Preservation of natural communities has historically consisted of measures protecting them from physical disturbance. Timber harvests and livestock grazing are usually excluded from preserves, and fire suppression has been practiced—within the U.S. system of national parks, for example. Ecologists and conservationists have come to recognize, however, that many forms of disturbance are important components of natural systems. Many plant communities and species are dependent on disturbance, especially for regeneration (Pickett & White 1985). Preserves should be large enough to allow the natural disturbance regime to operate and to support a mosaic of patches in different stages of disturbance, successional recovery, and community maturation (Pickett & Thompson 1978).

http://www.myxyz.org/phmurphy/dog/DisturbanceDiversityInvasion.pdf

Disturbance, Diversity, and Invasion: Implications for Conservation

The principles of classification and a classification of mammals. Bulletin of the AMNH ; v. 85

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

Methods for identifying species by using short orthologous DNA sequences, known as “DNA barcodes,” have been proposed and initiated to facilitate biodiversity studies, identify juveniles, associate sexes, and enhance forensic analyses. The cytochrome c oxidase 1 sequence, which has been found to be widely applicable in animal barcoding, is not appropriate for most species of plants because of a much slower rate of cytochrome c oxidase 1 gene evolution in higher plants than in animals. We therefore propose the nuclear internal transcribed spacer region and the plastid trnH-psbA intergenic spacer as potentially usable DNA regions for applying barcoding to flowering plants. The internal transcribed spacer is the most commonly sequenced locus used in plant phylogenetic investigations at the species level and shows high levels of interspecific divergence. The trnH-psbA spacer, although short (≈450-bp), is the most variable plastid region in angiosperms and is easily amplified across a broad range of land plants. Comparison of the total plastid genomes of tobacco and deadly nightshade enhanced with trials on widely divergent angiosperm taxa, including closely related species in seven plant families and a group of species sampled from a local flora encompassing 50 plant families (for a total of 99 species, 80 genera, and 53 families), suggest that the sequences in this pair of loci have the potential to discriminate among the largest number of plant species for barcoding purposes.

https://www.pnas.org/content/pnas/102/23/8369.full.pdf

Use of DNA barcodes to identify flowering plants

This paper is the first global study of the extent to which fire determines global vegetation patterns by preventing ecosystems from achieving the potential height, biomass and dominant functional types expected under the ambient climate (climate potential). To determine climate potential, we simulated vegetation without fire using a dynamic global-vegetation model. Model results were tested against fire exclusion studies from different parts of the world. Simulated dominant growth forms and tree cover were compared with satellite-derived land- and tree-cover maps. Simulations were generally consistent with results of fire exclusion studies in southern Africa and elsewhere. Comparison of global 'fire off' simulations with landcover and treecover maps show that vast areas of humid C(4) grasslands and savannas, especially in South America and Africa, have the climate potential to form forests. These are the most frequently burnt ecosystems in the world. Without fire, closed forests would double from 27% to 56% of vegetated grid cells, mostly at the expense of C(4) plants but also of C(3) shrubs and grasses in cooler climates. C(4) grasses began spreading 6-8 Ma, long before human influence on fire regimes. Our results suggest that fire was a major factor in their spread into forested regions, splitting biotas into fire tolerant and intolerant taxa.

/pdf/the-global-distribution-of-ecosystems-in-a-world-without-1aq6mksi7x.pdf

The global distribution of ecosystems in a world without fire

Aim This paper reviews the biogeography of the Australian monsoon tropical
biome to highlight general patterns in the distribution of a range of organisms
and their environmental correlates and evolutionary history, as well as to identify
knowledge gaps.
Location Northern Australia, Australian Monsoon Tropics (AMT). The AMT
is defined by areas that receive more than 85% of rainfall between November
and April.
Methods Literature is summarized, including the origin of the monsoon
climate, present-day environment, biota and habitat types, and phylogenetic and
geographical relationships of selected organisms.
Results Some species are widespread throughout the AMT while others are
narrow-range endemics. Such contrasting distributions correspond to presentday
climates, hydrologies (particularly floodplains), geological features (such as
sandstone plateaux), fire regimes, and vegetation types (ranging from rain forest
to savanna). Biogeographical and phylogenetic studies of terrestrial plants
(e.g. eucalypts) and animals (vertebrates and invertebrates) suggest that distinct
bioregions within the AMT reflect the aggregated effects of landscape and
environmental history, although more research is required to determine and
refine the boundaries of biogeographical zones within the AMT. Phylogenetic
analyses of aquatic organisms (fishes and prawns) suggest histories of associations
with drainage systems, dispersal barriers, links to New Guinea, and the existence
of Lake Carpentaria, now submerged by the Gulf of Carpentaria. Complex
adaptations to the landscape and climate in the AMT are illustrated by a number
of species.
Main conclusions The Australian monsoon is a component of a single global
climate system, characterized by a dominant equator-spanning Hadley cell.
Evidence of hot, seasonally moist climates dates back to the Late Eocene, implying
that certain endemic elements of the AMT biota have a long history. Vicariant
differentiation is inferred to have separated the Kimberley and Arnhem Land
bioregions from Cape York Peninsula/northern Queensland. Such older patterns
are overlaid by younger events, including dispersal from Southeast Asia, and
range expansions and contractions. Future palaeoecological and phylogenetic
investigations will illuminate the evolution of the AMT biome. Understanding the
biogeography of the AMT is essential to provide a framework for ecological
studies and the sustainable development of the region.

