A priori and a posteriori methods in comparative evolutionary studies of host–parasite associations

Brooks parsimony analysis (BPA) and reconciliation methods in studies of host–parasite associations differ fundamentally, despite using the same null hypothesis. Reconciliation methods may eliminate or modify input data to maximize fit of single parasite clades to a null hypothesis of cospeciation, by invoking different a priori assumptions, including a known host phylogeny. By examining the degree of phylogenetic congruence among multiple parasite clades, using hosts as analogs of taxa but not presuming a host phylogeny or any degree of cospeciation a priori, BPA modifies the null hypothesis of cospeciation if necessary to maintain the integrity of the input data. Two exemplars illustrate critical empirical differences between reconciliation methods and BPA: (1) reconciliation methods rather than BPA may select the incorrect general host cladogram for a set of data from different clades of parasites, (2) BPA rather than reconciliation methods provides the most parsimonious interpretation of all available data, and (3) secondary BPA, proposed in 1990, when applied to data sets in which host‐switching produces hosts with reticulate histories, provides the most parsimonious and biologically realistic interpretations of general host cladograms. The extent to which these general host cladograms, based on cospeciation among different parasite clades inhabiting the same hosts, correspond to host phylogeny can be tested, a posteriori, by comparison with a host phylogeny generated from nonparasite data. These observations lead to the conclusion that BPA and reconciliation methods are designed to implement different research programs based on different epistemologies. BPA is an a posteriori method that is designed to assess the host context of parasite speciation events, whereas reconciliation methods are a priori methods that are designed to fit parasite phylogenies to a host phylogeny. Host‐switching events are essential for explaining complex histories of host–parasite associations. BPA assumes coevolutionary complexity (historical contingency), relying on parsimony as an a posteriori explanatory tool to summarize complex results, whereas reconciliation methods, which embody formalized assumptions of maximum cospeciation, are based on a priori conceptual parsimony. Modifications of basic reconciliation methods, embodied in TreeMap 1.0 and TreeMap 2.02, represent the addition of weighting schemes in which the researcher specifies allowed departures from cospeciation a priori, with the result that TreeMap results more closely agree with BPA results than do reconciled tree analysis results.     

A Posteriori and a Priori Methodologies for Testing Hypotheses of Causal Processes in Vicariance Biogeography

Methods used in vicariance biogeography fall into the categories of a posteriori methods (e.g., Component Compatibility Analysis and Brooks Parsimony Analysis) and a priori methods (e.g., Component Analysis, Reconciled Tree Analysis, and Three Area Statement Analysis). Each category corresponds to a particular methodology that arrives at general area cladograms by testing null hypotheses in a particular way. A posteriori methods assume the process of vicariance only (A0) as a common cause of the distribution of different monophyletic groups of taxa under the null hypothesis. Whenever a parsimony analysis of combined data from these monophyletic groups results in a general area cladogram with homoplasy, the null hypothesis is rejected and extinction and dispersal are invoked a posteriori as ad hoc process explanations. A priori methods assume not only vicariance (A0) but also combinations of vicariance with the processes of extinction (A1) and dispersal (A2) as possible causes of the distribution of the taxa of different monophyletic groups. Each assumed set of processes corresponds to a different null hypothesis. Under the assumption of independence and thus additivity of the processes involved, the sets of area cladograms obtained under A0, A1, and A2 from data of each monophyletic group must be inclusive (requirement I). Whenever no congruent area cladograms are found in the intersection of sets of area cladograms derived under the same assumption for different monophyletic groups (II), the corresponding null hypothesis is rejected.     

