It is clear that the above can lead to confusion when scientists of different countries are trying to communicate with each other. Another example is the burrowing rodent called a gopher found throughout the western United States. In the southeastern United States the term gopher refers to a burrowing turtle very similar to the desert tortoise found in the American southwest. One final example; two North American mammals known as the elk and the caribou are known in Europe as the reindeer and the elk. We never sing “Rudolph the Red-nosed elk”! Confused? This was the reason for creating an internationally recognized system of naming organisms. To avoid confusion, living organisms are assigned a scientific name based on Latin or Latinized words. The English sparrow is Passer domesticus or Passer domesticus (italics or underlining these two names is the official written representation of a scientific name). Using a uniform naming system allows scientists from all over the world to recognize exactly which life form a scientist is referring to. The naming process is called the binomial system of nomenclature. Passer is comparable to a surname and is called the genus, while domesticus is the specific or species name (like your given name) of the English sparrow. Now scientists can give all sparrow-like birds the genus Passer but the species name will vary. All similar genera (plural for genus) can be grouped into another, “higher” category (see below). Study the following for a more through understanding of taxonomy. Taxonomy Analogy Kingdom: Animalia Country

Diversity of life

The Different Forms of Flowers on Plants of the Same Species: POLYGAMOUS, DIŒCTOUS, AND GYNO-DIŒCIOUS PLANTS

Large multi-gene phylogenetic trees of the grasses (Poaceae): progress towards complete tribal and generic level sampling.

The drying of the Tethys Sea—the progenitor of the modern Mediterranean, Black and Caspian seas—weakened the northern extension of the African monsoon and led to the creation of the Sahara desert about 7 million years ago. Most evidence suggests that the modern Sahara desert first arose between two and three million years ago, coinciding with the initiation of major glaciations in the Northern Hemisphere. This study puts Saharan origins much earlier. Zhongshi Zhang et al. show that the shrinkage of the Tethys Sea — the progenitor of the modern Mediterranean, Black and Caspian seas — weakened the northern extension of the African monsoon and led to the creation of the Sahara desert about seven million years ago. Such a dramatic revision could lead to new investigations of the Sahara in fields as diverse as geology, evolutionary biology and climatology. It is widely believed that the Sahara desert is no more than ∼2–3 million years (Myr) old1, with geological evidence showing a remarkable aridification of north Africa at the onset of the Quaternary ice ages2,3,4. Before that time, north African aridity was mainly controlled by the African summer monsoon (ASM)5,6,7,8, which oscillated with Earth’s orbital precession cycles. Afterwards, the Northern Hemisphere glaciation added an ice volume forcing on the ASM, which additionally oscillated with glacial–interglacial cycles2. These findings led to the idea that the Sahara desert came into existence when the Northern Hemisphere glaciated ∼2–3 Myr ago. The later discovery, however, of aeolian dune deposits ∼7 Myr old9 suggested a much older age, although this interpretation is hotly challenged1 and there is no clear mechanism for aridification around this time. Here we use climate model simulations to identify the Tortonian stage (∼7–11 Myr ago) of the Late Miocene epoch as the pivotal period for triggering north African aridity and creating the Sahara desert. Through a set of experiments with the Norwegian Earth System Model10 and the Community Atmosphere Model11, we demonstrate that the African summer monsoon was drastically weakened by the Tethys Sea shrinkage during the Tortonian, allowing arid, desert conditions to expand across north Africa. Not only did the Tethys shrinkage alter the mean climate of the region, it also enhanced the sensitivity of the African monsoon to orbital forcing, which subsequently became the major driver of Sahara extent fluctuations. These important climatic changes probably caused the shifts in Asian and African flora and fauna observed during the same period4,12,13,14, with possible links to the emergence of early hominins in north Africa15,16.

Aridification of the Sahara desert caused by Tethys Sea shrinkage during the Late Miocene

