandra (56), and Chamaecrista (57)]. In the Páramo biome of the Andes, analyses of net diversification (but not immigration) yielded the highest average rate compared with eight other hotspots and appear driven more by Pleistocene climate oscillations than orogeny (58).…”

Section: Discussionmentioning

confidence: 99%

Uplift-driven diversification in the Hengduan Mountains, a temperate biodiversity hotspot

Xing

Ree

2017

Proc. Natl. Acad. Sci. U.S.A.

459

473

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A common hypothesis for the rich biodiversity found in mountains is uplift-driven diversification-that orogeny creates conditions favoring rapid in situ speciation of resident lineages. We tested this hypothesis in the context of the Qinghai-Tibetan Plateau (QTP) and adjoining mountain ranges, using the phylogenetic and geographic histories of multiple groups of plants to infer the tempo (rate) and mode (colonization versus in situ diversification) of biotic assembly through time and across regions. We focused on the Hengduan Mountains region, which in comparison with the QTP and Himalayas was uplifted more recently (since the late Miocene) and is smaller in area and richer in species. Time-calibrated phylogenetic analyses show that about 8 million y ago the rate of in situ diversification increased in the Hengduan Mountains, significantly exceeding that in the geologically older QTP and Himalayas. By contrast, in the QTP and Himalayas during the same period the rate of in situ diversification remained relatively flat, with colonization dominating lineage accumulation. The Hengduan Mountains flora was thus assembled disproportionately by recent in situ diversification, temporally congruent with independent estimates of orogeny. This study shows quantitative evidence for uplift-driven diversification in this region, and more generally, tests the hypothesis by comparing the rate and mode of biotic assembly jointly across time and space. It thus complements the more prevalent method of examining endemic radiations individually and could be used as a template to augment such studies in other biodiversity hotspots.biogeography | vascular plants | molecular clocks | dispersal | speciation C entral to understanding global patterns of biodiversity are considerations of biotic assembly: For a given region, when and how did resident species accumulate? Of primary interest is tempo (the rate of accumulation) and mode (the process, whether by colonization via dispersal or in situ lineage diversification). We wish to know how and why these vary in time and space.For mountains, well-known for harboring a disproportionate fraction of terrestrial species, a common hypothesis is that of uplift-driven diversification-that orogeny creates conditions favoring in situ speciation of resident lineages (1-6). Among global biodiversity hotspots, the mountain ranges surrounding the Qinghai-Tibetan Plateau (QTP) are unusual and enigmatic: They harbor one of the world's richest temperate floras, and (unlike other hotspots) they are neither tropical nor Mediterranean in climate. Moreover, despite increasing interest from biogeographers, their biotic assembly remains poorly understood (3, 4, 7). The mountains form three distinct hotspots of biodiversity that respectively lie to the west, south, and east of the QTP's central high desert: the Central Asian mountains (Altai and Tianshan ranges), the Himalayas, and the Hengduan Mountains region (4) (Fig. 1). Of these, the richest in plant diversity is the Hengduan Mountains, with a vascular flor...

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Exploring the tempo of species diversification in legumes

Cited by 53 publications

References 72 publications

Phylogeny of the Rosidae: A dense taxon sampling analysis

Phylogeny of the Rosidae: A dense taxon sampling analysis

Estimating the normal background rate of species extinction

Uplift-driven diversification in the Hengduan Mountains, a temperate biodiversity hotspot

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