Assessing Modes of Speciation: Range Asymmetry and Biogeographical Congruence

Lynch [1989, in "Speciation and Its Consequences" (D. Otte and J. A. Endler, Eds.), pp. 527–553, Sinauer, Sunderland, MA, proposed a methodology for assessing the frequency of occurrence of various modes of initiating species formation, using a combination of phylogenetic relationships and relative size of geographic ranges for sister species and sister groups. Historical biogeography provides an alternative criterion for assessing modes of species formation. Species whose distributions conform to a general (replicated in multiple clades) pattern of area relationships are deemed to be the result of vicariance (including microvicariance) regardless of the details of current geographic range. Species exhibiting unique biogeographic distributions are the result of peripheral isolates speciation and postspeciation dispersal. Lineage duplications indicate sympatric speciation. An empirical assessment of this alternative approach was performed using the most recent phylogenetic trees and geographical distribution data on the Mesoamerican poeciliid fish comprising the genera Xiphophorus and Heterandria . The single area cladogram produced by secondary Brooks Parsimony Analysis indicates 3 vicariant events (accounting for seven extant species and the common ancestor of the northern swordtails, which are not further analyzed) and at least 13 episodes of peripheral isolates speciation. Two of the 10 areas considered in previous analyses are vicariant areas of endemism, 1 is historically unique due to a single episode of peripheral isolates speciation, and the remaining 7 have reticulated histories of speciation. The results corroborate inferences of speciation modes made by Lynch for the same data.     

Historical biogeography of some river basins in central Mexico evidenced by their goodeine freshwater fishes: a preliminary hypothesis using secondary Brooks parsimony analysis

Aims Our aim was to uncover and describe patterns of historical biogeography of the main river basins in central Mexico, based on a secondary Brooks parsimony analysis (BPA) of goodeine fishes, and to understand the processes that determine them with respect to the molecular clock of the goodeines and the geological events that have taken place in the region since the Miocene. Location The region covered in this study includes central Mexico, mostly the so‐called Mesa Central of Mexico, an area argued to be a transitional zone comprising several major river drainages from their headwaters at high elevations along the Transmexican Volcanic Belt to the coast of the Gulf of Mexico and the Pacific Ocean. Methods Based on a previous phylogenetic hypothesis regarding the Goodeidae, we built a data matrix using additive binary coding. First, we conducted a primary BPA to provide general explanations of the historical biogeography of Central Mexico. As ambiguity was found, a secondary BPA was conducted, and some areas were duplicated in order to explain the reticulated history of the area. Area cladograms were obtained by running a parsimony analysis. Instances of vicariance and non‐vicariance processes were described with reference to the cladogram obtained from secondary BPA. Results The study area was divided into 18 discrete regions. Primary BPA produced nine equally parsimonious cladograms with 129 steps, and a consistency index (CI) of 0.574. A strict consensus cladogram shows low resolution among some areas, but other area relationships are consistent. For secondary BPA, five of the 18 regions were duplicated (LEA, COT, AYU, CUT, PAN); one was triplicated (BAL); and one was quadruplicated (AME), suggesting that the pattern of distribution of species in these areas reflects multiple independent events. These areas correspond with the regions exhibiting the highest levels of diversification and the most complex geological history, and those for which river piracy events or basin connections have been proposed. The secondary BPA produced a single most parsimonious cladogram with 118 steps, and a CI of 0.858. This cladogram shows that none of the duplicated areas are nested together, reinforcing the idea of a reticulated history of the areas and not a single vicariant event. Main conclusions Although our results are preliminary and we cannot establish this as a general pattern, as the BPA is based on a single‐taxon cladogram, resolution obtained in the secondary BPA provides some insights regarding the historical biogeography of this group of fishes in river basins of central Mexico. Secondary BPA indicates that the historical biogeography of central Mexico, as shown by their goodeine freshwater fishes, is complex and is a result of a series of vicariant and non‐vicariant events such as post‐dispersal speciation and post‐speciation dispersal.     

Historical biogeography of New World emballonurid bats (tribe Diclidurini): taxon pulse diversification

