The role of disjunction and postglacial population expansion on phylogeographical history and genetic diversity of the circumboreal plant Chamaedaphne calyculata

In the last decade a number of studies has illustrated quite different phylogeographical patterns amongst plants with a northern present‐day geographical distribution, spanning the entire circumboreal region and/or circumarctic region and southern mountains. These works, employing several marker systems, have brought to light the complex evolutionary histories of this group. Here I focus on one circumboreal plant species, Chamaedaphne calyculata (leatherleaf), to unravel its phylogeographical history and patterns of genetic diversity across its geographical range. A survey of 29 populations with combined analyses of chloroplast DNA (cpDNA), internal transcribed spacer (ITS) and AFLP markers revealed structuring into two groups: Eurasian/north‐western North American, and north‐eastern North American. The present geographical distribution of C. calyculata has resulted from colonization from two putative refugial areas: east Beringia and south‐eastern North America. The variation of chloroplast DNA (cpDNA) and ITS sequences strongly indicated that the evolutionary histories of the Eurasian/north‐western North American and the north‐eastern North American populations were independent of each other because of a geographical disjunction in the distribution area and ice‐sheet history between north‐eastern and north‐western North America. Mismatch analysis using ITS confirmed that the present‐day population structure is the result of rapid expansion, probably since the last glacial maximum. The AFLP data revealed low genetic diversity of C. calyculata (P = 19.5%, H = 0.085) over the whole geographical range, and there was no evidence of loss of genetic diversity within populations in the continuous range, either at the margins or in formerly glaciated and nonglaciated regions. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 761–775.     

Genetic and phenotypic differentiation among Galaxias maculatus populations in a Patagonian postglacial lake system

Understanding the influence of landscape features on population differentiation is fundamental to evolutionary biology studies. We examined spatial patterns of genetic and phenotypic variability among Galaxias maculatus populations in a complex of four postglacial lakes in northwestern Patagonia differing in size and connectivity among them. A hierarchical Bayesian analysis grouped the individuals collected from eleven localities into three genetic clusters, first defining the populations of the two large lakes and separating the two small lakes in subsequent analysis. Genetic structuring was restricted within large lakes. It is known that the larval stage of Galaxias maculatus migrate to the limnetic zone of Patagonian lakes, possibly exerting an homogenizing effect on gene flow within lakes. Gene flow asymmetry and divergences among lakes can be explained by a combination of landscape characteristics and the presence of predators in the short streams that connect them. Individuals from the small lakes are the most divergent morphologically and genetically. The population in the isolated Redonda Lake, exhibits meristic differences as well, suggesting strong drift and environmental effects. This population is likely to have been isolated following the decline in water level of a paleolake that existed in this region approximately 13.2 kya BP. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

A morphologically intergrading population facilitates plastid introgression from diploid to tetraploid Dodecatheon (Primulaceae)

Polyploidy may promote diversification by generating reproductive isolation between ploidy levels, but this reproductive barrier may not be absolute. Several recent analyses of diploid–tetraploid contact zones have found evidence for hybridization. In these cases, inter‐cytotype gene flow is often associated with morphologically intergrading populations. In this study, we combine cytological, fitness and population genetic data to examine the evolutionary role of a morphologically intergrading population at a contact zone between species with different ploidy levels in Dodecatheon. Diploid D. frenchii and tetraploid D. meadia are usually distinguished by leaf‐shape characters. In southern Illinois, where these taxa occur in parapatry, a morphologically intergrading population includes the first documented tetraploid with D. frenchii morphology. Most plants in this intergrading population are fertile, and a nearby typical population of D. meadia has plastid DNA haplotypes that only occur in D. frenchii elsewhere in southern Illinois. These results suggest that fit neo‐tetraploids in this intergrading population have facilitated local introgression between ploidy levels. Similar patterns in other regions where these taxa co‐occur may explain weak range‐wide genetic differentiation between these species. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 168 , 91–100.     

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.     

