Legendre and Makarenkov
Abstract.A reticulogram is a general network capable of representing a reticulate evolutionary structure. It is particularly useful to portray relationships among organisms that may be related in a non-unique way to their common ancestor; a structure of this kind cannot be represented by a dendrogram or a phylogenetic tree. We are proposing a new method for construction of reticulograms representing a given distance matrix. Reticulate evolution applies first to phylogenetic problems; it has been found in nature, for example, in the within-species micro-evolution of eukaryotes and in lateral gene transfer in bacteria. In this paper, we are proposing a new method for reconstructing reticulation networks and developing applications of the reticulate evolution model to ecological biogeographic, population micro-evolutionary, and hybridization problems. The first example considers a spatially-constrained reticulogram representing the postglacial dispersal of freshwater fishes in the Quebec Peninsula; the reticulogram provides a better model of postglacial dispersal than a (bi)furcating tree model. The second example depicts the morphological similarities among local populations of muskrats in a river valley in Belgium; adding supplementary branches to a tree depicting the river network leads to a better representation of the morphological distances among local populations of muskrats than a (bi)furcating tree structure. A third example involves hybrids between plants of the genus Aphelandra.
Legendre et al.
Abstract.A new method, ParaFit, has been developed to test the significance of a global hypothesis of coevolution between parasites and their hosts. Individual host-parasite association links can also be tested. The test statistics are functions of the host and parasite phylogenetic trees and of the set of host-parasite association links. Numerical simulations are used to show that the method has correct rate of type I error and good power except under extreme error conditions. An application to real data (pocket gophers and chewing lice) is presented.
Funk et al.
Abstract.Conservation planning has tended to focus more on pattern (representation) than process (persistence) and, for the former, has emphasized species and ecosystem or community diversity over genetic diversity. Here I consider how best to incorporate knowledge of evolutionary processes and the distribution of genetic diversity into conservation planning and priority setting for populations within species and for biogeographic areas within regions. Separation of genetic diversity into two dimensions, one concerned with adaptive variation and the other with neutral divergence due to isolation, highlights different evolutionary processes and suggests alternative strategies for conservation. Planning for both species and areas should emphasize protection of historically isolated lineages ("Evolutionarily Significant Units") as these cannot be recovered. By contrast, adaptive features may best be protected by maintaining the context for selection, heterogeneous landscapes and viable populations, rather than by protecting specific phenotypes. A useful strategy may be to; (i) identify areas that are important to represent species and (vicariant) genetic diversity, and (ii) maximize within these protection of contiguous environmental gradients across which selection and migration can interact to maintain population viability and (adaptive) genetic diversity. These concepts are illustrated using recent results from analysis of a rainforest fauna from northeast Australia.
Perry et al.
Abstract.Biodiversity of North American freshwaters is among the highest in the world. This biodiversity is, however, also among the most threatened with extinction as a result of habitat degradation, pollution, and nonindigenous species, both Eurasian and North American. Unlike habitat degradation and pollution, nonindigenous species represent a permanent loss of biodiversity since their removal or control is often impossible. Most species introduced into non-native North American ranges, however, are not from Eurasia, instead the are introduced from geographically isolated regions within North America. Although the ecological effects of introduced species have been widely documented, the effects of hybridization, especially between closely related species, represents an equally serious mechanism of extinction but is often understudied. Identification of species likely to hybridize after contact is of critical importance to prevent the further loss of native species. Molecular phylogenetics serves as a powerful tool to identify freshwater species at risk of introgression assuming genetic distance is a good predictor of the potential for hybridization. While not a thorough review of all cases of hybridization, this review documents the extent and effects of hybridization in fishes, crayfishes, mussels, and other invertebrates in light of the currently accepted phylogenetic relationships. We suggest this approach may be the first step in addressing the potential threat of hybridization between many of the closely related species in North American fresh waters.
Sakai et al.
