Ecological coassociations influence species' responses to past climatic change: an example from a Sonoran Desert bark beetle

Ecologically interacting species may have phylogeographical histories that are shaped both by features of their abiotic landscape and by biotic constraints imposed by their coassociation. The Baja California peninsula provides an excellent opportunity to examine the influence of abiotic vs. biotic factors on patterns of diversity in plant-insect species. This is because past climatic and geological changes impacted the genetic structure of plants quite differently to that of codistributed free-living animals (e.g. herpetofauna and small mammals). Thus, ‘plant-like’ patterns should be discernible in host-specific insect herbivores. Here, we investigate the population history of a monophagous bark beetle, Araptus attenuatus, and consider drivers of phylogeographical patterns in the light of previous work on its host plant, Euphorbia lomelii. Using a combination of phylogenetic, coalescent-simulation-based and exploratory analyses of mitochondrial DNA sequences and nuclear genotypic data, we found that the evolutionary history of A. attenuatus exhibits similarities to its host plant that are attributable to both biotic and abiotic processes. Southward range expansion and recent colonization of continental Sonora from the Baja peninsula appear to be unique to this taxon pair and probably reflect influences of the host plant. On the other hand, abiotic factors with landscape-level influences on a diverse suite of codistributed arid-adapted taxa, such as Plio- and Pleistocene-aged marine incursions in the region, also left genetic signatures in beetle and host plant populations. Superimposed on these similarities, bark beetle-specific patterns and processes were also evident: our data revealed two secondarily sympatric, reproductively isolated genetic lineages, as well as a previously unrecognized mid-peninsular warm desert refuge. Taken together, this work illustrates that the evolutionary history of species-specific insect herbivores may represent a mosaic of influences, including—but not limited to—those imposed by the host plant.     

Geographic genetic architecture of pocket gopher (Thomomys bottae) populations in Baja California, Mexico

Phylogenetic analyses of complete mitochondrial cytochrome b sequences support the monophyly of pocket gopher (Thomomys bottae) populations from the 1000 km length of the Baja California peninsula of Mexico, relative to other geographical segments of the species range in western North America. The Baja California peninsula is an area that encompasses considerable ecomorphological and infraspecific diversity within this pocket gopher species. However, detailed population analyses encompassing 35 localities distributed over the southern half of the peninsula reveal only trivial phylogeographical structure. Rather, most of the 72 unique 500-base pair haplotypes examined from 142 individuals is restricted to single populations, although a few haplotypes are shared broadly across geography. Individual populations are typically comprised of haplotype sets from different branches in a network of relationships. Analysis of molecular variance (amova) indicates that approximately half of the total pool of variation is contained among individuals within local populations, and that only about 25% can be explained by the regional subdivisions of current subspecies distributions or physiographic realms. A hypothesized historical vicariant event that has been causally linked to the phylogeographical structure of other, codistributed species has had little influence on these pocket gopher populations, explaining only 13% of the total variation. The temporal depth, estimated by coalescence parameters, of the haplotype lineage in Baja California is relatively recent, approximately 300,000 generations; both the mismatch distribution of pairwise comparisons and a significantly positive exponential growth estimate support a recent history of expanding populations; but current, or recent past, migration estimates have remained small, are largely unidirectional from north to south, and weak isolation by distance is present. All data suggest that pocket gophers have relatively recently invaded the southern half of peninsular Baja California, with the genetic signature of expansion still evident but with sufficient time having lapsed to result in a weak isolation by distance pattern. The geographical assemblage of sampled populations thus appears as a meta-population, with limited gene flow contrasting with random haplotype loss due to drift in small, localized populations.     

