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Diversification of land plants: insights from a family-level phylogenetic analysis
Omar Fiz-Palacios, Harald Schneider, Jochen Heinrichs, Vincent Savolainen
BMC Evolutionary Biology , 2011, DOI: 10.1186/1471-2148-11-341
Abstract: We found evidence for the radiations of ferns and mosses in the shadow of angiosperms coinciding with the rather warm Cretaceous global climate. In contrast, gymnosperms and liverworts show a signature of declining diversification rates during geological time periods of cool global climate.This broad-scale phylogenetic analysis helps to reveal the successive waves of diversification that made up the diversity of land plants we see today. Both warm temperatures and wet climate may have been necessary for the rise of the diversity under a successive lineage replacement scenario.It is believed that climate change is one of the main factors affecting global biodiversity [1-3]. During the history of life, fluctuations of the world's climate have most likely caused major extinctions [4] and led to the development of new ecosystems, promoting new biotic interactions and the evolution of novel adaptive traits. The dynamics of such diversification events can be studied based on phylogenetic trees dated with fossils. Here we focus on land plants. The origin and diversification of land plants has intrigued biologists for centuries. According to the fossil record, land plants diverged from green algae before 475 million years ago (Ma; first land plant fossil) and led to the major clades found today [5,6]. These are liverworts (74 families, ca. 6,000 spp. [7]), mosses (112 families, ca. 12,000 spp. [8,9]), hornworts (five families, ca. 150 spp. [10]) and tracheophytes. The latter include ferns (45 families, ca. 9,000 spp. [11]), lycophytes (three families, ca. 1,200 spp. [12]), and seed plants, which in turn are separated into gymnosperms (14 families, ca. 1,000 spp. [13]) and angiosperms (456 families, ca. 260,000 spp. [13]).There are various possible scenarios to describe the processes that influenced land plant diversification throughout geological time. One frequently proposed scenario is based on a successive replacement of ancestral lineages by more derived lineages, which
Phylogenetic insights into Andean plant diversification  [PDF]
Federico Luebert,Maximilian Weigend
Frontiers in Ecology and Evolution , 2014, DOI: 10.3389/fevo.2014.00027
Abstract: Andean orogeny is considered as one of the most important events for the development of current plant diversity in South America. We compare available phylogenetic studies and divergence time estimates for plant lineages that may have diversified in response to Andean orogeny. The influence of the Andes on plant diversification is separated into four major groups: The Andes as source of new high-elevation habitats, as a vicariant barrier, as a North-South corridor, and as generator of new environmental conditions outside the Andes. Biogeographical relationships between the Andes and other regions are also considered. Divergence time estimates indicate that high-elevation lineages originated and diversified during or after the major phases of Andean uplift (Mid-Miocene to Pliocene), although there are some exceptions. As expected, Andean mid-elevation lineages tend to be older than high-elevation groups. Most clades with disjunct distribution on both sides of the Andes diverged during Andean uplift. Inner-Andean clades also tend to have divergence time during or after Andean uplift. This is interpreted as evidence of vicariance. Dispersal along the Andes has been shown to occur in either direction, mostly dated after the Andean uplift. Divergence time estimates of plant groups outside the Andes encompass a wider range of ages, indicating that the Andes may not be necessarily the cause of these diversifications. The Andes are biogeographically related to all neighboring areas, especially Central America, with floristic interchanges in both directions since Early Miocene times. Direct biogeographical relationships between the Andes and other disjunct regions have also been shown in phylogenetic studies, especially with the eastern Brazilian highlands and North America. The history of the Andean flora is complex and plant diversification has been driven by a variety of processes, including environmental change, adaptation, and biotic interactions.