Aim To reconstruct the biogeographical history of New World emballonurid bats (tribe Diclidurini). Although bats are the second most species‐rich order of mammals, they have not contributed substantially to our understanding of the historical biogeography of mammals in the Neotropics because of a poor fossil record. In addition, being the only group of mammals that fly, bats typically have large distributions with relatively few species endemic to restricted areas that are amenable to vicariant biogeographical approaches. Location Central and South America. Methods Phylogenetic analysis for comparing trees (PACT) is a new algorithm that incorporates all spatial information from taxon area cladograms into a general area cladogram. There were nine biogeographical areas identified in Central and South America for New World emballonurid bats. Molecular dating was used to incorporate the temporal aspect of historical biogeography. This method was compared with dispersal–vicariance analysis (DIVA), which assumes vicariance as the default mode of speciation. Results Of the 45 speciation events in a fully resolved phylogeny, eight that were hypothesized by DIVA as vicariance were considered by PACT as two peripheral isolations and six within‐area events. DIVA was less parsimonious because it required six more post‐speciation dispersal events in addition to the 73 hypothesized by PACT. DIVA reconstructed a widely distributed ancestor, suggesting that most dispersal events occurred earlier, whereas the ancestral area for PACT based on character optimization was the Northern Amazon, suggesting that dispersal events were more recent phenomena. Main conclusions The general area cladogram from PACT indicated that within‐area events, and not vicariance, provide the major mode of speciation for New World emballonurid bats. There was no biological evidence supporting or rejecting sympatric speciation in New World emballonurid bats. However, the geological history, combined with fluctuations in temperature and sea level, suggested within‐area speciation in a changing and heterogeneous environment in the Northern Amazon during the Miocene. This scenario is similar to the taxon‐pulse hypothesis of biotic diversification, which posits repeated episodes of range expansions and contractions from a stable core area such as the Guiana Shield within the Northern Amazon.     

Reticulate evolution on a global scale: a nuclear phylogeny for New World Dryopteris (Dryopteridaceae)

Reticulate, or non-bifurcating, evolution is now recognized as an important phenomenon shaping the histories of many organisms. It appears to be particularly common in plants, especially in ferns, which have relatively few barriers to intra- and interspecific hybridization. Reticulate evolutionary patterns have been recognized in many fern groups, though very few have been studied rigorously using modern molecular phylogenetic techniques in order to determine the causes of the reticulate patterns. In the current study, we examine patterns of branching and reticulate evolution in the genus Dryopteris, the woodferns. The North American members of this group have long been recognized as a classic example of reticulate evolution in plants, and we extend analysis of the genus to all 30 species in the New World, as well as numerous taxa from other regions. We employ sequence data from the plastid and nuclear genomes and use maximum parsimony (MP), maximum likelihood (ML), Bayesian inference (BI), and divergence time analyses to explore the relationships of New World Dryopteris to other regions and to reconstruct the timing and events which may have led to taxa displaying reticulate rather than strictly branching histories. We find evidence for reticulation among both the North and Central/South American groups of species, and our data support a classic hypothesis for reticulate evolution via allopolyploid speciation in the North America taxa, including an extinct diploid progenitor in this group. In the Central and South American species, we find evidence of extensive reticulation involving unknown ancestors from Asia, and we reject deep coalescent processes such as incomplete lineage sorting in favor of more recent intercontinental hybridization and chloroplast capture as an explanation for the origin of the Latin American reticulate taxa.     

A historical biogeographical protocol for studying biotic diversification by taxon pulses

Aim To present a historical biogeographical protocol for distinguishing biotic diversification by taxon pulse radiations from biotic diversification by vicariance. Location Mexico and northern Central America. Methods Brooks Parsimony Analysis (BPA), phylogenetic inference, linear correlation analysis. Results The taxon pulse radiation of 33 clades in nine areas of endemism in Mesoamerica is based on nine episodes of biotic expansion from three areas, and six episodes of vicariance, involving four geographical splits. Nineteen per cent of speciation events are due to vicariance, 25% to peripheral isolates speciation and 56% are within‐area events. The species–area curve has a correlation coefficient (r²) of 0.47. Extinction events and species richness are highly correlated (r² = 0.75), but colonization events and species richness are poorly correlated (r² = 0.36), suggesting that colonization is not the main determinant of the species–area relationship. Colonization events are more poorly correlated with size of area (r² = 0.05) than are in situ speciation events (r² = 0.60). Colonization events and in situ events are poorly correlated (r² = 0.02). All areas of endemism have reticulated histories, and have acted as both sources and islands at various times. Main conclusions Taxon pulses can be distinguished from maximum vicariance using this protocol; refining it requires a method for generating area cladograms from complex data and incorporation of direct dating of evolutionary events.     