The peninsula effect on species diversity: a reassessment of the avifauna of Baja California

The peninsula effect, a decrease in species diversity from the base to the tip of peninsulas, has been proposed to explain the relatively poor species diversity of mammals on North American peninsulas. Subsequent work has questioned both the existence of peninsular declines in diversity, as well as the proposed cause (immigration-extinction dynamics). Previous studies of the Baja California avifauna have shown a gradual decrease in the diversity of breeding birds from the base to the tip of the peninsula. Using newly published data on the breeding land birds, I found a decrease only from the base to the middle of the peninsula, with a slight increase in diversity from the middle to the tip. This result is similar to that for other highly vagile taxa (e.g., Chiroptera. Lepidoptera) and is largely due to the coneave diversity gradient of montane species along the peninsula. Habitat associations of the Baja avifauna and the location of potential source populations suggest that: 1) local habitat heterogeneity is likely the single most important factor influencing the avian diversity gradient along the peninsula; and 2) limited immigration of Neotropical species from mainland areas, and of Nearctic species from the base of the peninsula to the montane southern tip is partly responsible for the form of the diversity gradient along the southern half of the peninsula. My results along with those from previous studies, suggest that rather than colonization/extinction dynamics, habitat heterogeneity and the vagility of the taxa considered have the greatest impact on the observed patterns of species diversity along peninsulas,     

Deep biogeographical history and cytonuclear discordance in the black-tailed brush lizard (Urosaurus nigricaudus) of Baja California

Molecular tools help us deduce historical events such as vicariance, dispersal, gene flow and speciation. However, our inferences are inevitably linked to the nature of the characters that we use to infer history. For example, the difference in inheritance patterns of mitochondrial DNA (mtDNA) and nuclear DNA (non-recombining maternal vs. recombining biparental inheritance) may lead us to propose different intraspecific histories. The peninsula of Baja California of north-western Mexico, a region affected by a complex geological history involving temporary seaways, permits evaluation of differences between these character types. We sequenced 1966 bp of mtDNA to reconstruct the genealogical history of Urosaurus nigricaudus (black-tailed brush lizard) from samples spanning the entire peninsula. The genealogy revealed several deep divergences, congruent with temporary vicariance events in the mid-peninsular, Loreto and Cape regions, as well as a major split across the Isthmus of La Paz, possibly resulting from a late Miocene seaway. The results support an emerging picture of the historical biogeography of Baja California, which suggests that key vicariance events are older than commonly perceived. The maternal genealogy of U. nigricaudus sharply contrasts with variation in allozymes that suggests very little differentiation across mitochondrial breaks, consistent with a pattern of ongoing gene flow. We interpret this cytonuclear discordance in relation to the historical biogeography of the region.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 89–104.     

Historical vicariance and postglacial colonization effects on the evolution of genetic structure in Lophocereus,a Sonoran Desert columnar cactus

Distinguishing the historical effects of gene migration and vicariance on contemporary genetic structure is problematic without testable biogeographic hypotheses based on preexisting geological and environmental evidence. The availability of such hypotheses for North America's Sonoran Desert has contributed to our understanding of the effect of historical vicariance and dispersal events on the diversification of this region's vertebrate biota but have not yet been applied to its flora. In this paper we describe a detailed allozyme analysis of the population genetic structure and phylogeography of the Sonoran Desert columnar cactus, Lophocereus schottii (senita). Inferred phylogroup distributions reflect two historical vicariance events: (1) a middle Pliocene northward transgression of the Sea of Cortéz that is reflected in well-supported Baja California peninsular and continental phylogroups but not in current taxonomic treatments of the species; and (2) a late Pliocene transpeninsular seaway across southern Baja that is reflected in tentative support for peninsular and southern Cape Region phylogroups corresponding to taxonomic varieties L. schottii var. schottii and L. schottii var. australis, respectively. A middle Pleistocene midpeninsular seaway hypothesized to explain congruent phylogroup distributions in several vertebrate taxa is not reflected in L. s. var. schottii, nor is the distinction of a third variety, L. s. var. tenuis, from continental populations of L. s. var. schottii. Linear regression of pairwise estimates of interpopulation differentiation (M and F(ST)/[1 - F(ST)]) on interpopulation geographic distance revealed significant evidence of isolation by distance within peninsular and continental phylogroups but not between them, consistent with historical vicariance between but not within these regions. We also found significant evidence of isolation by distance between putative L. s. var. schottii and L. s. var. australis phylogroups, suggesting that reproductive isolation between peninsular and Cape Region forms is incomplete. Within peninsular, but not continental, phylogroups, northward range expansion from southern Pleistocene refugia is reflected in significant declines in genetic variation with increasing latitude and in an area phenogram in which populations are progressively nested from south (ancestral) to north (descendant) along the Baja peninsula. Although the geographic concordance of phylogenetic topologies suggests that ancient vicariance events, and not dispersal, have primarily influenced the biogeographic distributions of Baja's vertebrate biota, the phylogeographic structure of L. schottii suggests that Sonoran Desert plant species may exhibit genetic signatures of postglacial range expansion and gene flow as well as vicariance.     