Phylogenetic diversification of glycogen synthase kinase 3/SHAGGY-like kinase genes in plants
Mi-Jeong Yoo, Victor A Albert, Pamela S Soltis, Douglas E Soltis
BMC Plant Biology , 2006, DOI: 10.1186/1471-2229-6-3
Abstract: We found that the structure of GSK genes is generally conserved in Arabidopsis and rice, although we documented examples of exon expansion and intron loss. Our phylogenetic analyses of 139 sequences revealed four major clades of GSK genes that correspond to the four subgroups initially recognized in Arabidopsis. ESTs from basal angiosperms were represented in all four major clades; GSK homologs from the basal angiosperm Persea americana (avocado) appeared in all four clades. Gymnosperm sequences occurred in clades I, III, and IV, and a sequence of the red alga Porphyra was sister to all green plant sequences.Our results indicate that (1) the plant-specific GSK gene lineage was established early in the history of green plants, (2) plant GSKs began to diversify prior to the origin of extant seed plants, (3) three of the four major clades of GSKs present in Arabidopsis and rice were established early in the evolutionary history of extant seed plants, and (4) diversification into four major clades (as initially reported in Arabidopsis) occurred either just prior to the origin of the angiosperms or very early in angiosperm history.The glycogen synthase kinase 3 (GSK3)/SHAGGY-like kinases are non-receptor serine/threonine protein kinases that are involved in a variety of signal transduction pathways [1]. In animals, they are involved in cell fate determination, in metazoan pattern formation, and in tumorigenesis [2-6]. In mammals, two enzymes, GSK3α and GSK3β, are involved in the regulation of glycogen metabolism [7], in stability of the cytoskeleton [8], and in numerous processes related to oncogenesis [9]. In Saccharomyces cerevisiae, the GSK3 homologs MCK1 and MDS1 play a role in chromosomal segregation [10], and in Schizosaccharomyces pombe the GSK3 homolog Skp1 regulates cytokinesis [11].In contrast to the two members of the GSK3 family found in mammals, plants appear to have a much larger set of divergent GSK3/SHAGGY-like kinase genes [12-28], with functions as nume
Phylogenetic Patterns of Geographical and Ecological Diversification in the Subgenus Drosophila  [PDF]
Ramiro Morales-Hojas, Jorge Vieira
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0049552
Abstract: Colonisation of new geographic regions and/or of new ecological resources can result in rapid species diversification into the new ecological niches available. Members of the subgenus Drosophila are distributed across the globe and show a large diversity of ecological niches. Furthermore, taxonomic classification of Drosophila includes the rank radiation, which refers to closely related species groups. Nevertheless, it has never been tested if these taxonomic radiations correspond to evolutionary radiations. Here we present a study of the patterns of diversification of Drosophila to test for increased diversification rates in relation to the geographic and ecological diversification processes. For this, we have estimated and dated a phylogeny of 218 species belonging to the major species groups of the subgenus. The obtained phylogenies are largely consistent with previous studies and indicate that the major groups appeared during the Oligocene/Miocene transition or early Miocene, characterized by a trend of climate warming with brief periods of glaciation. Ancestral reconstruction of geographic ranges and ecological resource use suggest at least two dispersals to the Neotropics from the ancestral Asiatic tropical disribution, and several transitions to specialized ecological resource use (mycophagous and cactophilic). Colonisation of new geographic regions and/or of new ecological resources can result in rapid species diversification into the new ecological niches available. However, diversification analyses show no significant support for adaptive radiations as a result of geographic dispersal or ecological resource shift. Also, cactophily has not resulted in an increase in the diversification rate of the repleta and related groups. It is thus concluded that the taxonomic radiations do not correspond to adaptive radiations.
