Chloroplast DNA sequences are a primary source of data for plant molecular systematic studies. A few key papers have provided the molecular systematics community with universal primer pairs for noncoding regions that have dominated the field, namely trnL-trnF and trnK/matK. These two regions have provided adequate information to resolve species relationships in some taxa, but often provide little resolution at low taxonomic levels. To obtain better phylogenetic resolution, sequence data from these regions are often coupled with other sequence data. Choosing an appropriate cpDNA region for phylogenetic investigation is difficult because of the scarcity of information about the tempo of evolutionary rates among different noncoding cpDNA regions. The focus of this investigation was to determine whether there is any predictable rate heterogeneity among 21 noncoding cpDNA regions identified as phylogenetically useful at low levels. To test for rate heterogeneity among the different cpDNA regions, we used three species from each of 10 groups representing eight major phylogenetic lineages of phanerogams. The results of this study clearly show that a survey using as few as three representative taxa can be predictive of the amount of phylogenetic information offered by a cpDNA region and that rate heterogeneity exists among noncoding cpDNA regions.

The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis

Ribosomal ITS sequences and plant phylogenetic inference.

Fire is a major modifier of communities, but the evolutionary origins of its prevalent role in shaping current biomes are uncertain. Australia is among the most fire-prone continents, with most of the landmass occupied by the fire-dependent sclerophyll and savanna biomes. In contrast to biomes with similar climates in other continents, Australia has a tree flora dominated by a single genus, Eucalyptus, and related Myrtaceae. A unique mechanism in Myrtaceae for enduring and recovering from fire damage likely resulted in this dominance. Here, we find a conserved phylogenetic relationship between post-fire resprouting (epicormic) anatomy and biome evolution, dating from 60 to 62 Ma, in the earliest Palaeogene. Thus, fire-dependent communities likely existed 50 million years earlier than previously thought. We predict that epicormic resprouting could make eucalypt forests and woodlands an excellent long-term carbon bank for reducing atmospheric CO2 compared with biomes with similar fire regimes in other continents.

/pdf/flammable-biomes-dominated-by-eucalypts-originated-at-the-52c1kb9vgg.pdf

Flammable biomes dominated by eucalypts originated at the Cretaceous-Palaeogene boundary

The cotton genus ( Gossypium ) includes approximately 50 species distributed in arid to semi-arid regions of the tropic and subtropics. Included are four species that have independently been domesticated for their fiber, two each in Africa–Asia and the Americas. Gossypium species exhibit extraordinary morphological variation, ranging from herbaceous perennials to small trees with a diverse array of reproductive and vegetative characteristics. A parallel level of cytogenetic and genomic diversity has arisen during the global radiation of the genus, leading to the evolution of eight groups of diploid ( n =13) species (genome groups A–G, and K). The evolutionary history of the genus included multiple episodes of trans-oceanic dispersal, invasion of new ecological niches, and a surprisingly high frequency of natural interspecific hybridization among lineages that are presently both geographically isolated and intersterile. Recent investigations have clarified many aspects of this history, including relationships within and among the eight genome groups, the domestication history of each of the four cultivated species, and the origin of the allopolyploid cottons. Data implicate an origin for Gossypium 5–15 million years ago (mya) and a rapid early diversification of the major genome groups. Allopolyploid cottons appear to have arisen within the last million years, as a consequence of trans-oceanic dispersal of an A-genome taxon to the New World followed by hybridization with an indigenous D-genome diploid. Subsequent to formation, allopolyploids radiated into three modern lineages, including those containing the commercially important species G. hirsutum and G. barbadense . Genome doubling has led to an array of molecular genetic interactions, including inter-locus concerted evolution, differential rates of genomic evolution, inter-genomic genetic transfer, and probable alterations in gene expression. The myriad underlying mechanisms are also suggested to have contributed to both ecological success and agronomic potential.

https://www.fs.fed.us/pnw/pubs/journals/pnw_2002_wendel001.pdf

Polyploidy and the Evolutionary History of Cotton

The integration of phylogenetics, phylogeography and palaeoenvironmental studies is providing major insights into the historical forces that have shaped the Earth's biomes. Yet our present view is biased towards arctic and temperate/tropical forest regions, with very little focus on the extensive arid regions of the planet. The Australian arid zone is one of the largest desert landform systems in the world, with a unique, diverse and relatively well-studied biota. With foci on palaeoenvironmental and molecular data, we here review what is known about the assembly and maintenance of this biome in the context of its physical history, and in comparison with other mesic biomes. Aridification of Australia began in the Mid-Miocene, around 15 million years, but fully arid landforms in central Australia appeared much later, around 1-4 million years. Dated molecular phylogenies of diverse taxa show the deepest divergences of arid-adapted taxa from the Mid-Miocene, consistent with the onset of desiccation. There is evidence of arid-adapted taxa evolving from mesic-adapted ancestors, and also of speciation within the arid zone. There is no evidence for an increase in speciation rate during the Pleistocene, and most arid-zone species lineages date to the Pliocene or earlier. The last 0.8 million years have seen major fluctuations of the arid zone, with large areas covered by mobile sand dunes during glacial maxima. Some large, vagile taxa show patterns of recent expansion and migration throughout the arid zone, in parallel with the ice sheet-imposed range shifts in Northern Hemisphere taxa. Yet other taxa show high lineage diversity and strong phylogeographical structure, indicating persistence in multiple localised refugia over several glacial maxima. Similar to the Northern Hemisphere, Pleistocene range shifts have produced suture zones, creating the opportunity for diversification and speciation through hybridisation, polyploidy and parthenogenesis. This review highlights the opportunities that development of arid conditions provides for rapid and diverse evolutionary radiations, and re-enforces the emerging view that Pleistocene environmental change can have diverse impacts on genetic structure and diversity in different biomes. There is a clear need for more detailed and targeted phylogeographical studies of Australia's arid biota and we suggest a framework and a set of a priori hypotheses by which to proceed.