Cryptic vicariance in Gulf of California fishes parallels vicariant patterns found in Baja California mammals and reptiles

Comparisons across multiple taxa can often clarify the histories of biogeographic regions. In particular, historic barriers to movement should have affected multiple species and, thus, result in a pattern of concordant intraspecific genetic divisions among species. A striking example of such comparative phylogeography is the recent observation that populations of many small mammals and reptiles living on the Baja California peninsula have a large genetic break between northern and southern peninsular populations. In the present study, I demonstrate that five species of near-shore fishes living on the Baja coastline of the Gulf of California share this genetic pattern. The simplest explanation for this concordant genetic division within both terrestrial and marine vertebrates is that the Baja Peninsula was fragmented by a Plio-Pleistocene marine seaway and that this seaway posed a substantial barrier to movement for near-shore fishes. For some fish species, the signal of this vicariance in mtDNA has been eroded by gene flow and is not evident with classic, equilibrium measures of population structure. Yet, significant divisions are apparent in coalescent analyses that jointly estimate divergence with gene flow. The genetic divisions within Gulf of California fishes also coincide with recognized biogeographic regions based on fish community composition and several environmental factors. It is likely that adaptation to regional environments and present-day oceanographic circulation limit gene exchange between biogeographic regions and help maintain evidence of past vicariance.     

Evidence for range stasis during the latter Pleistocene for the Atlantic Coastal Plain endemic genus,Pyxidanthera Michaux

The general phylogeographical paradigm for eastern North America (ENA) is that many plant and animal species retreated into southern refugia during the last glacial period, then expanded northward after the last glacial maximum (LGM). However, some taxa of the Gulf and Atlantic Coastal Plain (GACP) demonstrate complex yet recurrent distributional patterns that cannot be explained by this model. For example, eight co‐occurring endemic plant taxa with ranges from New York to South Carolina exhibit a large disjunction separating northern and southern populations by >300 km. Pyxidanthera (Diapensiaceae), a plant genus that exhibits this pattern, consists of two taxa recognized as either species or varieties. We investigated the taxonomy and phylogeography of Pyxidanthera using morphological data, cpDNA sequences, and amplified fragment length polymorphism markers. Morphological characters thought to be important in distinguishing Pyxidanthera barbulata and P. brevifolia demonstrate substantial overlap with no clear discontinuities. Genetic differentiation is minimal and diversity estimates for northern and southern populations of Pxyidanthera are similar, with no decrease in rare alleles in northern populations. In addition, the northern populations harbour several unique cpDNA haplotypes. Pyxidanthera appears to consist of one morphologically variable species that persisted in or near its present range at least through the latter Pleistocene, while the vicariance of the northern and southern populations may be comparatively recent. This work demonstrates that the refugial paradigm is not always appropriate and GACP endemic plants, in particular, may exhibit phylogeographical patterns qualitatively different from those of other ENA plant species.     

