Niche evolution in a northern temperate tree lineage: biogeographical legacies in cork oaks (Quercus section Cerris).

Background And Aims: Cork oaks (Quercus section Cerris) comprise 15 extant species in Eurasia. Despite being a small clade, they display a range of leaf morphologies comparable to the largest sections (>100 spp.) in Quercus.

5S-IGS rDNA in wind-pollinated trees (Fagus L.) encapsulates 55 million years of reticulate evolution and hybrid origins of modern species.

Standard models of plant speciation assume strictly dichotomous genealogies in which a species, the ancestor, is replaced by two offspring species. The reality in wind-pollinated trees with long evolutionary histories is more complex: species evolve from other species through isolation when genetic drift exceeds gene flow; lineage mixing can give rise to new species (hybrid taxa such as nothospecies and allopolyploids). The multi-copy, potentially multi-locus 5S rDNA is one of few gene regions conserving signal from dichotomous and reticulate evolutionary processes down to the level of intra-genomic recombination.

Phylogenetic relationships in the southern African genus (Ruschioideae, Aizoaceae).

Background: , the only genus of the tribe Drosanthemeae, is widespread over the Greater Cape Floristic Region in southern Africa. With 114 recognized species, together with the highly succulent and species-rich tribe Ruschieae, constitute the 'core ruschioids' in Aizoaceae. Within , nine subgenera have been described based on flower and fruit morphology.

Evolutionary dynamics in the dispersal of sign languages.

The evolution of spoken languages has been studied since the mid-nineteenth century using traditional historical comparative methods and, more recently, computational phylogenetic methods. By contrast, evolutionary processes resulting in the diversity of contemporary sign languages (SLs) have received much less attention, and scholars have been largely unsuccessful in grouping SLs into monophyletic language families using traditional methods. To date, no published studies have attempted to use language data to infer relationships among SLs on a large scale.

Genomic landscape of the global oak phylogeny.

The tree of life is highly reticulate, with the history of population divergence emerging from populations of gene phylogenies that reflect histories of introgression, lineage sorting and divergence. In this study, we investigate global patterns of oak diversity and test the hypothesis that there are regions of the oak genome that are broadly informative about phylogeny. We utilize fossil data and restriction-site associated DNA sequencing (RAD-seq) for 632 individuals representing nearly 250 Quercus species to infer a time-calibrated phylogeny of the world's oaks.

Plant fossils reveal major biomes occupied by the late Miocene Old-World Pikermian fauna.

Reconstruction of palaeobiomes, ancient communities that exhibit a physiognomic and functional structure controlled by their environment, depends on proxies from different disciplines. Based on terrestrial mammal fossils, the late Miocene vegetation from China to the eastern Mediterranean and East Africa has been reconstructed as a single cohesive biome with increasingly arid conditions, with modern African savannahs the surviving remnant. Here, we test this reconstruction using plant fossils spanning 14-4 million years ago from sites in Greece, Bulgaria, Turkey, the Tian Shan Mountains and Baode County in China, and East Africa.

Comparative systematics and phylogeography of Section in western Eurasia: inferences from plastid and nuclear DNA variation.

Oaks () comprise more than 400 species worldwide and centres of diversity for most sections lie in the Americas and East/Southeast Asia. The only exception is the Eurasian sect. that comprises about 15 species, most of which are confined to western Eurasia.

Evolution of pollen morphology in Loranthaceae.

Earlier studies indicate a strong correlation of pollen morphology and ultrastructure with taxonomy in Loranthaceae. Using high-resolution light microscopy and scanning electron microscopy imaging of the same pollen grains, we document pollen types of 35 genera including 15 studied for the first time. Using a molecular phylogenetic framework based on currently available sequence data with good genus-coverage, we reconstruct trends in the evolution of Loranthaceae pollen and pinpoint traits of high diagnostic value, partly confirming earlier intuitive hypotheses based on morphological observations.

The fossil Osmundales (Royal Ferns)-a phylogenetic network analysis, revised taxonomy, and evolutionary classification of anatomically preserved trunks and rhizomes.

The Osmundales (Royal Fern order) originated in the late Paleozoic and is the most ancient surviving lineage of leptosporangiate ferns. In contrast to its low diversity today (less than 20 species in six genera), it has the richest fossil record of any extant group of ferns. The structurally preserved trunks and rhizomes alone are referable to more than 100 fossil species that are classified in up to 20 genera, four subfamilies, and two families.

Tiny pollen grains: first evidence of Saururaceae from the Late Cretaceous of western North America.

Background: The Saururaceae, a very small family of Piperales comprising only six species in four genera, have a relatively scanty fossil record outside of Europe. The phylogenetic relationships of the four genera to each other are resolved, with the type genus occurring in both eastern North America and East Asia. No extant species occurs in western Eurasia.

Ixora (Rubiaceae) on the Philippines - crossroad or cradle?

Background: The Philippine archipelago is globally one of the most important model island systems for studying evolutionary processes. However, most plant species on this archipelago have not yet been studied in sufficient detail. The main aim of this study is to unravel the evolutionary history and biogeographic relationships of the Philippine members of the pantropical genus Ixora.

