The ‘requirement of total evidence’ and its role in phylogenetic systematics

The question of whether or not to partition data for the purposes of inferring phylogenetic hypotheses remains controversial. Opinions have been especially divided since Kluge's (1989, Systematic Zoology 38, 7–25) claim that data partitioning violates the requirement of total evidence (RTE). Unfortunately, advocacy for or against the RTE has not been based on accurate portrayals of the requirement. The RTE is a basic maxim for non-deductive inference, stipulating that evidence must be considered if it has relevance to an inference. Evidence is relevant if it has a positive or negative effect on a given conclusion. In the case of ℈partitioned’ phylogenetic inferences, the RTE is violated, and the basis for rational belief in any conclusion is compromised, unless it is shown that the partitions are evidentially irrelevant to one another. The goal of phylogenetic systematics is to hypothesize past causal conditions to account for observed shared similarities among two or more species. Such inferences are non-deductive, necessitating consideration of the RTE. Some phylogeneticists claim the parsimony criterion as justification for the RTE. There is no relation between the two – parsimony is a relation between a hypothesis and causal question(s). Parsimony does not dictate the content of premises prior to an inference. ℈Taxonomic congruence,’ ℈supertrees,’ and ℈conditional combination’ methods violate the RTE. Taxonomic congruence and supertree methods also fail to achieve the intended goal of phylogenetic inference, such that ℈consensus trees’ and ℈supertrees’ lack an empirical basis. ℈Conditional combination’ is problematic because hypotheses derived from partitioned data cannot be compared – a causal hypothesis inferred to account for a set of effects only has relevance to those effects, not any comparative relevance to other causal hypotheses. A similar problem arises in the comparisons of hypotheses derived from different causal theories.     

NOTHOFAGUS AND PACIFIC BIOGEOGRAPHY

Abstract — Gondwanan biogeography, particularly the relationships between southern South America, New Zealand, Australia, New Guinea and New Caledonia, has been much studied. Nothofagus is often used as the "test taxon", and many papers have been directed at using Nothofagus to explain Gondwanan biogeography. Cladistic biogeographers, working on plant material, have generally failed to find congruence among taxa expected from the southern Pacific disjunctions. New morphological and molecular data on the phytogeny of Nothofagus have re-opened the issue, and we analysed these data to construct a new hypothesis of the biogeography of the genus. We assembled all plant taxa for which we could find reasonably robust phylogenetic hypotheses, and sought a parsimonious biogeographical pattern common to all. Two analyses, based on different assumptions, produced the same general areacladogram. We use the general area-cladogram, in conjunction with the fossil record of Nothofagus to construct a historical scenario for the evolution of the genus. This scenario indicates extensive extinction, but also suggests that Australia has a more recent relationship to New Zealand than to southern South America. This is not congruent with the current geological theories, nor with the patterns evident from insect biogeography. We suggest that concordant dispersal is an unlikely explanation for this pattern, and propose that the solution might be found in alternative geological hypotheses.     

Problems with the current deinococcal hypothesis: an alternative theory

All theories related to the evolution of Deinococcus radiodurans have a common denominator: the strong positive correlation between ionizing-radiation resistance and desiccation tolerance. Currently, the widespread hypothesis is that D. radiodurans’ ionizing-radiation resistance is a consequence of this organism’s adaptation to desiccation (desiccation adaptation hypothesis). Here, we draw attention to major discrepancy that has emerged between the “desiccation adaptation hypothesis” and recent findings in computational biology, experimental research, and terrestrial subsurface surveys. We explain why the alternative hypothesis, suggesting that D. radiodurans’ desiccation tolerance could be a consequence of this organism’s adaptation to ionizing radiation (radiation adaptation hypothesis), should be considered on equal basis with the “desiccation adaptation hypothesis”.     

How Willing Are You to Accept Sexual Requests from Slightly Unattractive to Exceptionally Attractive Imagined Requestors?