The Quaternary has been described as an important time for genetic diversification and speciation. This is based on the premise that Quaternary climatic conditions fostered the isolation of populations and, in some instances, allopatric speciation. However, the 'Quaternary Ice-Age speciation model' rests on two key assumptions: (i) that biotic responses to climate change during the Quaternary were significantly different from those of other periods in Earth's history; and (ii) that the mechanisms of isolation during the Quaternary were sufficient in time and space for genetic diversification to foster speciation. These assumptions are addressed by examining the plant fossil record for the Quaternary (in detail) and for the past 410 Myr, which encompasses previous intervals of icehouse Earth. Our examination of the Quaternary record indicates that floristic responses to climate changes during the past 1.8 Myr were complex and that a distinction has to be made between those plants that were able to withstand the extremes of glacial conditions and those that could not. Generation times are also important as are different growth forms (e.g. herbaceous annuals and arborescent perennials), resulting in different responses in terms of genetic divergence rates during isolation. Because of these variations in the duration of isolation of populations and genomic diversification rates, no canonical statement about the predominant floristic response to climatic changes during the Quaternary (i.e. elevated rates of speciation or extinction, or stasis) is currently possible. This is especially true because of a sampling bias in terms of the fossil record of tree species over that of species with non-arborescent growth forms. Nevertheless, based on the available information, it appears that the dominant response of arborescent species during the Quaternary was extinction rather than speciation or stasis. By contrast, our examination of the fossil record of vascular plants for the past 410 Myr indicates that speciation rates often increased during long intervals of icehouse Earth (spanning up to 50 Myr). Therefore, longer periods of icehouse Earth than those occurring during the Quaternary may have isolated plant populations for sufficiently long periods of time to foster genomic diversification and allopatric speciation. Our results highlight the need for more detailed study of the fossil record in terms of finer temporal and spatial resolution than is currently available to examine the significance of intervals of icehouse Earth. It is equally clear that additional and detailed molecular studies of extant populations of Quaternary species are required in order to determine the extent to which these 'relic' species have genomically diversified across their current populations.

/pdf/the-role-of-quaternary-environmental-change-in-plant-4rqxq2nvtz.pdf

The role of Quaternary environmental change in plant macroevolution: the exception or the rule?

The manipulation of DNA is routine practice in botanical research and has made a huge impact on plant breeding, biotechnology and biodiversity evaluation. DNA is easy to extract from most plant tissues and can be stored for long periods in DNA banks. Curation methods are well developed for other botanical resources such as herbaria, seed banks and botanic gardens, but procedures for the establishment and maintenance of DNA banks have not been well documented. This paper reviews the curation of DNA banks for the characterisation and utilisation of biodiversity and provides guidelines for DNA bank management. It surveys existing DNA banks and outlines their operation. It includes a review of plant DNA collection, preservation, isolation, storage, database management and exchange procedures. We stress that DNA banks require full integration with existing collections such as botanic gardens, herbaria and seed banks, and information retrieval systems that link such facilities, bioinformatic resources and other DNA banks. They also require efficient and well-regulated sample exchange procedures. Only with appropriate curation will maximum utilisation of DNA collections be achieved.

https://link.springer.com/content/pdf/10.1007%2Fs10265-006-0059-7.pdf

DNA banking for plant breeding, biotechnology and biodiversity evaluation

Part I. Introduction: 1. Integrating ecology and systematics in climate change research T. R. Hodkinson 2. Climate modelling and deep time climate change R. Caballero and P. Lynch 3. The perils of addressing long term challenges in a short term world: making descriptive taxonomy predictive R. M. Bateman Part II. Adaptation, Speciation and Extinction: 4. Global climate and extinction: evidence from the fossil record P. J. Mayhew 5. Long term fluctuations in atmospheric CO2 concentration influence plant speciation rate J. C. McElwain, K. K. Willis and K. J. Niklas 6. Wood anatomy and climate change P. Baas and E. A. Wheeler 7. Savanna biome evolution, climate change and the ecological expansion of C4 grasses Y. Bouchenak-Khelladi and T. R. Hodkinson 8. Climate warming results in phenotypic and evolutionary changes in spring events: a mini review A. Donnelly, A. Caffarra, E. Diskin, C. T. Kelleher, A. Pletsers, H. Proctor, R. Stirnemann, M. B. Jones, J. O'Halloran, B. F. O'Neill, J. Penuelas and T. Sparks 9. Terrestrial green algae: systematics, biogeography and expected responses to climate change F. Rindi Part III. Biogeography, Migration and Ecological Niche Modelling: 10. Biodiversity informatics for climate change studies A. Culham and C. Yesson 11. Climate envelope models in systematics and evolutionary research: theory and practice D. Roedder, S. Schmidtlein, S. Schick and S. Loetters 12. Biogeography of cyclamen: an application of phyloclimatic modelling C. Yesson and A. Culham 13. Cenozoic climate changes and the demise of Tethyan laurel forests: lessons for the future from an integrative reconstruction of the past F. Rodriguez-Sanchez and J. Arroyo 14. The impact of climate change on the origin and future of East African rain forest trees L. W. Chatrou, J. J. Wieringa and T. L. P. Couvreur 15. Hybridisation, introgression and climate change: a case study for the tree genus Fraxinus (Oleaceae) M. Thomasset, J. F. Fernandez-Manjarres, G. C. Douglas, N. Frascaria-Lacoste and T. R. Hodkinson Part IV. Conservation: 16. Assessing the effectiveness of a protected area network in the face of climatic change B. Huntley, D. G. Hole and S. G. Willis 17. Documenting plant species in a changing climate: a case study from Arabia M. Hall and A. G. Miller 18. A critical appraisal of the meaning and diagnosability of cryptic evolutionary diversity, and its implications for conservation in the face of climate change J. Bernardo 19. Climate change and Cyperaceae D. A. Simpson, C. Yesson, A. Culham, C. A. Couch and A. M. Muasya 20. An interdisciplinary review of climate change trends and uncertainties: lichen biodiversity, arctic alpine ecosystems and habitat loss C. J. Ellis and R. Yahr 21. Climate change and oceanic mountain vegetation: a case study of the montane heath and associated plant communities in western Irish mountains R. L. Hodd and M. J. Sheehy Skeffington.

