Parsimony analysis of endemicity describes but does not explain: an illustrated critique

Aim To demonstrate that parsimony analysis of endemicity (PAE) is not analogous to a cladistic biogeographical analysis. Location We used six data sets from previously published studies from around the world. Methods In order to test the efficiency of PAE in recovering historical relationships among areas, we performed an empirical comparison of nodes recovered with PAE, primary Brooks parsimony analysis (BPA), and an event‐based method using three models (maximum codivergence, reconciled trees, and the default model of the treefitter program) for six data sets. We measured the performance of PAE in recovering historical area relationships by counting the number and examining the content of nodes recovered by PAE and by historical methods. The dispersal/vicariance ratio was calculated to assess the prevalence of dispersal or vicariance in each reconstruction and its relationship to the performance of PAE. Results Our results show that PAE recovers an average of 17.25% of historical nodes. PAE and BPA tend to provide similar results; however, in relation to the event‐based models, PAE performance was poor under all the tested scenarios. Although in some cases PAE reconstructions are more resolved than historical reconstructions, this does not necessarily mean that PAE produces more informative answers. These additional nodes correspond to unsupported statements that are based solely on the distributional data of taxa and not on their phylogenetic history. In other words, these nodes were not found by the historical methods, which take phylogenetics into account. The number of historical nodes recovered using PAE was in general negatively correlated with the dispersal/vicariance ratio. Main conclusions Our results show that PAE is unable to recover historical patterns and therefore does not fit into the current paradigm of historical biogeography. These findings raise doubts regarding conclusions derived from biogeographical studies that interpret PAE trees as area cladograms. We acknowledge that PAE aims to describe but does not explain the current distribution of organisms. It is therefore a useful tool in other biogeographical or ecological analyses for exploring the distribution of taxa or for establishing hypotheses of primary homology between areas.     

Application of parsimony analysis of endemicity in Amazonian biogeography: an example with primates

The distributions of 51 non-human primate species are used for Parsimony Analysis of Endemicity (PAE) to determine the relationships among 14 interfluvial regions in the Amazon basin, South America. Two most parsimonious cladograms were found. The strict consensus tree of these cladograms suggests an early separation between Lower Amazonia (eastern) and Upper Amazonia (western). The major clusters of interfluvial regions identified in the PAE cladogram are congruent with the areas of endemism delimited for birds. When interfluvial regions are converted into avian areas of endemism, the PAE cladogram is congruent with one of the two general areas cladograms suggested for Amazonia based on phylogenies of several clades of forest birds. Our analysis suggests that PAE can be used as a tool to objectively identify areas of endemism at an intra-continental scale as well as to make historical inferences. However, the value of a PAE cladogram in this latter application should be always evaluated by congruence with area cladograms built upon cladistic biogeography procedures.     

Parsimony analysis of endemicity and analysis of endemicity: A fair comparison

Parsimony Analysis of Endemicity (PAE) has been compared with other methods regarding its performance to identify areas of endemism. It is frequently compared with the Analysis of Endemicity (AE), which seems to perform better than PAE to identify these areas. Here I compare PAE and AE considering the sympatric taxa diagnosed as endemic, being as strictly close as possible to sympatry, and using previously published data of Sciobius (Coleoptera: Curculionidae). AE identified more candidate areas of endemism than PAE, but the number of highly restricted endemic taxa to these areas was insufficient to support them as areas of endemism. Considering strictly sympatry (homopatry), PAE performed better than AE; however, both methods may identify areas with some grade of sympatry, but the recognition of which areas constitute real areas of endemism in the strict sense depends on the interpretation of the researcher.     

Critique of parsimony analysis of endemicity as a method of historical biogeography

Aim Assess the value of parsimony analysis of endemism as either an a priori (cladistic) and an a posteriori (phylogenetic) method of historical biogeography. Location World‐wide. Methods Parsimony analysis of endemicity (PAE) and Brooks parsimony analysis (BPA). Results Parsimony analysis of endemicity is capable of finding correct and unambiguous area relationships only under scenarios of vicariance in combination with non‐response to vicariance or extinction. An empirical comparison between PAE and BPA, using the poeciliid fish genera Heterandria and Xiphophorus, demonstrates that PAE fails to document much of the historical complexity in this relatively simple system. Main conclusions The a priori assumptions of PAE are far more restrictive than those made by other a priori methods, limiting its utility as a method of cladistic biogeography. The inability of PAE to detect perfect vicariance or biogeographical histories involving dispersal, renders it unsuitable as a method of phylogenetic biogeography.     

