Application of parsimony analysis of endemicity to Mexican gymnosperm distributions: grid-cells, biogeographical provinces and track analysis

Parsimony analysis of endemicity (PAE) was used to analyse the distributional patterns of 124 species of Mexican gymnosperms, using two different sample units: grid-cells and biogeographical provinces. PAE analyses were based on distributional data from herbarium specimens and specialized literature. Two data matrices were constructed for 60 grid-cells of 2° and 14 biogeographical provinces. The analysis of the 2° grid-cell matrix led to 7084 cladograms. The strict consensus cladogram showed several clades equivalent to the results obtained with the biogeographical provinces. Three clades agree with some principal regions of distribution of Mexican pines, previously identified by several authors, located at the northern portion of the Baja California peninsula, the Sierra Madre Occidental, and the Sierra Madre Oriental. These areas represent important centres of species diversity and endemism for Mexican gymnosperms. The analysis of the province matrix led to two most parsimonious cladograms, which only differed in the position of the Sierra Madre Occidental province. The iterative procedure PAE with progressive character elimination was applied to identify generalized tracks, where clades of provinces were considered equivalent to generalized tracks, and each time a cladogram was obtained, species defining its clades were deleted and a new run was undertaken. We found five generalized tracks, mainly located in montane provinces. The distribution patterns of gymnosperms agree with the existence of several Mexican biogeographical provinces, and a different historical biogeography of the Mexican peninsulas from the rest of the country is evident.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 405–417.     

Does the Trans‐mexican Volcanic Belt represent a natural biogeographical unit? An analysis of the distributional patterns of Coleoptera

Aim We analysed the geographical distribution of beetle species of the families Buprestidae, Cerambycidae, Dryophthoridae, Melolonthidae, Passalidae and Staphylinidae from the Trans‐mexican Volcanic Belt (TVB) through a track analysis and a parsimony analysis of endemicity (PAE), in order to test its naturalness and determine its affinities. Location The area analysed corresponds to the TVB, which is a biogeographical province of the Mexican Transition Zone. Methods The panbiogeographical analysis was based on the comparison of the individual tracks of 299 species of Buprestidae, Cerambycidae, Dryophthoridae, Melolonthidae, Passalidae and Staphylinidae (Coleoptera). The TVB was divided into 1^o × 1^o grid cells and we also included in the analysis the remaining Mexican biogeographical provinces. Parsimony analysis of endemicity with progressive character elimination (PAE‐PCE) was applied to classify areas by their shared taxa according to the most parsimonious cladograms. The nested sets of areas were represented as generalized tracks. Results Three generalized tracks were obtained: (1) grid cells 9C, 9D, 10D, 10E, Sierra Madre Oriental, Chiapas, Mexican Gulf and the Sierra Madre del Sur; (2) grid cells 3B, 3C, 4B, 4C, 5C, 6C, 7C, Sierra Madre Occidental, Sierra Madre del Sur, Balsas Basin and the Mexican Pacific Coast, and (3) grid cells 8D, 9C, 9D, 10D, 10E, Yucatán Peninsula, Chiapas, Sierra Madre Oriental and the Mexican Gulf. Main conclusions We conclude that the TVB does not represent a natural biogeographical unit because it shows different relationships with other biogeographical provinces, being clearly transitional between the Nearctic and Neotropical provinces. Some parts of the TVB are related to Neotropical provinces (Chiapas, Mexican Gulf and Mexican Pacific Coast) and others to the remaining provinces of the Mexican Transition Zone (Sierra Madre Oriental, Sierra Madre del Sur, Sierra Madre Occidental and Balsas Basin).     