Vicariance and dispersal form a ring distribution in nightsnakes around the Gulf of California

Plate tectonics can have profound effects on organismal distribution and is often the driving force in speciation. Through geologic processes, the Baja California Peninsula depicts two faunal patterns: one through southern vicariance with Cape separation, and the other through dispersal onto the northern peninsula, referred to as a ‘dual-peninsular effect.’ Here we apply a hierarchical sampling strategy that combines population-level sequence data (800 bp, nad4 region) with complete mt-genome data (aligned 15,549 bp) and 5 nuclear protein encoding loci (3315 bp), to test whether both patterns have occurred in one group of nightsnakes (Hypsiglena). The geologic formation of the peninsula is thought to have occurred in three stages: (1) Cape separation from mainland Mexico; (2) the northern peninsula separated, forming the northern Gulf of California; and (3) the peninsula was united through volcanic activity, while moving northward causing collision with southern California. However, the timing of events is debated. We explore phylogenetic relationships and estimate dates of divergence for nightsnakes using our hierarchical sampling strategy. Our data support both ‘southern-vicariance’ and ‘northern-dispersal’ have occurred in nightsnakes, forming a ring distribution around the Gulf of California. Two divergent forms are sympatric on the southern half of the peninsula with no indication of hybridization. Nightsnakes represent the first group to depict the ‘dual-peninsular effect’ with extensive overlap on the Baja California Peninsula.     

Species delimitation in the Acomys cahirinus–dimidiatus complex (Rodentia, Muridae) inferred from chromosomal and morphological analyses

Our earlier chromosome banding studies of Acomys cahirinus and Acomys dimidiatus (the latter long considered to be a subspecies of the former) revealed that, despite very close diploid numbers (36 vs. 38), these taxa possess sharply different karyotypes and undoubtedly belong to different species. In this context, the taxonomic status and the relationship between the two chromosomal forms in Sinai (2 n  = 36) and Israel (2 n  = 38), chromosomally homozygous across a vast range except for a very narrow hybrid zone, remain poorly documented. Neither of these forms have previously been studied by chromosome banding; thus, the exact nature of chromosomal differences as well as the species to which these forms should be assigned remain unknown. Here, we present the data on comparative G-banding analysis and morphometrics of Acomys from Israel, Sinai, and Saudi Arabia, and a hybrid obtained in laboratory crosses between latter two. The analysis revealed that karyotype of Acomys from Israel is identical to that of Acomys from Saudi Arabia and both are different from that of Acomys from Sinai by one Robertsonian fusion. Therefore, karyotypically, all three are very different from A. cahirinus . It follows from the study that Sinai and probably Arabian peninsula and Minor Asia must be excluded from geographical distribution of A. cahirinus , which is limited from West Sahara to Egypt along Nile river (except Sinai). Furthermore, the synthesis of chromosomal and recent molecular data suggests a phylogeographical scenario explaining the modern distribution of Acomys in the Sinai and Arabian peninsulas and permits the update of the taxonomic status of these populations.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 91 , 203–214.     

Italy as a major Ice Age refuge area for the bat Myotis myotis (Chiroptera: Vespertilionidae) in Europe

The distribution of biota from the temperate regions changed considerably during the climatic fluctuations of the Quaternary. This is especially true for many bat species that depend on warm roosts to install their nursery colonies. Surveys of genetic variation among European bats have shown that the southern peninsulas (Iberia and the Balkans) harbour endemic diversity, but to date, no such surveys have been conducted in the third potential glacial refuge area, the Apennine peninsula. We report here the phylogeographical analysis of 115 greater mouse-eared bats ( Myotis myotis ) sampled throughout Italy, and show that 15 of the 18 different haplotypes found in the mitochondrial control region of these bats were unique to the Apennine peninsula. Colonies within this region also showed substantial genetic structure at both mitochondrial ( Φ_ST  = 0.47, P  < 0.001) and nuclear markers ( F _ST = 0.039, P  < 0.001). Based on a comprehensive survey of 575 bats from Europe, these genetic markers further indicate that central Italian populations of M. myotis are more closely related to Greek samples from across the Adriatic Sea, than to other Italian bats. Mouse-eared bat populations from the Apennine peninsula thus represent a complex mixture of several endemic lineages, which evolved in situ , with others that colonized this region more recently along an Adriatic route. Our broad survey also confirms that the Alps represent a relatively impermeable barrier to gene flow for Apennine lineages, even for vagile animals such as bats. These results underline the conservation value of bats from this region and the need to include the Apennine peninsula in phylogeographical surveys in order to provide a more accurate view of the evolution of bats in Europe.     

