Disrupted phylogeographical microsatellite and chloroplast DNA patterns indicate a vicariance rather than long‐distance dispersal origin for the disjunct distribution of the Chilean endemic Dioscorea biloba (Dioscoreaceae) around the Atacama Desert

Aim The Chilean endemic Dioscorea biloba (Dioscoreaceae) is a dioecious geophyte that shows a remarkable 600 km north–south disjunction in the peripheral arid area of the Atacama Desert. Its restricted present‐day distribution and probable Neogene origin indicate that its populations have a history linked to that of the Atacama Desert, making this an ideal model species with which to investigate the biogeography of the region. Location Chile, Atacama Desert and peripheral arid area. Methods Two hundred and seventy‐five individuals from nine populations were genotyped for seven nuclear microsatellite loci, and plastid trnL–F and trnT–L sequences were obtained for a representative subset of these. Analyses included the estimation of genetic diversity and population structure through clustering, Bayesian and analysis of molecular variance analyses, and statistical parsimony networks of chloroplast haplotypes. Isolation by distance was tested against alternative dispersal hypotheses. Results Microsatellite markers revealed moderate to high levels of genetic diversity within populations, with those from the southern Limarí Valley showing the highest values and northern populations showing less exclusive alleles. Bayesian analysis of microsatellite data identified three genetic groups that corresponded to geographical ranges. Chloroplast phylogeography revealed no haplotypes shared between northern and southern ranges, and little haplotype sharing between the two neighbouring southern valleys. Dispersal models suggested the presence of extinct hypothetical populations between the southern and northern ranges. Main conclusions Our results are consistent with prolonged isolation of the northern and southern groups, mediated by the life‐history traits of the species. Significant isolation was revealed at both large and moderate distances as gene flow was not evident even between neighbouring valleys. Bayesian analyses of microsatellite and chloroplast haplotype diversity identified the southern area of Limarí as the probable area of origin of the species. Our data do not support recent dispersal of D. biloba from the southern range into Antofagasta, but indicate the fragmentation of an earlier wider range, concomitant with the Pliocene–Pleistocene climatic oscillations, with subsequent extinctions of the Atacama Desert populations and the divergence of the peripheral ones as a consequence of genetic drift.     

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.     

Biogeography of the octocorallian coelenterate fauna of southern Africa

The geographical and bathymetric distribution of southern African octocorals is analysed. Of the over 200 estimated species of regional octocorals, 81 confirmed and adequately described species are studied using a radial sector method. Two primary faunal components are recognized–endemic (53.3% of the fauna by numbers of species) and Indo-Pacific (39.4%). An Atlantic component contributes only minimally (about 1.7%), while the remaining fauna is made up of cosmopolites (2.8%) and scattered species (2.8%). A subantarctic component is not evident for the present-day, although evidence for previous contact is presented. A sister-group analysis using genera as a guide to sister species, shows the biogeographic affinities for the present-day fauna as a whole to be 45% Indo-Pacific, 31% cosmopolitan, 10% endemic, 10% Atlantic and 4% southern oceans (subantarctic). Applying the same method to only those genera with endemic species shows the affinities of the present-day endemic fauna to be 27.5% Indo-Pacific, 27.5% endemic, 24% cosmopolitan, 14% Atlantic and 7% subantarctic. Clearly defined boundaries for west, south, and east coast faunas (as recognized by previous authors in describing various intertidal faunas) are found not be present with regard to the octocoral fauna (largely due to its overwhelmingly subtidal nature). Instead two primary zoogeographic provinces are recognized–the Cape Endemic Province (extending from Liideritz to Inhaca Island) and the south-western fringe of the Indo-Pacific Province from East London north-eastwards. An overlap zone between these two is recognized between East London and Inhaca Island, with the region in the vicinity of Richards Bay having an essentially evenly mixed fauna (roughly 50% Cape Endemic Province and 50% Indo-Pacific). Of the 84 octocoral genera recorded for the region, seven (or 8.3%) are endemic, and of these, five are monotypic while two are ditypic. The fauna is shown to be predominantly sublittoral (about 95% by numbers of species), the shallow sublittoral (< 100 m in depth) being the region with highest species richness. Pennatulaceans are eurybathic (intertidal to 4756 m) and clearly show a high proportion of cosmopolites (20% of presently identified species). Soft corals are stenobathic and restricted to the intertidal, continental shelf and uppermost portion of the continental slope (<500m), while gorgonians are intermediate in depth distributon (intertidal to 1200 m). No cosmopolitan alcyonaceans are presently recorded. The centre of the Cape Endemic Province is the Agulhas Bank–an extensive region of shallow continential shelf (< 200 m in depth) between Cape Town and East London. Two regions of octocoral radiation for southern Africa are postulated–the Agulhas Bank and the western Indian Ocean.     