Panbiogeographical analysis of the genus Bomarea (Alstroemeriaceae)

Aim  A panbiogeographical analysis of the genus Bomarea was undertaken in order to determine generalized tracks and biogeographical nodes, and to evaluate the current distribution of the genus based on the available tectonic information and the biogeographical regionalization of Latin America.
Location  The Neotropical region from northern Mexico to northern Argentina, and the Nearctic and Andean regions.
Method  A total of 2205 records of 101 species were analysed, representing 95% of the species assigned to Bomarea . Localities were represented on maps and their individual tracks were drawn. Based on their comparison, generalized tracks were detected and mapped. Nodes were identified in the areas where different generalized tracks were superimposed.
Results  Five generalized tracks were recovered. One is located in the Eastern Central America and Western Panamanian Isthmus provinces (Caribbean subregion, Neotropical region), which was supported by three species of Central American distribution. The four remaining generalized tracks were located in South America, in the North Andean Paramo, Cauca and Puna biogeographical provinces. These tracks were supported by species of Bomarea with an Andean distribution. Biogeographical nodes were established in the Central Andean region of Colombia, central Ecuador and central Peru.
Main conclusions  The nodes obtained for Bomarea support a hybrid origin for the Andean region, which presents diverse components from both northern and southern South America. Likewise, the track recovered between Colombia and Ecuador includes Andean and Neotropical areas, providing further support for this hypothesis. The nodes obtained are coherent with vicariant elements evident for Bomarea. Species of three clades proposed for Bomarea are distributed in specific generalized tracks.     

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.     

Track analysis of the Mexican species of Buprestidae (Coleoptera): testing the complex nature of the Mexican Transition Zone

Aim  We analysed the geographical distributions of species of Buprestidae (Coleoptera) in Mexico by means of a panbiogeographical analysis, in order to identify their main distributional patterns and test the complex nature of the Mexican Transition Zone, located between the Nearctic and Neotropical regions.
Location  Mexico.
Methods  The geographical distributions of 228 species belonging to 33 genera of Buprestidae were analysed. Localities of the buprestid species were represented on maps and their individual tracks were drawn. Based on a comparison of the individual tracks, generalized tracks were detected and mapped. Nodes were identified as the areas where generalized tracks converged.
Results  Thirteen generalized tracks were obtained: one was restricted to the Mexican Transition Zone and five to the Neotropical region (Antillean and Mesoamerican dominions), a further two occurred in both the Nearctic region (Continental Nearctic dominion) and the Mexican Transition Zone, and a further five in both the Neotropical region (Mesoamerican dominion) and the Mexican Transition Zone. Seven nodes were identified at the intersections of the generalized tracks – in the Mesoamerican dominion (Mexican Pacific Coast, Mexican Gulf and Chiapas biogeographical provinces) and the Mexican Transition Zone (Trans-Mexican Volcanic Belt, Balsas Basin and Sierra Madre Oriental biogeographical provinces).
Main conclusions  We conclude that the geographical distribution of Buprestidae is mainly Neotropical, corresponding to the Mesoamerican dominion and the Antillean dominion of the Neotropical region, and the Mexican Transition Zone. Most of the generalized tracks and nodes correspond to the Mexican Transition Zone, thus confirming its complex nature. We suggest that the nodes we have identified could be particularly important areas to choose for conservation prioritization.     

Distributional modelling and parsimony analysis of endemicity of Senecio in the Mediterranean-type climate area of Central Chile

Aim Floristic blocks and areas of endemism resulting from a parsimony analysis of endemicity (PAE) using raw floristic data versus data generated from distributional modelling for 130 species in the genus Senecio Tourn. ex L. distributed in the Mediterranean‐type climate area of Central Chile were compared, and the results were used to identify conservation priorities for the flora of the region. Location Central Chile, between 30° and 38° S. Methods Using herbarium records, a species × area matrix consisting of presence/absence data was constructed from a 0.5° × 0.5° grid. Distributional modelling techniques incorporating vegetation formations, elevation and the contagion index were used to interpolate floristic composition of poorly known areas. Parsimony analysis of endemicity was used to identify floristic blocks and areas of endemism. Results Using the number of most parsimonious trees as an index, distributional modelling greatly optimized the results of the PAE analysis. Three floristic blocks and four areas of endemism were suggested based on the PAE results using potential distribution data not incorporating the contagion index, while four blocks and two areas of endemism were suggested from the PAE results using potential distribution data incorporating the contagion index. Floristic blocks for the northern coast, southern Andes, and northern/central Andes were found, with some blocks showing divisions within them representing distinct geographic subunits. Major breaks between and within floristic blocks were identified at 32.5°–33° S and 34.5°–35° S. Main conclusions The floristic blocks identified with the distributional modelling and PAE correspond well to results from some previous studies and support hypothesized biogeographic divisions within Central Chile. The results were similar to those obtained from parallel analysis of the entire tree flora of Central Chile. The vegetative formation‐based distributional modelling produced robust and reproducible results when used along with PAE, especially when the contagion index was incorporated, and is a useful technique for area classification. The results demonstrate the utility of Senecio as an indicator genus for biogeography and conservation in southern South America.     

