Phylogeography of the Trans‐Volcanic bunchgrass lizard (Sceloporus bicanthalis) across the highlands of south‐eastern Mexico

We quantify the population divergence processes that shaped population genetic structure in the Trans‐Volcanic bunchgrass lizard (Sceloporus bicanthalis) across the highlands of south‐eastern Mexico. Multilocus genetic data from nine nuclear loci and mitochondrial (mt)DNA were used to estimate the population divergence history for 47 samples of S. bicanthalis. Bayesian clustering methods partitioned S. bicanthalis into three populations: (1) a southern population in Oaxaca and southern Puebla; (2) a population in western Puebla; and (3) a northern population with a broad distribution across Hidalgo, Puebla, and Veracruz. The multilocus nuclear data and mtDNA both supported a Late Pleistocene increase in effective population size, and the nuclear data revealed low levels of unidirectional gene flow from the widespread northern population into the southern and western populations. Populations of S. bicanthalis experienced different demographic histories during the Pleistocene, and phylogeographical patterns were similar to those observed in many co‐distributed highland taxa. Although we recommend continuing to recognize S. bicanthalis as a single species, future research on the evolution of viviparity could gain novel insights by contrasting physiological and genomic patterns among the different populations located across the highlands of south‐eastern Mexico. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 852–865.     

On glacial refugia,genetic diversity,and microevolutionary processes: deep phylogeographical structure in the endemic newt Lissotriton italicus1

We investigated the phylogeographical patterns of Lissotriton italcus, a newt endemic to the Italian peninsula, aiming to determine why hotspots of intraspecific diversity so ‘hot’. We found two main mitochindrial DNA lineages (net sequence divergence of 6.8% at two fragments of total length of 1897 bp): one restricted to part of the Calabrian peninsula (i.e the southernmost portion of the species range) and the other widespread throughout the rest of the species range. Both lineages, which had a parapatric distribution, showed evidence of further subdivisions, with an overall number of eight terminal haplogroups, most of whose times to the most recent common ancestors were estimated at the Late Pleistocene. Analysis of molecular variance suggested that partitioning populations according to the geographical distribution of these haplogroups can explain 97% of the observed genetic variation. These results suggest that L. italicus underwent repeated cycles of allopatric fragmentation throughout the Pleistocene, and that it likely survived the Late Pleistocene paleoenvironmental changes within eight separate refugia. Thus, the current hotspot of intraspecific diversity of L. italicus (within the Calabrian peninsula) has not been moulded by long‐term stability of large populations but rather by multiple events of allopatric fragmentation and divergence. When compared with the patterns recently identified in other species, these results suggest that the occurrence of phases of allopatric divergence (eventually followed by secondary admixture) could be a common, albeit probably underrated feature in the history of formation of hotspots of intraspecific diversity. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 42–55.     

Pluvial Drainage Patterns and Holocene Desiccation Influenced the Genetic Architecture of Relict Dace,Relictus solitarius (Teleostei: Cyprinidae)

Changing drainage patterns have played a significant role in the evolution of western North American aquatic taxa. Relict dace, Relictus solitarius, is a Great Basin endemic cyprinid with a native range that is restricted to four valleys in eastern Nevada. Relictus solitarius now occupies spring systems that are the remnants of Pleistocene-era pluvial lakes, although it may have occurred in the area for much longer. Here we use mitochondrial DNA sequence data to assess range-wide genetic diversity of R. solitarius, and to estimate divergence times to determine whether pluvial drainages played an important role in shaping intraspecific genetic diversity. Genetic diversification within R. solitarius began during the early to mid-Pleistocene, separating populations within two sets of valleys (Butte/Ruby and Goshute/Steptoe). Additional diversification in each of the two sets of valleys occurred more recently, in the mid- to late-Pleistocene. Holocene desiccation has further isolated populations, and each population sampled contains unique mtDNA haplotypes. Pluvial drainage patterns did contribute to the genetic structure observed within R. solitarius, but most of the intraspecific diversification does not appear to be associated with the Last Glacial Maximum. Holocene desiccation has also contributed to the observed genetic structure. The relict dace populations we sampled are all unique, and we recommend that future management efforts should strive to preserve as much of the genetic diversity as possible.     