An integrative taxonomic revision of the Tarentola geckos (Squamata,Phyllodactylidae) of the Cape Verde Islands

Recent phylogeographical analyses using mitochondrial DNA (mtDNA) sequences indicate that the Tarentola geckos from the Cape Verde archipelago originated from a propagule that dispersed from the Canary Islands approximately 7.7 Mya and that underwent a fast evolutionary radiation. Molecular analyses carried out to date clearly show some incongruences with the current taxonomy of Tarentola from the Cape Verde Islands, with some species being paraphyletic or polyphyletic, and several independently evolving lineages needing formal taxonomic recognition. The aim of this study was to clarify the systematics of this group to unravel its taxonomy by applying an integrative approach based on information from three independent sources: mtDNA, nuclear genes, and morphology. As a result of this taxonomic revision, two novel species for the islands of S. Nicolau and Fogo are described and eight subspecies are upgraded to species level. Moreover, an identification key for the genus Tarentola from the Cape Verde archipelago is presented. This study reconciles taxonomy and phylogeny in this group, provides a better understanding of diversity patterns, new insights on evolutionary hypotheses, and supports the basic framework for the future management and conservation of this unique reptile radiation. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 164 , 328–360.     

Parallel divergence of sympatric genetic and body size forms of Arctic charr,Salvelinus alpinus,from two Scottish lakes

F _ST and R_ST estimates for Arctic charr from six microsatelite markers collected from two neighbouring Scottish lakes, Loch Maree and Loch Stack, confirm the presence of two distinct genetic groupings representing separate populations within each lake. In both lakes, there was also a clear body size dimorphism, with large and small body size forms that segregated according to genetic grouping. There was evidence of only subtle foraging ecology differences between morphs, with the small body size morph in both lakes being more generalist in its foraging in the summer (consuming mostly plankton but also some macrobenthos) than the large body size morph, which specialized on planktonic prey. Trophic morphology (head and mouth shape) did not differ significantly between morphs (although the small sample size for Maree makes this a preliminary finding). Cluster analysis of the microsatelite data and the presence of private alleles showed that morphologically similar forms in different lakes were not genetically similar, as would be expected under a multiple invasion hypothesis. Thus, the data do not support a hypothesis of a dual invasion of both lakes by two common ancestors but instead suggest an independent origin of the two forms in each lake. Thus parallel sympatric divergence as a result of common selection pressures in both lakes is the most parsimonious explanation of the evolutionary origin of these polymorphisms. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 748–757.     

Phylogeography of a pearl oyster (Pinctada maxima) across the Indo‐Australian Archipelago: evidence of strong regional structure and population expansions but no phylogenetic breaks

This study investigates the genetic structure and phylogeography of a broadcast spawning bivalve mollusc, Pinctada maxima, throughout the Indo‐West Pacific and northern Australia. DNA sequence variation of the mitochondrial cytochrome oxidase subunit I (COI) gene was analysed in 367 individuals sampled from nine populations across the Indo‐West Pacific. Hierarchical AMOVA indicated strong genetic structuring amongst populations (Φ_ST = 0.372, P < 0.001); however, sequence divergence between the 47 haplotypes detected was low (maximum 1.8% difference) and no deep phylogenetic divergence was observed. Results suggest the presence of genetic barriers isolating populations of the South China Sea and central Indonesian regions, which, in turn, show patterns of historical separation from northern Australian regions. In P. maxima, historical vicariance during Pleistocene low sea levels is likely to have restricted planktonic larval transport, causing genetic differentiation amongst populations. However, low genetic differentiation is observed where strong ocean currents are present and is most likely due to contemporary larval transport along these pathways. Geographical association with haplotype distributions may indicate signs of early lineage sorting arising from historical population separations, yet an absence of divergent phylogenetic clades related to geography could be the consequence of periodic pulses of high genetic exchange. We compare our results with previous microsatellite DNA analysis of these P. maxima populations, and discuss implications for future conservation management of this species. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 107 , 632–646.     

Exploring the history of Serapias politisii (Orchidaceae), a narrow endemic on the opposite coasts of the Otranto channel: insights from molecular investigations

Knowledge of genetic spatial structure may provide insights into the causes of population disjunctions in plants. Serapias politisii is a narrow endemic with only a few populations scattered along the opposite coasts of the Otranto strait (southern Adriatic Sea). It was originally considered to be of hybrid origin between S. vomeracea ssp. laxiflora and S. parviflora, a possibility suggested also by a DNA phylogenetic study that grouped Italian and Greek populations in two distinct clades. In this study we have carried out additional plastid DNA sequencing and an AFLP analysis of the three taxa. Whereas the geographical distribution of four plastid DNA haplotypes supports the likelihood of a double hybrid origin or of a plastid capture, AFLP data do not support such a hypothesis, because S. politisii shows several private alleles, some of which are shared by Italian and Greek populations. In light of the floristic specificity of the coasts bordering the Otranto strait, we consider that the present‐day disjunction of S. politisii could have originated either by a long‐distance seed dispersal or by a fragmentation of an old polymorphic population. The pairwise mismatch distribution excludes a recent expansion of the populations examined. In light of recent evidence concerning the Mediterranean Lago‐Mare period and the westward haplotype evolution detected in some Euro‐Mediterranean trees, we argue that fragmentation of a previously continuous population could be an intriguing possibility. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 162 , 572–580.     