A protocol for temporal calibration of general area cladograms

Aim To describe a protocol for incorporating a temporal dimension into historical biogeographical analysis, while maintaining the essential independence of all datasets, involving the generation of general area cladograms. Location Global. Methods General area cladograms (GACs) are a reconstruction of the evolutionary history of a set of areas and unrelated clades within those areas. Nodes on a GAC correspond to speciation events in a group of taxa; general nodes are those at which multiple unrelated clades speciate. We undertake temporal calibration of GACs using molecular clock estimates of splitting events between extant taxa as well as first appearance data from the fossil record. We present two examples based on re‐analysis of previously published data: first, a temporally calibrated GAC generated from secondary Brooks parsimony analysis (BPA) of six extant bird clades from the south‐west of North America using molecular clock estimates of divergence times; and second, an analysis of African Neogene mammals based on a phylogenetic analysis for comparing trees (PACT) analysis. Results A hypothetical example demonstrates how temporal calibration reveals potentially critical information about the timing of both unique and general events, while also illustrating instances of incongruence between dates generated from molecular clock estimates and fossils. For the African Neogene mammal dataset, our analysis reveals that most mammal clades underwent geodispersal associated with the Neogene climatic optimum (c. 16 Ma) and vicariant speciation in central Africa correlated with increased aridity and cooler temperatures around 2.5 Ma. Main conclusions Temporally calibrated GACs are valuable tools for assessing whether coordinated patterns of speciation are associated with large‐scale climatic or tectonic phenomena.     

Cladistic and phylogenetic biogeography: the art and the science of discovery

All methods used in historical biogeographical analysis aim to obtain resolved area cladograms that represent historical relationships among areas in which monophyletic groups of taxa are distributed. When neither widespread nor sympatric taxa are present in the distribution of a monophyletic group, all methods obtain the same resolved area cladogram that conforms to a simple vicariance scenario. In most cases, however, the distribution of monophyletic groups of taxa is not that simple. A priori and a posteriori methods of historical biogeography differ in the way in which they deal with widespread and sympatric taxa. A posteriori methods are empirically superior to a priori methods, as they provide a more parsimonious accounting of the input data, do not eliminate or modify input data, and do not suffer from internal inconsistencies in implementation. When factual errors are corrected, the exemplar presented by M.C. Ebach & C.J. Humphries (Journal of Biogeography, 2002, 29 , 427) purporting to show inconsistencies in implementation by a posteriori methods actually corroborates the opposite. The rationale for preferring a priori methods thus corresponds to ontological rather than to epistemological considerations. We herein identify two different research programmes, cladistic biogeography (associated with a priori methods) and phylogenetic biogeography (associated with a posteriori methods). The aim of cladistic biogeography is to fit all elements of all taxon–area cladograms to a single set of area relationships, maintaining historical singularity of areas. The aim of phylogenetic biogeography is to document, most parsimoniously, the geographical context of speciation events. The recent contribution by M.C. Ebach & C.J. Humphries (Journal of Biogeography, 2002, 29 , 427) makes it clear that cladistic biogeography using a priori methods is an inductivist/verificationist research programme, whereas phylogenetic biogeography is hypothetico‐deductivist/falsificationist. Cladistic biogeography can become hypothetic‐deductive by using a posteriori methods of analysis.     

Heterogeneity, speciation/extinction history and climate: explaining regional plant diversity patterns in the Cape Floristic Region

This paper investigates the role of heterogeneity and speciation/extinction history in explaining variation in regional scale (c. 0.1–3000 km²) plant diversity in the Cape Floristic Region of south‐western Africa, a species‐ and endemic‐rich biogeographical region. We used species‐area analysis and analysis of covariance to investigate geographical (east vs. west) and topographic (lowland vs. montane) patterns of diversity. We used community diversity as a surrogate for biological heterogeneity, and the diversity of naturally rare species in quarter degree squares as an indicator of differences in speciation/extinction histories across the study region. We then used standard statistical methods to analyse geographical and topographic patterns of these two measures. There was a clear geographical diversity pattern (richer in the west), while a topographic pattern (richer in mountains) was evident only in the west. The geographical boundary coincided with a transition from the reliable winter‐rainfall zone (west) to the less reliable non‐seasonal rainfall zone (east). Community diversity, or biological heterogeneity, showed no significant variation in relation to geography and topography. Diversity patterns of rare species mirrored the diversity pattern for all species. We hypothesize that regional diversity patterns are the product of different speciation and extinction histories, leading to different steady‐state diversities. Greater Pleistocene climatic stability in the west would have resulted in higher rates of speciation and lower rates of extinction than in the east, where for the most, Pleistocene climates would not have favoured Cape lineages. A more parsimonious hypothesis is that the more predictable seasonal rainfall of the west would have favoured non‐sprouting plants and that this, in turn, resulted in higher speciation and lower extinction rates. Both hypotheses are consistent with the higher incidence of rare species in the west, and higher levels of beta and gamma diversity there, associated with the turnover of species along environmental and geographical gradients, respectively. These rare species do not contribute to community patterns; hence, biological heterogeneity is uniform across the region. The weak topography pattern of diversity in the west arises from higher speciation rates and lower extinction rates in the topographically complex mountains, rather than from the influence of environmental heterogeneity on diversity.     