Glinal variation in morphology among eastern populations of the waterstrider, Aquarius remigis Say (Hemiptera: Gerridae)

We examined morphological variation among populations of the stream-dwelling waterstrider, Aquarius remigis. A previous analysis of allozyme variation along a transect from southern Quebec to southern North Carolina revealed two distinct 'types' of A. remigis, north and south of a transition zone in southern New York and northern Pennsylvania. To assess the concordance of morphological and allozyme differentiation, adults were sampled from 15 populations along the original transect, as well as 11 additional populations in New York, Connecticut and New Jersey. Eight measurements of leg and body size were taken of preserved individuals. Univariate and multivariate analyses (multiple regression, PCA, discriminant analysis) reveal significant differentiation between northern and southern populations with a transition zone between latitudes 39^oand 42^onorth. Strong clines within each region and a clear transition between regions support previous suggestions that there are two distinct 'types' of this species in eastern North America. The transition zone, in morphology coincides with that revealed by the allozyme variation, but extends further south. The covariance of allozyme frequency and morphometric traits suggests that differentiation has occurred through vicariance and secondary contact, and that in this system, cladistic and adaptive differentiation are coupled.     

The biogeography of Lessoniaceae,with special reference to Macrocystis C. Agardh (Phaeophyta: Laminariales)

The bipolar distributions of Lessoniaceae and Macrocystis have been explained by migration out of a ‘centre of origin’ and across the tropics by means of dispersal, but controversy centres on the issue: which sector is the true centre of origin? We provide biological, palaeo-oceanographic and geological evidence that leads us to reject the centre of origin/migration theory and methodology in explaining ‘bipolarity’. As an alternative, a process of vicariant differentiation out of a Pacific Ocean/Southern Ocean ancestral complex is proposed. Moreover the biogeographic relationship between the southwest and northeast Pacific is shown to be a general phenomenon and not restricted to marine algae.     

Vicariance across major marine biogeographic barriers: temporal concordance and the relative intensity of hard versus soft barriers

The marine tropics contain five major biogeographic regions (East Pacific, Atlantic, Indian Ocean, Indo-Australian Archipelago (IAA) and Central Pacific). These regions are separated by both hard and soft barriers. Reconstructing ancestral vicariance, we evaluate the extent of temporal concordance in vicariance events across three major barriers (Terminal Tethyan Event (TTE), Isthmus of Panama (IOP), East Pacific Barrier, EPB) and two incomplete barriers (either side of the IAA) for the Labridae, Pomacentridae and Chaetodontidae. We found a marked lack of temporal congruence within and among the three fish families in vicariance events associated with the EPB, TTE and IOP. Vicariance across hard barriers separating the Atlantic and Indo-Pacific (TTE, IOP) is temporally diffuse, with many vicariance events preceding barrier formation. In marked contrast, soft barriers either side of the IAA hotspot support tightly concordant vicariance events (2.5 Myr on Indian Ocean side; 6 Myr on Central Pacific side). Temporal concordance in vicariance points to large-scale temporally restricted gene flow during the Late Miocene and Pliocene. Despite different and often complex histories, both hard and soft barriers have comparably strong effects on the evolution of coral reef taxa.     

Land masses and oceanic currents drive population structure of Heritiera littoralis,a widespread mangrove in the Indo‐West Pacific

Phylogeographic forces driving evolution of sea‐dispersed plants are often influenced by regional and species characteristics, although not yet deciphered at a large spatial scale for many taxa like the mangrove species Heritiera littoralis. This study aimed to assess geographic distribution of genetic variation of this widespread mangrove in the Indo‐West Pacific region and identify the phylogeographic factors influencing its present‐day distribution. Analysis of five chloroplast DNA fragments’ sequences from 37 populations revealed low genetic diversity at the population level and strong genetic structure of H. littoralis in this region. The estimated divergence times between the major genetic lineages indicated that glacial level changes during the Pleistocene epoch induced strong genetic differentiation across the Indian and Pacific Oceans. In comparison to the strong genetic break imposed by the Sunda Shelf toward splitting the lineages of the Indian and Pacific Oceans, the genetic differentiation between Indo‐Malesia and Australasia was not so prominent. Long‐distance dispersal ability of H. littoralis propagules helped the species to attain transoceanic distribution not only across South East Asia and Australia, but also across the Indian Ocean to East Africa. However, oceanic circulation pattern in the South China Sea was found to act as a barrier creating further intraoceanic genetic differentiation. Overall, phylogeographic analysis in this study revealed that glacial vicariance had profound influence on population differentiation in H. littoralis and caused low genetic diversity except for the refugia populations near the equator which might have persisted through glacial maxima. With increasing loss of suitable habitats due to anthropogenic activities, these findings therefore emphasize the urgent need for conservation actions for all populations throughout the distribution range of H. littoralis.