Abstract.The Hawaiian flora, because of its great isolation, high levels of endemism, known lineages, and high rates of endangerment, offers unique opportunities to explore patterns of endangerment that may be shared by many islands or habitats that are ecological islands. Nine percent of the native flora of 1159 taxa are already extinct, and 52.5% are at risk (extinct, endangered, vulnerable, or rare). Patterns of endangerment are related to phylogeny, ecological and life history traits, and geographic patterns of taxa and lineages. Risk is strongly associated with limited geographic distribution at several different scales: endemic taxa (native only to the Hawaiian Islands) are at far greater risk than indigenous taxa (with Hawaiian and extra-Hawaiian ranges), single-island endemics are more at risk than multi-island endemics, small islands have the highest proportion of endemic taxa at risk, and endemics with more limited habitat distributions (elevation, community type) are more at risk. Among the major islands, Maui Nui has the highest percent of taxa that are extinct. Kaua'i has the lowest percent of extinct taxa and the highest proportion of single-island endemic taxa that are rare. Historic population density is a strong predictor of risk, and taxa with historically low population densities are at greatest risk with rapid anthropogenic changes. Endemic taxa at risk are associated with distributions in cliff habitats that serve as refugia from large herbivores, shrublands, forests, and bogs rather than coastal areas and grasslands. Endemic taxa with distributions in low elevation dry habitats have the highest proportion of taxa at risk, but the greatest absolute number of taxa at risk occur in mesic lowland and montane forests and wet montane forests. The life history patterns associated with risk are complicated, and inclusion of the effect of evolutionary relationships (lineages) is essential to prevent domination of these patterns by taxa in the largest lineages. The largest Hawaiian lineage is in the Campanulaceae, and as a result, species level analyses without respect to lineage shows risk associated with a monomorphic (hermaphroditic) breeding system and bird pollination. Analyses incorporating the effect of lineage greatly reduce the impact of these taxa, and result in an association of risk with insect pollination, with no effect of breeding system. There is no association of lineage size and the percent of taxa at risk within the lineage; endemic taxa from lineages with large radiations are at no greater risk than endemic single-taxon lineages. The percent of taxa at risk at the family level in the Hawaiian Islands and worldwide (excluding Hawaiian taxa) are positively correlated, although flowering plant families in the Hawaiian Islands have a much higher proportion of taxa at risk than worldwide. These patterns may be useful to inform management decisions in other island-like ecosystems under increasing threats around the world.
Funk and Richardson
Abstract.Systematic data in the form of collections data are useful in biodiversity studies in many ways, most importantly because they serve as the only direct evidence of species distributions. However, collecting bias has been demonstrated for most areas of the world and has led some to propose methods that circumvent the need for collections data. New methods that model collections data in combination with abiotic data and predict potential total species distribution are examined using 25,111 records representing 5,123 species of plants and animals from Guyana; some methods use the reduced number of 320 species. These modeled species distributions are evaluated and potential high priority biodiversity sites are selected using the concept of irreplaceability, a measure of uniqueness. The major impediments to using collections data are the lack of data available in a useful format and the reluctance of most systematists to become involved in biodiversity and conservation research.
Desmet et al.
Abstract.This paper explores the role that biosystematists can play in conservation planning. Conservation planning concerns the location and design of reserves that both represent a region's biodiversity and enable the persistence of its biodiversity by maintaining key ecological and evolutionary processes. For conservation planning to be effective quantitative targets are needed for the spatial components of a region that reflect evolutionary processes. Using examples from the southern Africa's Succulent Karoo, we demonstrate how spatially explicit data on morphological variation within taxa provides essential information for conservation planning in that it represents an important surrogate for the spatial component of lineage diversification. We also provide an example of how the spatial components of evolutionary processes can be identified and targeted for conservation action. Key to this understanding is the recognition and description of taxonomic units at all spatial scales. Without the recognition of subspecific variation it is difficult to formulate evolutionary hypotheses as well as set quantitative targets for the conservation of this variation. Given the escalating threats to biodiversity, and the importance of planning for persistence by incorporating ecological and evolutionary processes into conservation plans, it is essential that systematists develop hypotheses on the spatial surrogates for these processes for a wide range of lineages. The important questions for systematists to be asking are: (1) how is variation distributed in the landscape, and (2) how did it come about? Additionally, conservation planners need to highlight these spatial components for conservation action.
Abstract.Vast gaps in available information on the spatial distribution of biodiversity pose a major challenge for regional conservation planning in many parts of the world. This problem is often addressed by basing such planning on various biodiversity surrogates. In some situations, distributional data for selected taxa may be employed as surrogates for biodiversity as a whole. However, this approach is less effective in data-poor regions, where there may be little choice but to base conservation planning on some form of remote environmental mapping derived, for example, from interpretation of satellite imagery or from numerical classification of abiotic environmental layers. While this alternative approach confers obvious benefits in terms of cost-effectiveness and rapidity of application, problems may arise if there is poor congruence between mapped land-classes and actual biological distributions. I propose three strategies for making more effective use of available biological data and knowledge to alleviate such problems by: (1) more closely integrating biological and environmental data through predictive modeling, with an increased emphasis on modeling collective properties of biodiversity rather than individual entities; (2) making more rigorous use of remotely-mapped surrogates in conservation planning by incorporating knowledge of heterogeneity within land-classes, and varying levels of distinctiveness between classes, into measures of conservation priority and achievement; and (3) using relatively data-rich regions as test-beds for evaluating the performance of surrogates that are readily applicable across data-poor regions.