Phylogeography of Pseudacris regilla (Anura: Hylidae) in western North America, with a proposal for a new taxonomic rearrangement

The Baja California populations of Pseudacris regilla, a widespread species in Western North America ranging from British Columbia to southern Baja California, are characterized by extensive geographic fragmentation. We performed phylogeographic and historical demographic analyses on 609 bp of the cytochrome b mitochondrial gene of 110 individuals representing 28 populations to determine the relative influences of current and historical processes in shaping the present distribution of genetic diversity on the Baja California Peninsula. Haplotypes from this area were nested in a clade with three well-differentiated groups. Two of these groups are from Baja California Sur and another is from California and Baja California. The estimated date for the split of these groups, between 0.9-1 Ma, fits with previously proposed hypotheses of vicariance due to different transpeninsular seaways, although successive population fragmentation and expansion due to climatic oscillations during Pleistocene glaciations cannot be discarded. Historical demographic analyses detected signs of past population expansions, especially in the southernmost group. With respect to populations north of this region, two older clades were identified, one with haplotypes mainly distributed in central California, and the other corresponding to the northern half of the species range, in what apparently is a recurrent pattern in the Pacific coast of North America. Based on the concordance between mt-DNA and available allozyme data indicating that these species have a long independent evolutionary history, we propose to consider the three major clades as distinct species: P. regilla, P. pacifica, and P. hypochondriaca.     

Biogeography and endemism of ants (Hymenoptera: Formicidae) in Baja California, Mexico: afirst overview

Abstract Aims Ants (Hymenoptera: Formicidae) of the Baja California peninsula are poorly known, with information based largely on scattered museum and literature records. We provide the first comprehensive account of ant species occurring on the peninsula, we examine distribution patterns, and we assess the ‘peninsular effect’ which predicts that species richness declines from the base to the tip of a peninsula. Location Peninsula of Baja California, Mexico. Methods Data collection involved examining, identifying and recording label data from c. 2350 series of ants. These records provide a provisional, if incomplete, species list. We applied the incidence‐based estimator, Chao‐2, to our data base of specimen records to estimate the total number of ant species on the peninsula. We assessed endemism by comparing our peninsular species list to those from adjacent states. The peninsular effect was tested by comparing genus and species level richness between the two states of Baja California, and across five latitudinal blocks. Results We document 170 native ant species in thirty‐three genera, plus six non‐native species, in Baja California. It seems likely that additional species remain to be discovered: the Chao‐2 estimator of species richness, at 206.0 species, is about 20% higher than our observed species richness. About 30% of the species and 20% of the genera are restricted within Baja California to the relatively mesic California Floristic Province of north‐western Baja California. Nearly all of these species also occur in California. Forty‐seven species (27.6%) are peninsula endemics. Using our entire data set, the peninsular effect appears to be strong, with about twice as many species in the northern state of Baja California than are recorded from the southern state of Baja California Sur; the ratio of genera is 33 to 24. However, this effect becomes weak at the species level and absent at the genus level when minimizing habitat effects by omitting species restricted to the California Floristic Province. At a finer scale, across latitudinal blocks of about 1.9°, the number of species declines towards central portions of the peninsula and then increases in the Cape Region. Nine ant species display strongly disjunct distributions, and these occur in two general patterns: peninsula disjuncts and peninsula–mainland disjuncts. Main conclusions The Baja California peninsula supports a diverse and distinctive ant fauna, with the proportion of endemic species similar to that displayed by plants. Patterns of species and genus richness across the five latitudinal blocks provide poor support for the peninsular effect. Moreover, habitat diversity, especially that related to topographic relief, appears to be the most important factor affecting the gradient of ant species richness in Baja California. Additional collections are needed to develop a more complete species list and to determine the boundaries and status of many species. Nevertheless, the present data base provides a useful starting point for understanding the evolution of ant assemblages in Baja California and for comparison with peninsular patterns in other taxa.     