Plastome data reveal multiple geographic origins of Quercus Group Ilex.

Nucleotide sequences from the plastome are currently the main source for assessing taxonomic and phylogenetic relationships in flowering plants and their historical biogeography at all hierarchical levels. One major exception is the large and economically important genus Quercus (oaks). Whereas differentiation patterns of the nuclear genome are in agreement with morphology and the fossil record, diversity patterns in the plastome are at odds with established taxonomic and phylogenetic relationships.

Osmunda pulchella sp. nov. from the Jurassic of Sweden--reconciling molecular and fossil evidence in the phylogeny of modern royal ferns (Osmundaceae).

Background: The classification of royal ferns (Osmundaceae) has long remained controversial. Recent molecular phylogenies indicate that Osmunda is paraphyletic and needs to be separated into Osmundastrum and Osmunda s.str.

Fagaceae pollen from the early Cenozoic of West Greenland: revisiting Engler's and Chaney's Arcto-Tertiary hypotheses.

In this paper we document Fagaceae pollen from the Eocene of western Greenland. The pollen record suggests a remarkable diversity of the family in the early Cenozoic of Greenland. Extinct Fagaceae pollen types include , which extends at least back to the Paleocene, and two ancestral pollen types with affinities to the Eurasian Group Ilex and the western North American Group Protobalanus.

A phylogeny and biogeographic analysis for the Cape-Pondweed family Aponogetonaceae (Alismatales).

The monocot family Aponogetonaceae (Alismatales) consists only of Aponogeton, with 57 species occurring in Africa, Madagascar, India and Sri Lanka, Southeast Asia and Australia. Earlier studies inferred a Madagascan or Australian origin for the genus. Aponogeton-like pollen is documented from the Late Cretaceous of Wyoming, the early mid-Eocene of Canada, and the late mid-Eocene of Greenland.

pollen from the Cretaceous and Paleogene of North America and West Greenland: Implications for the origin and palaeobiogeography of the genus.

The fossil record of (Aponogetonaceae) is scarce and the few reported macrofossil findings are in need of taxonomic revision. pollen is highly diagnostic and when studied with light microscopy (LM) and scanning electron microscopy (SEM) it cannot be confused with any other pollen types. The fossil pollen described here represent the first reliable Cretaceous and Eocene records of this genus worldwide.

Phylogeography of the tropical planktonic foraminifera lineage globigerinella reveals isolation inconsistent with passive dispersal by ocean currents.

Morphologically defined species of marine plankton often harbor a considerable level of cryptic diversity. Since many morphospecies show cosmopolitan distribution, an understanding of biogeographic and evolutionary processes at the level of genetic diversity requires global sampling. We use a database of 387 single-specimen sequences of the SSU rDNA of the planktonic foraminifera Globigerinella as a model to assess the biogeographic and phylogenetic distributions of cryptic diversity in marine microplankton on a global scale.

Constructing phylogenies in the presence of intra-individual site polymorphisms (2ISPs) with a focus on the nuclear ribosomal cistron.

Nuclear DNA is widely used to estimate phylogenetic and phylogeographic relationships. Nuclear gene variants may be present in an individual's genome, and these result in Intra-Individual Site Polymorphisms (2ISP; pronounced "twisp") in direct-PCR or individual-consensus sequences based on a sample of clones or fragment sequences from next generation sequencing (NGS). 2ISPs can occur fairly often, especially within, but not restricted to, high-copy-number regions such as the widely used internal transcribed spacers of the nuclear ribosomal cistron.

A Clustering Optimization Strategy for Molecular Taxonomy Applied to Planktonic Foraminifera SSU rDNA.

Identifying species is challenging in the case of organisms for which primarily molecular data are available. Even if morphological features are available, molecular taxonomy is often necessary to revise taxonomic concepts and to analyze environmental DNA sequences. However, clustering approaches to delineate molecular operational taxonomic units often rely on arbitrary parameter choices.

Maximum Likelihood Analyses of 3,490 rbcL Sequences: Scalability of Comprehensive Inference versus Group-Specific Taxon Sampling.

The constant accumulation of sequence data poses new computational and methodological challenges for phylogenetic inference, since multiple sequence alignments grow both in the horizontal (number of base pairs, phylogenomic alignments) as well as vertical (number of taxa) dimension. Put aside the ongoing controversial discussion about appropriate models, partitioning schemes, and assembly methods for phylogenomic alignments, coupled with the high computational cost to infer these, for many organismic groups, a sufficient number of taxa is often exclusively available from one or just a few genes (e.g.

Using the Multiple Analysis Approach to Reconstruct Phylogenetic Relationships among Planktonic Foraminifera from Highly Divergent and Length-polymorphic SSU rDNA Sequences.

The high sequence divergence within the small subunit ribosomal RNA gene (SSU rDNA) of foraminifera makes it difficult to establish the homology of individual nucleotides across taxa. Alignment-based approaches so far relied on time-consuming manual alignments and discarded up to 50% of the sequenced nucleotides prior to phylogenetic inference. Here, we investigate the potential of the multiple analysis approach to infer a molecular phylogeny of all modern planktonic foraminiferal taxa by using a matrix of 146 new and 153 previously published SSU rDNA sequences.