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.     

Tree squirrels: A key to understand the historic biogeography of Mesoamerica?

A multi-taxon historical biogeography approach (Brooks Parsimony Analysis) was used to estimate relationships among the Mesoamerican lowland and highland areas and the particular biogeographic history of Mesoamerican squirrels (Sciurus, Microsciurus and Syntheosciurus species). A total of 15 lowland areas and 12 highland areas plus 41 clades comprising 240 species (45,135 records) were employed to obtain Taxon-Area Cladograms and Area Cladograms. A single most parsimonious General Area Cladogram indicated a strong vicariant relationship between Southern Mexico and the remainder of Mesoamerica, and identified several vicariant nodes (Modern Chiapanencan Volcanic Arc, Honduras’ Great Central Depression, and Nicaraguan Depression) as well as historically independent highland areas. A secondary BPA in relation with Sciurus species showed several instances of post speciation dispersal or range expansion, lack of response to vicariant events, and, possibly, lineage duplication. The results obtained suggest that Mesoamerican biotas have been subjected to several major vicariant events, but the reticulated nature of some of its areas also indicates that dispersal (post-speciation dispersal and range expansion) had been important in the diversification of the Mesoamerican biota. This trend was also observed in the particular biogeographic history of Mesoamerican tree squirrels.     

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.     

Explaining disparities in species richness between Mediterranean floristic regions: a case study in Gladiolus (Iridaceae)

Aim The causes of geographical variation in species richness in clades that do not follow the latitudinal diversity gradient have rarely been investigated. Here, we examine spatial asymmetries of diversity in Gladiolus (Iridaceae), a large genus (> 260 species) that is present in two mediterranean climate biomes: the Cape of southern Africa (106 species) and the Mediterranean Basin (7 species). Despite convergence of climatic conditions between the two regions, the species density of Gladiolus is over one order of magnitude higher in the Cape than in the Mediterranean Basin. We investigate whether the diversity disparities observed in the genus are better explained by recent colonization of species‐poor areas (temporal hypothesis) or by differential rates of diversification (evolutionary hypothesis). Location Africa, Madagascar and Eurasia Methods We employ a recently developed Bayesian method for the estimation of diversification rates and a biogeographical optimization approach within a phylogenetic framework. Results In Gladiolus, the ‘diversity anomaly’ between the two Mediterranean climate regions cannot be explained solely by the time available for speciation in the Cape, but is also due to locally reduced rates of diversification in the Mediterranean Basin. Furthermore, high overall diversity in southern Africa stems from an ancient origin in the Cape allied with high rates of diversification in the summer‐rainfall region of the subcontinent. Main conclusions Both evolutionary and temporal hypotheses must be taken into account in order to explain the diversity anomaly between the Mediterranean Basin and the Cape. Our results suggest that regions at comparable latitudes and/or with similar climate may not converge in diversity levels due to heterogeneity of diversification rates and contrasting biogeographical histories.     

Speciation within genomic networks: a case study based on Steatocranus cichlids of the lower Congo rapids

Hybridization in animals is a much more common phenomenon as previously thought and may have profound implications for speciation research. The cichlid genus Steatocranus (Teleostei: Cichlidae), a close relative to members of the East African cichlid radiations, radiated under riverine conditions in the lower Congo rapids and produced a small species flock. Previous phylogenetic analyses suggested that hybridization occurred and contributed to speciation in this genus. A re-analysis of an already published 2000 loci-AFLP data set explicitly testing for patterns of ancient gene flow provided strong evidence for a highly reticulate phylogenetic history of the genus. We provide, to our knowledge, the first example of a complex reticulate network in vertebrates, including multiple closely related species connected through ancient as well as recent gene flow. In this context, the limited validity of strictly bifurcating tree hypotheses as a phylogenetic basis for hypothesis testing in evolutionary biology is discussed.     