Intraspecific divergences of Rhodiola alsia (Crassulaceae) based on plastid DNA and internal transcribed spacer fragments

In the present study, we used two maternally inherited plastid DNA intergenic spacers, rpl20‐rps12 and trnS‐trnG, and the biparentally inherited nuclear ribosomal internal transcribed spacer (ITS) region to explore genetic variation and phylogeographical history of Rhodiola alsia, a herb endemic to the Qinghai‐Tibetan Plateau (QTP). Based on range‐wide sampling (18 populations and 227 individuals), we detected 45 plastid DNA haplotypes and 19 ITS sequence types. Only three plastid DNA haplotypes were widespread; most haplotypes were restricted to single sites or to neighbouring populations. Analysis of molecular variance revealed that most of the genetic variance was found within populations (51.24%) but that populations were also distinct (F_ST = 0.48759). We found three areas with relatively high plastid DNA diversity and these could further be recognized as potentially isolated divergence centres based on the ITS sequence type distribution. These represent three potentially isolated glacial refugia for R. alsia: one of them has long been recognized as an important refugium on the south‐eastern edge of the QTP, whereas the others are new and located in the north and south of the Tanggula Mountains on the plateau platform. Divergence time estimates based on ITS suggest that the main lineages of R. alsia diverged from each other 0.35–0.87 Mya, indicating that climatic oscillations during the Pleistocene may have been an important driver of intraspecific divergence in R. alsia. Rhodiola alsia probably experienced a phylogeographical history of retreat to isolated glacial refugia during Quaternary glaciations that led to different degrees of allopatric intraspecific divergence. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 168 , 204–215.     

Phylogeography of the pademelons (Marsupialia: Macropodidae: Thylogale) in New Guinea reflects both geological and climatic events during the Plio‐Pleistocene

Aim Alternative hypotheses concerning genetic structuring of the widespread endemic New Guinean forest pademelons (Thylogale) based on current taxonomy and zoogeography (northern, southern and montane species groupings) and preliminary genetic findings (western and eastern regional groupings) are investigated using mitochondrial sequence data. We examine the relationship between the observed phylogeographical structure and known or inferred geological and historical environmental change during the late Tertiary and Quaternary. Location New Guinea and associated islands. Methods We used primarily museum specimen collections to sample representatives from Thylogale populations across New Guinea and three associated islands. Mitochondrial cytochrome b and control region sequence data were used to construct phylogenies and estimate the timing of population divergence. Results Phylogenetic analyses indicated subdivision of pademelons into ‘eastern’ and ‘western’ regional clades. This was largely due to the genetic distinctiveness of north‐eastern and eastern peninsula populations, as the ‘western’ clade included samples from the northern, southern and central regions of New Guinea. Two tested island groups were closely related to populations north of the Central Cordillera; low genetic differentiation of pademelon populations between north‐eastern New Guinea and islands of the Bismarck Archipelago is consistent with late Pleistocene human‐mediated translocations, while the Aru Islands population showed divergence consistent with cessation of gene flow in the mid Pleistocene. There was relatively limited genetic divergence between currently geographically isolated populations in subalpine and nearby mid‐montane or lowland regions. Main conclusions Phylogeographical structuring does not conform to zoogeographical expectations of a north/south division across the cordillera, nor to current species designations, for this generalist forest species complex. Instead, the observed genetic structuring of Thylogale populations has probably been influenced by geological changes and Pleistocene climatic changes, in particular the recent uplift of the north‐eastern Huon Peninsula and the lowering of tree lines during glacial periods. Low sea levels during glacial maxima also allowed gene flow between the continental Aru Island group and New Guinea. More work is needed, particularly multi‐taxon comparative studies, to further develop and test phylogeographical hypotheses in New Guinea.     