In their classic study of differences in mating strategies, Clark and Hatfield (1989, Journal of Psychology and Human Sexuality, 2, 39–54) found that men and women demonstrated a striking difference in interest in casual sex. The current study examined the role of an imagined requestor’s physical attractiveness (slightly unattractive, moderately attractive, and exceptionally attractive) on men’s and women’s willingness to accept three different requests (go out, come to apartment, go to bed) as reflected in answers to a questionnaire. We tested two hypotheses with a sample of 427 men and 443 women from three countries. Hypothesis 1 states that men, relative to women, will demonstrate a greater willingness to accept the “come to apartment” and “go to bed” requests but not the “go out” request for all three levels of requestor attractiveness. This hypothesis reflects Clark and Hatfield’s main findings. Hypothesis 2 states that the physical attractiveness of a potential partner will have a greater effect on women’s than on men’s willingness to accept all three requests, and particularly for the explicit request for casual sex. The results partially supported Hypothesis 1 and fully supported Hypothesis 2. The discussion highlights limitations of the current research and presents directions for future research.     

Do geese fully develop brood patches? A histological analysis of lesser snow geese (<Emphasis Type="Italic">Chen caerulescens caerulescens</Emphasis>) and Ross’s geese (<Emphasis Type="Italic">C. rossii</Emphasis>)

Most birds develop brood patches before incubation; epidermis and dermis in the brood patch region thicken, and the dermal connective tissue becomes increasingly vascularized and infiltrated by leukocytes. However, current dogma states that waterfowl incubate without modifications of skin within the brood patch region. The incubation periods of lesser snow geese (Chen caerulescens caerulescens; hereafter called snow geese) and Ross’s geese (C. rossii) are 2–6 days shorter than those of other goose species; only females incubate. Thus, we hypothesized that such short incubation periods would require fully developed brood patches for sufficient heat transfer from incubating parents to eggs. We tested this hypothesis by analyzing the skin histology of abdominal regions of snow and Ross’s geese collected at Karrak Lake, Nunavut, Canada. For female snow geese, we found that epidermis and dermis had thickened and vascularization of dermis was 14 times greater, on average, than that observed in males (n=5 pairs). Our results for Ross’s geese (n=5 pairs) were more variable, wherein only one of five female Ross’s geese fully developed a brood patch. Our results are consistent with three hypotheses about brood patch development and its relationship with different energetic cost–benefit relationships, resulting from differences in embryonic development and body size.     

Darwin, historical biogeography, and the importance of overcoming binary opposites

It is well known that Darwin and Wallace came to discover the phenomenon of evolution through a historical approach to the geographical distribution of organisms. Before Darwin, evolution was a mere speculation that could be invoked to explain some facts. Darwin's biogeographical argument for evolution is based largely on three main explanatory hypotheses. The first is that the geographical distribution of organisms is historically informative. The second hypothesis is that long-distance dispersal over barriers is one main force (extinction is the other) that modifies the distribution of organisms. The third of Darwin's biogeographical hypotheses is that the factors that shape the distribution of organisms are mainly historical (large, often global and long temporal scales) rather than ecological (small spatial and short temporal scales). From the time of Darwin until now, a wide spectrum of biogeographical schools have provided new insights that challenge the central role of space, dispersal and history as the main explanatory hypotheses for the distribution of organisms, generating three binary opposites: (1) the spatial dimension of evolution: geographical distribution of organisms as historically informative vs. historically uninformative; (2) the processes that modify the geographical distribution of organisms: dispersal vs. vicariance; and (3) the explanation of geographical distribution: history vs. ecology. We analyse these three binary opposites to show that the components of each are complementary rather than antagonistic approaches to the study of biogeography.     