Molecular systematics of Selenops spiders (Araneae: Selenopidae) from North and Central America: implications for Caribbean biogeography

The Caribbean region includes a geologically complex mix of islands, which have served as a backdrop for some significant studies of biogeography, mostly with vertebrates. Here, we use the tropical/subtropical spider genus Selenops (Selenopidae) to obtain a finer resolution of the role of geology in shaping patterns of species diversity. We obtained a broad geographic sample from over 200 localities from both the islands and American mainland. DNA sequence data were generated for three mitochondrial genes and one nuclear gene for eleven outgroup taxa and nearly 60 selenopid species. Phylogenetic analysis of the data revealed several biogeographic patterns common to other lineages that have diversified in the region, the most significant being: (1) a distinct biogeographic break between Northern and Southern Lesser Antilles, although with a slight shift in the location of the disjunction; (2) diversification within the islands of Jamaica and Hispaniola; (3) higher diversity of species in the Greater Antilles relative to the Lesser Antilles. However, a strikingly unique pattern in Caribbean Selenops is that Cuban species are not basal in the Caribbean clade. Analyses to test competing hypotheses of vicariance and dispersal support colonization through GAARlandia, an Eocene–Oligocene land span extending from South America to the Greater Antilles, rather than over‐water dispersal. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 288–322.     

Across‐taxa incongruence in patterns of collecting bias

If biological collections tend to be taken near accessible areas, and the number of such areas is limited, then we should expect a similar spatial distribution of collecting effort across taxa. Alternatively, if researchers working on a given taxon pick collection localities based on idiosyncratic criteria, then there should be no spatial similarity in collecting effort. This study compares the spatial distribution of collecting effort for plants and birds in Amazonia. Collection localities were transformed into a Thiessen network where polygon size works as a surrogate for collecting effort. A correlation between botanical and ornithological datasets, with an adjustment for spatial autocorrelation, showed little congruence in the spatial distribution of collecting effort between the two taxa. This incongruence of the distribution of collection effort among taxa suggests that the identification of priority areas for research, and correction for Wallacean and Linnean shortfalls based on taxon‐specific studies, should not be generalized.     

Panbiogeographical analysis of the shark genus Rhizoprionodon (Chondrichthyes,Carcharhiniformes, Carcharhinidae)

The distributional patterns of the seven species of Rhizoprionodon were analysed using the panbiogeographical method of track analysis. The individual tracks of Rhizoprionodon suggest that the genus is mainly an Indian–Atlantic Ocean group. Five generalized tracks were found: (1) Caribbean, defined by R. porosus and R. terraenovae; (2) eastern coast of South America, defined by R. porosus and R. lalandei; (3) Indian Ocean, defined by R. acutus and R. oligolinx; (4) north‐western Australia, defined by R. acutus, R. oligolinx and R. taylori; (5) north‐north‐eastern Australia, defined by R. acutus and R. taylori. Only R. longurio was not included in any generalized track, and its distribution is restricted to the eastern Pacific Ocean. Two biogeographical nodes were found at the intersection of the generalized tracks 1 and 2 (Caribbean Sea) and generalized tracks 4 and 5 (north Australia). The generalized tracks overlap with those found in several unrelated marine taxa. Overall, the generalized tracks are associated with warm currents. The biogeographical nodes found (Caribbean and Australian) are coincident with the global distribution of mangroves.     