Phylogeography and species limits in the green woodpecker complex (Aves: Picidae): multiple Pleistocene refugia and range expansion across Europe and the Near East

The green woodpecker complex consists of the green woodpecker (Picus viridis), distributed from Western Europe to the Caucasus and Iran, and the related LeVaillant's woodpecker (P. vaillantii), distributed in north‐western Africa from central Morocco to Tunisia. Much of the habitat of green woodpeckers in Central and Northern Europe was covered by ice, tundra, steppe or other unsuitable habitat during the Pleistocene; consequently, they must have come to occupy most of their current range during the past 20 000 years. We used complete mitochondrial ND2 sequences from populations throughout the range to investigate the genetic structure and evolutionary history of this complex. Three well‐differentiated clades, corresponding to three biogeographical regions, were recovered; 89% of the total genetic variance was distributed among these three regions. The populations in North Africa were sister to those of Europe and, within Europe, Iberia was sister to the rest of Europe and the Near East. This suggests that the post‐glacial colonization of most of Europe occurred from a refuge east of Iberia, probably in Italy or the Balkans; there was no substantial divergence among these regions. In addition, a population sample from Iran was genetically distinct from those of Western Europe, indicating a history of genetic isolation and an additional Pleistocene refuge east of the well‐known Balkan refugia and south of the Caucasus. Within Europe, northern populations were less genetically variable than southern ones, consistent with recent colonization. There was significant isolation‐by‐distance across Europe, indicating restricted gene flow; this was particularly apparent between western populations and those of the Caucasus and Iran. We recognize four species in the complex. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 710–723.     

Speciation and anagenesis in the genus Cyprinella of Mexico (Teleostei: Cyprinidae): a case study of Model III allopatric speciation

Allozyme variation at 42 presumptive gene lociis presented for members of the C. formosa species group. This group iscorroborated as a monophyletic assemblage whosecommon ancestor occupied pluvial Lake Palomasof the Guzman Basin. With increasingaridity during the Pleistocene this basin andassociated populations of this commonancestor were fragmented into several lineagesthat diverged independently of oneanother. The pattern of relationships andlevels of anagenetic change observed inindependent lineages for this clade are notconsistent with expectations of the mostcommon modes of speciation, Model I large-scalevicariance or Model II peripheralisolation. Rather, divergence in these fishlineages is consistent with the rarely observedModel III allopatric speciation. Consistentwith predictions of this model, thephylogenetic pattern recovered revealspolychotomous relationships (a hard polytomy)and varied rates of anagenetic change acrossexamined lineages.     

Landscape genetic patterns of the rainbow darter Etheostoma caeruleum: a catchment analysis of mitochondrial DNA sequences and nuclear microsatellites

Catchment population structure and divergence patterns of the rainbow darter Etheostoma caeruleum (Percidae: Teleostei), an eastern North American benthic fish, are tested using a landscape genetics approach. Allelic variation at eight nuclear DNA microsatellite loci and two mitochondrial DNA regions [cytochrome (cyt) b gene and control region; 2056 aligned base pairs (bp)] is analysed from 89 individuals and six sites in the Lake Erie catchment (Blanchard, Chagrin, Cuyahoga and Grand Rivers) v. the Ohio River catchment (Big Darby Creek and Little Miami River). Genetic and geographic patterning is assessed using phylogenetic trees, pair‐wise F_ST analogues, AMOVA partitioning, Mantel regression, Bayesian assignment, 3D factorial correspondence and barrier analyses. Results identify 34 cyt b haplotypes, 22 control region haplotypes and 137 microsatellite alleles whose distributions demonstrate marked genetic divergence between populations from the Lake Erie and Ohio River catchments. Etheostoma caeruleum populations in the Lake Erie and Ohio River catchments diverged c. 1·6 mya during the Pleistocene glaciations. Greater genetic separations characterize the Ohio River populations, reflecting their older habitat age and less recent connectivity. Divergence levels within the Lake Erie catchment denote more recent post‐glacial origins. Notably, the western Lake Erie Blanchard River population markedly differs from the three central basin tributary samples, which are each genetically distinguishable using microsatellites. Overall relationships among the Lake Erie sites refute a genetic isolation by geographic distance hypothesis. Etheostoma caeruleum populations thus exchange few genes and have low migration among tributaries and catchments.     