Dispersal vs. vicariance in the Mediterranean: historical biogeography of the Palearctic Pachydeminae (Coleoptera, Scarabaeoidea)

Aim The geological evolution of the Mediterranean region is largely the result of the Tertiary collision of the African and Eurasian Plates, but also a mosaic of migrating island arcs, fragmenting tectonic belts, and extending back‐arc basins. Such complex paleogeography has resulted in a ‘reticulate’ biogeographical history, in which Mediterranean biotas repeatedly fragmented and merged as dispersal barriers appeared and disappeared through time. In this study, dispersal‐vicariance analysis (DIVA) is used to assess the relative role played by dispersal and vicariance in shaping distribution patterns in the beetle subfamily Pachydeminae Reitter, 1902 (Scarabaeoidea), an example of east–west Mediterranean disjunction. Location The Mediterranean region, including North Africa, the western Mediterranean, Balkans–Anatolia, Middle East, Caucasus, the Iranian Plateau, and Central Asia. Methods A phylogenetic hypothesis of the Palearctic genera of Pachydeminae in conjunction with distributional data was analysed using DIVA. This method reconstructs the ancestral distribution in a given phylogeny based on the vicariance model, while allowing dispersal and extinction to occur. Unlike other methods, DIVA does not enforce area relationships to conform to a hierarchical ‘area cladogram’, so it can be used to reconstruct ‘reticulate’ biogeographical scenarios. Results Optimal reconstructions, requiring 23 dispersal events, suggest that the ancestor of Pachydeminae was originally present in the south‐east Mediterranean region. Basal splitting within the subfamily was caused by vicariance events related to the late Tertiary collision of the African microplates Apulia and Arabia with Eurasia, and the resultant arise of successive dispersal barriers (e.g. the Red Sea, the Zagros Mountains). Subsequent diversification in Pachydeminae involved multiple speciation events within the Middle East and Iran–Afghanistan regions, which gave rise to the least speciose genera of Pachydeminae (e.g. Otoclinius Brenske, 1896). Finally, the presence of Pachydeminae in the western Mediterranean region seems to be the result of a recent dispersal event. The ancestor of the Iberian genera Ceramida Baraud, 1987 and Elaphocera Gené, 1836 probably dispersed from the Middle East to the Iberian Peninsula across North Africa and the Gibraltar Strait during the ‘Messinian salinity crisis’ at the end of the Miocene. Main conclusions Although the basal diversification of Pachydeminae around the Mediterranean appears to be related to vicariance events linked to the geological formation of the Mediterranean Basin, dispersal has also played a very important role. Nearly 38% of the speciation events in the phylogeny resulted from dispersal to a new area followed by allopatric speciation between lineages. Relationships between western and eastern Mediterranean disjuncts are usually explained by dispersal through Central Europe. The biogeographical history of the Pachydeminae corroborates other biogeographical studies that consider North Africa to be an alternative dispersal route by which Mediterranean taxa could have achieved circum‐Mediterranean distributions.     

Parsimony Analysis of Endemicity (PAE) of Mexican hydrological basins based on helminth parasites of freshwater fishes

Aim The distributional patterns of helminthological fauna of freshwater fishes were analysed to postulate a general hypothesis on the relationships of some Mexican hydrological systems. Location Eight hydrological systems of central and eastern Mexico were studied and compared with records from Nicaragua. Methods A Parsimony Analysis of Endemicity (PAE) was applied to the presence/absence of ninety‐two helminth parasite taxa (Monogeneans, Digeneans, Cestodes, Acanthocephalans and Nematodes) of freshwater fishes, from eight Mexican hydrological systems, using the Hennig86 program. Results The results represent the first attempt for a biogeographical analysis through application of the PAE method to the distributional patterns of helminth parasites of freshwater fishes in Mexico. A single most parsimonious cladogram was obtained, which grouped all the Neotropical systems in accordance with previous proposals based on other plant and animal taxa. Main conclusions The most basal systems were Santiago and Lerma basins, which exhibited Nearctic affinities. The remaining areas of the cladogram showed Neotropical affinities. All the southeastern systems were grouped in a clade with the Nicaragua system, providing support for a ‘Mesoamerican province’ based on helminth parasites of cichlids. The cladogram also suggests that the treatment of the Lerma‐Santiago basin as a single biogeographical unit is inaccurate and that they should be treated as separate systems.     