Areas of endemism and distribution patterns for Neotropical Piper species (Piperaceae)

Aim The study aimed to establish areas of endemism and distribution patterns for Neotropical species of the genus Piper in the Neotropical and Andean regions by means of parsimony analysis of endemicity (PAE) and track‐compatibility analysis. Location The study area includes the Neotropical region and the Northern Andean region (Páramo‐Punan subregion). Methods We used distribution information from herbarium specimens and recent monographic revisions for 1152 species of Piper from the Neotropics. First, a PAE was attempted in order to delimit the areas of endemism. Second, we performed a track‐compatibility analysis to establish distribution patterns for Neotropical species of Piper. Terminology for grouping Piper is based on recent phylogenetic analyses. Results The PAE yielded 104 small endemic areas for the genus Piper, 80 of which are in the Caribbean, Amazonian and Paranensis subregions of the Neotropical region, and 24 in the Páramo‐Punan subregion of the Andean region. Track‐compatibility analysis revealed 26 generalized tracks, one in the Páramo‐Punan subregion (Andean region), 19 in the Neotropical region, and six connecting the Andean and Neotropical regions. Both the generalized tracks and endemic areas indicate that distribution of Piper species is restricted to forest areas in the Andes, Amazonia, Chocó, Central America, the Guayana Shield and the Brazilian Atlantic coast. Main conclusions Piper should not be considered an Andean‐centred group as it represents two large species components with distributions centred in the Amazonian and Andean regions. Furthermore, areas of greater species richness and/or endemism are restricted to lowland habitats belonging to the Neotropical region. The distribution patterns of Neotropical species of Piper could be explained by recent events in the Neotropical region, as is the case for the track connecting Chocó and Central America, where most of the species rich groups of the genus are found. Two kinds of event could explain the biogeography of a large part of the Piper taxa with Andean–Amazonian distribution: pre‐Andean and post‐Andean events.     

Biogeographic analysis of endemic cacti of the Sierra Madre Oriental, Mexico

The distribution of cacti species that inhabit the Sierra Madre Oriental (SMO) was analysed. Grid-cells were analysed using parsimony analysis of endemicity (PAE) and endemism indices. Areas characterized by their diagnostic species were determined, aiming to propose areas for the conservation of threatened cacti. Distributional data were obtained from 1936 herbarium specimens, electronic information, and from field collections. Eight areas of endemism and three main clades were obtained from the grid-cell analysis. Areas obtained from the endemism indices are very similar to those obtained with the PAE, but differ in the association of grid-cells. PAE showed endemism patterns indicating that southern and central sections of the SMO province are the areas richest in geographically-restricted species. The results obtained with different endemism indices detected more or less the same areas, although the importance level is different. The corrected weighted endemism index can be considered as a reliable measure of endemism because it is unrelated to species richness. A regionalization of the SMO in three subprovinces is suggested, supported by characteristic cacti taxa and the existence of natural barriers.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 373–389.     

Island evolutionary biogeography: analysis of the weevils (Coleoptera: Curculionidae) of the Falkland Islands (Islas Malvinas)

Aim I analysed distributional and phylogenetic information on weevils (Coleoptera: Curculionidae) from the Falklands, and integrated it with molecular, palaeontological and geological information to infer a geobiotic scenario. Location Falkland Islands (Islas Malvinas). Methods The panbiogeographical analysis was based on data on 23 Falkland species and their related taxa from southern South America. For the cladistic biogeographical analysis I analysed six weevil taxa for which phylogenetic hypotheses are available (the generic groups Cylydrorhinus, Strangaliodes and Falklandius, and the genera Antarctobius, Germainiellus and Puranius). Results from this analysis were compared with previous regionalizations. Cenocrons (sets of taxa that share the same biogeographical history) were identified by considering temporal information provided by fossils and molecular clocks. Finally, a geobiotic scenario was proposed by integrating the available information. Results Six generalized tracks were detected: Maule–Valdivian forests, Magellanic forest, Magellanic moorland, Falkland Islands, Magellanic forest–Magellanic moorland, and Magellanic forest–Falkland Islands. A node was identified in the Magellanic forest, based on the overlap of two generalized tracks. A single general area cladogram was obtained, implying the following sequence: (Magellanic moorland (Maule–Valdivian forests (Magellanic forest, Falkland Islands))). The Falklands are classified here as a biogeographical province in the Austral realm, Andean region and Subantarctic subregion. Falkland weevils seem to belong to a single Subantarctic cenocron. The sequence of events deduced implies the following steps: development of the Subantarctic biota in southern South America, arrival of the Falkland crustal block from South Africa in the Early Cretaceous, geodispersal of the Subantarctic cenocron from southern South America to the Falklands during the Early Oligocene, vicariance of the Magellanic moorland, vicariance of the Maule–Valdivian forests, and final vicariance between the Magellanic forest and the Falkland Islands. Main conclusions The biotic components identified support the connection of the Falkland weevils with the Magellanic forest. Falkland weevils belong to a single cenocron, dated to at least the Early Oligocene, when geodispersal from southern South America may have occurred. An older African cenocron may have been replaced completely by the Subantarctic one when the proto‐Falklands made contact with the Patagonian continental shelf. A geobiotic scenario implying vicariance events related to sea‐level variations could explain the distributional patterns analysed herein.     