On the definition of element,chorotype and component in biogeography

Terms such as element, chorotype and component are widely used to indicate biogeographical units. As a result of variation in approaches and methodologies, these terms do not have a single definitive meaning, and similar concepts have been defined under different labels. As originally defined, element denotes a group of species that occur in previously defined biogeographical areas, while chorotype denotes a group of species with a similar distribution. The term component is widely used in ecology to denote the biotic or abiotic constituent of an ecosystem; within biogeography it has typically been used as a synonym for element. Applying the original meanings, current usage within the tradition of systematic biogeography should regard element as referring to groups of taxa defined according to the biogeographical areas they occupy. Within quantitative and evolutionary biogeography, chorotype should be used to define patterns of distribution that can be used to generate hypotheses about their causes and origins. In this paper I argue that component expresses a generic concept rather than a chorological category and should be avoided in biogeography.     

Global diversity of caddisflies (Trichoptera: Insecta) in freshwater

The not yet uploaded Trichoptera World Checklist (TWC) [], as at July 2006, recorded 12,627 species, 610 genera and 46 families of extant and in addition 488 species, 78 genera and 7 families of fossil Trichoptera. An analysis of the 2001 TWC list of present-day Trichoptera diversity at species, generic/subgeneric and family level along the selected Afrotropical, Neotropical, Australian, Oriental, Nearctic and Palaearctic (as a unit or assessed as Eastern and Western) regions reveals uneven distribution patterns. The Oriental and Neotropical are the two most species diverse with 47–77% of the species in widespread genera being recorded in these two regions. Five Trichoptera families comprise 55% of the world’s species and 19 families contain fewer than 30 species per family. Ten out of 620 genera contain 29% of the world’s known species. Considerable underestimates of Trichoptera diversity for certain regions are recognised. Historical processes in Trichoptera evolution dating back to the middle and late Triassic reveal that the major phylogenetic differentiation in Trichoptera had occurred during the Jurrasic and early Cretaceous. The breakup of Gondwana in the Cretaceous led to further isolation and diversification of Trichoptera. High species endemism is noted to be in tropical or mountainous regions correlated with humid or high rainfall conditions. Repetitive patterns of shared taxa between biogeographical regions suggest possible centres of origin, vicariant events or distribution routes. Related taxa associations between different regions suggest that an alternative biogeographical map reflecting Trichoptera distribution patterns different from the Wallace (The Geographical Distribution of Animals: With a Study of the Relations of Living and Extinct Faunas as Elucidating the Past Changes of the Earth’s Surface, Vol. 1, 503 pp., Vol. 2, 607 pp., Macmillan, London, 1876) proposed biogeography patterns should be considered. Anthropogenic development threatens biodiversity and the value of Trichoptera as important functional components of aquatic ecosystems, indicator species of deteriorating conditions and custodians of environmental protection are realised.     

Sexual coercion and forced in-pair copulation as sperm competition tactics in humans

Rape of women by men might be generated either by a specialized rape adaptation or as a by-product of other psychological adaptations. Although increasing number of sexual partners is a proposed benefit of rape according to the “rape as an adaptation” and the “rape as a by-product” hypotheses, neither hypothesis addresses directly why some men rape their long-term partners, to whom they already have sexual access. In two studies we tested specific hypotheses derived from the general hypothesis that sexual coercion in the context of an intimate relationship may function as a sperm competition tactic. We hypothesized that men’s sexual coercion in the context of an intimate relationship is related positively to his partner’s perceived infidelities and that men’s sexual coercion is related positively to their mate retention behaviors (behaviors designed to prevent a partner’s infidelity). The results from Study 1 (self-reports from 246 men) and Study 2 (partner-reports from 276 women) supported the hypotheses. The Discussion section addresses limitations of this research and highlights future directions for research on sexual coercion in intimate relationships.     