Phylogeography of European sea bass in the north‐east Atlantic: a correction and reanalysis of the mitochondrial DNA data from Coscia & Mariani (2011)

The re‐analysis of mtDNA sequence data on sea bass (Dicentrarchus labrax) in the north‐east Atlantic revealed the presence of a ‘slippage error’ in the alignment of the mitochondrial DNA (mtDNA) control region sequences. This induced an overestimation of the genetic variability within this species, and hence the inference of a striking multi‐clade partitioning of D. labrax populations within this area. After correction, the existence of highly distinct D. labrax haplogroups in Atlantic areas does not hold anymore, but the robust dichotomy between a single Mediterranean and a single Atlantic subgroup is confirmed. Here we present the new results related to the amended mtDNA control region alignment, and also summarize the key message in relation to the microsatellite data, which are unaffected by this revision. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106 , 455–458.     

Genetic and morphological differentiation of the mangrove crab Perisesarma guttatum (Brachyura: Sesarmidae) along an East African latitudinal gradient

The genetic structure and morphometric differentiation of mangrove crab Perisesarma guttatum populations were examined among shelf connected locations along a latitudinal gradient on the East African coast. Over 2200 specimens were sampled from 23 mangrove sites for geometric morphometrics analysis. Population genetic analyses of mitochondrial cytochrome c oxidase subunit I (COI) DNA sequences were used to evaluate connectivity among populations. A total of 73 haplotypes were detected, and almost no haplotypes were found in common between two highly supported phylogeographic clades: southern Mozambique (Inhaca Island and Maputo Bay) and a northern clade that included north Mozambique, Tanzania and Kenya. These two clades were identified based on the species' populations pairwise genetic differentiation and geographical location. Φ_ST values were considerably high between the two clades, indicating the presence of significant population genetic structure between Kenya and South Mozambique. However, each clade was composed of genetically similar populations along the latitudinal gradient, and no significant population structure was found within each clade because the Φ_st values were not significant. The morphometric analysis corroborated the division into two clades (i.e. Inhaca Island/Maputo Bay and northern populations) and also detected less shape variation among populations that were few kilometres apart. The significant spatial genetic structuring between the southern and the northern populations of P. guttatum along the geographic gradient under study, combined with morphological differences, suggests that these populations may be considered as cryptic species. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 28–46.     

Molecular taxonomy and population structure of the rough‐toothed dolphin Steno bredanensis (Cetartiodactyla: Delphinidae)

Several delphinid species have shown genetic population structure, both between and within ocean basins. We investigated genetic differentiation in the rough‐toothed dolphin, Steno bredanensis, using mitochondrial control region sequences from several localities worldwide (N = 112). Preliminary analyses indicated high levels of genetic differentiation between the Atlantic and Pacific/Indian Oceans, which were further investigated using complete cytochrome b sequences and mitogenomes. Phylogenetic analyses were inconclusive about the existence of cryptic speciation in the genus Steno. Notwithstanding this result, analysis of molecular variance and Φ‐statistics analyses revealed strong population differentiation not only between the Atlantic and Pacific, but also within the Atlantic, where three populations were detected: Caribbean, southeastern Brazil, and southern Brazil. We propose that these populations be considered management units for conservation purposes. Our results provide the first perspective on the worldwide genetic differentiation of S. bredanensis. © 2015 The Linnean Society of London     

Population genetics and conservation of critically small cycad populations: a case study of the Albany Cycad,Encephalartos latifrons (Lehmann)