/pdf/birth-of-a-biome-insights-into-the-assembly-and-maintenance-1kbja6w5q6.pdf

Birth of a biome: insights into the assembly and maintenance of the Australian arid zone biota.

Evolution of exceptional species richness among lineages of fleshy-fruited Myrtaceae.

Circumscriptions of the genus Hibiscus and the tribe Hibisceae (Malvaceae) are based on morphological features that are not unique in the family. An examination of the literature regarding putatively ancestral morphological features revealed that Hibiscus and Hibisceae may be defined by shared ancestral features, and thus are unlikely to be monophyletic groups. These phylogenetic hypotheses were tested using two chloroplast DNA sequences (a coding region— ndhF, and a non-coding region—the rpl16 intron). Several genera usually placed in Hibisceae were found to occupy positions sister to the rest of the family, as was predicted from our reevaluation of their morphological features. Although the earliest divergences in the family were not resolved by chloroplast DNA topologies alone, several morphological features, when analysed in combination with ndhF, suggested a possible resolution of the basal polytomy. These early divergences are represented by extant genera with relatively restricted distributions, which all possess Australasian species that are sister to more widespread and diverse lineages. This suggests the novel hypothesis that eastern Gondwana may be the centre of origin of the family. The pollen fossil record is consistent with this possibility, but does not support it unambiguously. Unexpectedly the tribes Decaschistieae and Malvavisceae as well as other genera of Hibisceae nest within Hibiscus. Nomen- clatural upheavals concerning Hibiscus, one of the world's most popular horticultural plant genera, will be difficult to avoid.

Phylogeny of Hibiscus and the Tribe Hibisceae (Malvaceae) Using Chloroplast DNA Sequences of ndhF and the rpl16 Intron

An infrageneric classification of Syzygium based upon evolutionary relationships as inferred from analyses of nuclear and plastid DNA sequence data, and supported by morphological evidence, is presented. Six subgenera and seven sections are recognised. An identification key is provided and names proposed for two species newly transferred to Syzygium.

/pdf/an-infrageneric-classification-of-syzygium-myrtaceae-86i01cztay.pdf

An infrageneric classification of Syzygium (Myrtaceae)

With as many as 1000 included species, Syzygium s.l. (including Syzygium and segregate genera such as Acmena, Acmenosperma, Cleistocalyx, Piliocalyx, and Waterhousea) comprises one of the major lineages within Myrtaceae, and is an important component of the Old-World tropical rainforest flora. As with other large genera, high species richness, an extensive distribution and relative homogeneity in morphology have hindered attempts to divide Syzygium s.l. Here, we investigate higher level relationships within the group, using parsimony and Bayesian analyses of cpDNA sequences from the matK and ndhF genes and the rpl 16 intron, generated for a total of 87 species from the Syzygium group and eight outgroup taxa. Within the ingroup, four major well supported clades are found, which form a basal polytomy along with S. wesa and monotypic Anetholea. Generally, the molecular data provide little support for traditional divisions of Syzygium s.l., and the recognition of segregate groups such as Acmena, Acmenosperma, Cleistocalyx, Piliocalyx and Waterhousea. While homoplasy amongst morphological characters has misled attempts to divide the group, detailed and critical assessments of placental, ovular and seed morphology may provide novel insights into evolutionary relationships, and are an important future step in the development of a sound higher level taxonomy for Syzygium s.l.

https://www.jstor.org/stable/pdfplus/25065530.pdf

Molecular systematics of Syzygium and allied genera (Myrtaceae): evidence from the chloroplast genome

Australian Gossypium consists of 17 species classified into three sections. The largest and most poorly understood is the group of 12 species in sect. Grandicalyx that occur in the Kimberley and Cobourg regions of NW Australia. These areas are characterized by annual monsoon rains and dry-season fires. Species in sect. Grandicalyx exhibit a suite of morphological and ecological features that are otherwise unknown in the genus and that apparently evolved in response to seasonal fires and ant mutualism. These features include an herbaceous perennial habit, the ability to regenerate from thickened rootstocks following fires and ex-

Lyn A. Craven

Papers

Evolution of exceptional species richness among lineages of fleshy-fruited Myrtaceae.

Phylogeny of Hibiscus and the Tribe Hibisceae (Malvaceae) Using Chloroplast DNA Sequences of ndhF and the rpl16 Intron

An infrageneric classification of Syzygium (Myrtaceae)

Molecular systematics of Syzygium and allied genera (Myrtaceae): evidence from the chloroplast genome

Molecular Systematics of Australian Gossypium section Grandicalyx (Malvaceae)