Wallace’s Other Line: Human Biogeography and Field Practice in the Eastern Colonial Tropics

This paper examines how the 19th-century British naturalist Alfred Russel Wallace used biogeographical mapping practices to draw a boundary line between Malay and Papuan groups in the colonial East Indies in the 1850s. Instead of looking for a continuous gradient of variation between Malays and Papuans, Wallace chose to look for a sharp discontinuity between them. While Wallace’s “human biogeography” paralleled his similar project to map plant and animal distributions in the same region, he invoked distinctive “mental and moral” features as more decisive than physical ones. By following Wallace in the field, we can see his field mapping practices in action – how he conquered the problem of local particularity in the case of human variation. His experiences on the periphery of expanding European empires, far from metropolitan centers, shaped Wallace’s observations in the field. Taking his cues from colonial racial categories and his experiences collaborating with local people in the field, Wallace constructed the boundary line between the Malay and Papuan races during several years of work in the field criss-crossing the archipelago as a scientific collector. This effort to map a boundary line in the field was a bold example of using the practices of survey science to raise the status of field work by combining fact gathering with higher-level generalizing, although the response back in the metropole was less than enthusiastic. Upon his return to Britain in the 1860s, Wallace found that appreciation for observational facts he had gathered in the field was not accompanied by agreement with his theoretical interpretations and methods for doing human biogeography.     

Working at the interface of phylogenetics and population genetics: a biogeographical analysis of Triaenops spp. (Chiroptera: Hipposideridae)

New applications of genetic data to questions of historical biogeography have revolutionized our understanding of how organisms have come to occupy their present distributions. Phylogenetic methods in combination with divergence time estimation can reveal biogeographical centres of origin, differentiate between hypotheses of vicariance and dispersal, and reveal the directionality of dispersal events. Despite their power, however, phylogenetic methods can sometimes yield patterns that are compatible with multiple, equally well-supported biogeographical hypotheses. In such cases, additional approaches must be integrated to differentiate among conflicting dispersal hypotheses. Here, we use a synthetic approach that draws upon the analytical strengths of coalescent and population genetic methods to augment phylogenetic analyses in order to assess the biogeographical history of Madagascar's Triaenops bats (Chiroptera: Hipposideridae). Phylogenetic analyses of mitochondrial DNA sequence data for Malagasy and east African Triaenops reveal a pattern that equally supports two competing hypotheses. While the phylogeny cannot determine whether Africa or Madagascar was the centre of origin for the species investigated, it serves as the essential backbone for the application of coalescent and population genetic methods. From the application of these methods, we conclude that a hypothesis of two independent but unidirectional dispersal events from Africa to Madagascar is best supported by the data.     

Size-assortative pairing in the lotic amphipod <Emphasis Type="Italic">Gammarus zaddachi</Emphasis>, an examination of hypotheses and the influence of current speed

Three main hypotheses have been put forward to explain size-assortative pairing in gammarid amphipods: microhabitat separation, sexual selection and loading constraint. In order to determine which hypothesis best explains this phenomenon in the estuarine species Gammarus zaddachi, I first measured the body lengths and dry weights of precopula pairs collected from two field sites with substantially different current speeds. Second, I performed three laboratory experiments in order to estimate the importance of the following processes: (1) male choice; (2) male–male competition and (3) male–female acceptability. The loading constraint hypothesis seemed best supported by the data in that field-collected male G. zaddachi size correlated well with female size in precopula pairing in both fast and slow flowing water. In the laboratory, males preferred females of their same size group (large versus small), and ‘won’ them in the male–male competition experiments. Size-assortative pairing is thus likely a consequence of the loading constraints imposed upon these males by virtue of them having to carry and manoeuvre their partners through flowing water, while attempting to maintain station in an optimal microhabitat. Males may therefore forego the largest, most fecund females, in favour of a practicable payload (small male–large female pairings were rare). However, there seems to be a lower limit to this selection, indicated by the high degree of cannibalism on small females by large males.     