Distributional patterns of the species of <Emphasis Type="Italic">Valeriana</Emphasis> (Valerianaceae) in southern South America

Distributional patterns of Valeriana species from southern South America were analyzed. We prepared a database with the records of 40 species from Argentina and Chile south of 33°S, obtained from herbarium specimens, published taxonomic studies and field trips. We undertook a track analysis and a parsimony analysis of endemicity (PAE), the latter with 134 grid cells of 1.5° latitude by 1.5° longitude. Three generalized tracks and one node were obtained, and three areas of endemism were identified. These general patterns of distribution in Valeriana were used to infer possible vicariance and dispersal events that might have shaped them. We identified a center of diversification in Central Chile and the Argentinean province of Neuquén. It represents a complex area that is related to both the Central Chilean and Subantarctic subregions.     

Influence of large South American rivers of the Plata Basin on distributional patterns of tropical snakes: a panbiogeographical analysis

Aim The main drainages of the Plata Basin – the Paraná, Paraguay and Uruguay rivers – begin in tropical latitudes and run in a north–south direction into subtropical–temperate latitudes. Consequently, the biota of these rivers has tropical elements that contrast with temperate biomes through which the rivers run. We apply a panbiogeographical approach, to test whether the large rivers of the Plata Basin have a differential influence on distributional patterns of tropical snakes in subtropical and temperate latitudes of South America. Location Subtropical and temperate sections of the major Plata Basin rivers, South America. Methods We compared the individual tracks of 94 snake taxa. The track analysis consisted of: (1) plotting the localities of each taxon on maps, (2) connecting the localities of each taxon using a minimal geographical proximity determinant of the ‘individual tracks’, and (3) superimposing the individual tracks to determine generalized tracks. To detect tropical snakes that reach higher latitudes through the rivers we used the preferential direction of distribution concept. For each taxon we measured the angular deviations between the line of its individual track and the course of the rivers in a 100 × 100 km scaled grid. Average angular values < 45° indicated a positive association with the rivers. Results Thirty‐five of 94 taxa showed distributions associated with the major rivers of the Plata Basin, including fauna from distinct biogeographical lineages, supported by the occurrence of five generalized tracks as follows: (1) the Paraguay–Middle Paraná, (2) the Paraguay–Paraná fluvial axis, Upper Paraná and Middle Paraná to Upper Delta, (3) the Lower Paraguay, Paraná and Uruguay rivers, excluding the sectors High Paraná and High Uruguay, (4) the Uruguay River and Upper Paraná, and (5) the High Paraná. The Atlantic species occurred with significantly higher frequency in the Uruguay River and High Paraná river sections, the Amazon species were found with significantly higher frequency in the Paraguay and Middle Paraná sections, and the species with a Pantanal distribution were found in all sections. Main conclusions The observed distributional patterns may be explained by the interaction of ecological, geographical and historical factors. Previous authors have developed ecological (hydrological or environmental similarity) or dispersalist (effect of rivers as migration routes) explanations. The coincidence between generalized tracks and past geomorphological events that caused displacements and changed relationships between the Paraguay, Paraná and Uruguay river sections supports hypotheses involving the strong influence of historical factors in the present configuration of tropical snake distribution in temperate latitudes.     