Climate change, ecology and systematics

Monitoring wetlands is necessary in order to understand and protect their ecohydrological balance. In Ireland, traditionally wetland-monitoring is carried out by manual field visits which can be very time-consuming. To automate the process, this study extends the ability of remote sensing-based monitoring of wetlands by combining RGB image processing, machine learning algorithms, and satellite data analysis to create seasonal maps of vegetation communities within the wetlands. The methodology matches multispectral and broad coverage of open-source Sentinel-2 (S2) imagery with the high spatial granularity of Unmanned Aerial Vehicles (UAV) or drone images. Single sensor drone imagery was captured, colour corrected and classified using random forest (RF) classifier for a subset of the wetland. The classified imagery was upsampled to satellite imagery scale to create training data for vegetation-segmentation in the entire wetland. The process was repeated for multiple seasons, and an annual map was created utilising the majority voting. The proposed framework has been evaluated on various wetlands across Ireland, with results presented herein for an ombrotrophic peatland complex, Clara Bog. The accuracy of the maps was checked utilising a set of area-based performance metric. The application of this method thereby reduces the number of field surveys typically required to assess the long-term ecological change of such wetland habitats. The performance of the proposed method demonstrates that the technique is a robust, quick, and cost-effective way to map wetland habitats seasonally and to explore their ecohydrological synergies.

A nested drone-satellite approach to monitoring the ecological conditions of wetlands

Colchicum autumnale L. (Colchicaceae) is classed as an endangered plant species in Ireland, with a highly localised distribution centred on the Nore Valley in the southeast. The high resolution Amplified Fragment Length Polymorphism genetic fingerprinting technique was used to clarify a question over the native status of the species and to assess its Irish conservation status through comparison with populations throughout northwestern Europe. The analysis of 20 populations with three selective primer pairs yielded 155 markers, 90% of which displayed polymorphism. Allele frequency was estimated using a Bayesian approach and based on this, total gene diversity (Ht) was 0.305 and mean within-population gene diversity (Hw) was 0.142. Irish populations contain comparatively moderate levels of genetic diversity and are unlikely to be susceptible to the deleterious effects of inbreeding depression. Analysis of Molecular Variance revealed that populations were significantly differentiated, with 68% of variation partitioned among populations and 32% within. Neighbour-joining and ordination analyses revealed a major biogeographic division between populations, suggesting that post-glacial migration in northwest Europe was driven from at least two separate glacial refugia and that the re-colonisation of Britain and Ireland is likely to have occurred via a western seaboard route from an Iberian glacial refugium. The total evidence points to C. autumnale being a native component of the Irish flora and its endangered IUCN (World Conservation Union) country status should therefore make it a priority for national conservation efforts. The study illustrates the point that a broader geographical perspective is fundamental to the assessment of the conservation status of regionally threatened plant species.

Patterns of genetic variation in Colchicum autumnale L. and its conservation status in Ireland: a broader perspective on local plant conservation.

Summary Parnell, J. & Waldren, S.: Detrended correspondence analysis in the ordination of data for phenetics and cladistics. - Taxon 45: 71-84. 1996. - ISSN 0040-0262. Most methods of morphometric and phylogenetic analysis do not permit the incorporation of both categorical and quantitative data. Detrended correspondence analysis (DCA) was used to produce ordination diagrams of strictly categorical data from a cladistic analysis, and mixed data from a morphometric study of hybridization. In both cases it proved preferable to standardize the data prior to DCA, because increased separation on ordination was found when larger scale ranges were used. A standardization is suggested, such that characters are scaled on a range from 1 to the total number of characters scored; this will produce more informative ordinations if large numbers of characters are scored. When used in conjunction with appropriate cladograms this phenetic technique may help reveal features such as homoplasy which are not readily apparent in cladograms, while the capability of DCA to combine both categorical and quantitative characters is especially useful in morphometric studies and in areas of evolutionary biology, e.g. chronistic studies of extinction events in morphospace.

Stephen Waldren

Papers

DNA banking for plant breeding, biotechnology and biodiversity evaluation

Climate change, ecology and systematics

A nested drone-satellite approach to monitoring the ecological conditions of wetlands

Patterns of genetic variation in Colchicum autumnale L. and its conservation status in Ireland: a broader perspective on local plant conservation.

Detrended correspondence analysis in the ordination of data for phenetics and cladistics