Evolutionary history of an alpine shrub Hippophae tibetana (Elaeagnaceae): allopatric divergence and regional expansion

Increasing evidence suggests that geological or climatic events in the past promoted allopatric speciation of alpine plants in the Qinghai‐Tibetan Plateau and adjacent region. However, few studies have been undertaken to examine whether such allopatric divergences also occurred within a morphologically uniform species. In the present study, we report the evolutionary history of an alpine shrub species, Hippophae tibetana, based on examining chloroplast DNA (cpDNA) and nuclear ribosomal internal transcribed spacer (ITS) DNA variations. We sequenced two cpDNA fragments (trnL‐F and trnS‐G) and the nuclear ITS region in 183 individuals collected from 21 natural populations. Ten chlorotypes and 17 ITS types were identified. Phylogenetic analyses of both chlorotypes and ITS sequence variations suggested two distinct lineages distributed in the eastern and western region, respectively. On the basis of the fast and low plant substitution rates, these two lineages were estimated to have diverged from each other between 1 and 4 million years ago, during the period of the major glaciations and orogenic processes. In addition, ITS has undergone the accelerated evolution in two populations in the southern Himalaya isolated by the high mountains with a surprising accumulation of the private variations. The east–west split was also supported by an analysis of molecular variance, which partitioned around 91% of the total cpDNA variance between these two groups of populations. A single chlorotype was found for most populations in eastern or western region, suggesting a recent postglacial expansion within each region. Star‐phylogeny and mismatch analyses of all chlorotypes within the eastern group of populations suggested an earlier regional expansion before the Last Glacial Maximum (LGM). The local fixture of the different chlorotypes in multiple populations suggested more than one refugia remained for eastern or western region. Coalescent tests rejected the hypothesis that all current populations originated from a single refugium during the LGM. Instead, they supported hypothesis that two lineages diverged before the late Pleistocene. These findings, when taken together, suggested that this species had experienced long allopatric divergence and recent regional range expansions in response to orogenic processes and the climate changes. The evolutionary history of this shrub species highlights importance of geographical isolations to the intraspecific divergence of alpine plants occurring in the world's ruff. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 37–50.     

Long‐term isolation of the coastal plant Calystegia soldanella (Convolvulaceae) in ancient freshwater Lake Biwa,Japan

Lake Biwa is an ancient freshwater lake that was formed approximately 4 Mya and harbours many coastal plants that commonly inhabit the seashore. We used chloroplast DNA haplotype analysis using two spacer sequences and simple sequence repeat (SSR) analysis using eight nuclear microsatellite markers to detect genomic signatures indicating long‐term isolation of inland populations of Calystegia soldanella in Lake Biwa from coastal populations. We used 348 samples from 63 populations for haplotype analysis and 478 samples from 27 populations for SSR analysis covering the inland and coastal distribution of the species. We detected seven haplotypes, and the distribution pattern of these haplotypes was geographically highly structured between Lake Biwa and the coast. Nuclear SSR analysis also supported genetic differentiation between Lake Biwa and coastal populations (analyses of molecular variance, 43%), and the grouping of Lake Biwa and coastal populations by a Neighbour‐joining tree. In addition, genetic diversity of the inland populations (mean H_E = 0.153) was significantly lower than that of coastal populations (mean H_E = 0.328). These results suggested that inland populations at Lake Biwa have been isolated from coastal populations for a very long time. The inland populations most likely experienced a bottleneck effect, resulting in sufficient in situ genetic divergence to clearly distinguish them from coastal populations. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 51–66.     

The birth of an endemic species flock: demographic history of the Bellamya group (Gastropoda,Viviparidae) in Lake Malawi

Changes in habitat stability may significantly shape evolutionary patterns and processes in ancient lakes. In the present study, we use a hierarchical combination of molecular phylogenetic and coalescent approaches to investigate the evolutionary history of the endemic species of the gastropod genus Bellamya in the African rift‐lake Malawi. By integrating our findings with reported palaeontological and palaeolimnological data, we demonstrate that all but one evolutionary lineage of the Pliocene Bellamya fauna in Lake Malawi became extinct. Coalescent analyses indicate that the modern radiation underwent both a sudden demographic and a spatial expansion after a genetic bottleneck. We argue that a reflooding of the lake after severe Pleistocene low stands offers a straightforward explanation for this pattern and may have triggered speciation processes in the modern endemic Bellamya radiation in Lake Malawi. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 130–143.     