Phylogeographic analysis of the nocturnal velvet ant genus Dilophotopsis (Hymenoptera: Mutillidae) provides insights into diversification in the Nearctic deserts

Understanding the history of diversification in the North American deserts has long been a goal of biogeographers and evolutionary biologists. Although it appears that a consensus is forming regarding the patterns of diversification in the Nearctic deserts in vertebrate taxa, little work has been done exploring the historical biogeography of widespread invertebrate taxa. Before a robust model of geobiotic change in the North American deserts can be proposed, it needs to be determined whether the same historical events affected vertebrate and invertebrate taxa in the same way. We explore the phylogeographic patterns in a widespread nocturnal wasp genus Dilophotopsis using two rDNA loci, the internal transcribed spacer regions 1 and 2 (ITS1 and ITS2). We use Bayesian phylogenetic analysis and haplotype network analysis to determine whether a consistent geographic pattern exists among species and populations within Dilophotopsis. We also used molecular dating techniques to estimate divergence dates of the major phylogenetic clades. Our analyses indicates that the species‐level divergences in Dilophotopsis occurred in the Neogene, and likely were driven by mountain building during the Miocene–Pliocene boundary (approximately 5 Mya) similar to the divergences in many vertebrate taxa. The population‐level divergences within species occurred during the Pleistocene (0.1–1.8 Mya). The present study shows that similar patterns of diversification exist in vertebrate and invertebrate taxa. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 360–375.     

Distributional patterns of the Neotropical humid montane forest avifaunas

The study of biogeographical patterns of the Neotropical humid montane forest avifauna has been prevented due to the lack of phylogenetic hypotheses for most taxa, and to the paucity of detailed studies about the geographical distribution for most of the species. Distributional patterns of this avifauna were explored by integrating predictive distributional models and Parsimony Analysis of Endemicity (PAE). Distributional maps were generated using the Genetic Algorithms for Rule Set Prediction for 442 species; this information was transformed into a data matrix for analysis with PAE. Hierarchical information corresponding to the genus level was incorporated to help resolve the relationships between areas. A strict consensus cladogram showed a clear separation between the Mesoamerican and South American avifaunas. Within the Mesoamerican clade, three geographically structured groups were obtained, whereas the South American clade showed a polytomy of three groups, with two of them, the South Andean Yungas and the Tepuis, located outside the main clade. The third group is a well resolved clade, including areas from eastern Panama and northern Venezuela to central Bolivia. Area relationships suggest a mixed history of dispersal and vicariant events, with the latter being the most important for explaining the biogeographical patterns found.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 175–194.     

Exploring the Afromontane centre of endemism: Kniphofia Moench (Asphodelaceae) as a floristic indicator

Aim The genus Kniphofia contains 71 species with an African–Malagasy distribution, including one species from Yemen. The genus has a general Afromontane distribution. Here we explore whether Kniphofia is a floristic indicator of the Afromontane centre of endemism and diversity. The South Africa Centre of diversity and endemism was explored in greater detail to understand biogeographical patterns. Location Africa, Afromontane Region, southern Africa, Madagascar and Yemen. Methods Diversity and endemism for the genus were examined at the continental scale using a chorological approach. Biogeographical patterns and endemism in the South Africa Centre were examined in greater detail using chorology, phenetics, parsimony analysis of endemicity (PAE) and mapping of range‐restricted taxa. Results Six centres of diversity were recovered, five of which are also centres of endemism. Eight subcentres of diversity are proposed, of which only two are considered subcentres of endemism. The South Africa Centre is the most species‐rich region and the largest centre of endemism for Kniphofia. The phenetic analysis of the South Africa Centre at the full degree square scale recovered three biogeographical areas that correspond with the subcentres obtained from the chorological analysis. The PAE (at the full degree square scale) and the mapping of range‐restricted taxa recovered two and six areas of endemism (AOEs), respectively. These latter two approaches produced results of limited value, possibly as a result of inadequate collecting of Kniphofia species. Only two AOEs were identified by PAE and these are embedded within two of the six AOEs recovered by the mapping of range‐restricted taxa. All the above AOEs are within the three subcentres found by chorological and phenetic analysis (at the full degree square scale) for the South Africa Centre. Main conclusions The centres for Kniphofia broadly correspond to the Afromontane regional mountain systems, but with some notable differences. We regard Kniphofia as a floristic indicator of the Afromontane Region sensu lato. In southern Africa, the phenetic approach at the full‐degree scale retrieved areas that correlate well with those obtained by the chorological approach.     