The role of the striatum in adaptation learning: a computational model

To investigate the functional role of the striatum in visuo-motor adaptation, we extend the DIRECT-model for visuo-motor reaching movements formulated by Bullock et al.(J Cogn Neurosci 5:408–435,1993) through two parallel loops, each modeling a distinct contribution of the cortico–cerebellar–thalamo–cortical and the cortico–striato–thalamo–cortical networks to visuo-motor adaptation. Based on evidence of Robertson and Miall(Neuroreport 10(5): 1029–1034, 1999), we implement the function of the cortico–cerebellar–thalamo–cortical loop as a module that gradually adapts to small changes in sensorimotor relationships. The cortico–striato–thalamo–cortical loop on the other hand is hypothesized to act as an adaptive search element, guessing new sensorimotor-transformations and reinforcing successful guesses while punishing unsuccessful ones. In a first step, we show that the model reproduces trajectories and error curves of healthy subjects in a two dimensional center-out reaching task with rotated screen cursor visual feedback. In a second step, we disable learning processes in the cortico–striato– thalamo–cortical loop to simulate subjects with Parkinson’s disease (PD), and show that this leads to error curves typical of subjects with PD. We conclude that the results support our hypothesis, i.e., that the role of the cortico–striato–thalamo–cortical loop in visuo-motor adaptation is that of an adaptive search element.     

Changes in the Range of Some Common Rocky Shore Species in Britain – A Response to Climate Change?

Since the 1990s there has been a period of rapid climate warming in Europe. Long-term broad scale datasets coupled with time series at specific locations for rocky intertidal species dating back to the 1950s have been collected in Britain and Ireland. Resurveys of the original locations in 2001–2003 have been undertaken to identify changes in the biogeographical range and abundance of these species. The results show that some ‘southern’ species including Osilinus lineatus da Costa and Gibbula umbilicalis da Costa have undergone north and north-eastern range extensions. Populations have increased in abundance and adult size has decreased since the previous surveys were conducted. These changes have been synchronous throughout Britain, strongly suggesting that climate is responsible. The use of intertidal species as indicators of climate change is proposed.     

Conservation Biogeography: assessment and prospect

There is general agreement among scientists that biodiversity is under assault on a global basis and that species are being lost at a greatly enhanced rate. This article examines the role played by biogeographical science in the emergence of conservation guidance and makes the case for the recognition of Conservation Biogeography as a key subfield of conservation biology delimited as: the application of biogeographical principles, theories, and analyses, being those concerned with the distributional dynamics of taxa individually and collectively, to problems concerning the conservation of biodiversity. Conservation biogeography thus encompasses both a substantial body of theory and analysis, and some of the most prominent planning frameworks used in conservation. Considerable advances in conservation guidelines have been made over the last few decades by applying biogeographical methods and principles. Herein we provide a critical review focussed on the sensitivity to assumptions inherent in the applications we examine. In particular, we focus on four inter‐related factors: (i) scale dependency (both spatial and temporal); (ii) inadequacies in taxonomic and distributional data (the so‐called Linnean and Wallacean shortfalls); (iii) effects of model structure and parameterisation; and (iv) inadequacies of theory. These generic problems are illustrated by reference to studies ranging from the application of historical biogeography, through island biogeography, and complementarity analyses to bioclimatic envelope modelling. There is a great deal of uncertainty inherent in predictive analyses in conservation biogeography and this area in particular presents considerable challenges. Protected area planning frameworks and their resulting map outputs are amongst the most powerful and influential applications within conservation biogeography, and at the global scale are characterised by the production, by a small number of prominent NGOs, of bespoke schemes, which serve both to mobilise funds and channel efforts in a highly targeted fashion. We provide a simple typology of protected area planning frameworks, with particular reference to the global scale, and provide a brief critique of some of their strengths and weaknesses. Finally, we discuss the importance, especially at regional scales, of developing more responsive analyses and models that integrate pattern (the compositionalist approach) and processes (the functionalist approach) such as range collapse and climate change, again noting the sensitivity of outcomes to starting assumptions. We make the case for the greater engagement of the biogeographical community in a programme of evaluation and refinement of all such schemes to test their robustness and their sensitivity to alternative conservation priorities and goals.     