A peninsula as an island: multiple forms of evidence for overwater colonization of Baja California by the gartersnake Thamnophis validus

The recent shift toward dispersal rather than vicariant explanations of disjunct distributions has been driven by the use of molecular data to estimate divergence dates between lineages. However, other kinds of evidence can also be critical in evaluating such biogeographic hypotheses. In the present study, we used a multifaceted approach employing diverse analyses of mitochondrial DNA sequences to assess explanations for the disjunct distribution of the gartersnake Thamnophis validus. The occurrence of this species in the Cape Region of the Baja California peninsula, isolated from mainland populations that occur along the west coast of Mexico, might be explained by: (1) separation of the peninsula from mainland Mexico through rifting 4–8 Mya (tectonic vicariance); (2) fragmentation of the range of this semi‐aquatic species because of post‐Pleistocene aridification (vicariance by aridification); (3) natural overwater dispersal across the Gulf of California; or (4) human introduction. Divergence dating indicates that peninsular and mainland T. validus separated from each other within the last 0.5 Myr, thus rejecting tectonic vicariance. In addition, the estimated closest mainland relatives of peninsular snakes are found farther north than expected under this hypothesis. Three findings argue against vicariance by aridification: (1) peninsular snakes and their closest mainland relatives are more genetically similar than predicted; (2) the location of closest mainland relatives is farther south than predicted; and (3) the species is absent from areas where one might expect to find relict populations. Taken together, refutation of the vicariance hypotheses and the fact that the estimated closest mainland relatives are found almost directly across the Gulf from the Cape Region supports some form of overwater colonization. Various additional arguments suggest that natural dispersal is more likely than human introduction. The present study emphasizes the need for multiple kinds of evidence, beyond divergence dates, to discriminate among hypotheses and to provide independent sources of corroboration or refutation in historical biogeography. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 409–424.     

Interglacial genetic diversification of Moussonia deppeana (Gesneriaceae), a hummingbird‐pollinated,cloud forest shrub in northern Mesoamerica

Recent empirical work on cloud forest‐adapted species supports the role of both old divergences across major geographical areas and more recent divergences attributed to Pleistocene climate changes. The shrub Moussonia deppeana is distributed in northern Mesoamerica, with geographically disjunct populations. Based on sampling throughout the species range and employing plastid and nuclear markers, we (i) test whether the fragmented distribution is correlated with main evolutionary lineages, (ii) reconstruct its phylogeographical history to infer the history of cloud forest in northern Mesoamerica and (iii) evaluate a set of refugia/vicariance scenarios for the region and demographic patterns of the populations whose ranges expanded and tracked cloud forest conditions during the Last Glacial Maximum. We found a deep evolutionary split in M. deppeana about 6–3 Ma, which could be consistent with a Pliocene divergence. Comparison of variation in plastid and nuclear markers revealed several lineages mostly congruent with their isolated geographical distribution and restricted gene flow among groups. Results of species distribution modelling and coalescent simulations fit a model of multiple refugia diverging during interglacial cycles. The demographic history of M. deppeana is not consistent with an expanding–contracting cloud forest archipelago model during the Last Glacial Maximum. Instead, our data suggest that populations persisted across the geographical range throughout the glacial cycles, and experienced isolation and divergence during interglacial periods.     

Comparative phylogeography of Australo‐Papuan mangrove‐restricted and mangrove‐associated avifaunas

The world's richest mangrove‐restricted avifauna is in Australia and New Guinea. The history of differentiation of the species involved and their patterns of intraspecific genetic variation remain poorly known. Here, we use sequence data derived from two mitochondrial protein‐coding genes to study the evolutionary history of eight co‐distributed mangrove‐restricted and mangrove‐associated birds from the Australian part of this region. Utilizing a comparative phylogeographical framework, we observed that the study species present concordantly located phylogeographical breaks across their shared geographical distribution, a plausible signature of common mechanisms of vicariance underlying this pattern. Barriers such as the Canning Gap, Bonaparte Gap, and the Carpentarian Gaps all had important but varying degrees of impact on the studied species. The Burdekin Gap along Australia's eastern seaboard probably had only a minor influence as a barrier to gene flow in mangrove birds. Statistical phylogeographical simulations were able to discriminate among alternative scenarios involving six different geographical and temporal population separations. Species exhibiting recent colonizations into mangroves include Rhipidura phasiana, Myiagra ruficollis, and Myzomela erythrocephala. By contrast, Peneoenanthe pulverulenta, Pachycephala melanura, Pachycephala lanioides, Zosterops luteus, and Colluricincla megarhyncha all had deeper histories, reflected as more marked phylogeographical divisions separating populations on the eastern seaboard/Cape York Peninsula from more western regions such as the Arnhem Land, the Pilbara, and the Kimberley. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 574–598.     