Biogeography of the Australian monsoon tropics

Aim To compare the phylogeny of the eucalypt and melaleuca groups with geological events and ages of fossils to discover the time frame of clade divergences.



Location Australia, New Caledonia, New Guinea, Indonesian Archipelago.



Methods We compare published molecular phylogenies of the eucalypt and melaleuca groups of the plant family Myrtaceae with geological history and known fossil records from the Cretaceous and Cenozoic.



Results The Australasian eucalypt group includes seven genera, of which some are relictual rain forest taxa of restricted distribution and others are species-rich and widespread in drier environments. Based on molecular and morphological data, phylogenetic analyses of the eucalypt group have identified two major clades. The monotypic Arillastrum endemic to New Caledonia is related in one clade to the more species-rich Angophora, Corymbia and Eucalyptus that dominate the sclerophyll vegetation of Australia. Based on the time of rifting of New Caledonia from eastern Gondwana and the age of fossil eucalypt pollen, we argue that this clade extends back to the Late Cretaceous. The second clade includes three relictual rain forest taxa, with Allosyncarpia from Arnhem Land the sister taxon to Eucalyptopsis of New Guinea and the eastern Indonesian archipelago, and Stockwellia from the Atherton Tableland in north-east Queensland. As monsoonal, drier conditions evolved in northern Australia, Arnhem Land was isolated from the wet tropics to the east and north during the Oligocene, segregating ancestral rain forest biota. It is argued also that the distribution of species in Eucalyptopsis and Eucalyptus subgenus Symphyomyrtus endemic in areas north of the stable edge of the Australian continent, as far as Sulawesi and the southern Philippines, is related to the geological history of south-east Asia-Australasia. Colonization (dispersal) may have been aided by rafting on micro-continental fragments, by accretion of arc terranes onto New Guinea and by land brought into closer proximity during periods of low sea-level, from the Late Miocene and Pliocene. The phylogenetic position of the few northern, non-Australian species of Eucalyptus subgenus Symphyomyrtus suggests rapid radiation in the large Australian sister group(s) during this time frame. A similar pattern, connecting Australia and New Caledonia, is emerging from phylogenetic analysis of the Melaleuca group (Beaufortia suballiance) within Myrtaceae, with Melaleuca being polyphyletic.



Main conclusion The eucalypt group is an old lineage extending back to the Late Cretaceous. Differentiation of clades is related to major geological and climatic events, including rifting of New Caledonia from eastern Gondwana, development of monsoonal and drier climates, collision of the northern edge of the Australian craton with island arcs and periods of low sea level. Vicariance events involve dispersal of biota.

Australian biogeographical connections and the phylogeny of large genera in the plant family Myrtaceae

/pdf/eucalypt-domestication-and-breeding-2nu4zylb7r.pdf

Eucalypt domestication and breeding

A review is presented of current knowledge of the tectonic rifting of eastern Gondwana in the context of possible land continuity between Australia and New Caledonia and the dating of events. Comment is made on the level of endemicity of the modern-day biota of New Caledonia, with examples of phylogenetic analyses, biogeographic patterns and estimated divergence dates among particular taxa, including birds (kagu-sunbittern clade), Nothofagus and Myrtaceae. The geological history of the region is complex but there is evidence of land persisting into the Cenozoic (Paleocene/Eocene) that possibly allowed old biota to persist. Vicariance explanations of divergences cannot be justifiably dismissed in favour of long-distance, over-water dispersal for such taxa.

Pauline Y. Ladiges

Papers

Biogeography of the Australian monsoon tropics

Australian biogeographical connections and the phylogeny of large genera in the plant family Myrtaceae

Eucalypt domestication and breeding

New Caledonia–Australian connections: biogeographic patterns and geology

Paralogy in cladistic biogeography and analysis of paralogy-free subtrees. American Museum novitates ; no. 3167