Phylogenetic diversification patterns and divergence times in ground beetles (Coleoptera: Carabidae: Harpalinae)
Karen A Ober, Thomas N Heider
BMC Evolutionary Biology , 2010, DOI: 10.1186/1471-2148-10-262
Abstract: According to molecular divergence date estimates, harpalines originated in the mid Cretaceous but did not diversify extensively until the late Cretaceous or early Paleogene about 32 million years after their origin. In a relatively small window of time, harpalines underwent rapid speciation. Harpalines have a relative high net diversification rate and increased cladogenesis in some regions of the clade. We did not see a significant decrease in diversification rate through time in the MCCR test, but a model of diversification with two shift points to lower diversification rates fit the harpaline lineage accumulation through time the best.Our results indicate harpalines are significantly more diverse and have higher diversification than their sistergroup. Instead of an immediate burst of explosive diversification, harpalines may have had a long "fuse" before major lineages diversified during the early Paleogene when other taxa such as mammals, birds, and some flowering plants were also rapidly diversifying.Ever since Darwin, biologists have been interested in using phylogenetic trees to investigate the pattern and tempo of lineage diversification. We see that the branching patterns in phylogenies contain information about the processes of speciation and extinction. Molecular phylogenies of species rich groups supply hypotheses of evolutionary relationships among higher taxa, and also allow us to test hypotheses about the tempo and pattern of diversification [1-4], revealing both the topology of ancestor-descendant relationships and the tempo of descent among members of a clade. It is clear that organismal diversification rates (speciation minus extinction) have been variable across lineages and through time, with some lineages showing slowing rates of lineage accumulation [5] and others showing rapid diversification [6] or radiations. Radiations are generally defined in a way that includes rapid cladogenesis from a common ancestor [7], yielding taxon rich clades. The
Phylogenetic Status and Timescale for the Diversification of Steno and Sotalia Dolphins  [PDF]
Haydée A. Cunha, Lucas C. Moraes, Bruna V. Medeiros, José Lailson-Brito, Vera M. F. da Silva, Antonio M. Solé-Cava, Carlos G. Schrago
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0028297
Abstract: Molecular data have provided many insights into cetacean evolution but some unsettled issues still remain. We estimated the topology and timing of cetacean evolutionary relationships using Bayesian and maximum likelihood analyses of complete mitochondrial genomes. In order to clarify the phylogenetic placement of Sotalia and Steno within the Delphinidae, we sequenced three new delphinid mitogenomes. Our analyses support three delphinid clades: one joining Steno and Sotalia (supporting the revised subfamily Stenoninae); another placing Sousa within the Delphininae; and a third, the Globicephalinae, which includes Globicephala, Feresa, Pseudorca, Peponocephala and Grampus. We also conclude that Orcinus does not belong in the Globicephalinae, but Orcaella may be part of that subfamily. Divergence dates were estimated using the relaxed molecular clock calibrated with fossil data. We hypothesise that the timing of separation of the marine and Amazonian Sotalia species (2.3 Ma) coincided with the establishment of the modern Amazon River basin.
Phylogenomics and Coalescent Analyses Resolve Extant Seed Plant Relationships  [PDF]
Zhenxiang Xi, Joshua S. Rest, Charles C. Davis
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0080870
Abstract: The extant seed plants include more than 260,000 species that belong to five main lineages: angiosperms, conifers, cycads, Ginkgo, and gnetophytes. Despite tremendous effort using molecular data, phylogenetic relationships among these five lineages remain uncertain. Here, we provide the first broad coalescent-based species tree estimation of seed plants using genome-scale nuclear and plastid data By incorporating 305 nuclear genes and 47 plastid genes from 14 species, we identify that i) extant gymnosperms (i.e., conifers, cycads, Ginkgo, and gnetophytes) are monophyletic, ii) gnetophytes exhibit discordant placements within conifers between their nuclear and plastid genomes, and iii) cycads plus Ginkgo form a clade that is sister to all remaining extant gymnosperms. We additionally observe that the placement of Ginkgo inferred from coalescent analyses is congruent across different nucleotide rate partitions. In contrast, the standard concatenation method produces strongly supported, but incongruent placements of Ginkgo between slow- and fast-evolving sites. Specifically, fast-evolving sites yield relationships in conflict with coalescent analyses. We hypothesize that this incongruence may be related to the way in which concatenation methods treat sites with elevated nucleotide substitution rates. More empirical and simulation investigations are needed to understand this potential weakness of concatenation methods.