Biogeography and conservation in Southeast Asia: how 2.7 million years of repeated environmental fluctuations affect today’s patterns and the future of the remaining refugial-phase biodiversity

Understanding the historical biogeography of this global biodiversity hotspot is as important to long-term conservation goals as ecology and evolution are to understanding current patterns and processes. Today’s geography is, however, misleading and typical of only ~2% of the last million years; >90% of that time the region’s land area was 1.5–2.0 times larger as mean sea levels were 62 m below today’s, climates were cooler, and extensive forests and savanna covered the emerged Sunda plains. The region’s land area varied two-fold as sea levels fluctuated up to ±50 m with each of ~50 Pleistocene glacial cycles, and forests expanded and contracted with oscillations in land area and seasonality. This dynamic geographic history is relevant to the development of biogeographic regionalism and shows that it is today’s forests that are refugial, not those of the Last Glacial Maximum. This history affects how species will adapt or shift their ranges in response to global warming and further decreases in land area (submergence of low-lying coastal areas) during the 21st century. The alternative is mass species extinction. The biota is also threatened by the continued destruction of forest, destruction of Mekong River flood-pulse based ecosystems, and continued human population growth. Human biogeography will become more important in conservation planning as tens of millions of people who depend on protected area forests, riverine ecosystems, and coastal habitats become environmental refugees. Conservation scientists need to become more involved in regional ecological education, environmental stewardship, and ecosystem-based adaptation to sustain as much as possible of this rich biota and the ecological services it provides.     

A Life More Ordinary: The Dull Life but Interesting Times of Joseph Dalton Hooker

The life of Joseph Dalton Hooker (1817–1911) provides an invaluable lens through which to view mid-Victorian science. A biographical approach makes it clear that some well-established narratives about this period need revising. For example, Hooker’s career cannot be considered an example of the professionalisation of the sciences, given the doubtful respectability of being paid to do science and his reliance on unpaid collectors with pretensions to equal scientific and/or social status. Nor was Hooker’s response to Darwin’s theories either straightforward or contradictory; it only makes sense as carefully crafted equivocation when seen in the context of his life and career. However, the importance of Hooker’s life is ultimately its typicality; what was true of Hooker was true of many other Victorian men of science.     

Biological images of geological history: through a glass darkly or brightly face to face?

Abstract Aim To explore the implications for historical biogeography of a recent review of island biogeographical theory in three main thematic areas and to suggest ways in which a synthesis between the two approaches might be achieved to the benefit of both. Location The Indo‐Australian tropics. Theme 1 discusses the relationship of species number to area, and how the nestedness of faunas may influence the methodology used for some types of analysis and also the quality of data expected from an archipelago embracing an extreme range of island sizes. Theme 2 examines the way in which the processes of speciation may lead to development of biogeographical patterns through a complex archipelago, illustrated in particular with reference to Sulawesi where biotic enrichment from different lepidopteran groups follows predictions from island biogeographical theory. This also has implications for patterns of endemism in the archipelago, another constraint on the quality of data available for historical biogeography. Theme 3 addresses ecological determinism as an influence in development of biogeographical pattern, focusing on the theme of specificity in insect–plant relationships and the potential for parallel development of pattern in an insect group and its particular plant host group. This theme is developed with particular reference to moth and plant groups that may represent Gondwanan elements in the Oriental fauna, with an analysis of Sarcinodes, a geometrid moth genus associated with Proteaceae. Main conclusions Prospects are assessed for the synthesis of the two approaches of island biogeography and historical biogeography. Modelling pattern development with the former may complement the methods of analysis of the latter, particularly if some satisfactory method for dating events of pattern development can also be incorporated.     

Hypothesis testing in biogeography

Often, biogeography is applied only as a narrative addition to phylogenetic studies and lacks scientific rigour. However, if research questions are framed as hypotheses, biogeographical scenarios become testable. In this review, we explain some problems with narrative biogeography and show how the use of explicit hypotheses is changing understanding of how organisms came to be distributed as they are. Developing synergies between biogeography, ecology, molecular dating and palaeontology are providing novel data and hypothesis-testing opportunities. New approaches are challenging the classic 'Gondwana' paradigm and a more complicated history of the Southern Hemisphere is emerging, involving not only general drivers such as continental drift and niche conservatism, but also drowning and re-emergence of landmasses, biotic turnover and long-distance colonization.