Phylogeny of species of Sciadicleithrum (Monogenoidea: Ancyrocephalinae), and their historical biogeography in the neotropics

The phylogenetic relationships and historical biogeography of species of Sciadicleithrum parasitizing Neotropical cichlid fishes were studied. Hypotheses were: Did the presence of Sciadicleithrum species in southeast Mexico (SM) and Central America (CA) result from early dispersal of cichlid species from South America (SA) to the north via the Antilles during the Tertiary (24 million years ago [mya]), or did it occur after emergence of the Panama Isthmus in the Pleistocene (2-5 mya)? The Sciadicleithrum phylogeny was based on 19 morphological transformation series, with species of Gussevia and Cichlidogyrus as outgroups. The most parsimonious cladogram had a 40% consistency index, with one clade including all the species of Sciadicleithrum from SA and all but one of those from CA and another with all the Sciadicleithrum species from SM and S. maculicaudae from CA. Results support the late dispersal hypothesis following emergence of the Panama Isthmus. Fifteen species of Sciadicleithrum parasitize 13 cichlid species from SA and CA. In contrast, only 4 species of Sciadicleithrum infect 14 cichlid species from SM. Parasite speciation appears to lag behind host speciation, with 2 equally possible explanations: loss of parasite species and host switching.     

COMPARISONS OF OBSERVED PHYLOGENETIC TOPOLOGIES WITH NULL EXPECTATIONS AMONG THREE MONOPHYLETIC LINEAGES

Three null models have been proposed to predict the relative frequencies of topologies of phylogenetic trees. One null model assumes each distinguishable n-member tree is equally likely (proportional-to-distinguishable-arrangements model). A second model assumes that each topological type is equally likely (equiprobable model). A third model assumes that the probability of each topological type is determined by random speciation (Markov model). We sampled published phylogenetic trees from three major groups of organisms: division Angiospermae, class Insecta, and superclass Tetrapoda. Our sampling was more restricted than previous studies and was designed to test whether observed topological frequencies were distinguishable from those predicted by the three null models. The pattern of evolution reflected in five-member phylogenetic trees is different from predictions of the equiprobable and Markov model but is indistinguishable from the proportional-to-distinguishable-arrangements model. This indicates that 1) speciation (and/or extinction) is not equally likely among all taxa, even for small phylogenies; or 2) systematists' attempts at reconstructing small phylogenies are, on average, indistinguishable from those expected if they had merely selected a tree at random from the pool of all possible trees. The topology frequencies were not different among the three groups of organisms, suggesting that factors shaping patterns of speciation and extinction are consistent among major taxonomic groups.     

Hidden histories of gene flow in highland birds revealed with genomic markers

Genomic studies are revealing that divergence and speciation are marked by gene flow, but it is not clear whether gene flow has played a prominent role during the generation of biodiversity in species‐rich regions of the world where vicariance is assumed to be the principal mode by which new species form. We revisit a well‐studied organismal system in the Mexican Highlands, Aphelocoma jays, to test for gene flow among Mexican sierras. Prior results from mitochondrial DNA (mtDNA) largely conformed to the standard model of allopatric divergence, although there was also evidence for more obscure histories of gene flow in a small sample of nuclear markers. We tested for these ‘hidden histories’ using genomic markers known as ultraconserved elements (UCEs) in concert with phylogenies, clustering algorithms and newer introgression tests specifically designed to detect ancient gene flow (e.g. ABBA/BABA tests). Results based on 4303 UCE loci and 2500 informative SNPs are consistent with varying degrees of gene flow among highland areas. In some cases, gene flow has been extensive and recent (although perhaps not ongoing today), whereas in other cases there is only a trace signature of ancient gene flow among species that diverged as long as 5 million years ago. These results show how a species complex thought to be a model for vicariance can reveal a more reticulate history when a broader portion of the genome is queried. As more organisms are studied with genomic data, we predict that speciation‐with‐bouts‐of‐gene‐flow will turn out to be a common mode of speciation.