A spruce gene map infers ancient plant genome reshuffling and subsequent slow evolution in the gymnosperm lineage leading to extant conifers  [cached]
Pavy Nathalie,Pelgas Betty,Laroche Jér?me,Rigault Philippe
BMC Biology , 2012, DOI: 10.1186/1741-7007-10-84
Abstract: Background Seed plants are composed of angiosperms and gymnosperms, which diverged from each other around 300 million years ago. While much light has been shed on the mechanisms and rate of genome evolution in flowering plants, such knowledge remains conspicuously meagre for the gymnosperms. Conifers are key representatives of gymnosperms and the sheer size of their genomes represents a significant challenge for characterization, sequencing and assembling. Results To gain insight into the macro-organisation and long-term evolution of the conifer genome, we developed a genetic map involving 1,801 spruce genes. We designed a statistical approach based on kernel density estimation to analyse gene density and identified seven gene-rich isochors. Groups of co-localizing genes were also found that were transcriptionally co-regulated, indicative of functional clusters. Phylogenetic analyses of 157 gene families for which at least two duplicates were mapped on the spruce genome indicated that ancient gene duplicates shared by angiosperms and gymnosperms outnumbered conifer-specific duplicates by a ratio of eight to one. Ancient duplicates were much more translocated within and among spruce chromosomes than conifer-specific duplicates, which were mostly organised in tandem arrays. Both high synteny and collinearity were also observed between the genomes of spruce and pine, two conifers that diverged more than 100 million years ago. Conclusions Taken together, these results indicate that much genomic evolution has occurred in the seed plant lineage before the split between gymnosperms and angiosperms, and that the pace of evolution of the genome macro-structure has been much slower in the gymnosperm lineage leading to extent conifers than that seen for the same period of time in flowering plants. This trend is largely congruent with the contrasted rates of diversification and morphological evolution observed between these two groups of seed plants.
A Comparative Study of Mammalian Diversification Pattern
Wenhua Yu, Junxiao Xu, Yi Wu, Guang Yang
International Journal of Biological Sciences , 2012,
Abstract: Although mammals have long been regarded as a successful radiation, the diversification pattern among the clades is still poorly known. Higher-level phylogenies are conflicting and comprehensive comparative analyses are still lacking. Using a recently published supermatrix encompassing nearly all extant mammalian families and a novel comparative likelihood approach (MEDUSA), the diversification pattern of mammalian groups was examined. Both order- and family-level phylogenetic analyses revealed the rapid radiation of Boreoeutheria and Euaustralidelphia in the early mammalian history. The observation of a diversification burst within Boreoeutheria at approximately 100 My supports the Long Fuse model in elucidating placental diversification progress, and the rapid radiation of Euaustralidelphia suggests an important role of biogeographic dispersal events in triggering early Australian marsupial rapid radiation. Diversification analyses based on family-level diversity tree revealed seven additional clades with exceptional diversification rate shifts, six of which represent accelerations in net diversification rate as compared to the background pattern. The shifts gave origin to the clades Muridae+Cricetidae, Bovidae+Moschidae+Cervidae, Simiiformes, Echimyidae, Odontoceti (excluding Physeteridae+Kogiidae+Platanistidae), Macropodidae, and Vespertilionidae. Moderate to high extinction rates from background and boreoeutherian diversification patterns indicate the important role of turnovers in shaping the heterogeneous taxonomic richness observed among extant mammalian groups. Furthermore, the present results emphasize the key role of extinction on erasing unusual diversification signals, and suggest that further studies are needed to clarify the historical radiation of some mammalian groups for which MEDUSA did not detect exceptional diversification rates.
Interpreting the γ Statistic in Phylogenetic Diversification Rate Studies: A Rate Decrease Does Not Necessarily Indicate an Early Burst  [PDF]
James A. Fordyce
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0011781
Abstract: Phylogenetic hypotheses are increasingly being used to elucidate historical patterns of diversification rate-variation. Hypothesis testing is often conducted by comparing the observed vector of branching times to a null, pure-birth expectation. A popular method for inferring a decrease in speciation rate, which might suggest an early burst of diversification followed by a decrease in diversification rate is the γ statistic.
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