East–west genetic differentiation in Musk Ducks (<Emphasis Type="Italic">Biziura lobata</Emphasis>) of Australia suggests late Pleistocene divergence at the Nullarbor Plain

Musk Ducks (Biziura lobata) are endemic to Australia and occur as two geographically isolated populations separated by the Nullarbor Plain, a vast arid region in southern Australia. We studied genetic variation in Musk Duck populations at coarse (eastern versus western Australia) and fine scales (four sites within eastern Australia). We found significant genetic structure between eastern and western Australia in the mtDNA control region (Φ_ST = 0.747), one nuclear intron (Φ_ST = 0.193) and eight microsatellite loci (F_ST = 0.035). In contrast, there was little genetic structure between Kangaroo Island and adjacent mainland regions within eastern Australia. One small population of Musk Ducks in Victoria (Lake Wendouree) differed from both Kangaroo Island and the remainder of mainland eastern Australia, possibly due to genetic drift exacerbated by inbreeding and small population size. The observed low pairwise distance between the eastern and western mtDNA lineages (0.36%) suggests that they diverged near the end of the Pleistocene, a period characterised by frequent shifts between wet and arid conditions in central Australia. Our genetic results corroborate the display call divergence and Mathews’ (Austral Avian Record 2:83–107, 1914) subspecies classification, and confirm that eastern and western populations of Musk Duck are currently isolated from each other.     

A cryptic and critically endangered species revealed by mitochondrial DNA analyses: the Western Ground Parrot

We examined cytochrome b sequence data to resolve the intraspecific taxonomy of ground parrots Pezoporus wallicus. The species occurs in fragmented coastal heaths in south-eastern and south-western Australia. Net nucleotide divergences among all eastern populations were very low (0.0–0.6%) and genetic diversity unstructured, suggesting relatively recent common ancestry. Gene flow among them was probably maintained via land bridges and the persistence of suitable habitat during the Pleistocene. In contrast, net nucleotide divergence was high (4.4–5.1%) between western and eastern populations, suggesting more ancient divergence about 2 million years ago. The magnitude of divergence between eastern and western lineages is similar to a wide range of avian congeners. Our data support the need to reconsider the intraspecific taxonomy of ground parrots, and we cautiously suggest the recognition of Western Ground Parrots as a species, P. flaviventris, for conservation prioritization, planning and management purposes. Given their recent precipitous decline to approximately 110 individuals, most of which occur at one location, this makes Western Ground Parrots one of the world’s most threatened bird species.     

The phylogeography of palm cockatoos, Probosciger aterrimus, in the dynamic Australo-Papuan region

Aims We aimed to investigate the effects of historical land–sea boundary and vegetation dynamics in the Australo‐Papuan region on the genetic structure of palm cockatoo populations. In doing so, we also sought to clarify the intraspecific taxonomic status of palm cockatoos, and to examine the potential conservation implications of our results. Location New Guinea and northern Australia. Methods We examined mtDNA (domain III, control region) genetic structure in 71 palm cockatoos from 17 locations across their Australo‐Papuan range. Results Twenty polymorphic sites over 242‐base pairs defined 12 haplotypes that were arranged in a 95% confidence parsimony network of six one‐step clades. Half of these were linked in one clade that included birds from eastern New Guinea–Australia, and the other half included birds from western New Guinea. Nested clade analyses revealed strong and significant genetic structure between these two clades. The average nucleotide divergence between eastern and western birds is c. 3.3%. Within the western clade there was a non‐random distribution of haplotypes according to sampling location alone, but the locations did not cluster significantly, probably due to low sample sizes. A non‐random distribution of haplotypes emerged within one of the one‐step clades from the east of the range (once rare haplotypes were removed), although the historic mechanism that may have created this pattern is unclear. The underlying low nucleotide divergence (0.39%) among haplotypes within the eastern clade suggests relatively recent common ancestry. Main conclusions Our results suggest genetic isolation of the eastern and western clades sometime during the Pleistocene. The continual reappearance of land bridges associated with Pleistocene glacio‐eustatic cycles within the eastern part of the range provides an explanation for our results. We suggest that the occurrence of two deep marine troughs maintained a narrow mountainous barrier between eastern and western birds throughout much of the Pleistocene at a time when extensive land bridges formed elsewhere in the species’ range, and that this has maintained their genetic distinctiveness. Our results provide little support for the current accepted subspecies; the western clade is roughly congruent with Probosciger aterrimus goliath (with caveats), but the otherwise unstructured small genetic distances cast considerable doubt on the remaining subspecies. The eastern and western lineages are endemic to each area and should therefore be considered for independent conservation status and management.     