Testing the emergence of New Caledonia: fig wasp mutualism as a case study and a review of evidence

While geologists suggest that New Caledonian main island (Grande Terre) was submerged until ca 37 Ma, biologists are struck by the presence of supposedly Gondwanan groups on the island. Among these groups are the Oreosycea fig trees (Ficus, Moraceae) and their Dolichoris pollinators (Hymenoptera, Agaonidae). These partners are distributed in the Paleotropics and Australasia, suggesting that their presence on New Caledonia could result from Gondwanan vicariance. To test this hypothesis, we obtained mitochondrial and nuclear markers (5.3 kb) from 28 species of Dolichoris, used all available sequences for Oreosycea, and conducted phylogenetic and dating analyses with several calibration strategies. All our analyses ruled out a vicariance scenario suggesting instead that New Caledonian colonization by Dolichoris and Oreosycea involved dispersal across islands from Sundaland ca 45.9-32.0 Ma. Our results show that successful long-distance dispersal of obligate mutualists may happen further suggesting that presence of intimate mutualisms on isolated islands should not be used as a priori evidence for vicariance. Comparing our results to a review of all the published age estimates for New Caledonian plant and animal taxa, we showed that support for a vicariant origin of the island biota is still lacking. Finally, as demonstrating a causal relationship between geology and biology requires independent evidence, we argue that a priori assumptions about vicariance or dispersal should not be used to constrain chronograms. This circular reasoning could lead to under or overestimation of age estimates.     

Diversification within glacial refugia: tempo and mode of evolution of the polytypic fish Barbus sclateri

A diversity of evolutionary processes can be responsible for generating and maintaining biodiversity. Molecular markers were used to investigate the influence of Plio-Pleistocene climatic oscillations on the evolutionary history of taxa restricted to the freshwaters of a classical glacial refugium. Population genetic, phylogenetic and phylogeographical methods allowed the inference of temporal dynamics of cladogenesis and processes shaping present-day genetic constitution of Barbus sclateri , a polytypic taxon found in several independent river drainages in southern Iberian Peninsula. Results from different analyses consistently indicate several range expansions, high levels of allopatric fragmentation, and admixture following secondary contacts throughout its evolutionary history. Using a Bayesian demographical coalescent model on mitochondrial DNA sequences calibrated with fossil evidence, all cladogenetic events within B. sclateri are inferred to have occurred during the Pleistocene and were probably driven by environmental factors. Our results suggest that glaciation cycles did not inhibit cladogenesis and probably interacted with regional geomorphology to promote diversification. We conclude that this polytypic taxon is a species complex that recently diversified in allopatry, and that Pleistocene glaciation–deglaciation cycles probably contributed to the generation of biological diversity in a classical glacial refugium with high endemicity.     