Historical relationships of the Mexican cloud forests: a preliminary vicariance model applying Parsimony Analysis of Endemicity to vascular plant taxa

Mexican cloud forests, situated between 600 and 3000 m of elevation, exhibit a remarkable high biotic diversity. They follow a fragmented pattern, similar to that of an archipelago, that makes them suitable to vicariance modelling. A Parsimony Analysis of Endemicity (PAE) was applied to the presence/absence of 1267 species of vascular plants (gymnosperms, angiosperms, and pteridophytes) from twenty-four patches of Mexican cloud forests, in order to postulate a preliminary hypothesis of relationships. The single cladogram obtained grouped the twenty-four cloud forests into five clades. These results indicate that the Sierra Madre Oriental, Sierra Madre del Sur, and Serranías Meridionales floristic provinces do not represent natural units. A preliminary vicariance model is presented to explain the sequence of fragmentation of the Mexican cloud forests.     

Parsimony analysis of endemicity (PAE) of Mexican terrestrial mammals at different area units: when size matters

Abstract Aim Parsimony analysis of endemicity (PAE) is a biogeographical method that uses a parsimony algorithm to obtain an area cladogram, based on taxa inhabiting the study areas. We compare its performance at different geographical units (½° and 1° quadrats, ecoregions and biogeographical provinces) to analyse distributional patterns of Mexican terrestrial mammals, in order to assess the importance of the size of area units. Location The area analysed corresponds to Mexico. Methods Parsimony analyses were based on 56,859 collection records, corresponding to 703 genera, species and subspecies. Four data matrices were constructed for: (1) 716 quadrats of ½° latitude × ½° longitude, (2) 230 quadrats of 1° latitude × 1° longitude, (3) forty‐five ecoregions and (4) fourteen biogeographical provinces. Results For the ½° quadrat matrix, we obtained six cladograms of 17,138 steps. For the 1° quadrat matrix, we obtained five cladograms (strict consensus with 9394 steps). For the matrix of ecoregions, we obtained twelve cladograms (strict consensus cladogram with 3009 steps). For the provinces, we obtained a single cladogram with 1603 steps. Main conclusions The best results were obtained with natural areas instead of quadrats. There seems to exist a trend to decrease the absolute number of steps and an increase in the absolute and relative number of synapomorphies as the size of the area units decreases, although this does not necessarily occur for the number of cladograms.     

Panbiogeographical study of hagfishes: an anachronistic analysis

In a recent paper by M. J. Cavalcanti and V. Gallo, 'Panbiogeographical analysis of distribution patterns in hagfishes (Craniata: Myxinidae)' ( Journal of Biogeography , 2008, 35 , 1258–1268), the authors studied the biogeography of an ancient fish family (Myxinidae) in the hope that the contemporary distributions of the species would reveal their past history and that of the ocean basins where they reside. In order to accomplish this task, there are several criteria that should have been met: (1) the ages of the taxa utilized (species) would have to be old enough to reflect the history of the areas where they are found, (2) the identification of the species as listed in the databases would have to be accurate, (3) the geographical locations indicated on the figures would have to be consistent with the statements in the text, and (4) the significance of the vicariant patterns would have to depend on evidence pertaining to the ages of such patterns. Unfortunately, it appears that none of these conditions has been met. It seems apparent that faith in an antiquated method of analysis led to neglect of the necessary steps in the analysis. This leaves little justification for publication of the paper, except to show that hagfishes are very widely distributed.     

Vicariance divergence and gene flow among islet populations of an endemic lizard

Allopatry and allopatric speciation can arise through two different mechanisms: vicariance or colonization through dispersal. Distinguishing between these different allopatric mechanisms is difficult and one of the major challenges in biogeographical research. Here, we address whether allopatric isolation in an endemic island lizard is the result of vicariance or dispersal. We estimated the amount and direction of gene flow during the divergence of isolated islet populations and subspecies of the endemic Skyros wall lizard Podarcis gaigeae, a phenotypically variable species that inhabits a major island and small islets in the Greek archipelago. We applied isolation-with-migration models to estimate population divergence times, population sizes and gene flow between islet-mainland population pairs. Divergence times were significantly correlated with independently estimated geological divergence times. This correlation strongly supports a vicariance scenario where islet populations have sequentially become isolated from the major island. We did not find evidence for significant gene flow within P. g. gaigeae. However, gene-flow estimates from the islet to the mainland populations were positively affected by islet area and negatively by distance between the islet and mainland. We also found evidence for gene flow from one subspecies (P. g. weigandi) into another (P. g. gaigeae), but not in the other direction. Ongoing gene flow between the subspecies suggests that even in this geographically allopatric scenario with the sea posing a strong barrier to dispersal, divergence with some gene flow is still feasible.     