Molecular phylogeny of the Eremias persica complex of the Iranian plateau (Reptilia: Lacertidae), based on mtDNA sequences

The Persian racerunner Eremias persica Blanford, 1875 is confined to the Iranian plateau, and forms one of the most widespread but rarely studied species of the family Lacertidae. With many local populations inhabiting a variety of habitats, and exhibiting considerable morphological, genetic, and ecological variations, it represents a species complex. We analysed sequences of mitochondrial cytochrome b and 12S ribosomal RNA (rRNA) genes derived from 13 geographically distant populations belonging to the E. persica complex. Using our knowledge of palaeogeographical events, a molecular clock was calibrated to assess the major events in fragmentation, radiation, and intraspecific variation. The sequence data strongly support a basal separation of the highland populations of western Iran from those of the open steppes and deserts, occurring in the east. The subsequent radiation, fragmentation, and evolution of these major assemblages have led to several discernable geographical lineages across the wide area of the Iranian plateau. The results indicate a middle‐Miocene origin for the clade as a whole. The first split, isolating the western and eastern clades, appears to have occurred 11–10 Mya. Further fragmentations and divergence within the major clades began about 8 Mya, with an evolutionary rate of 1.6% sequence divergence per million years among the lineages in the genes studied (combined data set). Molecular and morphological data strongly support a taxonomic revision of this species complex. At least four of the discovered clades should be raised to species, and two to subspecies, rank. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 158 , 641–660.     

Reevaluation of a classic phylogeographic barrier: new techniques reveal the influence of microgeographic climate variation on population divergence

We evaluated the mtDNA divergence and relationships within Geomys pinetis to assess the status of formerly recognized Geomys taxa. Additionally, we integrated new hypothesis‐based tests in ecological niche models (ENM) to provide greater insight into causes for divergence and potential barriers to gene flow in Southeastern United States (Alabama, Florida, and Georgia). Our DNA sequence dataset confirmed and strongly supported two distinct lineages within G. pinetis occurring east and west of the ARD. Divergence date estimates showed that eastern and western lineages diverged about 1.37 Ma (1.9 Ma–830 ka). Predicted distributions from ENMs were consistent with molecular data and defined each population east and west of the ARD with little overlap. Niche identity and background similarity tests were statistically significant suggesting that ENMs from eastern and western lineages are not identical or more similar than expected based on random localities drawn from the environmental background. ENMs also support the hypothesis that the ARD represents a ribbon of unsuitable climate between more suitable areas where these populations are distributed. The estimated age of divergence between eastern and western lineages of G. pinetis suggests that the divergence was driven by climatic conditions during Pleistocene glacial–interglacial cycles. The ARD at the contact zone of eastern and western lineages of G. pinetis forms a significant barrier promoting microgeographic isolation that helps maintain ecological and genetic divergence.     

Phylogeography of a mite,Halozetes fulvus,reflects the landscape history of a young volcanic island in the sub‐Antarctic

Previous studies of the microarthropods of Marion Island, Southern Ocean, documented high mitochondrial COI (cytochrome c oxidase subunit I) haplotype diversity and significant genetic structure, which were ascribed to landscape subdivision. In this paper we revisit these ideas in light of new geomorphological evidence indicating a major lineament orientated along N26.5°E. Using the microarthropod Halozetes fulvus, we test the hypothesis that the eastern and western sides of the island show different population genetic patterns, corresponding to the previously unrecognized geological separation of these regions, and perhaps also with differences in climates across the island and further landscape complexity. Mitochondrial COI data were collected for 291 H. fulvus individuals from 30 localities across the island. Notwithstanding our sampling effort, haplotype diversity was under‐sampled as indicated by rarefaction analyses. Overall, significant genetic structure was found across the island as indicated by Φ_ST analyses. Nested clade phylogeographical analyses suggested that restricted gene flow (with isolation‐by‐distance) played a role in shaping current genetic patterns, as confirmed by Mantel tests. At the local scale, coalescent modelling revealed two different genetic patterns. The first, characterizing populations on the south‐western corner of the island, was that of low effective population size and high gene flow. The converse was found on the eastern side of Marion Island. Taken together, substantial differences in spatial genetic structure characterize H. fulvus populations across Marion Island, in keeping with the hypothesis that the complex history of the island, including the N26.5°E geological lineament, has influenced population genetic structure. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 131–145.     