Declining populations of less than 250 mature individuals are symptomatic of many Critically Endangered cycads, which, globally, comprise the most threatened group of organisms as a result of collecting and habitat loss. Survival plans focus on law enforcement, reintroduction, and augmentation programmes using plants from the wild and botanical gardens. Augmentation is one of the few remaining options for cycad populations, although the assumed benefits remain untested and there is a possibility that augmentation from different sources could compromise the genetic integrity of existing populations, especially when garden plants have no provenance data. We studied Encephalartos latifrons, a South African endemic, which is a typical Critically Endangered cycad. We studied the extent and structure of genetic diversity in wild and ex situ populations to assess the potential benefits and risks associated with augmentation programmes. We examined 86 plants using amplified fragment length polymorphisms (AFLPs). The 417 AFLP markers thus generated yielded a unique DNA ‘fingerprint’ for each plant. Wild populations retain high levels of genetic diversity and this is reflected among the ex situ holdings at the Kirstenbosch Botanical Garden. No population differentiation is evident, indicating a single panmictic population, consistent with moderately high levels of gene flow between subpopulations and a sexual mode of reproduction. Bayesian clustering identified four genotype groups in the wild, as well as a genotype group only found in ex situ collections. Our results indicate that E. latifrons would benefit from augmentation programmes, including the use of undocumented collections, and careful management of breeding plants would increase the heterogeneity of propagules. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 293–308.     

Multiple glacial refugia and postglacial colonization routes inferred for a woodland geophyte,Cyclamen purpurascens: patterns concordant with the Pleistocene history of broadleaved and coniferous tree species

The phylogeographical history of mid‐altitude woodland herbs that depend on moist and shaded forest habitats is poorly understood. Here, we analysed the genetic structure of Cyclamen purpurascens, a mountainous calcicolous perennial, to test hypotheses regarding its glacial survival in single or multiple refugia and postglacial colonization routes, and to explore how they are congruent with the histories inferred for temperate trees and other mountainous herbs. We gathered AFLP data and chloroplast DNA sequences (trnD‐trnT region) from 68 populations spanning the entire distribution range (the Jura Mountains, Alps, western Carpathians, Dinarides). Both genetic markers revealed two main phylogeographical groups (phylogroups) in C. purpurascens. Additionally, AFLP data detected a more detailed structure of five phylogroups: two widespread, showing east?west geographical separation, and three local ones, restricted to somewhat disjunct, marginal regions of the species range. We suggest that C. purpurascens survived the last glaciation in two main regions, the foothills of the Southern Limestone Alps and the Karst area of the north‐western Dinarides, and possibly also in microrefugia in the Western Carpathians. The glacial persistence and colonization routes of this woodland herb are highly concordant with those inferred for several temperate trees, especially the European beech. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 741–760.     

Cytogenetic and molecular characterization of morphologically variable Sisyrinchium micranthum (Iridaceae) in southern Brazil

Sisyrinchium micranthum is native to southern Brazil and shows a wide range of morphological variation in this region. This study was performed to compare individuals of this species in terms of traits such as morphology, chromosome number, meiotic behaviour, pollen viability and genetic diversity using inter simple sequence repeat markers. First, general morphological aspects were evaluated and plants were classified into three morphological categories (CI, CII and CIII) to analyse the cytogenetic and genetic data. Three chromosome numbers corresponding to three ploidies were found: 2n = 2x = 16, 2n = 4x = 32 and 2n = 6x = 48. All morphological types showed regular meiotic behaviour and high meiotic index values and pollen viability. CII is the most frequent in southern Brazil. The most common haploid chromosome number, n = 8, has not been reported previously in this species. The percentage of polymorphic loci ranged from 6.45 to 61.29% for each accession. Molecular and cytogenetic analyses indicate that some S. micranthum accessions may have more than one ploidy. This study represents the first effort to characterize this taxonomically complex species based on cytogenetic and genetic aspects. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 169 , 350–364.     

Phenotypically Different Microalgal Morphospecies with Identical Ribosomal DNA: A Case of Rapid Adaptive Evolution?

The agents driving the divergence and speciation of free-living microbial populations are still largely unknown. We investigated the dinoflagellate morphospecies Scrippsiella hangoei and Peridinium aciculiferum, which abound in the Baltic Sea and in northern temperate lakes, respectively. Electron microscopy analyses showed significant interspecific differences in the external cellular morphology, but a similar plate pattern in the characteristic dinoflagellate armor. Experimentally, S. hangoei grew in a wide range of salinities (0–30), whereas P. aciculiferum only grew in low salinities (0–3). Despite these phenotypic differences and the habitat segregation, molecular analyses showed identical ribosomal DNA sequences (ITS1, ITS2, 5.8S, SSU, and partial LSU) for both morphospecies. Yet, a strong interspecific genetic isolation was indicated by amplified fragment length polymorphism (F _ST = 0.76) and cytochrome b (cob) sequence divergence (∼1.90%). Phylogenetic reconstructions based on ribosomal (SSU, LSU) and mitochondrial (cob) DNA indicated a recent marine ancestor for P. aciculiferum. In conclusion, we suggest that the lacustrine P. aciculiferum and the marine-brackish S. hangoei diverged very recently, after a marine–freshwater transition that exposed the ancestral populations to different selective pressures. This hypothetical scenario agrees with mounting data indicating a significant role of natural selection in the divergence of free-living microbes, despite their virtually unrestricted dispersal capabilities. Finally, our results indicate that identical ITS rDNA sequences do not necessarily imply the same microbial species, as commonly assumed.     