Towards a panbiogeography of the seas

A contrast is drawn between the concept of speciation favoured in the Darwin–Wallace biogeographic paradigm (founder dispersal from a centre of origin) and in panbiogeography (vicariance or allopatry). Ordinary ecological dispersal is distinguished from founder dispersal. A survey of recent literature indicates that ideas on many aspects of marine biology are converging on a panbiogeographic view. Panbiogeographic conclusions supported in recent work include the following observations: fossils give minimum ages for groups and most taxa are considerably older than their earliest known fossil; Pacific/Atlantic divergence calibrations based on the rise of the Isthmus of Panama at 3 Ma are flawed; for these two reasons most molecular clock calibrations for marine groups are also flawed; the means of dispersal of taxa do not correlate with their actual distributions; populations of marine species may be closed systems because of self‐recruitment; most marine taxa show at least some degree of vicariant differentiation and vicariance is surprisingly common among what were previously assumed to be uniform, widespread taxa; mangrove and seagrass biogeography and migration patterns in marine taxa are best explained by vicariance; the Indian Ocean and the Pacific Ocean represent major biogeographic regions and diversity in the Indo‐Australian Archipelago is related to Indian Ocean/Pacific Ocean vicariance; distribution in the Pacific is not the result of founder dispersal; distribution in the south‐west Pacific is accounted for by accretion tectonics which bring about distribution by accumulation and juxtaposition of communities; tectonic uplift and subsidence can directly affect vertical distribution of marine communities; substantial parallels exist between the biogeography of terrestrial and marine taxa; biogeographically and geologically composite areas are tractable using panbiogeographic analysis; metapopulation models are more realistic than the mainland/island dispersal models used in the equilibrium theory of island biogeography; and regional biogeography is a major determinant of local community composition. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society, 2005, 84 , 675–723.     

A biogeographical profile of the sand cockroach Arenivaga floridensis and its bearing on origin hypotheses for Florida scrub biota

Florida scrub is a xeric ecosystem associated with the peninsula's sand ridges, whose intermittent Pliocene–Pleistocene isolation is considered key to scrub endemism. One scrub origin hypothesis posits endemics were sourced by the Pliocene dispersal of arid‐adapted taxa from southwestern North America; a second invokes Pleistocene migration within eastern North America. Only one study to date has explicitly tested these competing hypotheses, supporting an eastern origin for certain scrub angiosperms. For further perspective, we conducted a genetic analysis of an endemic arthropod, the Florida sand cockroach (Arenivaga floridensis), with two aims: (1) to reconstruct the peninsular colonization and residence history of A. floridensis and (2) determine whether its biogeographic profile favors either origin hypothesis. We sequenced the cox2 mitochondrial gene for 237 specimens (65 populations) as well as additional loci (cox1, nuclear H3) for a subset of Florida roaches and congeners. Using Network and Bayesian inference methods, we identified three major lineages whose genetic differentiation and phylogeographical structure correspond with late Pliocene peninsula insularization, indicating Arenivaga was present and broadly distributed in Florida at that time. Stem and crown divergence estimates (6.36 Ma; 2.78 Ma) between A. floridensis and western sister taxa span a period of extensive dispersal by western biota along an arid Gulf Coast corridor. These phylogeographical and phylogenetic results yield a biogeographic profile consistent with the western origin hypothesis. Moreover, age estimates for the roach's peninsular residence complement those of several other endemics, favoring a Pliocene (or earlier) inception of the scrub ecosystem. We argue that eastern versus western hypotheses are not mutually exclusive; rather, a composite history of colonization involving disparate biotas better explains the diverse endemism of Florida scrub.     

Species delimitation in the Hwamei Garrulax canorus

Due to the male's elaborate songs, the Hwamei Garrulax canorus is the most popular caged bird in the global Chinese community. Three allopatric Hwamei subspecies have been described: G. c. canorus in central and southern China and northern Indochina, G. c. owstoni from Hainan and G. c. taewanus from Taiwan. We sequenced the entire mitochondrial cytochrome b gene to reconstruct the molecular intraspecific phylogeny of the Hwamei. Molecular phylogenetic trees indicated that individuals of the three subspecies formed three monophyletic clades with high bootstrap support (> 95%). The basal clade was G. c. taewanus . According to a conventional molecular clock (2% divergence per million years), G. c. taewanus split from the other Hwamei taxa around 1.5 million years ago, and G. c. owstoni diverged from G. c. canorus around 0.6 million years ago. Considering the periodic connection between the Asian mainland and nearby continental islands during the glacial periods, habitat vicariance may have played a more important role than geographical vicariance in facilitating the differentiation of these taxa. Molecular diagnosability, population integrity, and concordance between the population ranges and the topology of the phylogenetic tree suggested that the Hwamei should be delimited into at least two full species: G. canorus and G. taewanus . Our work represents one of the first attempts to re-evaluate the intraspecific systematics for an eastern Asian bird species using molecular data.