Evolution of Dendrocolaptes platyrostris (Aves: Furnariidae) between the South American open vegetation corridor and the Atlantic forest

The open vegetation corridor of South America is a region dominated by savanna biomes. It contains forests (i.e. riverine forests) that may act as corridors for rainforest specialists between the open vegetation corridor and its neighbouring biomes (i.e. the Amazonian and Atlantic forests). A prediction for this scenario is that populations of rainforest specialists in the open vegetation corridor and in the forested biomes show no significant genetic divergence. We addressed this hypothesis by studying plumage and genetic variation of the Planalto woodcreeper Dendrocolaptes platyrostris Spix (1824) (Aves: Furnariidae), a forest specialist that occurs in both open habitat and in the Atlantic forest. The study questions were: (1) is there any evidence of genetic continuity between populations of the open habitat and the Atlantic forest and (2) is plumage variation congruent with patterns of neutral genetic structure or with ecological factors related to habitat type? We used cytochrome b and mitochondrial DNA control region sequences to show that D. platyrostris is monophyletic and presents substantial intraspecific differentiation. We found two areas of plumage stability: one associated with Cerrado and the other associated with southern Atlantic Forest. Multiple Mantel tests showed that most of the plumage variation followed the transition of habitats but not phylogeographical gaps, suggesting that selection may be related to the evolution of the plumage of the species. The results were not compatible with the idea that forest specialists in the open vegetation corridor and in the Atlantic forest are linked at the population level because birds from each region were not part of the same genetic unit. Divergence in the presence of gene flow across the ecotone between both regions might explain our results. Also, our findings indicate that the southern Atlantic forest may have been significantly affected by Pleistocene climatic alteration, although such events did not cause local extinction of most taxa, as occurred in other regions of the globe where forests were significantly affected by global glaciations. Finally, our results neither support plumage stability areas, nor subspecies as full species. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 103 , 801–820.     

Variability,genetic structure and phylogeography of the dolomitophilous species Convolvulus boissieri (Convolvulaceae) in the Baetic ranges,inferred from AFLPs,plastid DNA and ITS sequences

Convolvulus boissieri is an edaphic endemic plant which grows in the Baetic ranges always in association with high mountain xeric dolomitic outcrops. As these dolomitic areas appear in a ‘soil‐island’ pattern, the distribution of this species is disjunct. Populations of this species frequently include a low number of individuals, which could have an important impact on their genetic diversity and viability. Convolvulus boissieri provides an excellent opportunity to study the genetic and phylogeographical aspects of species linked to dolomites. We used amplified fragment length polymorphism markers and nuclear (internal transcribed spacer region of the nuclear ribosomal cistron) and plastid sequences (trnL‐trnF, rpl32‐trnL and trnQ‐5′rps16). Data were generated from 15 populations, representing the distribution area of the species. For sequence analysis and estimation of divergence times we also used sequences from other Convolvulus species. Results revealed low intrapopulational genetic diversity and a strong interpopulational structure. Furthermore, we found clear‐cut differentiation caused by the existence of two large population groups separated by the Guadiana Menor river basin. Estimation of divergence times indicated that divergence took place during the Pleistocene glaciations. Genetic diversity and differentiation are similar to those other species exhibiting naturally fragmented distribution with a sky islands pattern. In phylogeographical terms, the successive glaciation–interglaciation cycles caused the species to spread from the western sites to eastern sites, the latter being more exposed to the effects of glaciation. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176 , 506–523.     

Bioacoustic and genetic divergence in a frog with a wide geographical distribution

The study of intraspecific variation of acoustic signals and its relationship with genetic divergence is important for understanding the origin of divergence in communication systems. We studied geographical variation in the acoustic structure of advertisement calls from five populations of the four‐eyed frog, Pleurodema thaul, and its relationship with the genetic divergence among these populations. By analyzing temporal and spectral parameters of the advertisement calls, we report that the signals of northern, central, and southern populations have remarkable differences between them. A phylogeographical analysis from a mitochondrial DNA fragment demonstrated three phylogenetic groups coincident with those found with the bioacoustics analysis. Furthermore, bioacoustic and genetic distances show significant correlations after controlling for geographical distance. These results suggest that behavioural divergence among populations of P. thaul has a phylogenetic basis, supporting three evolutionary units within this species, as well as prompting the exploration of divergence processes in the sound communication system of this species. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 142–155.