PACT: an efficient and powerful algorithm for generating area cladograms

Aim To introduce and describe the functioning of a new algorithm, phylogenetic analysis for comparing trees (PACT), for generating area cladograms that provide accurate representation of information contained in taxon–area cladograms. Methods PACT operates in the following steps. Convert all phylogenies to taxon–area cladograms. Convert all taxon–area cladograms to Venn diagrams. Choose any taxon–area cladogram from the set of taxon–area cladograms to be analysed and determine its elements. This will be the template area cladogram. Select a second taxon–area cladogram. Determine its elements. Document which elements in the second tree occur in the template tree (denoted by ‘Y’) and which do not (denoted by ‘N’). Each ‘Y’ indicates a match with previous pattern and these are combined. Each ‘N’ is a new element and is attached to the template area cladogram at the node where it is linked with a Y. This requires two rules: (1) ‘Y + Y = Y’ (combine common elements) as long as they are connected at the same node; and (2) ‘Y + N = YN’ (add novel elements to the template area cladogram at the node where they first appear). Once the novel elements in the second taxon–area cladogram have been added to the template area cladogram, see if any of them can be further combined. This requires three additional rules: (1) ‘Y(Y? = Y(Y?’ (do not combine Y's if they are attached at different nodes on the template area cladogram); (2) ‘Y + YN = YN’ (Y is part of group YN); and (3) ‘YN + YN = YNN’ (Y is the same for each, but each N is different). Repeat for all available taxon–area cladograms. Results Three exemplars demonstrate that PACT provides the most accurate area cladograms for vicariance‐driven biotic diversification, dispersal‐driven biotic diversification and taxon pulse‐driven biotic diversification. PACT can also be used as an a priori method of biogeographical analysis. Main conclusions PACT embodies all the strong points and none of the weaknesses of previously proposed methods of historical biogeography. It is most useful as an a posteriori method, but it is also superior to all previous a priori methods because it does not specify costs, or weights or probabilities, or likelihoods of particular biogeographical processes a priori and is thus sensitive to clade‐specific historical contingencies.     

基因组学: 理解植物入侵性的重要工具

入侵植物基因组学是一个新兴的研究领域, 它利用基因组学方法研究与植物入侵性相关的分子基础和表达调控机制, 甄别入侵性基因型, 进而在基因组水平上揭示外来种入侵性产生和进化的分子机制。本文扼要综述了可用于植物入侵生物学研究的主要基因组学方法, 包括比较基因组学、群体基因组学和表观基因组学等方法; 运用基因组学技术研究入侵植物除草剂抗性和根状茎发育的分子基础已取得了重要进展。然而, 入侵植物基因组学仍处于发展初期, 选择理想的入侵植物模式种, 建立入侵性研究的模式系统, 是当前亟待解决的问题。本文还提出了入侵植物基因组学研究值得关注的几个发展方向, 包括基因组信息的完善、不同环境条件下入侵植物的分子响应机制以及入侵性的系统生物学研究等。     

Distribution patterns of the genus Pacifigorgia (Octocorallia: Gorgoniidae): track compatibility analysis and parsimony analysis of endemicity