Distribution patterns and biogeographic analysis of Austral Polychaeta (Annelida)

Aim We investigate the biogeography of Austral Polychaeta (Annelida) using members of the families Eunicidae, Lumbrineridae, Oenonidae, Onuphidae, Serpulidae and Spionidae and Parsimony Analysis of Endemicity (PAE). We determine whether observed polychaete distribution patterns correspond to traditional shallow-water marine areas of endemism, estimate patterns of endemism and relationships between areas of endemism, and infer the biological processes that have caused these patterns. Location The study is concerned with extant polychaete taxa occupying shallow-water areas derived from the breakup of the Gondwana landmass (i.e. Austral areas). Methods Similarity was assessed using a significance test with Jaccard's indices. Areas not significantly different at 0.99 were combined prior to the PAE. Widespread species and genera (155 taxa) were scored for presence/absence for each area of endemism. PAE was used to derive hypotheses of area relationships. Hierarchical patterns in the PAE trees were identified by testing for congruence with patterns derived from cladistic biogeographic studies of other Gondwanan taxa and with geological evidence. Results The polychaete faunas of four area-pairs were not significantly different and the areas amalgamated: South-west Africa and South Africa, New Zealand South Island and Chatham Islands, Macquarie Island and Antipodean Islands, and West Antarctica and South Georgia. Areas with the highest levels of species endemism were southern Australia (67.0%), South-east South America (53.2%) and South Africa (40.4%). About 60% of species and 7.5% of genera occupied a single area of endemism. The remainder were informative in the PAE. Under a no long-distance dispersal assumption a single minimal-length PAE tree resulted (l=367; ci=0.42); under dispersal allowed, three minimal-length trees resulted (l=278; ci=0.56). In relation to the sister grouping of the New Zealand areas and Australia we find congruence between our minimal-length trees and those derived from a biogeographic study of land plants, and with area relationships predicted by the Expanding Earth Model. Main conclusions The polychaete distribution patterns in this study differ slightly from the classical areas of endemism, most notably in being broader, thereby bringing into question the value of using single provincial system for marine biogeographic studies. The Greater New Zealand region is found to be ‘monophyletic’ with respect to polychaetes, that is comprising a genuine biogeographical entity, and most closely related to the polychaete fauna of southern Australia. This finding is consistent with studies of land plants and with the Expanding Earth model, but disagrees with conventional geology and biogeographic hypothesis involving a ‘polyphyletic’ New Zealand. Both vicariance and concerted range expansion (=biotic dispersion) appear to have played important roles in shaping present-day distribution patterns of Austral polychaetes. Shallow-water ridge systems between the Australian and Greater New Zealand continental landmasses during the Tertiary are thought to have facilitated biotic dispersion.     

New Proboscideans (Mammalia) from the middle Miocene of Thailand

The proboscidean fauna of the middle Miocene of Thailand consists of five taxa, including four elephantoids and one deinothere. The Thai association is dominated by the genera Stegolophodon and Gomphotherium. Stegolophodon is represented by S. nasaiensis and S. praelatidens. The latter species, considered invalid and possibly conspecific with S. latidens, is re‐erected. Its phylogenetic relationships are discussed. The Thai Gomphotherium matches with G. browni from the middle Miocene of Indo‐Pakistan. However, the open nomenclature is employed for the Thai material because it differs from G. browni in terms of curvature of the upper tusk. Intraspecific molar size variation observed in G. cf. browni and Stegolophodon praelatidens is attributed to sexual dimorphism. The Thai proboscidean asssemblage is mainly endemic compared with other contemporaneous Asian faunas although the recognition of Gomphotherium cf. browni denotes faunal affinities with Pakistan. The biostratigraphical implications of the taxa are examined in a regional context. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 703–721.     

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.