Genetic structure of Eurasian badgers Meles meles (Carnivora: Mustelidae) and the colonization history of Ireland

The present study examined the contemporary genetic composition of the Eurasian badger, Meles meles, in Ireland, Britain and Western Europe, using six nuclear microsatellite loci and a 215‐bp fragment of the mitochondrial DNA control region. Significant population structure was evident within Europe (global multilocus microsatellite F_ST = 0.205, P < 0.001; global mitochondrial control region Φ_ST = 0.399, P < 0.001). Microsatellite‐based cluster analyses detected one population in Ireland, whereas badgers from Britain could be subdivided into several populations. Excluding the island populations of Ireland and Britain, badgers from Western Europe showed further structuring, with evidence of discrete Scandinavian, Central European, and Spanish populations. Mitochondrial DNA cluster analysis grouped the Irish population with Scandinavia and Spain, whereas the majority of British haplotypes grouped with those from Central Europe. The findings of the present study suggest that British and Irish badger populations colonized from different refugial areas, or that there were different waves of colonization from the source population. There are indications for the presence of an Atlantic fringe element, which has been seen in other Irish species. We discuss the results in light of the controversy about natural versus human‐mediated introductions. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

Phylogenetic analysis,taxonomic revision,and dental ontogeny of the Cretaceous Zhelestidae (Mammalia: Eutheria)

Iphisa elegans Gray, 1851 is a ground‐dwelling lizard widespread over Amazonia that displays a broadly conserved external morphology over its range. This wide geographical distribution and conservation of body form contrasts with the expected poor dispersal ability of the species, the tumultuous past of Amazonia, and the previously documented prevalence of cryptic species in widespread terrestrial organisms in this region. Here we investigate this homogeneity by examining hemipenial morphology and conducting phylogenetic analyses of mitochondrial (CYTB) and nuclear (C‐MOS) DNA sequence data from 49 individuals sampled across Amazonia. We detected remarkable variation in hemipenial morphology within this species, with multiple cases of sympatric occurrence of distinct hemipenial morphotypes. Phylogenetic analyses revealed highly divergent lineages corroborating the patterns suggested by the hemipenial morphotypes, including co‐occurrence of different lineages. The degrees of genetic and morphological distinctness, as well as instances of sympatry among mtDNA lineages/morphotypes without nuDNA allele sharing, suggest that I. elegans is a complex of cryptic species. An extensive and integrative taxonomic revision of the I. elegans complex throughout its wide geographical range is needed. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 166 , 361–376.     

Biogeography and diversity among montane populations of mouse shrew (Soricidae: Myosorex) in Tanzania

We assess variation in morphological and molecular characters among three species of Myosorex (the mouse shrew) –Myosorex geata, Myosorex kihaulei, and Myosorex zinki– as a means to test previously proposed biogeographic hypotheses for Tanzanian ‘sky islands’ and systematic hypotheses for Tanzanian mouse shrews. We analyse 17 cranial and dental variables using multivariate statistics and perform phylogenetic and phylogeographic analyses on sequences of mitochondrial and nuclear DNA; samples are drawn from every known Tanzanian population of Myosorex. Morphometric and phylogenetic analyses reveal that M. zinki is distinct, but that currently isolated populations of M. geata and M. kihaulei are relatively similar to one another, and may not have been isolated over geological time scales. Analyses of molecular variance identify statistically significant, but limited, genetic variation within and between isolated populations of M. geata and M. kihaulei. Between two putative regional biogeographic boundaries, greater genetic variation is explained by grouping populations on either side of the Ruaha River than by grouping populations on either side of the Makambako Gap. Our results are in agreement with recent studies illustrating the close relationship between faunas of the Southern Highlands and southern Eastern Arc Mountains, diminishing the apparent importance of the Makambako Gap as a historical biogeographic barrier. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100 , 669–680.