Aim We analysed the distribution patterns of the eastern Pacific octocoral genus Pacifigorgia and deduced its ancestral distribution to determine why Pacifigorgia is absent from the Gulf of Mexico, the Caribbean of central America, and the Antilles. We also examined the current patterns of endemism for Pacifigorgia to look for congruence between hot spots of endemism in the genus and generally recognized areas of endemism for the eastern Pacific. Location The tropical eastern Pacific and western Atlantic, America. Methods We used track compatibility analysis (TCA) and parsimony analysis of endemicity (PAE) to derive ancestral distribution patterns and hot spots of endemism, respectively. Distributional data for Pacifigorgia were gathered from several museum collections and from fieldwork, particularly in the Pacific of Costa Rica and Panama. Results A single generalized track joined the three main continental eastern Pacific biogeographical provinces and the western Atlantic. This track can be included within a larger eastern Atlantic–eastern Pacific transoceanic track that may be the oldest transoceanic track occurring in the region. PAE results designate previously recognized eastern Pacific biogeographical provinces as Pacifigorgia hot spots of endemism. The number of endemic species, which for other taxonomic groups is similar among the eastern Pacific provinces, is higher in the Panamic province for Pacifigorgia. Main conclusions We propose that the absence of Pacifigorgia from the Gulf of Mexico, the Caribbean of central America, and the Antilles is the result of an ancient absence of the genus from these areas rather than the consequence of a major, recent, extinction episode. The Cortez province and the Mexican province appear together as a result of either non‐response to vicariance or dispersal across the Sinaloan Gap. We posit that the Central American Gap acts as a barrier that separates the Panamic province from the northern Cortez–Mexican province.     

New insight into the phylogenetic and biogeographic history of genus Ficus: Vicariance played a relatively minor role compared with ecological opportunity and dispersal

Studies on the evolution of tropical taxa emphasize the role ofvicariance and the break-up of Gondwana in explaining modern distributions.Earlier studies on figs (Ficus spp.) support this view.In the current study,we used an expanded sample (208 spp.) and improved molecular dating techniques to reconstruct the phylogenetic and biogeographic history of Ficus.Consistent with previous studies,our biogeographic analysis indicated that the ancestor of Ficus was present in Gondwana.However,a relaxed clock analysis relying on uncorrelated rates in BEAST suggested that the Neotropical section Pharmacosycea split-off in South America 86.67 Mya,and that other Ficus lineage ancestors originated in India.Most of the basal lineages appeared to have diverged following KT extinction,then rapidly diversified after India collided with continental Asia.The Afrotropical species most likely evolved initially in the Indian subcontinent then dispersed to Africa,either in the late Cretaceous of Madagascar or even later,following the Eocene collision of India with Asia.The Neotropical section Americana,either islandhopped to South America or took a northern route to the Americas through Europe prior to the terminal Eocene global cooling event.Ficus may have arrived in eastern Malesia following the collision of India with Asia,then widely dispersed thereafter.Given the wide ranges in our date estimates,several other scenarios are possible.However,contrary to earlier reports,our analyses suggest that vicariance played a relatively minor role compared with ecological opportunity and dispersal in the diversification of genus Ficus.     

Short-faced bats (Phyllostomidae: Stenodermatina): a Caribbean radiation of strict frugivores

Aim  To test the hypothesis that Caribbean Short-faced bats descended from a single recent ancestor that originated in the continental Neotropics (Mexico, Central America and/or South America).
Location  The Neotropics, including the West Indies.
Methods  New mitochondrial cytochrome b and nuclear Rag2 sequences were combined with published molecular data to estimate phylogenetic relationships and sequence divergence among Short-faced bats. The resulting phylogenies were compared with those compatible with the single-origin hypothesis using two model-based statistical tests. Confidence limits on sequence divergence were estimated using a parametric bootstrap.
Results  All molecular phylogenies revealed two independent Caribbean lineages and showed that continental Short-faced bats share a recent common ancestor. Morphology-based trees compatible with the single-origin hypothesis were significantly worse at explaining the molecular data than any molecular phylogeny.
Main conclusions  The ancestor of all Short-faced bats reached the Antilles in the Miocene, too recently to have used a proposed Oligocene land bridge, and well before the Pleistocene glaciations that are thought to have facilitated dispersal for many bats. After a long period of isolation, Short-faced bats diversified quickly on the Caribbean islands. A single Short-faced lineage then reached the continent and subsequently expanded its range and diversified into the four extant genera. Among bats, independent lineages of aerial insectivores and nectarivores have also recolonized the continent after evolving in the West Indies. The evidence for an insular origin of the short-faced frugivorous radiation completes a dynamic model of Caribbean biogeography that encompasses an entire biological community.     

Image analysis as a tool for quantitative phycology: a computational approach to cyanobacterial taxa identification

In the following work we discuss the application of image processing and pattern recognition to the field of quantitative phycology. We overview the area of image processing and review previously published literature pertaining to the image analysis of phycological images and, in particular, cyanobacterial image processing. We then discuss the main operations used to process images and quantify data contained within them. To demonstrate the utility of image processing to cyanobacteria classification, we present details of an image analysis system for automatically detecting and classifying several cyanobacterial taxa of Lake Biwa, Japan. Specifically, we initially target the genus Microcystis for detection and classification from among several species of Anabaena. We subsequently extend the system to classify a total of six cyanobacteria species. High-resolution microscope images containing a mix of the above species and other nontargeted objects are analyzed, and any detected objects are removed from the image for further analysis. Following image enhancement, we measure object properties and compare them to a previously compiled database of species characteristics. Classification of an object as belonging to a particular class membership (e.g., “Microcystis,”“A. smithii,”“Other,” etc.) is performed using parametric statistical methods. Leave-one-out classification results suggest a system error rate of approximately 3%. Received: September 6, 1999 / Accepted: February 6, 2000     

The west Mediterranean orophilous taxa of Sideritis L. (Lamiaceae): a new species of subsection Hyssopifolia from south-eastern Spain

Orophilous taxa of Sideritis sect. Sideritis (Lamiaceae) are rare, although highly diversified in south-eastern Spain. Most of them belong to subsections Hyssopifolia and Fruticulosa and show very reduced distribution areas in the summits of the highest Betic mountains. The inaccessibility of their habitats has meant that many of them have been described only within the last twenty years. In this context, a new species Sideritis tugiensis is described in subsection Hyssopifolia , from the Oromediterranean summits of Sierra de Segura (south-eastern Spain). It is a woody, cushion-shaped plant, resembling both S. carbonellis Socorro (subsect. Hyssopifolia) and S. glacialis Boiss., s.l. (subsect. Fruticulosa) , though important morphological divergences warrant recognition at species rank. Data on morphology, ecology and chorology of the new species are reported, and affinities and differences with regard to close taxa from other subsections are presented. Evolutionary trends in the whole aggregate are briefly discussed.     

GeX: an automated tool for generating XYD files for analysis of endemicity using VNDM

In the last decade, a method widely used to delimit areas of endemism is the analysis of endemicity (AE), a non-hierarchical and grid-dependent algorithm implemented through the package NDM/VNDM. Its input files are based on lists of georeferenced taxa, and any mistakes in their preparation will influence the results of the analyses. We describe here a free online automated tool for generating the input files for VNDM from simple spreadsheets.     

Vicariance and dispersal in southern hemisphere freshwater fish clades: a palaeontological perspective

Widespread fish clades that occur mainly or exclusively in fresh water represent a key target of biogeographical investigation due to limited potential for crossing marine barriers. Timescales for the origin and diversification of these groups are crucial tests of vicariant scenarios in which continental break‐ups shaped modern geographic distributions. Evolutionary chronologies are commonly estimated through node‐based palaeontological calibration of molecular phylogenies, but this approach ignores most of the temporal information encoded in the known fossil record of a given taxon. Here, we review the fossil record of freshwater fish clades with a distribution encompassing disjunct landmasses in the southern hemisphere. Palaeontologically derived temporal and geographic data were used to infer the plausible biogeographic processes that shaped the distribution of these clades. For seven extant clades with a relatively well‐known fossil record, we used the stratigraphic distribution of their fossils to estimate confidence intervals on their times of origin. To do this, we employed a Bayesian framework that considers non‐uniform preservation potential of freshwater fish fossils through time, as well as uncertainty in the absolute age of fossil horizons. We provide the following estimates for the origin times of these clades: Lepidosireniformes [125–95 million years ago (Ma)]; total‐group Osteoglossomorpha (207–167 Ma); Characiformes (120–95 Ma; a younger estimate of 97–75 Ma when controversial Cenomanian fossils are excluded); Galaxiidae (235–21 Ma); Cyprinodontiformes (80–67 Ma); Channidae (79–43 Ma); Percichthyidae (127–69 Ma). These dates are mostly congruent with published molecular timetree estimates, despite the use of semi‐independent data. Our reassessment of the biogeographic history of southern hemisphere freshwater fishes shows that long‐distance dispersals and regional extinctions can confound and erode pre‐existing vicariance‐driven patterns. It is probable that disjunct distributions in many extant groups result from complex biogeographic processes that took place during the Late Cretaceous and Cenozoic. Although long‐distance dispersals likely shaped the distributions of several freshwater fish clades, their exact mechanisms and their impact on broader macroevolutionary and ecological dynamics are still unclear and require further investigation.